bluuebunny/crossref_metadata_2025_split huggingface dataset:
PathoGFAIR: a collection of FAIR and adaptable (meta)genomics workflows for (foodborne) pathogens detection and tracking
Authors: Nasr Engy , Henger Anna , Grüning Björn , Zierep Paul , Batut Bérénice 
Published: July 2024

AbstractBackgroundFood contamination by pathogens poses a global health threat, affecting an estimated 600 million people annually. During a foodborne outbreak investigation, microbiological analysis of food vehicles detects responsible pathogens and traces contamination sources. Metagenomic approaches offer a comprehensive view of the genomic composition of microbial communities, facilitating the detection of potential pathogens in samples. Combined with sequencing techniques like Oxford Nanopore sequencing, such metagenomic approaches become faster and easier to apply. A key limitation of these approaches is the lack of accessible, easy-to-use, and openly available pipelines for pathogen identification and tracking from (meta)genomic data.FindingsPathoGFAIR is a collection of Galaxy-based FAIR workflows employing state-of-the-art tools to detect and track pathogens from metagenomic Nanopore sequencing. Although initially developed to detect pathogens in food datasets, the workflows can be applied to other metagenomic Nanopore pathogenic data. PathoGFAIR incorporates visualisations and reports for comprehensive results. We tested PathoGFAIR on 130 samples containing different pathogens from multiple hosts under various experimental conditions. For all but one sample, workflows have successfully detected expected pathogens at least at the species rank. Further taxonomic ranks are detected for samples with sufficiently high Colony-forming unit (CFU) and low Cycle Threshold (Ct) values.ConclusionsPathoGFAIR detects the pathogens at species and subspecies taxonomic ranks in all but one tested sample, regardless of whether the pathogen is isolated or the sample is incubated before sequencing. Importantly, PathoGFAIR is easy to use and can be straightforwardly adapted and extended for other types of analysis and sequencing techniques, making it usable in various pathogen detection scenarios. PathoGFAIR homepage:https://usegalaxy-eu.github.io/PathoGFAIR/
Comprehensive characterization of mitochondrial bioenergetics at different larval stages reveals novel insights about the developmental metabolism ofCaenorhabditis elegans
Authors: Mello Danielle F. , Perez Luiza , Bergemann Christina M. , Morton Katherine S. , Ryde Ian T. , Meyer Joel N. 
Published: July 2024

AbstractMitochondrial bioenergetic processes are fundamental to development, stress responses, and health.Caenorhabditis elegansis widely used to study developmental biology, mitochondrial disease, and mitochondrial toxicity. Oxidative phosphorylation generally increases during development in many species, and genetic and environmental factors may alter this normal trajectory. Altered mitochondrial function during development can lead to both drastic, short-term responses including arrested development and death, and subtle consequences that may persist throughout life and into subsequent generations. Understanding normal and altered developmental mitochondrial biology inC. elegansis currently constrained by incomplete and conflicting reports on how mitochondrial bioenergetic parameters change during development in this species. We used a Seahorse XFe24 Extracellular Flux (XF) Analyzer to carry out a comprehensive analysis of mitochondrial and non-mitochondrial oxygen consumption rates (OCR) throughout larval development inC. elegans. We optimized and describe conditions for analysis of basal OCR, basal mitochondrial OCR, ATP-linked OCR, spare and maximal respiratory capacity, proton leak, and non-mitochondrial OCR. A key consideration is normalization, and we present and discuss results as normalized per individual worm, protein content, worm volume, mitochondrial DNA (mtDNA) count, nuclear DNA (ncDNA) count, and mtDNA:ncDNA ratio. Which normalization process is best depends on the question being asked, and differences in normalization explain some of the discrepancies in previously reported developmental changes in OCR inC. elegans. Broadly, when normalized to worm number, our results agree with previous reports in showing dramatic increases in OCR throughout development. However, when normalized to total protein, worm volume, or ncDNA or mtDNA count, after a significant 2-3-fold increase from L1 to L2 stages, we found small or no changes in most OCR parameters from the L2 to the L4 stage, other than a marginal increase at L3 in spare and maximal respiratory capacity. Overall, our results indicate an earlier cellular shift to oxidative metabolism than suggested in most previous literature.
Polyphyletic domestication and inter-lineage hybridization magnified genetic diversity of cultivated melon,Cucumis meloL
Authors: Tanaka Katsunori , Shigita Gentaro , Dung Tran Phuong , Nhi Phan Thi Phuong , Takahashi Mami , Monden Yuki , Nishida Hidetaka , Ishikawa Ryuji , Kato Kenji 
Published: July 2024

