bluuebunny/crossref_metadata_2025_split huggingface dataset:
NOVEL ACTIVE PROTEINS FOR SEPSIS PROGNOSIS REVEALED THROUGH ScRNA-seq AND QUANTITATIVE PROTEOMICS
Authors: Liu Hui , Xiong Wei , Zhong Wu , Hu Yingchun 
Published: June 2024

ABSTRACT

Objective: To uncover critical active proteins influencing sepsis outcomes through multiomics analysis. Methods: This study collected peripheral blood from sepsis patients (NS = 26, SV = 27) and controls (Con = 16). Cellular heterogeneity was assessed using scRNA-seq. Cellular populations were identified through clustering and annotation. Gene set variation analysis was employed to detect pathway alterations in sepsis, while the Viper algorithm estimated protein activity at the single-cell level. Signaling networks were investigated via cell-cell communication analysis. Differentially expressed proteins were identified by DIA proteomics and confirmed through integrated analysis. Prognostic value was evaluated via meta and survival analyses. Results: scRNA-seq of 22,673 features within 34,228 cells identified five cellular clusters and 253 active proteins via Viper, validated by DIA (FC > 2, P < 0.05). Four proteins (SPI1, MEF2A, CBX3, UBTF) with prognostic significance were discovered and mapped onto the cellular landscape. Gene set variation analysis enrichment analysis revealed that the NS group exhibited significant alterations in pathways related to cellular apoptosis and inflammatory responses, while the SV group displayed increased activity in DNA repair and cellular survival pathways. Conclusion: The study’s findings advance the understanding of sepsis pathophysiology by linking differentially active proteins to patient prognosis, paving the way for targeted therapeutic strategies.
Alterations of tau and Camk2 in acute stroke and effects of a multicomponent drug
Authors: Wu Yue , Zhou Rui , Wang Menglan , Xu Jing , Zhang Yi , Wei Junying , Yang Hongjun 
Published: June 2024

Abstract

Background
Stroke is one of the leading causes of death around the world. The sequelae of ischemic stroke cause drastic effects on the quality of life for patients. Sanwujiaowan (SWJW) is a mixture prepared with 5 herbal medicines (Aconiti Lateralis Radix Praeparata, Aconiti Kusnezoffii Radix, Polygoni Multiflori Radix, Aconiti Radix, and Olibanum), with a long history of application in treating the sequelae of stroke.

Objectives
To provide evidence and decipher the mechanism of SWJW in alleviating stroke.

Materials and Methods
In this article, we expanded the indicators of SWJW by an integrated strategy based on signature metabolomics, target proteins, and bioinformatics and probed into the mechanism of SWJW intervention in ischemic stroke in a rat model.

Results
The results indicated that SWJW protected rats from nerve damage during the acute phase of ischemic stroke by regulating tau phosphorylation via the PI3K/Akt pathway.

Conclusions
This study, for the first time, proved that the reduction of phosphorylated tau was harmful for the neural function in the acute phase of ischemic stroke. Meanwhile, the pathological changes of phosphorylated tau proteins were detected in stroke and recalled by SWJW. This finding may provide a new reference for formulating treatment strategies for the acute phase of ischemic stroke.
Comprehensive analysis of Perilla frutescens (L.) Britt. along the value chain in northeast Inner Mongolia
Authors: Chen Yuan , Niu Hui , Fan Lingling , Wen Chunxiu , Wei Xinxin , Zhao Zeyuan , Surenjidiin Seesregdorj , Aruhan  , Li Minhui 
Published: June 2024

Abstract

Objective
To ensure the quality of Perilla frutescens (L.) Britt. and improve the associated benefits for stakeholders, this study analyzed the influences of different circulation channels and stakeholders on the quality, price, and other factors of P. frutescens with consideration to P. frutescens distribution.

Method
We interviewed the local stakeholders and e-commerce platforms in Oroqen Autonomous Banner and Morin Dawa Daur Autonomous Banner regarding the origin, circulation, distribution, and prices of different medicinal parts of P. frutescens. In addition, the maximum entropy model was used to predict the potential distribution of P. frutescens in the study area. According to the Chinese Pharmacopeia (2020 edition), we measured the content of index components in the collected Perillae Folium, Perillae Caulis, and Perillae Fructus samples and evaluated the quality of the samples by quantitative and cluster analyses. Remote sensing was employed to distinguish and calculate the P. frutescens area in highly suitable regions. The autoregressive integrated moving average model was adopted to analyze the Perillae Fructus price in the study area.

