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White B, Ng SM, Agwu JC, Barrett TG, Birchmore N, Kershaw M, Drew J, Kavvoura F, Law J, Moudiotis C, Procter E, Paul P, Regan F, Reilly P, Sachdev P, Sakremath R, Semple C, Sharples K, Skae M, Timmis A, Williams E, Wright N, Soni A. A practical evidence-based approach to management of type 2 diabetes in children and young people (CYP): UK consensus. BMC Med 2024; 22:144. [PMID: 38561783 PMCID: PMC10986054 DOI: 10.1186/s12916-024-03349-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Type 2 diabetes in young people is an aggressive disease with a greater risk of complications leading to increased morbidity and mortality during the most productive years of life. Prevalence in the UK and globally is rising yet experience in managing this condition is limited. There are no consensus guidelines in the UK for the assessment and management of paediatric type 2 diabetes. METHODS Multidisciplinary professionals from The Association of Children's Diabetes Clinicians (ACDC) and the National Type 2 Diabetes Working Group reviewed the evidence base and made recommendations using the Grading Of Recommendations, Assessment, Development and Evaluation (GRADE) methodology. RESULTS AND DISCUSSION Young people with type 2 diabetes should be managed within a paediatric diabetes team with close working with adult diabetes specialists, primary care and other paediatric specialties. Diagnosis of diabetes type can be challenging with many overlapping features. Diabetes antibodies may be needed to aid diagnosis. Co-morbidities and complications are frequently present at diagnosis and should be managed holistically. Lifestyle change and metformin are the mainstay of early treatment, with some needing additional basal insulin. GLP1 agonists should be used as second-line agents once early ketosis and symptoms are controlled. Glycaemic control improves microvascular but not cardiovascular risk. Reduction in excess adiposity, smoking prevention, increased physical activity and reduction of hypertension and dyslipidaemia are essential to reduce major adverse cardiovascular events. CONCLUSIONS This evidence-based guideline aims to provide a practical approach in managing this condition in the UK.
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Affiliation(s)
- Billy White
- University College London Hospitals NHS Foundation Trust, London, UK
| | - S M Ng
- Mersey And West Lancashire Teaching Hospitals NHS Trust, Ormskirk, UK
| | - J C Agwu
- Wye Valley NHS Trust, Hereford, UK
| | - T G Barrett
- Birmingham Women's And Children NHS Foundation Trust, Birmingham, UK
| | - N Birchmore
- Great Ormond Street Hospital For Children, NHS Foundation Trust, London, UK
| | - M Kershaw
- Birmingham Women's And Children NHS Foundation Trust, Birmingham, UK
| | - J Drew
- Nottingham University Hospitals NHS Foundation Trust, Nottingham, UK
| | - F Kavvoura
- Royal Berkshire NHS Foundation Trust, Reading, UK
| | - J Law
- Nottingham University Hospitals NHS Foundation Trust, Nottingham, UK
| | - C Moudiotis
- Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - E Procter
- Nottingham University Hospitals NHS Foundation Trust, Nottingham, UK
| | - P Paul
- Alder Hey Children's NHS Foundation Trust, Liverpool, UK
| | - F Regan
- Guy's and St Thomas's NHS Foundation Trust, London, UK
| | - P Reilly
- Torbay and South Devon NHS Foundation Trust, Torquay, UK
| | - P Sachdev
- Nottingham University Hospitals NHS Foundation Trust, Nottingham, UK
| | - R Sakremath
- Shrewsbury and Telford Hospital NHS Trust, Shrewsbury, UK
| | - C Semple
- University Hospitals Bristol and Weston NHS Foundation Trust, Bristol, UK
| | | | - M Skae
- Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - A Timmis
- Countess of Chester Hospital NHS Foundation Trust, Chester, UK
| | - E Williams
- Hampshire Hospitals NHS Foundation Trust, Winchester, UK
| | - N Wright
- Sheffield Children's Hospital NHS Foundation Trust, Sheffield, S102TH, UK
| | - A Soni
- Sheffield Children's Hospital NHS Foundation Trust, Sheffield, S102TH, UK.
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Shapla SP, Rahman MM, Paul P, Begum M, Debnath MR, Jahan F, Ferdousi A, Saha T, Sultana H, Biswas R. Usefulness of Diagnostic Ultrasound for Detection of Common Shoulder Abnormalities Prior to MRI. Mymensingh Med J 2024; 33:16-22. [PMID: 38163768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Shoulder pain is a common musculoskeletal pain in the general population and results in significant disability, quality of life impairment and financial burden to the health care system. This cross-sectional study was carried out among purposively selected 61 adult patients with shoulder pain and or limited range of motion in the Department of Radiology and Imaging, Mymensingh Medical College Hospital, Mymensingh, Bangladesh from September 2018 to August 2020 to determine the usefulness of USG in detection of common shoulder abnormalities, as an initial imaging modality using MRI as reference standard. The majority of the patients 25(40.98%) were in age group of 51-60 years with mean age of 52.98±10.85 years. In the dectection of rotator cuff pathology, the overall sensitivity, specificity and accuracy of USG for any complete tear were 100.0% each, for any partial tear were 79.71%, 96.57% and 91.80%, for any rotator cuff tear were 83.33%, 96.25% and 91.80%, and for any tendinosis were 90.48%, 99.37% and 96.31% respectively. The sensitivity, specificity and accuracy of USG were 88.23%, 92.59% & 90.16% for long head of biceps tendon sheath effusion, 100.0% each for long head of biceps tendon dislocation, 71.11%, 87.50% and 75.41% for glenohumeral joint effusion, and 58.06%, 96.67% and 77.05% for bursal effusion respectively. From this study, it is concluded that high resolution USG showed high sensitivity, specificity and accuracy compared to MRI in detecting common shoulder abnormalities, and could be considered as the first line imaging modality in the evaluation of shoulder pain.
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Affiliation(s)
- S P Shapla
- Dr Sanchita Paul Shapla, MD Resident, Department of Radiology and Imaging, Mymensingh Medical College (MMC), Mymensingh, Bangladesh; E-mail:
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Gollapalli R, Phillips J, Paul P. Ultrasensitive Surface Plasmon Resonance Sensor with a Feature of Dynamically Tunable Sensitivity and High Figure of Merit for Cancer Detection. Sensors (Basel) 2023; 23:5590. [PMID: 37420756 DOI: 10.3390/s23125590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 07/09/2023]
Abstract
Cancer is one of the leading causes of death worldwide, and it is well known that an early detection of cancer in a human body will provide an opportunity to cure the cancer. Early detection of cancer depends on the sensitivity of the measuring device and method, where the lowest detectable concentration of the cancerous cell in a test sample becomes a matter of high importance. Recently, Surface Plasmon Resonance (SPR) has proven to be a promising method to detect cancerous cells. The SPR method is based on the detection of changes in refractive indices of samples under testing and the sensitivity of such a SPR based sensor is related to the smallest detectable change in the refractive index of the sample. There exist many techniques where different combinations of metals, metal alloys and different configurations have been shown to lead to high sensitivities of the SPR sensors. Based on the difference in the refractive index between a normal healthy cell and a cancerous cell, recently, SPR method has been shown to be applicable to detect different types of cancers. In this work, we propose a new sensor surface configuration that comprises of gold-silver-graphene-black phosphorus to detect different cancerous cells based on the SPR method. Additionally, recently we proposed that the application of electric field across gold-graphene layers that form the SPR sensor surface can provide enhanced sensitivity than that is possible without the application of electrical bias. We utilized the same concept and numerically studied the impact of electrical bias across the gold-graphene layers combined with silver and black Phosphorus layers which forms the SPR sensor surface. Our numerical results have shown that electrical bias across the sensor surface in this new heterostructure can provide enhanced sensitivity compared to the original unbiased sensor surface. Not only that, our results have shown that as the electrical bias increases, the sensitivity increases up to a certain value and stabilizes at a still improved sensitivity value. Such dependence of sensitivity on the applied bias provides a dynamic tunability of the sensitivity and figure-of-merit (FOM) of the sensor to detect different types of cancer. In this work, we used the proposed heterostructure to detect six different types of cancers: Basal, Hela, Jurkat, PC12, MDA-MB-231, and MCF-7. Comparing our results to work published recently, we were able to achieve an enhanced sensitivity ranging from 97.2 to 1851.4 (deg/RIU) and FOM values ranging from 62.13 to 89.81 far above the values presented recently by other researchers.
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Affiliation(s)
- Ravi Gollapalli
- Department of Engineering and Industrial Professions, University of North Alabama, Florence, AL 35632, USA
| | - Jonathan Phillips
- Department of Engineering and Industrial Professions, University of North Alabama, Florence, AL 35632, USA
| | - Puneet Paul
- Department of Engineering and Industrial Professions, University of North Alabama, Florence, AL 35632, USA
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Bi Y, Yassue RM, Paul P, Dhatt BK, Sandhu J, Do TP, Walia H, Obata T, Morota G. Evaluating metabolic and genomic data for predicting grain traits under high night temperature stress in rice. G3 (Bethesda) 2023; 13:7071564. [PMID: 36881928 PMCID: PMC10151405 DOI: 10.1093/g3journal/jkad052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/09/2023]
Abstract
The asymmetric increase in average nighttime temperatures relative to increase in average daytime temperatures due to climate change is decreasing grain yield and quality in rice. Therefore, a better genome-level understanding of the impact of higher night temperature stress on the weight of individual grains is essential for future development of more resilient rice. We investigated the utility of metabolites obtained from grains to classify high night temperature conditions of genotypes, and metabolites and single nucleotide polymorphisms to predict grain length, width, and perimeter phenotypes using a rice diversity panel. We found that the metabolic profiles of rice genotypes alone could be used to classify control and high night temperature conditions with high accuracy using random forest or extreme gradient boosting. Best linear unbiased prediction and BayesC showed greater metabolic prediction performance than machine learning models for grain-size phenotypes. Metabolic prediction was most effective for grain width, resulting in the highest prediction performance. Genomic prediction performed better than metabolic prediction. Integrating metabolites and genomics simultaneously in a prediction model slightly improved prediction performance. We did not observe a difference in prediction between the control and high night temperature conditions. Several metabolites were identified as auxiliary phenotypes that could be used to enhance the multi-trait genomic prediction of grain-size phenotypes. Our results showed that, in addition to single nucleotide polymorphisms, metabolites collected from grains offer rich information to perform predictive analyses, including classification modeling of high night temperature responses and regression modeling of grain size-related phenotypes in rice.
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Affiliation(s)
- Ye Bi
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Rafael Massahiro Yassue
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Department of Genetics, 'Luiz de Queiroz' College of Agriculture, University of Sã o Paulo, Sã o Paulo, 13418, Brazil
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Balpreet Kaur Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Thi Phuc Do
- Faculty of Biology, VNU University of Science, Vietnam National University, 334 Nguyen Trai, Thanh Xuan, Hanoi, Vietnam.,Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Gota Morota
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Center for Advanced Innovation in Agriculture, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
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Dharni JS, Dhatt BK, Paul P, Gao T, Awada T, Bacher H, Peleg Z, Staswick P, Hupp J, Yu H, Walia H. A non-destructive approach for measuring rice panicle-level photosynthetic responses using 3D-image reconstruction. Plant Methods 2022; 18:126. [PMID: 36443862 PMCID: PMC9703705 DOI: 10.1186/s13007-022-00959-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Our understanding of the physiological responses of rice inflorescence (panicle) to environmental stresses is limited by the challenge of accurately determining panicle photosynthetic parameters and their impact on grain yield. This is primarily due to the lack of a suitable gas exchange methodology for panicles and non-destructive methods to accurately determine panicle surface area. RESULTS To address these challenges, we have developed a custom panicle gas exchange cylinder compatible with the LiCor 6800 Infra-red Gas Analyzer. Accurate surface area measurements were determined using 3D panicle imaging to normalize the panicle-level photosynthetic measurements. We observed differential responses in both panicle and flag leaf for two temperate Japonica rice genotypes (accessions TEJ-1 and TEJ-2) exposed to heat stress during early grain filling. There was a notable divergence in the relative photosynthetic contribution of flag leaf and panicles for the heat-tolerant genotype (TEJ-2) compared to the sensitive genotype (TEJ-1). CONCLUSION The novelty of this method is the non-destructive and accurate determination of panicle area and photosynthetic parameters, enabling researchers to monitor temporal changes in panicle physiology during the reproductive development. The method is useful for panicle-level measurements under diverse environmental stresses and is sensitive enough to evaluate genotypic variation for panicle physiology and architecture in cereals with compact inflorescences.
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Affiliation(s)
- Jaspinder Singh Dharni
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Balpreet Kaur Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Tian Gao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Tala Awada
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Harel Bacher
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Jason Hupp
- LI-COR Inc., 4647 Superior Street, Lincoln, NE, 68505, USA
| | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA.
