A surrogate Bayesian framework for a SARS-CoV-2 data driven stochastic model

Dynamic compartmentalized data (DCD) and compartmentalized differential equations (CDEs) are key instruments for modeling transmission of pathogens such as the SARS-CoV-2 virus. We describe an effi-cient nowcasting algorithm for modeling transmission of SARS-CoV-2 with uncertainty quantification for the COVID-19 impact. A key concern for transmission of SARS-CoV-2 is under-reporting of cases, and this is addressed in our data-driven model by providing an estimate for the detection rate. Our novel top-down model is based on CDEs with stochastic constitutive parameters obtained from the DCD using Bayesian inference. We demonstrate the robustness of our algorithm for simulation studies using synthetic DCD, and nowcasting COVID-19 using real DCD from several regions across five continents.

A numerically stable T-matrix method for acoustic scattering by nonspherical particles with large aspect ratios and size parameters

We consider a two-part method for computing the acoustic scattering T-matrix of a three dimensional particle. The first part involves accurately computing the far fields by solving a number of particular scattering problems. The second part calculates the T-matrix from these far fields using the Fourier transform over the sphere. The two-part method was first introduced in Ganesh and Hawkins [J. Comput. Appl. Math. 234, 1702-1709]. The focus of this work is to demonstrate the numerical stability and physical correctness of the two-part method for scattering by nonspherical particles with large aspect ratios and size parameters that are at the upper limit of numerical stability for the current state-of-the-art algorithm. The numerical stability of the method is attributed to elimination of the Hankel functions by working with the far field. The numerical experiments use our recently developed open-source software package (TMATROM3) that implements the two-part method.

Role of Lipoprotein Associated Phospholipase A2 in Diagnosis of Coronary Artery Disease

Introduction: Cardiovascular Diseases (CVD) are a major cause of significant morbidity and mortality in industrialized countries, of which Coronary Artery Disease (CAD) is the commonest. The diagnostic workup of CAD has improved over the years starting from conventional investigations like ECG to invasive procedures like coronary angiogram. Moving forward, numerous novel inflammatory biomarkers are coming up to diagnose CAD. Aim: To assess the role of Lipoprotein associated Phospholipase A2 (LpPLA2) as an independent predictor of CAD. Materials and Methods: This case-control study was conducted in the Inpatient Department of Cardiology at Sri Ramachandra Medical College and Research Institute, Chennai, Tamil Nadu, India, from September 2014 to November 2014. Participants without significant blockage in the coronary arteries and without detectable atheroma served as controls and those with detectable atheroma and significant blockage in coronary arteries served as cases. Peripheral blood samples of 80 male patients aged over 40 years undergoing Coronary Angiography were processed for LpPLA2 levels. Mean and Standard deviation were calculated for the parameters included in the study. All statistical analyses were performed using Statistical Package for Social Sciences (SPSS) version 15.0. Results: Mean age of the participants in the controls group was 51.75±8.74 years and that of the cases group was 59.15±11.31 years. The mean LpPLA2 level in the cases was found to be higher than that in the controls and the difference was statistically significant (p-value <0.05). No correlation was noted between the age and BMI of both the groups with their respective LpPLA2 levels. Conclusion: The current study showed that LpPLA2 can be used as a potential independent predictor of CAD, thus minimising the usage of invasive investigations and favouring the psychosocial and economic welfare of the patients.

Treading the beaten path with old and new obstacles: a report from the Indian HIPEC registry

BACKGROUND

The Indian HIPEC registry is a self-funded registry instituted by a group of Indian surgeons for patients with peritoneal metastases (PM) undergoing surgical treatment. This work was performed to  • Evaluate outcomes of cytoreductive surgery ± HIPEC in patients enrolled in the registry.  • Identify operational problems.

METHODS

A retrospective analysis of patients enrolled in the registry from March 2016 to September 2017 was performed. An online survey was performed to study the surgeons' attitudes and existing practices pertaining to the registry and identify operational problems.

