bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nationwide Study on Clinical Outcomes of Endovascular Interventions for Cerebral Venous Thrombosis in Japan
Authors: Senda Atsushi , Suginaka Hiroshi , Morishita Koji , Fushimi Kiyohide 
Published: June 2024

AbstractBackgroundCerebral venous thrombosis (CVT) is a rare but devastating disease, with some patients experiencing disease deterioration despite treatment. Endovascular treatment is an anticipated option, but its clinical relevance is yet to be determined. This observational study aimed to assess the clinical effects and identify patient populations that may benefit from treatment.MethodsPatient data from April 2014 to March 2022 were extracted from a nationwide Japanese database. The primary outcome was in-hospital mortality, while secondary outcomes included modified Rankin Score (≥ 3) and posthospitalization complications. Severity adjustments were performed using a generalized linear mixed model and propensity score matching.ResultsThe analysis included 2901 patients; 240 patients in the endovascular treatment group were matched with 240 patients in the standard treatment group. After adjusting for background factors, endovascular treatment did not improve in-hospital mortality (adjusted odds ratio 1.45 [95% CI: 0.74–2.16]) or the modified Rankin Score (adjusted odds ratio 0.89 [95% CI: 0.56–1.23]). No subpopulations that could benefit from endovascular treatment were identified. However, posthospitalization intracranial complications did not increase with endovascular treatment (0.8% vs. 1.2% in the standard treatment group).ConclusionsEndovascular treatment did not show any clinical benefit in patients with CVT. These findings are crucial for guiding clinical decisions and suggest that further evidence is warranted.
Holistic Processing Strategy in Cross-Species Face Perception between Dogs and Humans
Authors: Park Soon Young , Niehorster Diederick C. , Huber Ludwig , Virányi Zsófia 
Published: June 2024

AbstractExtensive studies have shown that humans process faces holistically, considering not only individual features but also the relationships among them. Knowing where humans and dogs fixate first and the longest when they view faces is highly informative, because the locations can be used to evaluate whether they use a holistic face processing strategy or not. However, the conclusions reported by previous eye-tracking studies appear inconclusive. To address this, we conducted an experiment with humans and dogs, employing experimental settings and analysis methods that can enable direct cross-species comparisons. Our findings reveal that humans, unlike dogs, preferentially fixated on the central region, surrounded by the inner facial features, for both human and dog faces. This pattern was consistent for initial and sustained fixations over seven seconds, indicating a clear tendency towards holistic processing. Although dogs did not show an initial preference for what to look at, their later fixations may suggest holistic processing when viewing faces of their own species. We discuss various potential factors influencing species differences in our results, as well as differences compared to the results of previous studies.
Bacteroidesexpand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity
Authors: Saba Jason , Flores Katia , Marshall Bailey , Engstrom Michael D. , Peng Yikai , Garje Atharv S. , Comstock Laurie , Landick Robert 
Published: June 2024

SUMMARYHuman gutBacteroidesspecies encode numerous (eight or more) tightly regulated capsular polysaccharides (CPS). Specialized paralogs of the universal transcription elongation factor NusG, called UpxY (Y), and an anti-Y UpxZ (Z) are encoded by the first two genes of each CPS operon. The Y-Z regulators combine with promoter inversions to limit CPS transcription to a single operon in most cells. Y enhances transcript elongation whereas Z inhibits noncognate Ys. How Y distinguishes among cognate CPS operons and how Z inhibits only noncognate Ys are unknown. Using in-vivo nascent-RNA sequencing andpromoter-less invitrotranscription (PIVoT), we establish that Y recognizes a paused RNA polymerase via sequences in both the exposed non-template DNA and the upstream duplex DNA. Y association is aided by novel ‘pause-then-escape’ nascent RNA hairpins. Z binds non-cognate Ys to directly inhibit Y association. This Y-Z hierarchical regulatory program allowsBacteroidesto create CPS subpopulations for optimal fitness.
Decomposition of L-glutamine and accumulation of ammonium in cell culture media inhibit infectivity of influenza viruses
Authors: Kegel Nathanael B. , Kaufmann Andreas , Matrosovich Mikhail , Bauer Stefan , Dorna Jens 
Published: June 2024

AbstractCationic lysosomotropic molecules such as ammonium salts and chloroquine inhibit influenza A virus (IAV) infection in cell culture by counteracting endosomal acidification and hampering viral-endosomal fusion. Here, we studied the effects of storage of L-glutamine-supplemented cell culture media on accumulation of ammonium and inhibition of IAV infection. The storage-related inhibitory effect was observed in the case of DMEM and OptiMEM media, but not RPMI medium, and was more pronounced for the IAV with pH-stable hemagglutinin. Our results highlight the importance to consider potential presence of virus-inhibiting lysosomotropic agents and/or their production in culture media with negative effect on influenza virus infection.
Integrating Bioinformatics and Machine Learning to Investigate the Mechanisms by Which Three Major Respiratory Infectious Diseases Exacerbate Heart Failure
Authors: Yu Yiding , Zhang Juan , Shi Jingle , Yuan Huajing , Han Quancheng , Xue Yitao , Li Yan 
Published: June 2024

