bluuebunny/crossref_metadata_2025_split huggingface dataset:
PerturbAtlas: A Comprehensive Atlas of Public Genetic Perturbation Bulk RNA-seq Datasets
Authors: Zhang Yiming , Zhang Ting , Yang Gaoxia , Pan Zhenzhong , Tang Min , Wen Yue , He Ping , Wang Yuan , Zhou Ran 
Published: July 2024

ABSTRACTManipulating gene expression is crucial for understanding gene function, with high-throughput sequencing techniques such as RNA-seq elucidating the downstream mechanisms involved. However, the lack of a standardized metadata format for small-scale perturbation expression datasets in public repositories hinders their reuse. To address this issue, we developed PerturbAtlas, an add-value resource that re-analyzes publicly archived RNA-seq libraries to provide quantitative data on gene expression, transcript profiles, and alternative splicing events following genetic perturbation. PerturbAtlas assists users in identifying trends at the gene and isoform levels in perturbation assays by re-analyzing a curated set of 122,801 RNA-seq libraries across 13 species. This resource is freely available athttps://perturbatlas.kratoss.siteas both raw data tables and an interactive browser, allowing searches by species, tissue, or genomic features. The results provide detailed information on alterations following perturbations, accessible through both forward and reverse approaches, thereby enabling the exploration of perturbation consequences and the identification of potential causal perturbations.GRAPHICAL ABSTRACT
Coordinated regulation of chemotaxis and resistance to copper by CsoR inPseudomonas putida
Authors: He Meina , Tao Yongxin , Mu Kexin , Feng Haoqi , Fan Ying , Liu Tong , Huang Qiaoyun , Xiao Yujie , Chen Wenli 
Published: July 2024

AbstractCopper is an essential enzyme cofactor in bacteria, but excess copper is highly toxic. Bacteria can cope with copper stress by increasing copper resistance and initiating chemorepellent response. However, it remains unclear how bacteria coordinate chemotaxis and resistance to copper. By screening proteins that interacted with the chemotaxis kinase CheA, we identified a copper-binding repressor CsoR that interacted with CheA inPseudomonas putida. CsoR interacted with the HPT (P1), Dimer (P3), and HATPase_c (P4) domains of CheA and inhibited CheA autophosphorylation, resulting in decreased chemotaxis. The copper-binding of CsoR weakened its interaction with CheA, which relieved the inhibition of chemotaxis by CsoR. In addition, CsoR bound to the promoter of copper-resistance genes to inhibit gene expression, and copper-binding released CsoR from the promoter, leading to increased gene expression and copper resistance.P. putidacells exhibited a chemorepellent response to copper in a CheA-dependent manner, and CsoR inhibited the chemorepellent response to copper. Besides, the CheA-CsoR interaction also existed in proteins from several other bacterial species. Our results revealed a mechanism by which bacteria coordinately regulated chemotaxis and resistance to copper by CsoR.
Degradability tunes ECM stress relaxation and cellular mechanics
Authors: Narasimhan Badri Narayanan , Fraley Stephanie I. 
Published: July 2024

AbstractIn native extracellular matrices (ECM), cells can use matrix metalloproteinases (MMPs) to degrade and remodel their surroundings. Likewise, synthetic matrices have been engineered to facilitate MMP-mediated cleavage that enables cell spreading, migration, and interactions. However, the intersection of matrix degradability and mechanical properties has not been fully considered. We hypothesized that immediate mechanical changes result from the action of MMPs on the ECM and that these changes are sensed by cells. Using atomic force microscopy (AFM) to measure cell-scale mechanical properties, we find that both fibrillar collagen and synthetic degradable matrices exhibit enhanced stress relaxation after MMP exposure. Cells respond to these relaxation differences by altering their spreading and focal adhesions. We demonstrate that stress relaxation can be tuned through the rational design of matrix degradability. These findings establish a fundamental link between matrix degradability and stress relaxation, which may impact a range of biological applications.Table of contentsThis work reveals that matrix degradability, through its effects on stress relaxation, is an important cellular mechanotransduction cue. Cell-scale mechanical characterization shows that collagen gels and degradable synthetic gels display enhanced stress relaxation post-degradation. Stress relaxation is then tuned by systematically varying degradability, resulting in the regulation of cell spreading. This identifies degradability as a key chemomechanical design feature.
Biregional division angles generate sharp apex and concave joints in leaves
Authors: Wang Zining , Inoue Yasuhiro , Mochizuki Atsushi , Tsukaya Hirokazu 
Published: July 2024

