bluuebunny/crossref_metadata_2025_split huggingface dataset:
MDMD: a computational model for predicting drug-related microbes based on the aggregated metapaths from a heterogeneous network
Authors: Xing Jiajie , Zhang Xianguo , Wang Juan 
Published: October 2023

AbstractClinical studies have shown that microbes are closely related to the occurrence of diseases in the human body. It is beneficial for treating diseases by means of microbes to modulate the activity and toxicity of drugs. Therefore, it is significant in predicting associations between drugs and microbes. Recently, there are several computational models for addressing the issue. However, most of them only focus on drug-related microbes and neglect related diseases, which can lead to insufficient training. Here we introduce a new model (called MDMD) is proposed to predict drug-related microbes based on the Metapaths from a heterogeneous network constructed by using the data of Diseases, Microbes, Drugs, the associations of microbe-disease and disease-drug. The MDMD uses an aggregation of the metapath features that can effectively abundance the embedding of the features for different types of nodes and edges in the heterogeneous networks. Then, the MDMD uses the attention mechanism to mark the importance of the metapath vector for each node type which can improve the quality of feature embedding. Experimental results demonstrate that the MDMD improves accuracy by 1.9% compared with other models. The MDMD is also used to predict the microbes of two drugs Lamivudine and Tenofovir which are the antiretroviral drugs used to treat the Acquired Immune Deficiency Syndrome(AIDS). The results show that 90-95% of microbes are reported in the PubMed. Mycobacterium tuberculosis(Mtb) is a specific microbe only predicted by the MDMD. An online platform of the MDMD is available inhttps://mdmd2023.bit1024.top/, in which the source code of the MDMD and the data in the work can be downloaded.Author summaryMicrobes inhabit multiple organs of the human body that consist of bacteria, fungi, and viruses. Extensive research shows that the microbes can adjust the efficacy and toxicity of drugs to treat the disease. The efficient and accurate selection of drug-related microbes is important for drug research and disease treatment. However, screening of drug-related microbes relies on traditional lab experiments that are labor-intensive and costly. With the growth of high-throughput data, the research of drug-related microbes urgently needs a computational method in bioinformatics. However, most of them only focus on drug-related microbes and neglect related diseases, which can lead to insufficient training. Therefore, we propose a new method (called MDMD) based on the aggregation of the metapath to efficiently and accurately predict potential drug-related microbes within the microbes-disease-drug network.
Antiviral and Antibacterial Efficacy of Nanocomposite Amorphous Carbon Films with Copper Nanoparticles
Authors: Bakhet Shahd , Tamulevičienė Asta , Vasiliauskas Andrius , Andrulevičius Mindaugas , Meškinis Šarūnas , Tamulevičius Sigitas , Kašėtienė Neringa , Malakauskas Mindaugas , Lelešius Raimundas , Zienius Dainius , Šalomskas Algirdas , Šmits Krišjānis , Tamulevičius Tomas 
Published: October 2023

ABSTRACTCopper compound-rich films and coatings are effective against widespread viruses and bacteria. Even though the killing mechanisms are still debated it is agreed that the metal ion, nanoparticle release, and surface effects are of paramount importance in the antiviral and antibacterial efficacy of the surfaces. In this work we have investigated the behaviour of the reactive magnetron sputtered nanocomposite diamond-like carbon thin films with copper nanoparticles (DLC:Cu). The films were etched employing oxygen plasma and/or exposed to ultra-pure water aiming to investigate the differences of the Cu release in the medium and changes in film morphology. The presence of metallic copper and Cu2O phases were confirmed by multiple analytical methods. Pristine films were more effective in the Cu release reaching up to 1.3 mg/L/cm2concentration. Plasma processing resulted in the oxidation of the films which released less Cu but after exposure to water, their average roughness increased more, up to 5.5 nm. Pristine and O2plasma processed DLC:Cu films were effective against both model coronavirus and herpesvirus after 1-hour contact time and reached virus reduction up to 2.23 and 1.63 log10, respectively. Pristine DLC:Cu films were more effective than plasma-processed ones against herpesvirus, while less expressed difference was found for coronavirus. The virucidal efficacy over up to 24 h exposures in the aqueous medium was validated. A bactericidal study confirmed that pristine DLC:Cu films were effective against gram-negativeE. coliand gram-positiveE. faecalisbacteria. After 3 hours 100% antibacterial efficiency (ABE) was obtained forE. coliand 99.97% forE. faecalis. After 8 hours and longer exposures, 100% ABE was reached. The half-life inactivation of viruses was 8.10 – 11.08 minutes and forE. faecalis15.1 – 72.2 minutes.
Mechanistic insights into the function of 14-3-3 proteins as negative regulators of brassinosteroid signaling in Arabidopsis
Authors: Obergfell Elsa , Hohmann Ulrich , Moretti Andrea , Hothorn Michael 
Published: October 2023

