Miracle-dz/UniFAR-FTUs huggingface dataset:
Azadirachta indica Attenuates Colonic Mucosal Damage in Experimental Colitis Induced by Trinitrobenzene Sulfonic Acid

Azadirachta indica leaves indicated the presence of active principles with proven antioxidants, antiinflammatory, immunomodulatory, free radical scavenging and healing properties. In the present study we evaluated the healing effects of 50% ethanol extract of dried leaves of Azadirachta indica on trinitrobenzene sulfonic acid-induced colitis in rats. Azadirachta indica extract (500 mg/kg) was administered orally, once daily for 14 days and studied for its effects on diarrhoea, food and water intake, body weight changes, colonic damage and inflammation, histology, antibacterial activity and free radicals (nitric oxide and lipid peroxidation), antioxidants (superoxide dismutase, catalase and reduced glutathione) and myeloperoxidase activities in colonic tissue. Intracolonic trinitrobenzene sulfonic acid increased colonic mucosal damage and inflammation, diarrhea, but decreased body weight which were reversed by Azadirachta indica extract and sulfasalazine (positive control) treatments. Azadirachta indica extract showed antibacterial activity. Azadirachta indica extract and sulfasalazine enhanced the antioxidants but decreased free radicals and myeloperoxidase activities affected in trinitrobenzene sulfonic acid-induced colitis. Azadirachta indica extract, thus seemed to be effective in healing trinitrobenzene sulfonic acid-induced colitis in rats.
The strength of negative plant–soil feedback increases from the intraspecific to the interspecific and the functional group level

Abstract One of the processes that may play a key role in plant species coexistence and ecosystem functioning is plant–soil feedback, the effect of plants on associated soil communities and the resulting feedback on plant performance. Plant–soil feedback at the interspecific level (comparing growth on own soil with growth on soil from different species) has been studied extensively, while plant–soil feedback at the intraspecific level (comparing growth on own soil with growth on soil from different accessions within a species) has only recently gained attention. Very few studies have investigated the direction and strength of feedback among different taxonomic levels, and initial results have been inconclusive, discussing phylogeny, and morphology as possible determinants. To test our hypotheses that the strength of negative feedback on plant performance increases with increasing taxonomic level and that this relationship is explained by morphological similarities, we conducted a greenhouse experiment using species assigned to three taxonomic levels (intraspecific, interspecific, and functional group level). We measured certain fitness‐related aboveground traits and used them along literature‐derived traits to determine the influence of morphological similarities on the strength and direction of the feedback. We found that the average strength of negative feedback increased from the intraspecific over the interspecific to the functional group level. However, individual accessions and species differed in the direction and strength of the feedback. None of our results could be explained by morphological dissimilarities or individual traits. Synthesis. Our results indicate that negative plant–soil feedback is stronger if the involved plants belong to more distantly related species. We conclude that the taxonomic level is an important factor in the maintenance of plant coexistence with plant–soil feedback as a potential stabilizing mechanism and should be addressed explicitly in coexistence research, while the traits considered here seem to play a minor role.
A comprehensive benchmarking system for evaluating global vegetation models

We present a benchmark system for global vegetation models. This system provides a quantitative evaluation of multiple simulated vegetation properties, including primary production; seasonal net ecosystem production; vegetation cover; composition and height; fire regime; and runoff. The benchmarks are derived from remotely sensed gridded datasets and site-based observations. The datasets allow comparisons of annual average conditions and seasonal and inter-annual variability, and they allow the impact of spatial and temporal biases in means and variability to be assessed separately. Specifically designed metrics quantify model performance for each process, and are compared to scores based on the temporal or spatial mean value of the observations and a "random" model produced by bootstrap resampling of the observations. The benchmark system is applied to three models: a simple light-use efficiency and water-balance model (the Simple Diagnostic Biosphere Model: SDBM), the Lund-Potsdam-Jena (LPJ) and Land Processes and eXchanges (LPX) dynamic global vegetation models (DGVMs). In general, the SDBM performs better than either of the DGVMs. It reproduces independent measurements of net primary production (NPP) but underestimates the amplitude of the observed CO 2 seasonal cycle. The two DGVMs show little difference for most benchmarks (including the inter-annual variability in the growth rate and seasonal cycle of atmospheric CO 2 ), but LPX represents burnt fraction demonstrably more accurately. Benchmarking also identified several weaknesses common to both DGVMs. The benchmarking system provides a quantitative approach for evaluating how adequately processes are represented in a model, identifying errors and biases, tracking improvements in performance through model development, and discriminating among models. Adoption of such a system would do much to improve confidence in terrestrial model predictions of climate change impacts and feedbacks.
Quick change: post-transcriptional regulation in Pseudomonas

