The aim of the present study is to develop and verify the single film calibration procedure used in intensity-modulated radiation therapy (IMRT) quality assurance.
Radiographic films have been regularly used in routine commissioning of treatment modalities and verification of treatment planning system (TPS). The radiation dosimetery based on radiographic films has ability to give absolute two-dimension dose distribution and prefer for the IMRT quality assurance. However, the single therapy verification film gives a quick and significant reliable method for IMRT verification.
Materials and methods
A single extended dose rate (EDR 2) film was used to generate the sensitometric curve of film optical density and radiation dose. EDR 2 film was exposed with nine 6 cm × 6 cm fields of 6 MV photon beam obtained from a medical linear accelerator at 5-cm depth in solid water phantom. The nine regions of single film were exposed with radiation doses raging from 10 to 362 cGy. The actual dose measurements inside the field regions were performed using 0.6 cm3 ionization chamber. The exposed film was processed after irradiation using a VIDAR film scanner and the value of optical density was noted for each region. Ten IMRT plans of head and neck carcinoma were used for verification using a dynamic IMRT technique, and evaluated using the gamma index method with TPS calculated dose distribution.
Sensitometric curve has been generated using a single film exposed at nine field region to check quantitative dose verifications of IMRT treatments. The radiation scattered factor was observed to decrease exponentially with the increase in the distance from the centre of each field region. The IMRT plans based on calibration curve were verified using the gamma index method and found to be within acceptable criteria.
The single film method proved to be superior to the traditional calibration method and produce fast daily film calibration for highly accurate IMRT verification.
IMRT; EDR 2 film; Patient specific quality assurance; Sensitometric curve
Rabies is the most severe and neglected public health problem in India. Management of animal bite with post exposure prophylaxis is the only existent strategy to prevent rabies related deaths. Cost-effective and sustainable programme for provision of post exposure prophylaxis (PEP) is needed in India.
In this study, we have documented the experience of implementation of intra-dermal anti rabies vaccination in Animal Bite Management (ABM) clinic at Primary Health Centre (PHC). This study facility belonged to Comprehensive Rural Health Services Project, Ballabgarh in Faridabad district of Haryana. Hospital service record of ABM clinic was analyzed and various feasibility issues such as costing of services, vaccine wastage and other operational issues in providing PEP services at PHC level were documented.
A total of 619 patients were treated in the ABM clinic. Service utilization of ABM clinic was increased by 38% in the second year of implementation. Mean age of the patients was 23.9 years (SD: 18.8) and majority (70.4%) were males. Majority (86%) of the patients received the first dose of anti-rabies vaccine within the recommended 48 hours. A total 446 vaccine vials (1 ml) were consumed of which 20.8% was contributed in vaccine wastage. User-fee (350 Indian Rupees) collected from the patients. User-fee was re-used to purchase vaccines, intradermal (ID) syringes and other consumables required to ensure regular availability of ARV services at the PHC.
This study demonstrated the cost-effective and sustainable model of provision of PEP against rabies at primary care level. ID PEP provision at primary care level not only address the unmet need of animal bite management in the community also reduces the out of pocket expenditure of the patients.
Intra-dermal PEP; Rabies; Primary care; Rural; India
The purpose of this study was to compare the outcome of open treatment of mandibular fracture (symphysis or parasymphysis) using lag screw or mini plate clinically as well as radiologically in young (age range 12–45 years) and healthy individuals of poor socioeconomic status.
This prospective study was conducted on 30 patients diagnosed as cases of displaced mandibular anterior fractures treated with open reduction and internal fixation. The patients were then randomly allocated to either of two groups––Group A: Two 2.5 mm stainless steel lag screws were placed in 15 patients. Group B: Two 2.5 mm stainless steel mini plates were placed in 15 patients for the fixation of fractures. Subsequent follow up was done on 2nd, 4th, 6th and 8th week postoperatively. During every follow up patient was assessed clinically for infection, malocclusion, loosening of plate/screw, sensory disturbance, plate fracture, malunion/non-union, devitalisation of associated dentoalveolar segment and masticatory efficiency. Radiographs were taken if necessary and patients were further assessed for any complaint. Pain was objectively measured using a visual analogue scale, bite force was measured using a bite force transducer at biweekly interval. The data collected was subjected to unpaired t test and paired t test for statistical analysis.
