bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eclipse: A Python package for alignment of two or more nontargeted LC-MS metabolomics datasets
Authors: Hitchcock Daniel S. , Krejci Jesse N. , Sturgeon Chloe E. , Dennis Courtney A. , Jeanfavre Sarah T. , Avila-Pacheco Julian R. , Clish Clary B. 
Published: June 2023

ABSTRACTNontargeted LC-MS metabolomics datasets contain a wealth of information but present many challenges during analysis and processing. Often, two or more independently processed datasets must be aligned to form a complete dataset, but no available software meets our needs. For this, we have created an open-source Python package calledEclipse. Eclipseuses a novel graph-based subalignment approach to handle complex matching scenarios that arise fromn>2datasets.Eclipseis open source (https://github.com/broadinstitute/bmxp) and can be installed via “pip install bmxp”.
Homologous chromosome recognition via nonspecific interactions
Authors: Marshall Wallace F. , Fung Jennifer C. 
Published: June 2023

AbstractIn many organisms, most notablyDrosophila, homologous chromosomes in somatic cells associate with each other, a phenomenon known as somatic homolog pairing. Unlike in meiosis, where homology is read out at the level of DNA sequence complementarity, somatic homolog pairing takes place without double strand breaks or strand invasion, thus requiring some other mechanism for homologs to recognize each other. Several studies have suggested a “specific button” model, in which a series of distinct regions in the genome, known as buttons, can associate with each other, presumably mediated by different proteins that bind to these different regions. Here we consider an alternative model, which we term the “button barcode” model, in which there is only one type of recognition site or adhesion button, present in many copies in the genome, each of which can associate with any of the others with equal affinity. An important component of this model is that the buttons are non-uniformly distributed, such that alignment of a chromosome with its correct homolog, compared with a non-homolog, is energetically favored; since to achieve nonhomologous alignment, chromosomes would be required to mechanically deform in order to bring their buttons into mutual register. We investigated several types of barcodes and examined their effect on pairing fidelity. We found that high fidelity homolog recognition can be achieved by arranging chromosome pairing buttons according to an actual industrial barcode used for warehouse sorting. By simulating randomly generated non-uniform button distributions, many highly effective button barcodes can be easily found, some of which achieve virtually perfect pairing fidelity. This model is consistent with existing literature on the effect of translocations of different sizes on homolog pairing. We conclude that a button barcode model can attain highly specific homolog recognition, comparable to that seen in actual cells undergoing somatic homolog pairing, without the need for specific interactions. This model may have implications for how meiotic pairing is achieved.
Sociodemographic inequalities in COVID-19 booster vaccination in Peru: a GINI index decomposition analysis
Authors: Intimayta-Escalante Claudio , Tapia-Sequeiros Gustavo , Rojas-Bolivar Daniel 
Published: June 2023