AbstractA total of 212 melon accessions with diverse geographical origins were classified into large and small seed-types by length of seed at the boundary of 9 mm, and into five populations based on polymorphisms in the nuclear genome. They were further divided into three maternal lineages, Ia, Ib, and Ic, by polymorphisms in the chloroplast genome. By combining these three classifications, the Europe/US subsp.meloand the East Asian subsp.agrestiswere characterized as [large seed, Ib, PopA1 or A2] and [small seed, Ia, PopB1 or B2], respectively, indicating nearly perfect divergence in both nuclear and cytoplasm genomes. In contrast, in South and Southeast Asia, in addition to the Europe/US and East Asian types, recombinant types were also frequently found, indicating unclear genetic differentiation in South and Southeast Asia. Such an intermixed structure of genetic variation supported the Indian origin of Ia and Ib types of melon. Seed length was intermediate, between the large and small seed-types, and chloroplast type was a mixture of Ia and Ib in Momordica, suggesting its origin from the recombinant type. In Africa, three lineages of melon were distributed allopatrically and showed distinct divergence. Subsp.agrestisof the Ic type proved to be endemic to Africa, indicating its African origin.
Evaluating the Performance of Artificial Intelligence in Generating Differential Diagnoses for Infectious Diseases Cases: A Comparative Study of Large Language Models
Authors: Mondal Agnibho , Karad Rucha , Bhattacharjee Boudhayan , Saha Bibhuti 
Published: July 2024

AbstractBackgroundArtificial Intelligence (AI) has potential to transform healthcare including the field of infectious diseases diagnostics. This study assesses the capability of three large language models (LLMs), GPT 4, Llama 3, and Gemini 1.5 to generate differential diagnoses, comparing their outputs against those of medical experts to evaluate AI’s potential in augmenting clinical decision-making.MethodsThis study evaluates the differential diagnosis capabilities of three LLMs, GPT 4, Llama 3, and Gemini 1.5, using 50 simulated infectious disease cases. The cases were diverse, complex, and reflective of common clinical scenarios, including detailed histories, symptoms, lab results, and imaging findings. Each model received standardized case information and produced differential diagnoses, which were then compared to reference differential diagnosis lists created by medical experts. The analysis utilized the Jaccard index and Kendall’s Tau to assess similarity and order accuracy, summarizing findings with mean, standard deviation, and combined p-values.ResultsThe mean numbers of differential diagnoses generated by GPT 4, Llama 3, and Gemini 1.5 were 6.22, 5.06, and 10.02 respectively which was significantly different (p<0.001) from the medical experts. The mean Jac-card index of GPT 4, Llama 3, and Gemini 1.5 were 0.3, 0.21, and 0.24 while the mean Kendall’s Tau were 0.4, 0.7, and 0.33 respectively. The combined p-value of GPT 4, Llama 3, and Gemini 1.5 were 1, 1, 0.979 respectively indicating no significant association between the differential diagnosis generated by the LLMs and the medical experts.ConclusionAlthough LLMs like GPT 4, Llama 3, and Gemini 1.5 exhibit varying effectiveness, none align significantly with expert-level diagnostic accuracy, emphasizing the need for further development and refinement. The findings highlight the importance of rigorous validation, ethical considerations, and seamless integration into clinical workflows to ensure AI tools enhance healthcare delivery and patient outcomes effectively.
Co-occurrence of VIM-positive non-aeruginosa Pseudomonasspp. andPseudomonas aeruginosain the hospital: A detailed molecular comparison ofblaVIM-2-containing plasmids from environmental and clinical isolates
Authors: Pirzadian Jannette , Zandijk Willemien H. A. , Heikema Astrid P. , Koene Heidy H. H. T. , Goessens Wil H. F. , Vos Margreet C. , Klaassen Corné H. W. , Severin Juliëtte A. 
Published: July 2024

