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IMPORTANCE: The prevalence, pathophysiology, and long-term outcomes of COVID-19 (post-acute sequelae of SARS-CoV-2 [PASC] or Long COVID) in children and young adults remain unknown. Studies must address the urgent need to define PASC, its mechanisms, and potential treatment targets in children and young adults. OBSERVATIONS: We describe the protocol for the Pediatric Observational Cohort Study of the NIHs REsearching COVID to Enhance Recovery (RECOVER) Initiative. RECOVER-Pediatrics is an observational meta-cohort study of caregiver-child pairs (birth through 17 years) and young adults (18 through 25 years), recruited from more than 100 sites across the US. This report focuses on two of four cohorts that comprise RECOVER-Pediatrics: 1) a de novo RECOVER prospective cohort of children and young adults with and without previous or current infection; and 2) an extant cohort derived from the Adolescent Brain Cognitive Development (ABCD) study (n = 10,000). The de novo cohort incorporates three tiers of data collection: 1) remote baseline assessments (Tier 1, n = 6000); 2) longitudinal follow-up for up to 4 years (Tier 2, n = 6000); and 3) a subset of participants, primarily the most severely affected by PASC, who will undergo deep phenotyping to explore PASC pathophysiology (Tier 3, n = 600). Youth enrolled in the ABCD study participate in Tier 1. The pediatric protocol was developed as a collaborative partnership of investigators, patients, researchers, clinicians, community partners, and federal partners, intentionally promoting inclusivity and diversity. The protocol is adaptive to facilitate responses to emerging science. CONCLUSIONS AND RELEVANCE: RECOVER-Pediatrics seeks to characterize the clinical course, underlying mechanisms, and long-term effects of PASC from birth through 25 years old. RECOVER-Pediatrics is designed to elucidate the epidemiology, four-year clinical course, and sociodemographic correlates of pediatric PASC. The data and biosamples will allow examination of mechanistic hypotheses and biomarkers, thus providing insights into potential therapeutic interventions. CLINICAL TRIALS.GOV IDENTIFIER: Clinical Trial Registration: http://www.clinicaltrials.gov. Unique identifier: NCT05172011.

β2-glycoprotein I (β2-Gp1) is a cardiolipin-binding plasma glycoprotein. It is evolutionarily conserved from invertebrates, and cardiolipin-bound β2-Gp1 is a major target of antiphospholipid antibodies seen in autoimmune disorders. Cardiolipin is almost exclusively present in mitochondria, and mitochondria are present in circulating blood. We show that β2-Gp1 binds to cell-free mitochondria (CFM) in the circulation and promotes its phagocytosis by macrophages at physiological plasma concentrations. Exogenous CFM had a short circulation time of less than 10 minutes in mice. Following infusion of CFM, β2-Gp1-deficient mice had significantly higher levels of transfused mitochondria at 5 minutes (9.9 ± 6.4 pg/ml versus 4.0 ± 2.3 pg/ml in wildtype, p = 0.01) and at 10 minutes (3.0 ± 3.6 pg/ml versus 1.0 ± 0.06 pg/ml in wild-type, p = 0.033, n = 10). In addition, the splenic macrophages had less phagocytosed CFM in β2-Gp1-deficient mice (24.4 ± 2.72% versus 35.6 ± 3.5 in wild-type, p = 0.001, n = 5). A patient with abnormal β2-Gp1, unable to bind cardiolipin, has increased CFM in blood (5.09 pg/ml versus 1.26 ± 1.35 in normal) and his plasma induced less phagocytosis of CFM by macrophages (47.3 ± 1.6% versus 54.3 ± 1.3, p = 0.01) compared to normal plasma. These results show the evolutionarily conserved β2-Gp1 is one of the mediators of the clearance of CFM in circulation.

Cardiopulmonary and renal end organ (CPR) complications are associated with early mortality among individuals with sickle cell disease (SCD). However, there is limited knowledge regarding acute care utilization for individuals with SCD and CPR complications. Our objective was to determine the prevalence of CPR complications in a state specific SCD population and compare acute care utilization among individuals with and without CPR complications. We leveraged 2017-2020 data for individuals with SCD identified by the Sickle Cell Data Collection program in Wisconsin. The prevalence of CPR complications is determined for distinct age groups. Generalized linear models adjusted for age compared the rate of acute care visits/person/year among individuals who had cardiopulmonary only, renal only, both cardiopulmonary and renal, or no CPR complications. There were 1378 individuals with SCD, 52% females, mean (SD) age 28.3 (18.5) years; 48% had at least one CPR complication during the study period. The prevalence of CPR complications was higher in adults (69%) compared to pediatric (15%) and transition (51%) groups. Individuals with SCD and cardiopulmonary complications had higher acute visit rates than those without CPR complications (5.4 (IQR 5.0-5.8) vs 2.4 (IQR 2.1-2.5), p

ObjectivesTo propose a novel framework for COVID-19 vaccine allocation based on three components of Vulnerability, Vaccination, and Values (3Vs).MethodsA combination of geospatial data analysis and artificial intelligence methods for evaluating vulnerability factors at the local level and allocate vaccines according to a dynamic mechanism for updating vulnerability and vaccine uptake.ResultsA novel approach is introduced including (I) Vulnerability data collection (including country-specific data on demographic, socioeconomic, epidemiological, healthcare, and environmental factors), (II) Vaccination prioritization through estimation of a unique Vulnerability Index composed of a range of factors selected and weighed through an Artificial Intelligence (AI-enabled) expert elicitation survey and scientific literature screening, and (III) Values consideration by identification of the most effective GIS-assisted allocation of vaccines at the local level, considering context-specific constraints and objectives.ConclusionsWe showcase the performance of the 3Vs strategy by comparing it to the actual vaccination rollout in Kenya. We show that under the current strategy, socially vulnerable individuals comprise only 45% of all vaccinated people in Kenya while if the 3Vs strategy was implemented, this group would be the first to receive vaccines.

BackgroundParticipation in bowel cancer screening programs remains poor in many countries. Knowledge of geographical variation in participation rates may help design targeted interventions to improve uptake. This study describes small-area and broad geographical patterns in bowel screening participation in Australia between 2015-2020.MethodsPublicly available population-level participation data for Australia's National Bowel Cancer Screening Program (NBCSP) were modelled using generalized linear models to quantify screening patterns by remoteness and area-level disadvantage. Bayesian spatial models were used to obtain smoothed estimates of participation across 2,247 small areas during 2019-2020 compared to the national average, and during 2015-2016 and 2017-2018 for comparison. Spatial heterogeneity was assessed using the maximized excess events test.ResultsOverall, screening participation rates was around 44% over the three time-periods. Participation was consistently lower in remote or disadvantaged areas, although heterogeneity was evident within these broad categories. There was strong evidence of spatial differences in participation over all three periods, with little change in patterns between time periods. If the spatial variation was reduced (so low participation areas were increased to the 80th centile), an extra 250,000 screens (4% of total) would have been conducted during 2019-2020.ConclusionsDespite having a well-structured evidence-based government funded national bowel cancer screening program, the substantial spatial variation in participation rates highlights the importance of accounting for the unique characteristics of specific geographical regions and their inhabitants. Identifying the reasons for geographical disparities could inform interventions to achieve more equitable access and a higher overall bowel screening uptake.

One of the biggest challenges to be addressed in world agriculture is low nitrogen (N) use efficiency (

BackgroundThe mental wellbeing implications of a prostate cancer diagnosis are increasingly being realised. Significant mental health symptoms such as depression and anxiety, along with related constructs such as fear of cancer recurrence, body image and masculine self-esteem issues are prevalent. However, less is understood about potential prognostic factors for these outcomes in prostate cancer patients. Therefore, this study aims to primarily explore potential treatment, patient and oncological factors associated with mental wellbeing outcomes in the initial prostate cancer follow-up period.MethodsMIND-P is a multi-institutional prospective cohort study recruiting newly diagnosed prostate cancer patients for 12-month follow up. It will aim to recruit a final sample of 300 participants undergoing one of four treatment options: active surveillance, radical prostatectomy, radical radiotherapy, or hormone monotherapy. Questionnaire-based data collection consists of multiple validated mental, physical, and social wellbeing outcomes at baseline and 3-monthly intervals until study completion. Primary analysis will include evaluation of treatment undergone against multiple mental wellbeing outcomes. Secondary analysis will additionally explore multiple patient and oncological prognostic factors of potential importance, along with the cumulative incidence of these outcomes, symptom trajectory and their association with subsequent functional and social outcomes.ConclusionThis cohort study aims to add to the existing limited literature evaluating significant prognostic factors for multiple mental wellbeing outcomes in newly diagnosed prostate cancer patients. This may be of potential use for guiding future prognosis research and of clinical use for identifying individuals potentially requiring additional surveillance or support during routine cancer follow up.Study registrationThis study was prospectively registered on ClinicalTrials.gov (NCT04647474).