ABSTRACTBackgroundCOVID-19 vaccine coverage, especially in booster doses, remains a significant issue in Peru. This study aimed to analyze the social determinants that affect vaccine coverage and evaluate sociodemographic inequalities in COVID-19 booster dose vaccination in Peru.MethodsAn ecological study was conducted with 196 provinces in Peru. GINI index decomposition analysis was performed to assess the inequality of immunization coverage in these provinces, considering sociodemographic characteristics as sources of inequality (sex, age group, educational level, residence area, and ethnic group). The Oaxaca-Blinder method was utilized to decompose the GINI index into Sk (composition effect), Gk (redistribution effect), Rk (differential effect), share value, and percentage change. Bootstrap method based on percentiles was employed to determine 95% confidence interval values for each GINI index and percentage change in the decomposition analysis.ResultsA total of 196 Peruvian provinces were evaluated. Among these, 59.74% had higher education, while 10.37% had no education or only elementary education. White or mestizo individuals accounted for 51.62% of the population. The GINI index decomposition analysis, six months after the start of the third and fourth dose vaccination campaign, revealed higher Sk values for the white or mestizo ethnic group (Sk= 6.46 vs Sk= 3.03), people living in rural (Sk= 6.63 vs Sk= 2.76) or urban areas (Sk= 5.88 vs Sk= 2.76), and those aged between 30 and 64 years (Sk= 6.84 vs Sk= 3.20). The highest Gk values were observed for the Aymara (Gk= 0.92 vs Gk= 0.92), Afro-Peruvian (Gk= 0.61 vs Gk= 0.61), and Quechua (Gk= 0.53 vs Gk= 0.53) ethnic groups, in contrast to the white or mestizo group (Gk= 0.34 vs Gk= 0.34). Furthermore, Rk exhibited high positive values for individuals with university or postgraduate education (Rk= 0.59 vs Rk= 0.44) and those living in urban areas (Rk= 0.34 vs Rk= 0.28). Conversely, individuals living in rural areas (Rk= -0.34 vs Rk= -0.28), those with elementary education (Rk= -0.46 vs. Rk= -0.36), and those with no education or only preschool education (Rk= -0.41 vs. Rk= -0.32) displayed high negative Rk values.ConclussionSociodemographic inequalities exist in the coverage of third and fourth booster doses against COVID-19 in Peruvian provinces, particularly concerning geographic location, ethnicity, and educational level.
BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA
Authors: Gabriel Lars , Brůna Tomáš , Hoff Katharina J. , Ebel Matthis , Lomsadze Alexandre , Borodovsky Mark , Stanke Mario 
Published: June 2023

AbstractGene prediction has remained an active area of bioinformatics research for a long time. Still, gene prediction in large eukaryotic genomes presents a challenge that must be addressed by new algorithms. The amount and significance of the evidence available from transcriptomes and proteomes vary across genomes, between genes and even along a single gene. User-friendly and accurate annotation pipelines that can cope with such data heterogeneity are needed. The previously developed annotation pipelines BRAKER1 and BRAKER2 use RNA-seq or protein data, respectively, but not both. A further significant performance improvement was made by the recently released GeneMark-ETP integrating all three data types.We here present the BRAKER3 pipeline that builds on GeneMark-ETP and AUGUSTUS and further improves accuracy using the TSEBRA combiner. BRAKER3 annotates protein-coding genes in eukaryotic genomes using both short-read RNA-seq and a large protein database, along with statistical models learned iteratively and specifically for the target genome. We benchmarked the new pipeline on genomes of 11 species under assumed level of relatedness of the target species proteome to available proteomes. BRAKER3 outperformed BRAKER1 and BRAKER2. The average transcript-level F1-score was increased by∼20 percentage points on average, while the difference was most pronounced for species withlarge and complex genomes. BRAKER3 also outperformed other existing tools, MAKER2, Funannotate and FINDER. The code of BRAKER3 is available on GitHub and as a ready-to-run Docker container for execution with Docker or Singularity. Overall, BRAKER3 is an accurate, easy-to-use tool for eukaryotic genome annotation.
Effect of Dual Leucine Zipper Kinase Inhibitor GNE-3511 on Epileptogenesis and Cognitive and Behavioral Changes in a Temporal Lobe Epilepsy Model in Mice
Authors: Acar Dilan , Tunçcan Emre , Selek Serra Nur , Sayın İrem Ekin , Asaroğlu Can Berk , Tümentemur Gamze , Arslan Devrim Öz , Özdemir Samet , Süyen Güldal Güleç 
Published: June 2023

