bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating multiple omics levels using the human protein complexome as a framework, a multi-omics study of inborn errors of metabolism
Authors: Guharoy Mainak , Adant Isabelle , Bird Matthew , Pedrayes Andrea Jáñez , Botzki Alexander , Dehairs Jonas , Derveaux Stefaan , Devos Simon , Goeminne Geert , Impens Francis , Janky Rekin’s , Maes Ruth , Maia Teresa M. , Meersseman Wouter , Rymen Daisy , Swinnen Johannes V. , Van Haver Delphi , Witters Peter , Cassiman David , Ghesquiere Bart 
Published: December 2023

AbstractProteins organize into functional assemblies that drive diverse biological activities. Leveraging a comprehensive dataset of manually curated annotations for the human protein complexome, we investigated biological perturbations at the protein complex level. Using proteomics and transcriptomics data from fibroblasts of patients with inborn errors of metabolism (IEM) and control samples, we globally mapped information onto complex subunits to discern affected processes.Across the patient cohort (consisting of organic acidaemias, fatty acid oxidation defects and mitochondrial respiratory chain defect IEMs), mitochondrial oxidative phosphorylation emerged as the most perturbed pathway, identified through proteomics datasets. Simultaneously, metabolomics highlighted significant regulation of phospholipids in patients with Fatty Acid and Mitochondrial IEM. Moreover, proteomics analysis also revealed the dysregulation of protein complexes involved in histone (de)acetylation, a finding validated through Western Blot analysis measuring histone acetylation levels. This introduces a novel epigenetic dimension to IEM and metabolic research, suggesting avenues for further exploration.Our study demonstrates a multiomics data integration concept that maps proteomics and transcriptomics data onto model organism complexomes. This integrative approach can be extended to metabolomics and lipidomics, associating information with complexes having metabolic functions, such as enzymatic complexes. This global strategy for identifying disease-relevant perturbations offers a systems-wide perspective on molecular-level physiological and pathological changes. Such insights are crucial for devising clinical intervention strategies and prioritizing druggable pathways and complexes. The presented methodology provides a foundation for future investigations, emphasizing the importance of integrating multiomics data to comprehensively understand cellular machinery alterations and facilitate targeted therapeutic approaches.
The effects of phenotypic plasticity on diversification rates and adaptive evolution in simulated environments with different climatic and cost contexts
Authors: Barbosa Júnior Emerson Campos , Dodonov Pavel , Japyassú Hilton F. , Vilela Bruno 
Published: December 2023

AbstractPhenotypic plasticity can either hinder or facilitate genetic evolution, thus affecting macroevolution. However, the mechanisms and associations of phenotypic plasticity with biodiversity patterns remain unresolved. In this paper, we investigate the effect of phenotypic plasticity on adaptive evolution in the context of climatic changes and plasticity costs, specifically examining the rates of trait evolution, speciation, extinction, and diversification. We employed an eco-evolutionary agent-based model, incorporating body temperature as a plastic trait that dynamically responds to fluctuations in environmental temperature. We found the same pattern of results for both climate and plasticity cost contexts. We found that an increase in plasticity leads to a decrease in extinction and trait evolution rates, with high plasticity serving to postpone mass extinction events. Systems with plastic species experience higher speciation rates. Additionally, as plasticity increases in systems, diversification rates also increase. Our study supports the hypothesis that plasticity can facilitate adaptive evolution. It provides new insights into the effect of plasticity on adaptive evolution at larger scales, considering relevant mechanisms and factors such as population size, grouping, occupancy, plasticity extension, and dispersion.
MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions
Authors: Farr Elias , Dimitrov Daniel , Turei Denes , Schmidt Christina , Lobentanzer Sebastian , Dugourd Aurelien , Saez-Rodriguez Julio 
Published: December 2023