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Chandran AKN, Sandhu J, Irvin L, Paul P, Dhatt BK, Hussain W, Gao T, Staswick P, Yu H, Morota G, Walia H. Rice Chalky Grain 5 regulates natural variation for grain quality under heat stress. Front Plant Sci 2022; 13:1026472. [PMID: 36304400 PMCID: PMC9593041 DOI: 10.3389/fpls.2022.1026472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Heat stress occurring during rice (Oryza sativa) grain development reduces grain quality, which often manifests as increased grain chalkiness. Although the impact of heat stress on grain yield is well-studied, the genetic basis of rice grain quality under heat stress is less explored as quantifying grain quality is less tractable than grain yield. To address this, we used an image-based colorimetric assay (Red, R; and Green, G) for genome-wide association analysis to identify genetic loci underlying the phenotypic variation in rice grains exposed to heat stress. We found the R to G pixel ratio (RG) derived from mature grain images to be effective in distinguishing chalky grains from translucent grains derived from control (28/24°C) and heat stressed (36/32°C) plants. Our analysis yielded a novel gene, rice Chalky Grain 5 (OsCG5) that regulates natural variation for grain chalkiness under heat stress. OsCG5 encodes a grain-specific, expressed protein of unknown function. Accessions with lower transcript abundance of OsCG5 exhibit higher chalkiness, which correlates with higher RG values under stress. These findings are supported by increased chalkiness of OsCG5 knock-out (KO) mutants relative to wildtype (WT) under heat stress. Grains from plants overexpressing OsCG5 are less chalky than KOs but comparable to WT under heat stress. Compared to WT and OE, KO mutants exhibit greater heat sensitivity for grain size and weight relative to controls. Collectively, these results show that the natural variation at OsCG5 may contribute towards rice grain quality under heat stress.
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Affiliation(s)
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Banos, Philippines
| | - Tian Gao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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Mudgal M, Mudgal M, Paul P, Jayaprakash TP, Kyritsi M, Hady E, Waqas M, Murakonda P, Lebelt A, Russell R, Dharmarajan T, Kanagala M. De-Prescribing for Renal Function in Long-Term Care Residents with Chronic Kidney Disease. J Am Med Dir Assoc 2022. [DOI: 10.1016/j.jamda.2022.04.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Razi RZ, Ahmed AM, Sultana S, Amin K, Ahsan M, Akter P, Paul P, Sangma MA, Ferdousi RA, Jahan F, Hasan MS, Ahsan SB. Clinical and Haematological Findings in Dengue Fever. Mymensingh Med J 2022; 31:344-349. [PMID: 35383748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
From 2000 onwards dengue fever has been occurring at regular intervals in Bangladesh. Ultrasonography is a useful diagnostic procedure. This study was done, keeping this background in mind. Objective of this study was to identify the role of ultrasonography as a useful tool in early diagnosis of dengue haemorrhagic fever. This was a cross-sectional descriptive type of observational study. Results of ultrasonography, haematogy an immunology were observed in 2004 and 2019 in 32 patients on each occasion. In 2004 out of 32 patients 29 had positive ultrsonographic findings supported by corresponding haematological and immunological findings. In 2019 ultrsonography was done in three out of thirty two patients, all three had had positive ultra sonographic findings which were supported by haematological and immunological findings. Dengue fever has serious complications like plasma leakage which manifest in the form of ascites, pleural effusion, thick gallbladder wall etc. If such complications can be detected at an early stage many lives can be saved.
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Affiliation(s)
- R Z Razi
- Dr RMA Ziauddin Razi, Associate Professor, Department of Radiology & Imaging, Mymensingh Medical College (MMC), Mymensingh, Bangladesh; E-mail:
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9
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Gao T, Chandran AKN, Paul P, Walia H, Yu H. HyperSeed: An End-to-End Method to Process Hyperspectral Images of Seeds. Sensors (Basel) 2021; 21:8184. [PMID: 34960287 PMCID: PMC8703337 DOI: 10.3390/s21248184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/27/2021] [Accepted: 12/04/2021] [Indexed: 01/04/2023]
Abstract
High-throughput, nondestructive, and precise measurement of seeds is critical for the evaluation of seed quality and the improvement of agricultural productions. To this end, we have developed a novel end-to-end platform named HyperSeed to provide hyperspectral information for seeds. As a test case, the hyperspectral images of rice seeds are obtained from a high-performance line-scan image spectrograph covering the spectral range from 600 to 1700 nm. The acquired images are processed via a graphical user interface (GUI)-based open-source software for background removal and seed segmentation. The output is generated in the form of a hyperspectral cube and curve for each seed. In our experiment, we presented the visual results of seed segmentation on different seed species. Moreover, we conducted a classification of seeds raised in heat stress and control environments using both traditional machine learning models and neural network models. The results show that the proposed 3D convolutional neural network (3D CNN) model has the highest accuracy, which is 97.5% in seed-based classification and 94.21% in pixel-based classification, compared to 80.0% in seed-based classification and 85.67% in seed-based classification from the support vector machine (SVM) model. Moreover, our pipeline enables systematic analysis of spectral curves and identification of wavelengths of biological interest.
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Affiliation(s)
- Tian Gao
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Anil Kumar Nalini Chandran
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (A.K.N.C.); (P.P.); (H.W.)
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (A.K.N.C.); (P.P.); (H.W.)
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (A.K.N.C.); (P.P.); (H.W.)
| | - Hongfeng Yu
- School of Computing, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
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Dachrodt L, Arndt H, Bartel A, Kellermann LM, Tautenhahn A, Volkmann M, Birnstiel K, Do Duc P, Hentzsch A, Jensen KC, Klawitter M, Paul P, Stoll A, Woudstra S, Zuz P, Knubben G, Metzner M, Müller KE, Merle R, Hoedemaker M. Prevalence of disorders in preweaned dairy calves from 731 dairies in Germany: A cross-sectional study. J Dairy Sci 2021; 104:9037-9051. [PMID: 33985777 DOI: 10.3168/jds.2021-20283] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/04/2021] [Indexed: 11/19/2022]
Abstract
The objective of this cross-sectional study was to determine the prevalence of disorders in preweaned calves in 3 regions in Germany, exemplary for structural diversity in dairy farming. A farm visit was performed on a single occasion on 731 dairy farms in the northern, eastern, and southern regions of Germany between December 2016 and July 2019. Farms differed in herd size, geographical location, and management. In the northern region, the farms had a median of 90 milking cows and were often run as full-time family businesses, partly with external workers. The eastern region tended to have larger farms (a median of 251 milking cows), which were often large-scale agricultural enterprises with employees. In the southern region, the farms had a median of 39 milking cows and were often traditional family businesses, some of these being part-time businesses. Clinical examinations were performed on 14,164 preweaned dairy calves (median 12 calves per farm) by trained veterinarians. A complete data set was available for 13,656 calves. Almost half (42.0%) of the evaluated calves were classified as being affected by at least 1 of the common calf disorders. Omphalitis (O, 20.9%; n = 2,876) and diarrhea (D, 18.5%; n = 2,670) were the most frequently recorded diagnoses, whereas respiratory diseases (RD) were observed to a lesser extent (8.7%; n = 1,100). A striking feature was the fact that 7.1% (n = 987) of the calves were affected by more than 1 disorder at the same time (multimorbidity, M). The following combinations of disorders were frequently observed: O and D (n = 596), O and RD (n = 164), and D and RD (n = 140). Disorders such as O and D, as well as M, were predominantly observed in calves aged 2 wk. A gradual increase in the frequency of RD was observed with age. For all disorders except RD, male calves were more often affected than females. Omphalitis was predominantly diagnosed in the summer months, whereas RD, D, and M were more common in the fall. We detected several statistically significant differences in the prevalence of clinical signs and disorders in preweaned dairy calves between the 3 exemplary regions. The prevalence of RD was higher in the south (10.8%) than in the north (8.2%) and east (7.4%). In the north (33.2%), O was observed more frequently than in the other regions (east: 18.9%; south: 10.5%), whereas D was found less frequently in the north (13.8%) than in the east (21.6%) and south (20.0%).
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Affiliation(s)
- L Dachrodt
- Clinic for Cattle, University of Veterinary Medicine Hannover, Foundation, D-30173 Hannover, Germany
| | - H Arndt
- Clinic for Cattle, University of Veterinary Medicine Hannover, Foundation, D-30173 Hannover, Germany
| | - A Bartel
- Institute for Veterinary Epidemiology and Biostatistics, Department of Veterinary Medicine, Freie Universität Berlin, D-14163 Berlin, Germany
| | - L M Kellermann
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, D-85764 Oberschleissheim, Germany
| | - A Tautenhahn
- Clinic for Ruminants and Swine, Department of Veterinary Medicine, Freie Universität Berlin, D-14163 Berlin, Germany
| | - M Volkmann
- Institute for Veterinary Epidemiology and Biostatistics, Department of Veterinary Medicine, Freie Universität Berlin, D-14163 Berlin, Germany
| | | | - P Do Duc
- Clinic for Cattle, University of Veterinary Medicine Hannover, Foundation, D-30173 Hannover, Germany
| | - A Hentzsch
- Clinic for Ruminants and Swine, Department of Veterinary Medicine, Freie Universität Berlin, D-14163 Berlin, Germany
| | - K C Jensen
- Clinic for Cattle, University of Veterinary Medicine Hannover, Foundation, D-30173 Hannover, Germany
| | - M Klawitter
- Clinic for Ruminants and Swine, Department of Veterinary Medicine, Freie Universität Berlin, D-14163 Berlin, Germany
| | - P Paul
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, D-85764 Oberschleissheim, Germany
| | - A Stoll
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, D-85764 Oberschleissheim, Germany
| | - S Woudstra
- Clinic for Cattle, University of Veterinary Medicine Hannover, Foundation, D-30173 Hannover, Germany
| | - P Zuz
- Clinic for Ruminants and Swine, Department of Veterinary Medicine, Freie Universität Berlin, D-14163 Berlin, Germany
| | - G Knubben
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, D-85764 Oberschleissheim, Germany
| | - M Metzner
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität Munich, D-85764 Oberschleissheim, Germany
| | - K E Müller
- Clinic for Ruminants and Swine, Department of Veterinary Medicine, Freie Universität Berlin, D-14163 Berlin, Germany
| | - R Merle
- Institute for Veterinary Epidemiology and Biostatistics, Department of Veterinary Medicine, Freie Universität Berlin, D-14163 Berlin, Germany
| | - M Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine Hannover, Foundation, D-30173 Hannover, Germany.
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11
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Paul P, Das R, Drow T, Souza AD, Appakalai B, Davis D, Galipeau J. Pancreatic stellate cells maintain endocrine islet viability and function in vitro in a laminin-dependent mechanism. Cytotherapy 2021. [DOI: 10.1016/s1465324921002942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Zhu F, Paul P, Hussain W, Wallman K, Dhatt BK, Sandhu J, Irvin L, Morota G, Yu H, Walia H. SeedExtractor: An Open-Source GUI for Seed Image Analysis. Front Plant Sci 2021; 11:581546. [PMID: 33597957 PMCID: PMC7882627 DOI: 10.3389/fpls.2020.581546] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 12/18/2020] [Indexed: 06/12/2023]
Abstract
Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it can be modified by users to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were used for genome-wide association analysis. We identified known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrates the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops.
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Affiliation(s)
- Feiyu Zhu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Waseem Hussain
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kyle Wallman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Larissa Irvin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Gota Morota
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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13
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Dhatt BK, Paul P, Sandhu J, Hussain W, Irvin L, Zhu F, Adviento‐Borbe MA, Lorence A, Staswick P, Yu H, Morota G, Walia H. Allelic variation in rice Fertilization Independent Endosperm 1 contributes to grain width under high night temperature stress. New Phytol 2021; 229:335-350. [PMID: 32858766 PMCID: PMC7756756 DOI: 10.1111/nph.16897] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/09/2020] [Indexed: 05/23/2023]
Abstract
A higher minimum (night-time) temperature is considered a greater limiting factor for reduced rice yield than a similar increase in maximum (daytime) temperature. While the physiological impact of high night temperature (HNT) has been studied, the genetic and molecular basis of HNT stress response remains unexplored. We examined the phenotypic variation for mature grain size (length and width) in a diverse set of rice accessions under HNT stress. Genome-wide association analysis identified several HNT-specific loci regulating grain size as well as loci that are common for optimal and HNT stress conditions. A novel locus contributing to grain width under HNT conditions colocalized with Fie1, a component of the FIS-PRC2 complex. Our results suggest that the allelic difference controlling grain width under HNT is a result of differential transcript-level response of Fie1 in grains developing under HNT stress. We present evidence to support the role of Fie1 in grain size regulation by testing overexpression (OE) and knockout mutants under heat stress. The OE mutants were either unaltered or had a positive impact on mature grain size under HNT, while the knockouts exhibited significant grain size reduction under these conditions.
