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Cerebroside sulfotransferase (CST) is considered a target protein in developing substrate reduction therapy for metachromatic leukodystrophy. This study employed a multistep virtual screening approach for getting a specific and potent inhibitor against CST from 35 phytoconstituents of Bacopa monnieri (L.) Pennell and 31 phytoconstituents of Mucuna pruriens (L.) DC. from the IMPPAT 2.0 database. Using a binding score cutoff of -8.0 kcal/mol with ADME and toxicity screening, four phytoconstituents IMPHY009537 (Stigmastenol), IMPHY004141 (alpha-Amyrenyl acetate), IMPHY014836 (beta-Sitosterol), and IMPHY001534 (jujubogenin) were considered for in-depth analysis. In the binding pocket of CST, the major amino acid residues that decide the orientation and interaction of compounds are Lys85, His84, His141, Phe170, Tyr176, and Phe177. The molecular dynamics simulation with a 100ns time span further validated the stability and rigidity of the docked complexes of the four hits by exploring the structural deviation and compactness, hydrogen bond interaction, solvent accessible surface area, principal component analysis, and free energy landscape analysis. Stigmastenol from Bacopa monnieri with no potential cross targets was found to be the most potent and selective CST inhibitor followed by alpha-Amyrenyl acetate from Mucuna pruriens as the second-best performing inhibitor against CST. Our computational drug screening approach may contribute to the development of oral drugs against metachromatic leukodystrophy., Competing Interests: The authors declare that there are no competing interests associated with the manuscript., (Copyright: © 2024 Singh, Singh. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Epigenetic silencing through methylation is one of the major mechanisms for downregulation of tumor suppressor miRNAs in various malignancies. The aim of this study was to identify novel tumor suppressor miRNAs which are silenced by DNA hypermethylation and investigate the role of at least one of these in oral squamous cell carcinoma (OSCC) pathogenesis. We treated cells from an OSCC cell line SCC131 with 5-Azacytidine, a DNA methyltransferase inhibitor, to reactivate tumor suppressor miRNA genes silenced/downregulated due to DNA methylation. At 5-day post-treatment, total RNA was isolated from the 5-Azacytidine and vehicle control-treated cells. The expression of 2,459 mature miRNAs was analysed between 5-Azacytidine and control-treated OSCC cells by the microRNA microarray analysis. Of the 50 miRNAs which were found to be upregulated following 5-Azacytidine treatment, we decided to work with miR-6741-3p in details for further analysis, as it showed a mean fold expression of >4.0. The results of qRT-PCR, Western blotting, and dual-luciferase reporter assay indicated that miR-6741-3p directly targets the oncogene SRSF3 at the translational level only. The tumor-suppressive role of miR-6741-3p was established by various in vitro assays and in vivo study in NU/J athymic nude mice. Our results revealed that miR-6741-3p plays a tumor-suppressive role in OSCC pathogenesis, in part, by directly regulating SRSF3. Based on our observations, we propose that miR-6741-3p may serve as a potential biological target in tumor diagnostics, prognostic evaluation, and treatment of OSCC and perhaps other malignancies., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 More et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: Iron deficiency anemia (IDA) is a prevalent hematological complication associated with gastrointestinal (GI) cancers due to an increased loss of iron and decreased iron absorption. The purpose of this systematic review is to evaluate the use of parenteral iron to treat IDA in patients with GI cancer., Methods: PubMed, Cochrane, EMBASE, CINHAL and Scopus were searched from January 1, 2010 to September 29, 2023 with no language restrictions. We excluded editorials, case reports, abstracts, conference papers, and poster presentations. Studies were included if they discussed IDA, GI neoplasms, use of iron supplementation (with or without erythropoietin-stimulating agents [ESAs]), defined anemia and had an adult patient population. We assessed the efficacy of parenteral iron in comparison to other iron supplementation methods when treating IDA in patients with GI cancer. The Cochrane Risk of Bias Tool 2 (RoB 2) and the Risk Of Bias In Non-randomized Studies of Interventions (ROBINS-I) assessment tools were used to assess the quality of the included studies. Moreover, the Cochrane Effective Practice and Organization data collection form was used to collect pertinent study information., Results: Our search yielded 3,969 studies across all databases. Twenty-one studies were included (6 randomized control trials; 15 non-randomized studies). Of the 15 studies evaluating hemoglobin (Hb) response, seven studies found an increase in Hb levels when patients were treated with IV iron. The 14 studies evaluating red blood cell (RBC) transfusion rates found conflicting differences in RBC transfusion needs when treated with IV iron. Studies analyzing health related outcomes typically found an increase in quality of life and decreased post-operative complications., Discussion: This review demonstrates improved outcomes of IDA in patients with GI cancer treated with IV iron instead of other iron supplementation methods. Timely diagnosis and appropriate IDA management can greatly improve quality of life in this patient population, especially if myelosuppressive chemotherapy is required., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: Dr. Christine Brezden-Masley has received research funding from Novartis Pharmaceuticals Canada Inc., Eli Lilly Canada Inc., and Pfizer Canada Inc.; a travel grant from Knight, and honoraria; and has been involved as a consultant for Agendia Inc., Astellas, AstraZeneca, Bristol–Myers Squibb, Eisai, Eli Lilly Canada Inc., Gilead, Knight, Merck Sharp and Dohme LLC, Mylan, Novartis Pharmaceuticals Canada Inc., Pfizer Canada Inc., Roche, Sanofi, Seagen, and Taiho Pharma Canada Inc.., (Copyright: © 2024 Nandakumar et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

