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Marsch A, Khodosh R, Porter M, Raad J, Samimi S, Schultz B, Strowd LC, Vera L, Wong E, Smith GP. Implementing patient safety and quality improvement in dermatology. Part 1: Patient safety science. J Am Acad Dermatol 2023; 89:641-654. [PMID: 35143912 DOI: 10.1016/j.jaad.2022.01.049] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/23/2022]
Abstract
Patient safety (PS) and quality improvement (QI) have gained momentum over the last decade and are becoming more integrated into medical training, physician reimbursement, maintenance of certification, and practice improvement initiatives. While PS and QI are often lumped together, they differ in that PS is focused on preventing adverse events while QI is focused on continuous improvements to improve outcomes. The pillars of health care as defined by the 1999 Institute of Medicine report "To Err is Human: Building a Safer Health System" are safety, timeliness, effectiveness, efficiency, equity, and patient-centered care. Implementing a safety culture is dependent on all levels of the health care system. Part 1 of this CME will provide dermatologists with an overview of how PS fits into our current health care system and will include a focus on basic QI/PS terminology, principles, and processes. This article also outlines systems for the reporting of medical errors and sentinel events and the steps involved in a root cause analysis.
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Affiliation(s)
- Amanda Marsch
- University of California, San Diego Medical Center, San Diego, California
| | - Rita Khodosh
- Department of Dermatology, University of Massachusetts, Boston, Massachusetts
| | - Martina Porter
- Department of Dermatology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, Massachusetts
| | - Jason Raad
- American Academy of Dermatology, Rosemont, Illinois
| | - Sara Samimi
- University of Pennsylvania, Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Brittney Schultz
- Department of Dermatology, University of Minnesota, Minneapolis, Minnesota
| | | | - Laura Vera
- American Academy of Dermatology, Rosemont, Illinois
| | - Emily Wong
- San Antonio Uniformed Services Health Education Consortium, San Antonio, Texas
| | - Gideon P Smith
- Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts.
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Hatch MN, Etingen B, Raad J, Siddiqui S, Stroupe KT, Smith BM. Dual utilization of Medicare and VA outpatient care among Veterans with spinal cord injuries and disorders. J Spinal Cord Med 2023; 46:716-724. [PMID: 35108176 PMCID: PMC10446768 DOI: 10.1080/10790268.2022.2027321] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
OBJECTIVE Veterans with spinal cord injuries and disorders (SCI/D) utilizing Veterans Affairs healthcare facilities are also Medicare eligible. Use of multiple health care systems potentially duplicates or fragments care in this population; yet little is known about those using multiple systems. This study describes dual use of services paid for by VA and Medicare among Veterans with SCI/D. DESIGN Retrospective, cross-sectional, observational study. PARTICIPANTS Veterans with SCI/D (n = 13,902) who received healthcare services within the VA SCI System of Care and were eligible for or enrolled in Medicare in 2011. INTERVENTIONS N/A. OUTCOME MEASURES Patient characteristics, average number of visits and patient level frequencies of reasons for visits were determined for individuals within healthcare utilization (VA only, Medicare only, or dual VA/Medicare) groups. Multinomial logistic regression analyses were used to investigate associations of patient variables on dual use. RESULTS 65.3% of Veterans with SCI/D were VA only users for outpatient encounters, 4.4% had encounters paid for by Medicare only, and 30.3% were dual users. Veterans were less likely to be VA only users if they were older than 69 and if they had been injured for greater than ten years. African American Veterans with SCI (compared to white) were more likely to be VA only users. CONCLUSION A substantial number (∼30%) of Veterans with SCI/D are dual users. These numbers highlight the importance of improved strategies to coordinate care and increase health information sharing across systems.
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Affiliation(s)
- Maya N Hatch
- Spinal Cord Injury/Disorder Center, Long Beach Veterans Affairs (VA) Medical Center, Long Beach, California, USA
- Physical Medicine & Rehabilitation Department, UC Irvine School of Medicine, Irvine, California, USA
| | - Bella Etingen
- Center of Innovation for Complex Chronic Healthcare, Edward Hines Jr. Department of VA Hospital, Chicago, Illinois, USA
| | - Jason Raad
- Econometrica, Inc, Bethesda, Massachusetts, USA
| | - Sameer Siddiqui
- Spinal Cord Injury/Disorder Center, Louis Stokes Cleveland (VA) Medical Center, Cleveland, Ohio, USA
- Department of Physical Medicine & Rehabilitation, Case Western Reserve University, Cleveland, Ohio, USA
| | - Kevin T Stroupe
- Center of Innovation for Complex Chronic Healthcare, Edward Hines Jr. Department of VA Hospital, Chicago, Illinois, USA
| | - Bridget M Smith
- Center of Innovation for Complex Chronic Healthcare, Edward Hines Jr. Department of VA Hospital, Chicago, Illinois, USA
- Institute for Healthcare Studies, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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Bugnon LA, Edera AA, Prochetto S, Gerard M, Raad J, Fenoy E, Rubiolo M, Chorostecki U, Gabaldón T, Ariel F, Di Persia LE, Milone DH, Stegmayer G. Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches. Brief Bioinform 2022; 23:6606044. [PMID: 35692094 DOI: 10.1093/bib/bbac205] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION In contrast to messenger RNAs, the function of the wide range of existing long noncoding RNAs (lncRNAs) largely depends on their structure, which determines interactions with partner molecules. Thus, the determination or prediction of the secondary structure of lncRNAs is critical to uncover their function. Classical approaches for predicting RNA secondary structure have been based on dynamic programming and thermodynamic calculations. In the last 4 years, a growing number of machine learning (ML)-based models, including deep learning (DL), have achieved breakthrough performance in structure prediction of biomolecules such as proteins and have outperformed classical methods in short transcripts folding. Nevertheless, the accurate prediction for lncRNA still remains far from being effectively solved. Notably, the myriad of new proposals has not been systematically and experimentally evaluated. RESULTS In this work, we compare the performance of the classical methods as well as the most recently proposed approaches for secondary structure prediction of RNA sequences using a unified and consistent experimental setup. We use the publicly available structural profiles for 3023 yeast RNA sequences, and a novel benchmark of well-characterized lncRNA structures from different species. Moreover, we propose a novel metric to assess the predictive performance of methods, exclusively based on the chemical probing data commonly used for profiling RNA structures, avoiding any potential bias incorporated by computational predictions when using dot-bracket references. Our results provide a comprehensive comparative assessment of existing methodologies, and a novel and public benchmark resource to aid in the development and comparison of future approaches. AVAILABILITY Full source code and benchmark datasets are available at: https://github.com/sinc-lab/lncRNA-folding. CONTACT lbugnon@sinc.unl.edu.ar.