AbstractInflammation and neuronal loss are key factors in the pathophysiology of epilepsy. It is known that activation of Dual Leucine Zipper Kinase (DLK) in chronic neurodegenerative diseases causes neuron death and axon degeneration through apoptotic pathways. Genetic deletion of DLK (dual leucine zipper kinase, MAP3K12) or pharmacological inhibition by GNE-3511 or GNE-8505 was found to have benefits in mouse models of Alzheimer’s and ALS; however, there is no previous study that uses DLK inhibitors in epilepsy models. Therefore, the aim of our study is to suppress the DLK/JNK pathway with the DLK inhibitor GNE-3511 in the temporal lobe epilepsy model induced by pilocarpine and to determine the effect of this inhibition on cognitive and behavioural defects, as well as epileptogenesis. Open field, elevated plus maze, and Morris water maze tests were used to assess locomotor activity, anxiety and learning and memory, respectively. Following decapitation the hippocampi were removed and, histopathological and biochemical analyses were performed. Both treatment groups had less anxiety and locomotor activity as well as decreased impairment in memory and learning performance compared to SE group (p<0.001). Both doses of GNE-3511 prevented the spontaneous recurrent seizures in a dose dependent manner with respect to the SE group (p<0.01 and p<0.001, respectively). Histological examination of the hippocampus revealed a neuroprotective effect of both doses of treatment in the CA1 area and dentate gyrus (p<0.0001). Thus, DLK inhibitor GNE-3511 was found to be effective in preventing epileptogenesis, neuronal loss and cognitive and behavioural deficits due to pilocarpine induced SE.
Experimental testing of two urban stressors on freshwater biofilms
Authors: VRBA Romain , LAVOIE Isabelle , CREUSOT Nicolas , EON Mélissa , MILLAN-NAVARRO Débora , FEURTET-MAZEL Agnès , MAZZELLA Nicolas , MOREIRA Aurélie , PLANAS Dolors , MORIN Soizic 
Published: June 2023

AbstractAquatic ecosystems and their communities are exposed to numerous stressors of various natures (chemical and physical), which impacts are often poorly documented. In urban areas, the use of biocides such as dodecyldimethylbenzylammonium chloride (DDBAC) and their subsequent release in wastewater result in their transfer to urban aquatic ecosystems. DDBAC is known to be toxic to most aquatic organisms. Artificial light at night (ALAN) is another stressor that is increasing globally, especially in urban areas. ALAN may have a negative impact on photosynthetic cycles of periphytic biofilms, which in turn may result in changes in their metabolic functioning. Moreover, studies suggest that exposure to artificial light could increase the biocidal effect of DDBAC on biofilms. The present study investigates the individual and combined effects of DDBAC and/or ALAN on the functioning and structure of photosynthetic biofilms. We exposed biofilms in artificial channels to a nominal concentration of 30 mg.L-1of DDBAC and/or ALAN for 10 days. ALAN modified DDBAC exposure, decreasing concentrations in the water but not accumulation in biofilms. DDBAC had negative impacts on biofilm functioning and structure. Photosynthetic activity was inhibited by > 90% after 2 days of exposure, compared to the controls, and did not recover over the duration of the experiment. Biofilm composition was also impacted, with a marked decrease in green algae and the disappearance of microfauna under DDBAC exposure. The integrity of algal cells was compromised where DDBAC exposure altered the chloroplasts and chlorophyll content. Impacts on autotrophs were also observed through a shift in lipid profiles, in particular a strong decrease in glycolipid content was noted. We found no significant interactive effect of ALAN and DDBAC on the studied endpoints.Graphical abstract
Virtual tissue microstructure reconstruction across species using generative deep learning
Authors: Bettancourt Nicolás , Pérez Cristian , Candia Valeria , Guevara Pamela , Kalaidzidis Yannis , Zerial Marino , Segovia-Miranda Fabián , Morales-Navarrete Hernán 
Published: June 2023