With the onset of COVID-19, the development of ex vivo laboratory models became an urgent priority to study host-pathogen interactions in response to the pandemic. In this study, we aimed to establish an ex vivo mucosal tissue explant challenge model for studying SARS-CoV-2 infection and replication. Nasal or oral tissue samples were collected from eligible participants and explants generated from the tissue were infected with various SARS-CoV-2 strains, including IC19 (lineage B.1.13), Beta (lineage B.1.351) and Delta (lineage B.1.617.2). A qRT-PCR assay used to measure viral replication in the tissue explants over a 15-day period, demonstrated no replication for any viral strains tested. Based on this, the ex vivo challenge protocol was modified by reducing the viral infection time and duration of sampling. Despite these changes, viral infectivity of the nasal and oral mucosa was not improved. Since 67% of the enrolled participants were already vaccinated against SARS-CoV-2, it is possible that neutralizing antibodies in explant tissue may have prevented the establishment of infection. However, we were unable to optimize plaque assays aimed at titrating the virus in supernatants from both infected and uninfected tissue, due to limited volume of culture supernatant available at the various collection time points. Currently, the reasons for the inability of these mucosal tissue samples to support replication of SARS-CoV-2 ex vivo remains unclear and requires further investigation., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Gordhan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Most of the popular scion varieties of mango possess alternate/irregular bearing. There are many external and internal factors assigned, among them carbohydrate reserves, and nutrient content plays important roles in the floral induction process in many crop species. In addition to that rootstock can alter the carbohydrate reserve and nutrient acquisition of scion varieties in fruit crops. The present investigation was carried out to understand the effect of rootstocks on the physiochemical traits of leaf, and bud and nutrient content in regular and alternate bearing varieties of mango. The rootstock "Kurukkan" promoted starch content in leaves of both alternate bearing varieties 'Dashehari' (5.62 mg/g) and regular 'Amrapali' (5.49 mg/g) and encouraged higher protein content (6.71 mg/g) and C/N ratio (37.94) in buds of alternate bearing 'Dashehari'. While Olour rootstock upregulated the reducing sugar in leaves of 'Amrapali' (43.56 mg/g) and promoted K (1.34%) and B (78.58 ppm) content in reproductive buds of 'Dashehari'. Stomatal density in 'Dashehari' scion variety was found higher on Olour rootstock (700.40/mm 2), while the rootstock fails to modify stomatal density in the scion variety regular bearer 'Amrapali'. Further, a total of 30 carbohydrate metabolism-specific primers were designed and validated in 15 scion/rootstock combinations. A total of 33 alleles were amplified among carbohydrate metabolism-specific markers, which varied from 2 to 3 alleles with a mean of 2.53 per locus. Maximum and minimum PIC value was found for NMSPS10, and NMTPS9 primers (0.58). Cluster analysis revealed that scion grafted on Kurukkan rootstock clustered together except 'Pusa Arunima' on Olour rootstock. Our analysis revealed that Fe is the key component that is commonly expressed in both leaf and bud. Although Stomatal density (SD) and Intercellular CO2 Concentration (Ci) are more specific to leaf and Fe, B, and total sugar (TS) are abundant in buds. Based on the results it can be inferred that the physiochemical and nutrient responses of mango scion varieties are manipulated by the rootstock, hence, the scion-rootstock combination can be an important consideration in mango for selecting suitable rootstock for alternate/irregular bearer varieties., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Vittal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Oncogenic kinase inhibitors show short-lived responses in the clinic due to high rate of acquired resistance. We previously showed that pharmacologically exploiting oncogene-induced proteotoxic stress can be a viable alternative to oncogene-targeted therapy. Here, we performed extensive analyses of the transcriptomic, metabolomic and proteostatic perturbations during the course of treatment of Her2+ breast cancer cells with a Her2 inhibitor covering the drug response, resistance, relapse and drug withdrawal phases. We found that acute Her2 inhibition, in addition to blocking mitogenic signaling, leads to significant decline in the glucose uptake, and shutdown of glycolysis and of global protein synthesis. During prolonged therapy, compensatory overexpression of Her3 allows for the reactivation of mitogenic signaling pathways, but fails to re-engage the glucose uptake and glycolysis, resulting in proteotoxic ER stress, which maintains the protein synthesis block and growth inhibition. Her3-mediated cell proliferation under ER stress during prolonged Her2 inhibition is enabled due to the overexpression of the eIF2 phosphatase GADD34, which uncouples protein synthesis block from the ER stress response to allow for active cell growth. We show that this imbalance in the mitogenic and proteostatic signaling created during the acquired resistance to anti-Her2 therapy imposes a specific vulnerability to the inhibition of the endoplasmic reticulum quality control machinery. The latter is more pronounced in the drug withdrawal phase, where the de-inhibition of Her2 creates an acute surge in the downstream signaling pathways and exacerbates the proteostatic imbalance. Therefore, the acquired resistance mechanisms to oncogenic kinase inhibitors may create secondary vulnerabilities that could be exploited in the clinic., Competing Interests: KK is an employee of Champions Oncology Inc, and holds stocks there and at Pfizer Inc. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2022 Singh et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Our study aims to update knowledge about psychological distress and its changes in the Polish group of academic medical teachers after two years of a global pandemic. During the coronavirus disease, teachers were challenged to rapidly transition into remote teaching and adapt new assessment and evaluation systems for students, which might have been a completely novel situation that was not addressed before, especially in medical universities in Poland. We conducted a cross-sectional study at Poznan University of Medical Sciences from March to April 2022. The questionnaire included self-reported information on anxiety, stress, and depression. We found that post-pandemic levels of anxiety, stress, and depression have significantly (p<0.001) improved compared to initial levels at the beginning of coronavirus disease. In multivariate models, females had higher odds of improving levels of anxiety (OR  =  0.46; 95% CI  =  -1.58-(-0.03); p  =  0.04), stress (OR  =  0.36; 95% CI  =  -1.83-(-0.22); p  =  0.01), and depression (OR  =  0.0.37; 95% CI  =  -1.58-(-0.12); p  =  0.03). Anxiety, stress, or depression were not significantly associated with years of experience, the number of taught subjects, and weekly teaching hours, but only with the academic work during COVID-19 (Spearman ranxiety = 0.37, rstress = 0.32, rdepression = 0.37, p<0.001). For the virtual learning concerns, 79% of teachers reported that students might engage less; and it was correlated with higher weekly teaching hours (r = 0.19, p<0.05). Even though only 29.8% reported cheating as a concern, it was correlated with a higher number of taught subjects (r = 0.2, p<0.05). Levels of anxiety, stress, and depression have improved as time passed, not affecting teachers' academic performance. Concerns about virtual learning have been raised, suggesting it may be conjoined with classroom learning but not as an alternative. Universities should highlight the importance of seeking psychological support and provide essential programs to employees. Teachers' coping skills with psychological distress should be further studied., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2022 Wojtera et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Background: There are limited data on the experiences of children being treated for drug-resistant tuberculosis (DR-TB), and most work in the area has been done with older children and adolescents. Comprehensive explorations of the caregiver experiences in this area are also lacking., Objective: To describe the experiences of being treated for drug-resistant tuberculosis of children and their caregivers., Methods: This was a qualitative study done using focus group discussions (FGDs) among three different groups of participants: 1) health care providers involved in the care of children being treated for DR-TB (including physicians, nurses, and pharmacists)-herein referred to as providers; 2) household caregivers of children being treated for DR-TB-herein referred to as caregivers; and 3) children who were being treated for DR-TB-herein referred to as children. The population was a convenience sample and included children hospitalized between January 1, 2018, and June 30, 2020, ages 0-14 years old, as well as their caregivers and providers. Focus group transcripts and notes were analysed using a thematic network analysis based in grounded theory The analysis was iterative and the coding system developed focused on "stressful experiences" as well as ways to address them along the diagnostic and treatment journey. This paper follows the COREQ guidelines., Results: 16 children between the ages 7 and 14 years participated in 5 FGDs, 30 caregivers participated in 7 FGDs, and 12 providers participated in 3 FDGs. Data from the children and the caregivers were the focus of this analysis, although some themes were informed by the discussions with the providers as well. In general, it was reported that for a child diagnosed with DR-TB, there is a lived experience of stress that impacts their physical, mental, and social well-being. These pediatric patients and their families therefore develop strategies for coping with these disruptions to their lives. In general, there were major disruptive experiences that resulted from the process around receiving a diagnosis of DR-TB and second distinct set of stressful experiences that occurred during the treatment of DR-TB once the diagnosis had been made. These stresses occur in the physical, mental, and social realms, and families develop multiple strategies to cope with them, demonstrating resilience in the face of this disease., Conclusion: Addressing the stresses experienced by children and their caregivers through child-friendly DR-TB testing, treatment, and counseling is not only essential for ending TB but also for enacting a human-rights based approach to child health in general. Children with DR-TB are a vulnerable population, and they have often been the last to benefit from advances in general pediatric care and in DR-TB care more specifically., Competing Interests: The authors have declared that no competing interests exist.

Background: The population of patients with cancer requiring palliative care (PC) is on the rise in India. Family caregivers will be essential members of the care team in the provision of PC., Objective: We aimed to characterize provider perspectives of the challenges that Indian families face in taking on a palliative caregiving role., Method: Data for this analysis came from an evaluation of the PC-PAICE project, a series of quality improvement interventions for PC in India. We conducted 44 in-depth semi-structured interviews with organizational leaders and clinical team members at seven geographically and structurally diverse settings. Through thematic content analysis, themes relating to the caregivers' role were identified using a combination of deductive and inductive approaches., Result: Contextual challenges to taking up the PC caregiving role included family members' limited knowledge about PC and cancer, the necessity of training for caregiving responsibilities, and cultural preferences for pursuing curative treatments over palliative ones. Some logistical challenges include financial, time, and mental health limitations that family caregivers may encounter when navigating the expectations of taking on the caregiving role. Strategies to facilitate family buy-in for PC provision include adopting a family care model, connecting them to services provided by Non-Governmental Organizations, leveraging volunteers and social workers to foster PC awareness and training, and responding specifically to family's requests., Conclusion: Understanding and addressing the various challenges that families face in adopting the caregiver role are essential steps in the provision and expansion of PC in India. Locally initiated quality improvement projects can be a way to address these challenges based on the context., Competing Interests: The authors have declared that no competing interests exist.

Background: The Global Burden of Disease data suggest that respiratory diseases contribute to high morbidity in India. However, the factors responsible for high morbidity are not quite clear. Therefore, the Seasonal Waves Of Respiratory Disorders (SWORD) study was planned to estimate the point prevalence due to respiratory diseases in Indian OPD services and its association with risk factors and change in seasons., Methods: In this point prevalence observational multicenter study conducted during 2017-18, participating physicians recorded information of consecutive patients in response to a questionnaire. The study was conducted on four predetermined days representing transition of Indian seasons i.e., February (winter), May (summer), August (monsoon), and November (autumn)., Results: The eligible number of patients from across 302 sites in India was 25,177. The mean age of study population was 46.1±18.1 years, 14102(56.0%) were males and 11075(44.0%) females. The common diagnoses were: asthma(29.8%), chronic obstructive pulmonary disease (COPD),15.6%, respiratory tract infections (RTIs),11.3%, and tuberculosis(8.7%). All these conditions showed significant seasonal trends (Asthma 31.4% autumn vs. 26.5% summer, COPD 21.1% winter vs. 8.1% summer, RTIs 13.3% winter vs. 4.3% summer, and tuberculosis 12.5% autumn vs. 4.1% summer, p<0.001 for each respectively). After adjustment for risk factors, asthma was significantly associated with exposure to molds (OR:1.12,CI:1.03-1.22), pet animals (OR:1.07,CI:1.01-1.14), recent-travel (OR:1.22,CI:1.13-1.32), and rain-wetting (OR:1.27,CI:1.15-1.40); and RTIs with rain-wetting (OR:1.53,CI:1.34-1.74), and recent-travel (OR:1.17,CI:1.05-1.30)., Conclusions: The SWORD study showed wide seasonal variations in outpatient attendance of patients with common respiratory conditions. Novel risk-factors associated with respiratory diseases were also identified., Competing Interests: The authors have declared that no competing interests exist.

