MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis

Summary: MS-BID (MS Biomarker Discovery Platform) is an integrative computational pipeline for biomarker discovery using LC-MS-based comparative proteomic analysis. This platform consists of several computational tools for: (i) detecting peptides in the collected patterns; (ii) matching detected peptides across a number of LC-MS datasets and (iii) selecting discriminatory peptides between classes of samples. Availability: MS-BID source codes, binaries and documentations are freely available under LGPL from http://tools.proteomecenter.org/msBID.php. Contact: [email protected]

Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia

Hypoxia increases both active and repressive histone methylation levels via decreased activity of histone demethylases. However, how such increases coordinately regulate induction or repression of hypoxia-responsive genes is largely unknown. Here, we profiled active and repressive histone tri-methylations (H3K4me3, H3K9me3, and H3K27me3) and analyzed gene expression profiles in human adipocyte-derived stem cells under hypoxia. We identified differentially expressed genes (DEGs) and differentially methylated genes (DMGs) by hypoxia and clustered the DEGs and DMGs into four major groups. We found that each group of DEGs was predominantly associated with alterations in only one type among the three histone tri-methylations. Moreover, the four groups of DEGs were associated with different TFs and localization patterns of their predominant types of H3K4me3, H3K9me3 and H3K27me3. Our results suggest that the association of altered gene expression with prominent single-type histone tri-methylations characterized by different localization patterns and with different sets of TFs contributes to regulation of particular sets of genes, which can serve as a model for coordinated epigenetic regulation of gene expression under hypoxia.111Ysciescopu

Transcriptional regulatory networks underlying the reprogramming of spermatogonial stem cells to multipotent stem cells

Spermatogonial stem cells (SSCs) are germline stem cells located along the basement membrane of seminiferous tubules in testes. Recently, SSCs were shown to be reprogrammed into multipotent SSCs (mSSCs). However, both the key factors and biological networks underlying this reprogramming remain elusive. Here, we present transcriptional regulatory networks (TRNs) that control cellular processes related to the SSC-to-mSSC reprogramming. Previously, we established intermediate SSCs (iSSCs) undergoing the transition to mSSCs and generated gene expression profiles of SSCs, iSSCs and mSSCs. By comparing these profiles, we identified 2643 genes that were up-regulated during the reprogramming process and 15 key transcription factors (TFs) that regulate these genes. Using the TF-target relationships, we developed TRNs describing how these TFs regulate three pluripotency-related processes (cell proliferation, stem cell maintenance and epigenetic regulation) during the reprogramming. The TRNs showed that 4 of the 15 TFs (Oct4/Pou5f1, Cux1, Zfp143 and E2f4) regulated cell proliferation during the early stages of reprogramming, whereas 11 TFs (Oct4/Pou5f1, Foxm1, Cux1, Zfp143, Trp53, E2f4, Esrrb, Nfyb, Nanog, Sox2 and Klf4) regulated the three pluripotency-related processes during the late stages of reprogramming. Our TRNs provide a model for the temporally coordinated transcriptional regulation of pluripotency-related processes during the SSC-to-mSSC reprogramming, which can be further tested in detailed functional studies.111Ysciescopuskc

Prequips—an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data

Summary: We describe an integrative software platform, Prequips, for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)-based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies. Availability: http://prequips.sourceforge.net Contact: [email protected]

Cream: Visually-Situated Natural Language Understanding with Contrastive Reading Model and Frozen Large Language Models

Advances in Large Language Models (LLMs) have inspired a surge of research exploring their expansion into the visual domain. While recent models exhibit promise in generating abstract captions for images and conducting natural conversations, their performance on text-rich images leaves room for improvement. In this paper, we propose the Contrastive Reading Model (Cream), a novel neural architecture designed to enhance the language-image understanding capability of LLMs by capturing intricate details typically overlooked by existing methods. Cream integrates vision and auxiliary encoders, complemented by a contrastive feature alignment technique, resulting in a more effective understanding of textual information within document images. Our approach, thus, seeks to bridge the gap between vision and language understanding, paving the way for more sophisticated Document Intelligence Assistants. Rigorous evaluations across diverse tasks, such as visual question answering on document images, demonstrate the efficacy of Cream as a state-of-the-art model in the field of visual document understanding. We provide our codebase and newly-generated datasets at https://github.com/naver-ai/crea