AbstractInteractions between proteins and metabolites are key for cellular function, from the catalytic breakdown of nutrients to signaling. An important case is cell-cell communication, where cellular metabolites are secreted into the microenvironment and initiate a signaling cascade by binding to an intra- or extracellular receptor of another cell. While protein-protein mediated cell-cell communication is routinely inferred from transcriptomic data, for metabolite-protein interactions this is challenging due to the limitations of high-throughput single-cell and spatial metabolomics technologies, together with the absence of comprehensive prior knowledge resources that include metabolites. Here we report MetalinksDB, a comprehensive and flexible database of intercellular metabolite-protein interactions that is a magnitude larger than existing ones. MetalinksDB can be tailored to specific biological contexts such as diseases, pathways, or tissue/cellular locations by querying subsets of interactions using the web interface (https://metalinks.omnipathdb.org/) or the knowledge graph adapters. We showcase the use of MetalinksDB by identifying deregulated processes in renal cancer patients from multi-omics data as well as inferring metabolite-mediated cell-cell communication events driving acute kidney injury from spatial transcriptomic data. We anticipate that MetalinksDB will facilitate the study of metabolite-mediated communication processes.Graphical Abstract
Highly Accurate and Precise Determination of Mouse Mass Using Computer Vision
Authors: Guzman Malachy , Geuther Brian , Sabnis Gautam , Kumar Vivek 
Published: December 2023

1SummaryChanges in body mass are a key indicator of health and disease in humans and model organisms. Animal body mass is routinely monitored in husbandry and preclinical studies. In rodent studies, the current best method requires manually weighing the animal on a balance which has at least two consequences. First, direct handling of the animal induces stress and can have confounding effects on studies. Second, the acquired mass is static and not amenable to continuous assessment, and rapid mass changes can be missed. A noninvasive and continuous method of monitoring animal mass would have utility in multiple areas of biomedical research. Here, we test the feasibility of determining mouse body mass using video data. We combine computer vision methods with statistical modeling to demonstrate the feasibility of our approach. Our methods determine mouse mass with 4.8% error across highly genetically diverse mouse strains, with varied coat colors and mass. This error is low enough to replace manual weighing with image-based assessment in most mouse studies. We conclude that visual determination of rodent mass using video enables noninvasive and continuous monitoring and can improve animal welfare and preclinical studies.
Benefits and challenges of implementing green building development in Nigeria
Authors: Abdulsalam Rufai Salihu , Chan Melissa , Masrom Md. Asrul Nasid , Nawawi Abdul Hadi 
Published: December 2023

PurposeThe adoption of green building concepts and practices is rapidly gaining momentum globally due to their tendency to mitigate adverse effects of construction activities on the environment. The purpose of this study is to examine the challenges and benefits of implementing green building development in Nigeria.Design/methodology/approachPrimary data were collected from questionnaires administered to 122 participants selected using stratified sampling techniques in North-East Nigeria. Semi-structured interviews complemented survey findings with proposed solutions. The quantitative data were analysed using descriptive statistics to identify the benefits and challenges, while thematic analysis was used to identify effective measures to the challenges of green building.FindingsResults show that “conservation of natural resources”, “reducing maintenance” and “heightened aesthetic” were rated higher as environmental, economic and social benefits, and thus were significant to green building development. The study revealed “economic issues”, “government issues” and “absence of standard assessment system” were the key factors as internal, external and general challenges to green building. Most practical solutions were related broadly to policy, awareness and support as measures to challenges of green building development.Originality/valueThe study is imperative to bridge the knowledge gaps and provide empirical information for green building policy guidelines specific to North-East Nigeria’s built environment sector. The understanding of policy implications will assist in building regulatory and monitoring agencies in developing new internal management policies to inform the public and investors about the effects of green building development.
True knowledge vs empowering knowledge: conceptualizing a theory of mindfulness and knowledge transfer (TMKT)
Authors: Issac Abraham Cyril , Dhir Amandeep , Christofi Michael 
Published: December 2023