Result
The results showed 8 value chains for P. frutescens. The cooperation chain between farmers and enterprises in the study area could maximize the benefits for all stakeholders and guarantee the quality of the medicinal materials. The results of the regionalization analysis showed that the most suitable area for planting P. frutescens was the junction between Oroqen Autonomous Banner and Morin Dawa Daur Autonomous Banner. Chemical results showed that Perillae Fructus and Perillae Caulis samples were unqualified and mostly purchased from e-commerce platforms. We identified 5 land types, among which the cultivated land area was 3247.7501 km2. The price of Perillae Fructus in the study area showed a rising trend, although this trend slowed down.

Conclusion
This study involved various links in the production and circulation of medicinal materials from planting to consumption by consumers, which can help to facilitate the future research on any link. The findings help to guarantee the quality of medicinal materials and benefits of all stakeholders and promote the development of the P. frutescens industry in the study area.
Anti-acute gastric ulcer resistance of Aurantii Fructus Immaturus juice processing Atractylodis Macrocephalae Rhizoma by regulating PTGS2, MAPK1, and KDR targets based on metabolomics and integrated network pharmacology analysis
Authors: Xu Wanai , Wu Jingyu , Yang Danyang , Chen Yuxun , Wu Xiaoying , Wen Rou , Yan Liping , Li Chao , Yu Huan 
Published: June 2024

Abstract

Background
Currently, traditional methods of treating acute gastric ulcer (AGU) have many drawbacks, necessitating an alternative therapy with fewer adverse effects. Atractylodis Macrocephalae Rhizoma (BZ) is known for strengthening the spleen and harmonizing the stomach. BZ processed with Aurantii Fructus Immaturus juice (ZSZBZ), a classic decoction since the Han Dynasty, can enhance the efficacy of BZ. However, the key active components and targets of action of ZSZBZ remain undiscovered.

Aim of the study
This study aimed to investigate the bioactive chemical constituents of ZSZBZ against AGU and their possible mechanisms of action, elucidating the scientific content of ZSZBZ processing.

Materials and methods
Initially, we examined rat stomach histopathology and conducted ELISA for oxidative stress and inflammation. Subsequently, we investigated underlying mechanisms using metabolomics. Further analysis of potent components and key targets in ZSZBZ was conducted through liquid chromatography-mass spectrometry analysis combined with network pharmacology. Finally, key targets were analyzed by Western blot.

Results
ZSZBZ improved gastric histopathology, reversing high alcohol-induced oxidative stress (SOD, CAT) and inflammatory level (TNF-α, IL-6) disorders. This is associated with ZSZBZ’s regulation of amino acid metabolism, energy metabolism, and inflammatory response-related metabolic pathways, along with key targets PTGS2, MAPK1, and KDR. The significant increase in potency of ZSZBZ may be attributed to elevated levels of naringenin, hesperidin, hesperidin, and rhamnoceroside after concoction.

Conclusions
Combining metabolomics and network pharmacology, this study elucidated that ZSZBZ enhanced gastroprotection by modulating amino acid metabolism, antioxidant, and inflammation-related targets and pathways, providing insights into the bioactive compounds and potential mechanisms of herbal concoctions.
Genetic modifiers of somatic expansion and clinical phenotypes in Huntington’s disease reveal shared and tissue-specific effects
Authors:   Genetic Modifiers of Huntington’s Disease (GeM-HD) Consortium, Lee Jong-Min , McLean Zachariah L. , Correia Kevin , Shin Jun Wan , Lee Sujin , Jang Jae-Hyun , Lee Yukyeong , Kim Kyung-Hee , Choi Doo Eun , Long Jeffrey D. , Lucente Diane , Seong Ihn Sik , Pinto Ricardo Mouro , Giordano James V. , Mysore Jayalakshmi S. , Siciliano Jacqueline , Elezi Emanuela , Ruliera Jayla , Gillis Tammy , Wheeler Vanessa C. , MacDonald Marcy E. , Gusella James F. , Gatseva Anna , Ciosi Marc , Lomeikaite Vilija , Loay Hossameldin , Monckton Darren G. , Wills Christopher , Massey Thomas H. , Jones Lesley , Holmans Peter , Kwak Seung , Sampaio Cristina , Orth Michael , Bernhard Landwehrmeyer G. , Paulsen Jane S. , Ray Dorsey E. , Myers Richard H. 
Published: June 2024