Otosclerosis (OTSC) is the primary form of conductive hearing loss characterized by abnormal bone remodelling within the otic capsule of the human middle ear. A genetic association of the RELN SNP rs3914132 with OTSC has been identified in European population. Previously, we showed a trend towards association of this polymorphism with OTSC and identified a rare variant rs74503667 in a familial case. Here, we genotyped these variants in an Indian cohort composed of 254 OTSC cases and 262 controls. We detected a significant association of rs3914132 with OTSC (OR = 0.569, 95%CI = 0.386-0.838, p = 0.0041). To confirm this finding, we completed a meta-analysis which revealed a significant association of the rs3914132 polymorphism with OTSC (Z = 6.707, p<0.0001) across different ethnic populations. Linkage analysis found the evidence of linkage at RELN locus (LOD score 2.1059) in the OTSC family which has shown the transmission of rare variant rs74503667 in the affected individuals. To understand the role of RELN and its receptors in the development of OTSC, we went further to perform a functional analysis of RELN/reelin. Here we detected a reduced RELN (p = 0.0068) and VLDLR (p = 0.0348) mRNA levels in the otosclerotic stapes tissues. Furthermore, a reduced reelin protein expression by immunohistochemistry was confirmed in the otosclerotic tissues. Electrophoretic mobility shift assays for rs3914132 and rs74503667 variants revealed an altered binding of transcription factors in the mutated sequences which indicates the regulatory role of these variations in the RELN gene regulation. Subsequently, we showed by scanning electron microscopy a change in stapes bone morphology of otosclerotic patients. In conclusion, this study evidenced that the rare variation rs74503667 and the common polymorphism rs3914132 in the RELN gene and its reduced expressions that were associated with OTSC., Competing Interests: The authors have declared that no competing interests exist.

Sugar transporter proteins (STPs) are membrane proteins required for sugar transport throughout cellular membranes. They plays an imperative role in sugar transmission across the plant and determinants of crop yield. However, the analysis of these important STPs Sugars Will Eventually be Exported Transporters (SWEET) family in legumes is still not well-documented and remains unclear. Therefore, the in-silico analysis of STPs has been performed to unravel their cellular, molecular, and structural composition in legume species. This study conducted a systematic search for STPs in Cajanus cajan using the Blastp algorithm to understand its molecular basis. Here, we performed a comprehensive analysis of 155 identified SWEET proteins across 12 legumes species, namely (Cajanus cajan, Glycine max, Vigna radiate, Vigna angularis, Medicago truncatula, Lupinus angustifolius, Glycine soja, Spatholobus suberectus, Cicer arietinum, Arachis ipaensis, Arachis hypogaea, Arachis duranensis). The amino acid composition and motif analysis revealed that SWEET proteins are rich in essential amino acids such as leucine, valine, isoleucine, phenylalanine, and serine while less profuse in glutamine, tryptophan, cysteine, and histidine. A total of four main conserved motifs of SWEET proteins are also highly abundant in these amino acids. The present study deciphered the details on primary physicochemical properties, secondary, tertiary structure, and phylogenetic analysis of SWEETs protein. Majorities of SWEET proteins (72.26%) are in stable form with an average instability index of 36.5%, and it comprises a higher fraction of positively charged amino acid Arg + Lys residues. Secondary structure analysis shown that these proteins are richer in alpha-helix (40%) than extended strand (30%) and random coil (25%), respectively. Furthermore, to infer their mechanism at a structural and functional level which play an essential roles in growth, development, and stress responses. This study will be useful to examine photosynthetic productivity, embryo sugar content, seed quality, and yield enhancement in Fabaceae for a sustainable source of essential amino acids and carbon source., Competing Interests: The authors have declared that no competing interests exist.

Background: Iron metabolism is crucial to maintain optimal physiological homeostasis of every organism and any alteration of the iron concentration (i.e. deficit or excess) can have adverse consequences. Transferrins are glycoproteins that play important role in iron transportation and have been widely characterized in vertebrates and insects, but poorly studied in blood-feeding mosquitoes., Results: We characterized a 2102 bp long transcript AcTrf1a with complete CDS of 1872bp, and 226bp UTR region, encoding putative transferrin homolog protein from mosquito An. culicifacies. A detailed in silico analysis predicts AcTrf1a encodes 624 amino acid (aa) long polypeptide that carries transferrin domain. AcTrf1a also showed a putative N-linked glycosylation site, a characteristic feature of most of the mammalian transferrins and certain non-blood feeding insects. Structure modelling prediction confirms the presence of an iron-binding site at the N-terminal lobe of the transferrin. Our spatial and temporal expression analysis under altered pathophysiological conditions showed that AcTrf1a is abundantly expressed in the fat-body, ovary, and its response is significantly altered (enhanced) after blood meal uptake, and exogenous bacterial challenge. Additionally, non-heme iron supplementation of FeCl3 at 1 mM concentration not only augmented the AcTrf1a transcript expression in fat-body but also enhanced the reproductive fecundity of gravid adult female mosquitoes. RNAi-mediated knockdown of AcTrf1a causes a significant reduction in fecundity, confirming the important role of transferrin in oocyte maturation., Conclusion: All together our results advocate that detailed characterization of newly identified AcTrf1a transcript may help to select it as a unique target to impair the mosquito reproductive outcome., Competing Interests: the authors have declared that no competing interests exist.

Vigna stipulacea (Lam.) Kuntz., commonly known as Minni payaru is an underutilized legume species and has a great potential to be utilized as food crop. To evaluate and select the best germplasm to be harnessed in the breeding programme, we assessed the genetic diversity of V. stipulacea (94 accessions) conserved in the Indian National Genebank, based on morphological traits and microsatellite markers. Significant variation was recorded for the morphological traits studied. Euclidean distance using UPGMA method grouped all accessions into two major clusters. Accessions were identified for key agronomic traits such as, early flowering (IC331436, IC251436, IC331437); long peduncle length (IC553518, IC550531, IC553557, IC553540, IC550532, IC553564); and more number of seeds per pod (IC553529, IC622865, IC622867, IC553528). To analyse the genetic diversity among the germplasm 33 SSR primers were used anda total of 116 alleles were detected. The number of alleles varied from two to seven, with an average of 3.52 per loci. The polymorphic information content values varied from 0.20 to 0.74, with a mean of 0.40. The high number of alleles per locus and the allelic diversity in the studied germplasm indicated a relatively wider genetic base of V. stipulacea. Phylogenetic analysis clustered accessions into seven clades. Population structure analysis grouped them into five genetic groups, which were partly supported by PCoA and phylogenetic tree. Besides, PCoA and AMOVA also decoded high genetic diversity among the V. stipulacea accessions. Thus, morphological and microsatellite markers distinguished V. stipulacea accessions and assessed their genetic diversity efficiently. The identified promising accessions can be utilized in Vigna improvement programme through introgression breeding and/or can be used for domestication and enhanced utilization of V. stipulacea., Competing Interests: The authors have declared that no competing interests exist.

High throughput sequencing has previously identified differentially expressed genes (DEGs) and enriched signalling networks in human myometrium for term (≥37 weeks) gestation labour, when defined as a singular state of activity at comparison to the non-labouring state. However, transcriptome changes that occur during transition from early to established labour (defined as ≤3 and >3 cm cervical dilatation, respectively) and potentially altered by fetal membrane rupture (ROM), when adapting from onset to completion of childbirth, remained to be defined. In the present study, we assessed whether differences for these two clinically observable factors of labour are associated with different myometrial transcriptome profiles. Analysis of our tissue ('bulk') RNA-seq data (NCBI Gene Expression Omnibus: GSE80172) with classification of labour into four groups, each compared to the same non-labour group, identified more DEGs for early than established labour; ROM was the strongest up-regulator of DEGs. We propose that lower DEGs frequency for early labour and/or ROM negative myometrium was attributed to bulk RNA-seq limitations associated with tissue heterogeneity, as well as the possibility that processes other than gene transcription are of more importance at labour onset. Integrative analysis with future data from additional samples, which have at least equivalent refined clinical classification for labour status, and alternative omics approaches will help to explain what truly contributes to transcriptomic changes that are critical for labour onset. Lastly, we identified five DEGs common to all labour groupings; two of which (AREG and PER3) were validated by qPCR and not differentially expressed in placenta and choriodecidua., Competing Interests: The authors have declared that no competing interests exist.

