Multi-GWAS reveals significant genomic regions for Mungbean yellow mosaic India virus resistance in urdbean (Vigna mungo (L.) across multiple environments.

KEY MESSAGE: Unraveling genetic markers for MYMIV resistance in urdbean, with 8 high-confidence marker-trait associations identified across diverse environments, provides crucial insights for combating MYMIV disease, informing future breeding strategies. Globally, yellow mosaic disease (YMD) causes significant yield losses, reaching up to 100% in favorable environments within major urdbean cultivating regions. The introgression of genomic regions conferring resistance into urdbean cultivars is crucial for combating YMD, including resistance against mungbean yellow mosaic India virus (MYMIV). To uncover the genetic basis of MYMIV resistance, we conducted a genome-wide association study (GWAS) using three multi-locus models in 100 diverse urdbean genotypes cultivated across six individual and two combined environments. Leveraging 4538 high-quality single nucleotide polymorphism (SNP) markers, we identified 28 unique significant marker-trait associations (MTAs) for MYMIV resistance, with 8 MTAs considered of high confidence due to detection across multiple GWAS models and/or environments. Notably, 4 out of 28 MTAs were found in proximity to previously reported genomic regions associated with MYMIV resistance in urdbean and mungbean, strengthening our findings and indicating consistent genomic regions for MYMIV resistance. Among the eight highly significant MTAs, one localized on chromosome 6 adjacent to previously identified quantitative trait loci for MYMIV resistance, while the remaining seven were novel. These MTAs contain several genes implicated in disease resistance, including four common ones consistently found across all eight MTAs: receptor-like serine-threonine kinases, E3 ubiquitin-protein ligase, pentatricopeptide repeat, and ankyrin repeats. Previous studies have linked these genes to defense against viral infections across different crops, suggesting their potential for further basic research involving cloning and utilization in breeding programs. This study represents the first GWAS investigation aimed at identifying resistance against MYMIV in urdbean germplasm.

Pedigree-based relationship inference from complex DNA mixtures.

We present a general method for analysing DNA mixtures involving relatives that accounts for dropout and drop-in, mutations, silent alleles and population substructure. Whether the aim is to identify the contributors to a mixture who may be related, or to determine the relationship between individuals based on a DNA mixture, both types of problems can be handled by the method and software presented here. We focus on the latter scenario, motivated by non-invasive prenatal paternity testing where the profile of the child is available only in the form of a mixture with the mother's profile. Relationships are represented by pedigrees and can include kinship between more than two individuals. The software is freely available as a graphical user interface in the R package relMix.

Relationship inference based on DNA mixtures.

Today, there exists a number of tools for solving kinship cases. But what happens when information comes from a mixture? DNA mixtures are in general rarely seen in kinship cases, but in a case presented to the Norwegian Institute of Public Health, sample DNA was obtained after a rape case that resulted in an unwanted pregnancy and abortion. The only available DNA from the fetus came in form of a mixture with the mother, and it was of interest to find the father of the fetus. The mother (the victim), however, refused to give her reference data and so commonly used methods for paternity testing were no longer applicable. As this case illustrates, kinship cases involving mixtures and missing reference profiles do occur and make the use of existing methods rather inconvenient. We here present statistical methods that may handle general relationship inference based on DNA mixtures. The basic idea is that likelihood calculations for mixtures can be decomposed into a series of kinship problems. This formulation of the problem facilitates the use of kinship software. We present the freely available R package relMix which extends on the R version of Familias. Complicating factors like mutations, silent alleles, and θ-correction are then easily handled for quite general family relationships, and are included in the statistical methods we develop in this paper. The methods and their implementations are exemplified on the data from the rape case.

Prevalence of multidrug-resistant, coagulase-positive Staphylococcus aureus in nasal carriage, food, wastewater and paper currency in Jalandhar city (north-western), an Indian state of Punjab.

Development of multidrug-resistant pattern in the bacterial community is a major threat to the society. Staphylococcus aureus is perhaps the pathogen of the greatest concern because of its inherent virulence, its ability to cause a diverse array of life-threatening situations and capacity to adapt to different environmental conditions. The aims of this study is to investigate the multidrug-resistant pattern of the coagulase-positive S. aureus isolated from nasal carriage, food, paper currency and wastewater samples. We had also studied the multiple antibiotic resistance index and in vitro production of ß-lactamase. The study had found out 130 coagulase-positive S. aureus strains isolated from total of 595 samples such as anterior nares of preschool children (195), hospital nurses (100), drivers (76), food (86), wastewater (3) and paper currency (135) (Indian rupee). The biotypes pattern were as follows; A > D > B > C> UT. Multiple antibiotic resistance (MAR) value clearly defines the multidrug-resistant pattern of the S. aureus among different sources. Statistical analysis (one-way ANOVA) of results obtained indicated that the difference in the antibiotic resistance observed in the 130 bacterial isolates against the 23 different antibiotics used in this study was statically significant (p < 0.01).