AbstractLeaf apex, the distal end of the leaf blade, exhibits enormous shape variations across plant species. Among these variations, the sharp apex, characterized by its pointed tip, is important in species identification and environmental adaptation. Despite its taxonomic and ecological importance, the developmental mechanisms underlying the formation of a sharp apex remain unknown. The present study aims to investigate the curvature patterns and morphogenesis of the sharp apex to uncover these mechanisms usingTriadica sebiferaleaves. Our research revealed that the sharp apex marks the maximum positive curvature, and is flanked by concave joints with negative curvatures, suggestive of differential tissue growth and spatially regulated cellular behavior. Through a combination of wet experiments and numerical simulations, we demonstrated that biregional cell division angles, rather than locally differing cell expansion or division frequency, play a determining role in shaping distinct leaf morphology. Our study highlights the importance of spatiotemporal regulation of cell division angles during leaf development, suggesting that a biregional growth pattern and cellular behavior contribute to diversity in leaf apex morphology.
Designing a simple and efficient phage biocontainment system using the amber suppressor initiator tRNA
Authors: Tsoumbris Pamela R. , Vincent Russel M. , Jaschke Paul R. 
Published: July 2024

AbstractMultidrug-resistant infections are becoming increasingly prevalent worldwide. One of the fastest emerging alternative and adjuvant therapies being proposed is phage therapy. Naturally-isolated phages are used in the vast majority of phage therapy treatments today. Engineered phages are being developed to enhance the effectiveness of phage therapy, but concerns over their potential escape remains a salient issue. To address this problem, we designed a biocontained phage system based on conditional replication using amber stop codon suppression. This system can be easily installed on any natural phage with a known genome sequence. To test the system, we mutated the start codons of three essential capsid genes in the phage ϕX174 to the amber stop codon (TAG). These phages were able to efficiently infect host cells expressing the amber initiator tRNA, which suppresses the amber stop codon and initiates translation at TAG stop codons. The amber phage mutants were also able to successfully infect host cells and reduce their population on solid agar and liquid culture but could not produce infectious particles in the absence of the amber initiator tRNA or complementing capsid gene. We did not detect any growth-inhibiting effects onE. colistrains known to lack a receptor for ϕX174, and we show that engineered phages have a limited propensity for reversion. The approach outlined here may be useful to control engineered phage replication in both the lab and clinic.
Resource-efficiency of cyanobacterium production on Mars: Assessment and paths forward
Authors: Ramalho Tiago P. , Baumgartner Vincent , Kunst Nils , Rodrigues David , Bohuon Emma , Leroy Basile , Pillot Guillaume , Heinicke Christiane , Kerzenmacher Sven , Avila Marc , Verseux Cyprien 
Published: July 2024

ABSTRACTSpace agencies and private companies strive for a permanent human presence on the Moon and ultimately on Mars. Bioprocesses have been advocated as key enablers due to their ability to transform locally available resources into added-value materials. However, the resource-efficiency and scaling of space biosystems remain poorly understood, hindering quantitative estimates of their potential performance. We leveraged extensive cultivation experiments, where a cyanobacterium (Anabaenasp. PCC 7938) was subject to conditions attainable on Mars, to develop a model that can estimate bioprocess productivity and resource-efficiency as a function of water, light, temperature, regolith minerals and perchlorates, and atmospheric carbon and nitrogen. We show that a breakeven can be reached within a few years. We discuss research lines to improve both resource efficiency and the accuracy of the model, thereby reducing the need for costly tests in space and eventually leading to a biotechnology-supported, sustained human presence on Mars.TEASERBioprocess modeling shows that cyanobacterium-based biotechnologies can be a sustainable basis for resource production on Mars.
High-fat and high-sucrose diet-induced hypothalamic inflammation shows sex specific features in mice
Authors: De Paula Gabriela C. , Simões Rui F. , Garcia-Serrano Alba M. , Duarte João M. N. 
Published: July 2024

AbstractHypothalamic inflammation underlies diet-induced obesity and diabetes in rodent models. While diet normalization largely allows for recovery from metabolic impairment, it remains unknown whether long-term hypothalamic inflammation induced by obesogenic diets is a reversible process. In this study, we aimed at determining sex specificity of hypothalamic neuroinflammation and gliosis in mice fed a fat- and sugar-rich diet, and their reversibility upon diet normalization. Mice were fed a 60%-fat diet complemented by a 20% sucrose drink (HFHSD) for 3 days or 24 weeks, followed by a third group that had their diet normalized for the last 8 weeks of the study (reverse diet group, RevD). We determined the expression of pro- and anti-inflammatory cytokines, and of the inflammatory cell markers IBA1, CD68, GFAP and EMR1 in the hypothalamus, and analyzed morphology of microglia (IBA-1+cells) and astrocytes (GFAP+cells) in the arcuate nucleus. After 3 days of HFHSD feeding, male mice showed over-expression of IL-13, IL-18, IFN-γ, CD68 and EMR1 and reduced expression of IL-10, while females showed increased IL-6 and IBA1 and reduced IL-13, compared to controls. After 24 weeks of HFHSD exposure, male mice showed a general depression in the expression of cytokines, with prominent reduction of TNF-α, IL-6 and IL-13, but increased TGF-β, while female mice showed over-expression of IFN-γ and IL-18. Furthermore, both female and male mice showed some degree of gliosis after HFHSD feeding for 24 weeks. In mice of both sexes, diet normalization after prolonged HFHSD feeding resulted in partial neuroinflammation recovery in the hypothalamus, but gliosis was only recovered in females. In sum, HFHSD-fed mice display sex-specific inflammatory processes in the hypothalamus that are not fully reversible after diet normalization.
How do algorithms influence platform workers’ behavior? Relationship between algorithmic autonomy support and platform workers’ stress and incivility
Authors: Deng Ting , Tang Chunyong , Zhou Ang , Lai Yanzhao 
Published: July 2024