AbstractBackgroundPseudomonas aeruginosais a bacterial pathogen responsible for severe hospital-acquired infections, and is capable of forming persistent reservoirs in hospital sink drains, creating a transmission risk. In our hospital, we have cultured not only carbapenemase-producing, Verona Integron-encoded Metallo-beta-lactamase (VIM)-positiveP. aeruginosa, but also VIM-positive non-aeruginosa Pseudomonasspp., from sink drains. Previously, ablaVIM-2-containing, conjugative plasmid conferring carbapenem resistance was found in a clinicalP. aeruginosaisolate in our hospital.ObjectiveTo investigate if otherPseudomonasspp. from our hospital also carried ablaVIM-2-containing plasmid, genetically characterize these plasmids, and compare these plasmids to publicly-available plasmid sequences to identify their source.MethodsWhole-genome sequencing was used to sequence chromosomes and possible plasmids from VIM-positive non-aeruginosa Pseudomonasspp. and VIM-positiveP. aeruginosastrains. Hybrid assemblies were generated to reconstruct plasmid sequences. All isolates were obtained from environmental sampling or clinical cultures during a prolonged VIM-positiveP. aeruginosaoutbreak in our hospital.ResultsAn identicalblaVIM-2-containing plasmid was found in six non-aeruginosa Pseudomonas(P. carnis,P. oleovorans, and a novel species) and in threeP. aeruginosaisolates. The previously-reportedblaVIM-2-containing plasmid was found in three additionalP. aeruginosaisolates. AllP. aeruginosabelonged to high-risk clones ST111 or ST446. The two plasmids were derived from both clinical isolates and isolates from sink cultures, and were unique to our hospital when compared to other publicly-available plasmid sequences.ConclusionsDuring a VIM-positiveP. aeruginosaoutbreak in our hospital, two closely-related,blaVIM-2-containing plasmids co-occurred in multiple non-aeruginosa Pseudomonasspp. and in high-riskP. aeruginosaclones ST111 and ST446. Non-aeruginosa Pseudomonasspp. cultured from either patient or sink samples may be important sources of carbapenem resistance genes, and should not be overlooked during outbreak investigations. Moreover, plasmid analysis is essential to fully understand transmission routes in hospitals.
Dzyaloshinskii-Moriya interaction in Ni/Cu(001)
Authors: Allenspach R. , Bischof A. , Boehm B. , Drechsler U. , Reich O. , Sousa M. , Tacchi S. , Carlotti G. 
Published: July 2024

Dzyaloshinskii-Moriya interaction (DMI) is found in the epitaxial Ni/Cu(001) system by imaging magnetic domain wall profiles with high resolution and by Brillouin light scattering. The domain walls have right-handed chirality and deviate from both the Néel and Bloch configurations for Ni thicknesses up to 9 nm. From a detailed structural analysis it is found that strain in the Ni film is inhomogeneous with film thickness. We suggest that this strain field is responsible for the symmetry breaking that is required for a sizable DMI to appear, even in absence of a heavy metal.

Published by the American Physical Society
2024
Priming tourists with traditional gastronomic delicacies: embracing a responsible approach towards sustainable consumption practice
Authors: Samaddar Kaushik , Mondal Sanjana 
Published: July 2024

Purpose
Amidst the rising awareness of sustainable consumption, this study aims to delve into the dimensions shaping individuals' preferences for traditional gastronomic delicacies taking an emerging economy’s perspective, India.

Design/methodology/approach
A qualitative research methodology in the form of a Grounded Theory Approach is used to develop theories. Important dimensions that drive attitude and intention towards experiencing traditional gastronomic delicacies are explored. Based on literary inputs and qualitative study, a research framework is developed and empirically validated thereon with SEM analysis using SPSS-AMOS.