BackgroundHealthy NYC is an innovative survey panel created by the New York City (NYC) Department of Health and Mental Hygiene (DOHMH) that offers a cost-effective mechanism for collecting priority and timely health information. Between November 2020 and June 2021, invitations for six different surveys were sent to Healthy NYC panelists by postal mail, email, and text messages. Panelists had the option to complete surveys online or via paper survey.MethodsWe analyzed whether panelists varied by sociodemographic characteristics based on the contact mode they provided and the type of invitation that led to their response using logistic regression models. Poisson regression models were used to determine whether the number of invitations received before participating in a survey was associated with sociodemographic characteristics.ResultsYounger age and higher education were positively associated with providing an email or text contact. Furthermore, age, race, and income were significant predictors for invitation modes that led to a survey response. Black panelists had 72% greater odds (OR 1.72 95% CI: 1.11-2.68) of responding to a mail invite and 33% lesser odds (OR 0.67, 95% CI: 0.54-0.83) of responding to an email invite compared with White panelists. Additionally, in five of the six surveys, more than half of the respondents completed surveys after two invites. Email invitations garnered the highest participation rates.ConclusionsWe recommend using targeted invitation modes as an additional strategy to improve participation in panels. For lower-income panelists who do not provide an email address, it may be reasonable to offer additional response options that do not require internet access. Our study's findings provide insight into how panels can tailor outreach to panelists, especially among underrepresented groups, in the most economical and efficient ways.

BackgroundDespite ongoing recommendations to increase male engagement and gender-equity (GE) counseling in family planning (FP) services, few such programs have been implemented and rigorously evaluated. This study evaluates the impact of CHARM, a three-session GE+FP counseling intervention delivered by male health care providers to married men, alone (sessions 1&2) and with their wives (session 3) in India.Methods and findingsA two-armed cluster randomized controlled trial was conducted with young married couples (N = 1081 couples) recruited from 50 geographic clusters (25 clusters randomized to CHARM and a control condition, respectively) in rural Maharashtra, India. Couples were surveyed on demographics, contraceptive behaviors, and intimate partner violence (IPV) attitudes and behaviors at baseline and 9 &18-month follow-ups, with pregnancy testing at baseline and 18-month follow-up. Outcome effects on contraceptive use and incident pregnancy, and secondarily, on contraceptive communication and men's IPV attitudes and behaviors, were assessed using logistic generalized linear mixed models. Most men recruited from CHARM communities (91.3%) received at least one CHARM intervention session; 52.5% received the couple's session with their wife. Findings document that women from the CHARM condition, relative to controls, were more likely to report contraceptive communication at 9-month follow-up (AOR = 1.77, p = 0.04) and modern contraceptive use at 9 and 18-month follow-ups (AORs = 1.57-1.58, p = 0.05), and they were less likely to report sexual IPV at 18-month follow-up (AOR = 0.48, p = 0.01). Men in the CHARM condition were less likely than those in the control clusters to report attitudes accepting of sexual IPV at 9-month (AOR = 0.64, p = 0.03) and 18-month (AOR = 0.51, p = 0.004) follow-up, and attitudes accepting of physical IPV at 18-month follow-up (AOR = 0.64, p = 0.02). No significant effect on pregnancy was seen.ConclusionsFindings demonstrate that men can be engaged in FP programming in rural India, and that such an approach inclusive of GE counseling can improve contraceptive practices and reduce sexual IPV in married couples.Trial registrationClinicalTrials.gov NCT01593943.

Fetal nicotine exposure increased risk of developing cardiovascular disease later in life. The present study tested the hypothesis that perinatal nicotine-induced programming of heart ischemia-sensitive phenotype is mediated by enhanced reactive oxygen species (ROS) in offspring. Nicotine was administered to pregnant rats via subcutaneous osmotic minipumps from day 4 of gestation to day 10 after birth, in the absence or presence of a ROS inhibitor, N-acetyl-cysteine (NAC) in drinking water. Experiments were conducted in 8 month old age male offspring. Isolated hearts were perfused in a Langendorff preparation. Perinatal nicotine treatment significantly increased ischemia and reperfusion-induced left ventricular injury, and decreased post-ischemic recovery of left ventricular function and coronary flow rate. In addition, nicotine enhanced cardiac ROS production and significantly attenuated protein kinase Cε (PKCε) protein abundance in the heart. Although nicotine had no effect on total cardiac glycogen synthase kinase-3β (GSK3β) protein expression, it significantly increased the phosphorylation of GSK3β at serine 9 residue in the heart. NAC inhibited nicotine-mediated increase in ROS production, recovered PKCε gene expression and abrogated increased phosphorylation of GSK3β. Of importance, NAC blocked perinatal nicotine-induced increase in ischemia and reperfusion injury in the heart. These findings provide novel evidence that increased oxidative stress plays a causal role in perinatal nicotine-induced developmental programming of ischemic sensitive phenotype in the heart, and suggest potential therapeutic targets of anti-oxidative stress in the treatment of ischemic heart disease.

IntroductionQuality of life in prostate cancer survivorship is becoming increasingly important, with mental and social wellbeing recognised as key components. However, limited global evaluation of psychosocial challenges experienced after treatment exists. Therefore, we aimed to explore the lived experiences of men who underwent radical treatment, and its psychosocial impact.Material and methodsThis qualitative study was conducted using 19 men who had undergone radical treatment (prostatectomy or radiotherapy) for their cancer. Semi-structured interviews were conducted exploring lived experiences of men after treatment. A Structured thematic analysis of collected data was undertaken, with an inductive co-construction of themes through the lens of the biopsychosocial model. Themes generated were considered within a psychological, social, and physical wellbeing framework.ResultsAn initial knowledge gap meant mental wellbeing was strongly impacted initially leading to a 'Diagnostic Blow and the Search for Clarity'. Doubt over individuals' future resulted in 'An Uncertain Future' in many men. Once treatment was completed a 'Reflective journey' began, with men considering their outcomes and decisions made. Social wellbeing was also impacted with many identifying the 'Emotional Repercussions' on their relationships and the impact their diagnosis had on their partner and family. Many subsequently sought to increase their support through 'The Social Network and Advocacy', while physical changes led to an increased need for 'Social Planning'. Finally, physical wellbeing was highlighted by a continual acknowledgement of the 'Natural process of ageing' leading to a reluctancy to seek help, whilst simultaneously attempting to improve existing health via 'The Health Kick'.ConclusionsRadical treatments have a considerable impact on mental and social wellbeing of individuals. Anxiety after diagnosis and significant uncertainty over individual futures exist, with physical complications of treatment leading to social repercussions. Future research should aim to identify forms of support to improve quality of life of these men.

ObjectivesHypoglycemia unawareness (HUA) in patients with FCPD is common with an unclear etiology. We evaluated the prevalence, characteristics of HUA, glycemic variability (GV), its possible association with pancreatic glucagon secretion & cardiac autonomic function in patients with FCPD.MethodsA two-week ambulatory glucose profile (AGP) and cardiac autonomic function test was done in patients with FCPD (n = 60), and categorized into UNAWARE (n = 44) and AWARE (n = 16) groups based on the Hypoglycemia Unawareness Index (HUI) score. Glycaemic variability was assessed from the AGP data using Easy GV 9.0.2 software. A subset of patients from both the groups (n = 11) underwent a mixed-meal challenge test and were compared with healthy individuals (controls; n = 11).ResultsHUA was evidenced in 73% (44/60) of patients with FCPD. Significant hypoglycemia, nocturnal hypoglycemia, duration of hypoglycemia and poor cardiac autonomic functions (p = 0.01) were prominent in the UNAWARE group. The overall GV was greater in the UNAWARE group. In the UNAWARE group, significantly reduced fasting and post prandial glucagon levels negatively correlated with HUI (r = -0.74, p < 0.05) and GV-hypoglycemia indices (p < 0.05) In contrast, significantly higher post prandial glucagon levels in the AWARE group positively correlated with post prandial hyperglycemia (r = 0.61, p < 0.05).ConclusionHeterogeneity in patterns of glucagon secretion were significantly associated with HUA and GV. Reduced glucagon levels contribute to greater risks of HUA, nocturnal hypoglycemia and greater GV, while hyperglucagonemia predisposes to postprandial hyperglycemia and hypoglycemia awareness in patients with FCPD.

