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BackgroundCarpal instability is defined as a condition where wrist motion and/or loading creates mechanical dysfunction, resulting in weakness, pain and decreased function. When conventional methods do not identify the instability patterns, yet clinical signs of instability exist, the diagnosis of dynamic instability is often suggested to describe carpal derangement manifested only during the wrist's active motion or stress. We addressed the question: can advanced MRI techniques provide quantitative means to evaluate dynamic carpal instability and supplement standard static MRI acquisition? Our objectives were to (i) develop a real-time, three-dimensional MRI method to image the carpal joints during their active, uninterrupted motion; and (ii) demonstrate feasibility of the method for assessing metrics relevant to dynamic carpal instability, thus overcoming limitations of standard MRI.MethodsTwenty wrists (bilateral wrists of ten healthy participants) were scanned during radial-ulnar deviation and clenched-fist maneuvers. Images resulting from two real-time MRI pulse sequences, four sparse data-acquisition schemes, and three constrained image reconstruction techniques were compared. Image quality was assessed via blinded scoring by three radiologists and quantitative imaging metrics.ResultsReal-time MRI data-acquisition employing sparse radial sampling with a gradient-recalled-echo acquisition and constrained iterative reconstruction appeared to provide a practical tradeoff between imaging speed (temporal resolution up to 135 ms per slice) and image quality. The method effectively reduced streaking artifacts arising from data undersampling and enabled the derivation of quantitative measures pertinent to evaluating dynamic carpal instability.ConclusionThis study demonstrates that real-time, three-dimensional MRI of the moving wrist is feasible and may be useful for the evaluation of dynamic carpal instability.

Discriminating between black and white spruce (Picea mariana and Picea glauca) is a difficult palynological classification problem that, if solved, would provide valuable data for paleoclimate reconstructions. We developed an open-source visual recognition software (ARLO, Automated Recognition with Layered Optimization) capable of differentiating between these two species at an accuracy on par with human experts. The system applies pattern recognition and machine learning to the analysis of pollen images and discovers general-purpose image features, defined by simple features of lines and grids of pixels taken at different dimensions, size, spacing, and resolution. It adapts to a given problem by searching for the most effective combination of both feature representation and learning strategy. This results in a powerful and flexible framework for image classification. We worked with images acquired using an automated slide scanner. We first applied a hash-based "pollen spotting" model to segment pollen grains from the slide background. We next tested ARLO's ability to reconstruct black to white spruce pollen ratios using artificially constructed slides of known ratios. We then developed a more scalable hash-based method of image analysis that was able to distinguish between the pollen of black and white spruce with an estimated accuracy of 83.61%, comparable to human expert performance. Our results demonstrate the capability of machine learning systems to automate challenging taxonomic classifications in pollen analysis, and our success with simple image representations suggests that our approach is generalizable to many other object recognition problems.

The use of quality seeds is crucial to improve rice yield, food security, and farmers' livelihoods. The large informal seed system, limited access to quality seeds, and low seed replacement rate challenge increasing rice yield. Despite robust government initiatives to support the seed system, progress has been slow. Besides, the need for farmers' behavioural change, enhanced coordination, and communication at the local level has not received adequate attention. We investigate rice farmers' preferences for quality seed, packet sizes, types, and sources, and assess the impact of utilizing good quality seed. We collected quantitative data from 1196 rice farmers in northern Bangladesh in 2019. To identify major factors influencing farmers' preferences regarding quality seed, packet sizes, packet types, and seed sources, we employed ordered logit and multinomial logit models. Additionally, we used the propensity score matching procedure to assess the impact of good quality and formal seed sources on the rice yield. The findings revealed that farmers strongly prefer using seeds from formal sources despite limited accessibility. Of the total farmers, 34% use public source seeds, 33% use private source seeds, and the rest rely on their own saved seeds. The use of good quality seeds increased rice yields from the base yield by 0.07-0.28 t/ha. We found about a 48% gap in accessing good-quality seeds, indicating significant potential for scaling up the seed systems. Farmers using formal seed sources yielded 0.03-0.15 t/ha more than informal seed users. Farmers strongly prefer 5 kg packets due to their cost-effectiveness, easy storage, and handling convenience. Additionally, farmers prefer polycoated jute sacks for their versatility, multi-purpose applications, and resistance to pests. The econometric model results showed that farmers' preferences were significantly influenced by gender, farm type, crop yield, seed price, market distance, various stakeholders' advice, and seed supply systems' constraints. The government should implement policies and programs to strengthen a well-connected seed network in rural areas, promoting inclusivity, and enhancing rice productivity. Besides, farmers' needs and preferences should be considered in designing and implementing seed-related initiatives to foster sustainable agricultural development.

Apart from aerosols, contaminated surfaces with SARS-CoV-2 virus are the significant carriers of virus transmission. The disinfection and sanitization of the indoor and outdoor places are one among the powerful and effective strategies to avoid the surface-to-human transmission of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) through frequent touch and physical contact. Electrostatic spraying is one of the effective and efficient methods to apply the liquid-based sprays on surfaces to be disinfected or sanitized. This technique covers the directly exposed and obscured surfaces uniformly and reaches to hidden areas of the target. In this paper, the design and performance parameters of a motorized pressure-nozzle based handheld electrostatic disinfection device were optimized and the chargeability of ethanol (C2H5OH), formaldehyde (CH2O), glutaraldehyde (C5H8O2), hydrogen peroxide (H2O2), phenol (C6H5OH) and sodium hypochlorite (NaClO) has been critically investigated. The chargeability indicator for disinfectants was presented in terms of the charge-to-mass ratio. The significant value of the charge-to-mass ratio of 1.82 mC/kg was achieved at an applied voltage of 2.0 kV, the liquid flow rate and pressure of 28 ml/min and 5 MPa, respectively. The experimental results are well aligned to the proposed theoretical context.

This study investigated the current practices and challenges for the sustainable fashion of luxury boutique fashion brands (LBFBs) in Vietnam. A series of in-depth interviews with 20 founders and managers of LBFBs in Vietnam was conducted. Findings show that sustainable practices improve ethnic cultures, strengthen the usage of local resources, promote sustainable lifestyle, and thereby contributing to sustainable development of the boutique fashion brands. However, the brands face some challenges while dealing with their stakeholders such as shortage of available internal resources, bias in consumer perception and purchase behaviors, and legal barriers to achieve accredited environment certification that, in turn, weaken the sustainable practices in the local context. Results also provide some insightful information for small & medium sized enterprises (SMEs) to adjust their sustainability practices in order to improve their competitive advantages in the marketplace.

Nucleotide Sugar Transporters (NSTs) belong to the SLC35 family (human solute carrier) of membrane transport proteins and are crucial components of the glycosylation machinery. NSTs are localized in the ER and Golgi apparatus membranes, where they accumulate nucleotide sugars from the cytosol for subsequent polysaccharide biosynthesis. Loss of NST function impacts the glycosylation of cell surface molecules. Mutations in NSTs cause several developmental disorders, immune disorders, and increased susceptibility to infection. Atomic resolution structures of three NSTs have provided a blueprint for a detailed molecular interpretation of their biochemical properties. In this work, we have identified, cloned, and expressed 18 members of the SLC35 family from various eukaryotic organisms in Saccharomyces cerevisiae. Out of 18 clones, we determined Vrg4 from Chaetomium thermophilum (CtVrg4) is a GDP-mannose transporter with an enhanced melting point temperature (Tm) of 56.9°C, which increases with the addition of substrates, GMP and GDP-mannose. In addition, we report-for the first time-that the CtVrg4 shows an affinity to bind to phosphatidylinositol lipids.