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Affiliation(s)
- L A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - A A Edera
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - S Prochetto
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina.,IAL, CONICET, Ciudad Universitaria UNL, (3000) Santa Fe, Argentina
| | - M Gerard
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - J Raad
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - E Fenoy
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - M Rubiolo
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - U Chorostecki
- Barcelona Supercomputing Center (BSC-CNS), Institute of Research in Biomedicine (IRB), Spain
| | - T Gabaldón
- Barcelona Supercomputing Center (BSC-CNS), Institute of Research in Biomedicine (IRB), Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - F Ariel
- IAL, CONICET, Ciudad Universitaria UNL, (3000) Santa Fe, Argentina
| | - L E Di Persia
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - D H Milone
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
| | - G Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (CONICET-UNL), Ciudad Universitaria, Santa Fe, Argentina
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Bugnon LA, Raad J, Merino GA, Yones C, Ariel F, Milone DH, Stegmayer G. Deep Learning for the discovery of new pre-miRNAs: Helping the fight against COVID-19. Mach Learn Appl 2021; 6:100150. [PMID: 34939043 PMCID: PMC8427907 DOI: 10.1016/j.mlwa.2021.100150] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 01/29/2023] Open
Abstract
The Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) has been recently found responsible for the pandemic outbreak of a novel coronavirus disease (COVID-19). In this work, a novel approach based on deep learning is proposed for identifying precursors of small active RNA molecules named microRNA (miRNA) in the genome of the novel coronavirus. Viral miRNA-like molecules have shown to modulate the host transcriptome during the infection progression, thus their identification is crucial for helping the diagnosis or medical treatment of the disease. The existence of the mature miRNAs derived from computationally predicted miRNA precursors (pre-miRNAs) in the novel coronavirus was validated with small RNA-seq data from SARS-CoV-2-infected human cells. The results demonstrate that computational models can provide accurate and useful predictions of pre-miRNAs in the SARS-CoV-2 genome, underscoring the relevance of machine learning in the response to a global sanitary emergency. Moreover, the interpretability of our model shed light on the molecular mechanisms underlying the viral infection, thus contributing to the fight against the COVID-19 pandemic and the fast development of new treatments. Our study shows how recent advances in machine learning can be used, effectively, in response to public health emergencies. The approach developed in this work could be of great help in future similar emergencies to accelerate the understanding of the singularities of any viral agent and for the development of novel therapies. Data and source code available at: https://sourceforge.net/projects/sourcesinc/files/aicovid/.
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Affiliation(s)
- L A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina
| | - J Raad
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina
| | - G A Merino
- Bioengineering and Bioinformatics Research and Development Institute (IBB), FI-UNER, CONICET, Ruta 11 km 10.5, Oro Verde, Argentina
| | - C Yones
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina
| | - F Ariel
- Instituto de Agrobiotecnologia del Litoral (IAL), CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - D H Milone
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina
| | - G Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence (sinc(i)), FICH-UNL, CONICET, Ciudad Universitaria UNL, Santa Fe, Argentina
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Yones C, Raad J, Bugnon LA, Milone DH, Stegmayer G. High precision in microRNA prediction: A novel genome-wide approach with convolutional deep residual networks. Comput Biol Med 2021; 134:104448. [PMID: 33979731 DOI: 10.1016/j.compbiomed.2021.104448] [Citation(s) in RCA: 6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 11/30/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that have a key role in the regulation of gene expression. The importance of miRNAs is widely acknowledged by the community nowadays and computational methods are needed for the precise prediction of novel candidates to miRNA. This task can be done by searching homologous with sequence alignment tools, but results are restricted to sequences that are very similar to the known miRNA precursors (pre-miRNAs). Besides, a very important property of pre-miRNAs, their secondary structure, is not taken into account by these methods. To fill this gap, many machine learning approaches were proposed in the last years. However, the methods are generally tested in very controlled conditions. If these methods were used under real conditions, the false positives increase and the precisions fall quite below those published. This work provides a novel approach for dealing with the computational prediction of pre-miRNAs: a convolutional deep residual neural network (mirDNN). This model was tested with several genomes of animals and plants, the full-genomes, achieving a precision up to 5 times larger than other approaches at the same recall rates. Furthermore, a novel validation methodology was used to ensure that the performance reported in this study can be effectively achieved when using mirDNN in novel species. To provide fast an easy access to mirDNN, a web demo is available at http://sinc.unl.edu.ar/web-demo/mirdnn/. The demo can process FASTA files with multiple sequences to calculate the prediction scores and generates the nucleotide importance plots. FULL SOURCE CODE: http://sourceforge.net/projects/sourcesinc/files/mirdnn and https://github.com/cyones/mirDNN. CONTACT: gstegmayer@sinc.unl.edu.ar.
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Affiliation(s)
- C Yones
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - J Raad
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - L A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - D H Milone
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina
| | - G Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH-UNL, CONICET, Ciudad Universitaria UNL, 3000, Santa Fe, Argentina.
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Bourdel N, Huchon C, Abdel Wahab C, Azaïs H, Bendifallah S, Bolze PA, Brun JL, Canlorbe G, Chauvet P, Chereau E, Courbiere B, De La Motte Rouge T, Devouassoux-Shisheboran M, Eymerit-Morin C, Fauvet R, Gauroy E, Gauthier T, Grynberg M, Koskas M, Larouzee E, Lecointre L, Levêque J, Margueritte F, Mathieu D'argent E, Nyangoh-Timoh K, Ouldamer L, Raad J, Raimond E, Ramanah R, Rolland L, Rousset P, Rousset-Jablonski C, Thomassin-Naggara I, Uzan C, Zilliox M, Daraï E. Borderline ovarian tumors: Guidelines from the French national college of obstetricians and gynecologists (CNGOF). Eur J Obstet Gynecol Reprod Biol 2020; 256:492-501. [PMID: 33262005 DOI: 10.1016/j.ejogrb.2020.11.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 10/28/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 11/28/2022]
Abstract