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Affiliation(s)
- Balpreet K. Dhatt
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNE68583USA
| | - Puneet Paul
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNE68583USA
| | - Jaspreet Sandhu
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNE68583USA
| | - Waseem Hussain
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNE68583USA
| | - Larissa Irvin
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNE68583USA
| | - Feiyu Zhu
- Department of Computer Science and EngineeringUniversity of Nebraska‐LincolnLincolnNE68588USA
| | | | - Argelia Lorence
- Department of Chemistry and PhysicsArkansas Biosciences InstituteArkansas State UniversityJonesboroAR72467USA
| | - Paul Staswick
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNE68583USA
| | - Hongfeng Yu
- Department of Computer Science and EngineeringUniversity of Nebraska‐LincolnLincolnNE68588USA
| | - Gota Morota
- Department of Animal and Poultry SciencesVirginia Polytechnic Institute and State UniversityBlacksburgVA24061USA
| | - Harkamal Walia
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNE68583USA
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Paul P, Dhatt BK, Miller M, Folsom JJ, Wang Z, Krassovskaya I, Liu K, Sandhu J, Yu H, Zhang C, Obata T, Staswick P, Walia H. MADS78 and MADS79 Are Essential Regulators of Early Seed Development in Rice. Plant Physiol 2020; 182:933-948. [PMID: 31818903 PMCID: PMC6997703 DOI: 10.1104/pp.19.00917] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/27/2019] [Indexed: 05/20/2023]
Abstract
MADS box transcription factors (TFs) are subdivided into type I and II based on phylogenetic analysis. The type II TFs regulate floral organ identity and flowering time, but type I TFs are relatively less characterized. Here, we report the functional characterization of two type I MADS box TFs in rice (Oryza sativa), MADS78 and MADS79 Transcript abundance of both these genes in developing seed peaked at 48 h after fertilization and was suppressed by 96 h after fertilization, corresponding to syncytial and cellularized stages of endosperm development, respectively. Seeds overexpressing MADS78 and MADS 79 exhibited delayed endosperm cellularization, while CRISPR-Cas9-mediated single knockout mutants showed precocious endosperm cellularization. MADS78 and MADS 79 were indispensable for seed development, as a double knockout mutant failed to make viable seeds. Both MADS78 and 79 interacted with MADS89, another type I MADS box, which enhances nuclear localization. The expression analysis of Fie1, a rice FERTILIZATION-INDEPENDENT SEED-POLYCOMB REPRESSOR COMPLEX2 component, in MADS78 and 79 mutants and vice versa established an antithetical relation, suggesting that Fie1 could be involved in negative regulation of MADS78 and MADS 79 Misregulation of MADS78 and MADS 79 perturbed auxin homeostasis and carbon metabolism, as evident by misregulation of genes involved in auxin transport and signaling as well as starch biosynthesis genes causing structural abnormalities in starch granules at maturity. Collectively, we show that MADS78 and MADS 79 are essential regulators of early seed developmental transition and impact both seed size and quality in rice.
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Affiliation(s)
- Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Balpreet K Dhatt
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Michael Miller
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Jing J Folsom
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Zhen Wang
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Inga Krassovskaya
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Kan Liu
- School of Biological Science, University of Nebraska, Lincoln, Nebraska 68588
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Huihui Yu
- School of Biological Science, University of Nebraska, Lincoln, Nebraska 68588
| | - Chi Zhang
- School of Biological Science, University of Nebraska, Lincoln, Nebraska 68588
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska, Lincoln, Nebraska 68588
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, Nebraska 68583
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15
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Paul P, Dhatt BK, Sandhu J, Hussain W, Irvin L, Morota G, Staswick P, Walia H. Divergent phenotypic response of rice accessions to transient heat stress during early seed development. Plant Direct 2020; 4:e00196. [PMID: 31956854 PMCID: PMC6955394 DOI: 10.1002/pld3.196] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/05/2019] [Accepted: 12/19/2019] [Indexed: 05/03/2023]
Abstract
Increasing global surface temperatures is posing a major food security challenge. Part of the solution to address this problem is to improve crop heat resilience, especially during grain development, along with agronomic decisions such as shift in planting time and increasing crop diversification. Rice is a major food crop consumed by more than 3 billion people. For rice, thermal sensitivity of reproductive development and grain filling is well-documented, while knowledge concerning the impact of heat stress (HS) on early seed development is limited. Here, we aim to study the phenotypic variation in a set of diverse rice accessions for elucidating the HS response during early seed development. To explore the variation in HS sensitivity, we investigated aus (1), indica (2), temperate japonica (2), and tropical japonica (4) accessions for their HS (39/35°C) response during early seed development that accounts for transition of endosperm from syncytial to cellularization, which broadly corresponds to 24 and 96 hr after fertilization (HAF), respectively, in rice. The two indica and one of the tropical japonica accessions exhibited severe heat sensitivity with increased seed abortion; three tropical japonicas and an aus accession showed moderate heat tolerance, while temperate japonicas exhibited strong heat tolerance. The accessions exhibiting extreme heat sensitivity maintain seed size at the expense of number of fully developed mature seeds, while the accessions showing relative resilience to the transient HS maintained number of fully developed seeds but compromised on seed size, especially seed length. Further, histochemical analysis revealed that all the tested accessions have delayed endosperm cellularization upon exposure to the transient HS by 96 HAF; however, the rate of cellularization was different among the accessions. These findings were further corroborated by upregulation of cellularization-associated marker genes in the developing seeds from the heat-stressed samples.
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Affiliation(s)
- Puneet Paul
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Balpreet K. Dhatt
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Jaspreet Sandhu
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Waseem Hussain
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
- International Rice Research InstituteLos BanosPhilippines
| | - Larissa Irvin
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Gota Morota
- Department of Animal and Poultry SciencesVirginia Polytechnic Institute and State UniversityBlacksburgVAUSA
| | - Paul Staswick
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
| | - Harkamal Walia
- Department of Agronomy and HorticultureUniversity of Nebraska‐LincolnLincolnNEUSA
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16
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Sandhu J, Zhu F, Paul P, Gao T, Dhatt BK, Ge Y, Staswick P, Yu H, Walia H. PI-Plat: a high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits. Plant Methods 2019; 15:162. [PMID: 31889986 PMCID: PMC6933716 DOI: 10.1186/s13007-019-0545-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 12/09/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND Recent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics. However, more complex agronomic traits such as inflorescence architecture (IA), which predominantly contributes to grain crop yield are more challenging to quantify and hence are relatively less explored. Previous efforts to estimate inflorescence-related traits using image-based phenotyping have been limited to destructive end-point measurements. Development of non-destructive inflorescence phenotyping platforms could accelerate the discovery of the phenotypic variation with respect to inflorescence dynamics and mapping of the underlying genes regulating critical yield components. RESULTS The major objective of this study is to evaluate post-fertilization development and growth dynamics of inflorescence at high spatial and temporal resolution in rice. For this, we developed the Panicle Imaging Platform (PI-Plat) to comprehend multi-dimensional features of IA in a non-destructive manner. We used 11 rice genotypes to capture multi-view images of primary panicle on weekly basis after the fertilization. These images were used to reconstruct a 3D point cloud of the panicle, which enabled us to extract digital traits such as voxel count and color intensity. We found that the voxel count of developing panicles is positively correlated with seed number and weight at maturity. The voxel count from developing panicles projected overall volumes that increased during the grain filling phase, wherein quantification of color intensity estimated the rate of panicle maturation. Our 3D based phenotyping solution showed superior performance compared to conventional 2D based approaches. CONCLUSIONS For harnessing the potential of the existing genetic resources, we need a comprehensive understanding of the genotype-to-phenotype relationship. Relatively low-cost sequencing platforms have facilitated high-throughput genotyping, while phenotyping, especially for complex traits, has posed major challenges for crop improvement. PI-Plat offers a low cost and high-resolution platform to phenotype inflorescence-related traits using 3D reconstruction-based approach. Further, the non-destructive nature of the platform facilitates analyses of the same panicle at multiple developmental time points, which can be utilized to explore the genetic variation for dynamic inflorescence traits in cereals.
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Affiliation(s)
- Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Feiyu Zhu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, USA
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Tian Gao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, USA
| | - Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Yufeng Ge
- Biological Systems Engineering Department, University of Nebraska-Lincoln, Lincoln, USA
| | - Paul Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Hongfeng Yu
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, USA
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
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Paul P, Chouhan P, Zaveri A. Impact of child marriage on nutritional status and anaemia of children under 5 years of age: empirical evidence from India. Public Health 2019; 177:95-101. [DOI: 10.1016/j.puhe.2019.08.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/07/2019] [Accepted: 08/15/2019] [Indexed: 10/26/2022]
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18
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Dhatt BK, Abshire N, Paul P, Hasanthika K, Sandhu J, Zhang Q, Obata T, Walia H. Metabolic Dynamics of Developing Rice Seeds Under High Night-Time Temperature Stress. Front Plant Sci 2019; 10:1443. [PMID: 31781147 PMCID: PMC6857699 DOI: 10.3389/fpls.2019.01443] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 10/17/2019] [Indexed: 05/03/2023]
Abstract
High temperature stress during rice reproductive development results in yield losses. Reduced grain yield and grain quality has been associated with high temperature stress, and specifically with high night-time temperatures (HNT). Characterizing the impact of HNT on the phenotypic and metabolic status of developing rice seeds can provide insights into the mechanisms involved in yield and quality decline. Here, we examined the impact of warmer nights on the morphology and metabolome during early seed development in six diverse rice accessions. Seed size was sensitive to HNT in four of the six genotypes, while seed fertility and seed weight were unaffected. We observed genotypic differences for negative impact of HNT on grain quality. This was evident from the chalky grain appearance due to impaired packaging of starch granules. Metabolite profiles during early seed development (3 and 4 days after fertilization; DAF) were distinct from the early grain filling stages (7 and 10 DAF) under optimal conditions. We observed that accumulation of sugars (sucrose, fructose, and glucose) peaked at 7 DAF suggesting a major flux of carbon into glycolysis, tricarboxylic acid cycle, and starch biosynthesis during grain filling. Next, we determined hyper (HNT > control) and hypo (HNT < control) abundant metabolites and found 19 of the 57 metabolites to differ significantly between HNT and control treatments. The most prominent changes were exhibited by differential abundance of sugar and sugar alcohols under HNT, which could be linked to a protective mechanism against the HNT damage. Overall, our results indicate that combining metabolic profiles of developing grains with yield and quality parameters under high night temperature stress could provide insight for exploration of natural variation for HNT tolerance in the rice germplasm.
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Affiliation(s)
- Balpreet K. Dhatt
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Nathan Abshire
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Kalani Hasanthika
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Jaspreet Sandhu
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Qi Zhang
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Harkamal Walia
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
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Boissier R, Gondran-Tellier B, Francois P, Meunier M, Simoncini S, Lyonnet L, Legris T, Arnaud L, Magalon J, Giraudo L, Dignat-George F, Burtey S, Karsenty G, Lechevallier E, Sabatier F, Paul P. Utilisation de la graisse péri-rénale du donneur pour analyser la fonction/dysfonction endothéliale du transplant rénal. Prog Urol 2019. [DOI: 10.1016/j.purol.2019.08.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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20
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Sangma MA, Biswas N, Paul P. Relation of Hepatic Venous Doppler Sonography and Portal Flowmetry in Determination of Severity of Esophageal Varices in Liver Cirrhosis. Mymensingh Med J 2019; 28:727-733. [PMID: 31599233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Cirrhotic patients have hepatic vein waveform abnormalities (HVWA). Both Doppler ultrasonography of hepatic venous wave form (HVWF) and portal Doppler flowmetry (PDF) can non invasively recognize hepatic vein wave form abnormalities and determine severity of esophageal varices. Here we applied cross sectional study and found out the relation between HVWF and PDF and duration of the study from July 2016 to June 2017 in a tertiary Medical College Hospital, Bangladesh. 49 purposively taken diagnosed, hospital admitted, cirrhotic patients were included. Face to face interview and reviewing of records were the source of data and it was analyzed by SPSS windows version-12 software programs. At first, local ethical committee approved the study protocol, p<0.05 was statistically significant and 95% was confidence interval. Esophagogastroduodenoscopy is the gold standard for the diagnosis of esophageal varices. Alternative diagnostic investigations would be either HVWF or PDF. HVWF were normal triphasic. Abnormal biphasic and monophasic PDF consisted of the maximum values of portal flow velocity, portal vein flow volume, diameter of the portal vein, and congestion index. Small and large varices were the easiest form of endoscopic grading of esophageal varices. No clinical or echocardiographic feature of right sided heart failure had found in any patient. Both HVWF and PDF can certainly demonstrate the presence of varices but only HVWF detected severity of esophageal varices - monophasic wave (60.47%) in Doppler USG which signified (<0.05) large varices (67.44%) in endoscopy and in biphasic wave (31.53%) in Doppler USG which signified small varices (32.66%) in endoscopy. Patients who developed varices had portal vein diameter (PVD) and congestion index (CI) were higher (p<0.02) and portal vein velocity (PVV) was lower (p<0.05) than whom did not develop varices, but severity of varices could not be detected. Portal vein flow volume (PVFV) did not signify the presence or severity of varices. Moderately positive correlation (correlation co-efficient was 0.0064) was found between Doppler USG of HVWF and esophagogastroduodenoscopic in severity detection varices. In determination of severity of esophageal varices in patients with liver cirrhosis Hepatic venous Doppler sonography plays more vital role than PDF.
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Affiliation(s)
- M A Sangma
- Dr Mousumi Anuradha Sangma, Junior Consultant (Radiology & Imaging), Mymensingh Medical College Hospital (MMCH), Mymensingh, Bangladesh; E-mail: sumisangma @hotmail.com
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21
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Paul P, Laurence M, Gualter V, Isabelle R, Pierre M, Yves BJ, Patrice P, Mehdi B, Marie K, Armelle D, Pierre SM. EP-1608 Results of an aggressive local strategy after R1 or R2 unplanned surgery for soft tissue sarcomas. Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(19)32028-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Rahman A, Tauhid F, Begum S, Saifuddin M, Hossain MA, Paul P, Abdullah AA. Transmigrated and Impacted Upper 2nd Premolar Associated with Dentigerous Cyst. Mymensingh Med J 2019; 28:237-240. [PMID: 30755575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A male patient about 45 years old came to my private clinic "The Dental Aid", Dhanmondi, Dhaka, Bangladesh last year (February 2016) with the complaint of pain at right palatal premolar region. On clinical examination we found the absence of upper left 2nd premolar from the series of dentition but on the right side premolars are present. The oral mucosa was intact and normal in color. There was no caries, dental pocket or any other pathology in the teeth of both jaws. On palpation we found soft area on the right palatal side at the premolar area. We took intraoral peri-apical radiograph and found impacted left 2nd premolar whose crown was encircled by radiolucent area at the palatal side. Here, we present a rare case of transmigrated and impacted left 2nd maxillary premolar associated with dentigerous cyst. The cyst was successfully treated under general anaesthesia by enucleation along with extraction of the involved maxillary transposed and impacted left second premolar.
