Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphoproteomics Analysis Identifies Novel Candidate Substrates of the Nonreceptor Tyrosine Kinase, Src-related Kinase Lacking C-terminal Regulatory Tyrosine and N-terminal Myristoylation Sites (SRMS) *

SRMS (Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites), also known as PTK 70 (Protein tyrosine kinase 70), is a non-receptor tyrosine kinase that belongs to the BRK family of kinases (BFKs). To date less is known about the cellular role of SRMS primarily because of the unidentified substrates or signaling intermediates regulated by the kinase. In this study, we used phosphotyrosine antibody-based immunoaffinity purification in large-scale label-free quantitative phosphoproteomics to identify novel candidate substrates of SRMS. Our analyses led to the identification of 1258 tyrosine-phosphorylated peptides which mapped to 663 phosphoproteins, exclusively from SRMS-expressing cells. DOK1, a previously characterized SRMS substrate, was also identified in our analyses. Functional enrichment analyses revealed that the candidate SRMS substrates were enriched in various biological processes including protein ubiquitination, mitotic cell cycle, energy metabolism and RNA processing, as well as Wnt and TNF signaling. Analyses of the sequence surrounding the phospho-sites in these proteins revealed novel candidate SRMS consensus substrate motifs. We utilized customized high-throughput peptide arrays to validate a subset of the candidate SRMS substrates identified in our MS-based analyses. Finally, we independently validated Vimentin and Sam68, as bona fide SRMS substrates through in vitro and in vivo assays. Overall, our study identified a number of novel and biologically relevant SRMS candidate substrates, which suggests the involvement of the kinase in a vast array of unexplored cellular functions.
Retinal and Choroidal Microvasculature in Nonarteritic Anterior Ischemic Optic Neuropathy: An Optical Coherence Tomography Angiography Study.

Purpose To analyze retinal and choroidal microvasculature in patients with nonarteritic anterior ischemic optic neuropathy (NAION) by using optical coherence tomography angiography (OCT-A). Methods In this case-control retrospective observational study, patients with atrophic NAION (at least 3 months after onset of symptoms) and normal subjects underwent a complete ophthalmic examination including spectral-domain OCT, visual field (VF), and OCT-A. Whole en face image vessel density (wiVD) was used to assess retinal blood flow of the radial peripapillary capillaries (RPCs), circumpapillary RPC vessel density (cpVD), superficial capillary plexus (SCP), deep capillary plexus (DCP), and choriocapillaris (CC). Statistical correlations between wiVD measurements and visual acuity, VF parameters, retinal nerve fiber layer (RNFL), and combined thickness of retinal ganglion cell and inner plexiform layers were analyzed. Results Twenty-four patients (26 eyes) with NAION and 24 age-matched normal controls (NCs) (24 eyes) were included. OCT-A showed significant reduction of the RPC wiVD (P < 0.0001) and the cpVD (P < 0.0001) in NAION eyes compared with NC and correlated with RNFL thickness (P = 0.002, P = 0.004), visual acuity (P = 0.042), and mean deviation of the VF (P = 0.001). Macular OCT angiograms showed capillary rarefaction in the SCP (P < 0.0001) and DCP (P < 0.0001) in the NAION group, both correlated with visual acuity (P = 0.02, P = 0.024). However, wiVD of the CC was not significantly different between the two groups in the peripapillary (P = 0.218) and macular (P = 0.786) areas. Conclusions OCT-A provided detailed visualization of the peripapillary and macular retinal capillary rarefaction, correlated with VF and visual acuity loss. OCT-A could be a useful tool for quantifying and monitoring ischemia in NAION.
An evaluation and analysis of graph processing frameworks on five key issues