It is recommended to classify Borderline Ovarian Tumors (BOTs) according to the WHO classification. Transvaginal and suprapubic ultrasonography are recommended for the analysis of an ovarian mass (Grade A). In case of an undetermined ovarian lesion on ultrasonography, it is recommended to perform a pelvic MRI (Grade A) with a score for malignancy (ADNEX MR/O-RADS) (Grade C) included in the report and to formulate a histological hypothesis (Grade C). Pelvic MRI is recommended to characterize a tumor suspected of being BOT (Grade C). It is recommended to evaluate serum levels of HE4 and CA125 and to use the ROMA score for the diagnosis of indeterminate ovarian mass on imaging (grade A). If there is a suspicion of a mucinous BOT on imaging, serum levels of CA 19-9 may be proposed (Grade C). For Early Stages (ES) of BOT, if surgery without risk of tumor rupture is possible, laparoscopy with protected extraction is recommended over laparotomy (Grade C). For treatment of a bilateral serous ES BOT with a strategy to preserve fertility and/or endocrine function, bilateral cystectomy is recommended where possible (Grade B). For mucinous BOTs with a treatment strategy of fertility and/or endocrine function preservation, unilateral salpingo-oophorectomy is recommended (grade C). For mucinous BOTs treated by initial cystectomy, unilateral salpingo-oophorectomy is recommended (grade C). For serous or mucinous ES BOTs, routine hysterectomy is not recommended (Grade C). For ES BOTs, lymphadenectomy is not recommended (Grade C). For ES BOTs, appendectomy is recommended only in case of a macroscopically pathological appendix (Grade C). Restaging surgery is recommended in cases of serous BOTs with micropapillary architecture and an incomplete abdominal cavity inspection during initial surgery (Grade C). Restaging surgery is recommended for mucinous BOTs after initial cystectomy or in cases where the appendix was not examined (Grade C). If restaging surgery is decided for ES BOTs, the following procedures should be performed: peritoneal washing (grade C), omentectomy (grade B), complete exploration of the abdominal cavity with peritoneal biopsies (grade C), visualization of the appendix and appendectomy in case of a pathological macroscopic appearance (grade C) as well as unilateral salpingo-oophorectomy in case of a mucinous BOT initially treated by cystectomy (grade C). In advanced stages (AS) of BOT, it is not recommended to perform a lymphadenectomy as a routine procedure (Grade C). For AS BOT in a patient with a desire to fall pregnant, conservative treatment involving preservation of the uterus and all or part of the ovary may be proposed (Grade C). Restaging surgery aimed at removing all lesions, not performed initially, is recommended for AS BOTs (Grade C). After treatment, follow-up for a duration greater than 5 years is recommended due to the median recurrence time of BOTs (Grade B). It is recommended that a systematic clinical examination be carried out during follow-up of a treated BOT (Grade B). If the determination of tumor markers is normal preoperatively, the routine dosage of tumor markers in BOT follow-up is not recommended (Grade C). In case of an initial elevation in serum CA 125 levels, it is recommended to monitor CA 125 during follow up (Grade B). In case of conservative treatment, it is recommended to use transvaginal and transabdominal ultrasound during follow up of a treated BOT (Grade B). In the event of a BOT recurrence in a woman of childbearing age, a second conservative treatment may be proposed (Grade C). A consultation with a physician specialized in Assisted Reproductive Technique (ART) should be offered in the case of BOTs in women of childbearing age (Grade C). When possible, a conservative surgical strategy is recommended to preserve fertility in women of childbearing age (Grade C). In the case of optimally treated BOT, there is no evidence to contraindicate the use of ART. The use of hormonal contraception after serous or mucinous BOT is not contraindicated (Grade C). After management of mucinous BOT, for women under 45 years, given the benefit of Hormonal Replacement Therapy (HRT) on cardiovascular and bone risks, and the lack of hormone sensitivity of mucinous BOTs, it is recommended to offer HRT (Grade C). Over 45 years of age, HRT can be prescribed in case of a climacteric syndrome after individual benefit to risk assessment (Grade C).
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Affiliation(s)
- N Bourdel
- Service de Chirurgie Gynécologique, CHU de Clermont Ferrand, 1 Place Lucie Aubrac, 63 003 Clermont Ferrand, France
| | - C Huchon
- Service de Gynécologie & Obstétrique, Hopital Lariboisière, 2 rue Ambroise Paré, 75010 Paris, France; Université de Paris, Paris, France.
| | - C Abdel Wahab
- APHP.6 Service de Radiologie, Hôpital Tenon, 4 rue de la Chine, 75020, Paris, France; Faculté De Médecine UPMC, Sorbonne Université, France
| | - H Azaïs
- AP-HP, Hôpital Pitié-Salpêtrière, Service De Chirurgie Et Oncologie Gynécologique Et Mammaire, 75013 Paris, France; Faculté de Médecine UPMC, Sorbonne Université, France
| | - S Bendifallah
- Service De Gynécologie-Obstétrique Et Médecine De La Reproduction, Hôpital Tenon, Assistance Publique Des Hôpitaux De Paris (AP-HP), Institut Universitaire de Cancérologie (IUC), Centre CALG (Cancer Associé à La Grossesse), UMRS-938, Faculté de Médecine UPMC, Sorbonne Université, France
| | - P A Bolze
- Service De Chirurgie Gynécologique Et Oncologique, Obstétrique, 165 Chemin du Grand Revoyet, 69310, Lyon Sud, Pierre Bénite, France; Université Lyon 1, 43 Boulevard du 11 Novembre 1918, 69100, Villeurbanne, France
| | - J L Brun
- Service De Chirurgie Gynécologique, Centre Aliénor d'Aquitaine, Hôpital Pellegrin, 33076 Bordeaux, Société Française De Gynéco Pathologie, 81 Rue Verte, 76000 Rouen, France
| | - G Canlorbe
- AP-HP, Hôpital Pitié-Salpêtrière, Service De Chirurgie Et Oncologie Gynécologique Et Mammaire, 75013 Paris, France; Faculté de Médecine UPMC, Sorbonne Université, France
| | - P Chauvet
- Service de Chirurgie Gynécologique, CHU de Clermont Ferrand, 1 Place Lucie Aubrac, 63 003 Clermont Ferrand, France
| | - E Chereau
- Service De Gynécologie Obstétrique, Hopital Saint Joseph, Marseille, France
| | - B Courbiere
- Centre Clinico-Biologique d'AMP, Pôle Femmes - Parents- Enfants, AP-HM, Hôpital de La Conception, 147 Bd Baille, 13005 Marseille, France
| | | | - M Devouassoux-Shisheboran
- Institut De Pathologie Multi-Sites Des HOSPICES CIVILS De LYON, Centre Hospitalier Lyon Sud, Centre De Biologie Et Pathologie Sud, 165 Chemin Du Grand Revoyet, 69495 Pierre Bénite. Société Française de Gynéco Pathologie, 81 Rue Verte, 76000 Rouen, France
| | - C Eymerit-Morin
- Service d'Anatomie Et Cytologie Pathologiques, Hôpital Tenon, HUEP, UPMC Paris VI, Sorbonne Universities, 4 rue de la Chine, 75020 Paris, France; Institut de Pathologie de Paris, 35 boulevard Stalingrad, 92240 Malakoff, France
| | - R Fauvet
- Service de Gynécologie Obstétrique, Centre Hospitalier Universitaire de Caen, Caen, France
| | - E Gauroy
- Service de Gynécologie-Obstétrique, Hôpital Bichat, 46 Rue Henri Huchard, 75018 Paris, France; Université de Paris, Paris, France
| | - T Gauthier
- Service De Gynécologie-Obstétrique, Hôpital Mère-Enfant, CHU Limoges, 8 Av Dominique Larrey 87042 Limoges, France
| | - M Grynberg
- Service De Médecine De La Reproduction, Hôpital Antoine Béclère, 157 Rue De La Porte De Trivaux, 92140 Clamart, France
| | - M Koskas
- Service De Gynécologie-Obstétrique, Hôpital Bichat, 46 Rue Henri Huchard, 75018 Paris, France; Université de Paris, Paris, France
| | - E Larouzee
- Service de Gynécologie-Obstétrique, Hôpital Bichat, 46 Rue Henri Huchard, 75018 Paris, France; Université de Paris, Paris, France
| | - L Lecointre
- Centre Hospitalier Universitaire Hautepierre, Hôpital de Hautepierre, CHRU Strasbourg, 1 Avenue Molière, 67000 Strasbourg, France
| | - J Levêque
- Département De Gynécologie Obstétrique Et Reproduction Humaine, 16, Boulevard De Bulgarie, 35000 CHU Anne De Bretagne, UFR Médecine Université de Rennes 1, Rennes, Bretagne, France
| | - F Margueritte
- Service De Gynécologie-Obstétrique, Hôpital Mère-Enfant, CHU Limoges, 8 Av Dominique Larrey, 87042 Limoges, France
| | - E Mathieu D'argent
- Service de Gynécologie-Obstétrique Et Médecine De La Reproduction, Hôpital Tenon, Assistance Publique Des Hôpitaux De Paris (AP-HP), Institut Universitaire de Cancérologie (IUC), Centre CALG (Cancer Associé à La Grossesse), UMRS-938, Faculté de Médecine UPMC, Sorbonne Université, France
| | - K Nyangoh-Timoh
- Département De Gynécologie Obstétrique Et Reproduction Humaine, 16, Boulevard De Bulgarie, 35000 CHU Anne De Bretagne, UFR Médecine Université de Rennes 1, Rennes, Bretagne, France