AbstractBrassinosteroids (BRs) are vital plant steroid hormones sensed at the cell surface by a membrane signaling complex comprising the receptor kinase BRI1 and a SERK-family co-receptor kinase. Activation of this complex lead to dissociation of the inhibitor protein BKI1 from the receptor and to differential phosphorylation of BZR1/BES1 transcription factors by the glycogen synthase kinase 3 protein BIN2. Many phosphoproteins of the BR signaling pathway, including BRI1, SERKs, BKI1 and BZR1/BES1 can associate with 14-3-3 proteins. In this study, we use quantitative ligand binding assays to define the minimal 14-3-3 binding sites in the N-terminal lobe of the BRI1 kinase domain, in BKI1, and in BZR1 fromArabidopsis thaliana. All three motifs require to be phosphorylated to specifically bind 14-3-3s with mid- to low micromolar affinity. BR signaling components display minimal isoform preference within the 14-3-3 non-ε subgroup. 14-3-3ƛ and 14-3-3ω isoform complex crystal structures reveal that BKI1 and BZR1 bind as canonical type II 14-3-3 linear motifs. Disruption of key amino acids in the phosphopeptide binding site through mutation impairs the interaction of 14-3-3ƛ with all three linear motifs. Notably, quadruple loss-of-function mutants from the non-ε group exhibit gain-of-function brassinosteroid signaling phenotypes, suggesting a role for 14-3-3 proteins as overall negative regulators of the BR pathway. Collectively, our work provides further mechanistic and genetic evidence for the regulatory role of 14-3-3 proteins at various stages of the brassinosteroid signaling cascade.
Gene expression variation across genetically identical individuals predicts reproductive traits
Authors: Webster Amy K. , Willis John H. , Johnson Erik , Sarkies Peter , Phillips Patrick C. 
Published: October 2023

ABSTRACTIn recent decades, genome-wide association studies (GWAS) have been the major approach to understand the biological basis of individual differences in traits and diseases. However, GWAS approaches have limited predictive power to explain individual differences, particularly for complex traits and diseases in which environmental factors play a substantial role in their etiology. Indeed, individual differences persist even in genetically identical individuals, although fully separating genetic and environmental causation is difficult in most organisms. To understand the basis of individual differences in the absence of genetic differences, we measured two quantitative reproductive traits in 180 genetically identical young adultCaenorhabditis elegansroundworms in a shared environment and performed single-individual transcriptomics on each worm. We identified hundreds of genes for which expression variation was strongly associated with reproductive traits, some of which depended on individuals’ historical environments and some of which was random. Multiple small sets of genes together were highly predictive of reproductive traits, explaining on average over half and over a quarter of variation in the two traits. We manipulated mRNA levels of predictive genes to identify a set of causal genes, demonstrating the utility of this approach for both prediction and understanding underlying biology. Finally, we found that the chromatin environment of predictive genes was enriched for H3K27 trimethylation, suggesting that gene expression variation may be driven in part by chromatin structure. Together, this work shows that individual, non-genetic differences in gene expression are both highly predictive and causal in shaping reproductive traits.
A PARP14/TARG1-Regulated RACK1 MARylation Cycle Drives Stress Granule Dynamics in Ovarian Cancer Cells
Authors: Challa Sridevi , Nandu Tulip , Kim Hyung Bum , Gong Xuan , Renshaw Charles W. , Li Wan-Chen , Tan Xinrui , Aljardali Marwa W. , Camacho Cristel V. , Chen Jin , Kraus W. Lee 
Published: October 2023

