Miracle-dz/UniFAR-FTUs huggingface dataset:
Lactobacillus johnsonii alleviates colitis by TLR1/2-STAT3 mediated CD206+ macrophagesIL-10 activation

ABSTRACT Imbalance of gut microbiota homeostasis is related to the occurrence of ulcerative colitis (UC), and probiotics are thought to modulate immune microenvironment and repair barrier function. Here, in order to reveal the interaction between UC and gut microbiota, we screened a new probiotic strain by 16S rRNA sequencing from Dextran Sulfate Sodium (DSS)-induced colitis mice, and explored the mechanism and clinical relevance. Lactobacillus johnsonii (L. johnsonii), as a potential anti-inflammatory bacterium was decreased colonization in colitis mice. Gavage L. johnsonii could alleviate colitis by specifically increasing the proportion of intestinal macrophages and the secretion of Il-10 with macrophages depleted model and in Il10−/− mice. We identified this subset of immune cells activated by L. johnsonii as CD206+ macrophagesIL−10. Mechanistically, L. johnsonii supplementation enhanced the mobilization of CD206+ macrophagesIL−10 through the activation of STAT3 in vivo and in vitro. In addition, we revealed that TLR1/2 was essential for the activation of STAT3 and the recognition of L. johnsonii by macrophages. Clinically, there was positive correlation between the abundance of L. johnsonii and the expression level of MRC1, IL10 and TLR1/2 in UC tissues. L. johnsonii could activate native macrophages into CD206+ macrophages and release IL-10 through TLR1/2-STAT3 pathway to relieve experimental colitis. L. johnsonii may serve as an immunomodulator and anti-inflammatory therapeutic target for UC.
Current fluctuations in the zero-range process with open boundaries

We discuss the long-time limit of the integrated current distribution for the one-dimensional zero-range process with open boundaries. We observe that the current fluctuations become site dependent above some critical current and argue that this is a precursor of the condensation transition which occurs in such models. Our considerations for the totally asymmetric zero-range process are complemented by a Bethe ansatz treatment for the equivalent exclusion process.
Kinetic theory of quantum transport at the nanoscale

We present a quantum-kinetic scheme for the calculation of non-equilibrium transport properties in nanoscale systems. The approach is based on a Liouville-master equation for a reduced density operator and represents a generalization of the well-known Boltzmann kinetic equation. The system, subject to an external electromotive force, is described using periodic boundary conditions. We demonstrate the feasibility of the approach by applying it to a double-barrier resonant tunneling structure.
Evidence for a Merger-induced Shock Wave in ZwCl 0008.8+5215 with Chandra and Suzaku

We present the results from new deep Chandra (∼410 ks) and Suzaku (∼180 ks) observations of the merging galaxy cluster ZwCl 0008.8+5215 (z = 0.104). Previous radio observations revealed the presence of a double radio relic located diametrically west and east of the cluster center. Using our new Chandra data, we find evidence for the presence of a shock at the location of the western relic, RW, with a Mach number from the density jump. We also measure and from the temperature jump, with Chandra and Suzaku, respectively. These values are consistent with the Mach number estimate from a previous study of the radio spectral index, under the assumption of diffusive shock acceleration ( ). Interestingly, the western radio relic does not entirely trace the X-ray shock. A possible explanation is that the relic traces fossil plasma from nearby radio galaxies that is reaccelerated at the shock. For the eastern relic we do not detect an X-ray surface brightness discontinuity, despite the fact that radio observations suggest a shock with . The low surface brightness and reduced integration time for this region might have prevented the detection. The Chandra surface brightness profile suggests , while the Suzaku temperature measurements found . Finally, we also detect a merger-induced cold front on the western side of the cluster, behind the shock that traces the western relic.
Manuscript: Archives of sexual behavior Title: Impact of Migration and Acculturation on Turkish Men Who Have Sex With Men in Germany: Results From the 2010 European MSM Internet Survey