Abstract Pseudomonas species have evolved dynamic and intricate regulatory networks to fine-tune gene expression, with complex regulation occurring at every stage in the processing of genetic information. This approach enables Pseudomonas to generate precise individual responses to the environment in order to improve their fitness and resource economy. The weak correlations we observe between RNA and protein abundance highlight the significant regulatory contribution of a series of intersecting post-transcriptional pathways, influencing mRNA stability, translational activity and ribosome function, to Pseudomonas environmental responses. This review examines our current understanding of three major post-transcriptional regulatory systems in Pseudomonas spp. ; Gac/Rsm, Hfq and RimK, and presents an overview of new research frontiers, emerging genome-wide methodologies, and their potential for the study of global regulatory responses in Pseudomonas.
Neutralizing Activity of Broadly Neutralizing Anti-HIV-1 Antibodies against Clade B Clinical Isolates Produced in Peripheral Blood Mononuclear Cells

ABSTRACT Recently discovered broadly neutralizing antibodies (bNAbs) against HIV-1 demonstrate extensive breadth and potency against diverse HIV-1 strains and represent a promising approach for the treatment and prevention of HIV-1 infection. The breadth and potency of these antibodies have primarily been evaluated by using panels of HIV-1 Env-pseudotyped viruses produced in 293T cells expressing molecularly cloned Env proteins. Here we report on the ability of five bNAbs currently in clinical development to neutralize circulating primary HIV-1 isolates derived from peripheral blood mononuclear cells (PBMCs) and compare the results to those obtained with the pseudovirus panels used to characterize the bNAbs. The five bNAbs demonstrated significantly less breadth and potency against clinical isolates produced in PBMCs than against Env-pseudotyped viruses. The magnitude of this difference in neutralizing activity varied, depending on the antibody epitope. Glycan-targeting antibodies showed differences of only 3- to 4-fold, while antibody 10E8, which targets the membrane-proximal external region, showed a nearly 100-fold decrease in activity between published Env-pseudotyped virus panels and PBMC-derived primary isolates. Utilizing clonal PBMC-derived primary isolates and molecular clones, we determined that the observed discrepancy in bNAb performance is due to the increased sensitivity to neutralization exhibited by 293T-produced Env-pseudotyped viruses. We also found that while full-length molecularly cloned viruses produced in 293T cells exhibit greater sensitivity to neutralization than PBMC-derived viruses do, Env-pseudotyped viruses produced in 293T cells generally exhibit even greater sensitivity to neutralization. As the clinical development of bNAbs progresses, it will be critical to determine the relevance of each of these in vitro neutralization assays to in vivo antibody performance. IMPORTANCE Novel therapeutic and preventive strategies are needed to contain the HIV-1 epidemic. Antibodies with exceptional neutralizing activity against HIV-1 may provide several advantages to traditional HIV drugs, including an improved side-effect profile, a reduced dosing frequency, and immune enhancement. The activity of these antibodies has been established in vitro by utilizing HIV-1 Env-pseudotyped viruses derived from circulating viruses but produced in 293T cells by pairing Env proteins with a backbone vector. We tested PBMC-produced circulating viruses against five anti-HIV-1 antibodies currently in clinical development. We found that the activity of these antibodies against PBMC isolates is significantly less than that against 293T Env-pseudotyped viruses. This decline varied among the antibodies tested, with some demonstrating moderate reductions in activity and others showing an almost 100-fold reduction. As the development of these antibodies progresses, it will be critical to determine how the results of different in vitro tests correspond to performance in the clinic.
Health beliefs and breast cancer screening behaviors among Iranian female health workers.