| | - L Ouldamer
- Département De Gynécologie, Centre Hospitalier Universitaire De Tours, Hôpital Bretonneau, 2 Boulevard Tonnellé, 37000, Tours, France
| | - J Raad
- Service De Médecine De La Reproduction, Hôpital Antoine Béclère, 157 Rue De La Porte De Trivaux, 92140 Clamart, France
| | - E Raimond
- Département de Gynécologie Obstétrique, Institut Alix De Champagne, CHU Reims, Reims, France
| | - R Ramanah
- Pôle Mère-Femme, CHU Besançon, 3 Boulevard Fleming, 25000 Besançon, France
| | - L Rolland
- Centre Clinico-Biologique d'AMP, Pôle Femmes - Parents- Enfants, AP-HM, Hôpital de La Conception, 147 Bd Baille, 13005 Marseille, France
| | - P Rousset
- Service de Radiologie, Centre Hospitalier Lyon Sud, HCL, EMR 3738, 165 Chemin du Grand Revoyet, 69310, Lyon Sud, Pierre-Bénite, France; Université Lyon 1, 43 Boulevard Du 11 Novembre 1918, 69100, Villeurbanne, France
| | - C Rousset-Jablonski
- Centre Léon Bérard, 28 Rue Laënnec, 69008, Lyon, France; Centre Hospitalier Lyon Sud, Pierre-Bénite, France; Université Claude Bernard Lyon 1, EA 7425 Hesper, Health Service and Performance Research, Domaine Rockefeller, 8 Avenue Rockefeller, 69373, Lyon Cedex 8, France
| | - I Thomassin-Naggara
- APHP.6 Service de Radiologie, Hôpital Tenon, 4 rue de la Chine, 75020, Paris, France; Faculté de Médecine UPMC, Sorbonne Université, France
| | - C Uzan
- AP-HP, Hôpital Pitié-Salpêtrière, Service De Chirurgie Et Oncologie Gynécologique Et Mammaire, 75013 Paris, France; Faculté de Médecine UPMC, Sorbonne Université, France
| | - M Zilliox
- Centre Hospitalier Universitaire Hautepierre, Hôpital De Hautepierre, CHRU Strasbourg, 1 Avenue Molière, 67000 Strasbourg, France
| | - E Daraï
- Service de Gynécologie-Obstétrique Et Médecine De La Reproduction, Hôpital Tenon, Assistance Publique Des Hôpitaux De Paris (AP-HP), Institut Universitaire de Cancérologie (IUC), Centre CALG (Cancer Associé à La Grossesse), UMRS-938, Faculté de Médecine UPMC, Sorbonne Université, France
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Bugnon LA, Yones C, Raad J, Gerard M, Rubiolo M, Merino G, Pividori M, Di Persia L, Milone DH, Stegmayer G. DL4papers: a deep learning approach for the automatic interpretation of scientific articles. Bioinformatics 2020; 36:3499-3506. [DOI: 10.1093/bioinformatics/btaa111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/27/2019] [Accepted: 02/14/2020] [Indexed: 01/26/2023] Open
Abstract
Abstract
Motivation
In precision medicine, next-generation sequencing and novel preclinical reports have led to an increasingly large amount of results, published in the scientific literature. However, identifying novel treatments or predicting a drug response in, for example, cancer patients, from the huge amount of papers available remains a laborious and challenging work. This task can be considered a text mining problem that requires reading a lot of academic documents for identifying a small set of papers describing specific relations between key terms. Due to the infeasibility of the manual curation of these relations, computational methods that can automatically identify them from the available literature are urgently needed.
Results
We present DL4papers, a new method based on deep learning that is capable of analyzing and interpreting papers in order to automatically extract relevant relations between specific keywords. DL4papers receives as input a query with the desired keywords, and it returns a ranked list of papers that contain meaningful associations between the keywords. The comparison against related methods showed that our proposal outperformed them in a cancer corpus. The reliability of the DL4papers output list was also measured, revealing that 100% of the first two documents retrieved for a particular search have relevant relations, in average. This shows that our model can guarantee that in the top-2 papers of the ranked list, the relation can be effectively found. Furthermore, the model is capable of highlighting, within each document, the specific fragments that have the associations of the input keywords. This can be very useful in order to pay attention only to the highlighted text, instead of reading the full paper. We believe that our proposal could be used as an accurate tool for rapidly identifying relationships between genes and their mutations, drug responses and treatments in the context of a certain disease. This new approach can certainly be a very useful and valuable resource for the advancement of the precision medicine field.
Availability and implementation
A web-demo is available at: http://sinc.unl.edu.ar/web-demo/dl4papers/. Full source code and data are available at: https://sourceforge.net/projects/sourcesinc/files/dl4papers/.
Contact
lbugnon@sinc.unl.edu.ar
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- L A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
| | - C Yones
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
| | - J Raad
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
| | - M Gerard
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
| | - M Rubiolo
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
| | - G Merino
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
- Bioengineering and Bioinformatics Research and Development Institute, IBB, FIUNER-CONICET, Ruta Prov 11, Km 10.5, Oro Verde 3100, Argentina
| | - M Pividori
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA
| | - L Di Persia
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
| | - D H Milone
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
| | - G Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence, sinc(i), FICH/UNL-CONICET, Ciudad Universitaria, Santa Fe 3000, Argentina
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Raad J, Rolland L, Grynberg M, Courbiere B, Mathieu d'Argent E. [Borderline Ovarian Tumours: CNGOF Guidelines for Clinical Practice - Fertility]. ACTA ACUST UNITED AC 2020; 48:330-336. [PMID: 32004782 DOI: 10.1016/j.gofs.2020.01.020] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
OBJECTIVES Borderline ovarian tumours (BOT) represent around 15% of all ovarian neoplasms and are more likely to be diagnosed in women of reproductive age. Overall, given the epidemiological profile of BOT and their favourable prognosis, ovarian function and fertility preservation should be systematically considered in patients presenting these lesions. METHODS The research strategy was based on the following terms: borderline ovarian tumour, fertility, fertility preservation, infertility, fertility-sparing surgery, in vitro fertilization, ovarian stimulation, oocyte cryopreservation, using PubMed, in English and French. RESULTS AND CONCLUSIONS Fertility counselling should become an integral part of the clinical management of women with BOT. Patients with BOT should be informed that surgical management of BOT may cause damage ovarian reserve and/or peritoneal adhesions. Nomogram to predict recurrence, ovarian reserve markers and fertility explorations should be used to provide a clear and relevant information about the risk of infertility in patients with BOT. Fertility-sparing surgery should be considered for young women who wish preserving their fertility when possible. There is insufficient evidence to claim a causal relation between controlled ovarian stimulation (COS) and BOT. However, in case of poor prognosis factors, the use of COS should be considered cautiously through a multidisciplinary approach. In case of infertility after surgery for BOT, COS can be performed without delay, once histopathological diagnosis of BOT is confirmed. There is insufficient consistent evidence that fertility drugs and COS increase the risk of recurrence of BOT after conservative management. The conservative surgical treatment can be associated to oocyte cryopreservation considering the high risk of recurrence of the disease. In women with BOT recurrence in a single ovary and in women with bilateral ovarian involvement when the conservative management is not possible, other fertility preservation strategies are available, but still experimental.