Authors: Axel J Schmidt, Michael Ross, Rigmor C Berg, Peyman Altan 1 Sigma Research, Department of Public Health, Environments and Society, London School of Hygiene and Tropical Medicine, London, United Kingdom 2 Program in Human Sexuality, Department of Family Medicine, University of Minnesota Medical School, Minneapolis MN 55454, United States of America 3 Norwegian Institute of Public Health, Oslo, Norway, and University of Tromso, Department of Community Medicine, Tromso, Norway 4 Turkish Public Health Association *Corresponding author: LSHTM, 15-17 Tavistock Place, London WC1H 9SH, United Kingdom axel.j.schmidt@emis-project.eu
Associations Among Loneliness, Purpose in Life and Subjective Cognitive Decline in Ethnoracially Diverse Older Adults Living in the United States

Subjective cognitive decline (SCD), which precedes Mild Cognitive Impairment and dementia, may be affected by purpose in life (PiL) and loneliness in older adults. We investigated associations among PiL, loneliness, and SCD in US Latino (n = 126), Black (n = 74), Asian (n = 33), and White (n = 637) adults. Higher PiL predicted lower SCD in all groups (p-values < .012), except Black participants. Lower loneliness predicted lower SCD in Latino and White groups (p-values < .05), and PiL moderated this association in White adults. PiL and loneliness may play important roles in cognitive decline. Differential predictors of SCD suggest differential targets for preventing cognitive decline and dementia across ethnoracial groups.
Practical challenges of continuous real‐time functional magnetic resonance imaging neurofeedback with multiband accelerated echo‐planar imaging and short repetition times

Continuous real‐time functional magnetic resonance imaging (fMRI) neurofeedback is gaining increasing scientific attention in clinical neuroscience and may benefit from the short repetition times of modern multiband echoplanar imaging sequences. However, minimizing feedback delay can result in technical challenges. Here, we report a technical problem we experienced during continuous fMRI neurofeedback with multiband echoplanar imaging and short repetition times. We identify the possible origins of this problem, describe our current interim solution and provide openly available workflows and code to other researchers in case they wish to use a similar approach.
Introduction of gloved hand to cage induces 22-kHz ultrasonic vocalizations in male albino rats

Rodents emit ultrasonic vocalizations (USVs) above the human hearing threshold of ~ 20 kHz to communicate emotional states and to coordinate their social interactive behavior. Twenty-two kHz USVs emitted by adult rats have been reported in a variety of aversive social and behavioral situations. They occur not only under painful or restraining conditions but can also be evoked by gentle cutaneous touch or airflow. This study aimed to test if placement of a human hand in a cage can evoke 22-kHz USVs. It was found that 36% of the adult male Sprague-Dawley and 13% of the adult male Wistar Han rats emitted 22-kHz USVs when a gloved hand was introduced into the cages. Average vocalization onset latencies were 5.0 ± 4.4 s (Sprague-Dawley) and 7.4 ± 4.0 s (Wistar Han) and the USVs had a stable frequency (22 kHz) across the calls, ranging from 0.1 to 2.3 seconds in duration. Surprisingly, no 22-kHz USVs were found in any female Wistar Han rats tested. To further explore the mechanisms underlying this observation, we compared retinal function, basal serum corticosterone, and testosterone levels between the 22-kHz USV responders and non-responders. None of these parameters or endpoints showed any significant differences between the two cohorts. The results suggest that the introduction of a gloved-hand inside the cage can trigger adult male albino rats to emit 22-kHz ultrasonic vocalizations. This response should be considered in USV studies and animal welfare.
Transition to spatially periodic patterns in nematics under oscillatory shear flow: linear analysis

We consider the orientational instabilities, both homogeneous and spatially periodic, developing in a nematic liquid crystal under rectilinear oscillatory Couette flow for director alignment perpendicular to the flow plane. Using numerical and analytical approaches we determine the critical amplitude of oscillatory flow instabilities, the critical wave number and the symmetry of the destabilizing mode. It was found, that by varying of the oscillatory flow frequency the instability changes its temporal symmetry. The mechanism of this transition is coupled with the inertia of the nematic fluid. We also shown that an electric field applied to the nematic layer can induce switching between instabilities with different spatial and temporal symmetries. The complete phase diagram of the flow instabilities is presented
Application of T-method to AC problem based on boundary element method

A current vector potential (T) method using the BEM (boundary element method) to solve 3-D eddy current problems is described. The features of the method are that only one kind of variable (T) is needed in the conductor region and that the unknowns are only defined on the conductor surface. The derivation of the basic equations and a new technique that imposes a gage condition are presented. An application to an AC problem is examined with particular attention to the gage condition. >
Slip-Free Driving Method for Nonresonant Piezoelectric Actuator