Findings
Drawing on the Theory of Consumption Values and Stakeholder Theory, key influencers (consumption values) of traditional gastronomic delicacies were identified as Travel Motivation (Functional Values), Tourist Expectations (Emotional Values), Socio-economic Perspectives (Socio-economic Values), Mindful Consumption Practice (Epistemic Values), Community Awareness (Epistemic Values) and Sustainable Marketing Stimuli (Conditional Values).

Practical implications
This research has a multifaceted impact. At the macro-level, it supports stakeholders in Gastronomic Tourism (GT) – marketers, regional tourism bodies, policymakers and tour operators with distinct consumer values – in crafting regional culinary tourism, influencing economic policies and advocating for cultural conservation. At the micro-level, it aids scholars in initiating future research to elevate dining experiences, promote consumer education and tackle health and nutritional aspects within the evolving gastronomic industry.

Originality/value
This study makes a novel attempt to explore important drivers, categorizing the drivers into distinct consumer values that influence tourists and food connoisseurs towards traditional gastronomic delicacies by blending an innovative qualitative research methodology like grounded theory approach supported by the empirical validation process (quantitative). Additionally, it proposes a theoretical framework for future advancement of gastronomic literature.
“Don't you worry ‘bout a thing” – the moderating role of age in the relationship between qualitative job insecurity and career sustainability
Authors: Van der Heijden Beatrice , Hofer Annabelle , Semeijn Judith 
Published: July 2024

PurposeBuilding on a stress-related view, this study examines the impact of qualitative job insecurity on three indicators of career sustainability. It also examines the moderating role of employee age in this relationship.Design/methodology/approachDutch respondents (N = 398) working in various sectors responded to an online survey. Our hypotheses were tested using path modeling with Mplus.FindingsQualitative job insecurity was negatively related to job satisfaction, general health, and employability. Moreover, a moderating effect of employee age on the relationship between qualitative job insecurity and job satisfaction was found.Practical implicationsOrganizations need to take measures to prevent qualitative job insecurity, as this appears to be an essential hindering factor that might endanger an employee's career sustainability. Especially younger workers (<40 years) seem to suffer from qualitative job insecurity as this decreases their job satisfaction, urging management and HR professionals to protect them against it.Originality/valueBy focusing on qualitative job insecurity, this study helps to close an essential gap in the literature that so far has mainly focused on quantitative job insecurity. Besides, this is the very first empirical work investigating the link between qualitative job insecurity and multiple indicators of career sustainability. Finally, this research adds a developmental approach to sustainable careers by comparing younger and older workers.
CEO’s early-life extreme experiences and corporate social responsibility: the moderating role of CEO power
Authors: Liu Yanzhao , Hooy Wooi Chee 
Published: July 2024

Purpose
This study aims to explore the relation between CEO’s early-life extreme experiences and firm’s corporate social responsibility (CSR) taking while also examining the moderating influence of CEO power.

Design/methodology/approach
Using a sample of public listed companies in China over 2010–2020 (with 6,008 firm-year observations), this study examines the context of multiple early-life extreme experiences by dividing CEO’s early-life extreme experiences into two distinct types: environment-based and individual-based experiences. The environment based early-life experiences include that of World War II and the Great Famine era (1959–1961), while the individual based early-life experiences cover individual experiences from poor families and military services.

Findings
This study finds that firm with CEOs poses all these early-life experiences tends to have higher CSR taking. Moreover, this study also finds that CEO power enhances the effect of CEO’s early-life extreme experiences on CSR.