Inflammation is caused by a cascade of events, one of which is the metabolism of arachidonic acid, that begins with oxidation by the enzyme 5-lipoxygenase. 5-Lipoxygenase (5-LOX) plays an important role in the inflammation process by synthesizing leukotrienes and several lipid mediators and has emerged as a possible therapeutic target for treatment of inflammatory diseases such as asthma and rheumatoid arthritis. Most of the existing 5-LOX inhibitors are synthetic and exhibit adverse side effects. In view of this, there is need to search for an alternate source of 5-LOX inhibitor with minimal side effects. The essential oil of several species of Curcuma has received considerable attention in recent times in traditional system of medicine especially for treating various inflammatory disorders. Therefore, the present study was carried out to screen the most potential 5-LOX inhibitors from essential oil components of Curcuma species and elucidate their mechanisms of action through computational biology approaches. Twenty-three phytoconstituents derived from the essential oil of Curcuma species were docked and their predictive binding energies were calculated to select the best possible ligand for 5-LOX. The top 8 ranked compounds from docking was tested for drug-likeness properties, bioactivity score, and toxicity analysis. The phytoconstituents such as α-turmerone, β-turmerone, α-terpineol and dihydrocarveolshowed the best binding affinity with 5-LOX and displayed favorable physicochemical properties. Molecular dynamics simulation in POPC lipid bilayers was carried out to understand the intrinsic dynamics and flexibility of the 5-LOX (apo) and 5-LOX-complex (α-terpineol, α-turmerone, β-turmerone and dihydrocarveol) systems. The molecular dynamic results showed that these 4 phytoconstituents interacted stably with the 5-LOX active site residues and the important bonds that were observed in the initial ligand docked compounds did not alter during the course of simulation. In general, our integrative computational approach demonstrated that the natural compounds like α-turmerone, β-turmerone, α-terpineol, and dihydrocarveol could be considered for designing specific anti-inflammatory drugs using structure-based drug design.

Background Modeling studies estimated severe impacts of potential service delivery disruptions due to COVID-19 pandemic on maternal and child nutrition outcomes. Although anecdotal evidence exists on disruptions, little is known about the actual state of service delivery at scale. We studied disruptions and restorations, challenges and adaptations in health and nutrition service delivery by frontline workers (FLWs) in India during COVID-19 in 2020. Methods We conducted phone surveys with 5500 FLWs (among them 3118 Anganwadi Workers) in seven states between August–October 2020, asking about service delivery during April 2020 (T1) and in August-October (T2), and analyzed changes between T1 and T2. We also analyzed health systems administrative data from 704 districts on disruptions and restoration of services between pre-pandemic (December 2019, T0), T1 and T2. Results In April 2020 (T1), village centers, fixed day events, child growth monitoring, and immunization were provided by Conclusions Services to mothers and children were disrupted during stringent lockdown but restored thereafter, albeit not to pre-pandemic levels. Rapid policy guidance and adaptations by FLWs enabled restoration but little remains known about uptake by client populations. As COVID-19 continues to surge in India, focused attention to ensuring essential services is critical to mitigate these major indirect impacts of the pandemic.

High seed vigour ensures good quality seed and higher productivity. Early seedling growth parameters indicate seed vigour in rice. Seed vigour via physiological growth parameters is a complex trait controlled by many quantitative trait loci. A panel was prepared representing a population of 274 rice landraces by including genotypes from all the phenotypic groups of sixseedling stage physiological parameters including germination % for association mapping. Wide variations for the six studiedtraits were observed in the population. The population was classified into 3 genetic groups. Fixation indices indicated the presence of linkage disequilibrium in the population. The population was classified into subpopulations and each subpopulation showed correspondence with the 6 physiological traits. A total of 5 reported QTLs viz., qGP8.1 for germination % (GP); qSVII2.1, qSVII6.1 and qSVII6.2 for seed vigour index II (SVII), and qRSR11.1 for root-shoot ratio (RSR) were validated in this mapping population. In addition, 13 QTLs regulating the physiological parameters such as qSVI 11.1 for seed vigour index I; qSVI11.1 and qSVI12.1 for seed vigour index II; qRRG10.1, qRRG8.1, qRRG8.2, qRRG6.1 and qRRG4.1 for rate of root growth (RRG); qRSR2.1, qRSR3.1 and qRSR5.1 for root-shoot ratio (RSR) while qGP6.2 and qGP6.3 for germination %were identified. Additionally, co-localization or co-inheritance of QTLs, qGP8.1 and qSVI8.1 for GP and SVI-1; qGP6.2 and qRRG6.1 for GP and RRG, and qSVI11.1 and qRSR11.1 for SVI and RSR were detected. The QTLs identified in this study will be useful for improvement of seed vigour trait in rice.

BackgroundTransplant related toxicity is a major therapeutic challenge. We have previously reported that the toxicity of chemotherapy is largely not directly because of the drugs themselves; rather it is mainly due to DNA damage, apoptosis and hyper-inflammation triggered by cell-free chromatin particles that are released because of drug-induced host cell death. Cell-free chromatin particles can be inactivated by free-radicals which are generated when the nutraceuticals resveratrol and copper are administered orally. We investigated if a combination of resveratrol and copper would reduce transplant related toxicities in an exploratory, prospective dose-escalation study.Patients and methodsTwenty-five patients with multiple myeloma were enrolled between March 2017 to August 2019. Patients were divided into 3 groups: control (Group 1, N = 5) received vehicle alone; group 2 (N = 15) received resveratrol-copper at dose level I (resveratrol = 5.6 mg and copper = 560 ng); group 3 (N = 5) received resveratrol-copper at dose level II (resveratrol = 50 mg and copper = 5 μg). The dose was given twice daily with the first dose administered 48 hours before administering melphalan and continued until day +21 post-transplant. Common Terminology Criteria for Adverse Events version 4.02 was used to assess toxicities which included oral mucositis, nausea, vomiting and diarrhea. Measurement of inflammatory cytokines was done by ELISA.ResultsAll patients (100%) in the control group developed grade 3/4 oral mucositis compared to 8/20 (40%) in both resveratrol-copper group 2 plus group 3 combined (P = 0.039). Reduction in inflammatory cytokines: salivary TNF - α (p = 0.012) and IL-1β (p = 0.009) in dose level I but not in dose level II was observed.ConclusionsA combination of resveratrol-copper reduced transplant related toxicities in patients with multiple myeloma receiving high dose melphalan. We conclude that relatively inexpensive nutraceuticals may be useful as adjuncts to chemotherapy to reduce its toxicity.RegistrationThe trial was registered under Clinical Trial Registry of India (no.CTRI/2018/02/011905).

BackgroundNon-alcoholic fatty liver disease (NAFLD) is a spectrum of disease ranging from simple steatosis, non-alcoholic steatohepatitis (NASH), through to advanced fibrosis and cirrhosis. We assessed the prevalence, spectrum, and determinants of NAFLD among adults in urban and rural North India.MethodsA representative sample of adults aged 30-60 years were recruited from urban Delhi and rural Ballabhgarh during 2017-2019. Participants underwent abdominal ultrasonography (USG) and vibration controlled transient elastography (VCTE) with FibroScan to assess fatty liver and fibrosis, respectively. We estimated the age- and sex-standardised prevalence of NAFLD and its spectrum. The factors associated with 'ultrasound-diagnosed NAFLD' were identified using multivariate logistic regression.ResultsA total of 828 urban (mean ± SD age: 45.5 ± 8.0 years; women: 52.7%) and 832 rural (mean ± SD age: 45.1 ± 7.9 years; women: 62.4%) participants were recruited. The age- and sex-standardized prevalence of ultrasound-diagnosed NAFLD was 65.7% (95%CI: 60.3-71.2) in the urban and 61.1% (55.8-66.5) in the rural areas, respectively. The prevalence of NAFLD with elevated alanine transaminase (≥40IU/L) was 23.2% (19.8-26.6), and 22.5% (19.0-26.0) and any fibrosis by liver stiffness measurement on transient elastography (≥6.9 kPa) was 16.5% (13.8-19.8) and 5.2% (3.8-6.7) in urban and rural participants, respectively. In both urban and rural areas, diabetes, central obesity and insulin resistance were significantly associated with NAFLD.ConclusionNAFLD prevalence was high among rural and urban North Indian adults, including fibrosis or raised hepatic enzymes. The strong association of metabolic determinants confirms its linkage with metabolic syndrome.