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Affiliation(s)
- A Rahman
- Dr Arifur Rahman, Professor and Head, Department of Prosthodontics, Dental Unit, Holy Family Red Crescent Medical College & Hospital (HFRCMC&H), Dhaka, Bangladesh
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23
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Sandhu J, Zhu F, Paul P, Gao T, Dhatt BK, Ge Y, Staswick P, Yu H, Walia H. PI-Plat: a high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits. Plant Methods 2019. [PMID: 31889986 DOI: 10.1186/s13007-019-0545-542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
BACKGROUND Recent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics. However, more complex agronomic traits such as inflorescence architecture (IA), which predominantly contributes to grain crop yield are more challenging to quantify and hence are relatively less explored. Previous efforts to estimate inflorescence-related traits using image-based phenotyping have been limited to destructive end-point measurements. Development of non-destructive inflorescence phenotyping platforms could accelerate the discovery of the phenotypic variation with respect to inflorescence dynamics and mapping of the underlying genes regulating critical yield components. RESULTS The major objective of this study is to evaluate post-fertilization development and growth dynamics of inflorescence at high spatial and temporal resolution in rice. For this, we developed the Panicle Imaging Platform (PI-Plat) to comprehend multi-dimensional features of IA in a non-destructive manner. We used 11 rice genotypes to capture multi-view images of primary panicle on weekly basis after the fertilization. These images were used to reconstruct a 3D point cloud of the panicle, which enabled us to extract digital traits such as voxel count and color intensity. We found that the voxel count of developing panicles is positively correlated with seed number and weight at maturity. The voxel count from developing panicles projected overall volumes that increased during the grain filling phase, wherein quantification of color intensity estimated the rate of panicle maturation. Our 3D based phenotyping solution showed superior performance compared to conventional 2D based approaches. CONCLUSIONS For harnessing the potential of the existing genetic resources, we need a comprehensive understanding of the genotype-to-phenotype relationship. Relatively low-cost sequencing platforms have facilitated high-throughput genotyping, while phenotyping, especially for complex traits, has posed major challenges for crop improvement. PI-Plat offers a low cost and high-resolution platform to phenotype inflorescence-related traits using 3D reconstruction-based approach. Further, the non-destructive nature of the platform facilitates analyses of the same panicle at multiple developmental time points, which can be utilized to explore the genetic variation for dynamic inflorescence traits in cereals.
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Affiliation(s)
- Jaspreet Sandhu
- 1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Feiyu Zhu
- 2Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, USA
| | - Puneet Paul
- 1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Tian Gao
- 2Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, USA
| | - Balpreet K Dhatt
- 1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Yufeng Ge
- 3Biological Systems Engineering Department, University of Nebraska-Lincoln, Lincoln, USA
| | - Paul Staswick
- 1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Hongfeng Yu
- 2Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, USA
| | - Harkamal Walia
- 1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
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Benyamine A, Magalon J, Sabatier F, Kaplanski G, Mazodier K, Reynaud Gaubert M, Morange S, Rossi P, Dignat-George F, Paul P, Granel B. Les cellules natural killer de patients souffrant de sclérodermie systémique ont un profil phénotypique particulier et sont de puissants inducteurs de libération de microparticules endothéliales. Rev Med Interne 2018. [DOI: 10.1016/j.revmed.2018.10.287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Guha P, Cardoza F, Chen A, Dinh T, Paul P, DeStephano C. Choosing the Route of Morcellation for Minimally Invasive Gynecologic Surgeries. J Minim Invasive Gynecol 2018. [DOI: 10.1016/j.jmig.2018.09.742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Redondo MJ, Geyer S, Steck AK, Sharp S, Wentworth JM, Weedon MN, Antinozzi P, Sosenko J, Atkinson M, Pugliese A, Oram RA, Antinozzi P, Atkinson M, Battaglia M, Becker D, Bingley P, Bosi E, Buckner J, Colman P, Gottlieb P, Herold K, Insel R, Kay T, Knip M, Marks J, Moran A, Palmer J, Peakman M, Philipson L, Pugliese A, Raskin P, Rodriguez H, Roep B, Russell W, Schatz D, Wherrett D, Wilson D, Winter W, Ziegler A, Benoist C, Blum J, Chase P, Clare-Salzler M, Clynes R, Eisenbarth G, Fathman C, Grave G, Hering B, Kaufman F, Leschek E, Mahon J, Nanto-Salonen K, Nepom G, Orban T, Parkman R, Pescovitz M, Peyman J, Roncarolo M, Simell O, Sherwin R, Siegelman M, Steck A, Thomas J, Trucco M, Wagner J, Greenbaum ,CJ, Bourcier K, Insel R, Krischer JP, Leschek E, Rafkin L, Spain L, Cowie C, Foulkes M, Krause-Steinrauf H, Lachin JM, Malozowski S, Peyman J, Ridge J, Savage P, Skyler JS, Zafonte SJ, Kenyon NS, Santiago I, Sosenko JM, Bundy B, Abbondondolo M, Adams T, Amado D, Asif I, Boonstra M, Bundy B, Burroughs C, Cuthbertson D, Deemer M, Eberhard C, Fiske S, Ford J, Garmeson J, Guillette H, Browning G, Coughenour T, Sulk M, Tsalikan E, Tansey M, Cabbage J, Dixit N, Pasha S, King M, Adcock K, Geyer S, Atterberry H, Fox L, Englert K, Mauras N, Permuy J, Sikes K, Berhe T, Guendling B, McLennan L, Paganessi L, Hays B, Murphy C, Draznin M, Kamboj M, Sheppard S, Lewis V, Coates L, Moore W, Babar G, Bedard J, Brenson-Hughes D, Henderson C, Cernich J, Clements M, Duprau R, Goodman S, Hester L, Huerta-Saenz L, Karmazin A, Letjen T, Raman S, Morin D, Henry M, Bestermann W, Morawski E, White J, Brockmyer A, Bays R, Campbell S, Stapleton A, Stone N, Donoho A, Everett H, Heyman K, Hensley H, Johnson M, Marshall C, Skirvin N, Taylor P, Williams R, Ray L, Wolverton C, Nickels D, Dothard C, Hsiao B, Speiser P, Pellizzari M, Bokor L, Izuora K, Abdelnour S, Cummings P, Paynor S, Leahy M, Riedl M, Shockley S, Karges C, Saad R, Briones T, Casella S, Herz C, Walsh K, Greening J, Hay F, Hunt S, Sikotra N, Simons L, Keaton N, Karounos D, Oremus R, Dye L, Myers L, Ballard D, Miers W, Sparks R, Thraikill K, Edwards K, Fowlkes J, Kinderman A, Kemp S, Morales A, Holland L, Johnson L, Paul P, Ghatak A, Phelen K, Leyland H, Henderson T, Brenner D, Law P, Oppenheimer E, Mamkin I, Moniz C, Clarson C, Lovell M, Peters A, Ruelas V, Borut D, Burt D, Jordan M, Leinbach A, Castilla S, Flores P, Ruiz M, Hanson L, Green-Blair J, Sheridan R, Wintergerst K, Pierce G, Omoruyi A, Foster M, Linton C, Kingery S, Lunsford A, Cervantes I, Parker T, Price P, Urben J, Doughty I, Haydock H, Parker V, Bergman P, Liu S, Duncum S, Rodda C, Thomas A, Ferry R, McCommon D, Cockroft J, Perelman A, Calendo R, Barrera C, Arce-Nunez E, Lloyd J, Martinez Y, De la Portilla M, Cardenas I, Garrido L, Villar M, Lorini R, Calandra E, D’Annuzio G, Perri K, Minuto N, Malloy J, Rebora C, Callegari R, Ali O, Kramer J, Auble B, Cabrera S, Donohoue P, Fiallo-Scharer R, Hessner M, Wolfgram P, Maddox K, Kansra A, Bettin N, McCuller R, Miller A, Accacha S, Corrigan J, Fiore E, Levine R, Mahoney T, Polychronakos C, Martin J, Gagne V, Starkman H, Fox M, Chin D, Melchionne F, Silverman L, Marshall I, Cerracchio L, Cruz J, Viswanathan A, Miller J, Wilson J, Chalew S, Valley S, Layburn S, Lala A, Clesi P, Genet M, Uwaifo G, Charron A, Allerton T, Milliot E, Cefalu W, Melendez-Ramirez L, Richards R, Alleyn C, Gustafson E, Lizanna M, Wahlen J, Aleiwe S, Hansen M, Wahlen H, Moore M, Levy C, Bonaccorso A, Rapaport R, Tomer Y, Chia D, Goldis M, Iazzetti L, Klein M, Levister C, Waldman L, Muller S, Wallach E, Regelmann M, Antal Z, Aranda M, Reynholds C, Leech N, Wake D, Owens C, Burns M, Wotherspoon J, Nguyen T, Murray A, Short K, Curry G, Kelsey S, Lawson J, Porter J, Stevens S, Thomson E, Winship S, Wynn L, O’Donnell R, Wiltshire E, Krebs J, Cresswell P, Faherty H, Ross C, Vinik A, Barlow P, Bourcier M, Nevoret M, Couper J, Oduah V, Beresford S, Thalagne N, Roper H, Gibbons J, Hill J, Balleaut S, Brennan C, Ellis-Gage J, Fear L, Gray T, Pilger J, Jones L, McNerney C, Pointer L, Price N, Few K, Tomlinson D, Denvir L, Drew J, Randell T, Mansell P, Roberts A, Bell S, Butler S, Hooton Y, Navarra H, Roper A, Babington G, Crate L, Cripps H, Ledlie A, Moulds C, Sadler K, Norton R, Petrova B, Silkstone O, Smith C, Ghai K, Murray M, Viswanathan V, Henegan M, Kawadry O, Olson J, Stavros T, Patterson L, Ahmad T, Flores B, Domek D, Domek S, Copeland K, George M, Less J, Davis T, Short M, Tamura R, Dwarakanathan A, O’Donnell P, Boerner B, Larson L, Phillips M, Rendell M, Larson K, Smith C, Zebrowski K, Kuechenmeister L, Wood K, Thevarayapillai M, Daniels M, Speer H, Forghani N, Quintana R, Reh C, Bhangoo A, Desrosiers P, Ireland L, Misla T, Xu P, Torres C, Wells S, Villar J, Yu M, Berry D, Cook D, Soder J, Powell A, Ng M, Morrison M, Young K, Haslam Z, Lawson M, Bradley B, Courtney J, Richardson C, Watson C, Keely E, DeCurtis D, Vaccarcello-Cruz M, Torres Z, Alies P, Sandberg K, Hsiang H, Joy B, McCormick D, Powell A, Jones H, Bell J, Hargadon S, Hudson S, Kummer M, Badias F, Sauder S, Sutton E, Gensel K, Aguirre-Castaneda R, Benavides Lopez V, Hemp D, Allen S, Stear J, Davis E, Jones T, Baker A, Roberts A, Dart J, Paramalingam N, Levitt Katz L, Chaudhary N, Murphy K, Willi S, Schwartzman B, Kapadia C, Larson D, Bassi M, McClellan D, Shaibai G, Kelley L, Villa G, Kelley C, Diamond R, Kabbani M, Dajani T, Hoekstra F, Magorno M, Beam C, Holst J, Chauhan V, Wilson N, Bononi P, Sperl M, Millward A, Eaton M, Dean L, Olshan J, Renna H, Boulware D, Milliard C, Snyder D, Beaman S, Burch K, Chester J, Ahmann A, Wollam B, DeFrang D, Fitch R, Jahnke K, Bounmananh L, Hanavan K, Klopfenstein B, Nicol L, Bergstrom R, Noland T, Brodksy J, Bacon L, Quintos J, Topor L, Bialo S, Bream S, Bancroft B, Soto A, Lagarde W, Lockemer H, Vanderploeg T, Ibrahim M, Huie M, Sanchez V, Edelen R, Marchiando R, Freeman D, Palmer J, Repas T, Wasson M, Auker P, Culbertson J, Kieffer T, Voorhees D, Borgwardt T, DeRaad L, Eckert K, Gough J, Isaacson E, Kuhn H, Carroll A, Schubert M, Francis G, Hagan S, Le T, Penn M, Wickham E, Leyva C, Ginem J, Rivera K, Padilla J, Rodriguez I, Jospe N, Czyzyk J, Johnson B, Nadgir U, Marlen N, Prakasam G, Rieger C, Granger M, Glaser N, Heiser E, Harris B, Foster C, Slater H, Wheeler K, Donaldson D, Murray M, Hale D, Tragus R, Holloway M, Word D, Lynch J, Pankratz L, Rogers W, Newfield R, Holland S, Hashiguchi M, Gottschalk M, Philis-Tsimikas A, Rosal R, Kieffer M, Franklin S, Guardado S, Bohannon N, Garcia M, Aguinaldo T, Phan J, Barraza V, Cohen D, Pinsker J, Khan U, Lane P, Wiley J, Jovanovic L, Misra P, Wright