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Affiliation(s)
- J Raad
- Service de médecine de la reproduction, hôpital Antoine-Béclère, 157, rue de la Porte-de-Trivaux, 92140 Clamart, France.
| | - L Rolland
- Centre clinicobiologique d'AMP, pôle femmes-Parents-Enfants, hôpital de La Conception, AP-HM, 147, boulevard Baille, 13005 Marseille, France
| | - M Grynberg
- Service de médecine de la reproduction, hôpital Antoine-Béclère, 157, rue de la Porte-de-Trivaux, 92140 Clamart, France; Service de médecine de la reproduction, hôpital Jean-Verdier, avenue du 14-Juillet, 93140 Bondy, France; Unité Inserm U1133, université Paris-Diderot, 75013 Paris, France
| | - B Courbiere
- Centre clinicobiologique d'AMP, pôle femmes-Parents-Enfants, hôpital de La Conception, AP-HM, 147, boulevard Baille, 13005 Marseille, France; CNRS, IRD, IMBE, Aix-Marseille université, Avignon université, 13005 Marseille, France
| | - E Mathieu d'Argent
- Service de gynécologie-obstétrique et médecine de la reproduction, hôpital Tenon, Assistance publique-Hôpitaux de Paris, 4, rue de la Chine, 75020 Paris, France; UMR_S938 université Pierre-et-Marie-Curie, Paris 6, institut universitaire de cancérologie (IUC), Paris, France
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Raad J. The use of Functional and Psychosocial Measures Among Allied Health Professionals who treat SCI. Arch Phys Med Rehabil 2019. [DOI: 10.1016/j.apmr.2019.10.137] [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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Bugnon LA, Yones C, Raad J, Milone DH, Stegmayer G. Genome-wide hairpins datasets of animals and plants for novel miRNA prediction. Data Brief 2019; 25:104209. [PMID: 31453279 PMCID: PMC6700487 DOI: 10.1016/j.dib.2019.104209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 04/05/2019] [Revised: 06/16/2019] [Accepted: 06/25/2019] [Indexed: 01/19/2023] Open
Abstract
This article makes available several genome-wide datasets, which can be used for training microRNA (miRNA) classifiers. The hairpin sequences available are from the genomes of: Homo sapiens, Arabidopsis thaliana, Anopheles gambiae, Caenorhabditis elegans and Drosophila melanogaster. Each dataset provides the genome data divided into sequences and a set of computed features for predictions. Each sequence has one label: i) “positive”: meaning that it is a well-known pre-miRNA, according to miRBase v21; or ii) “unlabeled”: indicating that the sequence has not (yet) a known function and could be a possible candidate to novel pre-miRNA. Due to the fact that selecting an informative feature set is very important for a good pre-miRNA classifier, a representative feature set with large discriminative power has been calculated and it is provided, as well, for each genome. This feature set contains typical information about sequence, topology and structure. Dataset was publically shared in https://sourceforge.net/projects/sourcesinc/files/mirdata/.
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Affiliation(s)
- L A Bugnon
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (FICH-UNL/CONICET), Ciudad Universitaria, Santa Fe, Argentina
| | - C Yones
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (FICH-UNL/CONICET), Ciudad Universitaria, Santa Fe, Argentina
| | - J Raad
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (FICH-UNL/CONICET), Ciudad Universitaria, Santa Fe, Argentina
| | - D H Milone
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (FICH-UNL/CONICET), Ciudad Universitaria, Santa Fe, Argentina
| | - G Stegmayer
- Research Institute for Signals, Systems and Computational Intelligence sinc(i) (FICH-UNL/CONICET), Ciudad Universitaria, Santa Fe, Argentina
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Zeghari F, Sonigo C, Raad J, Sermondade N, Grynberg M. impact of breast cancer prognostic factors on the response to controlled ovarian stimulation patients undergoing fertility preservation. Fertil Steril 2018. [DOI: 10.1016/j.fertnstert.2018.07.260] [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: 11/15/2022]
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12
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Raad J, Sonigo C, Sermondade N, Zeghari F, Sifer C, Grynberg M. Influence of breast cancer prognostic factors on in-vitro maturation outcomes in patients seeking urgent fertility preservation. Fertil Steril 2018. [DOI: 10.1016/j.fertnstert.2018.07.547] [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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Abstract
Therapeutic advances in many medical fields have led to the need to consider patient quality of life after curative medico-surgical treatments for malignancy. Thus, it has become a major issue for young patients to preserve the ability to become "genetic" parents, with their own gametes. While the preservation of male fertility has been an established technique for more than 30 years, it is only in the last decade that progress in cryopreservation techniques has allowed surgeons to offer successful oocyte and ovarian tissue cryobanking. However, in addition to the still experimental nature of some fertility preservation techniques, this practice also raises many ethical and moral questions.
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Affiliation(s)
- C Vinolas
- Service de Médecine de la Reproduction & Préservation de la Fertilité, Hôpital Jean Verdier, Avenue du 14 Juillet, 93140 Bondy, France
| | - J Raad
- Service de Médecine de la Reproduction & Préservation de la Fertilité, Hôpital Jean Verdier, Avenue du 14 Juillet, 93140 Bondy, France
| | - C Sonigo
- Service de Médecine de la Reproduction & Préservation de la Fertilité, Hôpital Jean Verdier, Avenue du 14 Juillet, 93140 Bondy, France
| | - C Sifer
- Service de Cytogénétique et Biologie de la Reproduction, Hôpital Jean Verdier, Avenue du 14 Juillet, 93140 Bondy, France
| | - N Sermondade
- Service de Cytogénétique et Biologie de la Reproduction, Hôpital Jean Verdier, Avenue du 14 Juillet, 93140 Bondy, France
| | - M Grynberg
- Service de Médecine de la Reproduction & Préservation de la Fertilité, Hôpital Jean Verdier, Avenue du 14 Juillet, 93140 Bondy, France; Université Paris XIII, 93000 Bobigny, France; Unité Inserm U1133, Université Paris-Diderot, 75013 Paris, France.