With the continuously emerging applications in fields like social media analysis, mining massive graphs has drawn increasing attentions from industry and academia. To aid the development of distributed graph algorithms, various programming frameworks have been proposed. To better understand their performance differences under specific scenarios, we analyzed and compared a set of seven representative frameworks under five design aspects, including distribution policy, on-disk data organization, programming model, synchronization policy and message model. Our experiments reveal some interesting phenomena. For example, We observed that the vertex-cut method overweighs the edge-cut method on neighbor-based algorithms while leads to inefficiency for non-neighbor-based algorithms. Furthermore, we observed that using asynchronous update can reduce the total workload by 20% to 30%, but the processing time may still doubled due to fine-grained lock conflicts. Overall, we analyzed the pros and cons of each option for the five key issues. We believe our findings will help end-users choose a suitable framework, and designers improve current ones.
The Compensatory Reserve For Early and Accurate Prediction Of Hemodynamic Compromise: A Review of the Underlying Physiology

ABSTRACT Shock is deadly and unpredictable if it is not recognized and treated in early stages of hemorrhage. Unfortunately, measurements of standard vital signs that are displayed on current medical monitors fail to provide accurate or early indicators of shock because of physiological mechanisms that effectively compensate for blood loss. As a result of new insights provided by the latest research on the physiology of shock using human experimental models of controlled hemorrhage, it is now recognized that measurement of the body's reserve to compensate for reduced circulating blood volume is the single most important indicator for early and accurate assessment of shock. We have called this function the “compensatory reserve,” which can be accurately assessed by real-time measurements of changes in the features of the arterial waveform. In this paper, the physiology underlying the development and evaluation of a new noninvasive technology that allows for real-time measurement of the compensatory reserve will be reviewed, with its clinical implications for earlier and more accurate prediction of shock.
Dust Problem in silica Refractories

The paper briefly discusses the findings of an investigation into presence of respiarable free silica dust in the work atmosphere of three silica brick manufacturing plants, and its impact on the health of factory workers. The study showed the presence of silica dust in work atmosphere in excess of threshold limit values, and occurance of silicosis or other lung abnormalities among plant workers. The paper points out to the necessity for controlling dust at work place by source control; and to simultaneous need to wear personal protective devices by the workers so that manace of silicosis could be contained among them.
Infection and quantitative recovery of Salmonella typhimurium and Escherichia coli from within the lesser mealworm, Alphitobius diaperinus (panzer).

Abstract THE lesser mealworm, Alphitobius diaperinus (Panzer) has been considered only as a minor pest of grain, cereal products and related agricultural commodities although it is widely distributed throughout the world (Cotton, 1956; Harris, 1966; Lancaster and Simco, 1967). Infestations are noted frequently in damp and mouldy grain, the product having lost most of its food value prior to the insect infestation. The lesser mealworm has been noted also as a secondary but chronic problem in poultry brooder houses where it breeds and develops in feed and in corn cob litter (Gould and Moses, 1951; Harding and Bissell, 1958). It is apparent, however, that its diet in this environment is not restricted to plant products (Harris, 1966). Harris noted that the lesser mealworm bore into and apparently feed on the flesh and internal organs of moribund and dead baby chicks. During this feeding they may become contaminated with the avain leukosis .
Biochemical and Molecular Mechanisms Associated With the Resistance of the European Corn Borer (Lepidoptera: Crambidae) to Lambda-Cyhalothrin and First Monitoring Tool

Abstract The European corn borer (Ostrinia nubilalis (Hübner)) is one of the most serious corn pest in Europe where it is controlled with pesticides, in particular, pyrethroids. First control failures with this chemical family occurred on the field in 2008 in the center of France, and the first resistance case was described in 2012. In the present study, we investigate resistance mechanisms involved in seven French populations of O. nubilalis collected in the field. Resistances to deltamethrin and lambda-cyhalothrin were confirmed, with a higher resistance ratio for lambda-cyhalothrin (63.79 compared to 7.67). Resistance to the two active compounds was correlated except for one population, indicating a high probability of cross-resistance. Analyses of the activity of three major families of detoxification enzymes in resistant individuals showed a significant increase of the average MFO activity in males of four populations (activity ratios of 2.76–5.73) and higher GST activity in females of two other populations (activity ratios 4.48 and 5.21). Molecular investigation of the sodium channel gene sequence showed the presence of the kdr mutation in a highly resistant individual. We designed a PCR-RFLP screening tool to search for this mutation in the field, and we found it in five populations but not in the susceptible one. The resistance of O. nubilalis to pyrethroids in France seems to result from a combination of resistance mechanisms, possibly as a consequence of a selection pressure with an exceptional duration (almost 40 yr old).
Convex Combination Filtered-X Algorithms for Active Noise Control Systems