During follow up period a significant improvement in bite force was present in both the groups, with more improvement seen in the lag screw group (p < 0.01). There was a significant pain reduction present in the lag screw group (p < 0.01) and also masticatory efficiency showed a steadier improvement in lag screw group while mini plate group patients showed a tendency to masticate only food items of medium hard consistency.
The sample size is small to conclude lag screws are better than mini plates but the result of our study provides a basis for further studies done to conclude that the application of LAG SCREW is an effective, inexpensive, quick treatment modality to accelerate healing of fresh, displaced mandibular anterior fracture.
Mandibular anterior fracture; Lag screw; Miniplates; Bite force
A crossed-fused ectopic kidney is a rare congenital anomaly, and uncommonly we see an aberrant vessel as a cause of hydronephrosis in a kidney. We report a case of 4-year-old boy with crossed-fused right renal ectopia with hydronephrosis in the both kidneys. The aberrant renal vessel was found pressing the left pelvi-ureteric junction causing hydronephrosis. Dismembered pyeloplasty of the left kidney was performed anterior to the aberrant vessel. The patient is doing well in the follow-up visits and his renal function is stabilized. Aberrant blood supply may be a cause of hydronephrosis in the crossed-fused ectopic ipsilateral kidney. Keeping this entity in differential diagnosis will help in successful management of the crossed-fused ectopic kidney.
Crossed fused renal ectopia; Aberrant vessel; Hydronephrosis
Microalbuminuria is a risk factor for cardiovascular disease. It is gaining importance as a marker of atherogenic milieu and indicates the target organ damage and can be a valuable tool in screening and identification of patients with cardiovascular disease. Markers of inflammation, such as C-reactive protein (CRP), were found to be related to cardiovascular disease (CVD) events in patients with chest pain. In addition, recent studies have shown that, in the case of atherosclerosis, increased levels of CRP, reflects inflammatory condition of vessel wall. In the present study, CRP and microalbuminuria were estimated in patients of acute chest pain. The patients were divided into two study groups (gp-1 patients of chest pain with CVD and gp-2 patients of chest pain of causes other than CVD) along with one healthy control group. It was found that microalbuminuria was higher in CVD patients (RR = 6.250,95% CI 2.346–16.45,P < 0.05) and also CRP was much higher in CVD patients (RR = 13.667,95% CI 4.528–41.253, P < 0.05) as compared to other two groups. Sensitivity, specificity and positive predictive value of CRP and microalbuminuria were also higher in gp-1 (CVD) patients as compared to other two groups. Therefore, CRP and microalbuminuria can be used as important biomarkers in screening CVD.
Chest pain; Coronary disease; C-reactive protein; Microalbuminuria
In the generation of a traditional immune response against invading pathogens, innate cells guide T cells by programming their differentiation. However, here we demonstrate that αβ T cells play an essential role in priming innate immunity in the lung after Staphylococcus aureus enterotoxin A (SEA) inhalation. We found that SEA induces waves of cellular activation, cytokine production, and migration into the lung tissue and airways. However, this innate response was completely inhibited in the absence of αβ T cells. Specifically, we found that IL-17A was required for the recruitment of neutrophils and monocytes into the lung. The cellular source of IL-17A was γδ T cells, which increased their IL-17A production following SEA, but only in an αβ T cell-dependent manner. Thus, rapid T cell activation orchestrates innate immunity and may be a new point of therapeutic intervention for acute lung injury.
Acute kidney injury (AKI) promotes an abrupt loss of kidney function that results in substantial morbidity and mortality. Considerable effort has gone toward identification of diagnostic biomarkers and analysis of AKI-associated molecular events; however, most studies have adopted organ-wide approaches and have not elucidated the interplay among different cell types involved in AKI pathophysiology. To better characterize AKI-associated molecular and cellular events, we developed a mouse line that enables the identification of translational profiles in specific cell types. This strategy relies on CRE recombinase–dependent activation of an EGFP-tagged L10a ribosomal protein subunit, which allows translating ribosome affinity purification (TRAP) of mRNA populations in CRE-expressing cells. Combining this mouse line with cell type–specific CRE-driver lines, we identified distinct cellular responses in an ischemia reperfusion injury (IRI) model of AKI. Twenty-four hours following IRI, distinct translational signatures were identified in the nephron, kidney interstitial cell populations, vascular endothelium, and macrophages/monocytes. Furthermore, TRAP captured known IRI-associated markers, validating this approach. Biological function annotation, canonical pathway analysis, and in situ analysis of identified response genes provided insight into cell-specific injury signatures. Our study provides a deep, cell-based view of early injury-associated molecular events in AKI and documents a versatile, genetic tool to monitor cell-specific and temporal-specific biological processes in disease modeling.