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Hatch MN, Raad J, Suda K, Stroupe KT, Hon AJ, Smith BM. Evaluating the Use of Medicare Part D in the Veteran Population With Spinal Cord Injury/Disorder. Arch Phys Med Rehabil 2018; 99:1099-1107. [PMID: 29425699 DOI: 10.1016/j.apmr.2017.12.036] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/05/2017] [Accepted: 12/22/2017] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To examine the different sources of medications, the most common drug classes filled, and the characteristics associated with Medicare Part D pharmacy use in veterans with spinal cord injury/disorder (SCI/D). DESIGN Retrospective, cross-sectional, observational study. SETTING Outpatient clinics and pharmacies. PARTICIPANTS Veterans (N=13,442) with SCI/D using Medicare or Veteran Affairs pharmacy benefits. INTERVENTIONS Not applicable. MAIN OUTCOME MEASURES Characteristics and top 10 most common drug classes were examined in veterans who (1) used VA pharmacies only; (2) used both VA and Medicare Part D pharmacies; or (3) used Part D pharmacies only. Chi-square tests and multinomial logistic regression analyses were used to determine associations between various patient variables and source of medications. Patient level frequencies were used to determine the most common drug classes. RESULTS A total of 13,442 veterans with SCI/D were analyzed in this study: 11,788 (87.7%) used VA pharmacies only, 1281 (9.5%) used both VA and Part D pharmacies, and 373 (2.8%) used Part D pharmacies only. Veterans older than 50 years were more likely to use Part D pharmacies, whereas those with traumatic injury, or secondary conditions, were less associated with the use of Part D pharmacies. Opioids were the most frequently filled drug class across all groups. Other frequently used drug classes included skeletal muscle relaxants, gastric medications, antidepressants (other category), anticonvulsants, and antilipemics. CONCLUSIONS Approximately 12% of veterans with SCI/D are receiving medication outside the VA system. Polypharmacy in this population of veterans is relatively high, emphasizing the importance of health information exchange between systems for improved care for this medically complex population.
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Affiliation(s)
- Maya N Hatch
- Spinal Cord Injury and Disorders Center, Long Beach Veterans Affairs Medical Center, Long Beach, CA
| | - Jason Raad
- Center for Management of Complex Chronic Care, Edward Hines Jr. VA Hospital, Chicago, IL
| | - Katie Suda
- Center for Management of Complex Chronic Care, Edward Hines Jr. VA Hospital, Chicago, IL
| | - Kevin T Stroupe
- Center for Management of Complex Chronic Care, Edward Hines Jr. VA Hospital, Chicago, IL
| | - Alice J Hon
- Spinal Cord Injury and Disorders Center, Long Beach Veterans Affairs Medical Center, Long Beach, CA
| | - Bridget M Smith
- Center for Management of Complex Chronic Care, Edward Hines Jr. VA Hospital, Chicago, IL; Institute for Healthcare Studies, Feinberg School of Medicine, Northwestern University, Chicago, IL.
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Grynberg M, Raad J, Sifer C, Sermondade N, Sonigo C. BRCA 1/2 gene mutations do not affect the capacity of cumulo-oocyte-complexes to mature in vitro in breast cancer candidates for fertility preservation. Fertil Steril 2017. [DOI: 10.1016/j.fertnstert.2017.07.262] [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: 11/30/2022]
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16
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Schwertfeger J, Raad J. Measurement of Activity and Participation across Roles and Care Levels. Arch Phys Med Rehabil 2016. [DOI: 10.1016/j.apmr.2016.08.384] [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: 10/21/2022]
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Weissinger EM, Human C, Metzger J, Hambach L, Wolf D, Greinix HT, Dickinson AM, Mullen W, Jonigk D, Kuzmina Z, Kreipe H, Schweier P, Böhm O, Türüchanow I, Ihlenburg-Schwarz D, Raad J, Durban A, Schiemann M, Könecke C, Diedrich H, Holler E, Beutel G, Krauter J, Ganser A, Stadler M. The proteome pattern cGvHD_MS14 allows early and accurate prediction of chronic GvHD after allogeneic stem cell transplantation. Leukemia 2016; 31:654-662. [PMID: 27677743 DOI: 10.1038/leu.2016.259] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 08/24/2016] [Accepted: 08/30/2016] [Indexed: 12/14/2022]
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) may be curative, but is associated with significant morbidity and mortality. Chronic graft-versus-host disease (cGvHD), characterized by inflammation and fibrosis of multiple target organs, considerably contributes to the morbidity and mortality even years after allo-HSCT. Diagnosis of cGvHD is based on clinical features and histology of biopsies. Here, we report the generation of a urinary cGvHD-specific proteome-pattern (cGvHD_MS14) established by capillary electrophoresis-mass spectrometry to predict onset and severity of cGvHD as an unbiased laboratory test. cGvHD_MS14 was evaluated on samples from 412 patients collected prospectively in four transplant centers. Sensitivity and specificity was 84 and 76% by cGvHD_MS14 classification. Sensitivity further increased to 93% by combination of cGvHD_MS14 with relevant clinical variables to a logistic regression model. cGvHD was predicted up to 55 days prior to clinical diagnosis. Acute GvHD is not recognized by cGvHD_MS14. cGvHD_MS14 consists of 14 differentially excreted peptides, six of those have been sequenced to date and are fragments from thymosin β-4, eukaryotic translation initiation factor 4γ2, fibrinogen β-chain or collagens. In conclusion, the cGvHD_MS14-pattern allows early, highly sensitive and specific prediction of cGvHD as an independent diagnostic criterion of clinical diagnosis potentially allowing early therapeutic intervention.
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Affiliation(s)
- E M Weissinger
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - C Human
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - J Metzger
- Mosaiques-Diagnostics, Hannover, Germany
| | - L Hambach
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - D Wolf
- Department of Hematology and Oncology, University of Regensburg, Regensburg, Germany
| | - H T Greinix
- 1st Department of Internal Medicine, Medical University of Vienna, Vienna, Austria and Division of Hematology, Medical University of Graz, Graz, Austria
| | - A M Dickinson
- Institute of Cellular Medicine, Newcastle University, Newcastle-upon-Tyne, UK
| | - W Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - D Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Z Kuzmina
- 1st Department of Internal Medicine, Medical University of Vienna, Vienna, Austria and Division of Hematology, Medical University of Graz, Graz, Austria
| | - H Kreipe
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - P Schweier
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - O Böhm
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - I Türüchanow
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - D Ihlenburg-Schwarz
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - J Raad
- Mosaiques-Diagnostics, Hannover, Germany
| | - A Durban
- Mosaiques-Diagnostics, Hannover, Germany
| | | | - C Könecke
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - H Diedrich
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - E Holler
- Department of Hematology and Oncology, University of Regensburg, Regensburg, Germany
| | - G Beutel
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - J Krauter
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany.,Department of Hematology and Oncology, Klinikum Braunschweig, Braunschweig, Germany
| | - A Ganser
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
| | - M Stadler
- Department of Hematology, Hemostasis, Oncology and Stem cell transplantation, Hannover Medical School, Hannover, Germany
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Moore JL, Raad J, Ehrlich-Jones L, Heinemann AW. Development and use of a knowledge translation tool: the rehabilitation measures database. Arch Phys Med Rehabil 2013; 95:197-202. [PMID: 24076083 DOI: 10.1016/j.apmr.2013.09.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [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: 06/18/2013] [Revised: 09/18/2013] [Accepted: 09/21/2013] [Indexed: 10/26/2022]
Abstract
Clinical translation of research evidence is a challenge for rehabilitation clinicians. Publicly accessible and free, online educational resources that summarize research evidence can support implementation of research evidence into practice. Several online resources have been developed recently to overcome common knowledge translation barriers. The Rehabilitation Measures Database (RMD) is a free, web-based searchable database of standardized instruments that was designed to support knowledge translation. It helps clinicians select valid and sensitive instruments for screening patients, monitoring progress, and assessing rehabilitation outcomes. The RMD was developed using feedback from focus groups and beta-test participants. Since its launch in 2011, RMD use has grown to an average of 1851 hits per day from 168 countries. As of September 2013, 202 instrument summaries are viewable in the RMD. Most summaries are linked to copies of the instrument or to purchase instructions. A challenge in updating and expanding the RMD is securing the resources to ensure its future. Collaborative relationships with professional associations and graduate programs in the health sciences are critical in sustaining this resource.