Originality/value
This study provides a new perspective on the role of individual traits in driving altruistic CSR motivations by considering the impact of various events on the CEO’s values, perceptions and decision-making processes. In addition, this study also constructs a multiple-event measure of the early-life extreme experiences of CEOs that combines both external environmental and individual factors.
Revisiting the (disappearing) cost of data breach disclosures
Authors: Charoen Danuvasin , Khern-am-nuai Warut 
Published: July 2024

Purpose
The detrimental impact of data breaches on organizations and their customers has been well documented in the literature. These breaches expose sensitive information, raising concerns about reputational damage and substantial financial losses for affected firms. Prior research has consistently demonstrated the significant financial repercussions of data breach disclosures, with a significant decline in the market value of breached firms following the incident’s revelation. However, recent literature has documented the shift in consumer perception toward data breaches, warranting a revisit of this important and relevant issue with more recent data. This study aims to revisit the cost of data breach disclosures by empirically analyzing the impact of recent data breach incidents on the market value of affected firms.

Design/methodology/approach
The authors collect the data regarding data breach incidents among publicly traded companies in the USA listed in the S&P 500 index from 2013 to 2021. The empirical analysis relies on the event study approach, and the market value of each firm is estimated using the Fama-French three-factor model.

Findings
This study finds that the negative market reaction to data breach announcements in recent years has been significantly weaker than those reported in prior works from the past decade. This result confirms the shift in consumer perception toward data breaches in the market.

Originality/value
While prior research has quantified the cost of data breach disclosures, the authors posit that a renewed examination is essential within the contemporary digital environment. Consumer behavior and market sentiment have undergone significant transformations in recent years, necessitating a revisit of this important issue with updated data. This study not only documents this evolving phenomenon but also yields crucial policy recommendations. Notably, it challenges the conventional wisdom to rely on market forces as an adequate deterrent against data breaches. Consequently, updated regulations may be necessary to effectively navigate the complexities of the evolving digital landscape.
Role of e-learning for the continuing professional development of university librarians of Pakistan to deliver value-added services: an explanatory study
Authors: Shahzad Khurram , Khan Shakeel Ahmad 
Published: July 2024

Purpose
This study aims to identify the role of e-learning for the continuing professional development (CPD) of university librarians in Pakistan to deliver value-added library services.

Design/methodology/approach
Explanatory sequential design was applied to address this study’s objectives. First, quantitative data were gathered from 341 respondents working in 244 universities and then qualitative data were gathered through an interview guide from 27 subjects working in different university libraries of Pakistan.

Findings
The findings of this study revealed that respondents realized the benefits of e-learning for continuing professional development positively. E-learning enabled university librarians to perform IT-based tasks through an adequate usage of digital technologies. The findings also manifested that the majority of the respondents faced the challenges of the lack of technical support, and inadequate organizational support to adopt e-learning for CPD. Results displayed e-learning courses should be conducted by local trainers.

Originality/value
This study has provided pertinent theoretical, practical and social contributions by identifying the role of e-learning for the CPD of university librarians of Pakistan to deliver value-added services.
An artificial intelligence approach for the estimation of conduction heat transfer using deep neural networks
Authors: Edalatifar Mohammad , Shafi Jana , Khalid Majdi , Baro Manuel , Sheremet Mikhail A. , Ghalambaz Mohammad 
Published: July 2024

Purpose
This study aims to use deep neural networks (DNNs) to learn the conduction heat transfer physics and estimate temperature distribution images in a physical domain without using any physical model or mathematical governing equation.

Design/methodology/approach
Two novel DNNs capable of learning the conduction heat transfer physics were defined. The first DNN (U-Net autoencoder residual network [UARN]) was designed to extract local and global features simultaneously. In the second DNN, a conditional generative adversarial network (CGAN) was used to enhance the accuracy of UARN, which is referred to as CGUARN. Then, novel loss functions, introduced based on outlier errors, were used to train the DNNs.

Findings
A UARN neural network could learn the physics of heat transfer. Within a few epochs, it reached mean and outlier errors that other DNNs could never reach after many epochs. The composite outlier-mean error as a loss function showed excellent performance in training DNNs for physical images. A UARN could excellently capture local and global features of conduction heat transfer, whereas the composite error could accurately guide DNN to extract high-level information by estimating temperature distribution images.

Originality/value
This study offers a unique approach to estimating physical information, moving from traditional mathematical and physical models to machine learning approaches. Developing novel DNNs and loss functions has shown promising results, opening up new avenues in heat transfer physics and potentially other fields.