Appropriate descriptions of statistical methods are essential for evaluating research quality and reproducibility. Despite continued efforts to improve reporting in publications, inadequate descriptions of statistical methods persist. At times, reading statistical methods sections can conjure feelings of dèjá vu, with content resembling cut-and-pasted or “boilerplate text” from already published work. Instances of boilerplate text suggest a mechanistic approach to statistical analysis, where the same default methods are being used and described using standardized text. To investigate the extent of this practice, we analyzed text extracted from published statistical methods sections from PLOS ONE and the Australian and New Zealand Clinical Trials Registry (ANZCTR). Topic modeling was applied to analyze data from 111,731 papers published in PLOS ONE and 9,523 studies registered with the ANZCTR. PLOS ONE topics emphasized definitions of statistical significance, software and descriptive statistics. One in three PLOS ONE papers contained at least 1 sentence that was a direct copy from another paper. 12,675 papers (11%) closely matched to the sentence “a p-value < 0.05 was considered statistically significant”. Common topics across ANZCTR studies differentiated between study designs and analysis methods, with matching text found in approximately 3% of sections. Our findings quantify a serious problem affecting the reporting of statistical methods and shed light on perceptions about the communication of statistics as part of the scientific process. Results further emphasize the importance of rigorous statistical review to ensure that adequate descriptions of methods are prioritized over relatively minor details such as p-values and software when reporting research outcomes.

Both psychedelic drug experiences and near-death experiences can occasion changes in perspectives on death and dying, but there have been few direct comparisons of these phenomena. This study directly compared psychedelic occasioned and non-drug experiences which altered individuals' beliefs about death. Individuals who reported an experience that altered their beliefs about death occasioned by either a psychedelic drug or a near-death or other non-ordinary experience completed an online survey. Circumstances of the experience, mystical and near-death subjective features, changes in attitudes about death, and other persisting effects were evaluated. The study sample (n = 3192) included five groups: non-drug near-death or other non-ordinary experiences (n = 933), and drug experiences occasioned by lysergic acid diethylamide (LSD) (n = 904), psilocybin (n = 766), ayahuasca (n = 282), or N,N-dimethyltryptamine (DMT) (n = 307). Analyses of differences in experiences were adjusted statistically for demographic differences between groups. Compared to the psychedelic groups, the non-drug group was more likely to report being unconscious, clinically dead, and that their life was in imminent danger. The groups were remarkably similar in the reported changes in death attitudes attributed to the experience, including a reduced fear of death and high ratings of positive persisting effects and personal meaning, spiritual significance, and psychological insight. Although both psychedelic and non-drug participants showed robust increases on standardized measures of mystical and near-death experiences, these measures were significantly greater in the psychedelic participants. Non-drug participants were more likely to rate their experiences as the single most meaningful of their lives. Comparing across psychedelic substances, ayahuasca and DMT groups tended report stronger and more positive enduring consequences of the experience than the psilocybin and LSD groups, which were largely indistinguishable. These data provide a detailed characterization and comparison of psychedelic occasioned and non-drug experiences that changed attitudes about death and suggest the importance of future prospective psychedelic administration studies.

Understanding the spatial spreading patterns of plant-available sulphur (S) (AS) and plant-available micronutrients (available zinc (AZn), available iron (AFe), available copper (ACu), available manganese (AMn) and available boron (AB)) in soils, especially in coastal agricultural soils subjected to various natural and anthropogenic activities, is vital for sustainable crop production by adopting site-specific nutrient management (SSNM) strategies. We studied the spatial distribution patterns of AS, AZn, AFe, ACu, AMn, and AB in cultivated soils of coastal districts of India using geostatistical approaches. Altogether 39,097 soil samples from surface (0 to 15 cm depth) layers were gathered from farm lands of 68 coastal districts. The analysis of soil samples was carried out for soil pH, electrical conductivity (EC), soil organic carbon (SOC) and AS, AZn, AFe, ACu, AMn, and AB. Soil pH, EC and SOC varied from 3.70 to 9.90, 0.01 to 7.45 dS m-1 and 0.02 to 3.74%, respectively. The concentrations of AS, AZn, AFe, ACu, AMn, and AB varied widely in the study area with their corresponding mean values were 37.4±29.4, 1.50±1.53, 27.9±35.1, 2.14±1.74, 16.9±18.4 and 1.34±1.52 mg kg-1, respectively. The coefficient of variation values of analyzed soil parameters varied from 14.6 to 126%. The concentrations of AS, AZn, AFe, ACu, AMn, and AB were negatively and significantly correlated with soil pH and positively and significantly correlated with SOC. The geostatistical analysis indicated stable, Gaussian and exponential best-fit semivariogram models with moderate to strong spatial dependence for available nutrients. The generated spatial spreading maps revealed different distribution patterns for AS, AZn, AFe, ACu, AMn, and AB. There were variations in spatial spreading patterns of AS, AZn, AFe, ACu, AMn, and AB in east- and west-coastal area. About 62, 35, 12, 0.4, 23 and 45% of the study area had deficiency of AS, AZn, AFe, ACu, AMn, and AB, respectively. The spatial spreading maps will be highly useful for SSNM in the cultivated coastal soils of the country. This study could also be used as a base for assessing spatial spreading patterns of soil parameters in cultivated coastal areas of other parts of the world.

[This corrects the article DOI: 10.1371/journal.pone.0241607.].

Octamer-binding transcription factor 4 (Oct4) is a core regulator in the retention of stemness, invasive, and self-renewal properties in glioma initiating cells (GSCs) and its overexpression inhibits the differentiation of glioma cells promoting tumor cell proliferation. The Pit-Oct-Unc (POU) domain comprising POU-specific domain (POUS) and POU-type homeodomain (POUHD) subdomains is the most critical part of the Oct4 for the generation of induced pluripotent stem cells from somatic cells that lead to tumor initiation, invasion, posttreatment relapse, and therapeutic resistance. Therefore, the present investigation hunts for natural product inhibitors (NPIs) against the POUHD domain of Oct4 by employing receptor-based virtual screening (RBVS) followed by binding free energy calculation and molecular dynamics simulation (MDS). RBVS provided 13 compounds with acceptable ranges of pharmacokinetic properties and good docking scores having key interactions with the POUHD domain. More Specifically, conformational and interaction stability analysis of 13 compounds through MDS unveiled two compounds ZINC02145000 and ZINC32124203 which stabilized the backbone of protein even in the presence of linker and POUS domain. Additionally, ZINC02145000 and ZINC32124203 exhibited stable and strong interactions with key residues W277, R242, and R234 of the POUHD domain even in dynamic conditions. Interestingly, ZINC02145000 and ZINC32124203 established communication not only with the POUHD domain but also with the POUS domain indicating their incredible potency toward thwarting the function of Oct4. ZINC02145000 and ZINC32124203 also reduced the flexibility and escalated the correlations between the amino acid residues of Oct4 evidenced by PCA and DCCM analysis. Finally, our examination proposed two NPIs that can impede the Oct4 function and may help to improve overall survival, diminish tumor relapse, and achieve a cure not only in deadly disease GBM but also in other cancers with minimal side effects.

The rapid emergence of coronavirus disease 2019 (COVID-19) as a global pandemic affecting millions of individuals globally has necessitated sensitive and high-throughput approaches for the diagnosis, surveillance, and determining the genetic epidemiology of SARS-CoV-2. In the present study, we used the COVIDSeq protocol, which involves multiplex-PCR, barcoding, and sequencing of samples for high-throughput detection and deciphering the genetic epidemiology of SARS-CoV-2. We used the approach on 752 clinical samples in duplicates, amounting to a total of 1536 samples which could be sequenced on a single S4 sequencing flow cell on NovaSeq 6000. Our analysis suggests a high concordance between technical duplicates and a high concordance of detection of SARS-CoV-2 between the COVIDSeq as well as RT-PCR approaches. An in-depth analysis revealed a total of six samples in which COVIDSeq detected SARS-CoV-2 in high confidence which were negative in RT-PCR. Additionally, the assay could detect SARS-CoV-2 in 21 samples and 16 samples which were classified inconclusive and pan-sarbeco positive respectively suggesting that COVIDSeq could be used as a confirmatory test. The sequencing approach also enabled insights into the evolution and genetic epidemiology of the SARS-CoV-2 samples. The samples were classified into a total of 3 clades. This study reports two lineages B.1.112 and B.1.99 for the first time in India. This study also revealed 1,143 unique single nucleotide variants and added a total of 73 novel variants identified for the first time. To the best of our knowledge, this is the first report of the COVIDSeq approach for detection and genetic epidemiology of SARS-CoV-2. Our analysis suggests that COVIDSeq could be a potential high sensitivity assay for the detection of SARS-CoV-2, with an additional advantage of enabling the genetic epidemiology of SARS-CoV-2.