M, Cohen D, Huang K, Skiles M, Maxcy S, Pihoker C, Cochrane K, Nallamshetty L, Fosse J, Kearns S, Klingsheim M, Wright N, Viles L, Smith H, Heller S, Cunningham M, Daniels A, Zeiden L, Parrimon Y, Field J, Walker R, Griffin K, Bartholow L, Erickson C, Howard J, Krabbenhoft B, Sandman C, Vanveldhuizen A, Wurlger J, Paulus K, Zimmerman A, Hanisch K, Davis-Keppen L, Cotterill A, Kirby J, Harris M, Schmidt A, Kishiyama C, Flores C, Milton J, Ramiro J, Martin W, Whysham C, Yerka A, Freels T, Hassing J, Webster J, Green R, Carter P, Galloway J, Hoelzer D, Ritzie AQL, Roberts S, Said S, Sullivan P, Allen H, Reiter E, Feinberg E, Johnson C, Newhook L, Hagerty D, White N, Sharma A, Levandoski L, Kyllo J, Johnson M, Benoit C, Iyer P, Diamond F, Hosono H, Jackman S, Barette L, Jones P, Shor A, Sills I, Bzdick S, Bulger J, Weinstock R, Douek I, Andrews R, Modgill G, Gyorffy G, Robin L, Vaidya N, Song X, Crouch S, O’Brien K, Thompson C, Thorne N, Blumer J, Kalic J, Klepek L, Paulett J, Rosolowski B, Horner J, Terry A, Watkins M, Casey J, Carpenter K, Burns C, Horton J, Pritchard C, Soetaert D, Wynne A, Kaiserman K, Halvorson M, Weinberger J, Chin C, Molina O, Patel C, Senguttuvan R, Wheeler M, Furet O, Steuhm C, Jelley D, Goudeau S, Chalmers L, Wootten M, Greer D, Panagiotopoulos C, Metzger D, Nguyen D, Horowitz M, Christiansen M, Glades E, Morimoto C, Macarewich M, Norman R, Harding P, Patin K, Vargas C, Barbanica A, Yu A, Vaidyanathan P, Osborne W, Mehra R, Kaster S, Neace S, Horner J, McDonough S, Reeves G, Cordrey C, Marrs L, Miller T, Dowshen S, Doyle D, Walker S, Catte D, Dean H, Drury-Brown M, McGee PF, Hackman B, Lee M, Malkani S, Cullen K, Johnson K, Hampton P, McCarrell M, Curtis C, Paul E, Zambrano Y, Hess KO, Phoebus D, Quinlan S, Raiden E, Batts E, Buddy C, Kirpatrick K, Ramey M, Shultz A, Webb C, Romesco M, Fradkin J, Blumberg E, Beck G, Brillon D, Gubitosi-Klug R, Laffel L, Veatch R, Wallace D, Braun J, Lernmark A, Lo B, Mitchell H, Naji A, Nerup J, Orchard T, Steffes M, Tsiatis A, Zinman B, Loechelt B, Baden L, Green M, Weinberg A, Marcovina S, Palmer JP, Weinberg A, Yu L, Babu S, Winter W, Eisenbarth GS, Bingley P, Clynes R, DiMeglio L, Eisenbarth G, Hays B, Marks J, Matheson D, Rodriguez H, Wilson D, Redondo MJ, Gomez D, Zheng X, Pena S, Pietropaolo M, Batts E, Brown T, Buckner J, Dove A, Hammond M, Hefty D, Klein J, Kuhns K, Letlau M, Lord S, McCulloch-Olson M, Miller L, Nepom G, Odegard J, Ramey M, Sachter E, St. Marie M, Stickney K, VanBuecken D, Vellek B, Webber C, Allen L, Bollyk J, Hilderman N, Ismail H, Lamola S, Sanda S, Vendettuoli H, Tridgell D, Monzavi R, Bock M, Fisher L, Halvorson M, Jeandron D, Kim M, Wood J, Geffner M, Kaufman F, Parkman R, Salazar C, Goland R, Clynes R, Cook S, Freeby M, Gallagher MP, Gandica R, Greenberg E, Kurland A, Pollak S, Wolk A, Chan M, Koplimae L, Levine E, Smith K, Trast J, DiMeglio L, Blum J, Evans-Molina C, Hufferd R, Jagielo B, Kruse C, Patrick V, Rigby M, Spall M, Swinney K, Terrell J, Christner L, Ford L, Lynch S, Menendez M, Merrill P, Pescovitz M, Rodriguez H, Alleyn C, Baidal D, Fay S, Gaglia J, Resnick B, Szubowicz S, Weir G, Benjamin R, Conboy D, deManbey A, Jackson R, Jalahej H, Orban T, Ricker A, Wolfsdorf J, Zhang HH, Wilson D, Aye T, Baker B, Barahona K, Buckingham B, Esrey K, Esrey T, Fathman G, Snyder R, Aneja B, Chatav M, Espinoza O, Frank E, Liu J, Perry J, Pyle R, Rigby A, Riley K, Soto A, Gitelman S, Adi S, Anderson M, Berhel A, Breen K, Fraser K, Gerard-Gonzalez A, Jossan P, Lustig R, Moassesfar S, Mugg A, Ng D, Prahalod P, Rangel-Lugo M, Sanda S, Tarkoff J, Torok C, Wesch R, Aslan I, Buchanan J, Cordier J, Hamilton C, Hawkins L, Ho T, Jain A, Ko K, Lee T, Phelps S, Rosenthal S, Sahakitrungruang T, Stehl L, Taylor L, Wertz M, Wong J, Philipson L, Briars R, Devine N, Littlejohn E, Grant T, Gottlieb P, Klingensmith G, Steck A, Alkanani A, Bautista K, Bedoy R, Blau A, Burke B, Cory L, Dang M, Fitzgerald-Miller L, Fouts A, Gage V, Garg S, Gesauldo P, Gutin R, Hayes C, Hoffman M, Ketchum K, Logsden-Sackett N, Maahs D, Messer L, Meyers L, Michels A, Peacock S, Rewers M, Rodriguez P, Sepulbeda F, Sippl R, Steck A, Taki I, Tran BK, Tran T, Wadwa RP, Zeitler P, Barker J, Barry S, Birks L, Bomsburger L, Bookert T, Briggs L, Burdick P, Cabrera R, Chase P, Cobry E, Conley A, Cook G, Daniels J, DiDomenico D, Eckert J, Ehler A, Eisenbarth G, Fain P, Fiallo-Scharer R, Frank N, Goettle H, Haarhues M, Harris S, Horton L, Hutton J, Jeffrrey J, Jenison R, Jones K, Kastelic W, King MA, Lehr D, Lungaro J, Mason K, Maurer H, Nguyen L, Proto A, Realsen J, Schmitt K, Schwartz M, Skovgaard S, Smith J, Vanderwel B, Voelmle M, Wagner R, Wallace A, Walravens P, Weiner L, Westerhoff B, Westfall E, Widmer K, Wright H, Schatz D, Abraham A, Atkinson M, Cintron M, Clare-Salzler M, Ferguson J, Haller M, Hosford J, Mancini D, Rohrs H, Silverstein J, Thomas J, Winter W, Cole G, Cook R, Coy R, Hicks E, Lewis N, Marks J, Pugliese A, Blaschke C, Matheson D, Sanders-Branca N, Sosenko J, Arazo L, Arce R, Cisneros M, Sabbag S, Moran A, Gibson C, Fife B, Hering B, Kwong C, Leschyshyn J, Nathan B, Pappenfus B, Street A, Boes MA, Eck SP, Finney L, Fischer TA, Martin A, Muzamhindo CJ, Rhodes M, Smith J, Wagner J, Wood B, Becker D, Delallo K, Diaz A, Elnyczky B, Libman I, Pasek B, Riley K, Trucco M, Copemen B, Gwynn D, Toledo F, Rodriguez H, Bollepalli S, Diamond F, Eyth E, Henson D, Lenz A, Shulman D, Raskin P, Adhikari S, Dickson B, Dunnigan E, Lingvay I, Pruneda L, Ramos-Roman M, Raskin P, Rhee C, Richard J, Siegelman M, Sturges D, Sumpter K, White P, Alford M, Arthur J, Aviles-Santa ML, Cordova E, Davis R, Fernandez S, Fordan S, Hardin T, Jacobs A, Kaloyanova P, Lukacova-Zib I, Mirfakhraee S, Mohan A, Noto H, Smith O, Torres N, Wherrett D, Balmer D, Eisel L, Kovalakovska R, Mehan M, Sultan F, Ahenkorah B, Cevallos J, Razack N, Ricci MJ, Rhode A, Srikandarajah M, Steger R, Russell WE, Black M, Brendle F, Brown A, Moore D, Pittel E, Robertson A, Shannon A, Thomas JW, Herold K, Feldman L, Sherwin R, Tamborlane W, Weinzimer S, Toppari J, Kallio T, Kärkkäinen M, Mäntymäki E, Niininen T, Nurmi B, Rajala P, Romo M, Suomenrinne S, Näntö-Salonen K, Simell O, Simell T, Bosi E, Battaglia M, Bianconi E, Bonfanti R, Grogan P, Laurenzi A, Martinenghi S, Meschi F, Pastore M, Falqui L, Muscato MT, Viscardi M, Castleden H, Farthing N, Loud S, Matthews C, McGhee J, Morgan A, Pollitt J, Elliot-Jones R, Wheaton C, Knip M, Siljander H, Suomalainen H, Colman P, Healy F, Mesfin S, Redl L, Wentworth J, Willis J, Farley M, Harrison L, Perry C, Williams F, Mayo A, Paxton J, Thompson V, Volin L, Fenton C, Carr L, Lemon E, Swank M, Luidens M, Salgam M, Sharma V, Schade D, King C, Carano R, Heiden J, Means N, Holman L, Thomas I, Madrigal D, Muth T, Martin C, Plunkett C, Ramm C, Auchus R, Lane W, Avots E, Buford M, Hale C, Hoyle J, Lane B, Muir A, Shuler S, Raviele N, Ivie E, Jenkins M, Lindsley K, Hansen I, Fadoju D, Felner E, Bode B, Hosey R, Sax J, Jefferies C, Mannering S, Prentis R, She J, Stachura M, Hopkins D, Williams J, Steed L, Asatapova E, Nunez S, Knight S, Dixon P, Ching J, Donner T, Longnecker S, Abel K, Arcara K, Blackman S, Clark L, Cooke D, Plotnick L, Levin P, Bromberger L, Klein K, Sadurska K, Allen C, Michaud D, Snodgrass H, Burghen G, Chatha S, Clark C, Silverberg J, Wittmer C, Gardner J, LeBoeuf C, Bell P, McGlore O, Tennet H, Alba N, Carroll M, Baert L, Beaton H, Cordell E, Haynes A, Reed C, Lichter K, McCarthy P, McCarthy S, Monchamp T, Roach J, Manies S, Gunville F, Marosok L, Nelson T, Ackerman K, Rudolph J, Stewart M, McCormick K, May S, Falls T, Barrett T, Dale K, Makusha L, McTernana C, Penny-Thomas K, Sullivan K, Narendran P, Robbie J, Smith D, Christensen R, Koehler B, Royal C, Arthur T, Houser H, Renaldi J, Watsen S, Wu P, Lyons L, House B, Yu J, Holt H, Nation M, Vickers C, Watling R, Heptulla R, Trast J, Agarwal C, Newell D, Katikaneni R, Gardner C, Del Rio A, Logan A, Collier H, Rishton C, Whalley G, Ali A, Ramtoola S, Quattrin T, Mastrandea L, House A, Ecker M, Huang C, Gougeon C, Ho J, Pacuad D, Dunger D, May J, O’Brien C, Acerini C, Salgin B, Thankamony A, Williams R, Buse J, Fuller G, Duclos M, Tricome J, Brown H, Pittard D, Bowlby D, Blue A, Headley T, Bendre S, Lewis K, Sutphin K, Soloranzo C, Puskaric J, Madison H, Rincon M, Carlucci M, Shridharani R, Rusk B, Tessman E, Huffman D, Abrams H, Biederman B, Jones M, Leathers V, Brickman W, Petrie P, Zimmerman D, Howard J, Miller L, Alemzadeh R, Mihailescu D, Melgozza-Walker R, Abdulla N, Boucher-Berry C, Ize-Ludlow D, Levy R, Swenson Brousell C, Scott R, Heenan H, Lunt H, Kendall D, Willis J, Darlow B, Crimmins N, Edler D, Weis T, Schultz C, Rogers D, Latham D, Mawhorter C, Switzer C, Spencer W, Konstantnopoulus P, Broder S, Klein J, Bachrach B, Gardner M, Eichelberger D, Knight L, Szadek L, Welnick G, Thompson B, Hoffman R, Revell A, Cherko J, Carter K, Gilson E, Haines J, Arthur G, Bowen B, Zipf W, Graves P, Lozano R, Seiple D, Spicer K, Chang A, Fregosi J, Harbinson J, Paulson C, Stalters S, Wright P, Zlock D, Freeth A, Victory J, Maheshwari H, Maheshwari A, Holmstrom T, Bueno J, Arguello R, Ahern J, Noreika L, Watson V, Hourse S, Breyer P, Kissel C, Nicholson Y, Pfeifer M, Almazan S, Bajaj J, Quinn M, Funk K, McCance J, Moreno E, Veintimilla R, Wells A, Cook J, Trunnel S, Transue D, Surhigh J, Bezzaire D, Moltz K, Zacharski E, Henske J, Desai S, Frizelis K, Khan F, Sjoberg R, Allen K, Manning P, Hendry G, Taylor B, Jones S, Couch R, Danchak R, Lieberman D, Strader W, Bencomo M, Bailey T, Bedolla L, Roldan C, Moudiotis C, Vaidya B, Anning C, Bunce S, Estcourt S, Folland E, Gordon E, Harrill C, Ireland J, Piper J, Scaife L, Sutton K, Wilkins S, Costelloe M, Palmer J, Casas L, Miller C, Burgard M, Erickson C, Hallanger-Johnson J, Clark P, Taylor W, Galgani J, Banerjee S, Banda C, McEowen D, Kinman R, Lafferty A, Gillett S, Nolan C, Pathak M, Sondrol L, Hjelle T, Hafner S, Kotrba J, Hendrickson R, Cemeroglu A, Symington T, Daniel M, Appiagyei-Dankah Y, Postellon D, Racine M, Kleis L, Barnes K, Godwin S, McCullough H, Shaheen K, Buck G, Noel L, Warren M, Weber S, Parker S, Gillespie I, Nelson B, Frost C, Amrhein J, Moreland E, Hayes A, Peggram J, Aisenberg J, Riordan M, Zasa J, Cummings E, Scott K, Pinto T, Mokashi A, McAssey K, Helden E, Hammond P, Dinning L, Rahman S, Ray S, Dimicri C, Guppy S, Nielsen H, Vogel C, Ariza C, Morales L, Chang Y, Gabbay R, Ambrocio L, Manley L, Nemery R, Charlton W, Smith P, Kerr L, Steindel-Kopp B, Alamaguer M, Tabisola-Nuesca E, Pendersen A, Larson N, Cooper-Olviver H, Chan D, Fitz-Patrick D, Carreira T, Park Y, Ruhaak R, Liljenquist D. A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk. Diabetes Care 2018; 41:1887-1894. [PMID: 30002199 PMCID: PMC6105323 DOI: 10.2337/dc18-0087] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/06/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals. RESEARCH DESIGN AND METHODS We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables. RESULTS Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002). CONCLUSIONS The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.