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Affiliation(s)
- Jennifer L Moore
- Rehabilitation Institute of Chicago, Chicago, IL; Center for Rehabilitation Outcomes Research at the Rehabilitation Institute of Chicago, Chicago, IL.
| | - Jason Raad
- Rehabilitation Institute of Chicago, Chicago, IL; Center for Rehabilitation Outcomes Research at the Rehabilitation Institute of Chicago, Chicago, IL
| | - Linda Ehrlich-Jones
- Rehabilitation Institute of Chicago, Chicago, IL; Center for Rehabilitation Outcomes Research at the Rehabilitation Institute of Chicago, Chicago, IL; Department of Physical Medicine and Rehabilitation, Feinberg School of Medicine, Northwestern University, Chicago, IL; Center for Health Care Studies, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Allen W Heinemann
- Rehabilitation Institute of Chicago, Chicago, IL; Center for Rehabilitation Outcomes Research at the Rehabilitation Institute of Chicago, Chicago, IL; Department of Physical Medicine and Rehabilitation, Feinberg School of Medicine, Northwestern University, Chicago, IL; Center for Health Care Studies, Feinberg School of Medicine, Northwestern University, Chicago, IL
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Raad J, Moore J, Hamby J, Rivadelo RL, Straube D. A Brief Review of the Activities-Specific Balance Confidence Scale in Older Adults. Arch Phys Med Rehabil 2013. [DOI: 10.1016/j.apmr.2013.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Raad J, Moore J. Measurement Characteristics and Clinical Utility of the Craig Handicap Assessment and Reporting Technique Among Individuals With Spinal Cord Injury. Arch Phys Med Rehabil 2013. [DOI: 10.1016/j.apmr.2013.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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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21
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Raad J, Moore J. Measurement Characteristics and Clinical Utility of the Community Integration Questionnaire Among Individuals With Brain Injury. Arch Phys Med Rehabil 2013. [DOI: 10.1016/j.apmr.2013.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tappan R, Raad J, Moore J. Measurement Characteristics and Clinical Utility of the 6-Minute Walk Test Among Individuals With Spinal Cord Injury. Arch Phys Med Rehabil 2012. [DOI: 10.1016/j.apmr.2012.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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King RB, Hartke RJ, Houle T, Lee J, Herring G, Alexander-Peterson BS, Raad J. A problem-solving early intervention for stroke caregivers: one year follow-up. Rehabil Nurs 2012; 37:231-43. [PMID: 22949276 DOI: 10.1002/rnj.039] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
PURPOSE The study purposes were to assess the efficacy of a caregiver problem-solving intervention (CPSI) on stroke caregiver physical and psychosocial adaptation compared with a wait-list control (WLC) treatment, and to assess the mediation effects of coping on outcomes. METHODS A stress and coping model guided the study design. Outcomes were depression, anxiety, preparedness, life changes, and family functioning. CPSI started during acute rehabilitation and continued 3 months postdischarge. Data were collected at baseline (T1), postintervention (T2), and 6 (T3) and 12 months postdischarge (T4). RESULTS Of 255 caregivers, 75% were depressed at baseline. Repeated measures ANOVA of study completers (n = 121) indicated improved T2 depression, life change, and health (ps < .04) favoring the CPSI group. Improvements faded by 6 months. Although no group differences in outcomes were found in the intention-to-treat analysis, growth curve modeling indicated a difference in depression rate of change, favoring the CPSI (p = .04). Perceived health, threat appraisal and rational problem-solving were significant mediators (ps < .05). CONCLUSIONS Findings provide direction for future interventions to promote and sustain healthy caregiver adaptation.
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Affiliation(s)
- Rosemarie B King
- Northwestern University Feinberg School of Medicine, Department of Physical Medicine & Rehabilitation, Chicago, IL, USA.
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Abstract
UNLABELLED Liver transplantation for infants and children has been available in South Africa at a single centre, the only established service in Sub-Saharan Africa, for more than a decade. Current concerns have shifted from an initial target of early post-transplant survival to quality of life in the long-term. MATERIALS AND METHODS Since 1985, 225 infants and children have been assessed, with 146 accepted for transplantation. Sixty-nine have had 71 orthotopic liver transplants (OLTx). Biliary atresia was the most frequent diagnosis (54%) followed by acute liver failure (ALF) (15%). Waiting list mortality has remained high (23%), particularly for the ALF group (50%). Forty-three were reduced size transplants with donor: recipient weight ratios ranging from 2:1 to 11:1. Twenty-seven were <10 kg. RESULTS Fifty (74%) survive 1 month-12 years post-transplant. Actuarial survival after 1996 since HBV core antibody positive donor livers were refused and prophylactic IV ganciclovir used has been >82%. Early post-OLTx mortality was low (5%), one primary non-function, one IVC thrombosis, one PV thrombosis, but late morbidity and mortality (20%) was mainly due to viral infection: de novo hepatitis B (five patients, three deaths), EBV-related post-transplantation lymphoproliferative disease (PTLPD) (eight patients, six deaths) and CMV disease (11 patients, five deaths). Tuberculosis prophylaxis, required in six cases, resulted in major morbidity in two and mortality in one. Poor compliance played a significant role in seven deaths. Hypertension requiring medication along with some compromise of renal function has been present in all but two patients. However, all those of school-going age (25) attend school normally and remain in good health and only three of the survivors have abnormal liver function tests. CONCLUSIONS Successful liver transplantation is possible in a developing country with limited resources. Scarcity of virus-free donors (HBV and HIV) leading to waiting list mortality and infrequent re-transplantation along with long-term consequences of immunosuppression (infection, lymphoma and renal toxicity) remain problems. Intense education of the caregiver and close follow-up, particularly of those living at long distances has partly addressed the compliance problem.
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Affiliation(s)
- A J W Millar
- Department of Paediatric Surgery, Paediatrics, Medicine and Surgery, Red Cross Children's Hospital, Institute of Child Health and Medical Research Council Liver Research Centre, University of Cape Town, Cape Town, South Africa.