Background and objectivesCrohn's disease (CD) and Intestinal tuberculosis (ITB) are chronic inflammatory ulcero-constrictive intestinal diseases with similar phenotype. Although both are disease models of chronic inflammation and their clinical presentations, imaging, histological and endoscopic findings are very similar, yet their etiologies are diverse. Hence, we aimed to look at differences in the prevalence of pathobionts like adherent-invasive Escherichia coli (AIEC), Listeria monocytogenes, Campylobacter jejuni and Yersinia enterocolitica in CD and ITB as well as their associations with host-associated genetic polymorphisms in genes majorly involved in pathways of microbial handling and immune responses.MethodsThe study cohort included 142 subjects (69 patients with CD, 32 with ITB and 41 controls). RT- PCR amplification was used to detect the presence of AIEC, L. monocytogenes, C. jejuni, and Y. enterocolitica DNA in colonic mucosal biopsies. Additionally, we tested three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and one SNP in TNFRSF1A (rs4149570) by real-time PCR with SYBR green from peripheral blood samples in this cohort.ResultsIn patients with CD, AIEC was most frequently present (16/ 69, 23.19%) followed by L. monocytogenes (14/69, 20.29%), C. jejuni (9/69, 13.04%), and Y. enterocolitica (7/69, 10.14%). Among them, L. monocytogenes and Y. enterocolitica were significantly associated with CD (p = 0.02). In addition, we identified all the three SNPs in IRGM (rs13361189, rs10065172, and rs4958847), one SNP in ATG16L1 (rs2241880) and TNFRSF1A (rs4149570) with a significant difference in frequency in patients with CD compared with ITB and controls (pConclusionHigher prevalence of host gene polymorphisms, as well as the presence of pathobionts, was seen in the colonic mucosa of patients with CD as compared to ITB, although both are disease models of chronic inflammation.

The surge in the prevalence of drug-resistant bacteria in poultry is a global concern as it may pose an extended threat to humans and animal health. The present study aimed to investigate the colonization proportion of extended-spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae (EPE and CPE, respectively) in the gut of healthy poultry, Gallus gallus domesticus in Kaski district of Western Nepal. Total, 113 pooled rectal swab specimens from 66 private household farms and 47 commercial poultry farms were collected by systematic random sampling from the Kaski district in western Nepal. Out of 113 pooled samples, 19 (28.8%) samples from 66 backyard farms, and 15 (31.9%) from 47 commercial broiler farms were positive for EPE. Of the 38 EPE strains isolated from 34 ESBL positive rectal swabs, 31(81.6%) were identified as Escherichia coli, five as Klebsiella pneumoniae (13.2%), and one each isolate of Enterobacter species and Citrobacter species (2.6%). Based on genotyping, 35/38 examined EPE strains (92.1%) were phylogroup-1 positive, and all these 35 strains (100%) had the CTX-M-15 gene and strains from phylogroup-2, and 9 were of CTX-M-2 and CTX-M-14, respectively. Among 38 ESBL positive isolates, 9 (23.7%) were Ambler class C (Amp C) co-producers, predominant were of DHA, followed by CIT genes. Two (6.5%) E. coli strains of ST131 belonged to clade C, rest 29/31 (93.5%) were non-ST131 E. coli. None of the isolates produced carbapenemase. Twenty isolates (52.6%) were in-vitro biofilm producers. Univariate analysis showed that the odd of ESBL carriage among commercial broilers were 1.160 times (95% CI 0.515, 2.613) higher than organically fed backyard flocks. This is the first study in Nepal, demonstrating the EPE colonization proportion, genotypes, and prevalence of high-risk clone E. coli ST131 among gut flora of healthy poultry. Our data indicated that CTX-M-15 was the most prevalent ESBL enzyme, mainly associated with E. coli belonging to non-ST131clones and the absence of carbapenemases.

The efficient (site-specific) management of soil nutrients is possible by understanding the spatial variability in distribution of phyto-available nutrients (here after called available nutrients) and identifying the soil management zones (MZs) of agricultural landscapes. There is need for delineating soil MZs of agricultural landscapes of the world for efficient management of soil nutrients in order to obtain sustainability in crop yield. The present study was, therefore, undertaken to understand the spatial distribution pattern of available micronutrients (zinc (Zn), boron (B), iron (Fe), manganese (Mn) and copper (Cu)), available sulphur (S), and soil properties (soil acidity (pH), electrical conductivity (EC) and organic carbon (SOC) content) in soils of intensively cultivated Indo-Gangetic Plain (IGP) of India and to delineate soil MZs for efficient management of soil nutrients. Totally, 55101 soil samples from 0-15 cm depth were obtained from 167 districts of IGP during 2014 to 2017 and were analysed for different soil parameters. Soil pH, EC and SOC content varied from 4.44 to 9.80, 0.02 to 2.13 dS m-1 and 0.10 to 1.99%, respectively. The concentration of available Zn, B, Fe, Mn, Cu and S varied from 0.01 to 3.27, 0.01 to 3.51, 0.19 to 55.7, 0.05 to 49.0, 0.01 to 5.29 and 1.01 to 108 mg kg-1, respectively. Geostatistical analysis resulted in varied distribution pattern of studied soil parameters with moderate to strong spatial dependence. The extent (% area) of nutrient deficiencies in IGP followed the order: S > Zn > B > Mn > Cu > Fe. Principal component analysis and fuzzy c-means clustering produced six distinctly different soil MZs of IGP for implementation of zone-specific soil nutrient management strategies for attaining sustainability in crop yield. The developed MZ maps could also be utilized for prioritization and rationalization of nutrients supply in IGP of India.

OBJECTIVE:Patients with CAD have substantial residual risk of mortality, and whether hitherto unknown small-molecule metabolites and metabolic pathways contribute to this risk is unclear. We sought to determine the predictive value of plasma metabolomic profiling in patients with CAD. APPROACH AND RESULTS:Untargeted high-resolution plasma metabolomic profiling of subjects undergoing coronary angiography was performed using liquid chromatography/mass spectrometry. Metabolic features and pathways associated with mortality were identified in 454 subjects using metabolome-wide association studies and Mummichog, respectively, and validated in 322 subjects. A metabolomic risk score comprising of log-transformed HR estimates of metabolites that associated with mortality and passed LASSO regression was created and its performance validated. In 776 subjects (66.8 years, 64% male, 17% Black), 433 and 357 features associated with mortality (FDR-adjusted q

PurposeTo report the clinical presentation and management outcomes of glaucoma in the "Indian Twin cities retinopathy of prematurity (ROP) Screening database."MethodsAll children with diagnosis of ROP and glaucoma between 1997 and 2016 from a prospective database were included. Glaucoma was classified as open when anterior chamber (AC) was deep, closed when AC was shallow or flat and neovascular when there was extensive iris neovascularization. ROP was classified based on International classification of ROP.ResultsThe prevalence of secondary glaucoma in our cohort was 1.36% (82 eyes of 6000 children). Eighty-two eyes of 54 children with secondary glaucoma due to ROP where included in this study. The distribution of glaucoma among the ROP stages included, stage V (58.5%), stage 1V (24.3%), stage III (2.4%) and stage II (1.2%) eyes. Median (interquartile range) duration from birth to glaucoma diagnosis was 7.8 (4.2, 24.9) months. Type of glaucoma was angle closure in 39 (47.6%), open angle in 35 (42.7%) and neovascular in 8 (9.8%) eyes. Retinal interventions included vitreoretinal surgery in 59 (72%), retinal laser in 14 (17%) and intravitreal bevacizumab injection in 19 (23.1%) eyes. The mean (±standard deviation) IOP at presentation was 22.6 ±11.8 mm Hg. Glaucoma was managed medically in 66 (76%) and surgically in 16 (19.5%) eyes. The mean follow up for the entire cohort was 1.14±2.24 years. At final visit, 37% eyes with ROP and glaucoma had ambulatory vision with mean IOP of 16.0±8.1 mm Hg and 56 eyes (68.2%) needed glaucoma medications.ConclusionIn this large ROP cohort, 1.36% eyes developed secondary glaucoma. Majority of them had stage V or IV ROP and 1/5 of them needed glaucoma surgery. Around 1/3rd of the ROP eyes with glaucoma had ambulatory vision.