BackgroundChemical and physical restraints are associated with harm in older adults, but our understanding of their use during acute care hospitalizations is limited.ObjectivesTo (1) describe restraint use during acute care hospitalizations of older adults at the onset of the COVID-19 pandemic compared to pre-pandemic levels and (2) describe between-hospital variability in restraint use.DesignRetrospective cohort study with a time series analysis.ParticipantsAcute care hospital inpatients, aged 65 years or older, who were discharged from one of four Alberta hospitals or six Ontario hospitals in Canada, between November 1, 2019, and June 30, 2020.Main measuresWe used autoregressive linear models with restricted cubic splines to compare proportions of chemical restraint (that is, psychotropic medications, namely antipsychotics, benzodiazepines, and trazodone) and physical restraint (e.g., mittens) use immediately after the onset of the COVID-19 pandemic with pre-pandemic levels. We describe between-hospital variability in restraint use using intraclass correlation coefficients (ICC) and median odds ratios (OR).Key resultsWe included 71,004 hospitalizations. Adjusted for the prevalence of dementia and psychotic disorders, chemical restraint use increased in Ontario hospitals from a pre-pandemic average of 27.1% to 30.8% (pConclusionsThe COVID-19 pandemic impacted in-hospital use of chemical and physical restraints among older adults in Ontario but not Alberta. Substantial differences in chemical and physical restraint use by region and hospital suggests there are opportunities to improve best practices in geriatric care. Future research must support implementation of evidence-informed interventions that standardize appropriate restraint use.

BackgroundWhile Aboriginal and Torres Strait Islander peoples have poorer cancer survival than other Australians, absolute measures of survival disparities are lacking. This study quantified crude probabilities of deaths from cancer and other causes and estimated the number of avoidable deaths for Aboriginal and Torres Strait Islanders if these survival disparities were removed.MethodsFlexible parametric relative survival models were used to estimate reported measures for a population-based cohort of 709,239 Australians (12,830 Aboriginal and Torres Strait Islander peoples), 2005-2016.ResultsAmong Aboriginal and Torres Strait Islander peoples, the 5-year crude probability of cancer death was 0.44, while it was 0.07 for other causes of death. These probabilities were 0.07 and 0.03 higher than among other Australians, respectively. Magnitude of these disparities varied by cancer type and ranged for cancer deaths from ConclusionsStudy findings suggest the need to reduce the prevalence of risk factors prevalence, increase screening participation, and improve early detection, diagnosis and treatment rates to achieve more equitable outcomes for a range of cancer types. Reported measures provide unique insights into the impact of a cancer diagnosis among Aboriginal and Torres Strait Islander peoples from a different perspective to standard relative survival measures.

Previous studies have reported that perinatal nicotine exposure causes development of hypertensive phenotype in adult offspring.The present study was to determine whether perinatal nicotine exposure causes an epigenetic programming of vascular Angiotensin II receptors (ATRs) and their-mediated signaling pathway leading to heightened vascular contraction in adult offspring.Nicotine was administered to pregnant rats via subcutaneous osmotic minipumps from day 4 of gestation to day 10 after birth. The experiments were conducted at 5 months of age of male offspring.Nicotine treatment enhanced Angitension II (Ang II)-induced vasoconstriction and 20-kDa myosin light chain phosphorylation (MLC20-P) levels. In addition, the ratio of Ang II-induced tension/MLC-P was also significantly increased in nicotine-treated group compared with the saline group. Nicotine-mediated enhanced constrictions were not directly dependent on the changes of [Ca2+]i concentrations but dependent on Ca2+ sensitivity. Perinatal nicotine treatment significantly enhanced vascular ATR type 1a (AT1aR) but not AT1bR mRNA levels in adult rat offspring, which was associated with selective decreases in DNA methylation at AT1aR promoter. Contrast to the effect on AT1aR, nicotine decreased the mRNA levels of vascular AT2R gene, which was associated with selective increases in DNA methylation at AT2R promoter.Our results indicated that perinatal nicotine exposure caused an epigenetic programming of vascular ATRs and their-mediated signaling pathways, and suggested that differential regulation of AT1R/AT2R gene expression through DNA methylation mechanism may be involved in nicotine-induced heightened vasoconstriction and development of hypertensive phenotype in adulthood.

Purpose There is robust research examining the negative impact of racial and socioeconomic implicit bias on healthcare provider clinical decision-making. However, other under-studied important biases are likely to impact clinical care as well. The goal of this study was to explore the presence of bias against people with physical disability among a heterogeneous group of healthcare workers and trainees and to evaluate the effect of implicit association testing and an educational module on this bias. Method The study was composed of a one-hour web-based survey and educational module. The survey included an explicit disability bias assessment, disability Implicit Association Tests (IATs), demographic collection, and pre- and post- module clinical vignettes of prenatal patient scenarios. In addition to providing counseling to hypothetical patients, participants also indicated their personal preferences on genetic testing and termination. The educational module focused on the principles of patient-centered counseling. Results The collected data reflects responses from 335 participants. Within this sample, there were both explicit and implicit biases towards individuals with physical disabilities. Prior to the IAT and educational module, when respondents were tasked with providing genetic testing recommendations, implicit biases and personal preferences for genetic testing and termination influenced respondents’ clinical recommendations. Importantly, having previous professional experience with individuals with disabilities diminished biased clinical recommendations prior to the intervention. In response to the IAT and educational intervention, the effect of implicit bias and personal preferences on clinical recommendations decreased. Conclusions This study demonstrates how bias against a marginalized group exists within the medical community and that personal opinions can impact clinical counseling. Importantly, our findings suggest that there are strategies that can be easily implemented into curricula to address disability bias, including formal educational interventions and the addition of professional experiences into healthcare professional training programs.

Yellow Mosaic Disease (YMD) in mungbean [Vigna radiata (L.) R. Wilczek] is one of the most damaging diseases in Asia. In the northern part of India, the YMD is caused by Mungbean Yellow Mosaic India Virus (MYMIV), while in southern India this is caused by Mungbean Yellow Mosaic Virus (MYMV). The molecular mechanism of YMD resistance in mungbean remains largely unknown. In this study, RNA-seq analysis was conducted between a resistant (PMR-1) and a susceptible (Pusa Vishal) mungbean genotype under infected and control conditions to understand the regulatory network operating between mungbean-YMV. Overall, 76.8 million raw reads could be generated in different treatment combinations, while mapping rate per library to the reference genome varied from 86.78% to 93.35%. The resistance to MYMIV showed a very complicated gene network, which begins with the production of general PAMPs (pathogen-associated molecular patterns), then activation of various signaling cascades like kinases, jasmonic acid (JA) and brassinosteroid (BR), and finally the expression of specific genes (like PR-proteins, virus resistance and R-gene proteins) leading to resistance response. The function of WRKY, NAC and MYB transcription factors in imparting the resistance against MYMIV could be established. The string analysis also revealed the role of proteins involved in kinase, viral movement and phytoene synthase activity in imparting YMD resistance. A set of novel stress-related EST-SSRs are also identified from the RNA-Seq data which may be used to find the linked genes/QTLs with the YMD resistance. Also, 11 defence-related transcripts could be validated through quantitative real-time PCR analysis. The identified gene networks have led to an insight about the defence mechanism operating against MYMIV infection in mungbean which will be of immense use to manage the YMD resistance in mungbean.

A protocol for high-frequency direct organogenesis from root explants of Kachai lemon (Citrus jambhiri Lush.) was developed. Full-length roots (~3 cm) were isolated from the in vitro grown seedlings and cultured on Murashige and Skoog basal medium supplemented with Nitsch vitamin (MSN) with different concentrations of cytokinin [6-benzylaminopurine, (BAP)] and gibberellic acid (GA3). The frequency of multiple shoot proliferation was very high, with an average of 34.3 shoots per root explant when inoculated on the MSN medium supplemented with BAP (1.0 mg L-1) and GA3 (1.0 mg L-1). Optimal rooting was induced in the plantlets under half strength MSN medium supplemented with indole-3-acetic acid (IAA, 0.5-1.0 mg L-1). IAA induced better root structure than 1-naphthaleneacetic acid (NAA), which was evident from the scanning electron microscopy (SEM). The expressions of growth regulating factor genes (GRF1 and GRF5) and GA3 signaling genes (GA2OX1 and KO1) were elevated in the regenerants obtained from MSN+BAP (1.0 mg L-1)+GA3 (1.0 mg L-1). The expressions of auxin regulating genes were high in roots obtained in ½ MSN+IAA 1.0 mg L-1. Furthermore, indexing of the regenerants confirmed that there was no amplicons detected for Huanglongbing bacterium and Citrus tristeza virus. Random amplified polymorphic DNA (RAPD) and inter simple sequence repeat (ISSR) markers detected no polymorphic bands amongst the regenerated plants. This is the first report that describes direct organogenesis from the root explant of Citrus jambhiri Lush. The high-frequency direct regeneration protocol in the present study provides an enormous significance in Citrus organogenesis, its commercial cultivation and genetic conservation.