PurposeMindfulness is the human ability to be fully present, aware of where we are and what we're doing. This study explores on the impact of mindfulness on different elements of knowledge management, knowledge creation, knowledge sharing and knowledge hiding.Design/methodology/approachThe authors undertake an inductive reasoning approach whereby they try to generate themes from specific observations and conceptualize the theory of mindfulness and knowledge transfer.FindingsThis study finds out that mindfulness critically facilitates an open environment and enhances the clarity of thought which aids in effective knowledge creation. Such a realistic understanding about the present scenario encourages employees to share knowledge and equips them to collaborate and effectively work in teams. Surprisingly, this study also finds that mindfulness increases the result orientation to the extent that employees tried to hide knowledge from their co-workers targeting certain self-desired outcomes. In other words, similar to knowledge creation and knowledge sharing, mindfulness increases agenda-based knowledge hiding.Originality/valueThe theory of mindfulness and knowledge transfer states that mindfulness increases knowledge creation, knowledge sharing and agenda-based knowledge hiding.
A contribution-based indicator of research productivity: theoretical definition and empirical testing in the field of communication
Authors: Blasco-Blasco Olga , Demeter Márton , Goyanes Manuel 
Published: December 2023

Purpose The purpose of this article is to theoretically outline and empirically test two contribution-based indicators: (1) the scholars' annual contribution-based measurement and (2) the annual contribution modified h-index, computing six criteria: total number of papers, computed SCImago Journal Rank values, total number of authors, total number of citations of a scholar’s work, number of years since paper publication and number of annual paper citations.Design/methodology/approach Despite widespread scholarly agreement about the relevance of research production in evaluation and recruitment processes, the proposed mechanisms for gauging publication output are still rather elementary, consequently obscuring each individual scholar’s contributions. This study utilised the Technique for Order of Preference by Similarity to Ideal Solution method, and the authors built two indicators to value author's contribution.Findings To test both indicators, this study focussed on the most productive scholars in communication during a specific time period (2017–2020), ranking their annual research contribution and testing it against standard productivity measures (i.e. number of papers and h-index).Originality/value This article contributes to current scientometric studies by addressing some of the limitations of aggregate-level measurements of research production, providing a much-needed understanding of scholarly productivity based on scholars' actual contribution to research.
Validation of claims‐based algorithms for rheumatoid arthritis in Japan: Results from the VALIDATE‐J study
Authors: Sugiyama Naonobu , Kinjo Mitsuyo , Jinno Sadao , de Luise Cynthia , Morishima Toshitaka , Higuchi Takakazu , Katayama Kayoko , Chen Haoqian , Nonnenmacher Edward , Hase Ryota , Suzuki Daisuke , Tanaka Yoshiya , Setoguchi Soko 
Published: December 2023

AbstractAimValidity of Algorithms in Large Databases: Infectious Diseases, Rheumatoid Arthritis, and Tumor Evaluation in Japan (VALIDATE‐J) study examined algorithms for identifying rheumatoid arthritis (RA) in Japanese claims data.MethodsVALIDATE‐J was a multicenter, cross‐sectional retrospective study. Disease‐identifying algorithms were used to detect RA diagnosed between January 2012 and December 2016 using claims data from two Japanese hospitals. An RA diagnosis was confirmed using one of four gold standard definitions. Positive predictive values (PPVs) were calculated for prevalent (regardless of baseline RA‐free period) and incident (preceded by a 12‐month RA‐free period) cases.ResultsOf patients identified using claims‐based algorithms, a random sample of 389 prevalent and 134 incident cases of RA were included. Cases identified by an RA diagnosis, no diagnosis of psoriasis, and treatment with any disease‐modifying antirheumatic drugs (DMARDs) resulted in the highest PPVs versus other claims‐based treatment categories (29.0%–88.3% [prevalent] and 41.0%–78.2% [incident]); cases identified by an RA diagnosis, no diagnosis of psoriasis, and glucocorticoid‐only treatment had the lowest PPVs. Across claims‐based algorithms, PPVs were highest when a physician diagnosis or decision by adjudicators (confirmed and probable cases) was used as the gold standard and were lowest when American College of Rheumatology/European Alliance of Associations for Rheumatology 2010 criteria were applied. PPVs of claims‐based algorithms for RA in patients aged ≥66 years were slightly higher versus a USA Medicare population (maximum PPVs of 95.0% and 88.9%, respectively).ConclusionVALIDATE‐J demonstrated high PPVs for most claims‐based algorithms for diagnosis of prevalent and incident RA using Japanese claims data. These findings will help inform appropriate RA definitions for future claims database research in Japan.
Time Perception Scale: Measurement invariance between the United States and Japan
Authors: Yakin Syamil , Niiya Yu 
Published: December 2023