BACKGROUND Breast cancer is a serious health problem. Early detection is crucial for optimal treatment and reducing mortality. OBJECTIVE The aim of this study was to evaluate health beliefs concerning performance of breast self- examination (BSE) and mammography in a sample of Iranian female health workers. MATERIALS AND METHODS This cross-sectional study was performed among 441 female health care workers (physicians=88, nurses=163, midwives=38, officers=68, and others=84) in 3 different health centers in Yazd, Iran. Data were collected using a self administered questionnaire which included demographic characteristics and then Persian version of the Champion's Health Belief Model Scale (CHBMS). RESULTS The mean age of the participants was 34.7±13.7. It was found that 41.9% of the workers performed BSE in the past and 14.9% of them regularly, but only 10.6% of them had undergone a mammogram. Perceived barriers to BSE (F=6.351, P=0.021) and mammography (F=5.214, p=0.022) were significantly higher in officers than physicians, nurses or midwives. Perceived barriers were lower among those who had performed BSE and mammography, but not significant (p=0.34 and p=0.56, respectively). Furthermore, perceived susceptibility and perceived benefits of the workers who had BSE and mammography were significantly higher than who did not (p<0.05). Perceived seriousness was not a significant variable in BSE and mammography (p=0.71 and p=0.43, respectively). CONCLUSIONS The health beliefs of health workers concerning the perceived susceptibility of breast cancer and the perceived benefits BSE and mammography significantly impact their screening practices.
Colours and luminosities of z = 0.1 galaxies in the eagle simulation

We calculate the colours and luminosities of redshift z = 0.1 galaxies from the EAGLE simulation suite using the GALAXEV population synthesis models. We take into account obscuration by dust in birth clouds and diffuse ISM using a two-component screen model, following the prescription of Charlot and Fall. We compare models in which the dust optical depth is constant to models where it depends on gas metallicity, gas fraction and orientation. The colours of EAGLE galaxies for the more sophisticated models are in broad agreement with those of observed galaxies. In particular, EAGLE produces a red sequence of passive galaxies and a blue cloud of star forming galaxies, with approximately the correct fraction of galaxies in each population and with g-r colours within 0.1 magnitudes of those observed. Luminosity functions from UV to NIR wavelengths differ from observations at a level comparable to systematic shifts resulting from a choice between Petrosian and Kron photometric apertures. Despite the generally good agreement there are clear discrepancies with observations. The blue cloud of EAGLE galaxies extends to somewhat higher luminosities than in the data, consistent with the modest underestimate of the passive fraction in massive EAGLE galaxies. There is also a moderate excess of bright blue galaxies compared to observations. The overall level of agreement with the observed colour distribution suggests that EAGLE galaxies at z = 0.1 have ages, metallicities and levels of obscuration that are comparable to those of observed galaxies.
t4 report

Summary Read-across, i.e. filling toxicological data gaps by relating to similar chemicals, for which test data are available, is usually done based on chemical similarity. Besides structure and physico-chemical properties, however, biological similarity based on biological data adds extra strength to this process. In the context of developing Good Read-Across Practice guidance, a number of case studies were evaluated to demonstrate the use of biological data to enrich read-across. In the simplest case, chemically similar substances also show similar test results in relevant in vitro assays. This is a well-established method for the read-across of e.g. genotoxicity assays. Larger datasets of biological and toxicological properties of hundreds and thousands of substances become increasingly available enabling big data approaches in read-across studies. Several case studies using various big data sources are described in this paper. An example is given for the US EPA’s ToxCast dataset allowing read-across for high quality uterotrophic assays for estrogenic endocrine disruption. Similarly, an example for REACH registration data enhancing read-across for acute toxicity studies is given. A different approach is taken using omics data to establish biological similarity: Examples are given for stem cell models in vitro and short-term repeated dose studies in rats in vivo to support read-across and category formation. These preliminary biological data-driven read-across studies highlight the road to the new generation of read-across approaches that can be applied in chemical safety assessment.
Abstract 12723: Referral to Cardiac Rehabilitation After Percutaneous Coronary Intervention, Coronary Artery Bypass Surgery, and Valve Surgery: Data From the Clinical Outcomes Assessment Program