AbstractAnalyzing tissue microstructure is essential for understanding complex biological systems in different species. Tissue functions largely depend on their intrinsic tissue architecture. Therefore, studying the three-dimensional (3D) microstructure of tissues, such as the liver, is particularly fascinating due to its conserved essential roles in metabolic processes and detoxification. Here, we present TiMiGNet, a novel deep learning approach for virtual 3D tissue microstructure reconstruction using Generative Adversarial Networks (GANs) and fluorescence microscopy. TiMiGNet overcomes challenges such as poor antibody penetration and time-intensive procedures by generating accurate, high-resolution predictions of tissue components across large volumes without the need of paired images as input. We applied TiMiGNet to analyze tissue microstructure in mouse and human liver tissue. TiMiGNet shows high performance in predicting structures like bile canaliculi, sinusoids, and Kupffer cell shapes from actin meshwork images. Remarkably, using TiMiGNet we were able to computationally reconstruct tissue structures that cannot be directly imaged due experimental limitations in deep dense tissues, a significant advancement in deep tissue imaging. Our open-source virtual prediction tool facilitates accessible and efficient multi-species tissue microstructure analysis, accommodating researchers with varying expertise levels. TiMiGNet’s simplicity and independence from paired images make it a versatile asset. Overall, our method represents a powerful and efficient approach for studying tissue microstructure, with far-reaching applications in diverse biological contexts and species.
Quantitative comparison of a mobile, tablet-based and two stationary, video-based eye-trackers
Authors: König Aylin , Bremmer Frank , Dowiasch Stefan 
Published: June 2023

AbstractThe analysis of eye-movements is a non-invasive, reliable and fast method to detect and quantify brain (dys-)functions. Here, we investigated the performance of two novel eye-trackers: the Thomas-Oculus-Motus-research mobile (TOM-rm) and the TOM-research stationary (TOM-rs) and compared it with the performance of a well-established video-based eye-tracker, i.e., the EyeLink 1000 (EL). The TOM-rm is a fully integrated, tablet-based mobile device that presents visual stimuli and records head-unrestrained eye-movements at 30Hz without additional infrared (IR) illumination. The TOM-rs is a stationary, video-based eye-tracker that records eye-movements at either high spatial or high temporal resolution. We compared the performance of all three eye-trackers in two different behavioral tasks: pro– and anti-saccade and free viewing. We collected data from human subjects while running all three eye-tracking devices in parallel. Parameters requiring a high spatial or temporal resolution (e.g., saccade latency or gain), as derived from the data, differed significantly between the EL and the TOM-rm in the pro– and anti-saccade task. In the free viewing task, larger noise and the lower frame rate of the TOM-rm caused deviations of the results with respect to the EL. Differences between results derived from the TOM-rs and the EL were most likely due to experimental conditions, which could not be optimized for both systems simultaneously. We conclude that the TOM-rm can be used for measuring eye-movements reliably at comparably low spatial and temporal resolution. The TOM-rs, on the other hand, can provide high-resolution oculomotor data at least on a par with an established reference system.
Multi-criteria decision-making methods: application in humanitarian operations
Authors: Nain Aniruddh , Jain Deepika , Trivedi Ashish 
Published: June 2023

PurposeThis paper aims to examine and compare extant literature on the application of multi-criteria decision-making (MCDM) techniques in humanitarian operations (HOs) and humanitarian supply chains (HSCs). It identifies the status of existing research in the field and suggests a roadmap for academicians to undertake further research in HOs and HSCs using MCDM techniques.Design/methodology/approachThe paper systematically reviews the research on MCDM applications in HO and HSC domains from 2011 to 2022, as the field gained traction post-2004 Indian Ocean Tsunami phenomena. In the first step, an exhaustive search for journal articles is conducted using 48 keyword searches. To ensure quality, only those articles published in journals featuring in the first quartile of the Scimago Journal Ranking were selected. A total of 103 peer-reviewed articles were selected for the review and then segregated into different categories for analysis.FindingsThe paper highlights insufficient high-quality research in HOs that utilizes MCDM methods. It proposes a roadmap for scholars to enhance the research outcomes by advocating adopting mixed methods. The analysis of various studies revealed a notable absence of contextual reference. A contextual mind map specific to HOs has been developed to assist future research endeavors. This resource can guide researchers in determining the appropriate contextual framework for their studies.Practical implicationsThis paper will help practitioners understand the research carried out in the field. The aspiring researchers will identify the gap in the extant research and work on future research directions.Originality/valueTo the best of the authors’ knowledge, this is the first literature review on applying MCDM in HOs and HSCs. It summarises the current status and proposes future research directions.
Investigating the link between socially-responsible HRM and organizational sustainability performance – an HRD perspective
Authors: Nakra Neelam , Kashyap Vaneet 
Published: June 2023

Purpose
The paper aims to investigate the impact of socially-responsible human resource (SR-HR) practices on organizational sustainability performance (OSP) in Indian business organizations that are mandated to publish business sustainability and responsibility reporting.