Study undertaken to find any association of metformin intake to that of survival in ovarian cancer.
In this retrospective case control study, ovarian cancer patients who took metformin (cases) were compared with patients having ovarian cancer but no metformin (controls). Two-layered analysis was conducted. In preliminary analysis, all cases (OC cohort) were compared with controls in 1:2 ratio. Subsequently in definitive analysis, only Epithelial Ovarian Cancer cases (EOC cohort) were compared with controls in 1:3 ratio. In EOC cohort, cases were matched with controls for age (+/−5 years), FIGO stage and residual disease. Prognostic variables and Disease Specific Survival (DSS) were compared with Chi square, Kaplan-Meier (log rank) and Cox proportional hazards.
In the preliminary analysis on the OC cohort (72 cases, 143 controls), cases had a better survival (5 year DSS for cases 73% vs. controls 44%; p=0.0002). In the definitive analysis on the EOC cohort (61 cases, 178 controls) distribution of age, stage, optimal cytoreduction, serous histology and platinum chemotherapy remained similar amongst the cases and controls (p>0.05). Despite these similarities, cases had a significantly better survival (5 year DSS for cases 67% vs. controls 47%; p=0.007). On a multivariate analysis, metformin remained an independent predictor of survival (hazards ratio 3.7; 95% CI 1.6–9.0; p=0.002) after controlling for stage, grade, histology, chemotherapy, body mass index and surgical cytoreduction.
This study reports association rather than causation. Metformin intake was associated with better survival in ovarian cancer. Metformin is worthy of clinical trials in ovarian cancer.
Metformin; ovarian cancer; survival; drug repositioning
Recent observations suggest a lower incidence of malignancies in patients infected with HIV during treatment with Highly Active Anti-Retroviral Therapy (HAART) utilizing protease inhibitors. We investigated the effects of ritonavir, a FDA approved HIV protease inhibitor, on proliferation of pancreatic ductal adeno-carcinoma (PDAC) cell lines. Human PDAC cell lines BxPC-3, MIA PaCa-2, and PANC-1 were propagated under standard conditions and treated with serial dilutions of ritonavir. Ritonavir inhibited cell growth in a dose-dependent manner as well as activated the intrinsic apoptotic pathway in human pancreatic ductal adenocarcinoma (PDAC) cell lines. We observed down-modulation of cell-cycle promoting and up-regulation of cell-cycle inhibitory genes; enhanced interaction of retinoblastoma protein (RB) with E2F-1 transcription factor; inhibition of phosphorylation of RB, resulting in sequestration of E2F-1 and subsequent down-regulation of S phase genes; decreased interaction of E2F-1 with its consensus binding sites; inhibition of cell motility and invasiveness; and inhibition of the AKT pathway. Our results demonstrate a potential use of ritonavir as part of combination chemotherapy for PDAC. Since ritonavir is FDA approved for HIV, drug repositioning for PDAC would limit the costs and reduce risks.
ritonavir; pancreatic adenocarcinoma; AKT; retinoblastoma; 2F-1
Multiferroic materials, in which ferroelectric and magnetic ordering coexist, are of fundamental interest for the development of multi-state memory devices that allow for electrical writing and non-destructive magnetic read-out operation. The great challenge is to create multiferroic materials that operate at room-temperature and have a large ferroelectric polarization P. Cupric oxide, CuO, is promising because it exhibits a significant polarization, i.e. P ~ 0.1 μC.cm−2, for a spin-spiral multiferroic. Unfortunately CuO is only ferroelectric in a temperature range of 20 K, from 210 to 230 K. Here, using a combination of density functional theory and Monte Carlo calculations, we establish that pressure-driven phase competition induces a giant stabilization of the multiferroic phase of CuO, which at 20-40 GPa becomes stable in a domain larger than 300 K, from 0 to T > 300 K. Thus, under high-pressure, CuO is predicted to be a room-temperature multiferroic with large polarization.