ObjectivesTo evaluate the predictive performance of comb-push ultrasound shear elastography for the differentiation of reactive and metastatic axillary lymph nodes.MethodsFrom June 2014 through September 2018, 114 female volunteers (mean age 58.1±13.3 years; range 28-88 years) with enlarged axillary lymph nodes identified by palpation or clinical imaging were prospectively enrolled in the study. Mean, standard deviation and maximum shear wave elastography parameters from 117 lymph nodes were obtained and compared to fine needle aspiration biopsy results. Mann-Whitney U test and ROC curve analysis were performed.ResultsThe axillary lymph nodes were classified as reactive or metastatic based on the fine needle aspiration outcomes. A statistically significant difference between reactive and metastatic axillary lymph nodes was observed based on comb-push ultrasound shear elastography (CUSE) results (pConclusionsCUSE provided a quantifiable parameter that can be used for the assessment of enlarged axillary lymph nodes to differentiate between reactive and metastatic processes.

Automated quantification of behavior is increasingly prevalent in neuroscience research. Human judgments can influence machine-learning-based behavior classification at multiple steps in the process, for both supervised and unsupervised approaches. Such steps include the design of the algorithm for machine learning, the methods used for animal tracking, the choice of training images, and the benchmarking of classification outcomes. However, how these design choices contribute to the interpretation of automated behavioral classifications has not been extensively characterized. Here, we quantify the effects of experimenter choices on the outputs of automated classifiers of Drosophila social behaviors. Drosophila behaviors contain a considerable degree of variability, which was reflected in the confidence levels associated with both human and computer classifications. We found that a diversity of sex combinations and tracking features was important for robust performance of the automated classifiers. In particular, features concerning the relative position of flies contained useful information for training a machine-learning algorithm. These observations shed light on the importance of human influence on tracking algorithms, the selection of training images, and the quality of annotated sample images used to benchmark the performance of a classifier (the 'ground truth'). Evaluation of these factors is necessary for researchers to accurately interpret behavioral data quantified by a machine-learning algorithm and to further improve automated classifications.

BackgroundDue to improved treatment, there is an increasing focus on the reproductive potential of survivors of childhood cancer. Cytotoxic chemotherapy accelerates the decline in the number of primordial follicles within the mammalian ovary at all ages, but effects on the developmental potential of remaining oocytes following prepubertal cancer treatment are unclear.ObjectivesTo investigate whether cyclophosphamide (CY) exposure in the prepubertal period in female mice influences ovarian function and the functional competence of oocytes in adulthood.MethodsThis study used Swiss albino mice as the experimental model. Female mice were treated with 200 mg/kg CY on either postnatal day 14 (CY14), 21 (CY21) or 28 (CY28) i.e at a prepubertal and 2 young postpubertal ages. At 14 weeks of life, ovarian function, functional competence of oocytes, and embryo quality were assessed.ResultsThe number of primordial follicles decreased significantly in CY14 and CY21 groups compared to control (p < 0.01). The number of oocytes from superovulated was 8.5 ± 1.4, 24.1 ± 2.9 and 26.8 ± 2.1 in CY14, CY21 and CY28 respectively which was significantly lower than control (50.2 ± 3.2; p < 0.001). In vitro culture of CY14 embryos demonstrated only 55.4% blastocyst formation (p < 0.0001) and reduced ability of inner cell mass (ICM) to proliferate in vitro (p < 0.05) at 120 and 216 h post insemination respectively. On the other hand, ICM proliferation was unaltered in 2 young postpubertal ages.ConclusionOur results indicate long-term effects on the developmental competence of oocytes exposed to CY in early but not adult life. These data provide a mechanism whereby long-term fertility can be impaired after chemotherapy exposure, despite the continuing presence of follicles within the ovary, and support the need for fertility preservation in prepubertal girls before alkylating agent exposure.

Inflammation is a vital physiological response of the immune system meant to protect against the invasion of pathogens. However, accumulating evidence describes an intimate link between inflammation and thrombosis and cellular elements of the immune system of the immune system such as neutrophils and monocytes/macrophages are emerging as key players in the generation of a prothrombotic milieu suggesting that anti-inflammatory therapy may have a role in the management of thrombosis that is driven by inflammation. Tongji 2 (TJ2) is a traditional Chinese medication manufactured as granules by Tongji hospital of Tongji University (Shanghai, China) with known anti-inflammatory properties. In this study, we examine the effects of TJ2 on inflammation and thrombosis. Our study shows that TJ2 modulates NF-κB activation and thus generates a prominent anti-inflammatory effect. Further, we use mouse models of thrombosis to demonstrate that TJ2 has a beneficial effect in both arterial and venous thrombosis that occurs in the absence of alterations in platelet activation or coagulation.

A worldwide increase in the gastrointestinal colonization by extended-spectrum β-lactamase (ESBL)-producing bacteria has been observed. Their prevalence amongst Healthy People Living with HIV (HPLWH) has not been investigated adequately. The aim of this study was to determine and compare the rates of and risk factors for intestinal carriage and acquisition of extended-spectrum β-lactamase producing Enterobacteriaceae (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) among healthy people living with HIV (HPLWH) and healthy HIV negative population in the community. A cross-sectional study was conducted. Rectal swabs from HPLWH (n = 119) and HIV negative individuals (n = 357) from the community were screened for ESBL and CPE. Phenotypically confirmed ESBL-E strains were genotyped by multiplex PCR. The risk factors associated with ESBL-E colonization were analyzed by a multivariable conditional logistic regression analysis. Specimen from 357 healthy volunteers (213 female and 144 male) and 119 HPLWH (82 female and 37 male) with a median age of 30 [IQR 11-50] years were included in the study. ESBL colonization were found in 45 (37.82% [CI 29.09, 47.16]) and 246 (68.91% [CI 63.93, 73.49]), HPLWH and healthy HIV negative participants respectively. HPLWH had lower ESBL carriage rate (odds ratio 0.274 [CI 0.178, 0.423]) compared to healthy HIV negative subject's (p

INTRODUCTION:Malaria is a public health emergency in India and Odisha. The national malaria elimination programme aims to expedite early identification, treatment and follow-up of malaria cases in hot-spots through a robust health system, besides focusing on efficient vector control. This study, a result of mass screening conducted in a hot-spot in Odisha, aimed to assess prevalence, identify and estimate the risks and develop a management tool for malaria elimination. METHODS:Through a cross-sectional study and using WHO recommended Rapid Diagnostic Test (RDT), 13221 individuals were screened. Information about age, gender, education and health practices were collected along with blood sample (5 μl) for malaria testing. Altitude, forestation, availability of a village health worker and distance from secondary health center were captured using panel technique. A multi-level poisson regression model was used to analyze association between risk factors and prevalence of malaria, and to estimate risk scores. RESULTS:The prevalence of malaria was 5.8% and afebrile malaria accounted for 79 percent of all confirmed cases. Higher proportion of Pv infections were afebrile (81%). We found the prevalence to be 1.38 (1.1664-1.6457) times higher in villages where the Accredited Social Health Activist (ASHA) didn't stay; the risk increased by 1.38 (1.0428-1.8272) and 1.92 (1.4428-2.5764) times in mid- and high-altitude tertiles. With regard to forest coverage, villages falling under mid- and highest-tertiles were 2.01 times (1.6194-2.5129) and 2.03 times (1.5477-2.6809), respectively, more likely affected by malaria. Similarly, villages of mid tertile and lowest tertile of education had 1.73 times (1.3392-2.2586) and 2.50 times (2.009-3.1244) higher prevalence of malaria. CONCLUSION:Presence of ASHA worker in villages, altitude, forestation, and education emerged as principal predictors of malaria infection in the study area. An easy-to-use risk-scoring system for ranking villages based on these risk factors could facilitate resource prioritization for malaria elimination.