Sulfur mustard (SM) is a cytotoxic, vesicating, chemical warfare agent, first used in 1917; corneas are particularly vulnerable to SM exposure. They may develop inflammation, ulceration, neovascularization (NV), impaired vision, and partial/complete blindness depending upon the concentration of SM, exposure duration, and bio-physiological conditions of the eyes. Comprehensive in vivo studies have established ocular structural alterations, opacity, NV, and inflammation upon short durations (<4 min) of SM exposure. In this study, detailed analyses of histopathological alterations in corneal structure, keratocytes, inflammatory cells, blood vessels, and expressions of cyclooxygenase (COX)-2, matrix metalloproteinase (MMP)-9, vascular endothelial growth factor (VEGF), and cytokines were performed in New Zealand white rabbits, in a time-dependent manner till 28 days, post longer durations (5 and 7 min) of ocular SM exposure to establish quantifiable endpoints of injury and healing. Results indicated that SM exposure led to duration-dependent increases in corneal thickness, opacity, ulceration, epithelial-stromal separation, and epithelial degradation. Significant increases in NV, keratocyte death, blood vessels, and inflammatory markers (COX-2, MMP-9, VEGF, and interleukin-8) were also observed for both exposure durations compared to the controls. Collectively, these findings would benefit in temporal delineation of mechanisms underlying SM-induced corneal toxicity and provide models for testing therapeutic interventions., Competing Interests: The authors have declared that no competing interests exist.

Abiotic stress, especially a lack of water, can significantly reduce crop yields. In this study, we evaluated the physiological and biochemical effects of potassium sulfate (K2SO4) fertilizer and varied irrigation regimes on the economically significant oilseed crop, Brassica juncea L, under open field conditions. Two cultivars (RH-725 and RH-749) of B. juncea were used in a randomized complete block design experiment with three replicates. Irrigation regimes consisted of a control (double irrigation: once at the 50% flowering and another at 50% fruiting stages), early irrigation (at 50% flowering only), late irrigation (at 50% fruiting only) and stress (no irrigation). The K2SO4 applications were: control (K0, no fertilization); K1, 10 kg ha-1; and K2, 20 kg ha-1. We measured growth via fresh and dry plant weight, plant height, root length, and leaf area. All the growth parameters were higher in RH-749. The physiological attributes, including the membrane stability index and relative water content, were higher at the 50% flowering stage in RH-749. The amount of antioxidant enzymes (catalase (CAT), guaiacol peroxidase (POX), ascorbate peroxidase (APX), and superoxide dismutase (SOD)) was enhanced when both plants were fertilized during water stress. All of these enzymes had higher activity in RH-749. The total chlorophyll content and photosynthesis rate were considerably higher in RH-749, which leaked fewer electrolytes and maintained a less destructive osmotic potential under limited water conditions. The results indicated that it is water-stress tolerant when given a high concentration of K2SO4, which alleviated the adverse effects of water stress on growth and physiology., Competing Interests: The authors have declared that no competing interests exist.

Inflammation is thought to play a pivotal role in the onset of term and some forms of preterm labour. Although, we recently found that myometrial inflammation is a consequence rather than a cause of term labour, there are several other reproductive tissues, including amnion, choriodecidua parietalis and decidua basalis, where the inflammatory stimulus to labour may occur. To investigate this, we have obtained amnion, choriodecidual parietalis and decidua basalis samples from women at various stages of pregnancy and spontaneous labour. The inflammatory cytokine profile in each tissue was determine by Bio-Plex Pro® cytokine multiplex assays and quantitative RT-PCR. Active motif assay was used to study transcription activation in the choriodecidua parietalis. Quantitative RT-PCR was use to study the pro-labour genes (PGHS-2, PGDH, OTR and CX43) in all of the tissues at the onset of labour and oxytocin (OT) mRNA expression in the choriodecidual parietalis and decidua basalis. Statistical significance was ascribed to a P value <0.05. In the amnion and choriodecidua parietalis, the mRNA levels of various cytokines decreased from preterm no labour to term no labour samples, but the protein levels were unchanged. The choriodecidua parietalis showed increase in the protein levels of IL-1β and IL-6 in the term early labour samples. In the amnion and decidua basalis, the protein levels of several cytokines rose in term established labour. The multiples of the median derived from the 19-plex cytokine assay were greater in term early labour and term established labour samples from the choriodecidua parietalis, but only in term established labour for myometrium. These data suggest that the inflammatory stimulus to labour may begin in the choriodecidua parietalis, but the absence of any change in prolabour factor mRNA levels suggests that the cytokines may act on the myometrium where we observed changes in transcription factor activation and increases in prolabour gene expression in earlier studies., Competing Interests: The authors have declared that no competing interests exist.

Secretory proteins are important for microbial adaptation and survival in a particular environment. Till date, experimental secretomes have been reported for a few archaea. In this study, we have identified the experimental secretome of Picrophilous torridus and evaluated the efficacy of various signal peptide predictors (SPPs) in identifying signal peptides (SPs) in its experimental secretome. Liquid chromatography mass spectrometric (LC MS) analysis was performed for three independent P. torridus secretome samples and only those proteins which were common in the three experiments were selected for further analysis. Thus, 30 proteins were finally included in this study. Of these, 10 proteins were identified as hypothetical/uncharacterized proteins. Gene Ontology, KEGG and STRING analyses revealed that majority of the sercreted proteins and/or their interacting partners were involved in different metabolic pathways. Also, a few proteins like malate dehydrogenase (Q6L0C3) were multi-functional involved in different metabolic pathways like carbon metabolism, microbial metabolism in diverse environments, biosynthesis of antibiotics, etc. Multi-functionality of the secreted proteins reflects an important aspect of thermoacidophilic adaptation of P. torridus which has the smallest genome (1.5 Mbp) among nonparasitic aerobic microbes. SPPs like, PRED-SIGNAL, SignalP 5.0, PRED-TAT and LipoP 1.0 identified SPs in only a few secreted proteins. This suggests that either these SPPs were insufficient, or N-terminal SPs were absent in majority of the secreted proteins, or there might be alternative mechanisms of protein translocation in P. torridus., Competing Interests: The authors have declared that no competing interests exist.

Superoxide radicals and other reactive oxygen species (ROS) are implicated in influenza A virus-induced inflammation. In this in vitro study, we evaluated the effects of TG6-44, a novel quinazolin-derived myeloperoxidase-specific ROS inhibitor, on influenza A virus (A/X31) infection using THP-1 lung monocytic cells and freshly isolated peripheral blood mononuclear cells (PBMC). TG6-44 significantly decreased A/X31-induced ROS and virus-induced inflammatory mediators in THP-1 cells (IL-6, IFN-γ, MCP-1, TNF-α, MIP-1β) and in human PBMC (IL-6, IL-8, TNF-α, MCP-1). Interestingly, TG6-44-treated THP-1 cells showed a decrease in percent cells expressing viral nucleoprotein, as well as a delay in translocation of viral nucleoprotein into the nucleus. Furthermore, in influenza A virus-infected cells, TG6-44 treatment led to suppression of virus-induced cell death as evidenced by decreased caspase-3 activation, decreased proportion of Annexin V+PI+ cells, and increased Bcl-2 phosphorylation. Taken together, our results demonstrate the anti-inflammatory and anti-infective effects of TG6-44., Competing Interests: The authors have declared that no competing interests exist.

Previously, we showed that cAMP increased COX-2 expression in myometrial cells via MAPK. Here, we have extended these observations, using primary myometrial cell cultures to show that the cAMP agonist, forskolin, enhances IL-1β-driven COX-2 expression. We then explored the role of A-kinase interacting protein (AKIP1), which modulates the effect of PKA on p65 activation. AKIP1 knockdown reversed the effect of forskolin, such that its addition inhibited IL-1β-induced COX-2 mRNA expression and reduced the IL-1β-induced increase in nuclear levels of p65 and c-jun. Forskolin alone and with IL-1β increased IκBα mRNA expression suggesting that in the context of inflammation and in the presence of AKIP1, cAMP enhances p65 activation. AKIP1 knockdown reversed these changes. Interestingly, AKIP1 knockdown had minimal effect on the ability of forskolin to repress either basal OTR expression or IL-1β-stimulated OTR mRNA expression. AKIP1 was up-regulated by IL-1β, but not stretch and was repressed by cAMP. The mRNA expression of AKIP1 increased in early labour in tandem with an increase in COX-2 mRNA and protein. AKIP1 protein levels were also increased with inflammation and stretch-induced preterm labour. Our results identify a second important cAMP effector-switch occurring at term in human myometrium and suggest that a hitherto unrecognized interaction may exist between AKIP1, NFκB and AP-1. These data add to the proposition that cAMP acts as a key regulator of human myometrial contractility., Competing Interests: The authors have declared that no competing interests exist.