The recent experience with the emergence of the 2009 pandemic influenza A/H1N1 virus has highlighted the value of free and open access to influenza virus genome sequence data integrated with information about viral characteristics related to antiviral drug resistance and virulence. The Influenza Research Database (IRD, www.fludb.org) is a free, publicly accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases (NIAID) through the Bioinformatics Resource Centers (BRC) program. The IRD provides a comprehensive, integrated database, and analysis resource for influenza sequence, surveillance, and research data. It also provides user-friendly interfaces for data retrieval and visualization, comparative genomics analysis, and personal log in-protected “workbench” spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature. The goal of the IRD is to provide a resource that helps researchers identify root causes of virus pathogenicity and host range restriction, and facilitates the development of vaccines, diagnostics, and therapeutics.
To identify risk factors for endometrial cancer after benign results of endometrial biopsy or dilatation and curettage (D&C).
Nested case-control study from Rochester Epidemiology Project data. Among 370 Olmsted County, Minnesota, residents who received an endometrial cancer diagnosis between 1970 and 2008, we identified 90 patients (24.5%) who had previous benign endometrial biopsy or D&C results (no atypical hyperplasia). We compared them with 172 matched controls who had benign endometrial biopsy or D&C results without subsequent endometrial cancer.
Using a multivariable, conditional logistic regression model, we found that oral contraceptive use was protective (odds ratio [OR], 0.18; 95% confidence interval [CI], 0.08-0.45; P<.001), and personal history of colorectal cancer (OR, 4.44; 95% CI, 1.02-19.31; P<.05), endometrial polyp (OR, 4.12; 95% CI, 1.40-12.17; P=.01), and morbid obesity (OR, 3.40; 95% CI, 1.18-9.78; P<.03) were independently associated with subsequent endometrial cancer. Compared with the presence of no risk factor, presence of one and two or more risk factors increased the risk of endometrial cancer by 8.12 (95% CI, 3.08-21.44) and 17.87 (95% CI, 5.57-57.39) times, respectively. Assuming a 2.6% lifetime risk of EC, OR’s of 8.12 and 17.87 for 1 and 2 or more of the 4 afore-mentioned risk factors confer a lifetime risk of approximately 18% and 32%, respectively.
One-fourth of patients with endometrial cancer had previous benign endometrial biopsy or D&C results. Personal history of colorectal cancer, presence of endometrial polyps, and morbid obesity are the strongest risk factors for having endometrial cancer after a benign endometrial biopsy or D&C result, and oral contraceptive use is the strongest protective factor.
The scavenger receptor CD36 plays important roles in malaria, including the sequestration of parasite-infected erythrocytes in microvascular capillaries, control of parasitemia through phagocytic clearance by macrophages, and immunity. Although the role of CD36 in the parasite sequestration and clearance has been extensively studied, how and to what extent CD36 contributes to malaria immunity remains poorly understood. In this study, to determine the role of CD36 in malaria immunity, we assessed the internalization of CD36-adherent and CD36-nonadherent Plasmodium falciparum-infected red blood cells (IRBCs) and production of pro-inflammatory cytokines by DCs, and the ability of DCs to activate NK, and T cells. Human DCs treated with anti-CD36 antibody and CD36 deficient murine DCs internalized lower levels of CD36-adherent IRBCs and produced significantly decreased levels of pro-inflammatory cytokines compared to untreated human DCs and wild type mouse DCs, respectively. Consistent with these results, wild type murine DCs internalized lower levels of CD36-nonadherent IRBCs and produced decreased levels of pro-inflammatory cytokines than wild type DCs treated with CD36-adherent IRBCs. Further, the cytokine production by NK and T cells activated by IRBC-internalized DCs was significantly dependent on CD36. Thus, our results demonstrate that CD36 contributes significantly to the uptake of IRBCs and pro-inflammatory cytokine responses by DCs, and the ability of DCs to activate NK and T cells to produce IFN-γ. Given that DCs respond to malaria parasites very early during infection and influence development of immunity, and that CD36 contributes substantially to the cytokine production by DCs, NK and T cells, our results suggest that CD36 plays an important role in immunity to malaria. Furthermore, since the contribution of CD36 is particularly evident at low doses of infected erythrocytes, the results imply that the effect of CD36 on malaria immunity is imprinted early during infection when parasite load is low.
Paraneoplastic pemphigus (PNP) is often a fatal autoimmune bullous disease characterized by severe stomatitis, polymorphous skin eruptions, and underlying neoplasms. We describe a patient with PNP associated with follicular dendritic cell sarcoma (FDCS), a rare neoplasm originating from follicular dendritic cells, which are non-lymphoid, non-phagocytic accessory cells of the lymphoid system and play an integral role in regulation of the germinal center reaction and present antigens to B-cells. The presence of rich vascularity around the tumor and few hyalanized vascular follicles found in histopathological examination gives the clue that the tumor might have developed from Castleman's disease (CD). As for the mechanisms by which CD induces PNP, it has been proposed that autoantibodies secreted from the Castleman's tumor play pivotal role. This hypothesis seems to be supported by the present case, in which CD may have triggered both the FDCS and the PNP.