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Affiliation(s)
- Maria J. Redondo
- Texas Children’s Hospital, Baylor College of Medicine, Houston, TX
| | | | - Andrea K. Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO
| | - Seth Sharp
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | - John M. Wentworth
- Walter and Eliza Hall Institute of Medical Research and Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Michael N. Weedon
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
| | | | | | | | | | - Richard A. Oram
- Institute of Biomedical and Clinical Science, University of Exeter, Exeter, U.K
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Begum MS, Sarker UK, Islam MA, Sangma MA, Paul P, Rahman MA. Magnetic Resonance Imaging in Evaluation of Sinonasal Masses with Histopathological Correlation. Mymensingh Med J 2018; 27:26-33. [PMID: 29459588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Sinonasal mass is the abnormal growth of tissue from nasal cavity and mucosa of the paranasal sinuses. The growth may be benign or malignant. The benign lesion grows slowly and does not metastasize. The malignant lesion grows rapidly and metastasizes early. The aim of this study is to evaluate and diagnose the various types of sinonasal masses with MRI and its correlation with histopathological findings. This cross sectional descriptive study was carried out for a period of 02 years, from July 2015 to June 2017. The patients were selected from the ENT outpatient department and from the department Radiology & Imaging of Mymensingh Medical College Hospital, Mymensingh, Bangladesh who were reported as case of sinonasal masses. Thirty three (33) patients (17 males and 16 females) with sinonasal masses were included after fulfilling exclusion & inclusion criteria which was confirmed by proper clinical examination & were subjected to MRI and histopathological examination. The age range was 11 to 85 years. The nasal cavity was the most commonly involved site with sinonasal malignancies (were 4 cases, 12.12%) followed by the maxillary sinuses (were 2 cases, 6.06%). The least commonly affected site was the frontal sinuses (was 1 case, 3.03%). Histopathological findings shows benign sinonasal tumors were present in 25 cases. The most common benign lesion was sinonasal polyposis 10 cases (30.30%), followed by inverted papilloma 6 cases (18.18%) & juvenile nasopharyngeal angiofibroma 6 cases (18.18%), adenoma 02 cases (6.06%), and one case was rhinosporidiosis (3.03%). Malignant sinonasal tumors were present in 8 cases. Most common malignant tumors were nasopharyngeal carcinoma in 4 cases (12.12%), adenoid cystic carcinoma in 3 cases (9.09%) and non-Hodgkin lymphoma was present in 01 case (3.03%). MRI report shows benign masses in 23 cases of which nasopharyngeal polyposis was 10(30.30%), inverted papilloma 6(18.18%), juvenile angiofibroma 4(12.12%), adenoma 02(6.06%) & rhinosporidiosis 1(3.03%). Among 10 malignant tumors nasopharyngeal carcinoma were 6(18.18%), adenoid cystic carcinoma 3(9.09%) & non-Hodgkin lymphoma 1(3.03%). MRI findings of malignant sinonasal masses revealed that sensitivity 87.5%, specificity 40.0%, positive predictive value (PPV) 70% & negative predictive value 66%. Statistically significant association was observed between histopathology & MRI findings, p value was 0.305. Statistically significant association was found between histopathology & MRI findings.
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Affiliation(s)
- M S Begum
- Dr Mst Shahnwaz Begum, Assistant Professor, Prime Medical College & Hospital, Rangpur, Bangladesh
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Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017. [PMID: 28528990 DOI: 10.1016/j.prot.2017.05] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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Ghatak A, Chaturvedi P, Paul P, Agrawal GK, Rakwal R, Kim ST, Weckwerth W, Gupta R. Proteomics survey of Solanaceae family: Current status and challenges ahead. J Proteomics 2017; 169:41-57. [PMID: 28528990 DOI: 10.1016/j.jprot.2017.05.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/19/2017] [Accepted: 05/16/2017] [Indexed: 10/25/2022]
Abstract
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions. Among the Solanaceae members, most of the research has been focused on tomato (42%) followed by potato (28%) and tobacco (20%), owing to their economic importance. This review comprehensively covers the progress made so far in the field of Solanaceae proteomics including novel methods developed to isolate the proteins from different tissues. Moreover, key proteins presented in this review can serve as a resource to select potential targets for crop improvement. We envisage that information presented in this review would enable us to design the stress tolerant plants with enhanced yields.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Puneet Paul
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 68583-0915, USA
| | - Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal
| | - Randeep Rakwal
- Research Laboratory for Biotechnology and Biochemistry (RLABB), GPO Box 13265, Kathmandu, Nepal; GRADE Academy Private Limited, Adarsh Nagar-13, Birgunj, Nepal; Faculty of Health and Sport Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan; Global Research Center for Innovative Life Science, Peptide Drug Innovation, School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 4-41 Ebara 2-chome, Shinagawa, Tokyo 142-8501, Japan
| | - Sun Tae Kim
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Ravi Gupta
- Department of Plant Bioscience, Life and Industry Convergence Research Institute, Pusan National University, Miryang 627-707, Republic of Korea.
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Paul P, Talukder S, Sangma MA, Saha PL, Begum M, Razi AZ, Ferdousi RA, Sarkar SK, Rahman MM, Mirja TT, Sarker UK, Ahmed MU. Detection of Ovarian Tumor by Color Doppler Ultrasonography and CA-125. Mymensingh Med J 2017; 26:705-709. [PMID: 29208855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ovarian cancer is the most frequent cause of death from all gynaecological malignancies because of its insidious onset, vague symptoms and late presentation. This cross-sectional study was carried out on purposively selected 43 patients with suspected ovarian tumor in the Department of Radiology and Imaging in collaboration with the Department of Gynaecology and Obstetrics and Department of Pathology, Mymensingh Medical College Hospital, Bangladesh from January 2015 to December 2016 to assess the diagnostic performance of color Doppler ultrasonography and CA-125 in a combination described as Novel Index in detection of ovarian tumor. Highest number of patients of ovarian tumor 10(23.26%) were in age group 35 to 44 years and 45 to 54 years with a mean of 37.72±15.65 years with a range of 8-70 years. Histopathology findings revealed 19(44.18%) benign tumors and 24(55.82%) malignant tumors. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of Resistance Index (RI) in diagnosis of ovarian tumor were 91.67%, 89.47%, 91.67%, 89.47% and 90.69% respectively. Sensitivity, specificity, PPV, NPV and accuracy of serum CA-125 were 83.33%, 89.47%, 90.90%, 80.95% and 86.04% respectively. Sensitivity, specificity, PPV, NPV and accuracy of Novel index were 95.83%, 89.47%, 92.00%, 94.44% and 93.02% respectively. Novel index showed better diagnostic performance. Based on the current study it is concluded that the combination of color Doppler ultrasonography and serum CA-125 can be useful for diagnosis of ovarian tumor.
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Affiliation(s)
- P Paul
- Dr Pratima Paul, Assistant Professor, Department of Radiology and Imaging, Jahurul Islam Medical College & Hospital, Kishoregonj, Bangladesh
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Paul P, Chaturvedi P, Mesihovic A, Ghatak A, Weckwerth W, Schleiff E. Protocol for Enrichment of the Membrane Proteome of Mature Tomato Pollen. Bio Protoc 2017; 7:e2315. [PMID: 34541080 DOI: 10.21769/bioprotoc.2315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/01/2017] [Accepted: 05/02/2017] [Indexed: 11/02/2022] Open
Abstract
We established and elaborated on a method to enrich the membrane proteome of mature pollen from economically relevant crop using the example of Solanum lycopersicum (tomato). To isolate the pollen protein fraction enriched in membrane proteins, a high salt concentration (750 mM of sodium chloride) was used. The membrane protein-enriched fraction was then subjected to shotgun proteomics for identification of proteins, followed by in silico analysis to annotate and classify the detected proteins.
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Affiliation(s)
- Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany.,Current address: Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, USA
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Anida Mesihovic
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany.,Cluster of Excellence, Goethe University, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany, Germany
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Butt TE, Alam A, Gouda HM, Paul P, Mair N. Baseline study and risk analysis of landfill leachate - Current state-of-the-science of computer aided approaches. Sci Total Environ 2017; 580:130-135. [PMID: 27986314 DOI: 10.1016/j.scitotenv.2016.10.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 10/03/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
For the successful completion of a risk analysis process, its foundation (i.e. a baseline study) has to be well established. For this purpose, a baseline study needs to be more integrated than ever, particularly when environmental legislation is increasingly becoming stringent and integrated. This research investigates and concludes that no clear evidence of computer models for baseline study has been found in a whole-system and integrated format, which risk assessors could readily and effectively use to underpin risk analyses holistically and yet specifically for landfill leachate. This is established on the basis of investigation of software packages that are particularly closely related to landfills. Holistic baseline study is also defined along with its implications and in the context of risk assessment of landfill leachate. The study also indicates a number of factors and features that need to be added to baseline study in order to render it more integrated thereby enhancing risk analyses for landfill leachate.
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Affiliation(s)
- T E Butt
- Centre of Water Systems (CWS), College of Engineering, Mathematics & Physical Sciences (CEMPS), The University of Exeter, Harrison Building, North Park Road, Exeter PostCode: EX4 4QF, England, UK; School of Architecture, Built & Natural Environments (SABNE), Faculty of Architecture, Computing & Engineering (FACE), University of Wales Trinity Saint David (UWTSD), Mount Pleasant Campus, Swansea, PostCode: SA1 6ED, Wales, UK.
| | - A Alam
- College of Earth and Environmental Sciences, University of the Punjab, Lahore, Pakistan.
| | - H M Gouda
- Department of Geography and Environmental Management, University of the West of England, Coldharbour Lane, Bristol PostCode: BS16 1QY, England, UK.
| | - P Paul
- Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames, Surrey PostCode: KT1 2EE, England, UK.
| | - N Mair
- Environmental Leadership Ltd., 440 St. Helens Road, Bolton PostCode: BL3 3RS, England, UK.
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Benyamine A, Arnaud L, Lesavre N, Kaplanski G, Harlé J, Weiller P, Bernard-Guervilly F, Rossi P, Sabatier F, Paul P, Dignat-George F, Granel B. Taux sériques élevés de Fractalkine et mobilisation des cellules progénitrices endothéliales dans la sclérodermie systémique. Rev Med Interne 2016. [DOI: 10.1016/j.revmed.2016.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Paul P, Kuriakose T, John J, Raju R, George K, Amritanand A, Doss PA, Muliyil J. Prevalence and Visual Outcomes of Cataract Surgery in Rural South India: A Cross-Sectional Study. Ophthalmic Epidemiol 2016; 23:309-15. [PMID: 27552313 DOI: 10.1080/09286586.2016.1212991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE To determine the prevalence of cataract surgery and postoperative vision-related outcomes, especially with respect to sex, socioeconomic status (SES) and site of first contact with eye care, in a rural area of South India. METHODS In a population-based cross-sectional survey of 5530 individuals aged 50 years or older from 10 villages selected by cluster sampling, individuals who had undergone cataract surgery in one or both eyes were identified. Consenting participants were administered a questionnaire, underwent vision assessment and ophthalmic examination. Outcomes were classified as good if visual acuity of the operated eye was 6/18 or better, fair if worse than 6/18 but better than or equal to 6/60, and poor if worse than 6/60. RESULTS Prevalence of cataract surgery in this age group (771 persons) was 13.9% (95% confidence interval, CI, 13.0-14.9%). In the 1112 eyes of 749 persons studied, at presentation, 53.1% (95% CI 50.1-56.1%) of operated eyes had good, 38.1% (95% CI 35.2-41.0%) had fair, and 8.8% (95% CI 7.1-10.5%) had poor outcomes. With pinhole, 75.2% (95% CI 72.6-77.8%) had good, 17.2% (95% CI 14.9-19.5%) had fair, and 7.4% (95% CI 5.8-9.0%) had poor outcomes. In 76.3% of eyes with fair and poor presenting outcomes we detected an avoidable cause for the suboptimal visual acuity. Place of surgery and duration since surgery of 3 years or more were risk factors for blindness, while SES, sex and site of first eye care contact were not. CONCLUSION The high prevalence of avoidable causes of visual impairment in this rural setting indicates the scope for preventive strategies.
