bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term impacts of Legionnaires’ disease on health and well-being: rationale, study design and baseline findings of a matched cohort study (LongLEGIO)
Authors: Bigler Melina , Vaucher Malina , Wiederkehr Manuel , Brülisauer Sophia , Albrich Werner C. , Dräger Sarah , Gisler Valentin , Akers Isabel , Mäusezahl Daniel 
Published: August 2024

AbstractBackgroundThe long-term effects of Legionnaires’ disease beyond the acute infection and their impact on healthcare utilisation remain poorly understood. We present the rationale and study design of a matched prospective observational cohort study (LongLEGIO) aimed at investigating the persistent sequelae on patients’ health, well-being, and health service use following community-acquired Legionnaires’ disease, compared to other bacterial pneumonias that tested negative forLegionella.MethodsPatients with Legionnaires’ disease and other bacterialLegionellatest-negative pneumonia are recruited from secondary and tertiary care hospitals and matched for sex, age, hospital-level and date of diagnosis. Semi-structured interviews were conducted at baseline (shortly after the pneumonia diagnosis) and at two, six and 12 months following appropriate antibiotic therapy. Baseline assessments capture pre-existing conditions, illness experience, and disease severity, while follow-up assessments evaluate long-term symptoms, healthcare utilisation, quality of life (EQ-5D-5L), and social/work impacts. Data on case management and the disease severity are extracted from patient records.ResultsA total of 59 patients with community-acquired Legionnaires’ disease and 60 patients with other bacterialLegionellatest-negative pneumonia were enrolled. Both cohorts were representative of their respective condition. Key differences between Legionnaires’ disease and non-Legionellabacterial pneumonia patient groups emerged in terms of comorbidities, pneumonia severity, and self-reported quality of life. These differences will be accounted for in future analyses as part of theLongLEGIOstudy.ConclusionsTheLongLEGIOstudy will advance ongoing research on post-acute infection syndromes and provide a robust data foundation for more accurate assessments of the disease burden associated with Legionnaires’ disease.
A comprehensiveSchizosaccharomyces pombeatlas of physical transcription factor interactions with proteins and chromatin
Authors: Skribbe Merle , Soneson Charlotte , Stadler Michael B. , Schwaiger Michaela , Sreechakram Vishnu N. Suma , Iesmantavicius Vytautas , Hess Daniel , Moreno Eliza Pandini Figueiredo , Braun Sigurd , Seebacher Jan , Smallwood Sebastien A. , Bühler Marc 
Published: August 2024

SUMMARYTranscription factors (TFs) are key regulators of gene expression, yet many of their targets and modes of action remain unknown. InSchizosaccharomyces pombe, one-third of TFs are solely homology-predicted, with few experimentally validated. We created a comprehensive library of 89 endogenously taggedS. pombeTFs, mapping their protein and chromatin interactions using immunoprecipitation-mass spectrometry and chromatin immunoprecipitation sequencing. Our study identified protein interactors for half the TFs, with over a quarter potentially forming stable complexes. We discovered DNA binding sites for most TFs across 2,027 unique genomic regions, revealing motifs for 38 TFs and uncovering a complex regulatory network of extensive TF cross- and autoregulation. Characterization of the largest TF family revealed conserved DNA sequence preferences but diverse binding patterns, and identified a repressive heterodimer, Ntu1/Ntu2, linked to perinuclear gene localization. Our TFexplorer webtool makes all data interactively accessible, offering new insights into TF interactions and regulatory mechanisms with broad biological relevance.HIGHLIGHTSComprehensive strain library of endogenously taggedS. pombeTFsExperimentally determined atlas of TF interactions with proteins and chromatinTFexplorer web application for interactive exploration of TF interactomesIdentification of repressive Nattou complex linked to perinuclear gene localization
A Neural Basis for Mutant ATAXIN-1 Induced Respiratory Dysfunction in Mouse Models of Spinocerebellar Ataxia Type 1
Authors: Soles Alyssa , Grittner Jessica , Douglas Kaia , Yang Praseuth , Barnett Ryan , Chau Christine , Cosiquien Roj , Duvick Lisa , Rainwater Orion , Serres Shannah , Orr Harry , Dougherty Brendan , Cvetanovic Marija 
Published: August 2024

