bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein Embeddings Predict Binding Residues in Disordered Regions
Authors: Jahn Laura R. , Marquet Céline , Heinzinger Michael , Rost Burkhard 
Published: March 2024

AbstractThe identification of protein binding residues helps to understand their biological processes as protein function is often defined through ligand binding, such as to other proteins, small molecules, ions, or nucleotides. Methods predicting binding residues often err for intrinsically disordered proteins or regions (IDPs/IDPRs), often also referred to as molecular recognition features (MoRFs). Here, we presented a novel machine learning (ML) model trained to specifically predict binding regions in IDPRs. The proposed model, IDBindT5, leveraged embeddings from the protein language model (pLM) ProtT5 to reach a balanced accuracy of 57.2±3.6% (95% confidence interval). Assessed on the same data set, this did not differ at the 95% CI from the state-of-the-art (SOTA) methods ANCHOR2 and DeepDISOBind that rely on expert-crafted features and evolutionary information from multiple sequence alignments (MSAs). Assessed on differ data, methods such as SPOT-MoRF reached higher MCCs. IDBindT5’s SOTA predictions are much faster than other methods, easily enabling full-proteome analyses. Our findings emphasize the potential of pLMs as a promising approach for exploring and predicting features of disordered proteins. The model and a comprehensive manual are publicly available athttps://github.com/jahnl/binding_in_disorder.
Evolution of Tn4371family ICE;traRmediated coordination of cargo gene upregulation and horizontal transfer
Authors: Matsumoto Satoshi , Kishida Kouhei , Nonoyama Shouta , Sakai Keiichiro , Tsuda Masataka , Nagata Yuji , Ohtsubo Yoshiyuki 
Published: March 2024

AbstractICEKKS102Tn4677, which has been shown to transfer horizontally, carriesbphoperon for mineralization of PCBs/biphenyl and belongs to an ICE Tn4371family. In this study we investigated the role oftraRgene encoding a LysR-type transcriptional regulator, which is conserved in sequence, positioning, and directional orientation among Tn4371family ICEs. ThetraRbelonged tobphoperon and its overexpression on solid medium resulted in modest upregulation oftraG(3-fold) and marked upregulation ofxis(80-fold), and enhanced ICE excision, and notably ICE transfer frequency. We propose the evolutional roles oftraR, which upon insertion to the current position, connected the cargo gene activation and ICE-transfer. This property of ICE, transferring under environmental conditions that lead to cargo gene activation, would give fitness advantages to the host bacteria, thereby resulting in efficient dissemination of the Tn4371family ICEs.SignificanceOnly ICEKKS102Tn4677is proven to transfer among the widely disseminating Tn4371family ICEs from β and γ-proteobacteria. We showed that thetraRgene in ICEKKS102Tn4677conserved in the ICE family with fixed location and direction is co-transcribed with the cargo gene and activates ICE transfer. We propose that capturing oftraRby an ancestral ICE to the current position established ICE Tn4371family ICEs. Our findings provide insights into the evolutionary processes that led to the widespread distribution of the Tn4371family of ICEs across bacterial species.
High-throughput genetics enables identification of nutrient utilization and accessory energy metabolism genes in a model methanogen
Authors: Day Leslie A. , Carlson Hans K. , Fonseca Dallas R. , Arkin Adam P. , Price Morgan N. , Deutschbauer Adam M. , Costa Kyle C. 
Published: March 2024