Adaptive filtering schemes exhibit a compromise between convergence speed and steady-state mean square error. Trying to overcome this trade-off, convex combination of adaptive filters have been recently developed for system identification achieving better performance than traditional approaches. The purpose of this work is to apply the convex combination strategy to single-channel and multichannel active noise control systems. In these systems it is necessary to take into account the secondary path between the adaptive filter output and the error sensor and the possible unavailability of the disturbance signal, which depends on the filtering scheme considered. Even though this strategy involves a higher computational burden than the classic adaptive filters, it exhibits a good performance in terms of convergence speed and steady-state mean square error.
Overlap between irritable bowel syndrome and functional dyspepsia including subtype analyses

Coexistent gastrointestinal symptom profiles and prevalence or associated factors for the overlap between each functional dyspepsia (FD) and irritable bowel syndrome (IBS) group remain unclear. Thus, the aim of the present study was to evaluate the clinicodemographic features of FD, IBS, and IBS‐FD overlap and assess the risk factors thereof, including subtype and genetic polymorphisms for IBS‐FD.
Gastrointestinal Leakage Detected by Serum (1→3)-&bgr;-D-Glucan in Mouse Models and a Pilot Study in Patients with Sepsis

ABSTRACT Gastrointestinal (GI) leakage is believed to exacerbate sepsis and new, validated markers of GI barrier performance might benefit clinical decision-making. Serum (1→3)-&bgr;-D-glucan (BG) was evaluated as a potential GI leakage marker. Serum BG was tested in several mouse models of GI leakage, including dextran sulfate solution (DSS) administration, endotoxin (LPS) injection, and cecal ligation and puncture sepsis (CLP). Serum BG titer was also evaluated in patients with sepsis and septic shock, for comparison. With 0.75% DSS administration, BG increased only after oral administration of heat-killed C. albicans, but increased spontaneously with 1.5% DSS. In the LPS and CLP models, BG increased as early as 1 h and at 12 h after LPS administration and surgery, respectively. GI leakage was confirmed by orthogonal validation methods including FITC-dextran oral administration in the DSS, LPS, and CLP models and, in the DSS model, with urine sucralose after oral administration and serum endotoxemia. IL-6 increased in parallel with serum BG. Serum BG or IL-6, at 18 h, anticipated sepsis mortality in the CLP model. Analysis of serum BG from patients with febrile neutropenic sepsis (N = 49) and febrile non-neutropenic sepsis (N = 39) demonstrated BG elevation. Patients with bacterial septic shock had serum BG titers similar to levels observed in invasive fungal disease, regardless of febrile neutropenia. Serum BG was lower in less severe cases of bacterial sepsis. Elevated serum IL-6 was associated with GI leakage and elevated serum BG. Serum BG may have potential as a sepsis/septic shock biomarker and further study in this context is warranted.
Virginiamycin and laying hen performance.