AbstractSpinocerebellar ataxia type 1 (SCA1), a dominantly inherited neurodegenerative disorder caused by an expanded trinucleotide repeat in theATAXIN-1 (ATXN1)gene, is characterized by motor dysfunction, cognitive impairment, and death from compromised swallowing and respiration. To delineate specific cell types that contribute to respiratory dysfunction, we utilized the floxed conditional knock-inf-ATXN1146Q/2Qmouse. Whole body plethysmography during spontaneous respiration and respiratory challenge showed thatf-ATXN1146Q/2Qmice exhibit a spontaneous respiratory phenotype characterized by elevated respiratory frequency, volumes, and respiratory output. Consequently, the ability off-ATXN1146Q/2Qmice to increase ventilation during the challenge is impaired. To investigate the role of mutantATXN1expression in neural and skeletal muscle lineages,f-ATXN1146Q/2Qmice were bred toNestin-CreandActa1-Cremice respectively. These analyses revealed that the abnormal spontaneous respiration inf-ATXN1146Q/2Qmice involved two aspects: a behavioral phenotype in which SCA1 mice exhibit increased motor activity during respiratory testing and functional dysregulation of central respiratory control centers. Both aspects of spontaneous respiration were partially ameliorated by removing mutantATXN1from neural, but not skeletal muscle, cell lineages.
Insilicocharacterisation of PAL homologs and metabolomic profiling of shade response indicates potential presence of PTALs and Tyr as a probable precursor of lignin biosynthesis in conifers
Authors: Ranade Sonali Sachin , García-Gil María Rosario 
Published: August 2024

AbstractNorway spruce and Scots pine show enhanced lignin synthesis under shade along with differential expression of defense-related genes that renders disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants and tyrosine (Tyr) forms an additional lignin precursor in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed a relatively higher amount of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggests potential presence of PTALs in conifers, which is novel. Exome sequence analysis revealed latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and PTAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.
Boosting Proteasome Activity: A Novel Mechanism of NMDAR Blockers Against Neurodegeneration
Authors: Sahin Fikret , Gunel Aslihan , Atasoy Buse Turegun , Guler Ulku , Salih Bekir , Kuzu Isunsu , Taspinar Mehmet , Cinar Ozgur , Kahveci Selda 
Published: August 2024

SummaryNMDAR antagonists, such as memantine and ketamine, have shown efficacy in treating neurodegenerative diseases and major depression. The mechanism by which these drugs correct the aforementioned diseases is still unknown. Our study reveals that these antagonists significantly enhance 20S proteasome activity, crucial for degrading intrinsically disordered, oxidatively damaged, or misfolded proteins, factors pivotal in neurodegenerative diseases like Alzheimer’s and Parkinson’s. In a mouse model, ketamine administration notably altered brain synaptic protein profiles within two hours, downregulating proteins linked to neurodegenerative conditions. Furthermore, the altered proteins exhibited enrichment in terms related to plasticity and potentiation, including retrograde endocannabinoid signaling—a pivotal pathway in both short- and long-term plasticity that may elucidate the long-lasting effects of ketamine in major depression. Via the ubiquitin-independent 20S proteasome pathway (UIPS), these drugs maintain cellular protein homeostasis, crucial as proteasome activity declines with age leading to protein aggregation and disease symptoms. The elucidation of the mechanistic pathways underlying the therapeutic effects of NMDAR antagonists holds promise for developing new treatment strategies for brain diseases, including schizophrenia, Alzheimer’s, and Parkinson’s.
Silver chimaera genome assembly and identification of the holocephalan sex chromosome sequence
Authors: Teramura Akinori , Kadota Mitsutaka , Hirase Shotaro , Kuraku Shigehiro , Kikuchi Kiyoshi 
Published: August 2024