Comprehensive Proteome Profiling of Platelet Identified a Protein Profile Predictive of Responses to An Antiplatelet Agent Sarpogrelate

Sarpogrelate is an antiplatelet agent widely used to treat arterial occlusive diseases. Evaluation of platelet aggregation is essential to monitor therapeutic effects of sarpogrelate. Currently, no molecular signatures are available to evaluate platelet aggregation. Here, we performed comprehensive proteome profiling of platelets collected from 18 subjects before and after sarpogrelate administration using LC-MS/MS analysis coupled with extensive fractionation. Of 5423 proteins detected, we identified 499 proteins affected by sarpogrelate and found that they strongly represented cellular processes related to platelet activation and aggregation, including cell activation, coagulation, and vesicle-mediated transports. Based on the network model of the proteins involved in these processes, we selected three proteins (cut-like homeobox 1; coagulation factor XIII, B polypeptide; and peptidylprolyl isomerase D) that reflect the platelet aggregation-related processes after confirming their alterations by sarpogrelate in independent samples using Western blotting. Our proteomic approach provided a protein profile predictive of therapeutic effects of sarpogrelate. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.1

Correlates associated with participation in physical activity among adults: a systematic review of reviews and update

Background Understanding which factors influence participation in physical activity is important to improve the public health. The aim of the present review of reviews was to summarize and present updated evidence on personal and environmental factors associated with physical activity. Methods MEDLINE and EMBASE were searched for reviews published up to 31 Jan. 2017 reporting on potential factors of physical activity in adults aged over 18 years. The quality of each review was appraised with the Assessing the Methodological Quality of Systematic Reviews (AMSTAR) checklist. The corrected covered area (CCA) was calculated as a measure of overlap for the primary publications in each review. Results Twenty-five articles met the inclusion criteria which reviewed 90 personal and 27 environmental factors. The average quality of the studies was moderate, and the CCA ranged from 0 to 4.3%. For personal factors, self-efficacy was shown as the strongest factor for participation in physical activity (7 out of 9). Intention to exercise, outcome expectation, perceived behavioral control and perceived fitness were positively associated with physical activity in more than 3 reviews, while age and bad status of health or fitness were negatively associated with participation in physical activity in more than 3 reviews. For environmental factors, accessibility to facilities, presence of sidewalks, and aesthetics were positively associated with participation in physical activity. Conclusions The findings of this review of reviews suggest that some personal and environmental factors were related with participation in physical activity. However, an association of various factors with physical activity could not be established because of the lack of primary studies to build up the organized evidence. More studies with a prospective design should be conducted to understand the potential causes for physical activity

Phenotypic and Functional Changes of Peripheral Ly6C(+) T Regulatory Cells Driven by Conventional Effector T Cells

A relatively high affinity/avidity of T cell receptor (TCR) recognition for self-peptide bound to major histocompatibility complex II (self-pMHC) ligands is a distinctive feature of CD4 T regulatory (Treg) cells, including their development in the thymus and maintenance of their suppressive functions in the periphery. Despite such high self-reactivity, however, all thymic-derived peripheral Treg populations are neither homogenous in their phenotype nor uniformly immune-suppressive in their function under steady state condition. We show here that based on the previously defined heterogeneity in the phenotype of peripheral Treg populations, Ly6C expression on Treg marks a lower degree of activation, proliferation, and differentiation status as well as functional incompetence. We also demonstrate that Ly6C expression on Treg in a steady state is either up-or downregulated depending on relative amounts of tonic TCR signals derived from its contacts with self-ligands. Interestingly, peripheral appearance and maintenance of these Ly6C-expressing Treg cells largely differed in an age-dependent manner, with their proportion being continuously increased from perinatal to young adult period but then being gradually declined with age. The reduction of Ly6C(+) Treg in the aged mice was not due to their augmented cell death but rather resulted from downregulation of Ly6C expression. The Ly6C down-regulation was accompanied by proliferation of Ly6C(+) Treg cells and subsequent change into Ly6C-effector Treg with concomitant restoration of immune-suppressive activity. Importantly, we found that this phenotypic and functional change of Ly6C(+) Treg is largely driven by conventional effector T cell population. Collectively, these findings suggest a potential cross-talk between peripheral Treg subsets and effector T cells and provides better understanding for Treg homeostasis and function on maintaining self-tolerance.110Ysciescopu