Miracle-dz/UniFAR-FTUs huggingface dataset:
Risk prediction models for acute kidney injury in adults: An overview of systematic reviews

Background The incidence of Acute Kidney Injury (AKI) and its human and economic cost is increasing steadily. One way to reduce the burden associated with AKI is to prevent the event altogether. An important step in prevention lies in AKI risk prediction. Due to the increasing number of available risk prediction models (RPMs) clinicians need to be able to rely on systematic reviews (SRs) to provide an objective assessment on which RPM can be used in a specific setting. Our aim was to assess the quality of SRs of RPMs in AKI. Methods The protocol for this overview was registered in PROSPERO. MEDLINE and Embase were searched for SRs of RPMs of AKI in any setting from 2003 till August 2020. We used the ROBIS tool to assess the methodological quality of the retrieved SRs. Results Eight SRs were retrieved. All studies were assessed as being at high risk for bias using the ROBIS tool. Eight reviews had a high risk of bias in study eligibility criteria (domain 1), five for study identification and selection (domain 2), seven for data collection and appraisal (domain 3) and seven for synthesis and findings (domain 4). Five reviews were scored at high risk of bias across all four domains. Risk of bias assessment with a formal risk of bias tool was only performed in five reviews. Primary studies were heterogeneous and used a wide range of AKI definitions. Only 19 unique RPM were externally validated, of which 11 had only 1 external validation report. Conclusion The methodological quality of SRs of RPMs of AKI is inconsistent. Most SRs lack a formal risk of bias assessment. SRs ought to adhere to certain standard quality criteria so that clinicians can rely on them to select a RPM for use in an individual patient. Trial registration PROSPERO registration number is CRD 42020204236, available at https://www.crd. york.ac. uk/prospero/display_record. php? RecordID=204236.
Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood

Abstract Tension wood (TW) is a specialized xylem tissue developed under mechanical/tension stress in angiosperm trees. TW development involves transregulation of secondary cell wall genes, which leads to altered wood properties for stress adaptation. We induced TW in the stems of black cottonwood (Populus trichocarpa, Nisqually-1) and identified two significantly repressed transcription factor (TF) genes: class B3 heat-shock TF (HSFB3-1) and MYB092. Transcriptomic analysis and chromatin immunoprecipitation (ChIP) were used to identify direct TF–DNA interactions in P. trichocarpa xylem protoplasts overexpressing the TFs. This analysis established a transcriptional regulatory network in which PtrHSFB3-1 and PtrMYB092 directly activate 8 and 11 monolignol genes, respectively. The TF–DNA interactions were verified for their specificity and transactivator roles in 35 independent CRISPR-based biallelic mutants and overexpression transgenic lines of PtrHSFB3-1 and PtrMYB092 in P. trichocarpa. The gene-edited trees (mimicking the repressed PtrHSFB3-1 and PtrMYB092 under tension stress) have stem wood composition resembling that of TW during normal growth and under tension stress (i.e., low lignin and high cellulose), whereas the overexpressors showed an opposite effect (high lignin and low cellulose). Individual overexpression of the TFs impeded lignin reduction under tension stress and restored high levels of lignin biosynthesis in the TW. This study offers biological insights to further uncover how metabolism, growth, and stress adaptation are coordinately regulated in trees.
Healer-led vs. clinician-led training to improve personal protective equipment use among traditional healers in South Africa: a randomized controlled trial protocol