Expanding access to contraception and ensuring that need for family planning is satisfied are essential for achieving universal access to reproductive healthcare services, as called for in the 2030 Agenda for Sustainable Development. To quantify the gaps that remain in meeting needs among adolescents, this study provides a harmonised data set and global estimates and projections of family planning indicators for adolescents aged 15-19 years. We compiled a comprehensive dataset of family-planning indicators among women aged 15-19 from 754 nationally representative surveys. We used a Bayesian hierarchical model with country-specific annual trends to estimate contraceptive prevalence and unmet need for family planning, with 95% uncertainty intervals (UIs), for 185 countries, taking into account changes in proportions married or in a union and differences in sexual activity among unmarried women across countries. Among 300 million women aged 15-19 years in 2019, 29.8 million (95% UI 24.6-41.7) use any contraception, and 15.0 million (95% UI 12.1-29.2) have unmet need for family planning. Population growth and the postponement of marriage influence trends in the absolute number of adolescents using contraception or experiencing unmet need. Large gaps remain in meeting family-planning needs among adolescents. The proportion of the need satisfied by modern methods, Sustainable Development Goals (SDG) indicator 3.7.1, was 59.2% (95% UI 44.8-67.2) globally among adolescents, lower compared to 75.7% (95% UI 73.2%-78.0%) among all women age 15-49 years. It was less than one half of adolescents in need in Western Asia and Northern Africa (38.7%, 95%UI = 20.9-56.5), Central and Southern Asia (43.5%, 95%UI = 36.6-52.3), and sub-Saharan Africa (45.6%, 95%UI = 42.2-49.0). The main limitations of the study are: (i) the uncertainty surrounding estimates for countries with limited or biased data is large; and (ii) underreporting of contraceptive use and needs is likely, especially among unmarried adolescents.

Catechol-estrogens can cause genetic mutations and to counteract their oncogenicity, the catechol-O-methyltransferase (COMT) gene is capable of neutralizing these reactive compounds. In this study, we determined the functional effects and regulation of COMT in prostate cancer. Both the Cancer Genome Atlas (TCGA) and immunohistochemical analysis of clinical specimens demonstrated a reduction of COMT expression in prostate cancer. Also, western analyses of prostate cancer cell lines show COMT levels to be minimal in DuPro and DU145 and thus, these cells were used for further analyses. Re-expression of COMT led to suppressed migration ability (wound healing assay) and enhanced apoptosis (flow cytometric analyses), and when challenged with 4-hydroxyestradiol, a marked reduction of cell proliferation (MTT assay) was observed. Xenograft growth in athymic mice also resulted in inhibition due to COMT. As a mechanism, western analyses show cleaved CASP3 and BID were increased whereas XIAP and cIAP2 were reduced due to COMT. As COMT expression is low in prostate cancer, its regulation was determined. Databases identified several miRNAs capable of binding COMT and of these, miR-195 was observed to be increased in prostate cancer according to TCGA. Real-time PCR validated upregulation of miR-195 in clinical prostate cancer specimens as well as DuPro and DU145 and interestingly, luciferase reporter showed miR-195 capable of binding COMT and overexpressing miR-195 could reduce COMT in cells. These results demonstrate COMT to play a protective role by activating the apoptosis pathway and for miR-195 to regulate its expression. COMT may thus be a potential biomarker and gene of interest for therapeutic development for prostate cancer.

BackgroundCoal mine dust lung disease comprises a group of occupational lung diseases including coal workers pneumoconiosis. In many countries, there is a lack of robust prevalence estimates for these diseases. Our objective was to perform a systematic review and meta-analysis of published contemporary estimates on prevalence, mortality, and survival for coal mine dust lung disease worldwide.MethodsSystematic searches of PubMed, EMBASE and Web of Science databases for English language peer-reviewed articles published from 1/1/2000 to 30/03/2021 that presented quantitative estimates of prevalence, mortality, or survival for coal mine dust lung disease. Review was conducted per PRISMA guidelines. Articles were screened independently by two authors. Studies were critically assessed using Joanna Briggs Institute tools. Pooled prevalence estimates were obtained using random effects meta-analysis models. Heterogeneity was measured using the I2 statistics and publication bias using Egger's tests.ResultsOverall 40 studies were included, (31 prevalence, 8 mortality, 1 survival). Of the prevalence estimates, fifteen (12 from the United States) were retained for the meta-analysis. The overall pooled prevalence estimate for coal workers pneumoconiosis among underground miners was 3.7% (95% CI 3.0-4.5%) with high heterogeneity between studies. The pooled estimate of coal workers pneumoconiosis prevalence in the United States was higher in the 2000s than in the 1990s, consistent with published reports of increasing prevalence following decades of declining trends. Sub-group analyses also indicated higher prevalence among underground miners, and in Central Appalachia. The mortality studies were suggestive of reduced pneumoconiosis mortality rates over time, relative to the general population.ConclusionThe ongoing prevalence of occupational lung diseases among contemporary coal miners highlights the importance of respiratory surveillance and preventive efforts through effective dust control measures. Limited prevalence studies from countries other than the United States limits our understanding of the current disease burden in other coal-producing countries.

Viperin, an antiviral protein, has been shown to contain a CX(3)CX(2)C motif, which is conserved in the radical S-adenosyl-methionine (SAM) enzyme family. A triple mutant which replaces these three cysteines with alanines has been shown to have severe deficiency in antiviral activity. Since the crystal structure of Viperin is not available, we have used a combination of computational methods including multi-template homology modeling and molecular dynamics simulation to develop a low-resolution predicted structure. The results show that Viperin is an α-β protein containing iron-sulfur cluster at the center pocket. The calculations suggest that the removal of iron-sulfur cluster would lead to collapse of the protein tertiary structure. To verify these predictions, we have prepared, expressed and purified four mutant proteins. In three mutants individual cysteine residues were replaced by alanine residues while in the fourth all the cysteines were replaced by alanines. Conformational analyses using circular dichroism and steady state fluorescence spectroscopy indicate that the mutant proteins are partially unfolded, conformationally unstable and aggregation prone. The lack of conformational stability of the mutant proteins may have direct relevance to the absence of their antiviral activity.

BACKGROUND:In the US, medication assisted treatment, particularly with office-based buprenorphine, has been an important component of opioid dependence treatment among patients with iatrogenic addiction to opioid analgesics. The predictors of initiating buprenorphine for addiction among opioid analgesic patients have not been well-described. METHODS:We conducted a time-to-event analysis using data from the North Carolina (NC) Prescription Drug Monitoring Program (PDMP). Our outcome of interest was time-to-initiation of sublingual buprenorphine. Our study population was a prospective cohort of all state residents receiving a full-agonist opioid analgesic between 2011 and 2015. Predictors of initiation of sublingual buprenorphine examined included: age, gender, cumulative pharmacies and prescribers utilized, cumulative opioid intensity (defined as cumulative opioid exposure divided by duration of opioid exposure), and benzodiazepine dispensing. FINDINGS:Of 4.3 million patients receiving opioid analgesics in NC between 2011 and 2015 (accumulated 8.30 million person-years of follow-up), and a total of 28,904 patients initiated buprenorphine formulations intended for addiction treatment (overall rate 3.48 per 1,000 person-years). In adjusted multivariate models, the utilization of 3 or more pharmacies (HR: 2.93; 95% CI: 2.82, 3.05) or 6 or more controlled substance prescribers (HR: 12.09; 95% CI: 10.76, 13.57) was associated with buprenorphine initiation. A dose-response relationship was observed for cumulative opioid intensity (HR in highest decile relative to lowest decile: 5.05; 95% CI: 4.70, 5.42). Benzodiazepine dispensing was negatively associated with buprenorphine initiation (HR: 0.63; 95% CI: 0.61, 0.65). CONCLUSIONS:Opioid analgesic patients utilizing multiple prescribers or pharmacies are more likely to initiate sublingual buprenorphine. This finding suggests that patients with multiple healthcare interactions are more likely to be treated for high-risk opioid use, or may be more likely to be identified and treated for addiction. Future research should utilize prescription monitoring program data linked to electronic health records to include diagnosis information in analytic models.