AbstractArchaea are widespread in the environment and play fundamental roles in diverse ecosystems; however, characterization of their unique biology requires advanced tools. This is particularly challenging when characterizing gene function. Here, we generate randomly-barcoded transposon libraries in the model methanogenic archaeonMethanococcus maripaludisand use high-throughput growth methods to conduct fitness assays (RB-TnSeq) across over 100 unique growth conditions. Using our approach, we identified new genes involved in nutrient utilization and response to oxidative stress. We identified novel genes for the usage of diverse nitrogen sources inM. maripaludisincluding a putative regulator of alanine deamination and molybdate transporters important for nitrogen fixation. Furthermore, leveraging the fitness data, we provide the first evidence thatM. maripaludis can utilize the nitrogen sources L-glutamine, D-glucuronamide, and adenosine. Under autotrophic growth conditions, we identified a gene encoding a domain of unknown function (DUF166) that is important for fitness and hypothesize it has an accessory role in carbon dioxide assimilation. Finally, comparing fitness costs of oxygen versus sulfite stress, we identified a previously uncharacterized class of dissimilatory sulfite reductase-like proteins (Dsr-LP, group IIId) that is important during growth in the presence of sulfite. When overexpressed, Dsr-LP conferred sulfite resistance and enabled use of sulfite as the sole sulfur source. The high-throughput approach employed here allowed for generation of a large-scale dataset that can be used as a resource to further understand gene function and metabolism in the archaeal domain.Significance StatementArchaea are widespread in the environment, yet basic aspects of their biology remain underexplored. To address this, we apply randomly-barcoded transposon libraries (RB-TnSeq) to the model archaeonMethanococcus maripaludis.RB-TnSeq coupled with high-throughput growth assays across over 100 unique conditions identified roles for previously uncharacterized genes, including several encoding proteins with domains of unknown function (DUFs). We also expand on our understanding of carbon and nitrogen metabolism and characterize a group IIId dissimilatory sulfite reductase-like protein as a functional sulfite reductase. This dataset encompasses a wide range of additional conditions including stress, nitrogen fixation, amino acid supplementation, and autotrophy; thus, providing an extensive dataset for the archaeal community to mine for characterizing additional genes of unknown function.
A literature-based view on technology transfer and culture
Authors: Gambi Lillian Do Nascimento , Debackere Koenraad 
Published: March 2024

PurposeThe purpose of this paper is to examine the evolution of the literature on technology transfer and culture, identifying the main contents of the current body of knowledge encompassing culture and technology transfer (TT), thus contributing to a better understanding of the relationship between TT and culture based on bibliometric and multivariate statistical analyses of the relevant body of literature.Design/methodology/approachData for this study were collected from the Web of Science (WoS) Core Collection database. Based on a bibliometric analysis and in-depth empirical review of major TT subjects, supported by multivariate statistical analyses, over 200 articles were systematically reviewed. The use of these methods decreases biases since it adds rigor to the subjective evaluation of the relevant literature base.FindingsThe exploratory analysis of the articles shows that first, culture is an important topic for TT in the literature; second, the publication data demonstrate a great dynamism regarding the different contexts in which culture is covered in the TT literature and third, in the last couple of years the interest of stimulating a TT culture in the context of universities has continuously grown.Research limitations/implicationsThis study focuses on culture in the context of TT and identifies the main contents of the body of knowledge in the area. Based on this first insight, obtained through more detailed bibliometric and multivariate analyses, it is now important to develop and validate a theory on TT culture, emphasizing the dimensions of organizational culture, entrepreneurial culture and a culture of openness that fosters economic and societal spillovers, and to link those dimensions to the performance of TT activities.Practical implicationsFrom the practical point of view, managers in companies and universities should be aware of the importance of identifying those dimensions of culture that contribute most to the success of their TT activities.Originality/valueDespite several literature reviews on the TT topic, no studies focusing specifically on culture in the context of TT have been developed. Therefore, given the multifaceted nature of the research field, this study aims to expand and to deepen the analysis of the TT literature by focusing on culture as an important and commonly cited element influencing TT performance.
Human-centricity in Industry 5.0 – revealing of hidden research topics by unsupervised topic modeling using Latent Dirichlet Allocation
Authors: Madzik Peter , Falat Lukas , Jum’a Luay , Vrábliková Mária , Zimon Dominik 
Published: March 2024