ABSTRACT There are estimated two million traditional healers in sub-Saharan Africa (SSA), with more than 10% (200,000) working in South Africa. Traditional healers in SSA are frequently exposed to bloodborne pathogens through the widespread practice of traditional ‘injections’, in which the healers perform dozens of subcutaneous incisions to rub herbs directly into the bloodied tissue with their hands. Healers who report exposure to patient blood have a 2.2-fold higher risk of being HIV-positive than those who do not report exposure. We propose a randomized controlled trial (61 healers in the intervention group and 61 healers in the control group) in Mpumalanga Province. Healers will receive personal protective equipment (PPE) education and training, general HIV prevention education, and three educational outreach visits at the healer’s place of practice to provide advice and support for PPE use and disposal. Healers in the control arm will be trained by health care providers, while participants in the intervention arm will receive training and outreach from a team of healers who were early adopters of PPE. We will evaluate intervention implementation using data from surveys, observation, and educational assessments. Implementation outcomes of interest include acceptability and feasibility of PPE use during clinical encounters and fidelity of PPE use during treatments that involve blood exposure. We will test our two intervention strategies to identify an optimal strategy for PPE education in a region with high HIV prevalence.
Gender roles are related to cortisol habituation to repeated social evaluative stressors in adults: secondary analyses from a randomized controlled trial

Abstract Masculine and feminine gender roles influence stressor appraisals and coping in everyday life, but their effect on stress response systems like the hypothalamic-pituitary-adrenocortical axis is unclear. Accordingly, the present study tested the association between gender roles and cortisol responses to repeated stress as part of secondary analyses of data from a randomized controlled trial examining the effects of stress management interventions on cortisol habituation. Participants (Nfinal = 86; 72% female) completed a baseline survey assessing gender role endorsement using the Bem Sex Role Inventory, from which 4 groups were derived: masculine (n = 20), feminine (n = 20), androgynous (high masculinity, high femininity; n = 22), and undifferentiated (low masculinity, low femininity; n = 24). Following the stress management intervention (mindfulness-based stress reduction or cognitive-behavioral skills training) or waitlist period control, participants completed the Trier Social Stress Test on two laboratory visits (48 h apart). Salivary cortisol was assessed 0, 25, 35, and 60 min post-stressor during both laboratory visits. Androgynous and undifferentiated individuals both exhibited a significant decrease in total cortisol from visit 1 to visit 2 (i.e. habituation) whereas feminine and masculine individuals did not. Undifferentiated individuals exhibited greater habituation than feminine and masculine individuals, whereas androgynous individuals only exhibited greater habituation than the feminine group. Controlling for study condition assignment did not alter these results. Results imply that gender roles may be implicated in stress-related disease because of their association with HPA axis functioning during episodes of acute stress.
Organic carbon and nitrogen mineralization in a poorly‐drained mineral soil under transient waterlogged conditions: an incubation experiment

In poorly‐drained mineral soils, little interest has been shown on the effects of the duration and frequency of water saturation periods on carbon (C) and nitrogen (N) mineralization. This study investigates C and N mineralization rates in a poorly‐drained mineral soil in response to transient and permanent waterlogged conditions. Soil samples were incubated for 43 days at 20°C under three treatments: field capacity (T0), transient waterlogged conditions (T1) and permanent waterlogged conditions (T2). The carbon dioxide (CO2)‐C and nitrous oxide (N2O)‐N emissions, soil mineral N content (NH4+, NO2− and NO3−) and contents of organic acids were measured. Soil C mineralization rate during transient waterlogged periods (68.7 mg kg−1 after 38 days) was not significantly different to that at field capacity (58.6 mg kg−1 after 38 days) and was twice that of permanently waterlogged soil. In contrast, the N mineralization rate in soil under transient waterlogged conditions was half that of permanently waterlogged soil or soil at field capacity. An accumulation of acetate and formate was measured in the soil during waterlogged periods in treatments T1 and T2; in treatment T1, de‐saturation resulted in a significant decrease in their concentrations. Mineralization of C and N under transient waterlogged conditions was related to aerobic and anaerobic mineralization processes. Rapid mineralization under oxidizing conditions of labile transient organic compounds from anaerobic processes resulted in pulses of CO2‐C and N2O‐N emissions. This study shows that in poorly‐drained mineral soil, C and N mineralization rates at a given time depend not only on the current soil redox status, but also on that of previous soil conditions. Further investigation comparing different durations of waterlogged conditions could allow better understanding of the impact of previous redox conditions on the dynamics of organic acid, C and N mineralization during transient conditions.
The phase instability of molecular fluid mixtures : dipolar and neutral hard spheres