AbstractThe Time Perception Scale (Niiya, 2019, Journal of Happiness Studies) measures people's perception of time as zero‐sum (i.e., the perception that they are taking time away from others, that they are offering time to others, or that others are taking away time from them) and nonzero‐sum (i.e., the perception that time spent on others is time spent on themselves). This scale was validated in Japan, but whether people from a non‐Asian culture also perceive time as nonzero‐sum remained unknown. We tested the measurement invariance of the Time Perception Scale with 189 Americans and 240 Japanese and examined its correlations with psychological well‐being and cultural self‐construals. We confirmed the configural, metric, and partial scalar invariance of the scale and also found that zero‐sum and nonzero‐sum time perceptions were differently associated with basic needs satisfaction, life satisfaction, and interdependent self‐construal in both cultures. Nonzero‐sum time perception may provide a new possibility where a concept derived from East Asian philosophy can contribute to our psychological well‐being.
She wants the best: Maximizing tendency, work‐to‐family enrichment and female employee adaptivity
Authors: Jia Huiyuan , Li Mushi 
Published: December 2023

AbstractStereotypes often link female employees with increased family–work conflicts and low work outcomes. Nevertheless, female employees may excel in both home and work environments. This study aimed to examine the effect of maximizing tendency on female employees' family‐to‐work enrichment and adaptivity. A three‐wave survey involving 1074 female employees was conducted. Results indicated that maximizing tendency positively predicts adaptivity via family‐to‐work enrichment. Spousal relationship quality weakens the effect of maximizing on family‐to‐work enrichment and employee adaptivity. The findings highlight the benefits of maximizing tendency in female employees, suggesting a bright side to maximizing as it enhances adaptability in dynamic work situations. The study also identifies maximizing tendency as a novel personal characteristic that facilitates resource transfer from family to work domain. The findings offer a valuable perspective for promoting female employees' success in the workplace.
Function analysis and characterisation of a novel chitinase, MdCht9, in Musca domestica
Authors: Zhao Wen‐Jing , Li Yan , Jiao Zhen‐Long , Su Pei‐Pei , Yang Long‐Bing , Sun Chao‐Qin , Xiu Jiang‐Fan , Shang Xiao‐Li , Guo Guo 
Published: December 2023

AbstractInsect chitinases have been proposed as potential targets for pest control. In this work, a novel group IV chitinase gene, MdCht9, from Musca domestica was found to have multiple functions in the physiological activity, including chitin regulation, development and antifungal immunity. The MdCht9 gene was cloned and sequenced, its phylogeny was analysed and its expression was determined in normal and 20E treated larvae. Subsequently, RNA interference (RNAi)‐mediated MdCht9 knockdown was performed, followed by biochemical assays, morphological observations and transcriptome analysis. Finally, the recombinant protein MdCht9 (rMdCht9) was purified and tested for anti‐microbial activity and enzyme characteristics. The results showed that MdCht9 consists of three domains, highly expressed in a larval salivary gland. RNAi silencing of MdCht9 resulted in significant down‐regulation of chitin content and expression of 15 chitin‐binding protein (CBP) genes, implying a new insight that MdCht9 might regulate chitin content by influencing the expression of CBPs. In addition, more than half of the lethality and partial wing deformity appeared due to the dsMdCht9 treatment. In addition, the rMdCht9 exhibited anti‐microbial activity towards Candida albicans (fungus) but not towards Escherichia coli (G−) or Staphylococcus aureus (G+). Our work expands on previous studies of chitinase while providing a potential target for pest management.
Dissecting climate change risk and financial market instability: Implications for ecological risk management
Authors: Ma Feng , Cao Jiawei , Wang Yizhi , Vigne Samuel A. , Dong Dayong 
Published: December 2023