Introduction: Despite guideline recommendations that all patients undergoing percutaneous coronary intervention (PCI), coronary artery bypass surgery (CABG), or valve surgery be referred to cardiac rehabilitation, cardiac rehabilitation is underused. The objective of this study was to identify predictors of cardiac rehabilitation referral after PCI, CABG, and valve surgery. Methods: We analyzed data from the Clinical Outcomes Assessment Program (COAP), a registry of all non-federal hospitals performing PCI and cardiac surgery in Washington State. We included eligible PCI, CABG, and valve surgery patients from 2010 to 2015 who were discharged alive. We analyzed PCI and cardiac surgery separately by performing multivariate hierarchical logistic regression for the outcome of cardiac rehabilitation referral at discharge, clustered by hospital. Candidate predictors included age, gender, race/ethnicity, and comorbidities. Results: Cardiac rehabilitation referral was reported in 47% (32,049/67,556) of eligible P.
Genome-Wide Identification and Classification of Soybean C2H2 Zinc Finger Proteins and Their Expression Analysis in Legume-Rhizobium Symbiosis

Root nodule symbiosis (RNS) is one of the most productive and economical systems for nitrogen fixation, and previous studies have shown that several nodule-specific C2H2-zinc finger proteins (ZFPs) play important roles in symbiosis establishment and nodule function. However, C2H2-ZFPs are the most widespread ZFPs in eukaryotes, and a great variation of structure and function exist among the family members. It remains largely unclear whether or not special types of C2H2-ZF genes participate in symbiosis, especially in soybean. In the present study, we performed a genome-wide survey of soybean C2H2-ZF genes, and 321 soybean C2H2-ZF genes were identified and classified into 11 clearly distinguishable subsets (Gm-t1-SF, Gm-t2-SF, Gm-1i-Q-SF, Gm-1i-M-SF, Gm-1i-Z-SF, Gm-1i-D-SF, Gm-2i-Q-SF, Gm-2i-M-SF, Gm-2i-Mix-SF, Gm-3i-SF, and Gm-4i-SF) based on the arrangements, numbers, and types of C2H2-ZF domains. Phylogenetic and gene ontology analyses were carried out to assess the conserved sequence and GO function among these subsets, and the results showed that the classification of soybean C2H2-ZFPs was reasonable. The expression profile of soybean C2H2-ZFPs in multiple tissues showed that nearly half of soybean C2H2-ZFPs within different subsets had expressions in nodules, including a clustering branch consisting of 11 Gm-1i-Q-SF genes specifically expressed in symbiotic-relative tissues. RNA-Seq was used to identify symbiosis-related soybean C2H2-ZFPs, and the expression pattern of the soybean C2H2-ZFPs in roots and nodules at different development stages showed that soybean C2H2-ZFPs mainly played roles in nodule development or nodule function rather than nodulation signal transduction, and nearly half of these genes had high expressions and/or different expression patterns during soybean nodule development, especially for the six clustering branches of genes consisting of different subsets of C2H2-ZFPs. Furthermore, the selected symbiosis-related soybean C2H2-ZFPs might function in legume-rhizobium symbiosis through regulating or interacting with other key proteins. Taken together, our findings provided useful information for the study on classification and conservative function of C2H2-ZFPs, and offered solid evidence for investigation of rhizobium symbiosis-related C2H2-ZFPs in soybean or other legumes.
k-Same-Net: k-Anonymity with Generative Deep Neural Networks for Face Deidentification †