The many degrees of freedom in fluid mixtures of nonspherical molecules can lead to different kinds of phase transition. We propose to characterize the phase transition uniquely by the eigenvector belonging to the vanishing eigenvalue of the coefficient matrix which multiplies the fluctuation in an expansion of the free energy up to second order. As an example we study the phase transition of a mixture of dipolar hard spheres and neutral hard spheres. We evaluate the coefficient matrix from the calculated correlation functions and find a demixing phase transition combined with small total density changes.
The ecological impacts of multiple environmental stressors on coastal biofilm bacteria

Ecological communities are increasingly exposed to multiple interacting stressors. For example, warming directly affects the physiology of organisms, eutrophication stimulates the base of the food web, and harvesting larger organisms for human consumption dampens top‐down control. These stressors often combine in the natural environment with unpredictable results. Bacterial communities in coastal ecosystems underpin marine food webs and provide many important ecosystem services (e.g. nutrient cycling and carbon fixation). Yet, how microbial communities will respond to a changing climate remains uncertain. Thus, we used marine mesocosms to examine the impacts of warming, nutrient enrichment, and altered top‐predator population size structure (common shore crab) on coastal microbial biofilm communities in a crossed experimental design. Warming increased bacterial α‐diversity (18% increase in species richness and 67% increase in evenness), but this was countered by a decrease in α‐diversity with nutrient enrichment (14% and 21% decrease for species richness and evenness, respectively). Thus, we show some effects of these stressors could cancel each other out under climate change scenarios. Warming and top‐predator population size structure both affected bacterial biofilm community composition, with warming increasing the abundance of bacteria capable of increased mineralization of dissolved and particulate organic matter, such as Flavobacteriia, Sphingobacteriia, and Cytophagia. However, the community shifts observed with warming depended on top‐predator population size structure, with Sphingobacteriia increasing with smaller crabs and Cytophagia increasing with larger crabs. These changes could alter the balance between mineralization and carbon sequestration in coastal ecosystems, leading to a positive feedback loop between warming and CO2 production. Our results highlight the potential for warming to disrupt microbial communities and biogeochemical cycling in coastal ecosystems, and the importance of studying these effects in combination with other environmental stressors.
Non-equilibrium momentum exchange algorithm for molecular dynamics simulation of heat flow in multicomponent systems

A new non-equilibrium molecular dynamics algorithm is presented based on the original work of Müller-Plathe, (1997, J. chem. Phys., 106, 6082), for the non-equilibrium simulation of heat transport maintaining fixed the total momentum as well as the total energy of the system. The presented scheme preserves these properties but, unlike the original algorithm, is able to deal with multicomponent systems, that is with particles of different mass independently of their relative concentration. The main idea behind the new procedure is to consider an exchange of momentum and energy between the particles in the hot and cold regions, to maintain the non-equilibrium conditions, as if they undergo a hypothetical elastic collision. The new algorithm can also be employed in multicomponent systems for molecular fluids and in a wide range of thermodynamic conditions.
Anchoring of Phosphonate and Phosphinate Coupling Molecules on Titania Particles

Titanium oxide particles were treated using six organophosphorus compounds chosen as model coupling molecules: phenylphosphonic and diphenylphosphinic acids, their ethyl esters, and their trimethylsilyl esters. The ability of all of these coupling molecules to modify the surface of the TiO2 particles was demonstrated by elemental analysis, thermogravimetric analysis, and nitrogen adsorption. The bonding modes on the surface were investigated by means of diffuse reflectance IR Fourier transform (DRIFT) and 31P solid-state MAS NMR spectroscopy. Upon irradiation in water, a marked trend to the photooxidative degradation of the anchored organophosphorus groups was evidenced, especially in the case of phosphinate groups.
LATE ELONGATED HYPOCOTYL potentiates resistance conferred by CIRCADIAN CLOCK ASSOCIATED1 to aphid by co-regulating the expression of indole glucosinolate biosynthetic genes