AbstractMono(ADP-ribosyl)ation (MARylation) is emerging as a critical regulator of ribosome function and translation. Herein, we demonstrate that RACK1, an integral component of the ribosome, is MARylated on three acidic residues by the mono(ADP-ribosyl) transferase (MART) PARP14 in ovarian cancer cells. MARylation of RACK1 is required for stress granule formation and promotes the colocalization of RACK1 in stress granules with G3BP1, eIF3η, and 40S ribosomal proteins. In parallel, we observed reduced translation of a subset of mRNAs, including those encoding key cancer regulators (e.g., AKT). Treatment with a PARP14 inhibitor or mutation of the sites of MARylation on RACK1 blocks these outcomes, as well as the growth of ovarian cancer cells in culture and in vivo. To re-set the system after prolonged stress and recovery, the ADP-ribosyl hydrolase TARG1 deMARylates RACK1, leading to the dissociation of the stress granules and the restoration of translation. Collectively, our results demonstrate a therapeutically targetable pathway that controls stress granule assembly and disassembly in ovarian cancer cells.SummaryWe have discovered a druggable PARP14/TARG1-regulated pathway that mediates site- specific mono(ADP-ribosyl)ation of RACK1, a ribosomal protein. This pathway controls stress granule assembly and disassembly, as well as the translation of a subset of mRNAs, to modulate the growth of ovarian cancer cells in culture and in vivo.
Representations of the intrinsic value of information in mouse orbitofrontal cortex
Authors: Bussell Jennifer J. , Badman Ryan P. , Márton Christian D. , Bromberg-Martin Ethan S. , Abbott L.F. , Rajan Kanaka , Axel Richard 
Published: October 2023

AbstractAnimals are motivated to seek information that does not influence reward outcomes, suggesting that information has intrinsic value. We have developed an odor-based information seeking task that reveals that mice choose to receive information even though it does not alter the reward outcome. Moreover, mice are willing to pay for information by sacrificing water reward, suggesting that information is of intrinsic value to a mouse. We used a microendoscope to reveal neural activity in orbitofrontal cortex (OFC) while mice learned the information seeking task. We observed the emergence of distinct populations of neurons responsive to odors predictive of information and odors predictive of water reward. A latent variable model recapitulated these different representations in the low-dimensional dynamics of OFC neuronal population activity. These data suggest that mice have evolved separate pathways to represent the intrinsic value of information and the extrinsic value of water reward. Thus, the desire to acquire knowledge is observed in mice, and the value of this information is represented in the OFC. The mouse now provides a facile experimental system to study the representation of the value of information, a higher cognitive variable.
Learner support services at distance higher education institutions in the union territory of Jammu and Kashmir
Authors: Wani Shabir Ahmed , Asgar Ali , Srivastava Manjulika 
Published: October 2023