ABSTRACTHuntington’s disease (HD), due to expansion of a CAG repeat inHTT, is representative of a growing number of disorders involving somatically unstable short tandem repeats. We find that overlapping and distinct genetic modifiers of clinical landmarks and somatic expansion in blood DNA reveal an underlying complexity and cell-type specificity to the mismatch repair-related processes that influence disease timing. Differential capture of non-DNA-repair gene modifiers by multiple measures of cognitive and motor dysfunction argues additionally for cell-type specificity of pathogenic processes. Beyondtransmodifiers, differential effects are also illustrated atHTTby a 5’-UTR variant that promotes somatic expansion in blood without influencing clinical HD, while, even after correcting for uninterrupted CAG length, a synonymous sequence change at the end of the CAG repeat dramatically hastens onset of motor signs without increasing somatic expansion. Our findings are directly relevant to therapeutic suppression of somatic expansion in HD and related disorders and provide a route to define the individual neuronal cell types that contribute to different HD clinical phenotypes.
BiomiX, a User-Friendly Bioinformatic Tool for Automatized Multiomics Data Analysis and Integration
Authors: Iperi Cristian , Fernández-Ochoa Álvaro , Barturen Guillermo , Pers Jacques-Olivier , Foulquier Nathan , Bettacchioli Eleonore , Alarcón-Riquelme Marta ,   PRECISESADS Flow Cytometry Study Group,   PRECISESADS Clinical Consortium, Cornec Divi , Bordron Anne , Jamin Christophe 
Published: June 2024

AbstractBiomiX addresses the data analysis bottleneck in high-throughput omics technologies, enabling the efficient, integrated analysis of multiomics data obtained from two cohorts. BiomiX incorporates diverse omics data. DESeq2/Limma packages analyze transcriptomics data, while statistical tests determine metabolomics peaks. The metabolomics annotation uses the mass-to-charge ratio in the CEU Mass Mediator database and fragmentation spectra in the TidyMass package while Methylomics analysis is performed using the ChAMP R package. Multiomics Factor Analysis (MOFA) integration and interpretation identifies common sources of variations among omics. BiomiX provides comprehensive outputs, including statistics and report figures, also integrating EnrichR and GSEA for biological process exploration. Subgroup analysis based on user gene panels enhances comparisons. BiomiX implements MOFA automatically, selecting the optimal MOFA model to discriminate the two cohorts being compared while providing interpretation tools for the discriminant MOFA factors. The interpretation relies on innovative bibliography research on Pubmed, which provides the articles most related to the discriminant factor contributors. The interpretation is also supported by clinical data correlation with the discriminant MOFA factors and pathways analyses of the top factor contributors. The integration of single and multi-omics analysis in a standalone tool, together with the implementation of MOFA and its interpretability by literature, constitute a step forward in the multi-omics landscape in line with the FAIR data principles. The wide parameter choice grants a personalized analysis at each level based on the user requirements. BiomiX is a user-friendly R-based tool compatible with various operating systems that aims to democratize multiomics analysis for bioinformatics non-experts.Key pointsBiomiX is the first user-friendly multiomics tool to perform single omics analysis for transcriptomics, metabolomics and methylomics and their data integration by MOFA in the same platform.MOFA algorithm was made accessible to non-bioinformaticians and improved to select the best model automatically, testing the MOFA factor’s performance in groups separation.Large improvement of MOFA factor’s interpretability by correlation, pathways analysis and innovative bibliography research.BiomiX is embedded in a network of other online tools as GSEA, metaboanalyst EnrichR etc, to provide a format compatible with further analyses in these tools.Interface and usage are intuitive and compatible with all the main operating systems, and rich parameters are set to grant personalized analysis based on the user’s needs.
Improving Inverse Folding models at Protein Stability Prediction without additional Training or Data
Authors: Dutton Oliver , Bottaro Sandro , Invernizzi Michele , Redl Istvan , Chung Albert , Hoffmann Falk , Henderson Louie , Ruschetta Stefano , Airoldi Fabio , Owens Benjamin M J , Foerch Patrik , Fisicaro Carlo , Tamiola Kamil 
Published: June 2024