ABSTRACT CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY) are core components of the circadian clock in Arabidopsis thaliana that impacts plant response to biotic stresses. Their clock-regulating functions are believed to be partially redundant, and mutation of either gene leads to shortened periods of the circadian cycle. Our recent study has demonstrated that CCA1 promotes plant resistance to the green peach aphid (Myzus persicae) through modulation of indole glucosinolate biosynthesis, but the role of LHY remains to be elucidated. Here we showed that, similar to cca1-11, single mutant lhy-21 became more susceptible to aphid infestation. Damage to the cca1-11 lhy-21 double mutant by aphids was most pronounced, indicating that the defensive roles of CCA1 and LHY were not entirely redundant. Also, the cyclic expression pattern of key indole glucosinolate biosynthetic genes was considerably disturbed in both single mutants and this was more severe in the double mutant. Apparently, both CCA1 and LHY were necessary for circadian-regulated indole glucosinolate biosynthesis. Taken together, LHY-CCA1 coordination in transcriptional regulation of indole glucosinolate biosynthetic genes most likely contributed to plant defensive capacity against aphids.
Research priorities for elder abuse screening and intervention: A Geriatric Emergency Care Applied Research (GEAR) network scoping review and consensus statement

ABSTRACT The Geriatric Emergency Care Applied Research (GEAR) Network (1) conducted a scoping review of the current literature on the identification of and interventions to address elder abuse among patients receiving care in emergency departments and (2) used this review to prioritize research questions for knowledge development. Two questions guided the scoping review: What is the effect of universal emergency department screening compared to targeted screening or usual practice on cases of elder abuse identified, safety outcomes, and health care utilization? ; and What is the safety, health, legal, and psychosocial impact of emergency department-based interventions vs. usual care for patients experiencing elder abuse? We searched five article databases. Additional material was located through reference lists of identified publications, PsychInfo, and Google Scholar. The results were discussed in a consensus conference; and stakeholders voted to prioritize research questions. No studies were identified that directly addressed the first question regarding assessment strategies, but four instruments used for elder abuse screening in the emergency department were identified. For the second question, we located six articles on interventions for elder abuse in the emergency department; however, none directly addressed the question of comparative effectiveness. Based on these findings, GEAR participants identified five questions as priorities for future research – two related to screening, two related to intervention, and one encompassed both. In sum, research to identify best practices for elder abuse assessment and intervention in emergency departments is still needed. Although there are practical and ethical challenges, rigorous experimental studies are needed.
Healthy versus inflamed lung environments differentially affect mesenchymal stromal cells

Background Despite increased interest in mesenchymal stromal cell (MSC)-based cell therapies for acute respiratory distress syndrome (ARDS), clinical investigations have not yet been successful and our understanding of the potential in vivo mechanisms of MSC actions in ARDS remains limited. ARDS is driven by an acute severe innate immune dysregulation, often characterised by inflammation, coagulation and cell injury. How this inflammatory microenvironment influences MSC functions remains to be determined. Aim The aim of this study was to comparatively assess how the inflammatory environment present in ARDS lungs versus the lung environment present in healthy volunteers alters MSC behaviour. Methods Clinical-grade human bone marrow-derived MSCs (hMSCs) were exposed to bronchoalveolar lavage fluid (BALF) samples obtained from ARDS patients or from healthy volunteers. Following exposure, hMSCs and their conditioned media were evaluated for a broad panel of relevant properties, including viability, levels of expression of inflammatory cytokines, gene expression, cell surface human leukocyte antigen expression, and activation of coagulation and complement pathways. Results Pro-inflammatory, pro-coagulant and major histocompatibility complex (self-recognition) related gene expression was markedly upregulated in hMSCs exposed ex vivo to BALF obtained from healthy volunteers. These changes were less apparent and often opposite in hMSCs exposed to ARDS BALF samples. Conclusion These data provide new insights into how hMSCs behave in healthy versus inflamed lung environments, and strongly suggest that the inflamed environment in ARDS induces hMSC responses that are potentially beneficial for cell survival and actions. This further highlights the need to understand how different disease environments affect hMSC functions. MSCs exposed to a healthy lung environment induce an inflammatory response with increased gene/protein expression associated with self- versus non-self-recognition. These changes were absent or opposite in MSCs exposed to an inflamed ARDS environment. https://bit.ly/3eombO8
MutSα mismatch repair protein stability is governed by subunit interaction, acetylation, and ubiquitination