PurposeThis paper presents the features and relevance of open distance learning in the context of the socio-economic conditions of people living in the Union Territory of Jammu and Kashmir (J&K) in India. Although the primary purpose of the present study was to ascertain the effectiveness of the learner support services (LSSs) and different facilities offered by the open distance learning (ODL) institutions in that specific region. On the basis of these findings, few suggestions are made for the improvement in the support services, in order to make the ODL system more responsive to the area-specific needs of the learners, especially those residing in inaccessible areas such as J&K.Design/methodology/approachA survey-based descriptive methodology was applied to conduct this study. The data extracted from primary and secondary sources were analysed to reach certain conclusions. In total, 1,200 distance learners constituted the sample of the research. A semi-structured questionnaire was designed and distributed amongst learners and academics in the region to obtain their feedback and opinion on different aspects of support services and facilities offered to ODL learners.FindingsResults of the study revealed that overall, the LSSs were satisfactory on different parameters, although they slightly varied from institution to institution. However, there was still scope for improvement in certain areas, where institutions further need to make serious efforts to address the identified gaps for improving the LSS and make teaching-learning more learner-centric in view of their specific requirements and local circumstances of J&K.Research limitations/implicationsThe present study focusses on presenting an overview of the only major components of LSS offered by ODL institutions and covers six distance education institutions (DEIs) located in different geographical locations within the limited jurisdiction of J&K. There is still scope to make focused (institution-wise) studies in a more specific situation and context to ascertain the problems in a more realistic way.Practical implicationsAlthough the study has been conducted in a specific territory of J&K, the findings reported in the paper may be equally useful for the other ODL institutions with similar characteristics or located in similar geographical locations, as support services are essential common components of institutions offering distance education programmes or courses.Originality/valueThe study is original research work conducted in the specific context of J&K, and its findings are based on the primary and secondary data collected from learners and other stakeholders of the selected ODL institutions. This work may be significant for the DEIs of J&K to get familiar with the essential components of LSS and develop a mechanism to further improve the academic and administrative support services for distance learners.
Accessing collective memory: the role of oral history in building an inclusive archives reflecting a people’s archives
Authors: Schellnack-Kelly Isabel 
Published: October 2023

Purpose
The purpose of this article is to discuss accessing oral history in building an inclusive archives from communities that once dwelled in the Kruger National Park. In March 2022, in the Daily Maverick, the South African Minister of Forestry, Fisheries and the Environment, Barbara Creecy stated that there is a need for a shift to an Africanised conservation approach that embraces the diverse cultures, traditions and knowledge systems in South Africa. It is, thus, important for wilderness areas in South Africa to undertake projects to collect and share indigenous knowledge that can be captured and used to conserve wilderness areas.

Design/methodology/approach
The research methodology that was applied for the purpose of this study is a multimethod approach but is dominated by a qualitative approach.

Findings
During three interviews, three focus groups of five persons and three onsite visits, several concerns were identified as requiring more investigations and efforts to ensure archives can be publicly accessible.

Originality/value
History on Africa has largely been written by the global north and kept behind expensive paywalls (Fengu, 2022). The oral history projects being undertaken in South Africa are to be commended in for filling gaps in the historical discourse neglected by the colonial and apartheid dispensations.
Inequality, poverty, and resilience to economic shrinking
Authors: Smythe Anthony , Martins Igor , Andersson Martin 
Published: October 2023

Purpose
With the recognition that generating economic growth is not the same as sustaining it, the challenge to catch-up and growth literature is discerning between these processes. Recent research suggests that the decline in the frequency of “shrinking” episodes is more important for long-term development than higher growth rates. By using a framework centred around social capabilities, this study aims to investigate the effects of income inequality and poverty on economic shrinking frequency, as opposed to previous literature that has exclusively had a growth focus. The aim is to investigate how and why some societies might be more resilient to economic shrinking.

Design/methodology/approach
The research is a quantitative study, and the authors build a longitudinal data set including 23 developing countries throughout 42 years to test the paper’s purpose. This study uses country and period fixed-effects specifications as well as cross-sectional graphical representations to investigate the relationship between proxies of economic inclusivity and the frequency of shrinking episodes.

Findings
The authors demonstrate that while inclusive societies are more resilient to shrinking overall, it is changes in poverty levels, but not changes in income inequality, that appear to be correlated with economic shrinking frequency. Inequality, while still an important element to explain countries’ growth potential as an initial condition, does not seem to make the sample more resilient to shrinking. The authors conclude that the mechanisms in which poverty and inequality are correlated with the catch-up process must run through different channels. Ultimately, processes that explain growth may intersect but not always overlap with the ones that explain resilience to shrinking.