It is generally considered that in the ultrasonic motor the motion always slips and scratches. The nonresonant ultrasonic motor (NRUSM) expected for future precision stage systems should, however, overcome the difficulties of the wear of friction materials, which has been encountered in the use of conventional ultrasonic motors. The wear occurs by slipping and may be reduced by material selection. In this paper, we focus on the control method at actuation to prevent slipping. The advantages of NRUSM in the ability to control the drive frequency as well as the drive amplitude are shown, and this is effective in reducing wear and obtaining long-term stability. The drive frequency condition for no slippage under sinusoidal waveforms was calculated. The experimental results correspond to the theoretical calculated drive frequency. Because the resultant values of the frequencies are low for practical applications, we present the slip-free actuation method of using the new actuator's driving waveform and time chart in order to drive the stage at constant accelerated motion.
Comparing the effect of physiotherapy and physiotherapy plus corticosteroid injection on pain intensity, disability, quality of life, and treatment effectiveness in patients with Subacromial Pain Syndrome: a randomized controlled trial

Abstract Purpose To compare the short and medium-term effects of physiotherapy plus corticosteroid injection (combined) with physiotherapy alone on pain intensity, disability, Quality of Life (QoL), and treatment effectiveness in patients with Subacromial Pain Syndrome (SAPS). Methods In this double-blind, parallel Randomized Controlled Trial (RCT), 50 patients with SAPS were randomly assigned into combined (N = 25, a single injection 3–6 days before physiotherapy) and physiotherapy alone group (N = 25). Pain, disability, QoL, and treatment-effectiveness were measured at pre-intervention, post-intervention, and 3 and 6-month follow-up with Visual Analog Scale (VAS), Shortened Disability of the Arm, Shoulder, and Hand (Quick-DASH), Shoulder Pain and Disability Index (SPADI) (primary outcome measure), Western Ontario Rotator Cuff (WORC), and Global Rating of Change (GRC) respectively. A 2 × 4 (group × time) mixed model analysis of variance (ANOVA) was applied for analysis. Results The ANOVA revealed statistically significant group-in-time interaction for all outcome measures (p-value < 0.05). The independent t-test showed more effectiveness in the combined group at medium-term, as the mean scores of almost all outcome measures were substantially lesser (p < 0.01). Moreover, in short-time, despite a greater number of patients stating “completely recovered” in the combined group, there was no statistically significant difference between groups. Conclusions Effects of physiotherapy plus corticosteroid injection could be more long-lasting than physiotherapy alone in improving pain intensity, disability, QoL, and treatment effectiveness in patients with SAPS. Trial registration number IRCT20201010048980N1. IMPLICATIONS FOR REHABILITATION Shoulder pain is common, persistent, and predominantly results from subacromial pain syndrome (SAPS). Physiotherapy and corticosteroid injections are effective interventions for this condition. Comprehensive physiotherapy alone can be as effective as corticosteroid injection combined with physiotherapy in the short term. A combined approach versus physiotherapy alone may have more medium-term effects on SAPS patients’ pain, disability, quality of life, and treatment effectiveness.
Genome-wide characterization of circRNA expression profile in overexpression of RIP2 chicken macrophages associated with avian pathogenic E.coli infection

ABSTRACT Avian pathogenic E. coli (APEC) can cause localized and systemic diseases in poultry, threatening human health via meat or egg contamination and resulting in considerable economic losses to the poultry industry globally. Increasing evidence shows circRNAs were widely involved in various biological processes. However, the role of circRNAs in the host response against APEC infection, especially correlated with the regulation of RIP2, remains unclear. Herein, the RNAseq technology was used to identify the circRNA expression profiles in the overexpression of RIP2 macrophages with or without APEC infection. A total of 256 and 287 differentially expressed (DE) circRNAs were identified in the overexpression of RIP2 group (oeRIP2) vs. the wild-type group (WT) and oeRIP2 + APEC vs. APEC, respectively, whose parental genes were involved in MAPK signalling pathway, Wnt signalling pathway, focal adhesion, tight junction, and VEGF signalling pathways. Specifically, the key circRNAs, such as 5:814443-825127, 10:18922360-18928461, 2:8746306-8750639, and 2:124177751-124184063 might play a critical role in APEC infection and the regulation of RIP2. As a whole, these findings will facilitate understanding the molecular mechanism underlying circRNAs, especially related to the regulation of the RIP2 gene. Meanwhile, the study may offer new ideas to improve host immune and inflammatory response against APEC infection.
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt

Abstract The Open Targets Platform (https://platform.opentargets.org/) is an open source resource to systematically assist drug target identification and prioritisation using publicly available data. Since our last update, we have reimagined, redesigned, and rebuilt the Platform in order to streamline data integration and harmonisation, expand the ways in which users can explore the data, and improve the user experience. The gene–disease causal evidence has been enhanced and expanded to better capture disease causality across rare, common, and somatic diseases. For target and drug annotations, we have incorporated new features that help assess target safety and tractability, including genetic constraint, PROTACtability assessments, and AlphaFold structure predictions. We have also introduced new machine learning applications for knowledge extraction from the published literature, clinical trial information, and drug labels. The new technologies and frameworks introduced since the last update will ease the introduction of new features and the creation of separate instances of the Platform adapted to user requirements. Our new Community forum, expanded training materials, and outreach programme support our users in a range of use cases.
Cab45 deficiency leads to the mistargeting of progranulin and prosaposin and aberrant lysosomal positioning

The trans‐Golgi Network (TGN) sorts molecular “addresses” and sends newly synthesized proteins to their destination via vesicular transport carriers. Despite the functional significance of packaging processes at the TGN, the sorting of soluble proteins remains poorly understood. Recent research has shown that the Golgi resident protein Cab45 is a significant regulator of secretory cargo sorting at the TGN. Cab45 oligomerizes upon transient Ca2+ influx, recruits soluble cargo molecules (clients), and packs them in sphingomyelin‐rich transport carriers. However, the identity of client molecules packed into Cab45 vesicles is scarce. Therefore, we used a precise and highly efficient secretome analysis technology called hiSPECs. Intriguingly, we observed that Cab45 deficient cells manifest hypersecretion of lysosomal hydrolases. Specifically, Cab45 deficient cells secrete the unprocessed precursors of prosaposin (PSAP) and progranulin (PGRN). In addition, lysosomes in these cells show an aberrant perinuclear accumulation suggesting a new role of Cab45 in lysosomal positioning. This work uncovers a yet unknown function of Cab45 in regulating lysosomal function.
A novel peptide ligand-coated nano-siRNA-lipoplex technology for kidney targeted gene therapy.

OBJECTIVES Small interfering RNA (siRNA) that silences specific disease-related genes holds the promise for the treatment of renal disease. However, delivery to the intended site of action remains a major obstacle. The goal of this study was to develop glomerulus-specific siRNA particles for targeted gene therapy of kidney diseases. METHODS We used a novel nanoparticle-based system comprised of siRNA in cationic liposomes (Lip) coated with non-inhibitory plasminogen activator inhibitor 1R (PAI-1R) that selectively targets glomerular cells and tested it with transforming growth factor-beta 1 (TGF-β1)-siRNA in nephritic rat model. RESULTS At the optimized ratio of components, three of PAI-1R, Lip and siRNA formed the compact nanostructured particles with close to neutral surface charge (+5.63 ± 1.45 mV) and relatively uniform size (68.9 ± 4.73 nm). When the fluorescence-conjugated siRNA was used, the labeled siRNA nanoparticles appeared specifically in glomeruli. Targeted delivery of siRNA specific to the TGFβ1 gene reduced elevated TGFβ1 mRNA expression and protein production in glomeruli, but had no effect on TGFβ1 mRNA levels in lung, spleen, artery or renal medulla, and in nephritic rats induced by injection of OX-7, for up to 5 days. PAI-1R-Lip-TGF-β1 siRNA administration significantly reduced increases in glomerular matrix accumulation and expression of PAI-1 and fibronectin. CONCLUSIONS We conclude that a single dose of PAI-1R-Lip-TGF-β1 siRNA inhibited glomerular TGF-β1 gene expression thereby ameliorating glomerulosclerosis specifically and efficiently in nephritic rats without affecting most of other organs. The target silencing of genes critical for glomerular diseases may represent a promising treatment strategy for kidney disease.
Abundance Analyses of Field RV Tauri Stars. V. DS Aquarii, UY Arae, TW Camelopardalis, BT Librae, U Monocerotis, TT Ophiuchi, R Scuti, and RV Tauri

