Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed.
Comparative effects of sodium selenite and selenomethionine upon nutritional muscular dystrophy, selenium-dependent glutathione peroxidase, and tissue selenium concentrations of turkey poults.

Day-old poults from hens depleted of Se were fed low-Se basal diets (containing corn, soybean meal, and torula yeast but no added vitamin E) with graded levels of Se supplied by Na2SeO3 or seleno-DL-methionine for 28 and 35 days in Experiments 1 and 2, respectively. Adding . 04 ppm Se to the basal diet significantly increased body weight and reduced both the incidence of gizzard myopathy and plasma glutamic-oxaloacetic transaminase (PGOT) activity. Further plasma Se and Se-dependent glutathione peroxidase (SeGSHpx) were elevated by increasing levels of dietary Se. There were no differences in these parameters due to the Se compound fed. Plasma SeGSHpx was significantly correlated with both dietary and plasma Se levels. Poults fed selenomethionine had significantly higher concentrations of Se in the gizzard, breast muscle, and pancreas, but not in the liver and heart, compared to poults fed Na2SeO3. These studies indicate that the utilization of Se in both Na2SeO3 and selenomethionine is approximately equal in young turkey poults.
Spatial Ecology of the Coachwhip, Masticophis flagellum (Squamata: Colubridae), in Eastern Texas

Abstract We radio-tracked nine Masticophis flagellum (Coachwhips) to determine home range, habitat use, and movements in eastern Texas from April to October 2000. Home ranges of Coachwhips contained more oak savanna macrohabitat than early-successional pine plantation or forested seep, based on the availability of these three macrohabitats in the study area. Likewise, within their individual home ranges, Coachwhips used oak savanna more than the other two macrohabitats, based on availability. An analysis of microhabitat use revealed that, relative to random sites within their home range, Coachwhips were found at sites with fewer pine trees and more herbaceous vegetation taller than 30 cm. Results of the two analyses, macrohabitat and microhabitat, were consistent: oak savannas contained relatively few pine trees but much herbaceous vegetation taller than 30 cm. Coachwhips made frequent long-distance moves, which resulted in large home ranges. Core activity areas, however, were small. These core activity areas were always within the oak savanna macrohabitat. Long movements, large home ranges, and small core activity areas likely were a result of the preferred oak savanna macrohabitat being patchily distributed in the landscape.
Oxidative Stress-Induced miR-200c Disrupts the Regulatory Loop Among SIRT1, FOXO1, and eNOS.

AIMS Reactive oxygen species (ROS) play a pivotal role in different pathologic conditions, including ischemia, diabetes, and aging. We previously showed that ROS enhance miR-200c expression, causing endothelial cell (EC) apoptosis and senescence. Herein, we dissect the interaction among miR-200c and three strictly related proteins that modulate EC function and ROS production: sirtuin 1 (SIRT1), endothelial nitric oxide synthase (eNOS), and forkhead box O1 (FOXO1). Moreover, the role of miR-200c on ROS modulation was also investigated. RESULTS We demonstrated that miR-200c directly targets SIRT1, eNOS, and FOXO1; via this mechanism, miR-200c decreased NO and increased the acetylation of SIRT1 targets, that is, FOXO1 and p53. FOXO1 acetylation inhibited its transcriptional activity on target genes, that is, SIRT1 and the ROS scavengers, catalase and manganese superoxide dismutase. In keeping, miR-200c increased ROS production and induced p66Shc protein phosphorylation in Ser-36; this mechanism upregulated ROS and inhibited FOXO1 transcription, reinforcing this molecular circuitry. These in vitro results were validated in three in vivo models of oxidative stress, that is, human skin fibroblasts from old donors, femoral arteries from old mice, and a murine model of hindlimb ischemia. In all cases, miR-200c was higher versus control and its targets, that is, SIRT1, eNOS, and FOXO1, were downmodulated. In the mouse hindlimb ischemia model, anti-miR-200c treatment rescued these targets and improved limb perfusion. Innovation and Conclusion: miR-200c disrupts SIRT1/FOXO1/eNOS regulatory loop. This event promotes ROS production and decreases NO, contributing to endothelial dysfunction under conditions of increased oxidative stress such as aging and ischemia. Antioxid. Redox Signal. 27, 328-344.
Effects of methionine and valine on growth and antibody production in chicks infected with live or killed Newcastle disease virus.