Ensuring affordable, reliable, sustainable and modern energy for all by 2030 is part of the internationally agreed Sustainable Development Goals (SDG7). With roughly 3 billion people still lacking access to clean cooking solutions in 2017, this remains an ambitious task. The use of solid biomass such as wood and cow dung for cooking causes household air pollution resulting in severe health hazards. In this context, the Indian government has set up a large program promoting the use of liquefied petroleum gas (LPG) in rural areas. While this has led millions of households to adopt LPG, a major fraction of them continues to rely heavily on solid biomass for their daily cooking. In this paper, we evaluate the effect of simple health messaging on the propensity of these households to use LPG more regularly. Our results from rural Rajasthan are encouraging. They show that health messaging increases the reported willingness to pay for LPG, and substantially increases actual consumption. We measure this based on a voucher, which can only be used if LPG consumption is doubled until a certain deadline. Households exposed to health messaging use the voucher about 30% more often than households exposed to a placebo treatment. We further show that the impact of our very brief, but concrete health messaging is close to the effect of a 10% price reduction for a new LPG cylinder. Finally, our study raises some interesting questions about gender-related effects that would be worth consideration in future research.

The rapid deployment of 5G spectrum by the telecommunication industry is intended to promote better connectivity and data integration among various industries. However, since exposures to radio frequency radiations (RFR) >2.4 GHz are still uncommon, concerns about their potential health impacts are ongoing. In this study, we used the embryonic zebrafish model to assess the impacts of a 3.5 GHz RFR on biology- a frequency typically used by 5G-enabled cell phones and lies within the 4G and 5G bandwidth. We established a plate-based exposure setup for RFRs, exposed developing zebrafish to 3.5 GHz RFR, specific absorption rate (SAR) ≈ 8.27 W/Kg from 6 h post fertilization (hpf) to 48 hpf, and measured a battery of morphological and behavioral endpoints at 120 hpf. Our results revealed no significant impacts on mortality, morphology or photomotor response and a modest inhibition of startle response suggesting some levels of sensorimotor disruptions. This suggests that the cell phone radiations at low GHz-level frequencies are likely benign, with subtle sensorimotor effects. Through this assessment, we have established a robust setup for zebrafish RFR exposures readily amenable to testing various powers and frequencies. Future developmental exposure studies in zebrafish will evaluate a wider portion of the radio frequency spectrum to discover the bioactive regions, the potential molecular targets of RFR and the potential long-term effects on adult behavior.

BackgroundNeoadjuvant chemotherapy (NAC) is the standard of care for patients with locally advanced breast cancer (LABC). The study was conducted to investigate the utility of quantitative ultrasound (QUS) carried out during NAC to predict the final tumour response in a multi-institutional setting.MethodsFifty-nine patients with LABC were enrolled from three institutions in North America (Sunnybrook Health Sciences Centre (Toronto, Canada), MD Anderson Cancer Centre (Texas, USA), and Princess Margaret Cancer Centre (Toronto, Canada)). QUS data were collected before starting NAC and subsequently at weeks 1 and 4 during chemotherapy. Spectral tumour parametric maps were generated, and textural features determined using grey-level co-occurrence matrices. Patients were divided into two groups based on their pathological outcomes following surgery: responders and non-responders. Machine learning algorithms using Fisher's linear discriminant (FLD), K-nearest neighbour (K-NN), and support vector machine (SVM-RBF) were used to generate response classification models.ResultsThirty-six patients were classified as responders and twenty-three as non-responders. Among all the models, SVM-RBF had the highest accuracy of 81% at both weeks 1 and week 4 with area under curve (AUC) values of 0.87 each. The inclusion of week 1 and 4 features led to an improvement of the classifier models, with the accuracy and AUC from baseline features only being 76% and 0.68, respectively.ConclusionQUS data obtained during NAC reflect the ongoing treatment-related changes during chemotherapy and can lead to better classifier performances in predicting the ultimate pathologic response to treatment compared to baseline features alone.

Lifelong noninvasive rejection monitoring in heart transplant patients is a critical clinical need historically poorly met in adults and unavailable for children and infants. Cell-free DNA (cfDNA) donor-specific fraction (DF), a direct marker of selective donor organ injury, is a promising analytical target. Methodological differences in sample processing and DF determination profoundly affect quality and sensitivity of cfDNA analyses, requiring specialized optimization for low cfDNA levels typical of transplant patients. Using next-generation sequencing, we previously correlated elevated DF with acute cellular and antibody-mediated rejection (ACR and AMR) in pediatric and adult heart transplant patients. However, next-generation sequencing is limited by cost, TAT, and sensitivity, leading us to clinically validate a rapid, highly sensitive, quantitative genotyping test, myTAIHEART®, addressing these limitations. To assure pre-analytical quality and consider interrelated cfDNA measures, plasma preparation was optimized and total cfDNA (TCF) concentration, DNA fragmentation, and DF quantification were validated in parallel for integration into myTAIHEART reporting. Analytical validations employed individual and reconstructed mixtures of human blood-derived genomic DNA (gDNA), cfDNA, and gDNA sheared to apoptotic length. Precision, linearity, and limits of blank/detection/quantification were established for TCF concentration, DNA fragmentation ratio, and DF determinations. For DF, multiplexed high-fidelity amplification followed by quantitative genotyping of 94 SNP targets was applied to 1168 samples to evaluate donor options in staged simulations, demonstrating DF call equivalency with/without donor genotype. Clinical validation studies using 158 matched endomyocardial biopsy-plasma pairs from 76 pediatric and adult heart transplant recipients selected a DF cutoff (0.32%) producing 100% NPV for ≥2R ACR. This supports the assay's conservative intended use of stratifying low versus increased probability of ≥2R ACR. myTAIHEART is clinically validated for heart transplant recipients ≥2 months old and ≥8 days post-transplant, expanding opportunity for noninvasive transplant rejection assessment to infants and children and to all recipients >1 week post-transplant.

BackgroundThere is currently no effective treatment for promoting regeneration of injured nerves in patients who have sustained injury to the central nervous system such as spinal cord injury. Chondroitinase ABC is an enzyme, which promotes neurite outgrowth and regeneration. It has shown considerable promise as a therapy for these conditions. The aim of the study is to determine if targeting chondroitinase ABC expression to the neuronal axon can further enhance its ability to promote axon outgrowth. Long-distance axon regeneration has not yet been achieved, and would be a significant step in attaining functional recovery following spinal cord injury.Methodology/principal findingsTo investigate this, neuronal cultures were transfected with constructs encoding axon-targeted chondroitinase, non-targeted chondroitinase or GFP, and the effects on neuron outgrowth and sprouting determined on substrates either permissive or inhibitory to neuron regeneration. The mechanisms underlying the observed effects were also explored. Targeting chondroitinase to the neuronal axon markedly enhances its ability to promote neurite outgrowth. The increase in neurite length is associated with an upregulation of β-integrin staining at the axonal cell surface. Staining for phosphofocal adhesion kinase, is also increased, indicating that the β-integrins are in an activated state. Expression of chondroitinase within the neurons also resulted in a decrease in expression of PTEN and RhoA, molecules which present a block to neurite outgrowth, thus identifying two of the pathways by which ChABC promotes neurite outgrowth.Conclusions / significanceThe novel finding that targeting ChABC to the axon significantly enhances its ability to promote neurite extension, suggests that this may be an effective way of promoting long-distance axon regeneration following spinal cord injury. It could also potentially improve its efficacy in the treatment of other pathologies, where it has been shown to promote recovery, such as myocardial infarction, stroke and Parkinson's disease.

BackgroundGlyco-lipopeptides, a form of lipid-tailed glyco-peptide, are currently under intense investigation as B- and T-cell based vaccine immunotherapy for many cancers. However, the cellular and molecular mechanisms of glyco-lipopeptides (GLPs) immunogenicity and the position of the lipid moiety on immunogenicity and protective efficacy of GLPs remain to be determined.Methods/Principal FindingsWe have constructed two structural analogues of HER-2 glyco-lipopeptide (HER-GLP) by synthesizing a chimeric peptide made of one universal CD4+ epitope (PADRE) and one HER-2 CD8+ T-cell epitope (HER420–429). The C-terminal end of the resulting CD4–CD8 chimeric peptide was coupled to a tumor carbohydrate B-cell epitope, based on a regioselectively addressable functionalized templates (RAFT), made of four α-GalNAc molecules. The resulting HER glyco-peptide (HER-GP) was then linked to a palmitic acid moiety, attached either at the N-terminal end (linear HER-GLP-1) or in the middle between the CD4+ and CD8+ T cell epitopes (branched HER-GLP-2). We have investigated the uptake, processing and cross-presentation pathways of the two HER-GLP vaccine constructs, and assessed whether the position of linkage of the lipid moiety would affect the B- and T-cell immunogenicity and protective efficacy. Immunization of mice revealed that the linear HER-GLP-1 induced a stronger and longer lasting HER420–429-specific IFN-γ producing CD8+ T cell response, while the branched HER-GLP-2 induced a stronger tumor-specific IgG response. The linear HER-GLP-1 was taken up easily by dendritic cells (DCs), induced stronger DCs maturation and produced a potent TLR- 2-dependent T-cell activation. The linear and branched HER-GLP molecules appeared to follow two different cross-presentation pathways. While regression of established tumors was induced by both linear HER-GLP-1 and branched HER-GLP-2, the inhibition of tumor growth was significantly higher in HER-GLP-1 immunized mice (p

