Galaxy is an open source web based framework for data intensive biomedical research. It is an environment for interactive analysis that transparently tracks the details of analyses, a workflow system for convenient reuse, data management, sharing and publishing of the results. In this paper we describe extending the Galaxy framework to the GARUDA Grid computing infrastructure for running bioinformatics applications on various grid. This involves developing a grid job adaptor for the Galaxy workflow. GARUDA grid is an aggregation of heterogeneous resources and advanced capabilities for scientific applications. Gridway is the metascheduler for running the jobs on the Garuda grid. Here we present the integration of Galaxy workflow with the Gridway middleware by developing a grid job runner to interface. This grid enabled galaxy facilitates computational biologists to perform complex problems on the grid environment through a web browser.
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pandemic has adversely affected humankind and caused millions of deaths globally since January 2020. Robust and quick serological tests such as antibody detection assays for SARS-CoV-2 provide relevant information and aid in the process of vaccine development and diagnostics, as well as in sero-epidemiological monitoring of antibody response to the virus. The receptor-binding domain (RBD) of spike and nucleocapsid protein are specific targets for detecting SARS-CoV-2 antibodies. Here, we present the development of a stable spike (S) and nucleocapsid (N) protein-based ELISA antibody detection test “CoroSuchak,” with 99% sensitivity, 98% specificity, cost-effective, and detection in a minimum time for serodiagnosis and mass screening of the population for antibodies against SARS-CoV-2. Blood samples were analyzed from 374 SARS-CoV-2 reverse transcription-polymerase chain reaction (RT-PCR) positive, 772 negative and asymptomatic, and 874 random groups of subjects. We found that the antibody titer was significantly higher ( p < 0.0001) in infected and vaccinated group compared to the only vaccinated and only infected group. Using enzyme-linked immunosorbent assay (ELISA), we detected SARS-CoV-2 immunoglobulin G (IgG) antibodies in 118/123 (96%) infected individuals, 570/653 (87%) non-infected but vaccinated individuals, 231/237 (97%) individuals who were both infected and vaccinated, and 499/874 (57%) from randomly selected individuals from the first and second waves of the pandemic. Similarly in the third wave, 14/14 (100%) infected and 16/20 (80%) RT-PCR-negative but symptomatic subjects were detected. Thus, the highly sensitive and specific in-house developed ELISA antibody detection kit “CoroSuchak” is extremely useful to determine the seroprevalence of SARS-CoV-2 antibodies in the coronavirus-exposed population. Key points • Indigenous kit using a combination of spike and nucleocapsid proteins and peptide sequences. • High sensitivity and specificity to detect variants. • Highly sensitive for mass screening. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-12113-8.
INTRODUCTIONIntrauterine Insemination (IUI) along with controlled ovarian stimulation has been a widely used method in management of women with infertility. IUI remains a relatively inexpensive, less invasive and easy to perform procedure, which if timed well can give favorable results. It is used in male factor infertility, minimal to mild endometriosis, PCOS, cervical factor or unexplained infertility. IUI has various determinants of success. Of these, sperm morphology, method of sperm preparation, cause of infertility, ovulation induction regime used, agent for ovulation trigger, etc. are important. Along with these, time interval between ovulation induction and IUI and time interval between sperm preparation and IUI are of definite clinical relevance.The timing of IUI, in the majority of published studies, is 32-36 h following hCG administration (used for ovulation trigger).1 Cochrane review compared the different time intervals from hCG trigger to IUI ranging from 24 to 48 hours and found that there is no difference ABSTRACT Background: The study was aimed to assess the difference in IUI outcome depending on the interval between hCG trigger and IUI and sperm preparation and IUI. Methods: The study was conducted in the Department of Obstetrics and Gynecology in Infertility unit at King George's Medical University, Lucknow from January-December 2016. All the women eligible for IUI were included in the study. Once the follicle attained size of 17-18 mm, IUI was planned 36-48 hours after Inj. hCG 10,000 IU im. Semen processing was done in laboratory and time noted between sperm preparation and IUI. Outcome was confirmation of pregnancy by urine test. Cases were women in whom IUI was done 36-40 hours after hCG as against controls (>40 hours). Interval between sperm preparation and IUI was <30 minutes in cases and ≥30 minutes in controls. Results: A total of 624 cycles were included in the study. Clomiphene was used in 582/624 cycles (93.3%) gonadotropins used in 42/624 cycles (2.7%). There was a total of 23 conceptions in study (3.7%). Of these 8/98 (8.2%) were seen when the interval between ovulation trigger and IUI was 36-40 hours and 15/526 in cycles (2.9%) when the interval was more than 40 hours (p=0.023; OR-3.028 95% CI -1.247-7.352). Of a total of 23 conceptions in the study, 18/324 conceptions were seen when IUI was done within 30 minutes of sperm preparation as compared to 5/300 when interval was more than 30 minutes (p=0.01). Conclusions: IUI with ovarian stimulation is a simple and effective procedure and its outcome can be maximized keeping in consideration the availability of gametes. IUI performed within 36-40 hours of hCG trigger and within 30 minutes of sperm preparation can increase conception rates.
Introduction: Many advanced techniques and materials have been introduced in the recent years with the advent of the new designing technology. Hence, in our study, we aimed to compare in maxillofacial trauma, the three-dimensional (3D) plating systems. Materials and Methods: We piloted a prospective clinical study among 50 subjects of both genders with mandibular parasymphysis fracture. We compared the 3D miniplates with the two-dimensional (2D) miniplates where the subjects were divided into 2 groups equally. The clinical parameters were compared at different times of follow-up after the surgery. Results: We observed that there was a similar distribution of the genders and the side of the fracture of the parasymphysis. There was a significant difference between the groups for the mouth opening while there was no significant difference for the sensory deficit. The subjects recovered better with the 3D mini-plates. Conclusion: The mandibular fractures can be successfully treated with the 3D miniplates that help in a quick and efficient recovery.
Schimke immunoosseous dysplasia is an autosomal recessive disorder characterized by spondyloepiphyseal dysplasia, lymphopenia with defective cellular immunity, and renal insufficiency. It is caused by a biallelic mutation in SMARCAL 1 gene. In this study, we described clinical and genetic diagnosis of a 5 years old girl who presented to our centre with short stature and repeated infections in the past. She had one episode of stroke in the past due to infarction and she was diagnosed with hypertension 1 year back. Last admission in the hospital, she had new stroke episode and found to have steroid resistant nephrotic syndrome.
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