Abstract IN PREVIOUS experiments (Bhargava et al., 1970) it was reported that the antibody titer was higher for chicks receiving 0.3 to 0.6% l -methionine levels than for chicks receiving 0.7 to 1.1% l -methionine. The optimum requirement of methionine for growth was about 0.7% while for antibody production it was considerably lower. The reverse was true with valine. As the level of valine in the diet was increased, the antibody titer increased. The requirement of valine for maximum growth response was 0.9% but for optimum antibody production it was higher. Gill and Gershoff (1967), using synthetic antigen, have reported that antibody production was increased by methionine deficiency and decreased by excess methionine in monkeys. However, in 1968, Gershoff et al. did not observe any change in antibody production in rats due to deficiency or excess of methionine using synthetic antigen or sheep red blood cell antigen. Ishiguro and Koyanagi (1968) observed that…
IONet: Learning to Cure the Curse of Drift in Inertial Odometry

Inertial sensors play a pivotal role in indoor localization, which in turn lays the foundation for pervasive personal applications. However, low-cost inertial sensors, as commonly found in smartphones, are plagued by bias and noise, which leads to unbounded growth in error when accelerations are double integrated to obtain displacement. Small errors in state estimation propagate to make odometry virtually unusable in a matter of seconds. We propose to break the cycle of continuous integration, and instead segment inertial data into independent windows. The challenge becomes estimating the latent states of each window, such as velocity and orientation, as these are not directly observable from sensor data. We demonstrate how to formulate this as an optimization problem, and show how deep recurrent neural networks can yield highly accurate trajectories, outperforming state-of-the-art shallow techniques, on a wide range of tests and attachments. In particular, we demonstrate that IONet can generalize to estimate odometry for non-periodic motion, such as a shopping trolley or baby-stroller, an extremely challenging task for existing techniques.
FAST implementation in Bangladesh: high frequency of unsuspected tuberculosis justifies challenges of scale-up.

SETTING National Institute of Diseases of the Chest and Hospital, Dhaka; Bangladesh Institute of Research and Rehabilitation in Diabetes, Endocrine and Metabolic Disorders, Dhaka; and Chittagong Chest Disease Hospital, Chittagong, Bangladesh. OBJECTIVE To present operational data and discuss the challenges of implementing FAST (Find cases Actively, Separate safely and Treat effectively) as a tuberculosis (TB) transmission control strategy. DESIGN FAST was implemented sequentially at three hospitals. RESULTS Using Xpert® MTB/RIF, 733/6028 (12.2%, 95%CI 11.4-13.0) patients were diagnosed with unsuspected TB. Patients with a history of TB who were admitted with other lung diseases had more than twice the odds of being diagnosed with unsuspected TB as those with no history of TB (OR 2.6, 95%CI 2.2-3.0, P < 0.001). Unsuspected multidrug-resistant TB (MDR-TB) was diagnosed in 89/1415 patients (6.3%, 95%CI 5.1-7.7). Patients with unsuspected TB had nearly five times the odds of being diagnosed with MDR-TB than those admitted with a known TB diagnosis (OR 4.9, 95%CI 3.1-7.6, P < 0.001). Implementation challenges include staff shortages, diagnostic failure, supply-chain issues and reliance on external funding. CONCLUSION FAST implementation revealed a high frequency of unsuspected TB in hospitalized patients in Bangladesh. Patients with a previous history of TB have an increased risk of being diagnosed with unsuspected TB. Ensuring financial resources, stakeholder engagement and laboratory capacity are important for sustainability and scalability.
Exclusive Breastfeeding Is More Common Among HIV-Infected Than HIV-Uninfected Kenyan Mothers at 6 Weeks and 6 Months Postpartum.