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Affiliation(s)
- P Paul
- a Department of Ophthalmology , Christian Medical College , Vellore , India
| | - T Kuriakose
- a Department of Ophthalmology , Christian Medical College , Vellore , India
| | - J John
- b Department of Community Health , Christian Medical College , Vellore , India
| | - R Raju
- a Department of Ophthalmology , Christian Medical College , Vellore , India
| | - K George
- b Department of Community Health , Christian Medical College , Vellore , India
| | - A Amritanand
- a Department of Ophthalmology , Christian Medical College , Vellore , India
| | - P A Doss
- a Department of Ophthalmology , Christian Medical College , Vellore , India
| | - J Muliyil
- b Department of Community Health , Christian Medical College , Vellore , India
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Paul P, Röth S, Schleiff E. Importance of organellar proteins, protein translocation and vesicle transport routes for pollen development and function. Plant Reprod 2016; 29:53-65. [PMID: 26874709 DOI: 10.1007/s00497-016-0274-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/18/2016] [Indexed: 05/27/2023]
Abstract
Protein translocation. Cellular homeostasis strongly depends on proper distribution of proteins within cells and insertion of membrane proteins into the destined membranes. The latter is mediated by organellar protein translocation and the complex vesicle transport system. Considering the importance of protein transport machineries in general it is foreseen that these processes are essential for pollen function and development. However, the information available in this context is very scarce because of the current focus on deciphering the fundamental principles of protein transport at the molecular level. Here we review the significance of protein transport machineries for pollen development on the basis of pollen-specific organellar proteins as well as of genetic studies utilizing mutants of known organellar proteins. In many cases these mutants exhibit morphological alterations highlighting the requirement of efficient protein transport and translocation in pollen. Furthermore, expression patterns of genes coding for translocon subunits and vesicle transport factors in Arabidopsis thaliana are summarized. We conclude that with the exception of the translocation systems in plastids-the composition and significance of the individual transport systems are equally important in pollen as in other cell types. Apparently for plastids only a minimal translocon, composed of only few subunits, exists in the envelope membranes during maturation of pollen. However, only one of the various transport systems known from thylakoids seems to be required for the function of the "simple thylakoid system" existing in pollen plastids. In turn, the vesicle transport system is as complex as seen for other cell types as it is essential, e.g., for pollen tube formation.
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Affiliation(s)
- Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany
| | - Sascha Röth
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt Am Main, Germany.
- Cluster of Excellence Frankfurt, Goethe University, 60438, Frankfurt Am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, 60438, Frankfurt Am Main, Germany.
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Powell K, Kwee E, Nutter B, Herderick E, Paul P, Thut D, Boehm C, Muschler G. Variability in subjective review of umbilical cord blood colony forming unit assay. Cytometry 2016; 90:517-524. [DOI: 10.1002/cyto.b.21376] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 03/16/2016] [Accepted: 04/05/2016] [Indexed: 11/11/2022]
Affiliation(s)
- K. Powell
- Biomedical Informatics; the Ohio State University; Columbus OH
| | - E. Kwee
- Biomedical Engineering; Case Western Reserve University; Cleveland OH
- Biomedical Engineering; Cleveland Clinic; Cleveland OH
| | - B. Nutter
- Quantitative Health Sciences; Cleveland Clinic; Cleveland OH
| | | | - P. Paul
- Cleveland Cord Blood Center; Cleveland OH
| | - D. Thut
- Cleveland Cord Blood Center; Cleveland OH
| | - C. Boehm
- Biomedical Engineering; Cleveland Clinic; Cleveland OH
| | - G. Muschler
- Biomedical Engineering; Cleveland Clinic; Cleveland OH
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Fragkostefanakis S, Mesihovic A, Simm S, Paupière MJ, Hu Y, Paul P, Mishra SK, Tschiersch B, Theres K, Bovy A, Schleiff E, Scharf KD. HsfA2 Controls the Activity of Developmentally and Stress-Regulated Heat Stress Protection Mechanisms in Tomato Male Reproductive Tissues. Plant Physiol 2016; 170:2461-77. [PMID: 26917685 PMCID: PMC4825147 DOI: 10.1104/pp.15.01913] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 02/23/2016] [Indexed: 05/18/2023]
Abstract
Male reproductive tissues are more sensitive to heat stress (HS) compared to vegetative tissues, but the basis of this phenomenon is poorly understood. Heat stress transcription factors (Hsfs) regulate the transcriptional changes required for protection from HS In tomato (Solanum lycopersicum), HsfA2 acts as coactivator of HsfA1a and is one of the major Hsfs accumulating in response to elevated temperatures. The contribution of HsfA2 in heat stress response (HSR) and thermotolerance was investigated in different tissues of transgenic tomato plants with suppressed HsfA2 levels (A2AS). Global transcriptome analysis and immunodetection of two major Hsps in vegetative and reproductive tissues showed that HsfA2 regulates subsets of HS-induced genes in a tissue-specific manner. Accumulation of HsfA2 by a moderate HS treatment enhances the capacity of seedlings to cope with a subsequent severe HS, suggesting an important role for HsfA2 in regulating acquired thermotolerance. In pollen, HsfA2 is an important coactivator of HsfA1a during HSR HsfA2 suppression reduces the viability and germination rate of pollen that received the stress during the stages of meiosis and microspore formation but had no effect on more advanced stages. In general, pollen meiocytes and microspores are characterized by increased susceptibility to HS due to their lower capacity to induce a strong HSR This sensitivity is partially mitigated by the developmentally regulated expression of HsfA2 and several HS-responsive genes mediated by HsfA1a under nonstress conditions. Thereby, HsfA2 is an important factor for the priming process that sustains pollen thermotolerance during microsporogenesis.
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Affiliation(s)
- Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Anida Mesihovic
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Marine Josephine Paupière
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Yangjie Hu
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Shravan Kumar Mishra
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Bettina Tschiersch
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Klaus Theres
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Arnaud Bovy
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
| | - Klaus-Dieter Scharf
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, D-60438 Frankfurt am Main, Germany (S.F., A.M., S.S., Y.H., P.P., S.K.M., E.S., K.-D.S.);Cluster of Excellence Frankfurt, Goethe University, D-60438 Frankfurt am Main, Germany (S.S., E.S.);Plant Breeding, Wageningen University, Wageningen 6708PB, The Netherlands (M.J.P., A.B.);Leibniz Institute of Plant Biochemistry, D-06120 Halle (Saale), Germany (B.T., K.-D.S.);Max Planck Institute for Plant Breeding Research, D-50829 Cologne, Germany (K.T.); andBuchmann Institute for Molecular Life Sciences, Goethe University, D-60438 Frankfurt am Main, Germany (E.S.)
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Abstract
Autophagy is an important cellular catabolic process conserved from yeast to man. Double-membrane vesicles deliver their cargo to the lysosome for degradation. Hence, autophagy is one of the key mechanisms mammalian cells deploy to rid themselves of intracellular pathogens including viruses. However, autophagy serves many more functions during viral infection. First, it regulates the immune response through selective degradation of immune components, thus preventing possibly harmful overactivation and inflammation. Additionally, it delivers virus-derived antigens to antigen-loading compartments for presentation to T lymphocytes. Second, it might take an active part in the viral life cycle by, eg, facilitating its release from cells. Lastly, in the constant arms race between host and virus, autophagy is often hijacked by viruses and manipulated to their own advantage. In this review, we will highlight key steps during viral infection in which autophagy plays a role. We have selected some exemplary viruses and will describe the molecular mechanisms behind their intricate relationship with the autophagic machinery, a result of host-pathogen coevolution.
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Affiliation(s)
- P Paul
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - C Münz
- Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland.
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Paul P, Chaturvedi P, Selymesi M, Ghatak A, Mesihovic A, Scharf KD, Weckwerth W, Simm S, Schleiff E. The membrane proteome of male gametophyte in Solanum lycopersicum. J Proteomics 2016; 131:48-60. [DOI: 10.1016/j.jprot.2015.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 09/21/2015] [Accepted: 10/08/2015] [Indexed: 12/11/2022]
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Ghatak A, Paul P, Hawcutt DB, White HD, Furlong NJ, Saunders S, Morrison G, Langridge P, Weston PJ. UK service level audit of insulin pump therapy in paediatrics. Diabet Med 2015; 32:1652-7. [PMID: 25884635 DOI: 10.1111/dme.12782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/15/2015] [Indexed: 12/01/2022]
Abstract
AIM To conduct an audit of insulin pump therapy in the UK after the issue of guidelines for the use of continuous subcutaneous insulin infusion by NICE in 2008 (Technology Appraisal 151). METHODS All centres in the UK, providing pump services to children and young people were invited to participate in an online audit. Audit metrics were aligned to NICE Technology Appraisal 151 and an electronic data collection tool was used. RESULTS Of the 176 UK centres identified as providing pump services, 166 (94.3%) participated in the study. A total of 5094 children and young people were identified as using continuous subcutaneous insulin infusion (19% of all paediatric patients with Type 1 diabetes), with a median (range) of 16.9 (0.67-69.4)% per centre. Units had a median of 0.58 consultant sessions, 0.43 full-time equivalent diabetic specialist nurses, and 0.1 full-time equivalent dieticians delivering the pump service. The majority of this time was not formally funded. Families could access 24-h clinical and technical support (83% units), although the delivery varied between consultant, diabetic specialist nurse and company representatives. Only 53% of units ran, or accessed, structured education programmes for continuous subcutaneous insulin infusion use. Most units (86%) allowed continuous subcutaneous insulin infusion use for paediatric inpatients, but only 56% had written guidelines for this scenario. Nine percent of units had encountered funding refusal for a patient fulfilling NICE (Technology Appraisal 151) criteria. CONCLUSION The number of children and young people on continuous subcutaneous insulin infusion therapy is consistent with numbers estimated by NICE. There is a worrying lack of funded healthcare professional time. The audit also identified gaps in the provision of structured education and absence of written inpatient guidelines.
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Affiliation(s)
- A Ghatak
- Alder Hey Children's Hospital, Liverpool, UK
| | - P Paul
- Alder Hey Children's Hospital, Liverpool, UK
| | - D B Hawcutt
- Alder Hey Children's Hospital, Liverpool, UK
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - H D White
- Aintree University Hospital NHS Trust, Liverpool, UK
| | - N J Furlong
- St Helens and Knowsley NHS Trust, St Helens, UK
| | - S Saunders
- Warrington and Halton Hospitals NHS Trust, Warrington, UK
| | - G Morrison
- The Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
| | | | - P J Weston
- The Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UK
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Mansencal N, Arslan M, Richard P, Guerard S, Brion R, Paul P, Dubourg O, Komajda M, Isnard R, Charron P. 2 Borderline hypertrophic cardiomyopathy or athlete's heart: what is the role for imaging and genetic testing in athletes? Archives of Cardiovascular Diseases Supplements 2015. [DOI: 10.1016/s1878-6480(15)30240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Fragkostefanakis S, Simm S, Paul P, Bublak D, Scharf KD, Schleiff E. Chaperone network composition in Solanum lycopersicum explored by transcriptome profiling and microarray meta-analysis. Plant Cell Environ 2015; 38:693-709. [PMID: 25124075 DOI: 10.1111/pce.12426] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 08/05/2014] [Indexed: 05/28/2023]
Abstract
Heat shock proteins (Hsps) are molecular chaperones primarily involved in maintenance of protein homeostasis. Their function has been best characterized in heat stress (HS) response during which Hsps are transcriptionally controlled by HS transcription factors (Hsfs). The role of Hsfs and Hsps in HS response in tomato was initially examined by transcriptome analysis using the massive analysis of cDNA ends (MACE) method. Approximately 9.6% of all genes expressed in leaves are enhanced in response to HS, including a subset of Hsfs and Hsps. The underlying Hsp-Hsf networks with potential functions in stress responses or developmental processes were further explored by meta-analysis of existing microarray datasets. We identified clusters with differential transcript profiles with respect to abiotic stresses, plant organs and developmental stages. The composition of two clusters points towards two major chaperone networks. One cluster consisted of constitutively expressed plastidial chaperones and other genes involved in chloroplast protein homeostasis. The second cluster represents genes strongly induced by heat, drought and salinity stress, including HsfA2 and many stress-inducible chaperones, but also potential targets of HsfA2 not related to protein homeostasis. This observation attributes a central regulatory role to HsfA2 in controlling different aspects of abiotic stress response and tolerance in tomato.