Neisseria meningitidis is the primary cause of bacterial meningitis in many parts of the world, with considerable mortality rates among neonates and adults. In Saudi Arabia, serious outbreaks of N. meningitidis affecting several hundreds of pilgrims attending Hajj in Makkah were recorded in the 2000-2001 season. Evidence shows increased rates of bacterial resistance to penicillin and other antimicrobial agents that are used in the treatment of the meningococcal disease. The host's immune system becomes unable to recognize the polysialic acid capsule of the resistant N. meningitidis that mimics the mammalian cell surface. The biosynthetic pathways of sialic acid (i.e., N-acetylneuraminic acid [NANA]) in bacteria, however, are somewhat different from those in mammals. The largest obstacle facing previously identified inhibitors of NANA synthase (NANAS) in N. meningitidis is that these inhibitors feature undesired chemical and pharmacological characteristics. To better comprehend the binding mechanism underlying these inhibitors at the catalytic site of NANAS, we performed molecular modeling studies to uncover essential structural aspects for the ultimate recognition at the catalytic site required for optimal inhibitory activity. Applying two virtual screening candidate molecules and one designed molecule showed promising structural scaffolds. Here, we report ethyl 3-benzoyl-2,7-dimethyl indolizine-1-carboxylate (INLZ) as a novel molecule with high energetic fitness scores at the catalytic site of the NmeNANAS enzyme. INLZ represents a promising scaffold for NmeNANAS enzyme inhibitors, with new prospects for further structural development and activity optimization.

BackgroundCarpal instability is defined as a condition where wrist motion and/or loading creates mechanical dysfunction, resulting in weakness, pain and decreased function. When conventional methods do not identify the instability patterns, yet clinical signs of instability exist, the diagnosis of dynamic instability is often suggested to describe carpal derangement manifested only during the wrist's active motion or stress. We addressed the question: can advanced MRI techniques provide quantitative means to evaluate dynamic carpal instability and supplement standard static MRI acquisition? Our objectives were to (i) develop a real-time, three-dimensional MRI method to image the carpal joints during their active, uninterrupted motion; and (ii) demonstrate feasibility of the method for assessing metrics relevant to dynamic carpal instability, thus overcoming limitations of standard MRI.MethodsTwenty wrists (bilateral wrists of ten healthy participants) were scanned during radial-ulnar deviation and clenched-fist maneuvers. Images resulting from two real-time MRI pulse sequences, four sparse data-acquisition schemes, and three constrained image reconstruction techniques were compared. Image quality was assessed via blinded scoring by three radiologists and quantitative imaging metrics.ResultsReal-time MRI data-acquisition employing sparse radial sampling with a gradient-recalled-echo acquisition and constrained iterative reconstruction appeared to provide a practical tradeoff between imaging speed (temporal resolution up to 135 ms per slice) and image quality. The method effectively reduced streaking artifacts arising from data undersampling and enabled the derivation of quantitative measures pertinent to evaluating dynamic carpal instability.ConclusionThis study demonstrates that real-time, three-dimensional MRI of the moving wrist is feasible and may be useful for the evaluation of dynamic carpal instability.

PurposeTo determine the impact of imaging parameters on the temporal signal-to-noise ratio (TSNR) of quantitative cardiac magnetic resonance (MR) in humans, and to determine applicability of the physiological noise covariance (PNC) model for physiological noise (PN).MethodsWe conducted MRI experiments in four healthy volunteers, and obtained series of short-axis cardiac images acquired with snapshot balanced steady-state free precession (bSSFP) and snapshot gradient echo (GRE) using a broad range of spatial resolutions and parallel imaging acceleration factors commonly used in quantitative cardiac MR. We measured regional SNR and TSNR in these datasets and fit the measurements to the PNC model for PN, which assumes that PN scales with signal strength.ResultsThe relationship between SNR and TSNR in human cardiac MR without contrast preparation was well modeled by the PNC model. SNR consistently decreased as the spatial resolution (matrix size) and acceleration factor (R) increased for both GRE and bSSFP imaging. TSNR varied linearly with SNR using GRE imaging, when SNR was low (SNR < 20), and approached an asymptotic limit using bSSFP imaging, when SNR was high (SNR > 40).ConclusionsThe PNC model can be used to guide the choice of matrix size and acceleration factor to optimize TSNR in stable contrast cardiac MR, such as T2-prepared Blood-Oxygen-Level-Dependent (BOLD) and several variants of Arterial Spin Labeled (ASL) cardiac MR.

It is increasingly evident that cytokines and growth factors produced in the decidua play a pivotal role in the regulation of the local immune microenvironment and the establishment of pregnancy. One of the major growth factors produced in the decidua is vascular endothelial growth factor (VEGF), which acts not only on endothelial cells, but also on multiple other cell types, including macrophages. We sought to determine whether decidua-derived VEGF affects macrophage recruitment and polarization using human endometrial/decidual tissue samples, primary human endometrial stromal cells (ESCs), and the human monocyte cell line THP1. In situ hybridization was used for assessment of local VEGF expression and immunohistochemistry was used for identification and localization of CD68-positive endometrial macrophages. Macrophage migration in culture was assessed using a transwell migration assay, and the various M1/M2 phenotypic markers and VEGF expression were assessed using quantitative real-time PCR (qRT-PCR). We found dramatic increases in both VEGF levels and macrophage numbers in the decidua during early pregnancy compared to the secretory phase endometrium (non-pregnant), with a significant increase in M2 macrophage markers, suggesting that M2 is the predominant macrophage phenotype in the decidua. However, decidual samples from preeclamptic pregnancies showed a significant shift in macrophage phenotype markers, with upregulation of M1 and downregulation of M2 markers. In THP1 cultures, VEGF treatment significantly enhanced macrophage migration and induced M1 macrophages to shift to an M2 phenotype. Moreover, treatment with conditioned media from decidualized ESCs induced changes in macrophage migration and polarization similar to that of VEGF treatment. These effects were abrogated by the addition of a potent VEGF inhibitor. Together these results suggest that decidual VEGF plays a significant role in macrophage recruitment and M2 polarization, and that inhibition of VEGF signaling may contribute to the shift in macrophage polarity observed in different pregnancy disorders, including preeclampsia.

OBJECTIVES:To compare different anthropometric indices, Body composition analysis and lipid profile markers in terms of their ability to predict prediabetes (PD). METHODS:We enrolled 83 subjects with PD and 84 normoglycemic subjects who were matched for age and gender. The diagnosis of prediabetes was done according to the American Diabetes Association (ADA) criteria. All subjects were aged between 30-55 years of age and visited the outpatient department of tertiary care hospital. Anthropometric and lipid profile measurements were obtained. Analysis of body composition was done using Bodystat 1500MDD Instrument. Backward logistic regression was performed for detecting the predictors of PD. A receiver operator characteristic curve (ROC) with area under curve (AUC) was utilized for the accuracy of the predictors of PD. RESULTS:Comparison of anthropometric measurement and body composition analysis parameters between the two groups showed that Waist circumference (WC), Body mass index, Body Fat% were significantly higher whereas Extracellular water and Dry lean weight in percentage (ECW% and DLW%) were found to be lower in PD (p< 0.05). Higher triglyceride (TG) levels and lower high-density cholesterol (HDL-C) with high TG/HDL-C were seen in subjects with PD. Backward logistic regression analysis found the combination of Body Fat % with WC, TG, ECW% and DLW% as strong predictors of PD. In ROC analysis, ECW% (AUC = 0.703) was the most predictive measure, followed by WC (AUC = 0.702). CONCLUSION:This study demonstrated that estimation of Body Fat % combined with waist circumference, Extracellular water and Dry lean weight in percentage are valuable in screening and diagnosis of prediabetes. Plasma levels of TG in lipid profile measurements can also serve as an additional marker for prediction of prediabetes.