AbstractCartilaginous fishes are divided into holocephalans and elasmobranchs, and comparative studies involving them are expected to elucidate how variable phenotypes and distinctive genomic properties were established in those ancient vertebrate lineages. To date, molecular-level studies on holocephalans have concentrated on the family Callorhinchidae, with a chromosome-scale genome assembly ofCallorhinchus miliiavailable. In this study, we focused on the most species-rich holocephalan family Chimaeridae and sequenced the genome of its member, silver chimaera (Chimaera phantasma). We report the first chromosome-scale genome assembly of the Chimaeridae, with high continuity and completeness, which exhibited a large intragenomic variation of chromosome lengths, which is correlated with intron size. This pattern is observed more widely in vertebrates and at least partly accounts for cross-species genome size variation. A male-female comparison identified a silver chimaera genomic scaffold with a double sequence depth for females, which we identify as an X chromosome fragment. This is the first DNA sequence-based evidence of a holocephalan sex chromosome, suggesting a male heterogametic sex determination system. This study, allowing the first chromosome-level comparison among holocephalan genomes, will trigger in-depth understanding of the genomic diversity among vertebrates as well as species’ population genetic structures based on the genome assembly of high completeness.
Cost-Effectiveness Analysis of Deep Brain Stimulation for the Treatment of Alcohol Use Disorder and Alcoholic Liver Disease
Authors: Abiola O.A. , Lehmann C. , Moussawi K. , Jalal H. 
Published: August 2024

AbstractBackgroundAlcohol use disorder (AUD) is a major public health concern and cause of mortality and morbidity. Alcohol-associated liver disease (ALD) is a debilitating complication of AUD, mitigated by abstinence from alcohol use. Deep brain stimulation (DBS) is emerging as a potential treatment for AUD. However, its cost-effectiveness compared to the standard medical treatment is unclear.ObjectiveTo estimate the cost-effectiveness of DBS compared to medical management for patients with AUD and ALD.MethodsWe utilized a decision analytic model based on published literature to conduct a cost-effectiveness analysis of costs and health outcomes for DBS and medical management in patients with AUD and ALD. We also carried out a threshold analysis to determine the probability of success necessary for DBS to be cost-effective. Costs were measured in 2024 US dollars and effectiveness in quality-adjusted life years (QALYs). We used a time horizon of 1-2 years and adopted a societal perspective.ResultsOur results show that for AUD patients in general, DBS is not cost-effective at any DBS success rate. However, for advanced ALD patients, defined as fibrosis stage 3 or beyond DBS becomes cost-effective. For these patients, DBS is cost-effective over a two-year period at a $100,000 willingness-to-pay threshold at DBS success rates greater than 53%. For advanced decompensated ALD patients, DBS is cost-effective over a one-year period at DBS success rate greater than 35%.ConclusionShould it prove efficacious, DBS may be cost-effective for patients with AUD and ALD. Thus, future randomized controlled trials to evaluate its efficacy are warranted.
Leveraging Large Language Models for Identifying Interpretable Linguistic Markers and Enhancing Alzheimer’s Disease Diagnostics
Authors: Mo Tingyu , Lam Jacqueline C. K. , Li Victor O. K. , Cheung Lawrence Y. L. 
Published: August 2024

AbstractAlzheimer’s disease (AD) is a progressive and irreversible neurodegenerative disorder. Early detection of AD is crucial for timely disease intervention. This study proposes a novel LLM frame-work, which extracts interpretable linguistic markers from LLM models and incorporates them into supervised AD detection models, while evaluating their model performance and interpretability. Our work consists of the following novelties: First, we design in-context few-shot and zero-shot prompting strategies to facilitate LLMs in extracting high-level linguistic markers discriminative of AD and NC, providing interpretation and assessment of their strength, reliability and relevance to AD classification. Second, we incorporate linguistic markers extracted by LLMs into a smaller AI-driven model to enhance the performance of downstream supervised learning for AD classification, by assigning higher weights to the high-level linguistic markers/features extracted from LLMs. Third, we investigate whether the linguistic markers extracted by LLMs can enhance theaccuracy and interpretability of the downstream supervised learning-based models for AD detection. Our findings suggest that the accuracy of the LLM-extracted linguistic markers-led supervised learning model is less desirable as compared to their counterparts that do not incorporate LLM-extracted markers, highlighting the tradeoffs between interpretability and accuracy in supervised AD classification. Although the use of these interpretable markers may not immediately lead to improved detection accuracy, they significantly improve medical diagnosis and trustworthiness. These interpretable markers allow healthcare professionals to gain a deeper understanding of the linguistic changes that occur in individuals with AD, enabling them to make more informed decisions and provide better patient care.
Genomic Surveillance and Evolutionary Dynamics of Influenza A Virus in Sri Lanka
Authors: Pramanayagam Jayadas Tibutius Thanesh , Jeewandara Chandima , Senadheera Bhagya , Kuruppu Heshan , Wickramanayake Rivindu , Bary Farha , Wijewickrama Ananda , Manilgama Suranga , Gamage Manouri , Perera Nilanka , Ogg Graham S. , Malavige Gathsaurie Neelika 
Published: August 2024