Abstract In eukaryotes, DNA mismatch recognition is accomplished by the highly conserved MutSα (Msh2/Msh6) and MutSβ (Msh2/Msh3) complexes. Previously, in the yeast Saccharomyces cerevisiae, we determined that deleting MSH6 caused wild-type Msh2 levels to drop by ∼50%. In this work, we determined that Msh6 steady-state levels are coupled to increasing or decreasing levels of Msh2. Although Msh6 and Msh2 are reciprocally regulated, Msh3 and Msh2 are not. Msh2 missense variants that are able to interact with Msh6 were destabilized when Msh6 was deleted; in contrast, variants that fail to dimerize were not further destabilized in cells lacking Msh6. In the absence of Msh6, Msh2 is turned over at a faster rate and degradation is mediated by the ubiquitin-proteasome pathway. Mutagenesis of certain conserved lysines near the dimer interface restored the levels of Msh2 in the absence of Msh6, further supporting a dimer stabilization mechanism. We identified two alternative forms of regulation both with the potential to act via lysine residues, including acetylation by Gcn5 and ubiquitination by the Not4 ligase. In the absence of Gcn5, Msh2 levels were significantly decreased; in contrast, deleting Not4 stabilized Msh2 and Msh2 missense variants with partial function. The stabilizing effect on Msh2 by either the presence of Msh6 or the absence of Not4 are dependent on Gcn5. Taken together, the results suggest that the wild-type MutSα mismatch repair protein stability is governed by subunit interaction, acetylation, and ubiquitination.
Imaging error compensation method for through‐focus scanning optical microscopy images based on deep learning

Through‐focus scanning optical microscopy (TSOM) is a model‐based nanoscale metrology technique which combines conventional bright‐field microscopy and the relevant numerical simulations. A TSOM image is generated after through‐focus scanning and data processing. However, the mechanical vibration and optical noise introduced into the TSOM image during image generation can affect the measurement accuracy. To reduce this effect, this paper proposes a imaging error compensation method for the TSOM image based on deep learning with U‐Net. Here, the simulated TSOM image is regarded as the ground truth, and the U‐Net is trained using the experimental TSOM images by means of a supervised learning strategy. The experimental TSOM image is first encoded and then decoded with the U‐shaped structure of the U‐Net. The difference between the experimental and simulated TSOM images is minimised by iteratively updating the weights and bias factors of the network, to obtain the compensated TSOM image. The proposed method is applied for optimising the TSOM images for nanoscale linewidth estimation. The results demonstrate that the proposed method performs as expected and provides a significant enhancement in accuracy.
Individuality decoded by running patterns: Movement characteristics that determine the uniqueness of human running

Human gait is as unique to an individual as is their fingerprint. It remains unknown, however, what gait characteristics differentiate well between individuals that could define the uniqueness of human gait. The purpose of this work was to determine the gait characteristics that were most relevant for a neural network to identify individuals based on their running patterns. An artificial neural network was trained to recognize kinetic and kinematic movement trajectories of overground running from 50 healthy novice runners (males and females). Using layer-wise relevance propagation, the contribution of each variable to the classification result of the neural network was determined. It was found that gait characteristics of the coronal and transverse plane as well as medio-lateral ground reaction forces provided more information for subject identification than gait characteristics of the sagittal plane and ground reaction forces in vertical or anterior-posterior direction. Additionally, gait characteristics during the early stance were more relevant for gait recognition than those of the mid and late stance phase. It was concluded that the uniqueness of human gait is predominantly encoded in movements of the coronal and transverse plane during early stance.