Advancing automobile identification and brand discrimination from tyre rubber through Machine learning algorithms for forensic investigations.

Criminal instances involving collision accidents, hit-and-run incidents, abduction, hostage-taking, and the unauthorised transit of forbidden items generally include evidence involving rubber traces from automobile tyres. These traces can be located on the road surface, in clothing, on the victim(s) themselves, or on items as skid marks following sudden stopping and spinning around. These traces serve as crucial evidence by reducing the range of suspects by revealing linkages between the getaway vehicle, the site of the crime, and the perpetrator through the tyre's brand, producer, or origin. This study offered a way for classifying 220 tyre rubber samples from different brands using various machine learning algorithms in PyCaret in conjunction with rapid and non-destructive ATR-FTIR spectroscopy equipped with diamond crystal. On spectral information from ATR-FTIR, pre-processing tools such as baseline correction, smoothing, derivatization, and normalisation were also implemented prior to machine learning. This approach has the potential to be advantageous for efficiently and non-destructively identifying rubber traces as forensic evidence and for facilitating brand recognition of automobile tyres.

Biochemical and physiological changes in Fenugreek (Trigonella foenum- graecum L.) leaves during storage under modified atmosphere packaging.

Fenugreek (Trigonella foenum-graecum L.), is a highly respiring leafy vegetable enriched with many nutrients and other active ingredients such as protein, vitamin C, niacin, potassium, alkaloids, lysine and L-tryptophan as well as steroidal saponins which are beneficial for human health. Both, quantitative and qualitative losses in this vegetable can be reduced by appropriate packaging and storage techniques which have not been applied hitherto. This study was taken upon to assess the potential of macro-perforated MAP for storage of fenugreek leaves. Packages (bag area: 0.075 m(2)) made from polypropylene (PP) film (Thickness: 35 µmm) were selected for the storage studies. The leaves were packaged in macro-perforated (2 perforations, perforation diameter: 0.3 mm each, with and without mustard seeds as natural absorbents) as well as in non-perforated PP film packages with and without mustard seeds. 10 g of mustard seeds were placed inside the packages to check water accumulation. The packaged samples were stored for 6 days at 75% relative humidity (RH) at 15°C to check water accumulation, if any. Different physiological and biochemical characteristics which generally affect the post-harvest life of the produce were monitored during the storage period. Results of the study suggested that among all the treatments, packaging of fenugreek in two perforation packets with mustard seeds resulted in best maintenance of chlorophyll, ascorbic acid, phenols and aroma. Water accumulation was also consoled due to mustard seeds after 6 days of storage.

A nationwide survey on the preference of Indian undergraduate medical students to go abroad for higher studies and residency.

Context: Getting residency training abroad is a critical motivator in the emigration of Indian medical students. Brain drain is an emerging issue, especially for developing countries as it causes a shortage of trained staff in the donor country. Aim: We aimed to survey Indian medical students to know about their intentions to get trained abroad and to understand the factors influencing their decision. Materials and Methods: In this cross-sectional observational study, we surveyed Indian undergraduate medical students of all professional years, including internship. A validated questionnaire collected data on students' demographics and educational characteristics, intention to study overseas or stay back in India, and factors influencing their decision. Results: Out of a total of 1199 responses (51.1% males, 48.9% females), 45.0% partakers had planned to pursue their residency abroad, while 33.8% wanted to stay in India and 21.2% were undecided. Better lifestyle and higher pay grades overseas were viewed as the most significant barriers to staying back in India and a key influencer in decision-making among the maximum number of students (412; 76.3%). On the other hand, a whopping 58.2% of participants opined that they wanted to stay back in India for taking care of their parents. Conclusions: Source countries with better healthcare facilities and better incomes tend to attract medical students. Awareness among medical educators regarding constantly changing curricula, a shift to a competency-based education system, better pay grades, limited working hours, and interventions to mitigate workplace violence could help prevent brain drain among Indian medical students and graduates.

Age-specific trends in intravenous thrombolysis and mechanical thrombectomy utilization in acute ischemic stroke in children under age 18.