Purpose
Drawing upon the needs–supplies fit theory, this study aims to examine how the expected and perceived algorithmic autonomy support (AAS) influences platform workers’ work stress and incivility, with a focus on the moderating role of self-direction.

Design/methodology/approach
Using data collected from 422 platform workers in China through multiple waves, the model is tested through polynomial regression and response surface analysis.

Findings
The results indicate that a mismatch between expected and perceived AAS is associated with higher levels of incivility among platform workers, and this relationship is mediated by work stress. These findings are particularly salient when self-direction is emphasized.

Practical implications
This study suggests that a universally high level of AAS may not necessarily reduce workers’ stress and incivility. Instead, it is important for platforms to ensure that their workers’ expectations of autonomy support are met and for workers to be given the space to exercise self-direction.

Originality/value
Previous studies have highlighted the need to pay attention to workers in mobile and ambiguous environments, and this study adds to this literature by focusing specifically on platform organizations and workplaces. This study provides valuable insights into the relationship between AAS, work stress and platform workers’ incivility.
Multiaxial low-cycle fatigue life model for notched specimens considering small sample characteristics
Authors: Wu Shenglei , Liu Jianhui , Wang Yazhou , Lu Jumei , Zhang Ziyang 
Published: July 2024

PurposeSufficient sample data are the necessary condition to ensure high reliability; however, there are relatively poor fatigue test data in the engineering, which affects fatigue life's prediction accuracy. Based on this, this research intends to analyze the fatigue data with small sample characteristics, and then realize the life assessment under different stress levels.Design/methodology/approachFirstly, the Bootstrap method and the principle of fatigue life percentile consistency are used to realize sample aggregation and information fusion. Secondly, the classical outlier detection algorithm (DBSCAN) is used to check the sample data. Then, based on the stress field intensity method, the influence of the non-uniform stress field near the notch root on the fatigue life is analyzed, and the calculation methods of the fatigue damage zone radius and the weighting function are revised. Finally, combined with Weibull distribution, a framework for assessing multiaxial low-cycle fatigue life has been developed.FindingsThe experimental data of Q355(D) material verified the model and compared it with the Yao’s stress field intensity method. The results show that the predictions of the model put forward in this research are all located within the double dispersion zone, with better prediction accuracies than the Yao’s stress field intensity method.Originality/valueAiming at the fatigue test data with small sample characteristics, this research has presented a new method of notch fatigue analysis based on the stress field intensity method, which is combined with the Weibull distribution to construct a low-cycle fatigue life analysis framework, to promote the development of multiaxial fatigue from experimental studies to practical engineering applications.
Social media platforms use in startups’ international marketing strategies: a multiple case study
Authors: Olivieri Mirko , Testa Ginevra 
Published: July 2024

PurposeThis paper aims to investigate how social media support startups in accessing international markets and interacting with foreign customers and stakeholders, focusing primarily on the social network LinkedIn.Design/methodology/approachGiven the explorative research aim, the paper adopts a multiple case study approach, analyzing seven Italian food tech startups. 15 semi-structured interviews were conducted, also involving startup accelerators and a business angel to deepen the knowledge on the investigated phenomenon. In addition, a content analysis of the LinkedIn pages of the seven selected startups was conducted using NVivo 14 software.FindingsThe results of this study show that social media support startups to (1) diffuse brand awareness in international markets, (2) position their offering abroad and (3) develop relationships with international stakeholders to penetrate the local business. Furthermore, the main challenges and difficulties related to the use of social media by startups for these purposes were identified.Practical implicationsThis study provides useful managerial implications to enable startups to strategically use social media to access international markets and connect with key foreign networks. Also from a policy perspective, incentives to support the expansion and consolidation of startups into international markets are crucial.Originality/valueAlthough a vast literature has dealt with internationalization strategies, this study clarifies the role of social media in changing these dynamics speeding up startups’ access to foreign markets and identifying key local stakeholders.
Intellectual capital through decarbonization for achieving Sustainable Development Goal 8: a systematic literature review and future research directions
Authors: Di Vaio Assunta , Zaffar Anum , Chhabra Meghna 
Published: July 2024