PurposeThe set of 2,509 documents related to the human-centric aspect of manufacturing were retrieved from Scopus database and systmatically analyzed. Using an unsupervised machine learning approach based on Latent Dirichlet Allocation we were able to identify latent topics related to human-centric aspect of Industry 5.0.Design/methodology/approachThis study aims to create a scientific map of the human-centric aspect of manufacturing and thus provide a systematic framework for further research development of Industry 5.0.FindingsIn this study a 140 unique research topics were identified, 19 of which had sufficient research impact and research interest so that we could mark them as the most significant. In addition to the most significant topics, this study contains a detailed analysis of their development and points out their connections.Originality/valueIndustry 5.0 has three pillars – human-centric, sustainable, and resilient. The sustainable and resilient aspect of manufacturing has been the subject of many studies in the past. The human-centric aspect of such a systematic description and deep analysis of latent topics is currently just passing through.
A review of and future research agenda on women entrepreneurship in Africa
Authors: Woldesenbet Beta Kassa , Mwila Natasha Katuta , Ogunmokun Olapeju 
Published: March 2024

PurposeThis paper seeks to systematically review and synthesise existing research knowledge on African women entrepreneurship to identify gaps for future studies.Design/methodology/approachThe paper conducted a systematic literature review of published studies from 1990 to 2020 on women entrepreneurship in Africa using a 5M gender aware framework of Brush et al. (2009).FindingsThe systematic literature review of published studies found the fragmentation, descriptive and prescriptive orientation of studies on Africa women entrepreneurship and devoid of theoretical focus. Further, women entrepreneurship studies tended to be underpinned from various disciplines, less from the entrepreneurship lens, mostly quantitative, and at its infancy stage of development. With a primary focus on development, enterprise performance and livelihood, studies rarely attended to issues of motherhood and the nuanced understanding of women entrepreneurship’s embeddedness in family and institutional contexts of Africa.Research limitations/implicationsThe paper questions the view that women entrepreneurship is a “panacea” and unravels how family context, customary practices, poverty and, rural-urban and formal/informal divide, significantly shape and interact with African women entrepreneurs’ enterprising experience and firm performance.Practical implicationsThe findings and analyses indicate that any initiatives to support women empowerment via entrepreneurship should consider the socially constructed nature of women entrepreneurship and the subtle interplay of the African institutional contexts’ intricacies, spatial and locational differences which significantly influence women entrepreneurs’ choices, motivations and goals for enterprising.Originality/valueThe paper contributes to a holistic understanding of women entrepreneurship in Africa by using a 5M framework to review the research knowledge. In addition, the paper not only identifies unexplored/or less examined issues but also questions the taken-for-granted assumptions of existing knowledge and suggest adoption of context- and gender-sensitive theories and methods.
Research performance evaluation model in university: evidence from Indonesia
Authors: Hermanu Adhi Indra , Sari Diana , Sondari Mery Citra , Dimyati Muhammad 
Published: March 2024

PurposeThis research aimed to examine the impact of input, process, output, productivity and outcome variables on university research performance and the indicators that represent them in order to improve academic quality and contribute to government policy.Design/methodology/approachThe quantitative approach was used through a survey method that obtained samples using questionnaires from 150 leaders of research institutions and continued analysis using the structural equation modeling-partial least square (SEM-PLS) to test the developed model.FindingsExcept for the relationship between process and productivity variables, all variable relationships had a positive and significant effect. Furthermore, the input, process, output, productivity and outcome variables each include seven, twelve, four and ten indicators.Research limitations/implicationsThis study has several ramifications because it provides a clear policy input and advances science. As a prelude to developing research performance assessment tools that take into account variances in a tertiary institution, this research aids in the implementation of national policies for assessing research performance in postsecondary institutions.Originality/valueTo improve the accuracy of the information acquired, we conducted a survey among the heads of research units at various higher-ranking Indonesian universities, taking into consideration their skill and experience in leading research organizations and conducting research. Other than that, our belief in the originality of our manuscript is strengthened by the way we applied systems theory to construct a performance evaluation model that examines each contribution made by each system aspect.
Effects of energy price shock on the macroeconomic indicators of India: a new measure
Authors: Raj Karan , Sharma Devashish 
Published: March 2024

Purpose
The purpose of this study is to construct a new index to assess the impact of an energy price shock on macroeconomic indicators of India. This paper also shows a comparative analysis of the constructed index along with pre-existing World Bank and International Monetary Fund indices on energy.