Two experiments were conducted for five 28-day periods each. In Experiments 1 and 2, Hyline W-36 hens, 36 and 26 weeks of age, respectively, were used. Experiment 1 was designed to measure the effect of virginiamycin on hen performance and egg characteristics when supplementing a diet having low pigmentation potential. In Experiment 2, the diet contained 3% added fat with 0, 10, and 20 ppm virginiamycin. In Experiment 1, virginiamycin-supplemented hens showed increased (P less than or equal to .05) egg production, body weight, and improved feed efficiency. When egg production and feed efficiency were ranked by quartiles within the control and virginiamycin-supplemented groups, virginiamycin was shown to benefit only the poorer producing hens. In Experiment 2, added fat improved feed efficiency; however, the response to virginiamycin, as observed in Experiment 1, did not occur.
Blood Pressure Trajectories From Childhood to Young Adulthood Associated With Cardiovascular Risk: Results From the 23-Year Longitudinal Georgia Stress and Heart Study

The purpose of this study is to identify subgroups of individuals with similar trajectories in blood pressure (BP) from childhood to young adulthood and to determine the relationship of BP trajectories with carotid intima–media thickness (IMT) and left ventricular mass index (LVMI). BP was measured ⩽16 times during a 23-year period in 683 participants from childhood to young adulthood. IMT and LVMI were measured in 551 participants and 546 participants, respectively. Using latent class models, 3 trajectory groups in BP from childhood to young adulthood were identified, including high-increasing, moderate-increasing, and low-increasing groups. We found that trajectory of systolic BP was a significant predictor of both IMT and LVMI with increased rate of growth in systolic BP associated with higher levels of IMT and LVMI (Pfor trend <0.001). Similar to the BP trajectory groups from childhood to young adulthood, 3 trajectory groups in BP during childhood (⩽18 years) were identified, and participants in the high-increasing group had thicker IMT (P<0.001) and increased LVMI (P=0.043) in comparison with those in the low-increasing group. Results were similar for mid-BP trajectories but not for diastolic BP trajectories. Our results suggested that different BP trajectories exist from childhood to young adulthood, and the trajectories were independently associated with IMT and LVMI. We, for the first time, reported the association between systolic BP trajectories derived from childhood with subclinical cardiovascular risk in young adulthood, indicating that monitoring trajectories of BP from childhood may help identify a high cardiovascular risk population in early life.
Phylogenetic diversity of bacterial endosymbionts in the gutless marine oligochete Olavius loisae (Annelida)

Endosymbiotic associations with more than 1 bacterial phylotype are rare among chemoautotrophic hosts. In gutless marine oligochetes 2 morphotypes of bacterial endosymbionts occur just below the cuticle between extensions of the epidermal cells. Using phylogenetic analysis, in situ hybridization, and denaturing gradient gel electrophoresis based on 16S ribosomal RNA genes, it is shown that in the gutless oligochete Olavius loisae, the 2 bacterial morphotypes correspond to 2 species of diverse phylogenetic origin. The larger symbiont belongs to the gamma subclass of the Proteobacteria and clusters with other previously described chemoautotrophic endosymbionts. The smaller symbiont represents a novel phylotype within the alpha subclass of the Proteobacteria. This is distinctly different from all other chemoautotrophic hosts with symbiotic bacteria which belong to either the gamma or epsilon Proteobacteria. In addition, a third bacterial morphotype as well as a third unique phylotype belonging to the spirochetes was discovered in these hosts. Such a phylogenetically diverse assemblage of endosymbiotic bacteria is not known from other marine invertebrates.
Efficient Model-Based Deep Reinforcement Learning with Variational State Tabulation

Modern reinforcement learning algorithms reach super-human performance on many board and video games, but they are sample inefficient, i.e. they typically require significantly more playing experience than humans to reach an equal performance level. To improve sample efficiency, an agent may build a model of the environment and use planning methods to update its policy. In this article we introduce Variational State Tabulation (VaST), which maps an environment with a high-dimensional state space (e.g. the space of visual inputs) to an abstract tabular model. Prioritized sweeping with small backups, a highly efficient planning method, can then be used to update state-action values. We show how VaST can rapidly learn to maximize reward in tasks like 3D navigation and efficiently adapt to sudden changes in rewards or transition probabilities.
Möbius: an integrated discrete-event modeling environment