Castleman's disease; follicular dendritic cell sarcoma; paraneoplatic pemphigus
Studies have shown that glycosylphosphatidylinositols (GPIs) of Plasmodium faciparum activate macrophages mainly through TLR2- and to certain extent through TLR4-mediated signaling to induce proinflammatory cytokine production. However, the ability of parasite GPIs to activate DCs has not been reported. Here, we show that, parasite GPIs efficiently activate DCs through TLR2-mediated signaling mechanism and induce the production of TNF-α and IL-12. We also studied the role of scavenger receptor CD36 in P. falciparum GPI- and merozoite-induced cytokine responses by DCs. The results indicate that CD36 modulates the cytokine-inducing activity of the parasite GPIs by collaborating with TLR2 in DCs. Furthermore, our data reveal that CD36 modulates the activity of P. falciparum merozoites, likely by the contribution of phagocytosis-coupled CD36-mediated signaling to the signaling induced by merozoites. Altogether, these results contribute toward understanding of signaling mechanisms in malaria parasite-induced activation of the innate immune system.
Plasmodium falciparum; Glycosylphosphatidylinositols; Merozoites; Dendritic cells; Toll-like receptors; CD36; Proinflammatory cytokines
An efficient protocol for rapid in vitro clonal propagation of spine gourd (Momordica dioica Roxb.) genotype RSR/DR15 (female) and DR/NKB-28 (male) was developed through enhanced axillary shoot proliferation from nodal segments. Maximum shoot proliferation of 6.2 shoots per explant with 100 % shoot regeneration frequency was obtained from the female genotype on Murashige and Skoog’s (1962) medium supplemented with 0.9 μM N6-benzyladenine (BA) and 200 mg l-1 casein hydrolysate (CH). While from the male genotype the optimum shoot regeneration frequency (86.6 %) and 6.4 shoots per explant was obtained on MS medium supplemented with 2.2 μM BA. CH induced vigorous shoots, promoted callus formation, and proved inhibitory for shoot differentiation and shoot length, especially in explants from male genotype. Rooting was optimum on half-strength MS medium (male 92.8 %, female 74.6 %) containing 4.9 μM indole-3-butyric acid (IBA). Plantlets were transferred to plastic cups containing a mixture of cocopit and perlite (1:1 ratio) and then to soil after 2–3 weeks. 84 % female and 81 % male regenerated plantlets survived and grew vigorously in the field. Genetic stability of the regenerated plants was assessed using random amplified polymorphic DNA (RAPD). The amplification products were monomorphic in the in vitro propagated plants and similar to those of mother plant. No polymorphism was detected revealing the genetic integrity of in vitro propagated plants. This micropropagation procedure could be useful for raising genetically uniform planting material of known sex for commercial cultivation or build-up of plant material of a specific sex-type.
Momordica dioica; Dioecious; Axillary shoot proliferation; Micropropagation; Nodal explants; Genetic fidelity
Obstructive lesions in the inflow of the systemic ventricle in congenitally corrected transposition of the great arteries are rare. It is important to identify such lesion which could alter the surgical outcome if not recognized. We report the echocardiographic findings in a patient with supratricuspid obstructive membrane with corrected transposition of the great arteries.
Corrected transposition of great arteries; echocardiography; supratricuspid membrane
We are reporting a case of an asthmatic patient who presented to us with retrosternal chest pain, constipation, and shortness of breath, with features which were suggestive of a hydropneumothorax and shock. On recovery from the shock, the patient was found to have increased chest tube drainage, which was suggestive of an oesophageal rupture. The Computerized Tomography (CT) scan showed a fistulous track. The patient was diagnosed as a case of a spontaneous oesophageal pleural fistula (Spontaneous EPF) on the basis of her clinical and radiological findings.