AbstractBackgroundInfluenza A has been named as a priority pathogen by the WHO due to the potential to cause pandemics. Genomic sequencing of influenza strains is important to understand the evolution of the influenza strains and also to select the appropriate influenza vaccines to be used in the different influenza seasons in Sri Lanka. Therefore, we sought to understand the molecular epidemiology of the influenza viruses in the Western Province of Sri Lanka, including mutational analysis to investigate the evolutionary dynamics.MethodologyA total of 349 individuals presenting with fever and respiratory symptoms were enrolled in this study from November 2022 to May 2024. Nasopharyngeal and oropharyngeal specimens were collected and screened using quantitative PCR to detect Influenza A, Influenza B, and SARS-CoV-2. Subtyping and genomic sequencing was carried out on influenza A strains using Oxford Nanopore Technology.ResultsInfluenza A was detected in 49 (14 %) patients, influenza B in 20 (5.7%) and SARS-CoV-2 in 41 (11.7%). Co-infections were observed in five participants. The phylogenetic analysis assigned the H1N1 HA gene sequences within the 6B.1A.5a.2a clade. The HA gene of the H1N1 sequences in 2023 were assigned as belonging to the subclades C.1, C.1.2, and C.1.8, while the 2024 sequences were assigned to subclades C.1.8 and C.1.9. The H3N2 sequences from 2023 were assigned to the 3C.2a1b.2a.2a.1b clade and subclade G.1.1.2, while the 2024 sequences were assigned to the 3C.2a1b.2a.2a.3a.1 clade and subclade J.2. The K54Q, A186T, Q189E, E224A, R259K, K308R, I418V, and X215A amino acid substitutions were seen in the H1N1 in the 2023 and 2024 sequences. The 2024 H1N1 sequences additionally exhibited further substitutions, such as V47I, I96T, T120A, A139D, G339X, K156X, and T278S.ConclusionIn this first study using genomic sequencing to characterize the influenza A strains in Sri Lanka, which showed different influenza A viruses circulating in an 18-month period. As the Sri Lankan strains also had certain mutations of unknown significance, it would be important to continue detailed surveillance of the influenza strains in Sri Lanka to choose the most suitable vaccines for the population and the timing of vaccine administration.
Randomized Crossover Clinical Trial of Nicotinamide Riboside and Coenzyme Q10 on Metabolic Health and Mitochondrial Bioenergetics in CKD
Authors: Ahmadi Armin , Valencia Ana P. , Begue Gwénaëlle , Norman Jennifer E. , Fan Sili , Durbin-Johnson Blythe P. , Jenner Bradley N. , Campbell Matthew D. , Reyes Gustavo , Kapahi Pankaj , Himmelfarb Jonathan , de Boer Ian H. , Marcinek David J. , Kestenbaum Bryan R. , Gamboa Jorge L. , Roshanravan Baback 
Published: August 2024