The transient build-up of DNA supercoiling during the translocation of replication forks threatens genome stability and is controlled by DNA topoisomerases (TOPs). This crucial process has been exploited with TOP poisons for cancer chemotherapy. However, pinpointing cellular determinants of the best clinical response to TOP poisons still remains enigmatic. Here, we present an integrated approach and demonstrate that endogenous and exogenous expression of the oncofetal high-mobility group AT-hook 2 (HMGA2) protein exhibited broad protection against the formation of hydroxyurea-induced DNA breaks in various cancer cells, thus corroborating our previously proposed model in which HMGA2 functions as a replication fork chaperone that forms a protective DNA scaffold at or close to stalled replication forks. We now further demonstrate that high levels of HMGA2 also protected cancer cells against DNA breaks triggered by the clinically important TOP1 poison irinotecan. This protection is most likely due to the recently identified DNA supercoil constraining function of HMGA2 in combination with exclusion of TOP1 from binding to supercoiled substrate DNA. In contrast, low to moderate HMGA2 protein levels surprisingly potentiated the formation of irinotecan-induced genotoxic covalent TOP1-DNA cleavage complexes. Our data from cell-based and several in vitro assays indicate that, mechanistically, this potentiating role involves enhanced drug-target interactions mediated by HMGA2 in ternary complexes with supercoiled DNA. Subtelomeric regions were found to be extraordinarily vulnerable to these genotoxic challenges induced by TOP1 poisoning, pointing at strong DNA topological barriers located at human telomeres. These findings were corroborated by an increased irinotecan sensitivity of patient-derived xenografts of colorectal cancers exhibiting low to moderate HMGA2 levels. Collectively, we uncovered a therapeutically important control mechanism of transient changes in chromosomal DNA topology that ultimately leads to enhanced human subtelomere stability.

Mangroves are an important ecosystem-based protection against cyclonic storm surge. As the surge moves through the mangrove forest, the tree roots, trunks, and leaves obstruct the flow of water. Damage to adjacent coastal lands is attenuated mainly by reducing (i) surge height, which determines the area and depth of inundation and (ii) water flow velocity. But the extent of mangrove protection depends on the density of tree plantings and the diameter of trunks and roots, along with an array of other forest characteristics (e.g., floor shape, bathymetry, spectral features of waves, and tidal stage at which waves enter the forest). Making efficient use of mangroves' protective capacity has been hindered by a lack of location-specific information. This study helps to fill that gap by estimating reduction in storm surge height and water flow velocity from mangroves at selected sites in cyclone-prone, coastal Bangladesh. A hydrodynamic model for the Bay of Bengal, based on the MIKE21FM system, was run multiple times to simulate the surge of cyclone Sidr (2007) at the Barisal coast. Estimates of surge height and water flow velocity were recorded first without mangroves and then with mangroves of various forest widths and planting densities, including specific information on local topography, bathymetry, and Manning's coefficients estimated from species' root and trunk systems. The results show a significant reduction in water flow velocity (29-92%) and a modest reduction in surge height (4-16.5 cm). These findings suggest that healthy mangroves can contribute to significant savings in rehabilitation and maintenance costs by protecting embankments from breaching, toe-erosion, and other damage.

Sphingosine Kinase-2 (Sphk2) is responsible for the production of the bioactive lipid Sphingosine-1 Phosphate, a key regulator of tissue repair. Here we address the in vivo significance of Sphingosine Kinase -2 in renal inflammation/fibrosis in response to unilateral ureteral obstruction using both genetic and pharmacological strategies. Obstructed kidneys of Sphk2-/- mice showed reduced renal damage and diminished levels of the renal injury markers TGFβ1 and αSMA when compared to wild type controls. We found a consistently significant increase in anti-inflammatory (M2) macrophages in obstructed Sphk2-/- kidneys by flow cytometry and a decrease in mRNA levels of the inflammatory cytokines, MCP1, TNFα, CXCL1 and ILβ1, suggesting an anti-inflammatory bias in the absence of Sphk2. Indeed, metabolic profiling showed that the pro-inflammatory glycolytic pathway is largely inactive in Sphk2-/- bone marrow-derived macrophages. Furthermore, treatment with the M2-promoting cytokines IL-4 or IL-13 demonstrated that macrophages lacking Sphk2 polarized more efficiently to the M2 phenotype than wild type cells. Bone marrow transplant studies indicated that expression of Sphk2-/- on either the hematopoietic or parenchymal cells did not fully rescue the pro-healing phenotype, confirming that both infiltrating M2-macrophages and the kidney microenvironment contribute to the damaging Sphk2 effects. Importantly, obstructed kidneys from mice treated with an Sphk2 inhibitor recapitulated findings in the genetic model. These results demonstrate that reducing Sphk2 activity by genetic or pharmacological manipulation markedly decreases inflammatory and fibrotic responses to obstruction, resulting in diminished renal injury and supporting Sphk2 as a novel driver of the pro-inflammatory macrophage phenotype.

Patients with chronic kidney disease (CKD) are at an increased risk of developing end-stage renal disease (ESRD). We assessed for the first time whether urinary free light chains (FLC) are independently associated with risk of ESRD in patients with CKD, and whether they offer incremental value in risk stratification.We measured urinary FLCs in 556 patients with CKD from a prospective cohort study. The association between urinary kappa/creatinine (KCR) and lambda/creatinine (LCR) ratios and development of ESRD was assessed by competing-risks regression (to account for the competing risk of death). The change in C-statistic and integrated discrimination improvement were used to assess the incremental value of adding KCR or LCR to the Kidney Failure Risk Equation (KFRE).136 participants developed ESRD during a median follow-up time of 51 months. Significant associations between KCR and LCR and risk of ESRD became non-significant after adjustment for estimated glomerular filtration rate (eGFR) and albumin/creatinine ratio (ACR), although having a KCR or LCR >75th centile remained independently associated with risk of ESRD. Neither KCR nor LCR as continuous or categorical variables provided incremental value when added to the KFRE for estimating risk of ESRD at two years.Urinary FLCs have an association with progression to ESRD in patients with CKD which appears to be explained to a degree by their correlation with eGFR and ACR. Levels above the 75th centile do have an independent association with ESRD, but do not improve upon a current model for risk stratification.

The goal of this study was to investigate associations between admissions criteria and performance in Ph.D. programs at Boston University School of Medicine. The initial phase of this project examined student performance in the classroom component of a newly established curriculum named "Foundations in Biomedical Sciences (FiBS)". Quantitative measures including undergraduate grade point average (GPA), graduate record examination (GRE; a standardized, computer-based test) scores for the verbal (assessment of test takers' ability to analyze, evaluate, and synthesize information and concepts provided in writing) and quantitative (assessment of test takers' problem-solving ability) components of the examination, previous research experience, and competitiveness of previous research institution were used in the study. These criteria were compared with competencies in the program defined as students who pass the curriculum as well as students categorized as High Performers. These data indicated that there is a significant positive correlation between FiBS performance and undergraduate GPA, GRE scores, and competitiveness of undergraduate institution. No significant correlations were found between FiBS performance and research background. By taking a data-driven approach to examine admissions and performance, we hope to refine our admissions criteria to facilitate an unbiased approach to recruitment of students in the life sciences and to share our strategy to support similar goals at other institutions.

[This corrects the article DOI: 10.1371/journal.pone.0171706.].

Many modern applications of AI such as web search, mobile browsing, image processing, and natural language processing rely on finding similar items from a large database of complex objects. Due to the very large scale of data involved (e.g., users' queries from commercial search engines), computing such near or nearest neighbors is a non-trivial task, as the computational cost grows significantly with the number of items. To address this challenge, we adopt Locality Sensitive Hashing (a.k.a, LSH) methods and evaluate four variants in a distributed computing environment (specifically, Hadoop). We identify several optimizations which improve performance, suitable for deployment in very large scale settings. The experimental results demonstrate our variants of LSH achieve the robust performance with better recall compared with "vanilla" LSH, even when using the same amount of space.