RESULTS

During the study period, 332 patients were enrolled in 8 participating centres. The common indication was ovarian cancer for three centres and pseudomyxoma peritonei for three others. The median PCI ranged from 3 to 23. A CC-0/1 resection was obtained in 94.7%. There was no significant difference in the morbidity (p = .25) and mortality (p = .19) rates between different centres. There was a high rate of failure-to-rescue (19.3%) patients with complications and the survival in patients with colorectal PM was inferior. A lack of dedicated personnel for data collection and entry was the main reason for only 10/43 surgeons contributing data. The other problem was the lack of complete electronic medical record systems at all centres.

CONCLUSIONS

These results validate existing practices and identify country-specific problems that need to be addressed. Despite operational problems, the registry is an invaluable tool for audit and research. It shows the feasibility of fruitful collaboration between surgeons in the absence of any regulatory body or funding for the project.

Efficacy of silver diamine fluoride as an antibacterial as well as antiplaque agent compared to fluoride varnish and acidulated phosphate fluoride gel: an in vivo study

BACKGROUND

Silver diamine fluoride (SDF) is already proven as an antibacterial agent in vitro. Present study was formulated to compare the efficacy of SDF as an antibacterial as well as antiplaque agent in vivo with fluoride varnish and acidulated phosphate fluoride (APF) gel.

STUDY DESIGN

Total 123 children (male = 82, female = 41) were included in the study for a period of 18 months. Children were divided into three different groups-Group 1: SDF; Group 2: fluoride varnish; and Group 3: APF gel. All subjects were evaluated via plaque score at 6 th, 12 th, and 18 th months as well as Streptococcus mutans counts in saliva at 72 h, 6 th, 12 th, and 18 th months of follow-up.

RESULTS

Significant reduction was found in plaque score as well as S. mutans counts irrespective of group division. On intergroup comparison, no statistically significant difference was found in plaque score, but significant reduction in S. mutans counts was found in Group 1 as compared with Groups 2 and 3, while no significant difference was found between Groups 2 and 3.

CONCLUSION

In vivo application of SDF on enamel significantly decreases S. mutans counts as compared to fluoride varnish and APF gel.

Hepcidin-minireview

Iron related disorders are encountered in daily clinical settings. Maintenance of stable extracellular iron concentrations requires the coordinate regulation of iron transport into plasma from dietary sources in the duodenum, from recycled senescent red cells in macrophages and from storage in hepatocytes. Hepcidin acts as a systemic iron-regulatory hormone. Many human diseases are associated with alterations in hepcidin concentrations. This review has focused on hepcidin structure, kinetics and function, its correlation with iron metabolism disorders, the therapeutic potential for modulating hepcidin expression and the diagnostic potential of hepcidin measurements in clinical practice.

Evaluation of the remineralization potential of amorphous calcium phosphate and fluoride containing pit and fissure sealants using scanning electron microscopy

AIM

To evaluate the remineralization potential of Amorphous Calcium Phosphate (ACP) and Fluoride containing pit and Fissure Sealants using Scanning Electron Microscopy.

MATERIALS AND METHODS

Thirty maxillary first premolars were divided into three groups of ten each and were randomly selected for ACP containing (Aegis- Opaque White, Bosworth Co. Ltd.), Fluoride containing (Teethmate F1 Natural Clear, Kuraray Co. Ltd.), resin based (Concise- Opaque White, 3M ESPE Co. Ltd.) pit and fissure sealant applications. The Concise group served as a control. The teeth weresubjected to the pH-cycling regimen for a period of two weeks. After two weeks, the teeth were sectioned bucco-lingually into 4mm sections and were observed under Scanning Electron Microscope at 50X, 250X, 500X, 1000X and 1500X magnifications. The qualitative changes at the tooth surface and sealant interface were examined and presence of white zone at the interface was considered positive for remineralization.

RESULTS

Both ACP containing (Aegis) and Fluoride containing (Teethmate F1) group showed white zone at the tooth surface-sealant interface. The resin based group (Concise) showed regular interface between the sealant and the tooth structure, but no clear cut white zone was observed.

CONCLUSION

Both, Aegis and Teethmate F1 have the potential to remineralize. Release of Amorphous Calcium Phosphate molecules in Aegis group and formation of Fluoroapetite in Teethmate F1 group, were probably responsible for the remineralization.

Prevalence and characteristics of Molar Incisor Hypomineralisation (MIH) in the child population residing in Gandhinagar, Gujarat, India

Most prevalence studies on Molar Incisor Hypomineralisation (MIH) have been carried out in European countries and data from Asia especially south Asian populations are lacking.