Synapse associated protein of 97KDa (SAP97) belongs to a family of scaffolding proteins, the membrane-associated guanylate kinases (MAGUKs), that are highly enriched in the postsynaptic density of synapses and play an important role in organizing protein complexes necessary for synaptic development and plasticity. The Dlg-MAGUK family of proteins are structurally very similar, and an effort has been made to parse apart the unique function of each Dlg-MAGUK protein by characterization of knockout mice. Knockout mice have been generated and characterized for PSD-95, PSD-93, and SAP102, however SAP97 knockout mice have been impossible to study because the SAP97 null mice die soon after birth due to a craniofacial defect. We studied the transcriptomic and behavioral consequences of a brain-specific conditional knockout of SAP97 (SAP97-cKO). RNA sequencing from hippocampi from control and SAP97-cKO male animals identified 67 SAP97 regulated transcripts. As large-scale genetic studies have implicated MAGUKs in neuropsychiatric disorders such as intellectual disability, autism spectrum disorders, and schizophrenia (SCZ), we analyzed our differentially expressed gene (DEG) set for enrichment of disease risk-associated genes, and found our DEG set to be specifically enriched for SCZ-related genes. Subjecting SAP97-cKO mice to a battery of behavioral tests revealed a subtle male-specific cognitive deficit and female-specific motor deficit, while other behaviors were largely unaffected. These data suggest that loss of SAP97 may have a modest contribution to organismal behavior. The SAP97-cKO mouse serves as a stepping stone for understanding the unique role of SAP97 in biology.

[This corrects the article DOI: 10.1371/journal.pone.0151482.].

[This corrects the article DOI: 10.1371/journal.pone.0199665.].

Radioresistance is one of the main determinants of treatment outcome in oral squamous cell carcinoma (OSCC), but its prediction is difficult. Several authors aimed to establish radioresistant OSCC cell lines to identify genes with altered expression in response to radioresistance. The development of OSCC is a multistep carcinogenic process that includes activation of several oncogenes and inactivation of tumour suppressor genes. TGM-3 is a tumour suppressor gene and contributes to carcinogenesis process. The aim of this study was to estimate serum and tissue expression of TGM-3 and its correlation with clinico-pathological factors and overall survival in patients of OSCC undergoing chemo-radiotherapy. Tissue expression was observed in formalin fixed tissue biopsies of 96 cases of OSCC and 32 healthy controls were subjected to immunohistochemistry (IHC) by using antibody against TGM-3 and serum level was estimated by ELISA method. mRNA expression was determined by using Real-Time PCR. Patients were followed for 2 year for chemo radiotherapy response. In OSCC, 76.70% cases and in controls 90.62% were positive for TGM-3 IHC expression. TGM-3 expression was cytoplasmic and nuclear staining expressed in keratinized layer, stratum granulosum and stratum spinosum in controls and tumour cells. Mean serum TGM-3 in pre chemo-radiotherapy OSCC cases were 1304.83±573.55, post chemo-radiotherapy samples were 1530.64±669.33 and controls were 1869.16±1377.36, but difference was significant in pre chemo-radiotherapy samples as compared to controls (p

The contribution of the tumor microenvironment to the development of pancreatic adenocarcinoma (PDAC) is unclear. The LSL-KrasG12D/+;LSL-p53R172H/+;Pdx-1-Cre (KPC) tumor model, which is widely utilized to faithfully recapitulate human pancreatic cancer, depends on Cre-mediated recombination in the epithelial lineage to drive tumorigenesis. Therefore, specific Cre-loxP recombination in stromal cells cannot be applied in this model, limiting the in vivo investigation of stromal genetics in tumor initiation and progression. To address this issue, we generated a new Pdx1FlpO knock-in mouse line, which represents the first mouse model to physiologically express FlpO recombinase in pancreatic epithelial cells. This mouse specifically recombines Frt loci in pancreatic epithelial cells, including acinar, ductal, and islet cells. When combined with the Frt-STOP-Frt KrasG12D and p53Frt mouse lines, simultaneous Pdx1FlpO activation of mutant Kras and deletion of p53 results in the spectrum of pathologic changes seen in PDAC, including PanIN lesions and ductal carcinoma. Combination of this KPF mouse model with any stroma-specific Cre can be used to conditionally modify target genes of interest. This will provide an excellent in vivo tool to study the roles of genes in different cell types and multiple cell compartments within the pancreatic tumor microenvironment.

Cooling towers (CTs) are a leading source of outbreaks of Legionnaires' disease (LD), a severe form of pneumonia caused by inhalation of aerosols containing Legionella bacteria. Accordingly, proper maintenance of CTs is vital for the prevention of LD. The aim of this study was to determine the distribution of Legionella in a subset of regionally diverse US CTs and characterize the associated microbial communities. Between July and September of 2016, we obtained aliquots from water samples collected for routine Legionella testing from 196 CTs located in eight of the nine continental US climate regions. After screening for Legionella by PCR, positive samples were cultured and the resulting Legionella isolates were further characterized. Overall, 84% (164) were PCR-positive, including samples from every region studied. Of the PCR-positive samples, Legionella spp were isolated from 47% (78), L. pneumophila was isolated from 32% (53), and L. pneumophila serogroup 1 (Lp1) was isolated from 24% (40). Overall, 144 unique Legionella isolates were identified; 53% (76) of these were Legionella pneumophila. Of the 76 L. pneumophila isolates, 51% (39) were Lp1. Legionella were isolated from CTs in seven of the eight US regions examined. 16S rRNA amplicon sequencing was used to compare the bacterial communities of CT waters with and without detectable Legionella as well as the microbiomes of waters from different climate regions. Interestingly, the microbial communities were homogenous across climate regions. When a subset of seven CTs sampled in April and July were compared, there was no association with changes in corresponding CT microbiomes over time in the samples that became culture-positive for Legionella. Legionella species and Lp1 were detected frequently among the samples examined in this first large-scale study of Legionella in US CTs. Our findings highlight that, under the right conditions, there is the potential for CT-related LD outbreaks to occur throughout the US.

A mapping population of recombinant inbred lines (RILs) derived from TMV 2 and its mutant, TMV 2-NLM was employed for mapping important taxonomic and productivity traits using genic and non-genic transposable element markers in peanut. Single nucleotide polymorphism and copy number variation using RAD-Sequencing data indicated very limited polymorphism between TMV 2 and TMV 2-NLM. But phenotypically they differed significantly for many taxonomic and productivity traits. Also, the RIL population showed significant variation for a few additional agronomic traits. A genetic linkage map of 1,205.66 cM was constructed using 91 genic and non-genic Arachis hypogaea transposable element (AhTE) markers. Using single marker analysis and QTL analysis, the markers with high phenotypic variance explained (PVE) were identified for branching pattern (32.3%), number of primary and secondary branches (19.9% and 28.4%, respectively), protein content (26.4%), days to 50% flowering (22.0%), content of oleic acid (15.1%), test weight (13.6%) and pod width (12.0%). Three genic markers (AhTE0357, AhTE0391, AhTE0025) with Arachis hypogaea miniature inverted-repeat transposable element (AhMITE1) activity in the genes Araip.TG1BL (B02 chromosome), Aradu.7N61X (A09 chromosome) and Aradu.7065G (A07 chromosome), respectively showed strong linkage with these taxonomic, productivity and quality traits. Since TMV 2 and TMV 2-NLM differed subtly at DNA level, the background noise in detecting the marker-trait associations was minimum; therefore, the markers identified in this study for the taxonomic and productivity traits may be significant and useful in peanut molecular breeding.

[This corrects the article DOI: 10.1371/journal.pone.0096758.].