OBJECTIVES: To evaluate current trends in the utilization of intravenous thrombolysis (IV-tPA) and mechanical thrombectomy (MT) in acute ischemic stroke (AIS) in various age groups of children in the United States. METHODS: We conducted a serial cross-sectional study using primary AIS admissions in children ⩽ 17 years (weighted n = 2807) contained in the 2009-2019 KIDS Inpatient Database. Age-specific utilization frequency of IV-tPA and MT were calculated. Multivariable-adjusted models were used to evaluate demographic predictors of treatment. RESULTS: From 2009 to 2019, there were 2807 AIS admissions in children in the KID of which 55.9% were in boys and 29.9% were 15-17 years old.128 (4.6%) received IV-tPA. IV-tPA utilization differed by age (5-9 years: 3.1%, 15-17 years 8.1% p value < 0.001). Overall MT usage was 2.3% and this also varied by age (1-4 years: 0.9% and 15-17years 4.0%, p value = 0.006). IV-tPA utilization almost tripled across the study period (2.5% 2009 to 6.5% in 2019, p value = 0.001) while MT use more than doubled over time (1.2% in 2009 and 3.0% in 2019, p value = 0.048). Increased IV-tPA utilization was seen primarily in children 10-14 years (0.8% in 2009 to 7.2% 2019, p value = 0.005) and 15-17 years (5.4% in 2009 to 10.4% in 2019, p value = 0.045). Utilization in younger age groups remained unchanged over time. MT usage was very variable across various age groups over time. IV-tPA and MT utilization increased over time in nonchildren's hospitals (both p values < 0.05) but usage in designated children's hospitals did not change significantly over time. In multivariable models, there was no significant difference in odds of IV-tPA and MT use by sex, race or insurance status. CONCLUSION: IV-tPA and MT utilization in pediatric AIS increased in the United States over the past decade mainly in older children 10-17 years. Utilization increased mainly in patients hospitalized in nonchildren's hospitals. Usage in children's hospitals did not change significantly over time.

Peduncular hallucinosis after a thalamic stroke.

Peduncular hallucinosis is a rare form of hallucinations consisting of vivid and nonthreatening colourful visual hallucinations. It was first described by French neurologist Jean Lhermitte in 1922. It sometimes includes distorted images of animals and people. Peduncular hallucinosis has been described after vascular and infective lesions of the mesencephalon and thalamus.We present a case of peduncular hallucinosis after a right thalamic infarction. This is a case of a 75-year-old Caucasian man with a previous medical history of hypertension and hyperlipidaemia who presented as a transfer from an outside hospital with transient left facial palsy, upper and lower extremity weakness. His symptoms resolved on arrival. CTA head and neck revealed focal filling defect in the basilar artery and a right posterior cerebral artery (PCA) occlusion at its origin. MRI brain without contrast revealed a right thalamic infarct. The patient had vivid hallucinations including his wife sleeping on his hospital bed, seeing his favourite book on the table while he had left it at home, seeing his dogs and a TV show on his room television while it was off. He was easily redirectable, and the hallucinations resolved over 2 days without pharmacological intervention. In cases of thalamic, midbrain or peduncular infarctions, physicians should be cognizant of the possibility of peduncular hallucinosis and inquire about hallucinations. New onset hallucinations in a patient with no prior psychiatric history presenting with concerns for stroke should prompt physicians to strongly consider peduncular hallucinosis.

Theory-Guided Randomized Neural Networks for Decoding Medication-Taking Behavior.

Long-term endocrine therapy (e.g. Tamoxifen, aromatase inhibitors) is crucial to prevent breast cancer recurrence, yet rates of adherence to these medications are low. To develop, evaluate, and sustain future interventions, individual-level modeling can be used to understand breast cancer survivors' behavioral mechanisms of medication-taking. This paper presents interdisciplinary research, wherein a model employing randomized neural networks was developed to predict breast cancer survivors' daily medication-taking behavior based on their survey data over three time periods (baseline, 4 months, 8 months). The neural network structure was guided by random utility theory developed in psychology and behavioral economics. Comparative analysis indicates that the proposed model outperforms existing computational models in terms of prediction accuracy under conditions of randomness.

Independent evolution of functional Pm3 resistance genes in wild tetraploid wheat and domesticated bread wheat.

The Pm3 alleles of cultivated bread wheat confer gene for gene resistance to the powdery mildew fungus. They represent a particular case of plant disease resistance gene evolution, because of their recent origin and possible evolution after the formation of hexaploid wheat. The Pm3 locus is conserved in tetraploid wheat, thereby allowing the comparative evolutionary study of the same resistance locus in a domesticated species and in one of its wild ancestors. We have identified 61 Pm3 allelic sequences from wild and domesticated tetraploid wheat subspecies. The Pm3 sequences corresponded to 24 different haplotypes. They showed low sequence diversity, differing by only a few polymorphic sequence blocks that were further reshuffled between alleles by gene conversion and recombination. Polymorphic sequence blocks are different from the blocks found in functional Pm3 alleles of hexaploid wheat, indicating an independent evolution of the Pm3 loci in the two species. A new functional gene was identified in a wild wheat accession from Syria. This gene, Pm3k, conferred intermediate race-specific resistance to powdery mildew, and consists of a mosaic of gene segments derived from non-functional alleles. This demonstrates that Pm3-based resistance is not very frequent in wild tetraploid wheat, and that the evolution of functional resistance genes occurred independently in wild tetraploid and bread wheat. The Pm3 sequence variability and geographic distribution indicated that diversity was higher in wild emmer wheat from the Levant area, compared with the accessions from Turkey. Further screens for Pm3 functional genes in wild wheat should therefore focus on accessions from the Levant region.