AIM

To investigate the prevalence and clinical characteristics of MIH in children residing in a western region of India.

METHOD

A cross-sectional survey including 1,366 children from 5 age cohorts, 8-12 years, studying in primary schools or attending the University Department, was carried out in the area of Gandhinagar, Gujarat, India. The dental examination was performed by a single well-trained and calibrated examiner in day light conditions. Full mouth inspection of wet teeth was conducted using the EAPD 2003 criteria for diagnosis of MIH. Results were recorded and statistically analysed using Chi-square test, independent sample t-test and Pearson correlations.

RESULTS

Prevalence of MIH was 9.2% in the examined population. Males and females were equally affected. Among 12 index teeth involved in the examination, the most commonly affected were in descending order 46, 36, 16, 11 [FDI] and the least 42, 32, and 22. 17.4% of the cases revealed only molars involved, the remaining 72.6% having both molars and incisors affected; all four first permanent molars showed in 23% of the cases while no cases of only affected incisors were found. Of the MIH teeth 77.3% revealed mild defects and 22.7% severe defects. All incisors were mildly affected, as compared with only 67.1% of the molars, the remaining 32.9% being severely affected. As age increased, a statistically significant larger total number and severity level of affected teeth were recorded.

CONCLUSION

Prevalence of MIH using EAPD 2003 criteria was found to be similar to other studies evaluating children in different geographic locations such as Europe, South America etc. Using the EAPD standardised criteria, more studies should be conducted in other Indian regions, in order to further evaluate prevalence, characteristics and treatment needs for this clinically demanding condition.

The effectiveness of a musical toothbrush for dental plaque removal: a comparative study

BACKGROUND AND OBJECTIVES

the purpose of this study was to clinically evaluate and compare the efficacy of "Brush Buddies" musical tooth brush and Colgate Smile tooth brush in the reduction of established plaque and gingivitis.

MATERIALS AND METHODS

for this study, 120 healthy kids (73 boys and 47 Girls) were selected. The subjects were randomly assigned into two groups by a second examiner; one group used Colgate Smile brush and the other group used "Brush Buddies" musical tooth brush. Plaque index (Quigley and Hein), Modified Gingival Index (Lobene and Associates) and Gingival Bleeding Index (Ainamo and Bay) were assessed at baseline, 30th day, 60th day, and 90th day.

RESULTS

all the baseline indices appeared to be well balanced. At the end of the study, reduction in plaque index, modified gingival index and gingival bleeding index were statistically highly significant during each interval for both the toothbrushes. For "Brush Buddies" musical tooth brush, the reduction in all clinical parameters were statistically significant for 30 days and 60 days interval, while nonsignificant at 90 days interval.

INTERPRETATION AND CONCLUSION

both the tooth brushes used in this study were clinically effective in removing plaque, improving gingival health. Musical tooth brush is more effective initially but as the time period increases both tooth brushes give almost similar results.

Electron beam characteristics at extended source-to-surface distances for irregular cut-outs

Electron beam therapy is widely used in the management of cancers. The rapid dose fall-off and the short range of an electron beam enable the treatment of lesions close to the surface, while sparing the underlying tissues. In an extended source-to-surface (SSD) treatment with irregular field sizes defined by cerrobend cutouts, underdosage of the lateral tissue may occur due to reduced beam flatness and uniformity. To study the changes in the beam characteristics, the depth dose, beam profile, and isodose distributions were measured at different SSDs for regular 10 × 10 cm² and 15 × 15 cm² cone, and for irregular cutouts of field size 6.5 × 9 cm² and 11.5 × 15 cm² for beam energies ranging from 6 to 20 MeV. The PDD, beam flatness, symmetry and uniformity index were compared. For lower energy (6 MeV), there was no change in the depth of maximum dose (R100) as SSD increased, but for higher energy (20 MeV), the R₁₀₀ depth increased from 2 cm to 3 cm as SSD increased. This shows that as SSD increases there is an increase in the depth of the maximum dose for higher energy beams. There is a +7 mm shift in the R₁₀₀ depth when compared with regular and irregular field sizes. The symmetry was found to be within limits for all the field sizes as the treatment distance extended as per International Electro technical Commision (IEC) protocol. There was a loss of beam flatness for irregular fields and it was more pronounced for lower energies as compared with higher energies, so that the clinically useful isodose level (80% and 90%) width decreases with increase in SSD. This suggests that target coverage at extended SSD with irregular cut-outs may be inadequate unless relatively large fields are used.