Background: Healthcare workers (HCW) are at increased risk of SARS-CoV-2 infection from both patients and other HCW with coronavirus disease 2019 (COVID-19). RT-PCR cycle threshold (Ct) values of SARS-CoV-2 ≤ 34 and the first 7-9 days of symptoms are associated with enhanced infectivity. We determined Ct values and duration of symptoms of HCW with a positive SARS-CoV-2 test. As HCW often assume their greatest risk of acquiring SARS-CoV-2 is working on a COVID-19 unit, we also determined Ct values and symptom duration of inpatients with a positive SARS-CoV-2 test., Methods: From 6/24/2020-8/23/2020, Ct values and duration of symptoms from 13 HCW, 12 outpatients, and 28 inpatients who had a positive nasopharyngeal swab for SARS-CoV-2 were analyzed., Results: Among HCW with a positive SARS-CoV-2 test, 46.2% (6/13) were asymptomatic and requested testing due to an exposure to someone with COVID-19; 83.3% (5/6) of those exposures occurred in the community rather than in the hospital. The median Ct value of HCW was 23.2, and 84.6% (11/13) had a Ct value ≤ 34. The median Ct value of 29.0 among outpatients with COVID-19 did not significantly differ from HCW. In contrast, inpatients with a positive SARS-CoV-2 test had a median Ct value of 34.0 (p = 0.003), which translated into a median ~1,000-fold lower viral load than observed in HCW. Among those with symptoms related to COVID-19, no (0/6) HCW compared to 50% (6/12) of inpatients had symptoms for at least one week (p = 0.04)., Conclusions: At our institution, asymptomatic COVID-19 accounted for nearly half of the cases among HCW. Symptomatic HCW had high viral loads and short duration of symptoms, both of which are associated with peak infectivity. Infection prevention programs should educate HCW on these findings in an effort to increase adherence to the requirement to maintain six feet separation in workspaces and breakrooms, in addition to consistently wearing personal protection equipment., Competing Interests: Dr. Clancy has been awarded investigator-initiated research grants from Astellas, Merck, Melinta, and Cidara for studies unrelated to this project, served on advisory boards or consulted for Astellas, Merck, the Medicines Company, Cidara, Scynexis, Shionogi, Qpex and Needham & Company, and spoken at symposia sponsored by Merck and T2Biosystems. The other authors report no conflicts. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

Rapid urban expansion has important health implications. This study examines trends and inequalities in undernutrition and overnutrition by gender, residence (rural, urban slum, urban non-slum), and wealth among children and adults in India. We used National Family Health Survey data from 2006 and 2016 (n = 311,182 children 0-5y and 972,192 adults 15-54y in total). We calculated differences, slope index of inequality (SII) and concentration index to examine changes over time and inequalities in outcomes by gender, residence, and wealth quintile. Between 2006 and 2016, child stunting prevalence dropped from 48% to 38%, with no gender differences in trends, whereas child overweight/obesity remained at ~7-8%. In both years, stunting prevalence was higher in rural and urban slum households compared to urban non-slum households. Within-residence, wealth inequalities were large for stunting (SII: -33 to -19 percentage points, pp) and declined over time only in urban non-slum households. Among adults, underweight prevalence decreased by ~13 pp but overweight/obesity doubled (10% to 21%) between 2006 and 2016. Rises in overweight/obesity among women were greater in rural and urban slum than urban non-slum households. Within-residence, wealth inequalities were large for both underweight (SII -35 to -12pp) and overweight/obesity (+16 to +29pp) for adults, with the former being more concentrated among poorer households and the latter among wealthier households. In conclusion, India experienced a rapid decline in child and adult undernutrition between 2006 and 2016 across genders and areas of residence. Of great concern, however, is the doubling of adult overweight/obesity in all areas during this period and the rise in wealth inequalities in both rural and urban slum households. With the second largest urban population globally, India needs to aggressively tackle the multiple burdens of malnutrition, especially among rural and urban slum households and develop actions to maintain trends in undernutrition reduction without exacerbating the rapidly rising problems of overweight/obesity., Competing Interests: The authors have declared that no competing interests exist.

Evaluation of nasal spray drug absorption has been challenging because deposited particles are consistently transported away by mucociliary clearance during diffusing through the mucus layer. This study developed a novel approach combining Computational Fluid Dynamics (CFD) techniques with a 1-D mucus diffusion model to better predict nasal spray drug absorption. This integrated CFD-diffusion approach comprised a preliminary simulation of nasal airflow, spray particle injection, followed by analysis of mucociliary clearance and drug solute diffusion through the mucus layer. The spray particle deposition distribution was validated experimentally and numerically, and the mucus velocity field was validated by comparing with previous studies. Total and regional drug absorption for solute radius in the range of 1 - 110nm were investigated. The total drug absorption contributed by the spray particle deposition was calculated. The absorption contribution from particles that deposited on the anterior region was found to increase significantly as the solute radius became larger (diffusion became slower). This was because the particles were consistently moved out of the anterior region, and the delayed absorption ensured more solute to be absorbed by the posterior regions covered with respiratory epithelium. Future improvements in the spray drug absorption model were discussed. The results of this study are aimed at working towards a CFD-based integrated model for evaluating nasal spray bioequivalence., Competing Interests: The authors have declared that no competing interests exist.

Our previous work has shown myometrial PKA activity declines in term and twin-preterm labour in association with an increase in the expression of the oxytocin receptor (OTR). Here we investigate the action of cAMP/PKA in basal conditions, with the addition of progesterone (P4) and/or IL-1β to understand how cAMP/PKA acts to maintain pregnancy and whether the combination of cAMP and P4 would be a viable therapeutic combination for the prevention of preterm labour (PTL). Further, given that we have previously found that cAMP enhances P4 action we wanted to test the hypothesis that changes in the cAMP effector system are responsible for the functional withdrawal of myometrial P4 action. Myometrial cells were grown from biopsies obtained from women at the time of elective Caesarean section before the onset of labour. The addition of forskolin, an adenylyl cyclase activator, repressed basal OTR mRNA levels at all doses and P4 only enhanced this effect at its highest dose. Forskolin repressed the IL-1β-induced increase in OTR mRNA and protein levels in a PKA-dependent fashion and repressed IL-1β-activation and nuclear transfer of NFκB and AP-1. P4 had similar effects and the combination P4 and forskolin had greater effects on OTR and NFκB than forskolin alone. While PKA knockdown had no effect on the ability of P4 to repress IL-1β-induced OTR expression it reversed the repressive effect of the combination of P4 and forskolin and resulted in a greater increase than observed with IL-1β alone. These studies suggest that cAMP acts via PKA to repress inflammation-driven OTR expression, but that when PKA activity is reduced, the combination of cAMP and P4 actually enhances the OTR response to inflammation, promoting the onset of labour and suggesting that changes in the cAMP effector system can induce a functional P4 withdrawal., Competing Interests: The authors have declared that no competing interests exist.

We previously reported that at term pregnancy, a decline in myometrial protein kinase A (PKA) activity leads to an exchange protein activated by cyclic AMP (Epac1)-dependent increase in oxytocin receptor (OTR) expression, promoting the onset of labour. Here, we studied the changes in the cyclic adenosine monophosphate (cAMP) effector system present in different phenotypes of preterm labour (PTL). Myometrial biopsies obtained from women with phenotypically distinct forms of PTL and the levels of PKA and OTR were examined. Although we found similar changes in the cAMP effector pathway in all forms of PTL, only in the case of twin PTL (T-PTL) was myometrial OTR levels increased in association with these results. Although there were several changes in the mRNA levels of components of the cAMP synthetic pathway, the total myometrial cAMP levels did not change with the onset of any subtype of PTL. With regards to the expression of cAMP-responsive genes, we found that the mRNA levels of 4 of the 5 cAMP-down-regulated genes were increased in T-PTL, similar to our findings in term labour. These data signify that although changes in the cAMP effector system were common to all forms of PTL, only in T-PTL were OTR levels increased. Similarly, the mRNA levels of cAMP-repressed genes were only increased in T-PTL supporting the concept that the decline in PKA levels influences myometrial function driving the onset of T-PTL., Competing Interests: The authors have declared that no competing interests exist.

The novel coronavirus 2019 (COVID-19) global pandemic has drastically affected the world economy, raised public anxiety, and placed a substantial psychological burden on the governments and healthcare professionals by affecting over 4.7 million people worldwide. As a preventive measure to minimise the risk of community transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in India, a nationwide lockdown was imposed initially for 21 days to limit the movement of 1.3 billion people. These restrictions continue in most areas, with a conditional relaxation occurring in a few Indian states. In an attempt to assess the emerging mutants of SARS-CoV-2 and determine their spread in India, we analysed 112 complete genomes of SARS-CoV-2 in a time-lapse manner. We found 72 distinct SARS-CoV-2 haplotypes, defined by 143 polymorphic sites and high haplotype diversity, suggesting that this virus possesses a high evolutionary potential. We also demonstrated that early introduction of SARS-CoV-2 into India was from China, Italy and Iran and observed signs of community spread of the virus following its rapid demographic expansion since its first outbreak in the country. Additionally, we identified 18 mutations in the SARS-CoV-2 spike glycoprotein and a few selected mutations showed to increase stability, binding affinity, and molecular flexibility in the overall tertiary structure of the protein that may facilitate interaction between the receptor binding domain (RBD) of spike protein and the human angiotensin-converting enzyme 2 (ACE2) receptor. The study provides a pragmatic view of haplotype-dependent spread of SARS-CoV-2 in India which could be important in tailoring the pharmacologic treatments to be more effective for those infected with the most common haplotypes. The findings based on the time-lapse sentinel surveillance of SARS-CoV-2 will aid in the development of a real-time practical framework to tackle the ongoing, fast-evolving epidemic challenges in the country., Competing Interests: Dr. Mukesh Thakur is a PLOS ONE Academic Editor. However, this does not alter the authors' adherence to all the PLOS ONE policies including sharing data, materials and peer review process.