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Millar AJW, Steinberg RM, Raad J, Rode H. Anal achalasia after pull-through operations for Hirschsprung's disease -- preliminary experience with topical nitric oxide. Eur J Pediatr Surg 2002; 12:207-11. [PMID: 12101506 DOI: 10.1055/s-2002-32722] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [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] [Indexed: 01/28/2023]
Abstract
INTRODUCTION Following definitive pull-through for Hirschsprung's disease (HD), a minority of patients develop constipation, incontinence and enterocolitis. The cause for these symptoms in some of the patients is believed to be "internal sphincter achalasia" related to abnormal innervation of the sphincter, with an absent anorectal relaxation reflex. Transanal myectomy, posterior sagittal rectal myectomy, anal dilatation and even intrasphincter injection of botulinum toxin have been used to solve this problem. Nitric oxide (NO) has been identified as the chemical messenger of the intrinsic non-adrenergic, non-cholinergic pathway mediating relaxation of the normal internal anal sphincter when applied topically. BACKGROUND/PURPOSE To evaluate the effect of topical isosorbide dinitrate (DTN) applied to the anus and its role in the management of patients with HD after pull-through who have ongoing difficulties in stool evacuation. MATERIAL AND METHODS Four children, aged 2, 5, 7 and 13 years, who all underwent the Soave operation for Hirschsprung's disease, were assessed. Three patients had recurrent episodes of enterocolitis, and all had symptoms of difficulty in rectal/colonic evacuation. Conservative treatment of repeated anal dilatation under anaesthesia had failed to improve symptoms. A rectal myectomy and conversion of Soave to Duhamel procedure had been done in 2 without significant improvement in symptoms. In all patients, ano-rectal manometry was performed before and after application of DTN paste (1 mg/kg/day in two separate doses) which was continued for a minimum period of 3 weeks. Results. Marked symptom improvement was noted in all 4 children. On manometric assessment the median maximum pressure (pre-DTN application) was 165 mm Hg (range 96 - 250), the median sphincter length 2.7 cm (range 2.3 - 3.1) and the high-pressure zone (HPZ) median length 1.6 cm (range 1.2 - 2.1). After application of DTN paste, the maximum pressure dropped by a median of 88 mm Hg (range 46 - 90), total sphincter length shortened to a median of 2.1 cm and the HPZ by a median total length of 1.4 cm (range 0.01 - 0.9). In addition, vector volume was reduced by a median of 59 % (range 40.5 - 77). CONCLUSION From these results, it is evident that DTN paste is not only an adjunct in the investigation, but can also be used as a temporary form of treatment of obstructive symptoms in Hirschsprung's disease patients.
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Affiliation(s)
- A J W Millar
- Department of Paediatric Surgery, Red Cross War Memorial Children's Hospital & Institute of Child Health, University of Cape Town, Rondebosch, Cape Town, South Africa.
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Cardenas V, Sanchez C, De la Hoz F, Jara JH, Velandia M, Martinez M, Raad J. Columbian field epidemiology training program. Am J Public Health 1998; 88:1404-5. [PMID: 9736889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- V Cardenas
- National Institute of Health, Bogotá, Columbia
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28
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Abi-Fadel W, Afif N, Farah S, Haddad A, Rizk K, Raad J. [Vertebral hemangioma symptomatic during pregnancy. A case report and review of the literature]. J Gynecol Obstet Biol Reprod (Paris) 1997; 26:90-4. [PMID: 9091551] [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] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Vertebral hemangioma is a relatively frequent but rarely symptomatic tumor. Physiologic changes during pregnancy may lead to spinal cord compression due to tumor expansion. We report a case of vertebral hemangioma during pregnancy: a 28-year-old woman, third trimester, third gestation, consulted for paraplegia of rapid onset; Magnetic resonance imaging showed a lesion of the 9th thoracic vertebra; a cesarean section was done, followed by laminectomy with partial symptom relief; pathology showed a benign vertebral hemangioma and treatment was completed with radiotherapy.
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Affiliation(s)
- W Abi-Fadel
- Département de Gynécologie-Obstétrique, Hôpital du Sacré-Coeur, Beyrouth, Liban
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29
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Abstract
We report a postmortem cesarean section resulting in fetal survival, performed 25 minutes after maternal blast injury. The time interval between cardiopulmonary arrest and delivery, prior maternal health status, and continued cardiopulmonary resuscitation represent important determinants of fetal survival. Improvement in maternal hemodynamic condition may potentially occur following the procedure. Postmortem cesarean section is advised in the event of fatal maternal trauma since it may result in fetal salvage.
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Affiliation(s)
- J T Awwad
- Department of Obstetrics and Gynecology, American University of Beirut Medical Center, Lebanon
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30
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Núñez RM, Raad J, Núñez CA. Antibodies against spermatozoids. Studies in homosexuals, AIDS and infertile men. Allergol Immunopathol (Madr) 1987; 15:215-9. [PMID: 3318351] [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: 01/05/2023]
Abstract
The presence of antibodies against spermatozoids was evaluated in one person with AIDS and six homosexuals (HS). Indirect immunofluorescence was utilized along with immunoenzymatic trial with peroxidase (ELISA) in order to detect antibodies class IgG towards spermatozoids and their membrane proteins. Optic densities of the following groups of patients were compared: 1) One patient with AIDS. 2) Six homosexuals (HS). 3) Three HS with cells OKT8 greater than 30%. 4) Three HS with cells OKT8 less than 30%. 5) Three men with auto-antibodies against spermatozoids + infertility. 6) Two men without auto-antibodies against spermatozoids + infertility. 7) Five women, spouses of the infertile men. 8) Five multiparous with more than 3 pregnancies. 9) One man with orchitis. 10) Ten fertile and healthy (C.G.) heterosexual persons. The patient with AIDS and the one with orchitis had the highest optic densities (OD), (groups 1 and 9). Groups 8 and 10 had the lowest, non-significant values. Groups 2, 5 and 7 ranked second in place in reference to O.D. Groups 3, 4 and 6 ranked third in O.D. values. Groups 8 and 10 differed significantly at P less than 0.005 compared with the others. The presence of antibodies against spermatozoids was considered as an important factor associated with AIDS and previous states of the AIDS detected by OKT8 greater than 30% of lymphocytes. The IIF and ELISA were able to detect antigenic system in spermatozoids with allelic form, which may be similar to the mice locus t, or a new tissue specific system.
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Affiliation(s)
- R M Núñez
- Departamento de Pediatria, Hospital Infantil, Universidad de Caldas, Manizales, Colombia
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Ghosn G, Tayah S, Raad J. [5 cases of uterine inversion]. Bull Fed Soc Gynecol Obstet Lang Fr 1971; 23:385-90. [PMID: 5153214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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32
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Ghosn G, Naffah J, Tayah S, Raad J, Hayek G, Braidi G. [A special case of intersexuality: testicular feminization or real hermaphroditism]. Bull Fed Soc Gynecol Obstet Lang Fr 1971; 23:379-84. [PMID: 5153213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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