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Affiliation(s)
- Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, 60438, Frankfurt/Main, Germany; Cluster of Excellence Frankfurt, Goethe University, 60438, Frankfurt/Main, Germany
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Simm S, Fragkostefanakis S, Paul P, Keller M, Einloft J, Scharf KD, Schleiff E. Identification and Expression Analysis of Ribosome Biogenesis Factor Co-orthologs in Solanum lycopersicum. Bioinform Biol Insights 2015; 9:1-17. [PMID: 25698879 PMCID: PMC4325683 DOI: 10.4137/bbi.s20751] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/17/2014] [Accepted: 11/21/2014] [Indexed: 12/12/2022] Open
Abstract
Ribosome biogenesis involves a large inventory of proteinaceous and RNA cofactors. More than 250 ribosome biogenesis factors (RBFs) have been described in yeast. These factors are involved in multiple aspects like rRNA processing, folding, and modification as well as in ribosomal protein (RP) assembly. Considering the importance of RBFs for particular developmental processes, we examined the complexity of RBF and RP (co-)orthologs by bioinformatic assignment in 14 different plant species and expression profiling in the model crop Solanum lycopersicum. Assigning (co-)orthologs to each RBF revealed that at least 25% of all predicted RBFs are encoded by more than one gene. At first we realized that the occurrence of multiple RBF co-orthologs is not globally correlated to the existence of multiple RP co-orthologs. The transcript abundance of genes coding for predicted RBFs and RPs in leaves and anthers of S. lycopersicum was determined by next generation sequencing (NGS). In combination with existing expression profiles, we can conclude that co-orthologs of RBFs by large account for a preferential function in different tissue or at distinct developmental stages. This notion is supported by the differential expression of selected RBFs during male gametophyte development. In addition, co-regulated clusters of RBF and RP coding genes have been observed. The relevance of these results is discussed.
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Affiliation(s)
- Stefan Simm
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany. ; Cluster of Excellence Frankfurt, Goethe University, Frankfurt/Main, Germany
| | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany. ; Cluster of Excellence Frankfurt, Goethe University, Frankfurt/Main, Germany
| | - Puneet Paul
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Mario Keller
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Jens Einloft
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Klaus-Dieter Scharf
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt/Main, Germany. ; Center of Membrane Proteomics, Goethe University, Frankfurt/Main, Germany. ; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt/Main, Germany
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Gupta H, Paul P, Kumar N, Baxi S, Das DP. One pot synthesis of water-dispersible dehydroascorbic acid coated Fe3O4 nanoparticles under atmospheric air: Blood cell compatibility and enhanced magnetic resonance imaging. J Colloid Interface Sci 2014; 430:221-8. [DOI: 10.1016/j.jcis.2014.05.043] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 05/12/2014] [Accepted: 05/17/2014] [Indexed: 11/25/2022]
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Paul P, Simm S, Mirus O, Scharf KD, Fragkostefanakis S, Schleiff E. The complexity of vesicle transport factors in plants examined by orthology search. PLoS One 2014; 9:e97745. [PMID: 24844592 PMCID: PMC4028247 DOI: 10.1371/journal.pone.0097745] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/24/2014] [Indexed: 11/18/2022] Open
Abstract
Vesicle transport is a central process to ensure protein and lipid distribution in eukaryotic cells. The current knowledge on the molecular components and mechanisms of this process is majorly based on studies in Saccharomyces cerevisiae and Arabidopsis thaliana, which revealed 240 different proteinaceous factors either experimentally proven or predicted to be involved in vesicle transport. In here, we performed an orthologue search using two different algorithms to identify the components of the secretory pathway in yeast and 14 plant genomes by using the 'core-set' of 240 factors as bait. We identified 4021 orthologues and (co-)orthologues in the discussed plant species accounting for components of COP-II, COP-I, Clathrin Coated Vesicles, Retromers and ESCRTs, Rab GTPases, Tethering factors and SNAREs. In plants, we observed a significantly higher number of (co-)orthologues than yeast, while only 8 tethering factors from yeast seem to be absent in the analyzed plant genomes. To link the identified (co-)orthologues to vesicle transport, the domain architecture of the proteins from yeast, genetic model plant A. thaliana and agriculturally relevant crop Solanum lycopersicum has been inspected. For the orthologous groups containing (co-)orthologues from yeast, A. thaliana and S. lycopersicum, we observed the same domain architecture for 79% (416/527) of the (co-)orthologues, which documents a very high conservation of this process. Further, publically available tissue-specific expression profiles for a subset of (co-)orthologues found in A. thaliana and S. lycopersicum suggest that some (co-)orthologues are involved in tissue-specific functions. Inspection of localization of the (co-)orthologues based on available proteome data or localization predictions lead to the assignment of plastid- as well as mitochondrial localized (co-)orthologues of vesicle transport factors and the relevance of this is discussed.
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Affiliation(s)
- Puneet Paul
- Department of Biosciences Molecular Cell Biology of Plants
| | - Stefan Simm
- Department of Biosciences Molecular Cell Biology of Plants
| | - Oliver Mirus
- Department of Biosciences Molecular Cell Biology of Plants
| | | | | | - Enrico Schleiff
- Department of Biosciences Molecular Cell Biology of Plants
- Cluster of Excellence Frankfurt
- Center of Membrane Proteomics; Goethe University Frankfurt, Frankfurt/Main, Germany
- * E-mail:
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White HD, Goenka N, Furlong NJ, Saunders S, Morrison G, Langridge P, Paul P, Ghatak A, Weston PJ. The U.K. service level audit of insulin pump therapy in adults. Diabet Med 2014; 31:412-8. [PMID: 24117515 DOI: 10.1111/dme.12325] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/27/2013] [Accepted: 09/19/2013] [Indexed: 11/30/2022]
Abstract
AIMS The National Institute for Health and Clinical Excellence (NICE) published guidelines for the use of continuous subcutaneous insulin infusion in 2008 (technology appraisal 151). The first U.K.-wide insulin pump audit took place in 2012 with the aim of determining adherence to the guidance issued in NICE technology appraisal 151. The results of the adult service level audit are reported here. METHODS All centres providing continuous subcutaneous insulin infusion services to adults with diabetes in the U.K. were invited to participate. Audit metrics were aligned to technology appraisal 151. Data entry took place online using a DiabetesE formatted data collection tool. RESULTS One hundred and eighty-three centres were identified as delivering adult continuous subcutaneous insulin infusion services in the U.K., of which 178 (97.3%) participated in the audit. At the time of the audit, 13 428 adults were using insulin pump therapy, giving an estimated prevalence of use of 6%. Ninety-three per cent of centres did not report any barriers in obtaining funding for patients who fulfilled NICE criteria. The mean number of consultant programmed activities dedicated to continuous subcutaneous insulin infusion services was 0.96 (range 0-8), mean whole-time equivalent diabetes specialist nurses was 0.62 (range 0-3) and mean whole-time equivalent dietitian services was 0.3 (range 0-2), of which 39, 61 and 60%, respectively, were not formally funded. CONCLUSIONS The prevalence of continuous subcutaneous insulin infusion use in the U.K. falls well below the expectation of NICE (15-20%) and that of other European countries (> 15%) and the U.S.A. (40%). This may be attributable, in part, to lack of healthcare professional time needed for identification and training of new pump therapy users.
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Affiliation(s)
- H D White
- Aintree University Hospital NHS Trust, Liverpool, UK
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Castle PE, Qiao YL, Zhao FH, Chen W, Valdez M, Zhang X, Kang LN, Bansil P, Paul P, Bai P, Peck R, Li J, Chen F, Jeronimo J. Clinical determinants of a positive visual inspection after treatment with acetic acid for cervical cancer screening. BJOG 2014; 121:739-46. [PMID: 24575872 DOI: 10.1111/1471-0528.12646] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/30/2013] [Indexed: 11/30/2022]
Affiliation(s)
- PE Castle
- Global Cancer Initiative; Chestertown MD USA
| | - Y-L Qiao
- Cancer Institute and Hospital; Chinese Academy of Medical Sciences; Peking Union Medical College; Beijing China
| | - F-H Zhao
- Cancer Institute and Hospital; Chinese Academy of Medical Sciences; Peking Union Medical College; Beijing China
| | - W Chen
- Cancer Institute and Hospital; Chinese Academy of Medical Sciences; Peking Union Medical College; Beijing China
| | | | - X Zhang
- Cancer Institute and Hospital; Chinese Academy of Medical Sciences; Peking Union Medical College; Beijing China
| | - L-N Kang
- Cancer Institute and Hospital; Chinese Academy of Medical Sciences; Peking Union Medical College; Beijing China
| | | | | | - P Bai
- Cancer Institute and Hospital; Chinese Academy of Medical Sciences; Peking Union Medical College; Beijing China
| | | | - J Li
- Cancer Institute and Hospital; Chinese Academy of Medical Sciences; Peking Union Medical College; Beijing China
| | - F Chen
- Cancer Institute and Hospital; Chinese Academy of Medical Sciences; Peking Union Medical College; Beijing China
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Rebbeck T, Macedo L, Paul P, Trevena L, Cameron ID. General practitioners' knowledge of whiplash guidelines improved with online education. AUST HEALTH REV 2014; 37:688-94. [PMID: 24160566 DOI: 10.1071/ah13057] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 08/02/2013] [Indexed: 11/23/2022]
Abstract
OBJECTIVE The primary objective of this study was to evaluate the effect of an online education program used to implement the Australian (New South Wales) whiplash guidelines with general practitioners (GP). The secondary aim was to identify factors associated with learning. METHODS An online educational and evaluation activity was developed to reflect the key messages for GP from the Australian whiplash guidelines. The educational activity was hosted on the Royal Australian College of General Practitioners' website (www.gplearning.com.au) for a period of 3 years. Participants were recruited through advertisement and media releases. Participants completed a baseline evaluation of their knowledge, participated in the interactive educational activity and completed a post-knowledge questionnaire. The primary outcome was change in professional knowledge, predictors of learning were computed using linear regression. RESULTS Two hundred and fifteen GP participated. Knowledge significantly improved between baseline and post-knowledge questionnaire scores (P < 0.00001). A total of 57.2% of participants improved their knowledge by more than 20%, indicating a large effect. Low baseline knowledge predicted learning, accounting for 71% of the variance. CONCLUSIONS Online education of GP significantly improved their knowledge in relation to guidelines for whiplash. Those with low baseline knowledge improved their knowledge the most, suggesting that implementation strategies should be targeted at this group.
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Affiliation(s)
- T Rebbeck
- Discipline of Physiotherapy, Faculty of Health Science, The University of Sydney, Lidcombe, NSW 2141, Australia
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Butt TE, Gouda HM, Baloch MI, Paul P, Javadi AA, Alam A. Literature review of baseline study for risk analysis - the landfill leachate case. Environ Int 2014; 63:149-162. [PMID: 24295846 DOI: 10.1016/j.envint.2013.09.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 09/16/2013] [Accepted: 09/23/2013] [Indexed: 06/02/2023]
Abstract
There is growing awareness and public concern about environmental impacts of waste management and disposal. Environmental policy instruments have been strengthened and associated governmental programmes have increased in recent years, resulting in high level strategies for waste management. Risk assessment is now an essential tool in the prioritisation of environmental and human health protection. However, regulators need to compare the full range of risks on a sound and consistent basis. Comparing risks from such diverse sources poses a significant challenge, and traditional hazard and risk assessments are no longer sufficient. Consideration now needs to be given to a much wider range of factors if risk assessment is to be used as an aid to more integrated decision-making process. For this purpose, baseline study - the foundation of risk assessment - can play a crucial role. To date limited research has been conducted on the need, parameters, requirements, and constituents of baseline study particularly in the context of how, why, and what information is to be collated in order to render risk assessments more appropriately integrated and complete. To establish the 'state-of-the-art' of baseline study, this paper comprehensively reviews the literature regarding environmental risk assessment in general terms, and then proceeds to review work that is specifically related to landfills and landfill leachate, thereby identifying knowledge gaps and shortfall areas. This review concludes that a holistic baseline study procedure for waste disposal sites, which risk assessors could use for carrying out risk analyses specifically for landfill leachate, does not as yet exist.
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Affiliation(s)
- T E Butt
- Centre of Water Systems (CWS), College of Engineering, Mathematics & Physical Sciences, The University of Exeter, Harrison Building, North Park Road, Exeter, EX4 4QF England, UK.
| | - H M Gouda
- Department of Geography and Environmental Management, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY England, UK
| | - M I Baloch
- Utilities Business Unit, Jacobs, 1180 Eskdale Road, Winnersh, Wokingham, RG41 5TU England, UK
| | - P Paul
- School of Engineering and Design, Brunel University, Uxbridge, UB8 3PH England, UK
| | - A A Javadi
- Department of Engineering, College of Engineering, Mathematics & Physical Sciences (CEMPS), The University of Exeter, Harrison Building, North Park Road, Exeter, EX4 4QF England, UK
| | - A Alam
- Sustainable Development Study Center, Government College University, Katchery Road, Lahore, Pakistan
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Romain C, Paul P, Qiao J, Chung D. Targeting Aurora Kinase A Inhibits Hypoxia-Mediated Neuroblastoma Tumor Progression. J Surg Res 2014. [DOI: 10.1016/j.jss.2013.11.967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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