Chickpea (Cicer arietinum L.) is the second largest pulse crop grown worldwide and ascochyta blight caused by Ascochyta rabiei (Pass.) Labr. is the most devastating disease of the crop in all chickpea growing areas across the continents. The pathogen A. rabiei is highly variable. The resistant sources available are not sufficient and new sources needs to be identified from time to time as resistance breakdown in existing chickpea varieties is very frequent due to fast evolution of new pathotypes of the pathogen. Therefore, this work was undertaken to evaluate the existing chickpea germplasm diversity conserved in Indian National Genebank against the disease under artificial epiphytotic conditions. An artificial standard inoculation procedure was followed for uniform spread of the pathogen. During the last five winter seasons from 2014-15 to 2018-19, a total of 1,970 accessions have been screened against the disease and promising accessions were identified and validated. Screening has resulted in identification of some promising chickpea accessions such as IC275447, IC117744, EC267301, IC248147 and EC220109 which have shown the disease resistance (disease severity score ≤3) in multiple seasons and locations. Promising accessions can serve as the potential donors in chickpea improvement programs. The frequency of resistant and moderately resistant type accessions was comparatively higher in accessions originated from Southwest Asian countries particularly Iran and Syria than the accessions originated from Indian sub-continent. Further large scale screening of chickpea germplasm originated from Southwest Asia may result in identifying new resistant sources for the disease., Competing Interests: The authors have declared that no competing interests exist.

Rice root-knot nematode (RRKN), Meloidogyne graminicola is one of the major biotic constraints in rice-growing countries of Southeast Asia. Host plant resistance is an environmentally-friendly and cost-effective mean to mitigate RRKN damage to rice. Considering the limited availability of genetic resources in the Asian rice (Oryza sativa) cultivars, exploration of novel sources and genetic basis of RRKN resistance is necessary. We screened 272 diverse wild rice accessions (O. nivara, O. rufipogon, O. sativa f. spontanea) to identify genotypes resistant to RRKN. We dissected the genetic basis of RRKN resistance using a genome-wide association study with SNPs (single nucleotide polymorphism) genotyped by 50K "OsSNPnks" genic Affymetrix chip. Population structure analysis revealed that these accessions were stratified into three major sub-populations. Overall, 40 resistant accessions (nematode gall number and multiplication factor/MF < 2) were identified, with 17 novel SNPs being significantly associated with phenotypic traits such as number of galls, egg masses, eggs/egg mass and MF per plant. SNPs were localized to the quantitative trait loci (QTL) on chromosome 1, 2, 3, 4, 6, 10 and 11 harboring the candidate genes including NBS-LRR, Cf2/Cf5 resistance protein, MYB, bZIP, ARF, SCARECROW and WRKY transcription factors. Expression of these identified genes was significantly (P < 0.01) upregulated in RRKN-infected plants compared to mock-inoculated plants at 7 days after inoculation. The identified SNPs enrich the repository of candidate genes for future marker-assisted breeding program to alleviate the damage of RRKN in rice., Competing Interests: The authors have declared that no competing interests exist.

The primary objective of this research was to extract the essential information needed for setting atomization break up models, specifically, the Linear Instability Sheet Atomization (LISA) breakup model, and alternative hollow cone models. A secondary objective was to gain visualization and insight into the atomization break up mechanism caused by the effects of viscosity and surface tension on primary break-up, sheet disintegration, ligament and droplet formation. High speed imaging was used to capture the near-nozzle characteristics for water and drug formulations. This demonstrated more rapid atomization for lower viscosities. Image processing was used to analyze the near-nozzle spray characteristics during the primary break-up of the liquid sheet into ligament formation. Edges of the liquid sheet, spray break-up length, break-up radius, cone angle and dispersion angle were obtained. Spray characteristics pertinent for primary breakup modelling were determined from high speed imaging of multiple spray actuations. The results have established input data for computational modelling involving parametrical analysis of nasal drug delivery., Competing Interests: The authors have declared that no competing interests exist.

Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding., Competing Interests: The authors have declared that no competing interests exist.

Objective: We examined the incremental cost-effectiveness between two mHealth programs, implemented from 2011 to 2015 in rural Bangladesh: (1) Comprehensive mCARE package as an intervention group and (2) Basic mCARE package as a control group., Methods: Both programs included a core package of census enumeration and pregnancy surveillance provided by an established cadre of digitally enabled community health workers (CHWs). In the comprehensive mCARE package, short message service (SMS) and home visit reminders were additionally sent to pregnant women (n = 610) and CHWs (n = 70) to promote the pregnant women's care-seeking of essential maternal and newborn care services. Economic costs were assessed from a program perspective inclusive of development, start-up, and implementation phases. Effects were calculated as disability adjusted life years (DALYs) and the number of newborn deaths averted. For comparative purposes, we normalized our evaluation to estimate total costs and total newborn deaths averted per 1 million people in a community for both groups. Uncertainty was assessed using probabilistic sensitivity analyses with Monte Carlo simulation., Results: The addition of SMS and home visit reminders based on a mobile phone-facilitated pregnancy surveillance system was highly cost effective at a cost per DALY averted of $31 (95% uncertainty range: $19-81). The comprehensive mCARE program had at least 88% probability of being highly cost-effective as compared to the basic mCARE program based on the threshold of Bangladesh's GDP per capita., Conclusion: mHealth strategies such as SMS and home visit reminders on a well-established pregnancy surveillance system may improve service utilization and program cost-effectiveness in low-resource settings., Competing Interests: The authors have declared that no competing interests exist.

Accurate and timely diagnosis is very critical for management, control and elimination of the malaria. Malaria rapid diagnostic tests (RDTs) have improved the diagnosis and management of malaria in remote areas, community and places where microscopy is not available for diagnosis. According to WHO report 2018, Plasmodium falciparum malaria constitutes more than 50% of malaria cases in India. Most of the RDTs used for diagnosis of falciparum malaria today employ HRP2 as a target antigen. However, low density parasitemia and deletion of hrp-2 gene in P. falciparum leads to false negative results and necessitates the development of alternative/ new or improved RDT for malaria diagnosis. We have analysed the genetic diversity and homology modelling of Pfgdh (glutamate dehydrogenase), ldh (lactate dehydrogenase) and aldolase genes in P. falciparum isolates from the eight endemic states of India to assess their potential as antigen for RDT development. We observed negligible sequence diversity in Pfgdh in comparison to the low level of diversity in ldh and aldolase gene. No structural or functional changes were observed in modelling studies and all three genes were under negative purifying selection pressure. The highly conserved nature of pfgdh gene suggests that GDH could be a potential target molecule for Pan/Pf diagnostic test for malaria., Competing Interests: The authors have declared that no competing interests exist.

Integrated crop-livestock (ICL) system is beneficial in enhancing soil organic carbon and nutrient cycling. However, the benefits of the ICL system on mitigation of GHG emissions are poorly understood. Thus, the present study was initiated in 2011 to assess the effect of crop rotation diversity and grazing managed under the ICL system on GHG emissions. The cropping system investigated here included spring wheat grown continuously for five years and a 5-yr crop rotation (spring wheat-cover crops-corn-pea/barley-sunflower). Each phase was present each year. Yearling steers grazed only the pea/barley, corn and cover crops plots in 2016 and 2017. Exclusion areas avoided the grazing in these crops to compare the GHG fluxes under grazed vs. non-grazed areas. The GHG fluxes were measured weekly from all crop phases during the growing season for both years using a static chamber. Cumulative CO2 and CH4 fluxes were similar from all crop phases over the study period. However, continuous spring wheat recorded higher cumulative N2O fluxes (671 g N ha-1) than that under spring wheat in rotation (571 g N ha-1). Grazing decreased cumulative CO2 fluxes (359 kg C ha-1) compared to ungrazed (409 kg C ha-1), however, no effect from grazing on cumulative CH4 and N2O fluxes over the study period were found. The present study shows that grazing and crop rotational diversity affected carbon and nitrogen inputs, which in turn affected soil CO2 and N2O fluxes. Long-term monitoring is needed to evaluate the response of soil GHG emissions to grazing and crop rotation interactions under the ICL system., Competing Interests: The authors have declared that no competing interests exist.