AbstractDeep learning protein sequence models have shown outstanding performance atde novoprotein design and variant effect prediction. We substantially improve performance without further training or use of additional experimental data by introducing a second term derived from the models themselves which align outputs for the task of stability prediction. On a task to predict variants which increase protein stability the absolute success probabilities of ProteinMPNN and ESMifare improved by 11% and 5% respectively. We term these models ProteinMPNN-ddG and ESMif-ddG.
Enhancing Blood Availability in Latin America: A Study on Public Perceptions and Barriers to Blood Donation in Guatemala during the COVID-19 Pandemic
Authors: Perez-Iglesias Carolina Torres , Monzon Jose C. , Faria Isabella , Kundu Shreenik , Zil-E-Ali Ahsan , Jhunjhunwala Rashi , Raykar Nakul , Asturias Sabrina 
Published: June 2024

ABSTRACTObjectivesGuatemala faces a significant challenge with one of the lowest voluntary blood donation rates in Latin America, a problem further exacerbated by the COVID-19 pandemic. This study aimed to investigate the population factors influencing blood donation behavior in Guatemala during the COVID-19 pandemic.MethodsConducted between August and September 2020, this cross-sectional electronic anonymous survey employed purposive sampling. Participants were questioned about their donation history, knowledge of donation processes, preferences, and barriers and motivators for blood donation. Quantitative and qualitative data were collected and analyzed.Comparative analyses were conducted based on gender, age, and education level. Regression analysis was used to identify predictors of blood donation behavior. Open-ended responses were studied via thematic content analysis.ResultsAmong the 1141 respondents, 53.5% reported a history of blood donation. Most donations occurred via referred donations to family or friends (78.5%). Factors such as male gender, older age, and higher education were associated with previous blood donation.Familiarity with donation centers and willingness to donate strongly influenced donation behavior. Among never donors, 89% expressed willingness to donate. Constraints in accessing donation centers, limited operation hours, insufficient knowledge about the donation process, and concerns over hygiene and safety were identified as the most prevalent barriers to donation.ConclusionsRespondents demonstrated a strong willingness to donate blood voluntarily. Understanding demographic and population factors is critical to inform tailored initiatives to facilitate access to voluntary blood donation in Guatemala.
Combining ability analysis ofCucurbita moschataD. in Cote d’Ivoire and classification of promising lines based on their gca effects
Authors: Kouago Badié Arnaud , Seka Dagou , Brou Kouakou Fulgence , Bonny Beket Severin , Koffi Konan Henri Joel , Adjoumani Koffi , Sie Raoul Sylvère 
Published: June 2024

AbstractTwelve hybrids and their four parental lines were evaluated for their general performances, combining abilities, potency ratio and heterosis effects. Taller plants and smaller fruits characterized the parental lineLong, while theSoubreparent showed favorable fruit and seed traits but with a small number of seeds. The lineZouan-Hexhibited performances that are close toSoubrebut with a smaller number of fruits per plant, higher number of seeds per fruit and the weight of the fruit is one-half that of theSoubreline. TheOvalparent is characterized by a high number of seeds per fruit, smaller fruits and shorter plants. Significant effects of heterosis were observed in different hybrids for different characters. And the computed values of potency ratio indicated that gene(s) expressions were characterized by partial dominance in many cases and super dominance in some other cases. The variance of the effect of the general combining ability of the female parent was highly significant for all the evaluated traits. The variance of the effect of the general combining ability for the male parent was significant for some characters. The variance due to the effect of the specific combining ability was also highly significant for all the traits evaluated. It showed that the effects of additive genes and non-additive genes contributed to the expressions of the characters. However, the general predictive ratio was closer to 1.00 for all the fruit-related traits implying the strong effects of additive genes in the determination of the fruit-related characters. A classification of the parental lines based on the effects of their general combining ability grouped theSoubrelines as promising contributors to fruit yield. The parental linesLongandOvalformed another group likely on the basis of the small size of their fruits, the small pulps, the smaller number of fruits per plant and the high number of seeds per fruit.Longwould be a candidate parent for the development of cultivars with longer vegetative growth. The parental lineZouan-Hformed the third group and it was mostly characterized by its advantageous seed traits.
Elasticity and Thermal Stability are Key Determinants of Hearing Rescue by Mini-Protocadherin-15 Proteins
Authors: De-la-Torre Pedro , Wen Haosheng , Brower Joseph , Martínez-Pérez Karina , Narui Yoshie , Yeh Frank , Hale Evan , Ivanchenko Maryna V. , Corey David P. , Sotomayor Marcos , Indzhykulian Artur A. 
Published: June 2024