Evaluation of antibacterial activity, phenol and flavonoid contents of Thespesia populnea flower extracts

Flavonoids which were reported as having many pharmacological activities, antimicrobial, antioxidant, cytotoxic, chemoprevention activities and they possess strong antiproliferative effects related to inhibition of cell cycle progression and apoptosis induction. On the basis of this Thespesia populnea (L.) Sol. Ex Correa (Family-Malvaceae) was selected and it is having the major composition of flavonoids and the antibacterial activity of methanolic extract of Thespesia populnea flowers was investigated by agar well diffusion method. Furthermore our phytochemical studies indicated that methanolic extract of Thespesia populnea flowers contains flavonoids, alkaloids, tannins and anthroquinone glycosides. Moreover the individual components were identified by thin layer chromatography and Rf value was compared with standard flavonoid quercetin. The total phenolic and flavonoid content studies were also quantified. The bacteria used for antibacterial study were Shigella flexneri (NCIM 4924), Rhodococcus terrae (NCIM 5126), Escherichiae coli (ATCC 11775), Streptococcus faecalis (NCIB 2406), Klebsiella pneumoniae (ATCC 13883),Brevibacterium luteum (NCIM 2923), Micrococcus flavum (NCIM 2376), Proteus mirabilis (NCIB 8268), Bacillus licheniformis (NCIM 2468), Micrococcus luteus (ATCC 2984), Flavobacterium devorans (NCIM 2581), Shigella sonei(ATCC 29930), Shigella boydii (ATCC 8700) and Shigella dysentriae (ATCC 13313).According to our results in the lowest tested concentration of 62.5 microg/ml and 125mug/ml 7.2% of the plant extract were active, 5% active in the concentration of 250 microg/ml, 75.7% active in the concentration of 500 microg/ml and 92.8% active at the concentration of 1000 microg/ml in a dose dependent manner.

Extractive separation and determination of chromium in tannery effluents and electroplating waste water using tribenzylamine as the extractant

A simple extractive separation method has been developed for the determination of chromium based on the extraction of Cr (VI) as its ion-pair with tribenzylamine (TBA). The ion-pair is extracted at acidic pH using toluene as the diluent. The concentration of chromium in the organic phase was measured spectrophotometrically at 309 nm. The influence of experimental variables such as pH, sample volume, equilibration time, diverse ions etc. has been studied in detail. The extracted chromium (VI) could be stripped to the aqueous phase using NaOH as the stripping agent. The extracts were characterized using FT-IR spectroscopy. A detection limit of 0.08 microg mL(-1) could be achieved and the validity of the method was checked in real tannery effluent, electroplating waste water and spiked water samples.

Clinical evaluation of FUJI VII sealant material

200 children of the age groups of 3-5 years and 6-7 years were selected for sealant application, each consisting of 100 children. The clinical retention of Fuji VII was tested in both primary and permanent molar teeth at time intervals of 6 months, 12 months and 24 months follow-up and compared with a resin based sealant, Concise. Results demonstrated that there was no difference in the performance of the materials in primary and permanent teeth.

A validated method for halquinol extraction from chicken liver matrix for residual HPLC studies

Extraction is the key step in the analysis of food samples, from either plant or animal sources for residues of veterinary drugs and pesticides. Such residues pose an unacceptable risk to the consumer and information is insufficient to allow a full assessment. This paper presents a method for extracting and determining Halquinol, a veterinary drug in liver of chicken. The first step of the study was to establish and validate a method for determination of Halquinol, which was achieved using HPLC equipped with a C18 reversed-phase, monomeric column and a MWD-UV detector. In the second step, we extracted and purified the liver samples. Liver samples were homogenized in buffer, extracted with ethyl acetate, and cleaned up using a solid-phase extraction column. The limit of quantification of the method was 0.1 microg/l mL, and detection limit was 0.01 microg/l mL. Mean recoveries in chicken liver ranged from 57% to 91%.