Wilson disease (WD) is an autosomal recessive disorder, characterized by excessive deposition of copper in various parts of the body, mainly in the liver and brain. It is caused by mutations in ATP7B. We report here the genetic analysis of 102 WD families from a south Indian population. Thirty-six different ATP7B mutations, including 13 novel ones [p.Ala58fs*19, p.Lys74fs*9, p.Gln281*, p.Pro350fs*12, p.Ser481*, p.Leu735Arg, p.Val752Gly, p.Asn812fs*2, p.Val845Ala, p.His889Pro, p.Ile1184fs*1, p.Val1307Glu and p.Ala1339Pro], were identified in 76/102 families. Interestingly, the mutation analysis of affected individuals in two families identified two different homozygous mutations in each family, and thus each affected individual from these families harbored two mutations in each ATP7B allele. Of 36 mutations, 28 were missense, thus making them the most prevalent mutations identified in the present study. Nonsense, insertion and deletion represented 3/36, 2/36 and 3/36 mutations, respectively. The haplotype analysis suggested founder effects for all the 14 recurrent mutations. Our study thus expands the mutational landscape of ATP7B with a total number of 758 mutations. The mutations identified during the present study will facilitate carrier and pre-symptomatic detection, and prenatal genetic diagnosis in affected families., Competing Interests: The authors have declared that no competing interests exist.

Mycobacterium tuberculosis (Mtb) secretes proteases and peptidases to subjugate its host. Out of its sixty plus proteases, atleast three are reported to reach host macrophages. In this study, we show that Mtb also delivers a lysyl alanine aminopeptidase, PepN (Rv2467) into host macrophage cytosol. Our comparative in silico analysis shows PepNMtb highly conserved across all pathogenic mycobacteria. Non-pathogenic mycobacteria including M. smegmatis (Msm) also encode pepN. PepN protein levels in both Mtb (pathogenic) and Msm (non-pathogenic) remain uniform across all in vitro growth phases. Despite such tight maintenance of PepNs' steady state levels, upon supplementation, Mtb alone allows accumulation of any excessive PepN. In contrast, Msm does not. It not only proteolyzes, but also secretes out the excessive PepN, be it native or foreign. Interestingly, while PepNMtb is required for modulating virulence in vivo, PepNMsm is essential for Msm growth in vitro. Despite such essentiality difference, both PepNMtb and PepNMsm harbor almost identical N-terminal M1-type peptidase domains that significantly align in their amino acid sequences and overlap in their secondary structures. Their C-terminal ERAP1&#95;C-like domains however align much more moderately. Our in vitro macrophage-based infection experiments with MtbΔpepN-expressing pepNMsm reveals PepNMsm also retaining the ability to reach host cytosol. Lastly, but notably, we determined the PepNMtb and PepNMsm interactomes and found them to barely coincide. While PepNMtb chiefly interacts with Mtb's secreted proteins, PepNMsm primarily coimmunoprecipitates with Msm's housekeeping proteins. Thus, despite high sequence homology and several common properties, our comparative analytical study reveals host-centric traits of pathogenic and bacterial-centric traits of non-pathogenic PepNs., Competing Interests: All authors declare that this research was conducted with no commercial or financial gains and thus declare no conflict of interest with all contents of this article. K.A.’s collaboration with S.K. towards generation of Mass Spectrometric data had no commercial interests or bearings to and with Thermo Fisher Scientific Pvt. Ltd., INDIA. All authors (including S.K.) declare that this commercial affiliation does not alter our adherence to all PLOS ONE policies on sharing data and materials.

Background: Artificial intelligence (AI) techniques are increasingly applied to cardiovascular (CV) medicine in arenas ranging from genomics to cardiac imaging analysis. Cardiac Phase Space Tomography Analysis (cPSTA), employing machine-learned linear models from an elastic net method optimized by a genetic algorithm, analyzes thoracic phase signals to identify unique mathematical and tomographic features associated with the presence of flow-limiting coronary artery disease (CAD). This novel approach does not require radiation, contrast media, exercise, or pharmacological stress. The objective of this trial was to determine the diagnostic performance of cPSTA in assessing CAD in patients presenting with chest pain who had been referred by their physician for coronary angiography., Methods: This prospective, multicenter, non-significant risk study was designed to: 1) develop machine-learned algorithms to assess the presence of CAD (defined as one or more ≥ 70% stenosis, or fractional flow reserve ≤ 0.80) and 2) test the accuracy of these algorithms prospectively in a naïve verification cohort. This report is an analysis of phase signals acquired from 606 subjects at rest just prior to angiography. From the collective phase signal data, features were extracted and paired with the known angiographic results. A development set, consisting of signals from 512 subjects, was used for machine learning to determine an algorithm that correlated with significant CAD. Verification testing of the algorithm was performed utilizing previously untested phase signals from 94 subjects., Results: The machine-learned algorithm had a sensitivity of 92% (95% CI: 74%-100%) and specificity of 62% (95% CI: 51%-74%) on blind testing in the verification cohort. The negative predictive value (NPV) was 96% (95% CI: 85%-100%)., Conclusions: These initial multicenter results suggest that resting cPSTA may have comparable diagnostic utility to functional tests currently used to assess CAD without requiring cardiac stress (exercise or pharmacological) or exposure of the patient to radioactivity., Competing Interests: Authors SR, TB, PG, AK, IS, WES are employees of A4L or Analytics For Life (https://www.analytics4life.com/) and receive salary for that employment. This does not alter our adherence to all the PLOS ONE policies on sharing data and materials. There are no patents, products in development or marketed products to declare. All other authors have no competing interests to declare.

Introduction: There is lack of information on the proportion of new smear-positive pulmonary tuberculosis (PTB) patients treated with a 6-month thrice-weekly regimen under Revised National Tuberculosis Control Programme (RNTCP) who develop recurrent TB after successful treatment outcome., Objective: To estimate TB recurrence among newly diagnosed PTB patients who have successfully completed treatment and to document endogenous reactivation or re-infection. Risk factors for unfavourable outcomes to treatment and TB recurrence were determined., Methodology: Adult (aged ≥ 18 yrs) new smear positive PTB patients initiated on treatment under RNTCP were enrolled from sites in Tamil Nadu, Karnataka, Delhi, Maharashtra, Madhya Pradesh and Kerala. Those declared "treatment success" at the end of treatment were followed up with 2 sputum examinations each at 3, 6 and 12 months after treatment completion. MIRU-VNTR genotyping was done to identify endogenous re-activation or exogenous re-infection at TB recurrence. TB recurrence was expressed as rate per 100 person-years (with 95% confidence interval [95%CI]). Regression models were used to identify the risk factors for unfavourable response to treatment and TB recurrence., Results: Of the1577 new smear positive PTB patients enrolled, 1565 were analysed. The overall cure rate was 77% (1207/1565) and treatment success was 77% (1210 /1565). The cure rate varied from 65% to 86%. There were 158 of 1210 patients who had TB recurrence after treatment success. The pooled TB recurrence estimate was 10.9% [95%CI: 0.2-21.6] and TB recurrence rate per 100 person-years was 12.7 [95% CI: 0.4-25]. TB recurrence per 100 person-years varied from 5.4 to 30.5. Endogenous reactivation was observed in 56 (93%) of 60 patients for whom genotyping was done. Male gender was associated with TB recurrence., Conclusion: A substantial proportion of new smear positive PTB patients successfully treated with 6 -month thrice-weekly regimen have TB recurrence under program settings., Competing Interests: The authors have declared that no competing interests exist.

Immune activating cytokines Interferon (IFN)-γ and Tumor necrosis factor (TNF)-α are known to activate macrophages for killing of Leishmania parasite. IFN-γ provides therapeutic potential while TNF-α has been recognized to mediate protection in visceral model of infection. In the present study we investigated whether combination of IFN-γ and TNF-α has better therapeutic strength than individually using one of these cytokines in Visceral Leishmaniasis (VL) patients. We performed combined blockade of IFN-γ and TNF-α in VL splenic biopsies and demonstrated it's impact on number of viable amastigotes and cytokine production. Additionally, selective depletion of splenic cell subsets was performed to establish the cellular sources of IFN-γ and TNF-α. Treatment of splenic aspirate cells with combination of anti-IFN-γ and anti-TNF-α monoclonal antibodies for 72 hours enabled no direct additive impact of these cytokines on parasite replication and IL-10 secretion, but IL-4 production was induced. Further assessment of splenic biopsies put forward CD4+ T cells as a source of IFN-γ whereas CD14+ cells contribute towards TNF-α production. Overall our results suggest, the interplay of pro-inflammatory cytokines IFN-γ derived from CD4+T lymphocytes and TNF-α from CD14+ cells has no direct additive impact on parasite replication but induces IL-4 production. Our data does not support direct targeting of IFN-γ and TNF-α for combination therapy but targeting these cytokines as an adjuvant in patients with exaggerated tissue inflammatory responses can have favourable patient outcome., Competing Interests: The authors have declared that no competing interests exist.