PurposeThe aim of this study is to review the literature on how intellectual capital (IC) contributes to the decarbonization efforts of firms. It explores how carbon accounting can measure the components of IC in decarbonization efforts to balance profitability with environmental and social goals, particularly in promoting decent work and economic growth (Sustainable Development Goal [SDG] 8 and its targets [2, 5, 6, 8]). Moreover, it emphasises the importance of multi-stakeholder partnerships for sharing knowledge, expertise, technology, and financial resources (SDG17-Target 17.G) to meet SDG8.Design/methodology/approachAs a consolidated methodological approach, a systematic literature review (SLR) was used in this study to fill the existing research gaps in sustainability accounting. To consolidate and clarify scholarly research on IC towards decarbonization, 149 English articles published in the Scopus database and Google Scholar between 1990 and 2024 were reviewed.FindingsThe results highlight that the current research does not sufficiently cover the intersection of carbon accounting and IC in the analysis of decarbonization practices. Stakeholders and regulatory bodies are increasingly pressuring firms to implement development-focused policies in line with SDG8 and its targets, requiring the integration of IC and its measures in decarbonization processes, supported by SDG17-Target 17.G. This integration is useful for creating business models that balance profitability and social and environmental responsibilities.Originality/valueThe integration of social dimension to design sustainable business models for emission reduction and provide a decent work environment by focusing on SDG17-Target 17.G has rarely been investigated in terms of theory and practice. Through carbon accounting, IC can be a key source of SDG8-Targets 8.[2, 5, 6, 8] and SDG17-Target 17.G. Historically, these major issues are not easily aligned with accounting research or decarbonization processes.
Navigating egalitarian culture and accountability pressures: shared instructional leadership practices of Danish school leaders
Authors: Laursen Ronni , Gümüş Sedat , Walker Allan David 
Published: July 2024

PurposeOur study presents insights from an exploratory qualitative case study conducted in three primary and lower secondary schools in Denmark, a country renowned for its collaborative and egalitarian culture, to unravel the complexities of shared instructional leadership.Design/methodology/approachInterviews with principals, middle leaders, and teachers and document analysis were used to identify themes according to shared and instructional leadership perspectives.FindingsThe study yielded three major findings. First, Danish principals structure schools to prioritize student learning outcomes and distribute responsibility to middle leaders and teachers. Second, reflection among teachers and leaders better prepares them for future demands and obligations. Third, collaboration underpins principals’ vision of reflection and professional development.Practical implicationsThe research team’s reflection on the data collected can be used to build future strategies to address unpredictable student learning progression and poor-performing teachers.Originality/valueTogether, these findings contribute to the broader understanding of shared instructional leadership and demonstrate how principals face external pressure for accountability and how egalitarian culture influences principals’ practices.
Integrated model between Three Pillars of Institutions and Mair Noboa model to determine social entrepreneurial intention
Authors: Iqbal Mehree , Geneste Louis , Weber Paull 
Published: July 2024

Purpose
This study aims to expand antecedent roles on social entrepreneurial behavioural intention by integrating both the Three Pillars of Institutions and the Mair Noboa model. The literature lacks in investigating both institutional- and individual-level antecedents to determine social entrepreneurial behavioural intention. This proposed integrated model was developed in which the Mair Noboa's model antecedents mediates the positive relationship between the antecedents of Three Pillars of Institutions and social entrepreneurial intention.

Design/methodology/approach
This study uses quantitative research methodologies to answer the research question of the extent that institutional-level antecedents in turn influence individual antecedents and thus determine social entrepreneurial intention. To explore this, a Web-based survey distributed across Bangladesh (n = 412). The confirmation of hypotheses involved using covariance-based structural equation modelling (SEM) for data analysis. The resulting measurement and structural models successfully met all criteria for reliability, model fit, convergent validity and discriminant validity. The hypotheses were subsequently assessed by examining both direct relationships and mediating effects.

Findings
The findings demonstrated a significant relationship between the antecedents of the Three Pillars of Institutions and the Mair Noboa model. The results suggest that the Mair Noboa model antecedents can mediate the relationship between the Three Pillars of Institutions and social entrepreneurial intention.

Originality/value
This paper advances the existing knowledge of social entrepreneurial intention, through the novel lens of combined institutional and individual antecedents. This paper fills an important knowledge gap by exploring both institutional- and individual-level antecedents to determine social entrepreneurial intention. This study findings yield fresh theoretical and practical insights into how institutional and individual antecedents jointly influence social entrepreneurial intention.