Abundance analyses are presented and discussed for eight RV Tauri variables. The RVB star UY Ara shows the abundance anomalies seen in other RVB stars, namely, elements that condense into grains at high temperature are underabundant, but elements of low condensation temperature are much less underabundant. This pattern is ascribed to a separation of dust from gas with accretion of gas but not dust by the atmosphere. Abundances for two RVC stars with earlier results for other RVC stars show that these intrinsically metal-poor stars do not show effects of dust-gas separation. Analyses of five RVA stars show that these cooler stars are very largely unaffected by dust-gas separation. It is proposed that the deeper convective envelope of cooler stars dilutes anomalies resulting from dust-gas separation. Possible sites for dust formation and dust-gas separation—the dusty wind off the RV Tauri variable or a dusty circumbinary disk—are reviewed and observational tests suggested.
Medical Text Simplification Using Reinforcement Learning (TESLEA): Deep Learning–Based Text Simplification Approach

Background In most cases, the abstracts of articles in the medical domain are publicly available. Although these are accessible by everyone, they are hard to comprehend for a wider audience due to the complex medical vocabulary. Thus, simplifying these complex abstracts is essential to make medical research accessible to the general public. Objective This study aims to develop a deep learning–based text simplification (TS) approach that converts complex medical text into a simpler version while maintaining the quality of the generated text. Methods A TS approach using reinforcement learning and transformer–based language models was developed. Relevance reward, Flesch-Kincaid reward, and lexical simplicity reward were optimized to help simplify jargon-dense complex medical paragraphs to their simpler versions while retaining the quality of the text. The model was trained using 3568 complex-simple medical paragraphs and evaluated on 480 paragraphs via the help of automated metrics and human annotation. Results The proposed method outperformed previous baselines on Flesch-Kincaid scores (11.84) and achieved comparable performance with other baselines when measured using ROUGE-1 (0.39), ROUGE-2 (0.11), and SARI scores (0.40). Manual evaluation showed that percentage agreement between human annotators was more than 70% when factors such as fluency, coherence, and adequacy were considered. Conclusions A unique medical TS approach is successfully developed that leverages reinforcement learning and accurately simplifies complex medical paragraphs, thereby increasing their readability. The proposed TS approach can be applied to automatically generate simplified text for complex medical text data, which would enhance the accessibility of biomedical research to a wider audience.
Stakeholder outcome prioritization in the Biologic Abatement and Capturing Kids' Outcomes and Flare Frequency in Juvenile Spondyloarthritis (BACK‐OFF JSpA) trial

The Biologic Abatement and Capturing Kids’ Outcomes and Flare Frequency in Juvenile Spondyloarthritis (BACK‐OFF JSpA) study is a randomized, pragmatic trial investigating different tumour necrosis factor inhibitor de‐escalation strategies for children with sustained inactive disease. In this project, we elicited concept rankings that aided in the selection of the patient‐reported outcome (PRO) measures that should be examined as part of the BACK‐OFF JSpA trial.
Didactic Physician Assistant Students’ Perceptions of Evidence-Based Medicine Resources: A Preliminary Investigation

Abstract Evidence-Based Medicine (EBM) instruction is required for physician Assistant (PA) students. This pilot study surveyed didactic PA students at three geographically diverse PA programs at the end of their didactic EBM course to understand which attributes of EBM resources they find most and least useful, and their self-efficacy in searching and appraising medical literature. Thematic analysis identified the most important student-reported attributes of a resource. PA students in this sample preferred UpToDate and PubMed as their top EBM tools based on attribute ratings. However, each database included in this pilot study received positive feedback, despite a low usage rate across institutions. The most important attributes were ease of use/search, information presentation, and conclusion/critical appraisal skill. After one EBM course, on average, students rated their self-efficacy searching the literature and appraising the literature as “moderately confident. ” This suggests that instructors and librarians have an opportunity to expose students to more tools as well as encourage “the right tool for the right job. ”