Fever work-up unfolds a rare diagnosis of native valve endocarditis caused by Mycobacterium abscessus.

Endocarditis caused by Mycobacterium abscessus is rare and often missed without appropriate blood cultures. It does not respond to standard antitubercular treatment and is also resistant to many other antibiotics. The course of the disease may be indolent and often results in a fatal outcome. Accurate identification and sensitivity, combination therapy, and prolonged duration of antibiotics are, therefore, important for a successful outcome.

Anti-inflammatory effect of methanolic extract of Gmelina arborea bark and its fractions against carrageenan induced paw oedema in rats.

Gmelina arborea has been traditionally used for treatment of abdominal pain, burning sensation and as stomachic. The anti-inflammatory effect of aqueous and methanol extract of this plant has been studied but detailed investigations on anti-inflammatory activity of G. arborea stem bark are still not available. Therefore, the present study was designed to evaluate the anti-inflammatory activity of methanol extract and its fractions using carrageenan induced paw oedema model. Methanol extract at the dose of 500 mg/kg and its ethyl acetate fraction at 50 mg/kg showed significant reduction in paw oedema in comparison with standard drug. Ethyl acetate fraction was subjected to column chromatography which resulted in isolation of a new flavonoid (GM-01). Anti-inflammatory effect of methanol extract and its fractions can be attributed to the presence of the flavonoid GM-01. Further studies are underway for evaluation of anti-inflammatory effect of GM-01 and identification of active constituents present in ethyl acetate fraction.

Role of oxidative stress in lansoprazole-mediated gastric and hepatic protection in Wistar rats.

BACKGROUND AND AIM: Lansoprazole, a benzimidazole derivative, is a widely-used proton-pump inhibitor. In addition, it has been reported to have an independent gastroprotective action. Since free radicals and antioxidant mechanisms appear to counter-act tissue-related injury, we studied the effect of lansoprazole on oxidative stress in acid-ethanol gastric injury. As this drug is metabolized in the liver, we also studied its effect on the liver. METHODS: Wistar rats were divided into three groups: control group, group I (vehicle treatment) and group II (lansoprazole treatment for eight days). In all the groups, injury was induced by ethanol-HCl administration. The effect of lansoprazole on free-radical generation and various antioxidants, e.g. superoxide dismutase (SOD), catalase, reduced glutathione (GSH), glutathione-s-transferase (GST) and glutathione reductase was evaluated in the gastric mucosal and liver homogenates. RESULTS: Ethanol-HCl administration initiated injury as shown by increase in malondialdehyde (MDA) levels in both gastric mucosa and liver. There was an increase in SOD and GST activity and a decrease in catalase, glutathione reductase and GSH in the gastric mucosa. In liver, ethanol-HCl administration decreased the activity of SOD, catalase and GSH and increased GST activity. Lansoprazole pretreatment led to decrease in the levels of MDA and increase in SOD, catalase, GSH, glutathione reductase and GST in both the gastric mucosa and liver. CONCLUSIONS: Lansoprazole has a protective action on gastric mucosa and the liver. This protection is mediated by a decrease in oxidative stress and a concomitant in-crease in antioxidants.

Regression models for DNA-mixtures.

This paper deals with the statistical interpretation of DNA mixture evidence. The conventional methods used in forensic casework today use something like 16 STR-markers. Power can be increased by rather using SNP-markers. New statistical methods are then needed, and we present a regression framework. The basic idea is that the traditional forensic hypotheses, commonly denoted HD and HP, are replaced by parametric versions: a person contributes to a mixture if and only if the fraction he contributes is greater than 0. This contributed fraction is a parameter of the regression model. The regression model uses the peak heights directly and there is no need to specify or estimate the number of contributors to the mixture. Also, drop-in and drop-out pose no principal problems. Data from 25 controlled blinded experiments were used to test the model. The number of contributors varied between 2 and 5, and the fractions contributed ranged from 0.01 to 0.99. The fractions were accurately estimated by the regression analyses. There were no false positives (i.e., in no cases were non-contributors declared to contributors). Some false negatives occurred for fractions of 0.1 or lower. Simulations were performed to test the model further. The analyses show that useful estimates can be obtained from a relatively small number of SNP-markers. Reasonable results are achieved using 300 markers which is close to the 313 SNPs in the controlled experiment. Increasing the number of SNPs, the analyses demonstrate that individuals contributing as little as 1% can reliably be detected, which suggests that cases beyond the reach of conventional forensic methods today can be reported.