OBJECTIVE To compare breastfeeding practices determined by mothers' own recall versus a stable isotope technique (deuterium oxide dilution) among human immunodeficiency virus (HIV)-infected and HIV-uninfected mothers at 6 weeks and 6 months postpartum. METHODS Exclusive breastfeeding (EBF) rates were assessed cross-sectionally at 6 weeks and 6 months postpartum among 75 HIV-positive and 68 HIV-negative women attending postnatal care. EBF was derived from maternal 24-hour recall of foods that were fed to the infant and by objective measurement of nonhuman milk-water intake using deuterium oxide (DO) dilution technique. RESULTS Multivariable logistic analyses were adjusted for infant sex, gravidity, maternal age, marital status, and maternal education. Using recall method, a greater proportion of HIV-infected mothers exclusively breastfed than HIV-uninfected mothers both at 6 weeks postpartum [94.1% versus 76.9%, respectively (adjusted odds ratio [aOR] 7.81; 95% confidence interval [CI] 1.9-31.6, p = 0.004)] and at 6 months postpartum [75% versus 59.7%, respectively (aOR 2.27; 95% CI 1.0-5.3, p = 0.058)]. At 6 weeks postpartum EBF rates from the DO technique were 23.5% and 13.8% for HIV-positive and HIV-negative mothers, respectively (aOR 0.35; 95% CI 0.11-1.04, p = 0.059). At 6 months postpartum, the DO technique determined EBF rates were 43.3% among HIV-positive and 24.2% among HIV-negative mothers, respectively (aOR 2.4; 95% CI 1.0-5.7, p = 0.048). CONCLUSIONS HIV-infected mothers are more likely to exclusively breastfeed compared with HIV-uninfected mothers. In this resource-poor setting, maternal recall overestimates EBF rates as compared with the deuterium oxide dilution technique. Validating EBF recall data using the objective DO technique is highly recommended for accurate tracking toward global targets on breastfeeding practices.
Netazepide, a gastrin/cholecystokinin‐2 receptor antagonist, can eradicate gastric neuroendocrine tumours in patients with autoimmune chronic atrophic gastritis

AIMS Netazepide, a gastrin/cholecystokinin 2 receptor antagonist, once daily for 12 weeks reduced the number of tumours and size of the largest one in 16 patients with autoimmune chronic atrophic gastritis (CAG), achlorhydria, hypergastrinaemia and multiple gastric neuroendocrine tumours (type 1 gastric NETs), and normalized circulating chromogranin A (CgA) produced by enterochromaffin-like cells, the source of the tumours. The aim was to assess whether longer-term netazepide treatment can eradicate type 1 gastric NETs. METHODS After a mean 14 months off netazepide, 13 of the 16 patients took it for another 52 weeks. Assessments were: gastroscopy; gene-transcript expression in corpus biopsies using quantitative polymerase chain reaction; blood CgA and gastrin concentrations; and safety assessments. RESULTS While off-treatment, the number of tumours, the size of the largest one, and CgA all increased again. Netazepide for 52 weeks: cleared all tumours in 5 patients; cleared all but one tumour in one patient; reduced the number of tumours and size of the largest one in the other patients; normalized CgA in all patients; and reduced mRNA abundances of CgA and histidine decarboxylase in biopsies. Gastrin did not increase further, confirming that the patients had achlorhydria. Netazepide was safe and well tolerated. CONCLUSIONS A gastrin/cholecystokinin 2 receptor antagonist is a potential medical and targeted treatment for type 1 gastric NETs, and an alternative to regular gastroscopy or surgery. Treatment should be continuous because the tumours will regrow if it is stopped. Progress can be monitored by CgA in blood or biomarkers in mucosal biopsies.
Prevalence and Predictors of Periodontal Disease among Pregnant Women in Mali, West Africa

Background: Epidemiologic reports on dental or oral health in Mali West Africa are rare. The prevalence of periodontal disease (PD) has not been well established among pregnant women in this sub-Saharan nation. Aim: The purpose of this study was three-fold: to describe oral health self-care behaviors; to measure the prevalence of PD; and to determine predictors of PD among pregnant women in southeastern Mali. Methods and Subjects: In this cross-sectional, correlational study, the Ramfjord Periodontal Index (PDI) and the Community Periodontal Index (CPI) were used to assess levels of PD. Seventy-four pregnant women were surveyed for oral self-care behaviors and examined for PD. Results: Almost all women said they brushed their teeth daily. Years of schooling was a statistically significant predictor of brushing frequency (P=0.005). 81% of the women had never had a professional dental exam. Based on the PDI, 24% were diagnosed with gingivitis and 49% with periodontitis. According to the CPI, 47% had pathological pockets in the periodontium. A history of previous oral/dental problems was a predictor of the severity of periodontal disease (P <.001). Conclusion: The presence of periodontal disease among this sample of Malian women was high; oral hygiene behaviors and use of dental professionals were low. Screening for PD should be included as a routine part of antenatal care. Research is needed in Mali to determine if PD is a risk factor for adverse pregnancy outcomes.
New pharmacological insights of Galactia glaucescens