AbstractThis research investigates the impact of climate challenges on financial markets by introducing an innovative approach to measure climate risk, specifically the aggregate climate change concern (ACCC) index. The study aims to assess and quantify the potential influence of climate change and risk‐related factors on the performance and dynamics of financial markets. In this paper, concern is defined as the attention paid to the risk of climate change and the associated negative consequences. The findings demonstrate that the aggregate index exhibits robust predictability of market risk premiums, both within the sample and out‐of‐sample. By comparison, the index contains additional information beyond 14 economic predictors and 12 risk/uncertainty indexes in forecasting stock market return. In addition, the index proves valuable for mean–variance investors in asset allocation, leading to significant economic gains. The study identifies the index's ability to capture the reversal of temporary price crashes caused by overreactions to climate change risk. Furthermore, it exhibits stronger return forecasting capability for green stocks, non‐state‐owned enterprise (non‐SOE) stocks, and stocks in regions with low air pollution. Particularly during periods of low air pollution and relaxed regulation, the index displays an enhanced ability to forecast returns. The study's findings provide valuable insights for policymakers and financial institutions as they address 21st‐century environmental challenges. Moreover, these findings can inform the design of adaptive measures and interventions aimed at mitigating ecological risks and promoting sustainable economic growth.
More than a name: Mid‐Cretaceous amber fossils link crickets and mole crickets (Orthoptera, Ensifera)
Authors: Gu Jun‐Jie , Yuan Wei , Ma Li‐Bin , Nel André , Xu Zi‐Qiang , Wang Ning , Jiang Chunxian , Ren Dong , Yue Yanli 
Published: December 2023

AbstractGrylloidea (crickets) and Gryllotalpoidea (mole crickets and ant crickets) are relatively ancient lineages within Orthoptera but their fossil records are not very rich. They are currently considered sister clades within the Gryllidea but with obvious differences in morphology and ecological adaptations. We report a new gryllidean family, †Pseudogryllotalpidae fam. nov. with three new genera and four new species, viz. †Pseudogryllotalpa scalprata gen. et sp. nov., †Unidigitus longialatus gen. et sp. nov., †Petilus zhengi gen. et sp. nov. and †Chunxiania fascia sp. nov. from the mid‐Cretaceous of northern Myanmar (ca. 99 million years ago). Their external and short ovipositors and their modified fossorial forelegs suggest a soil‐inhabiting preference. This new family exhibits a series of ‘intermediate’ character states between Grylloidea and Gryllotalpoidea and seems to be a ‘transitional’ fossil group linking these two superfamilies. This new family was resolved as a sister group of the extant Gryllotalpoidea and provides a new insight into the relationship and evolution of Grylloidea and Gryllotalpoidea.
Intrauterine devices are a safe form of contraception in users with solid organ transplantation: A single‐center experience
Authors: Amaya Stephanie I. , Wolff Sharon F. , Ross Meghan , French Valerie A. 
Published: December 2023

AbstractPatients who undergo organ transplantation are advised to use contraception for health optimization, yet limited data exists on safe contraceptive options for this population. This study investigates the infection risk of intrauterine devices (IUDs) in patients who have received a solid organ transplant by evaluating the incidence of pelvic inflammatory disease (PID). We performed a retrospective chart review of subjects with a solid organ transplant who used an IUD between the years of January 2007 to February 2021. We included subjects ages 22–55 years at the time of IUD placement. We abstracted demographic information, transplant type, IUD type, immunosuppressive medications, screening for sexually transmitted infections, and diagnosis of PID. We identified 29 subjects that met the inclusion criteria. Six subjects had a copper IUD (21%) and 23 had a levonorgestrel IUD (79%). The most common organ transplanted was a kidney (n = 10) and liver (n = 10) while five subjects had multiple organs transplanted. Twenty‐five (86.2%) subjects took immunosuppressive medications at the time of IUD insertion. Twenty‐four (82.8%) patients had their IUD placed after transplantation. The average time of IUD use was 2.5 years. . In our study of IUD use in patients with solid organ transplantation, no patients developed PID. IUDs are a safe contraceptive option for immunosuppressed transplant patients.
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