Evaluation of Anti-inflammatory activity and toxicity studies of Chloroxylon sweitenia in Rats

The extract of Chloroxylon sweitenia (Family: Rutaceae) leaves were investigated for its anti-inflammatory activity at the different doses in the standard animal models. The experimental paradigms used were carrageenan induced rat paw oedema (acute), and cotton pellet induced granuloma (chronic) models in rats for anti-inflammatory activity. In rats the toxicity was also performed for the extract by oral administration. The chloroform extract of Chloroxylon sweitenia (CECS) exhibited significant anti-inflammatory effect at the dose 50, 100 and 200 mg/kg. Maximum inhibition (55.32 %) was noted at the dose of 200 mg/kg after 3 h of drug treatment in carrageenan induced paw oedema, whereas the Diclofenac (standard drug) produced 61.33 % of inhibition. In the chronic model (cotton pellet induced granuloma) the CECS (200 mg/kg) and standard drug showed decreased formation of granuloma tissue by 52.32 % and 56.32 % (p < 0.001) respectively. The CECS further evaluated for their toxicity effect at the doses of 100 mg/kg administered for 14 days to orally in rats. At the end of experiments the blood, liver function and kidney metabolism was observed. The effect of CECS was assessed by the change in the body weight, lipid peroxidation and glutathione content (GSH) activities were measured from hepatic tissues. The hematological profile and different biochemical parameters such as SGOT, SGPT, and ALP were also estimated. Thus, the present study revealed that the chloroform extract of Chloroxylon sweitenia exhibited significant anti-inflammatory activity in the tested models Toxicity study indicates that the extract is non-toxic at the tested doses.

Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes

Regions of the genome not coding for proteins or not involved in cis-acting regulatory activities are frequently viewed as lacking in functional value. However, a number of recent large-scale studies have revealed significant regulated transcription of unannotated portions of a variety of plant and animal genomes, allowing a new appreciation of the widespread transcription of large portions of the genome. High-resolution mapping of the sites of transcription of the human and fly genomes has provided an alternative picture of the extent and organization of transcription and has offered insights for biological functions of some of the newly identified unannotated transcripts. Considerable portions of the unannotated transcription observed are developmental or cell-type-specific parts of protein-coding transcripts, often serving as novel, alternative 5' transcriptional start sites. These distal 5' portions are often situated at significant distances from the annotated gene and alternatively join with or ignore portions of other intervening genes to comprise novel unannotated protein-coding transcripts. These data support an interlaced model of the genome in which many regions serve multifunctional purposes and are highly modular in their utilization. This model illustrates the underappreciated organizational complexity of the genome and one of the functional roles of transcription from unannotated portions of the genome.

Prolonged feeding practice and its effects on developing dentition

Muscular activity of the lips, cheeks, and the tongue are important factors, which not only guide the occlusal development but also affect the growth of the jaws. Bottle feeding has been known to cause a myriad of changes in the oro-facial development. But the adverse effects of feeding practices with respect to developing dentition has been a subject of controversy. Hence a study was designed with the aim and objectives to check the commonly adopted feeding practices in South Kanara, to compare the occlusion of 3- to 5-year-old children with breast feeding, bottle feeding or combination, and to check whether prolonged feeding has any adverse influence on developing dentition. A total of 250 questionnaires were distributed to parents of 3- to 5-year-old children of which 153 were chosen for recording the impression and for studying the occlusion under various parameters. The results of the study indicated definite potential hazards of prolonged breast and bottle feeding especially with a tendency to develop openbite and posterior crossbite. It also suggested that an early preventive and interceptive approach.

Spatio-temporal pattern formation on spherical surfaces: numerical simulation and application to solid tumour growth