Type IV secretion systems (T4SS) are multi-protein complexes in a number of bacterial pathogens that can translocate proteins and DNA to the host. Most T4SSs function in conjugation and translocate DNA; however, approximately 13% function to secrete proteins, delivering effector proteins into the cytosol of eukaryotic host cells. Upon entry, these effectors manipulate the host cell's machinery for their own benefit, which can result in serious illness or death of the host. For this reason recognition of T4SS effectors has become an important subject. Much previous work has focused on verifying effectors experimentally, a costly endeavor in terms of money, time, and effort. Having good predictions for effectors will help to focus experimental validations and decrease testing costs. In recent years, several scoring and machine learning-based methods have been suggested for the purpose of predicting T4SS effector proteins. These methods have used different sets of features for prediction, and their predictions have been inconsistent. In this paper, an optimal set of features is presented for predicting T4SS effector proteins using a statistical approach. A thorough literature search was performed to find features that have been proposed. Feature values were calculated for datasets of known effectors and non-effectors for T4SS-containing pathogens for four genera with a sufficient number of known effectors, Legionella pneumophila, Coxiella burnetii, Brucella spp, and Bartonella spp. The features were ranked, and less important features were filtered out. Correlations between remaining features were removed, and dimensional reduction was accomplished using principal component analysis and factor analysis. Finally, the optimal features for each pathogen were chosen by building logistic regression models and evaluating each model. The results based on evaluation of our logistic regression models confirm the effectiveness of our four optimal sets of features, and based on these an optimal set of features is proposed for all T4SS effector proteins.

Human papillomavirus (HPV) causes tumors primarily Cervical cancer. Recently, inconsistent reports came up in Breast cancer (BC) too. In India, despite treatment 70,218 BC patients die each year. So, we explored the association of HPV, if any, with BC prognosis in Indian pre-therapeutic (PT) and Neo-adjuvant chemotherapy (NACT) patients with subsequent analysis of HPV profile.HPV prevalence was checked and analysis of physical status, copy number, genome variation, promoter methylation and expression (mRNA and protein) of the prevalent subtype was done.High prevalence of HPV was observed in both PT (64.0%) and NACT (71.0%) cases with significant association with younger (20-45 yrs) PT patients. Interestingly, HPV infection was significantly increased from adjacent normal breast (9.5%, 2/21), fibro adenomas (30%, 3/10) to tumors (64.8%, 203/313) samples. In both PT and NACT cases, HPV16 was the most prevalent subtype (69.0%) followed by HPV18 and HPV33. Survival analysis illustrated hrHPV infected PT patients had worst prognosis. So, detailed analysis of HPV16 profile was done which showed Europian-G350 as the most frequent HPV16 variant along with high rate of integration. Moreover, low copy number and hyper-methylation of P97 early promoter were concordant with low HPV16 E6 and E7 mRNA and protein expression. Notably, four novel variations (KT020838, KT020840, KT020841 and KT020839) in the LCR region and two (KT020836 and KT020837) in the E6 region were identified for the first time along with two novel E6^E7*I (KU199314) and E6^E7*II (KU199315) fusion transcript variants.Thus, significant association of hrHPV with prognosis of Indian BC patients led to additional investigation of HPV16 profile. Outcomes indicated a plausible role of HPV in Indian BC patients.

Bovine serum albumin (BSA) is an important transport protein of the blood and its aggregation/fibrillation would adversely affect its transport ability leading to metabolic disorder. Therefore, understanding the mechanism of fibrillation/aggregation of BSA and design of suitable inhibitor molecules for stabilizing its native conformation, are of utmost importance. The qualitative and quantitative aspects of the effect of osmolytes (proline, hydroxyproline, glycine betaine, sarcosine and sorbitol) on heat induced aggregation/fibrillation of BSA at physiological pH (pH 7.4) have been studied employing a combination of fluorescence spectroscopy, Rayleigh scattering, isothermal titration calorimetry (ITC), dynamic light scattering (DLS) and transmission electron microscopy (TEM). Formation of fibrils by BSA under the given conditions was confirmed from increase in fluorescence emission intensities of Thioflavin T over a time period of 600 minutes and TEM images. Absence of change in fluorescence emission intensities of 8-Anilinonaphthalene-1-sulfonic acid (ANS) in presence of native and aggregated BSA signify the absence of any amorphous aggregates. ITC results have provided important insights on the energetics of interaction of these osmolytes with different stages of the fibrillar aggregates of BSA, thereby suggesting the possible modes/mechanism of inhibition of BSA fibrillation by these osmolytes. The heats of interaction of the osmolytes with different stages of fibrillation of BSA do not follow a trend, suggesting that the interactions of stages of BSA aggregates are osmolyte specific. Among the osmolytes used here, we found glycine betaine to be supporting and promoting the aggregation process while hydroxyproline to be maximally efficient in suppressing the fibrillation process of BSA, followed by sorbitol, sarcosine and proline in the following order of their decreasing potency: Hydroxyproline> Sorbitol> Sarcosine> Proline> Glycine betaine.

This paper presents experimental evidence for the existence of a set of unique force modulation strategies during manual soft tissue palpation to locate hard abnormalities such as tumors. We explore the active probing strategies of defined local areas and outline the role of force control. In addition, we investigate whether the applied force depends on the non-homogeneity of the soft tissue. Experimental results on manual palpation of soft silicone phantoms show that humans have a well defined force control pattern of probing that is used independently of the non-homogeneity of the soft tissue. We observed that the modulations of lateral forces are distributed around the mean frequency of 22.3 Hz. Furthermore, we found that the applied normal pressure during probing can be modeled using a second order reactive autoregressive model. These mathematical abstractions were implemented and validated for the autonomous palpation for different stiffness parameters using a robotic probe with a rigid spherical indentation tip. The results show that the autonomous robotic palpation strategy abstracted from human demonstrations is capable of not only detecting the embedded nodules, but also enhancing the stiffness perception compared to static indentation of the probe.

We have developed a new litmus paper test (DipTest) for detecting Escherichia coli (E. coli) in water samples by performing enzymatic reactions directly on the porous paper substrate. The paper strip consists of a long narrow piece of cellulose blotting paper coated with chemoattractant (at bottom edge), wax hydrophobic barrier (at the top edge), and custom formulated chemical reagents (at reaction zone immediately below the wax hydrophobic barrier). When the paper strip is dipped in water, E. coli in the water sample is attracted toward the paper strip due to a chemotaxic mechanism followed by the ascent along the paper strip toward the reaction zone due to a capillary wicking mechanism, and finally the capillary motion is arrested at the top edge of the paper strip by the hydrophobic barrier. The E. coli concentrated at the reaction zone of the paper strip will react with custom formulated chemical reagents to produce a pinkish-red color. Such a color change on the paper strip when dipped into water samples indicates the presence of E. coli contamination in potable water. The performance of the DipTest device has been checked with different known concentrations of E. coli contaminated water samples using different dip and wait times. The DipTest device has also been tested with different interfering bacteria and chemical contaminants. It has been observed that the different interfering contaminants do not have any impact on the DipTest, and it can become a potential solution for screening water samples for E. coli contamination at the point of source.

There is very little reported in the literature about the relationship between modifications of bacterial proteins and their secretion by mammalian cells that synthesize them. We previously reported that the secretion of the bacterial enzyme Chondroitinase ABC by mammalian cells requires the strategic removal of at least three N-glycosylation sites. The aim of this study was to determine if it is possible to enhance the efficacy of the enzyme as a treatment for spinal cord injury by increasing the quantity of enzyme secreted or by altering its cellular location.To determine if the efficiency of enzyme secretion could be further increased, cells were transfected with constructs encoding the gene for chondroitinase ABC modified for expression by mammalian cells; these contained additional modifications of strategic N-glycosylation sites or alternative signal sequences to direct secretion of the enzyme from the cells. We show that while removal of certain specific N-glycosylation sites enhances enzyme secretion, N-glycosylation of at least two other sites, N-856 and N-773, is essential for both production and secretion of active enzyme. Furthermore, we find that the signal sequence directing secretion also influences the quantity of enzyme secreted, and that this varies widely amongst the cell types tested. Last, we find that replacing the 3'UTR on the cDNA encoding Chondroitinase ABC with that of β-actin is sufficient to target the enzyme to the neuronal growth cone when transfected into neurons. This also enhances neurite outgrowth on an inhibitory substrate.Some intracellular trafficking pathways are adversely affected by cryptic signals present in the bacterial gene sequence, whilst unexpectedly others are required for efficient secretion of the enzyme. Furthermore, targeting chondroitinase to the neuronal growth cone promotes its ability to increase neurite outgrowth on an inhibitory substrate. These findings are timely in view of the renewed prospects for gene therapy, and of direct relevance to strategies aimed at expressing foreign proteins in mammalian cells, in particular bacterial proteins.