Design/methodology/approach
Data were obtained from 620 working professionals employed in the organizations listed on National Stock Exchange in India. The proposed hypotheses were tested by deploying the statistical technique of multiple regression analysis using SPSS Version-21.

Findings
The results demonstrated that overall, SR-HR practices impact OSP. More precisely, all the dimensions of SR practices are positively associated with the organization’s financial performance, environmental performance and social performance (SP). There was a relatively higher significant impact of legal-oriented human resource management (HRM) on organizational economic and ecological performance. However, in the case of SP, a substantial effect of employee-oriented HRM was found.

Practical implications
Study findings encourage HR practitioners to invest in SR-HR practices to build and strengthen employees’ abilities and contributing to sustainability goals.

Originality/value
This study is one of the few studies conducted in the Indian context that highlights the relevance of the convergence of HRM, human resource development and corporate social responsibility to realize sustainability goals.
Understanding how indoor environmental classroom conditions influence academic performance in higher education
Authors: Brink Henk W. , Lechner Stefan C.M. , Loomans Marcel G.L.C. , Mobach Mark P. , Kort Helianthe S.M. 
Published: June 2023

Purpose
This study aims to qualitatively examine the relationship between the indoor environmental quality (IEQ), lecturers’ and students’ perceived internal responses and academic performance.

Design/methodology/approach
To capture user experiences with the IEQ in classrooms, semi-structured interviews with 11 lecturers and three focus group discussions with 24 students were conducted, transcribed, coded and analyzed using direct content analysis.

Findings
The findings show that lecturers and students experience poor thermal, lighting, acoustic and indoor air quality (IAQ) conditions that may influence their ability to teach and learn. Maintaining acceptable thermal and IAQ conditions was difficult for lecturers, as opening windows or doors caused noise disturbances. In uncomfortable conditions, lecturers may decide to give a break earlier or shorten a lecture. When students experienced discomfort, it may affect their ability to concentrate, their emotional status and their quality of learning.

Research limitations/implications
The findings originate from a relatively small sample, which might have limited the number and variety of identified associations between environment and users.

Practical implications
Maintaining acceptable air and thermal conditions will mitigate the need to open windows and doors. Keeping doors and windows closed will prevent noise disturbances and related distractions. This will support the quality of learning in classrooms. This study reveals the end users’ perspectives and preferences, which can inspire designers of new school buildings in higher education.

Originality/value
This study emphasizes the importance of creating and maintaining optimal IEQ conditions to support the quality of teaching and learning. These conditions are particularly relevant when classroom occupancy rates are high or outdoor conditions are unfavourable.
Data literacy training needs of researchers at South African universities
Authors: Moyo Mathew , Bangani Siviwe 
Published: June 2023

Purpose
The aim of this study was to determine data literacy (DL) training needs of researchers at South African public universities. The outcome of this study would assist librarians and researchers in developing a DL training programme which addressed identified needs.

Design/methodology/approach
A survey research method was used to gather data from researchers at these universities by convenience. Online questionnaires were distributed to public universities through library directors for further distribution to researchers.

Findings
The results indicate low levels of DL training at the respondent South African public universities with most researchers indicating that they had not received any formal training on DL. A few researchers indicated that they would welcome DL training.

Research limitations/implications
This study was exploratory in nature and data was received from eight universities, which is not representative of all the 26 public universities in South Africa. Nonetheless, the low DL confirmed by the majority in the realised sample is indicative of the need to further investigate the subject.

Practical implications
Librarians and research support personnel should collaborate on the development of DL training courses, workshops and materials used by researchers at institutions of higher learning to enhance DLs on campus.

Originality/value
This study may be novel in South Africa in investigating the DL training needs of researchers at several universities and contributes to the growing body of literature on research data management