Abstract Galactia glaucescens leaves are popularly used against snakebites in Brazil. The hydroethanolic extract from aerial parts of G. glaucescens (HEGg) was assayed against the neurotoxicity and myotoxicity induced by Bothrops jararacussu venom. A traditional myographic technique was applied for neurotoxicity and the resulting muscles were treated routinely by light microscopy analysis for myotoxicity. Additionally, the antimicrobial potential of HEGg was evaluated against Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa strains, as well as Rutin was isolated for the first time in this specie using chromatographic and spectroscopic methods and its antiophidian property was assessed. HEGg totally prevents the neurotoxicity and myotoxicity effects caused by B. jararacussu, but did not show any antimicrobial effect. Concluding, HEGg and Rutin were able to counteract the toxic effects of the venom and confirmed the antiophidian potential, but not antimicrobial, of G. glaucescens as an alternative for neutralization of B. jararacussu venom.
Levels of various elements of concern in feed phosphates of domestic and foreign origin.

Thirty-six feed phosphates, including nine mono-dicalcium phosphates (M-DCP, 21% P), 13 di-monocalcium phosphates (D-MCP, 18.5% P), and 14 thermochemically produced defluorinated phosphates (DFP, 18.0% P), were analyzed for moisture, Ca, P, and 9 essential minerals (K, Mg, Na, Cl, Fe, Cu, Mn, Se, and Zn). Also, nine potentially toxic elements (Al, F, As, Cd, Cr, Hg, Pb, Ni, and V) were determined. All of the M-DCP were of domestic origin; 5 of the 13 D-MCP samples were obtained in Algeria, Peru, Holland, and South Africa. The DFP samples included 10 domestic products, 2 samples from Russia, 1 from Poland, and 1 from Japan. Levels of Na were high in the DFP samples (3.96 to 5.78%), except for the two Russian samples, which contained only . 16 and . 19%. Magnesium levels varied from . 09 to . 76%, . 02 to 1.21%, and . 01 to 1.54% in the M-DCP, D-MCP, and DFP samples, respectively. Two Russian DFP samples contained 1.51 and 1.54% Mg. Chlorine levels were generally quite low (.002 to .020%); however, two precipitated D-MCP samples contained . 12 and 1.47% Cl. Iron levels were high (.24 to 1.41%) in all samples except the bone-precipitated D-MCP (.039%), and the reference standard, calcium phosphate, dibasic dihydrate, USP (.029%). Levels of Cu, Mn, and Zn were quite variable. Cadmium varied from < 1 ppm in the DFP samples to 67 ppm in one experimental M-DCP. Vanadium levels varied from 20 to 796 ppm in one experimental M-DCP sample. Fluorine levels were in the acceptable range, . 05 to . 21%. (ABSTRACT TRUNCATED AT 250 WORDS)
The histopathologic reliability of tissue taken from cadavers within the gross anatomy laboratory

The purpose of this study was to examine the histopathologic reliability of embalmed cadaveric tissue taken from the gross anatomy laboratory. Tissue samples from hearts, livers, lungs, and kidneys were collected after the medical students’ dissection course was completed. All of the cadavers were embalmed in a formalin‐based fixative solution. The tissue was processed, embedded in paraffin, sectioned at six micrometers, and stained with H&E. The microscope slides were evaluated by a board certified pathologist to determine whether the cellular components of the tissues were preserved at a high enough quality to allow for histopathologic diagnosis. There was a statistically significant relationship between ratings and organ groups. Across all organs, there was a smaller proportion of “poor” ratings. The lung group had the highest percentage of “poor” ratings (23.1%). The heart group had the least “poor” ratings (0.0%). The largest percentage of “satisfactory” ratings were in the lung group (52.8%), and the heart group contained the highest percentage of “good” ratings (58.5%) The lung group had the lowest percentage of “good” ratings (24.2%). These results indicate that heart tissue is more reliable than lung, kidney, or liver tissue when utilizing tissue from the gross anatomy laboratory for research and/or educational purposes. This information advises educators and researchers about the quality and histopathologic reliability of tissue samples obtained from the gross anatomy laboratory. Anat Sci Educ 11: 207–214. © 2017 American Association of Anatomists.
Thermophilic Alkaline Fermentation Followed by Mesophilic Anaerobic Digestion for Efficient Hydrogen and Methane Production from Waste-Activated Sludge: Dynamics of Bacterial Pathogens as Revealed by the Combination of Metagenomic and Quantitative PCR Analyses