Design/methodology/approach
This paper uses three vector autoregressions and compute the long-term impact of the indices on the considered macroeconomic variables through impulse response functions.

Findings
This paper finds that an energy price shock has a detrimental impact on the macroeconomic indicators of India in the long run. This study also finds that the constructed index acts as a relatively more sensitive index in comparison to the International Monetary Fund and World Bank indices, which is bespoke to a developing economy case. This sensitivity is ascribed to dynamic weighting for a different basket of energy components, which are more pertinent to an Indian context.

Originality/value
The novelty of this research lies in the construction of a new index and its comparison to the existing ones. This study justifies why a developing economy would require a different measure of energy as opposed to the existing indices.
Unpacking place-based narratives: enhancing campus community participation in watershed conservation
Authors: Abd. Kadir Siti Norasiah , MacBride-Stewart Sara , Mohamad Zeeda Fatimah 
Published: March 2024

Purpose
The study aims to identify the evoked “sense of place” that the campus community attributes to a watershed area in a Malaysian higher institution, aiming to enhance their participation in watershed conservation. Central to this objective is the incorporation of the concept of a watershed as a place, serving as the conceptual framework for analysis.

Design/methodology/approach
This case study explores an urban lake at Universiti Malaya, Malaysia’s oldest higher institution. It uses diverse qualitative data, including document analysis, semi-structured interviews, vox-pop interviews and a co-production workshop, to generate place-based narratives reflecting the meanings and values that staff and students associate with the watershed. Thematic analysis is then applied for further examination.

Findings
The data patterns reveal shared sense of place responses on: campus as a historic place, student, staff and campus identity, in-place learning experiences and interweaving of community well-being and watershed health. Recommendations advocate translating these narratives into campus sustainability communication through empirical findings and continuous co-production of knowledge and strategies with the campus community.

Practical implications
The research findings play a critical role in influencing sustainable campus planning and community inclusion by integrating place-based frameworks into sustainable development and watershed management. The study recommends the process of identifying place-based narratives with implications for the development of sustainability communication in a campus environment.

Originality/value
This paper contributes both conceptually and empirically to the sustainable management of a campus watershed area through place-based thinking. It outlines a process for enhancing campus sustainability communication strategies.
Ultra-high cycle fatigue and ultra-slow crack growth behavior of additively manufactured AlSi7Mg alloy
Authors: Zhao Qiuchen , Li Xue , Hu Junchao , Jiang Yuehui , Yang Kun , Wang Qingyuan 
Published: March 2024

PurposeThe purpose of this paper is to determine the ultra-high cycle fatigue behavior and ultra-slow crack propagation behavior of selective laser melting (SLM) AlSi7Mg alloy under as-built conditions.Design/methodology/approachConstant amplitude and two-step variable amplitude fatigue tests were carried out using ultrasonic fatigue equipment. The fracture surface of the failure specimen was quantitatively analyzed by scanning electron microscope (SEM).FindingsThe results show that the competition of surface and interior crack initiation modes leads to a duplex S–N curve. Both manufacturing defects (such as the lack of fusion) and inclusions can act as initially fatal fatigue microcracks, and the fatigue sensitivity level decreases with the location, size and type of the maximum defects.Originality/valueThe research results play a certain role in understanding the ultra-high cycle fatigue behavior of additive manufacturing aluminum alloys. It can provide reference for improving the process parameters of SLM technology.
Building community is the first thing HR leaders need to do
Authors: Freed Jann E. 
Published: March 2024

Purpose
This paper aims to help HR leaders understand the value of building community and advice on how they can build community in their teams and organizations.