In this paper we examine spatio-temporal pattern formation in reaction-diffusion systems on the surface of the unit sphere in 3D. We first generalise the usual linear stability analysis for a two-chemical system to this geometrical context. Noting the limitations of this approach (in terms of rigorous prediction of spatially heterogeneous steady-states) leads us to develop, as an alternative, a novel numerical method which can be applied to systems of any dimension with any reaction kinetics. This numerical method is based on the method of lines with spherical harmonics and uses fast Fourier transforms to expedite the computation of the reaction kinetics. Numerical experiments show that this method efficiently computes the evolution of spatial patterns and yields numerical results which coincide with those predicted by linear stability analysis when the latter is known. Using these tools, we then investigate the rĵle that pre-pattern (Turing) theory may play in the growth and development of solid tumours. The theoretical steady-state distributions of two chemicals (one a growth activating factor, the other a growth inhibitory factor) are compared with the experimentally and clinically observed spatial heterogeneity of cancer cells in small, solid spherical tumours such as multicell spheroids and carcinomas. Moreover, we suggest a number of chemicals which are known to be produced by tumour cells (autocrine growth factors), and are also known to interact with one another, as possible growth promoting and growth inhibiting factors respectively. In order to connect more concretely the numerical method to this application, we compute spatially heterogeneous patterns on the surface of a growing spherical tumour, modelled as a moving-boundary problem. The numerical results strongly support the theoretical expectations in this case. Finally in an appendix we give a brief analysis of the numerical method.

Extramedullary plasmacytoma presenting as upper back pain

Extramedullary plasmacytoma (EMP) is a rare soft tissue plasma cell tumour, usually presenting as a mass within the upper respiratory tract. It is most unusual for it to present in the posterior mediastinum as a primary solitary lesion. Discussed here is the case report of a patient who initially presented with musculoskeletal pain. Subsequent investigations, however, revealed the cause to be an EMP; diagnosis was made on finding aggregates of plasma cells on histological examination of the tissue specimen. The latter had been obtained by way of a computerised tomography scan guided biopsy of the tumour. Bone marrow aspiration studies showed no evidence of multiple myelomatosis. There was significant clinical improvement in response to radiotherapy. It is possible that this might represent one of the first documented reports of a primary solitary EMP in the posterior mediastinum.

Penetrance and expressivity of the gene for double podding in chickpea

The double-pod per peduncle trait is known to contribute to increased seed yield in chickpea (Cicer arietinum L.). A cross was made between the single-podded variety ICCV 2 and the double-podded variety JG 62 in 1993. Penetrance and expressivity of the gene for double podding was studied in an F2 population and F10 recombinant inbred lines (RILs) of this cross. Homozygous recessive allele of this gene (ss) governs the production of double flowers and pods per peduncle. Results indicated that the s allele has unstable penetrance and variable expressivity. The penetrance of this allele was 53% for the F2 and 84.5% for the RILs. The ranges for the expression of this trait among the penetrant F2 individuals and the penetrant RILs were 1.1-14.8% and 0.1-33.0%. These were 8.3-30.8% for early sown and 17.1-68.7% for the late sown double-podded parent JG 62. Thus it appears that the allele shows greater penetrance and enhanced expressivity under soil moisture stress. In the F2 the seed yield advantage of the double-podded over the single-podded plants was 18%, whereas among the RILs it was 7%. The increased number of pods and seeds contributed to the higher yield. However, there was a slight decrease in seed size of the double-podded genotypes. An increase in the size of seed may have a role in the decreased penetrance and expressivity of this allele among the double-podded segregants of the ICCV 2 x JG 62 chickpea cross.

DataFoundry: information management for scientific data

Data warehouses and data marts have been successfully applied to a multitude of commercial business applications. They have proven to be invaluable tools by integrating information from distributed, heterogeneous sources and summarizing this data for use throughout the enterprise. Although the need for information dissemination is as vital in science as in business, working warehouses in this community are scarce because traditional warehousing techniques do not transfer to scientific environments. There are two primary reasons for this difficulty. First, schema integration is more difficult for scientific databases than for business sources, because of the complexity of the concepts and the associated relationships. While this difference has not yet been fully explored, it is an important consideration when determining how to integrate autonomous sources. Second, scientific data sources have highly dynamic data representations (schemata). When a data source participating in a warehouse changes its schema, both the mediator transferring data to the warehouse and the warehouse itself need to be updated to reflect these modifications. The cost of repeatedly performing these updates in a traditional warehouse, as is required in a dynamic environment, is prohibitive. This paper discusses these issues within the context of the DataFoundry project, an ongoing research effort at Lawrence Livermore National Laboratory. DataFoundry utilizes a unique integration strategy to identify corresponding instances while maintaining differences between data from different sources, and a novel architecture and an extensive meta-data infrastructure, which reduce the cost of maintaining a warehouse.