ABSTRACT Thermophilic alkaline fermentation followed by mesophilic anaerobic digestion (TM) for hydrogen and methane production from waste-activated sludge (WAS) was investigated. The TM process was also compared to a process with mesophilic alkaline fermentation followed by a mesophilic anaerobic digestion (MM) and one-stage mesophilic anaerobic digestion (M) process. The results showed that both hydrogen yield (74.5 ml H2/g volatile solids [VS]) and methane yield (150.7 ml CH4/g VS) in the TM process were higher than those (6.7 ml H2/g VS and 127.8 ml CH4/g VS, respectively) in the MM process. The lowest methane yield (101.2 ml CH4/g VS) was obtained with the M process. Taxonomic results obtained from metagenomic analysis showed that different microbial community compositions were established in the hydrogen reactors of the TM and MM processes, which also significantly changed the microbial community compositions in the following methane reactors compared to that with the M process. The dynamics of bacterial pathogens were also evaluated. For the TM process, the reduced diversity and total abundance of bacterial pathogens in WAS were observed in the hydrogen reactor and were further reduced in the methane reactor, as revealed by metagenomic analysis. The results also showed not all bacterial pathogens were reduced in the reactors. For example, Collinsella aerofaciens was enriched in the hydrogen reactor, which was also confirmed by quantitative PCR (qPCR) analysis. The study further showed that qPCR was more sensitive for detecting bacterial pathogens than metagenomic analysis. Although there were some differences in the relative abundances of bacterial pathogens calculated by metagenomic and qPCR approaches, both approaches demonstrated that the TM process was more efficient for the removal of bacterial pathogens than the MM and M processes. IMPORTANCE This study developed an efficient process for bioenergy (H2 and CH4) production from WAS and elucidates the dynamics of bacterial pathogens in the process, which is important for the utilization and safe application of WAS. The study also made an attempt to combine metagenomic and qPCR analyses to reveal the dynamics of bacterial pathogens in anaerobic processes, which could overcome the limitations of each method and provide new insights regarding bacterial pathogens in environmental samples.
Predictors of Hearing Protection Use Among Industrial Workers

Promoting the use of hearing protection devices (HPDs) can prevent noise-induced hearing loss (NIHL) among workers who are exposed to excessive noise. In the present study, the authors examine factors that may explain HPD use among industrial workers from 15 manufacturing plants in Thailand. Participants consisted of 268 randomly selected workers exposed to harmful noise levels for which routine HPD use was required. Logistic regression analysis of study variables revealed the most powerful predictors of HPD use were perceived hearing status (b = 0.66, p < .001) and interpersonal factors (i.e., role modeling and interpersonal support; b = 0.20, p < .001). Together, these variables correctly classified 63.4% of the cases. These findings have implications for interventions aimed at motivating workers to use HPDs regularly.
Pfam 10 years on: 10 000 families and still growing

Classifications of proteins into groups of related sequences are in some respects like a periodic table for biology, allowing us to understand the underlying molecular biology of any organism. Pfam is a large collection of protein domains and families. Its scientific goal is to provide a complete and accurate classification of protein families and domains. The next release of the database will contain over 10,000 entries, which leads us to reflect on how far we are from completing this work. Currently Pfam matches 72% of known protein sequences, but for proteins with known structure Pfam matches 95%, which we believe represents the likely upper bound. Based on our analysis a further 28,000 families would be required to achieve this level of coverage for the current sequence database. We also show that as more sequences are added to the sequence databases the fraction of sequences that Pfam matches is reduced, suggesting that continued addition of new families is essential to maintain its relevance.