Asthma; Shock; Oesophageal pleural fistula; Rupture
Desmoid tumors (also called desmoids fibromatosis) are rare slow growing benign and musculoaponeurotic tumors. Although these tumors have a propensity to invade surrounding tissues, they are not malignant. These tumors are associated with women of fertile age, especially during and after pregnancy. We report a young female patient with a giant desmoid tumor of the anterior abdominal wall who underwent primary resection. The patient had no history of an earlier abdominal surgery. Preoperative evaluation included abdominal ultrasound, computed tomography, and magnetic resonance imaging. The histology revealed a desmoid tumor. Primary surgical resection with immediate reconstruction of abdominal defect is the best management of this rarity. To the best of our knowledge and PubMed search, this is the first case ever reported in the medical literature of such a giant desmoid tumor arising from anterior abdominal wall weighing 6.5 kg treated surgically with successful outcome.
We report a case of retained wooden foreign body in the zygomatic region which posed a considerable diagnostic difficulty and was the source of persistent draining sinus and other distressing symptoms. The patient was not aware of the foreign body in the maxillofacial region. In such cases a thorough history of the patient is of utmost importance. The case has been described to highlight the problems associated in managing unlikely foreign bodies at unusual facial sites when there is a possibility that radiolucent material is embedded in the wound.
Foreign body; Maxillofacial region; Trismus
Extracellular matrices in diverse biological systems are crosslinked by dityrosine covalent bonds catalyzed by the peroxidase/oxidase system. We show that the Immunomodulatory Peroxidase (IMPer), an enzyme secreted by the mosquito Anopheles gambiae midgut, and dual oxidase (Duox) form a dityrosine network that decreases gut permeability to immune elicitors and protects the microbiota by preventing activation of epithelial immunity. It also provides a suitable environment for malaria parasites to develop within the midgut lumen without inducing nitric oxide synthase expression. Disruption of this barrier results in strong and effective pathogen-specific immune responses.
malaria; A. gambiae; mosquito; Plasmodium; immunomodulatory peroxidase; IMPer; dual oxidase; Duox; epithelial immunity; dityrosine
Chronological aging of yeast cells is commonly used as a model for aging of human post-mitotic cells. The yeast Saccharomyces cerevisiae grown on glucose in the presence of ammonium sulphate is mainly used in yeast aging research. We have analyzed chronological aging of the yeast Hansenula polymorpha grown at conditions that require primary peroxisome metabolism for growth.
The chronological lifespan of H. polymorpha is strongly enhanced when cells are grown on methanol or ethanol, metabolized by peroxisome enzymes, relative to growth on glucose that does not require peroxisomes. The short lifespan of H. polymorpha on glucose is mainly due to medium acidification, whereas most likely ROS do not play an important role. Growth of cells on methanol/methylamine instead of methanol/ammonium sulphate resulted in further lifespan enhancement. This was unrelated to medium acidification. We show that oxidation of methylamine by peroxisomal amine oxidase at carbon starvation conditions is responsible for lifespan extension. The methylamine oxidation product formaldehyde is further oxidized resulting in NADH generation, which contributes to increased ATP generation and reduction of ROS levels in the stationary phase.
We conclude that primary peroxisome metabolism enhanced chronological lifespan of H. polymorpha. Moreover, the possibility to generate NADH at carbon starvation conditions by an organic nitrogen source supports further extension of the lifespan of the cell. Consequently, the interpretation of CLS analyses in yeast should include possible effects on the energy status of the cell.
Several viruses within the Coronaviridae family have been categorized as either emerging or re-emerging human pathogens, with Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) being the most well known. The NIAID-sponsored Virus Pathogen Database and Analysis Resource (ViPR, www.viprbrc.org) supports bioinformatics workflows for a broad range of human virus pathogens and other related viruses, including the entire Coronaviridae family. ViPR provides access to sequence records, gene and protein annotations, immune epitopes, 3D structures, host factor data, and other data types through an intuitive web-based search interface. Records returned from these queries can then be subjected to web-based analyses including: multiple sequence alignment, phylogenetic inference, sequence variation determination, BLAST comparison, and metadata-driven comparative genomics statistical analysis. Additional tools exist to display multiple sequence alignments, view phylogenetic trees, visualize 3D protein structures, transfer existing reference genome annotations to new genomes, and store or share results from any search or analysis within personal private ‘Workbench’ spaces for future access. All of the data and integrated analysis and visualization tools in ViPR are made available without charge as a service to the Coronaviridae research community to facilitate the research and development of diagnostics, prophylactics, vaccines and therapeutics against these human pathogens.
virus; database; bioinformatics; Coronavirus; SARS; SARS-CoV; Coronaviridae; comparative genomics