Dramatic increase of diabetes over the globe is in tandem with the increase in insulin requirement. This is because destruction and dysfunction of pancreatic β-cells are of common occurrence in both Type1 diabetes and Type2 diabetes, and insulin injection becomes a compulsion. Because of several problems associated with insulin injection, orally active insulin mimetic compounds would be ideal substitute. Here we report a small molecule, a peroxyvanadate compound i.e. DmpzH[VO(O2)2(dmpz)], henceforth referred as dmp, which specifically binds to insulin receptor with considerable affinity (KD-1.17μM) thus activating insulin receptor tyrosine kinase and its downstream signaling molecules resulting increased uptake of [14C] 2 Deoxy-glucose. Oral administration of dmp to streptozotocin treated BALB/c mice lowers blood glucose level and markedly stimulates glucose and fatty acid uptake by skeletal muscle and adipose tissue respectively. In db/db mice, it greatly improves insulin sensitivity through excess expression of PPARγ and its target genes i.e. adiponectin, CD36 and aP2. Study on the underlying mechanism demonstrated that excess expression of Wnt3a decreased PPARγ whereas dmp suppression of Wnt3a gene increased PPARγ expression which subsequently augmented adiponectin. Increased production of adiponectin in db/db mice due to dmp effected lowering of circulatory TG and FFA levels, activates AMPK in skeletal muscle and this stimulates mitochondrial biogenesis and bioenergetics. Decrease of lipid load along with increased mitochondrial activity greatly improves energy homeostasis which has been found to be correlated with the increased insulin sensitivity. The results obtained with dmp, therefore, strongly indicate that dmp could be a potential candidate for insulin replacement therapy.

Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network that cycles to the cell surface through exocytic and endocytic pathways. Unlike other members of the metallocarboxypeptidase family, CPD is a multicatalytic enzyme with three carboxypeptidase-like domains, although only the first two domains are predicted to be enzymatically active. To investigate the enzymatic properties of each domain in human CPD, a critical active site Glu in domain I and/or II was mutated to Gln and the protein expressed, purified, and assayed with a wide variety of peptide substrates. CPD with all three domains intact displays >50% activity from pH 5.0 to 7.5 with a maximum at pH 6.5, as does CPD with mutation of domain I. In contrast, the domain II mutant displayed >50% activity from pH 6.5-7.5. CPD with mutations in both domains I and II was completely inactive towards all substrates and at all pH values. A quantitative peptidomics approach was used to compare the activities of CPD domains I and II towards a large number of peptides. CPD cleaved C-terminal Lys or Arg from a subset of the peptides. Most of the identified substrates of domain I contained C-terminal Arg, whereas comparable numbers of Lys- and Arg-containing peptides were substrates of domain II. We also report that some peptides with C-terminal basic residues were not cleaved by either domain I or II, showing the importance of the P1 position for CPD activity. Finally, the preference of domain I for C-terminal Arg was validated through molecular docking experiments. Together with the differences in pH optima, the different substrate specificities of CPD domains I and II allow the enzyme to perform distinct functions in the various locations within the cell.

It has long been established that active agents in seminal fluid are key to initiating and coordinating mating-induced immunomodulation. This is in part governed by the actions of a network of cytokine interactions which, to date, remain largely undefined, and whose interspecific evolutionary conservation is unknown. This study applied Bayesian methods to illustrate the interrelationships between seminal profiles of interleukin (IL)-1alpha, IL-1beta, IL-2, IL-4, IL-5, IL-6, IL-9, IL-10, IL-12 (p70), IL-13, IL-17, eotaxin, granulocyte-colony stimulating factor (G-CSF), granulocyte macrophage-colony stimulating factor (GM-CSF), interferon (IFN)-gamma, keratinocyte-derived chemokine (KC), monocyte chemoattractant protein (MCP-1), macrophage inflammatory protein (MIP-1) alpha, MIP-1beta, regulated on activation normal T cell expressed and secreted (RANTES), tumour necrosis factor (TNF)-alpha, leptin, inducible protein (IP)-10 and vascular endothelial growth factor (VEGF) in a rat model. IL-2, IL-9, IL-12 (p70), IL-13, IL-18, eotaxin, IFN-gamma, IP-10, KC, leptin, MCP-1, MIP-1alpha and TNF-alpha were significantly higher in serum, whilst IL-1beta, IL-5, IL-6, IL-10, IL-17, G-CSF and GM-CSF were significantly higher in seminal fluid. When compared to mouse profiles, only G-CSF was present at significantly higher levels in the seminal fluid in both species. Bayesian modelling highlighted key shared features across mouse and rat networks, namely TNF-alpha as the terminal node in both serum and seminal plasma, and MCP-1 as a central coordinator of seminal cytokine networks through the intermediary of KC and RANTES. These findings reveal a marked interspecific conservation of seminal cytokine networks.

Chemical reduction of graphene oxide (GO) to graphene employs the use of toxic and environmentally harmful reducing agents, hindering mass production of graphene which is of tremendous technological importance. In this study we report a green approach to the synthesis of graphene, bio-reduced by crude polysaccharide. The polysaccharide reduces exfoliated GO to graphene at room temperature in an aqueous medium. Transmission electron microscopy image provides clear evidence for the formation of few layer graphene. Characterization of the resulting polysaccharide reduced GO by Raman spectroscopy, Fourier transform infrared spectroscopy and Energy dispersive X-ray analysis confirms reduction of GO to graphene. We also investigated the degree of biosafety of the reduced GO and found it to be safe under 100 μg/ml.

Type I interferons (IFNα, IFNβ) are key regulators of innate and adaptive immunity, modulating the severity of both viral and bacterial infections. While type I IFN signaling leads to improved outcomes in viral infections, its role in bacterial infections is more contextual and depends on the specific pathogen and route of infection. Given the limited evidence on whether type I IFN signaling affects enteric bacterial pathogens, we investigated the role of this signaling pathway in Salmonella enterica serovar Typhimurium (S. typhimurium)-induced colitis. Comparing mice deficient in IFNAR1- the common receptor for IFNα and IFNβ- with wild-type mice, we found that type I IFN signaling leads to more rapid death, more severe colonic inflammation, higher serum levels of pro-inflammatory cytokines, and greater bacterial dissemination. Specific ablation of plasmacytoid dendritic cells (pDCs), which are prominent producers of type I IFNs in antiviral responses, did not alter survival after infection. This result established that pDCs do not play a major role in the pathogenesis of S. typhimurium colitis. Flow cytometric analysis of macrophages and conventional dendritic cells (cDCs) during active colitis demonstrated an increase in CD11c- macrophages and CD103+ cDCs in the colon of Ifnar1-/- animals. Interestingly, cells expressing the anti-inflammatory cytokine receptor IL-10R are more abundant within these subsets in Ifnar1-/- than in wild-type mice. Moreover, blockade of IL-10R in Ifnar1-/- mice increased their susceptibility to S. typhimurium colitis, suggesting that altered numbers of these immunoregulatory cells may underlie the difference in disease severity. This cross-talk between type I IFN and IL-10R signaling pathways may represent a key host cellular mechanism to investigate further in order to unravel the balance between pathogenic inflammation and homeostasis of the colon. Taken together, our data clearly demonstrate that type I IFN signaling is pathogenic in S. typhimurium colitis.

In resting platelets, the integrin αIIbβ3 is present in a low-affinity "bent" state. During platelet aggregation, intracytoplasmic signals induce conformational changes (inside-out signaling) that result in a "swung-out" conformation competent to bind ligands such as fibrinogen. The cytoskeleton plays an essential role in αIIbβ3 activation. We investigated the role of the actin interacting protein Wdr1 in αIIbβ3 activation. Wdr1-hypomorphic mice had a prolonged bleeding time (> 10 minutes) compared to that of wild-type mice (2.1 ± 0.7 minutes). Their platelets had impaired aggregation to collagen and thrombin. In a FeCl3 induced carotid artery thrombosis model, vessel occlusion in Wdr1-hypomorphic mice was prolonged significantly compared to wild-type mice (9.0 ± 10.5 minutes versus 5.8 ± 12.6 minutes (p = 0.041). Activation-induced binding of JON/A (a conformation-specific antibody to activated αIIbβ3) was significantly less in Wdr1-hypomorphic platelets at various concentrations of collagen, indicating impaired inside-out activation of αIIbβ3, despite a normal calcium response. Actin turnover, assessed by measuring F-actin and G-actin ratios during collagen- and thrombin-induced platelet aggregation, was highly impaired in Wdr1-hypomorphic platelets. Furthermore, talin failed to redistribute and translocate to the cytoskeleton following activation in Wdr1-hypomorphic platelets. These studies show that Wdr1 is essential for talin-induced activation of αIIbβ3 during platelet activation.