Originality/value
The need for inclusive growth in long-term development has been championed for decades, yet inclusion has seldom been explored from the shrinking perspective. Though poverty reduction is already an important mainstream political objective, this paper differentiates itself by providing an alternate viewpoint of why this is important. Income inequality could have more of an economic growth limiting effect, while poverty reduction could be required to build resilience to economic shrinking. Developing countries will need both growth and resilience to shrinking, to catch-up with higher-income economies, which policymakers might need to balance carefully.
Change agents under tensions: a paradox approach to strategies for transforming higher education toward sustainability
Authors: Bohunovsky Lisa , Radinger-Peer Verena , Zint Michaela , Penker Marianne 
Published: October 2023

Purpose
Guided by paradox theory, the study aims to significantly advance Sustainability in Higher Education Institutions (SHEI) scholarship and inform change agents’ (CAs) practices by uncovering the tensions underlying the challenges CAs face in embedding sustainability in their universities and learning about potential strategies to manage these tensions.

Design/methodology/approach
The authors conducted a multi-step, mix-methods study including interviews (n = 15), an online survey (n = 36) and focus groups (n = 29) with CAs from 17 of Austria’s 22 public universities. Participating CAs consisted of faculty, staff and administrators with leading roles in their Higher Education Institutions’ sustainability change processes.

Findings
Austrian SHEI CAs’ responses revealed 15 tensions at and between the individual, organizational and system level addressing academic, organizational and external stakeholder engagement aspects. Six tensions were selected for more in-depth exploration including elaboration of management strategies, building on CAs’ experiences. Results revealed examples of acceptance, separation and synthesis strategies.

Research limitations/implications
Based on the exploratory nature of our study, the authors do not claim to have identified a comprehensive list of tensions underlying the challenges faced by SHEI CAs, nor of all potential management strategies.

Practical implications
Although this study focused exclusively on Austrian SHEI CAs, the challenges they shared were consistent with those in the literature and, thus, insights should also support the CAs’ efforts in other countries.

Originality/value
This study offers novel perspectives on how to manage the challenges to SHEI. To the best of the authors’ knowledge, it is the first to describe paradox theory-informed management strategies recommended by a heterogenous group of SHEI CAs to address the barriers they face in transforming their universities toward sustainability.
Capital requirements – risk taking/stability nexus during the global financial crisis and COVID-19: international evidence of Islamic banks
Authors: Ding Xiao Ling , Haron Razali , Hasan Aznan 
Published: October 2023

Purpose
This study aims to determine how Basel III capital requirements affect the stability of Islamic banks globally during the global financial crisis and the COVID-19 pandemic.

Design/methodology/approach
The secondary data for all Islamic banks worldwide from 2004 to 2021 is obtained from the FitchConnect database. The main technique was a two-step generalized method of moment (GMM) system, and the data were tested using pooled ordinary least squares, fixed effects and difference GMM models for robustness checks.

Findings
Regression results support the moral hazard hypothesis based on evidence that both the total capital ratio and the Tier 1 capital ratio have a statistically significant positive impact on the stability of Islamic banks globally. Furthermore, neither the global financial crisis of 2008–2009 nor COVID-19 (2020–2021) significantly impacted the stability of Islamic banks worldwide. The results are robust across alternative measures of stability, capital buffers, dummy variables and estimation techniques. According to the descriptive statistics, the number of Islamic banks that disclose their regulatory capital ratios to the public has increased over the study period, and the mean of total capital and Tier 1 ratios are considerably greater than what is required by Basel II and Basel III.

Research limitations/implications
Bankers, regulators and policymakers should benefit from the evidence on capital and risk management in Islamic banking according to Basel Committee on Banking Supervision (BCBS) and Islamic financial services board (IFSB) international standards in various jurisdictions.

Originality/value
This research builds on earlier studies that were both beneficial and instructive by exploring the relationship between BCBS and IFSB capital guidelines and the trustworthiness of Islamic banks in greater depth. This study uses numerous capital ratios, buffers and stability measures to provide an international context for research on Islamic banking. In addition, the database is up-to-date to include information about the COVID-19 pandemic aftereffects in the year 2021. This study also introduces the Basel membership of Islamic banks to provide context for countries still at the Basel II stage or are yet to begin implementing the Basel III international standard.