An attempt was made to compare between easy and inexpensive qualitative method (ammonia vapour test) and analytical methods (thin layer chromatography and enzyme-linked immunosorbent assay) for identification of aflatoxigenic isolates of Aspergillus flavus in maize. In this comparative study the toxicity level of A. flavus isolates exhibited 100% agreement among ammonia vapour test, ELISA and TLC for highly toxigenic (>2000 ppb) and toxigenic (501-2000 ppb) isolates while 88.5% agreement observed for least toxic (<20 ppb) isolates. In ammonia vapour test 51% of A. flavus isolates showed creamish or no colour change corresponding to least toxic/atoxic (<20ppb) category estimated by ELISA. Similarly 22% highly toxic isolates exhibited plum red colour, 12% moderately toxic indicated pink colour and 10% toxic isolates showed red colour. However, 11.5% isolates were found to be false positive in cream colour category (least toxic) and 28.5% false negatives in pink colour (moderately toxic) category. The isolates from different agroclimatic zones of maize in India showed high variability for aflatoxin B1 (AFB1) production potential ranging from 0.214-8116.61 ppb. Toxigenic potential of Aspergillus flavus isolates in culture was further validated by inoculating maize grain sample with four different isolates with varied toxin producing ability. With good agreement percentage between cultural and analytical methods the study concludes the ammonia vapour test to be easy, inexpensive, reliable and time saving method that can be used for segregating or pre-screening of contaminated samples from bulk food/feed stock.

Direct smear microscopy of sputum forms the mainstay of TB diagnosis in resource-limited settings. Stained sputum smear slides can serve as a ready-made resource to transport sputum for molecular drug susceptibility testing. However, bio-safety is a major concern during transport of sputum/stained slides and for laboratory workers engaged in processing Mycobacterium tuberculosis infected sputum specimens. In this study, a bio-safe USP (Universal Sample Processing) concentration-based sputum processing method (Bio-safe method) was assessed on 87 M. tuberculosis culture positive sputum samples. Samples were processed for Ziehl-Neelsen (ZN) smear, liquid culture and DNA isolation. DNA isolated directly from sputum was subjected to an IS6110 PCR assay. Both sputum DNA and DNA extracted from bio-safe ZN concentrated smear slides were subjected to rpoB PCR and simultaneously assessed by DNA sequencing for determining rifampin (RIF) resistance. All sputum samples were rendered sterile by Bio-safe method. Bio-safe smears exhibited a 5% increment in positivity over direct smear with a 14% increment in smear grade status. All samples were positive for IS6110 and rpoB PCR. Thirty four percent samples were RIF resistant by rpoB PCR product sequencing. A 100% concordance (κ value = 1) was obtained between sequencing results derived from bio-safe smear slides and bio-safe sputum. This study demonstrates that Bio-safe method can address safety issues associated with sputum processing, provide an efficient alternative to sample transport in the form of bio-safe stained concentrated smear slides and can also provide information on drug (RIF) resistance by direct DNA sequencing.

Carbidopa is a drug that blocks conversion of levodopa to dopamine outside of central nervous system (CNS) and thus inhibits unwanted side effects of levodopa on organs located outside of CNS during management of Parkinson's Disease (PD). PD is associated with increased expression of inflammatory genes in peripheral and central nervous system (CNS), infiltration of immune cells into brain, and increased numbers of activated/memory T cells. Animal models of PD have shown a critical role of T cells in inducing pathology in CNS. However, the effect of carbidopa on T cell responses in vivo is unknown. In this report, we show that carbidopa strongly inhibited T cell activation in vitro and in vivo. Accordingly, carbidopa mitigated myelin oligodendrocyte glycoprotein peptide fragment 35-55 (MOG-35-55) induced experimental autoimmune encephalitis (EAE) and collagen induced arthritis in animal models. The data presented here suggest that in addition to blocking peripheral conversion of levodopa, carbidopa may inhibit T cell responses in PD individuals and implicate a potential therapeutic use of carbidopa in suppression of T cell mediated pathologies.

The genetic diversity in Plasmodium falciparum antigens is a major hurdle in developing an effective malaria vaccine. Protective efficacy of the vaccine is dependent on the polymorphic alleles of the vaccine candidate antigens. Therefore, we investigated the genetic diversity of the potential vaccine candidate antigens i.e. msp-1, msp-2, glurp, csp and pfs25 from field isolates of P.falciparum and determined the natural immune response against the synthetic peptide of these antigens. Genotyping was performed using Sanger method and size of alleles, multiplicity of infection, heterogeneity and recombination rate were analyzed. Asexual stage antigens were highly polymorphic with 55 and 50 unique alleles in msp-1 and msp-2 genes, respectively. The MOI for msp-1 and msp-2 were 1.67 and 1.28 respectively. A total 59 genotype was found in glurp gene with 8 types of amino acid repeats in the conserved part of RII repeat region. The number of NANP repeats from 40 to 44 was found among 55% samples in csp gene while pfs25 was found almost conserved with only two amino acid substitution site. The level of genetic diversity in the present study population was very similar to that from Asian countries. A higher IgG response was found in the B-cell epitopes of msp-1 and csp antigens and higher level of antibodies against csp B-cell epitope and glurp antigen were recorded with increasing age groups. Significantly, higher positive responses were observed in the csp antigen among the samples with ≥42 NANP repeats. The present finding showed extensive diversity in the asexual stage antigens.

Introduction: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is of growing concern globally. The risk for transmission of antimicrobial resistant organisms across several continents to the Caribbean is a real one given its tourism industry. After a cluster of cases of CRKP were detected, several studies detailed in this report were initiated to better characterize the problem., Methods: A hospital-wide point prevalence study and active surveillance were performed at Queen Elizabeth Hospital (QEH) in Barbados in 2013 to assess the prevalence of CRKP infection/colonization. Following this, a 1-year longitudinal study measured the prevalence of CRKP isolates in the hospital and across all healthcare facilities in the country., Results: In 2013, eleven viable isolates of CRKP from cluster of cases were sent for molecular epidemiology studies. When sequenced, they were found to be the ST-258 clone. Identification of a cluster of cases of CRKP ST-258/512 clones indicated person-to-person transmission. In September 2013, the hospital-wide point prevalence study revealed 18% of patients (53/299) at the hospital were either colonized or infected with CRKP. The infection to colonization ratio was 1:7. Patients who were infected/colonized vs. non-colonized were older (64.7 vs. 48.7 years, p<0.0001), were hospitalized longer (42.5 days vs. 27 days, p = 0.0042), were more likely to have an invasive device (66% vs. 32%, p<0.0001), especially urinary catheters (55% vs. 24%, p<0.0001), and were more likely to have used antimicrobials within the prior 14 days (91% vs. 46%, p<0.0001). Specific antimicrobials, including fluoroquinolones and piperacillin-tazobactam, were significantly associated with infection/colonization. In 2014, the 12-month period prevalence of CRKP in Barbados was 49.6 per 100,000 population and of blood stream infections was 3.2 per 100,000 population., Conclusions: This point prevalence study identified patients at-risk of acquisition of CRKP and allowed QEH to implement interventions aimed at decreasing the prevalence of CRKP. Organization of a National and regional Infection Prevention and Control Committee in 2014 aimed to strengthen antimicrobial resistance surveillance programs across the English-speaking Caribbean were established.

The rodent malaria parasite Plasmodium berghei is an excellent model organism for laboratory-based experimental evaluation of anti-malarial therapeutics prior to studies with human malaria parasites. The rodent model is especially important for evaluation of pre-erythrocytic (PE) stage therapies, especially as current efforts to develop new PE vaccines and drugs is limited by access to P. falciparum and P. vivax sporozoites. Developing a more effective method for cryopreservation of sporozoites would help improve access to sporozoites for laboratories lacking suitable insectary facilities. In this study, P. berghei GFP-expressing sporozoites were purified from infected mosquitoes by manual dissection of salivary glands and different commercially-available, serum-free cryopreservative solutions were evaluated for efficient cryopreservation of the sporozoites. The cryopreservative solutions evaluated included CryoStor CS2, CryoSolutions DX5, CryoSolutions MC, Hestar 200, Voluven, Hetastarch, and Glycerolyte 57. The viability of fresh and post-thaw cryopreserved sporozoites was determined as a function of the relative sporozoite infectivity by infecting HC-04 cells in vitro, monitoring invasion and growth and development of liver stage parasites. Flow cytometer-based counting provided unbiased and fast quantitative assessment of parasite in vitro infection in infected HC-04 and in vivo infectivity was validated by injecting sporozoites IV into mice. CryoStor CS2 delivered the highest post-thaw recovery and infectivity of cryopreserved sporozoites. Sporozoites cryopreserved in CryoStor CS2 achieved 38% complete development of hepatic stages in HC-04 and 100% infectivity in mice. The cryopreservation method described here demonstrates a viable alternative for fresh Plasmodium sporozoites. The use of cryopreserved sporozoites should facilitate greater access to sporozoites for chemotherapeutic and vaccine research.