Image and video data are today being shared between government entities and other relevant stakeholders on a regular basis and require careful handling of the personal information contained therein. A popular approach to ensure privacy protection in such data is the use of deidentification techniques, which aim at concealing the identity of individuals in the imagery while still preserving certain aspects of the data after deidentification. In this work, we propose a novel approach towards face deidentification, called k-Same-Net, which combines recent Generative Neural Networks (GNNs) with the well-known k-Anonymitymechanism and provides formal guarantees regarding privacy protection on a closed set of identities. Our GNN is able to generate synthetic surrogate face images for deidentification by seamlessly combining features of identities used to train the GNN model. Furthermore, it allows us to control the image-generation process with a small set of appearance-related parameters that can be used to alter specific aspects (e.g., facial expressions, age, gender) of the synthesized surrogate images. We demonstrate the feasibility of k-Same-Net in comprehensive experiments on the XM2VTS and CK+ datasets. We evaluate the efficacy of the proposed approach through reidentification experiments with recent recognition models and compare our results with competing deidentification techniques from the literature. We also present facial expression recognition experiments to demonstrate the utility-preservation capabilities of k-Same-Net. Our experimental results suggest that k-Same-Net is a viable option for facial deidentification that exhibits several desirable characteristics when compared to existing solutions in this area.
Development of resilient modulus prediction models for base and subgrade pavement layers from in situ devices test results

Currently, the design of flexible pavements is generally conducted based on static properties such as California Bearing Ratio and soil support value. These properties do not represent the actual response of the pavement layers under traffic loadings. Recognizing this deficiency, the current and the 2002 mechanistic –empirical guide for design of pavement structures recommended the use of resilient modulus for characterizing the base and subgrade soil and for the design of flexible pavements. The objective of this study was to develop models to estimate the resilient modulus of base and subgrade soils from in situ test devices. Two types of cohesive soils and three types of granular soils commonly used in Louisiana were considered. Three types of in situ devices Geogauge, Light Falling Weight Deflectometer, Dynamic Cone Penetrometer and a laboratory repeated triaxial test were conducted on the soil types evaluated at various moisture content and dry density combinations. Statistical models for predicting the resilient modulus were developed based on the field and laboratory test results. These models correlate the resilient modulus to the in-situ test devices test results and basic soil properties. Good agreement was observed between predicted and measured values of the resilient modulus from the laboratory triaxial test.
Association of History of Gestational Diabetes With Long-term Cardiovascular Disease Risk in a Large Prospective Cohort of US Women

Importance Previous studies identify gestational diabetes (GD) as a risk factor for intermediate markers of cardiovascular disease (CVD) risk; however, few are prospective, evaluate hard CVD end points, or account for shared risk factors including body weight and lifestyle. Objective To prospectively evaluate history of GD in relation to incident CVD risk. Design, Setting, and Participants The Nurses’ Health Study II (NHS II) is an observational cohort study of US female nurses established in 1989, with ongoing follow-up. Biennial questionnaires updated behavioral characteristics, health outcomes, and lifestyle factors. Multivariable Cox models estimated the hazard ratio (HR) and 95% CI for CVD risk. We included 89 479 women who reported at least 1 pregnancy and were free of CVD and cancer at baseline. Follow-up through May 31, 2015, was complete for more than 90% of eligible participants. Exposures History of GD was self-reported at baseline (1989) via questionnaire and updated every 2 years. Main Outcomes and Measures We observed 1161 incident self-reported nonfatal or fatal myocardial infarction or stroke, confirmed via medical records. Results Participants had a mean (SD) age of 34.9 (4.7) years. Adjusting for age, prepregnancy body mass index, and other covariates, GD vs no GD was associated with subsequent CVD (HR, 1.43; 95% CI, 1.12-1.81). Additional adjustment for weight gain since pregnancy and updated lifestyle factors attenuated the association (HR, 1.29; 95% CI, 1.01-1.65). Classifying GD by progression to T2D in relation to CVD risk indicated a positive association for GD with progression to T2D vs no GD or T2D (HR, 4.02; 95% CI, 1.94-8.31), and an attenuated relationship for GD only (HR, 1.30; 95% CI, 0.99-1.71). Conclusions and Relevance Gestational diabetes was positively associated with CVD later in life, although the absolute rate of CVD in this younger cohort of predominantly white women was low. This relationship is possibly mediated in part by subsequent weight gain and lack of healthy lifestyle.