HPV is the major causative agent for cervical cancer. Study on the risk of cervical cancer associated with different hr-HPV genotypes would be useful for disease management and new vaccine strategy. With limited reports available, the present study aimed to investigate the pattern of HPV genotypes coinfections and risk of cervical carcinoma associated with them in Indian population. 15 HPV genotypes were detected by E6/E7 multiplex nested type-specific PCR in the HPV-positive cervical samples of 172 cervical cancer cases and 174 subjects with normal cytology. Association between the genotypes and cervical cancer was estimated by calculating the Odds ratio and 95% confidence interval. Risk of cervical carcinoma was associated with multiple genotypes excluding HPV16 (OR:5.87; 95% CI-1.28-26-29; p = .02), multiple genotypes excluding HPV18 (OR = 2.5; 95% CI = 1.09-6.05; p = .03), multiple genotypes of α9 species(OR = 5.3 95% CI = 1.14-24.03; p = .007), and multiple genotypes of α7 species (OR = 2.5; 95% CI = .49-13.45; p = .2). Genotypes not targeted by quadrivalent vaccine types (OR = 2.94 95% CI = 1.48-5.80; p = .001) conferred 2.94 fold higher risk of cervical carcinoma. Cases those coinfected with phylogenetically related genotypes (OR = 2.29; 95% CI(.69-7.59) p = .17) were at 2.9 fold higher risk of invasive cervical carcinoma than those infected with other genotypes although it is not statistically significant. Whereas phylogenetically unrelated genotypes coinfection is negatively associated with cervical carcinoma (OR = .44 95% CI (.244-.8) p = .007) and it is statistically significant.Genotypes not targeted by 9-valent vaccines (OR = .40; 95% CI = .19-.85; p = .017) associated with lesser risk of cervical carcinoma as compared to other genotypes. Subjects infected with any HPV genotype/genotypes excluding HPV16 in association with HPV 18 (OR = 4.1; 95% CI = 1.81-9.25 P = < .001) were at 4.1 fold higher risk of developing invasive cervical carcinoma.In conclusion, the risk of development of cervical cancer is genotype specific and might be associated with type-specific interactions between the genotypes in multiple infections.

A hallmark of the immune response to influenza is repeated encounters with proteins containing both genetically conserved and variable components. Therefore, the B and T cell repertoire is continually being remodeled, with competition between memory and naïve lymphocytes. Our previous work using a mouse model of secondary heterosubtypic influenza infection has shown that this competition results in a focusing of CD4 T cell response specificity towards internal virion proteins with a selective decrease in CD4 T cell reactivity to the novel HA epitopes. Strikingly, this shift in CD4 T cell specificity was associated with a diminished anti-HA antibody response. Here, we sought to determine whether the loss in HA-specific reactivity that occurs as a consequence of immunological memory could be reversed by selectively priming HA-specific CD4 T cells prior to secondary infection. Using a peptide-based priming strategy, we found that selective expansion of the anti-HA CD4 T cell memory repertoire enhanced HA-specific antibody production upon heterosubtypic infection. These results suggest that the potentially deleterious consequences of repeated exposure to conserved influenza internal virion proteins could be reversed by vaccination strategies that selectively arm the HA-specific CD4 T cell compartment. This could be a potentially useful pre-pandemic vaccination strategy to promote accelerated neutralizing antibody production on challenge with a pandemic influenza strain that contains few conserved HA epitopes.

Rice-rice system and rice fallows are no longer productive in Southeast Asia. Crop and varietal diversification of the rice based cropping systems may improve the productivity and profitability of the systems. Diversification is also a viable option to mitigate the risk of climate change. In Eastern India, farmers cultivate rice during rainy season (June-September) and land leftovers fallow after rice harvest in the post-rainy season (November-May) due to lack of sufficient rainfall or irrigation amenities. However, in lowland areas, sufficient residual soil moistures are available in rice fallow in the post-rainy season (November-March), which can be utilized for raising second crops in the region. Implementation of suitable crop/varietal diversification is thus very much vital to achieve this objective. To assess the yield performance of rice varieties under timely and late sown conditions and to evaluate the performance of dry season crops following them, three different duration rice cultivars were transplanted in July and August. In dry season several non-rice crops were sown in rice fallow to constitute a cropping system. The results revealed that tiller occurrence, biomass accumulation, dry matter remobilization, crop growth rate, and ultimately yield were significantly decreased under late transplanting. On an average, around 30% yield reduction obtained under late sowing may be due to low temperature stress and high rainfall at reproductive stages of the crop. Dry season crops following short duration rice cultivars performed better in terms of grain yield. In the dry season, toria was profitable when sown earlier and if sowing was delayed greengram was suitable. Highest system productivity and profitability under timely sown rice may be due to higher dry matter remobilization from source to sink. A significant correlation was observed between biomass production and grain yield. We infer that late transplanting decrease the tiller occurrence and assimilate remobilization efficiency, which may be responsible for the reduced grain yield.

OBJECTIVE:To develop and evaluate a framework for simulating low-field proton-density weighted MRI acquisitions based on high-field acquisitions, which could be used to predict the minimum B0 field strength requirements for MRI techniques. This framework would be particularly useful in the evaluation of de-noising and constrained reconstruction techniques. MATERIALS AND METHODS:Given MRI raw data, lower field MRI acquisitions can be simulated based on the signal and noise scaling with field strength. Certain assumptions are imposed for the simulation and their validity is discussed. A validation experiment was performed using a standard resolution phantom imaged at 0.35 T, 1.5 T, 3 T, and 7 T. This framework was then applied to two sample proton-density weighted MRI applications that demonstrated estimation of minimum field strength requirements: real-time upper airway imaging and liver proton-density fat fraction measurement. RESULTS:The phantom experiment showed good agreement between simulated and measured images. The SNR difference between simulated and measured was ≤ 8% for the 1.5T, 3T, and 7T cases which utilized scanners with the same geometry and from the same vendor. The measured SNR at 0.35T was 1.8- to 2.5-fold less than predicted likely due to unaccounted differences in the RF receive chain. The predicted minimum field strength requirements for the two sample applications were 0.2 T and 0.3 T, respectively. CONCLUSIONS:Under certain assumptions, low-field MRI acquisitions can be simulated from high-field MRI data. This enables prediction of the minimum field strength requirements for a broad range of MRI techniques.

Association of Mycobacterium avium subspecies paratuberculosis (MAP) and Crohn's disease (CD) has been controversial due to contradictory reports. Therefore, we determined the prevalence of MAP in patients with CD and intestinal tuberculosis (ITB) and its association with clinical course.Blood and intestinal biopsies were taken from 69 CD, 32 ITB patients and 41 patients with haemorrhoidal bleed who served as controls. qPCR targeting of MAP-specific IS900 gene was used to detect the presence of MAP DNA. qPCR results were further validated by sequencing. Immunohistochemistry (IHC) was used to detect the presence of MAP antigen in biopsy specimens. CD and ITB patients were followed-up for disease course and response to therapy.The frequency of MAP-specific DNA in biopsies by qPCR was significantly higher in CD patients (23.2%, p = 0.03) as compared to controls (7.3%). No significant difference in intestinal MAP presence was observed between ITB patients (12.5%, p = 0.6) and controls (7.3%). MAP presence in blood of CD patients was 10.1% as compared to 4.9% in controls while no patients with ITB were found to be positive (p = 0.1). Using IHC for detection of MAP antigen, the prevalence of MAP in CD was 2.9%, 12.5% in ITB patients and 2.4% in controls. However, long-term follow-up of the patients revealed no significant associations between clinical characteristics and treatment outcomes with MAP positivity.We report significantly high prevalence of MAP in intestinal biopsies of CD patients. However, the presence of MAP does not affect the disease course and treatment outcomes in either CD or ITB patients.

Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright's F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.

Allometric relationships among morphological traits underlie important patterns in ecology. These relationships are often phylogenetically shared; thus quantifying allometric relationships may allow for estimating difficult-to-measure traits across species. One such trait, proboscis length in bees, is assumed to be important in structuring bee communities and plant-pollinator networks. However, it is difficult to measure and thus rarely included in ecological analyses. We measured intertegular distance (as a measure of body size) and proboscis length (glossa and prementum, both individually and combined) of 786 individual bees of 100 species across 5 of the 7 extant bee families (Hymenoptera: Apoidea: Anthophila). Using linear models and model selection, we determined which parameters provided the best estimate of proboscis length. We then used coefficients to estimate the relationship between intertegular distance and proboscis length, while also considering family. Using allometric equations with an estimation for a scaling coefficient between intertegular distance and proboscis length and coefficients for each family, we explain 91% of the variance in species-level means for bee proboscis length among bee species. However, within species, individual-level intertegular distance was a poor predictor of individual proboscis length. To make our findings easy to use, we created an R package that allows estimation of proboscis length for individual bee species by inputting only family and intertegular distance. The R package also calculates foraging distance and body mass based on previously published equations. Thus by considering both taxonomy and intertegular distance we enable accurate estimation of an ecologically and evolutionarily important trait.