UNLABELLED Möbius has found numerous applications in computational biology to build and solve stochastic models of biological processes. It provides the user with a modeling workflow and several sophisticated features that are not available in the simulation tools commonly used by computational biologists. AVAILABILITY Möbius is free for academic users. It can be downloaded from www.mobius. uiuc.edu
Leptospira Immunoglobulin-Like Protein B Interacts with the 20th Exon of Human Tropoelastin Contributing to Leptospiral Adhesion to Human Lung Cells

Leptospira immunoglobulin-like protein B (LigB), a surface adhesin, is capable of mediating the attachment of pathogenic leptospira to the host through interaction with various components of the extracellular matrix (ECM). Human tropoelastin (HTE), the building block of elastin, confers resilience and elasticity to lung, and other tissues. Previously identified Ig-like domains of LigB, including LigB4 and LigB12, bind to HTE, which is likely to promote Leptospira adhesion to lung tissue. However, the molecular mechanism that mediates the LigB-HTE interaction is unclear. In this study, the LigB-binding site on HTE was further pinpointed to a N-terminal region of the 20th exon of HTE (HTE20N). Alanine mutants of basic and aromatic residues on HTE20N significantly reduced binding to the LigB. Additionally, HTE-binding site was narrowed down to the first β-sheet of LigB12. On this binding surface, residues F1054, D1061, A1065, and D1066 were critical for the association with HTE. Most importantly, the recombinant HTE truncates could diminish the binding of LigB to human lung fibroblasts (WI-38) by 68%, and could block the association of LigA-expressing L. biflexa to lung cells by 61%. These findings should expand our understanding of leptospiral pathogenesis, particularly in pulmonary manifestations of leptospirosis.
The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia

Despite increasing data on the impact of the microbiome on cancer, the dynamics and role of the microbiome in infection during therapy for acute myelogenous leukemia (AML) are unknown. Therefore, the authors sought to determine correlations between microbiome composition and infectious outcomes in patients with AML who were receiving induction chemotherapy (IC).
Mindfulness-based cognitive therapy v. treatment as usual in adults with ADHD: a multicentre, single-blind, randomised controlled trial

Abstract Background There is a high need for evidence-based psychosocial treatments for adult attention-deficit hyperactivity disorder (ADHD) to offer alongside treatment as usual (TAU). Mindfulness-based cognitive therapy (MBCT) is a promising psychosocial treatment. This trial investigated the efficacy of MBCT + TAU v. TAU in reducing core symptoms in adults with ADHD. Methods A multicentre, single-blind, randomised controlled trial (ClinicalTrials.gov: NCT02463396). Participants were randomly assigned to MBCT + TAU (n = 60), an 8-weekly group therapy including meditation exercises, psychoeducation and group discussions, or TAU only (n = 60), which reflected usual treatment in the Netherlands and included pharmacotherapy and/or psychoeducation. Primary outcome was ADHD symptoms rated by blinded clinicians. Secondary outcomes included self-reported ADHD symptoms, executive functioning, mindfulness skills, self-compassion, positive mental health and general functioning. Outcomes were assessed at baseline, post-treatment, 3- and 6-month follow-up. Post-treatment effects at group and individual level, and follow-up effects were examined. Results In MBCT + TAU patients, a significant reduction of clinician-rated ADHD symptoms was found at post-treatment [M difference = −3.44 (−5.75, −1.11), p = 0.004, d = 0.41]. This effect was maintained until 6-month follow-up. More MBCT + TAU (27%) than TAU participants (4%) showed a ⩽30% reduction of ADHD symptoms (p = 0.001). MBCT + TAU patients compared with TAU patients also reported significant improvements in ADHD symptoms, mindfulness skills, self-compassion and positive mental health at post-treatment, which were maintained until 6-month follow-up. Although patients in MBCT + TAU compared with TAU reported no improvement in executive functioning at post-treatment, they did report improvement at 6-month follow-up. Conclusions MBCT might be a valuable treatment option alongside TAU for adult ADHD aimed at alleviating symptoms.