Design/methodology/approach
The author draws from recent data about loneliness and community and incorporates real-world strategies and suggestions.

Findings
Building community is often overlooked or undervalued, but HR leaders can take steps to help employees feel as though they are part of a community and be more engaged in their work.

Originality/value
This paper fulfills a need that has been identified across major publications in the USA in recent years: how HR leaders can help employees combat loneliness and social isolation and feel more engaged at work.
Bank Supervision and Organizational Capital: The Case of Minority Lending
Authors: AN BYEONGCHAN , BUSHMAN ROBERT , KLEYMENOVA ANYA , TOMY RIMMY E. 
Published: March 2024

ABSTRACTWe investigate whether improvements in banks' organizational capital and control systems facilitate increased loan origination to minority borrowers. We focus on bank supervisors' enforcement decisions and orders (EDOs) against banks and hypothesize that EDO‐imposed improvements in loan policies, internal governance, and employee training mitigate deficiencies in credit assessments and lending decisions that previously disadvantaged minority borrowers. We find that mortgage origination to minority borrowers increases following the resolution of EDOs, and more so for banks with stricter supervisors or more severe EDOs. Using a semisupervised machine learning method to analyze the text of EDOs, we find that such increases are higher for EDOs specifying revisions of loan policies, implementation of formal internal governance procedures, or more employee training. Overall, we find that EDO‐driven improvements in organizational capital generate unintended, positive social externalities that enhance access to credit for minority borrowers.
Comparing practice‐ and results‐based agri‐environmental schemes controlled by remote sensing: An application to olive groves in Spain
Authors: Villanueva Anastasio J. , Granado‐Díaz Rubén , Colombo Sergio 
Published: March 2024

AbstractFarmers' preferences toward practice‐ and results‐based agri‐environmental schemes (AES) are analysed using a labelled choice experiment. The analysis focuses on schemes involving an innovative satellite‐based monitoring system, with different environmental objectives. Olive groves in southern Spain are used as a case study. Results show no statistically significant differences in farmers' willingness to accept (WTA) payment for participating in practice‐ versus results‐based AES when the scheme targets carbon sequestration. By contrast, farmers require a significantly higher WTA payment for results‐based AES when targeting biodiversity (using bird species as an indicator), mostly due to the uncertainties related to its provision and monitoring. WTA significantly increases with provision level and remote sensing monitoring, regardless of the type of scheme. Significant preference heterogeneity is observed, partly explained by farmers' attitudes toward risk and their beliefs about environmental service provision and monitoring capacity. The results suggest useful policy implications, including the potential of making use of joint provision of environmental services in the design of results‐based AES and accompanying them with uncertainty mitigating measures.
Forensic analysis of iOS binary cookie files
Authors: Studiawan Hudan 
Published: March 2024

AbstractiPhone operating system (iOS) devices utilize binary cookies as a data storage tool, encoding user‐specific information within an often‐neglected element of smartphone analysis. This binary format contains details such as cookie flags, expiration, and creation dates, domain, and value of the cookie. These data are invaluable for forensic investigations. This study presents a comprehensive methodology to decode and extract valuable data from these files, enhancing the ability to recover user activity information from iOS devices. This paper provides an in‐depth forensic investigation into the structure and function of iOS binary cookie files. Our proposed forensic technique includes a combination of reverse engineering and custom‐built Python scripts to decode the binary structure. The results of our research demonstrate that these cookie files can reveal an array of important digital traces, including user preferences, visited websites, and timestamps of online activities. It concludes that the forensic analysis of iOS binary cookie files can be a tool for forensic investigators and cybersecurity professionals. In the rapidly evolving domain of digital forensics, this research contributes to our understanding of less‐explored data sources within iOS devices and their potential value in investigative contexts.