ABSTRACTProtocadherin-15 is a core protein component of inner-ear hair-cell tip links pulling on transduction channels essential for hearing and balance. Protocadherin-15 defects can result in non-syndromic deafness or Usher syndrome type 1F (USH1F) with hearing loss, balance deficits, and progressive blindness. Three rationally engineered shortened versions of protocadherin-15 (mini-PCDH15s) amenable for gene therapy have been used to rescue function in USH1F mouse models. Two can successfully or partially rescue hearing, while another one fails. Here we show that despite varying levels of hearing rescue, all three mini-PCDH15 versions can rescue hair-cell mechanotransduction. Negative-stain electron microscopy shows that all three versions form dimers like the wild-type protein, while crystal structures of some engineered fragments show that these can properly fold and bind calcium ions essential for function. In contrast, simulations predict distinct elasticities and nano differential scanning fluorimetry shows differences in melting temperature measurements. Our data suggest that elasticity and thermal stability are key determinants of sustained hearing rescue by mini-PCDH15s.
Enhancing Phylogenetic Independent Contrasts: Addressing Abrupt Evolutionary Shifts with Outlier- and Distribution-Guided Correlation
Authors: Chen Zheng-Lin , Huang Rui , Guo Hong-Ji , Niu Deng-Ke 
Published: June 2024

AbstractPhylogenetic comparative methods are indispensable for analyzing cross-species data while accounting for evolutionary relationships. Traditional methods like phylogenetically independent contrasts (PIC) and phylogenetic generalized least squares (PGLS) are well-suited for gradual evolution under Brownian motion (BM) or similar assumptions. However, their effectiveness diminishes under abrupt evolutionary shifts or heterogeneous evolutionary processes. We introduce a hybrid framework, outlier-guided correlation (OGC) for large datasets and outlier- and distribution-guided correlation (ODGC) for small datasets, collectively termed O(D)GC, which integrates Pearson and Spearman correlation analyses to handle outliers and non-normal data dynamically. Using simulations across diverse evolutionary scenarios, we compared PIC-O(D)GC with a comprehensive range of methods, including eight robust regression approaches (PIC-MM, PIC-L1, PIC-S, PIC-M, and their PGLS counterparts); PGLS optimized using five evolutionary models: BM, lambda, Ornstein–Uhlenbeck random (OU-random), OU-fixed, and Early-burst; Corphylo (an OU-based method); PIC-Pearson; and two advanced models, phylogenetic generalized linear mixed models (PGLMM) and multi-response phylogenetic mixed models (MR-PMM). Our results demonstrate that PIC-O(D)GC and PIC-MM consistently exhibit superior performance under conditions with evolutionary shifts, maintaining low false positive rates and high accuracy. In no-shift scenarios, PIC-O(D)GC and PIC-MM perform comparably to other reliable methods, underscoring their adaptability and robustness across varied datasets. Furthermore, PIC-O(D)GC offers computational efficiency and flexibility, making it particularly suitable for large-scale datasets. These findings underscore the value of adaptive, nonparametric frameworks like PIC-O(D)GC in complementing traditional phylogenetic approaches. By bridging computational simplicity with methodological robustness, O(D)GC provides a versatile tool for trait correlation analysis in both stable and dynamic evolutionary contexts.