AbstractBackgroundMitochondria-driven oxidative/redox stress and inflammation play a major role in chronic kidney disease (CKD) pathophysiology. Compounds targeting mitochondrial metabolism may improve mitochondrial function, inflammation, and redox stress; however, there is limited evidence of their efficacy in CKD.MethodsWe conducted a randomized, double-blind, placebo-controlled crossover trial comparing the effects of 1200 mg/day of coenzyme Q10 (CoQ10) or 1000 mg/day of nicotinamide riboside (NR) supplementation to placebo in 25 people with moderate-to-severe CKD (eGFR <60mL/min/1.73 m2). We assessed changes in the blood transcriptome using 3’-Tag-Seq gene expression profiling and changes in pre-specified secondary outcomes of inflammatory and oxidative stress biomarkers. For a subsample of participants (n=14), we assessed lymphocyte and monocyte bioenergetics using an extracellular flux analyzer.ResultsThe (mean±SD) age, eGFR, and BMI of the participants were 61±11 years, 37±9 mL/min/1.73m2, and 28±5 kg/m2respectively. Of the participants, 16% had diabetes and 40% were female. Compared to placebo, NR-mediated transcriptomic changes were enriched in gene ontology (GO) terms associated with carbohydrate/lipid metabolism and immune signaling while, CoQ10 changes were enriched in immune/stress response and lipid metabolism GO terms. NR increased plasma IL-2 (estimated difference, 0.32, 95% CI of 0.14 to 0.49 pg/mL), and CoQ10 decreased both IL-13 (estimated difference, –0.12, 95% CI of –0.24 to –0.01 pg/mL) and CRP (estimated difference, –0.11, 95% CI of –0.22 to 0.00 mg/dL) compared to placebo. Both NR and CoQ10 reduced 5 series F2-Isoprostanes (estimated difference, –0.16 and –0.11 pg/mL, respectively; P<0.05 for both). NR, but not CoQ10, increased the bioenergetic health index (BHI) (estimated difference, 0.29, 95% CI of 0.06 to 0.53) and spare respiratory capacity (estimated difference, 3.52, 95% CI of 0.04 to 7 pmol/min/10,000 cells) in monocytes.ConclusionSix weeks of NR and CoQ10 improved in oxidative stress, inflammation, and cell bioenergetics in persons with moderate to severe CKD.
Gate operations for superconducting qubits and non-Markovianity
Authors: Nakamura Kiyoto , Ankerhold Joachim 
Published: August 2024

While the accuracy of qubit operations has been greatly improved in the last decade, further development is demanded to achieve the ultimate goal: a fault-tolerant quantum computer that can solve real-world problems more efficiently than classical computers. With growing fidelities even subtle effects of environmental noise such as qubit–reservoir correlations and non-Markovian dynamics turn into the focus for both circuit design and control. To guide progress, we disclose, in a numerically rigorous manner, a comprehensive picture of the single-qubit dynamics in presence of a broad class of noise sources and for entire sequences of gate operations. Thermal reservoirs ranging from Ohmic to deep 1/fɛ-like sub-Ohmic behavior are considered to imitate realistic scenarios for superconducting qubits. Apart from dynamical features, fidelities of the qubit performance over entire sequences are analyzed as a figure of merit. The relevance of retarded feedback and long-range qubit–reservoir correlations is demonstrated on a quantitative level, thus, providing a deeper understanding of the limitations of performances for current devices and guiding the design of future ones.

Published by the American Physical Society
2024
Do all roads lead to Rome? CEO narcissism and the role of ethnic courtiers
Authors: Dung Luu Tien 
Published: August 2024

Purpose
Inspired by the internationalisation paths to prosperity of small and medium-sized enterprises (SMEs), where narcissistic leaders are diligent about organisations but also pursue their dark goals, this study aims to concurrently examine two avenues for the internationalisation of narcissistic leaders in SMEs concerning the function of team organisational citizenship behaviours (OCB): corporate social irresponsibility (CSI) and digital business model innovation (BMI).

Design/methodology/approach
This study utilised a quantitative design emphasising mature theory research, and data was analysed using multiple regression analysis and Hayes' process model. The data for this study was collected via surveys from 270 SMEs in Vietnam.

Findings
The study showed that narcissistic Chief Executive Officers (CEOs) can penetrate the global market profoundly by utilising both the righteous path, which is based on the power of the times via BMI, and the unethical path, CSI. However, team devotion via OCB can mitigate the unethical conduct of narcissistic CEOs.

Practical implications
The study endeavoured to find a path to internationalisation for SMEs in emerging markets with high economic openness and increasingly close connections with international markets, via two strategies for SMEs to conquer the international market more successfully, and with utilising the foundations of CEO narcissism and team citizenship behaviour.

Originality/value
This study contributed to the theory of SME internationalisation by employing the resource-based view and upper-echelon theory, with the updated Uppsala model as its foundation.