AbstractBackgroundHeart failure (HF) is a severe cardiovascular disease often worsened by respiratory infections like influenza, COVID-19, and community-acquired pneumonia (CAP). This study aims to uncover the molecular commonalities among these respiratory diseases and their impact on HF, identifying key mediating genes.MethodsDatasets from the GEO database were analyzed for differential expression to find common molecular features of the three respiratory diseases. Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify gene modules associated with HF. GO and KEGG enrichment analyses determined the biological processes and pathways involved in HF exacerbation by respiratory diseases. Key genes were screened using LASSO, RF, and SVM-RFE machine learning algorithms, with accuracy validated by ROC curves. Single-sample GSEA (ssGSEA) was performed, and the Drug Signature Database (DSigDB) was used for drug prediction. Immune infiltration analysis was conducted using CIBERSORT.ResultsWe identified 51 characteristic genes of respiratory diseases and 10 potential genes exacerbating HF, primarily involved in innate immune response, inflammation, and coagulation pathways. Machine learning algorithms identified RSAD2 and IFI44L as key genes with high accuracy (AUC > 0.7). ssGSEA indicated RSAD2’s involvement in complement and coagulation cascades, while IFI44L is associated with myocardial contraction in HF progression. DSigDB predicted six potential therapeutic drugs. Immune infiltration analysis revealed significant differences in eight immune cell types between HF patients and healthy controls.ConclusionOur findings enhance the understanding of molecular interactions between respiratory diseases and heart failure, paving the way for future research and therapeutic strategies.
Backtranslation of human RNA biosignatures of tuberculosis disease risk into the preclinical pipeline is condition dependent
Authors: Painter Hannah , Larsen Sasha E. , Williams Brittany D. , Abdelaal Hazem F. M. , Baldwin Susan L. , Fletcher Helen A. , Fiore-Gartland Andrew , Coler Rhea N. 
Published: June 2024

AbstractIt is not clear whether human progression to active tuberculosis disease (TB) risk signatures are viable endpoint criteria for evaluations of treatments in clinical or preclinical development. TB is the deadliest infectious disease globally and more efficacious vaccines are needed to reduce this mortality. However, the immune correlates of protection for either preventing infection withMycobacterium tuberculosisor preventing TB disease have yet to be completely defined, making the advancement of candidate vaccines through the pipeline slow, costly, and fraught with risk. Human-derived correlate of risk (COR) gene signatures, which identify an individual’s risk to progressing to active TB disease, provide an opportunity for evaluating new therapies for TB with clear and defined endpoints. Though prospective clinical trials with longitudinal sampling are prohibitively expensive, characterization of COR gene signatures is practical with preclinical models. Using a 3Rs (Replacement, Reduction and Refinement) approach we reanalyzed heterogeneous publicly available transcriptional datasets to determine whether a specific set of COR signatures are viable endpoints in the preclinical pipeline. We selected RISK6, Sweeney3 and BATF2 human-derived blood-based RNA biosignatures because they require relatively few genes to assign a score and have been carefully evaluated across several clinical cohorts. Excitingly, these data provide proof-of-concept that human COR signatures seem to have high fidelity across several tissue types in the preclinical TB model pipeline and show best performance when the model most closely reflected human infection or disease conditions. Human-derived COR signatures offer an opportunity for high-throughput preclinical endpoint criteria of vaccine and drug therapy evaluations.One Sentence SummaryHuman-derived biosignatures of tuberculosis disease progression were evaluated for their predictive fidelity across preclinical species and derived tissues using available public data sets.
Characterizing neuroinvasion and neuropathology of SARS-CoV-2 by using AC70 human ACE2 transgenic mice
Authors: Hsu Jason C. , Saenkham-Huntsinger Panatda , Huang Pinghan , Octaviani Cassio Pontes , Drelich Aleksandra K. , Peng Bi-Hung , Tseng Chien-Te K. 
Published: June 2024

ABSTRACTCOVID-19 presents with a plethora of neurological signs and symptoms despite being characterized as a respiratory disease, including seizures, anxiety, depression, amnesia, attention deficits, and alterations in consciousness. The olfactory nerve is widely accepted as the neuroinvasive route by which the etiological agent SARS-CoV-2 enters the brain, but the trigeminal nerve is an often-overlooked additional route. Based on this consensus, we initially conducted a pilot experiment investigating the olfactory nerve route of SARS-CoV-2 neuroinvasion via intranasal inoculation in AC70 human ACE2 transgenic mice. Notably, we found that the trigeminal ganglion is an early and highly efficient site of viral replication, which then rapidly spread widely throughout the brain where neurons were primarily targeted. Despite the extensive viral infection across the brain, obvious evidence of tissue pathology including inflammatory infiltration, glial activation, and apoptotic cell deaths were not consistently observed, albeit inflammatory cytokines were significantly induced. However, the expression levels of different genes related to neuronal function, including the neurotransmitter dopamine pathway as well as synaptic function, and markers of neuronal damage were altered as compared to mock-infected mice. Our findings suggest that the trigeminal nerve can be a neuroinvasive route complementary to the olfactory nerve and that the ensuing neuroinvasion presented a unique neuropathological profile. This study provides insights into potential neuropathogenic mechanisms utilized by coronaviruses.IMPORTANCECOVID-19 presents with extrapulmonary signs and symptoms, the most notable of which involve the central nervous system, such as seizures and alterations in consciousness, and can eventually lead to death if severe enough. Some neurological signs and symptoms may continue to persist in some patients even after the resolution of active viral infection in the form of post-acute sequelae. Since the trigeminal nerve is a commonly under-studied route of entry into the brain in studies of coronaviruses and the neuropathogenic mechanisms of COVID-19 are not entirely elucidated, there is a need to thoroughly investigate this route of neuroinvasion. The significance of our research is in providing insights into the possible routes of SARS-CoV-2 neuroinvasion as well as the discovery of potential neuropathogenic mechanisms which may help guide the development of novel medical countermeasures.
RecA is a reliable marker for bacterial taxonomy, even in the Candidate Phyla Radiation
Authors: Sterzi Lodovico , Panelli Simona , Bonaiti Clara , Papaleo Stella , Bettoni Giorgia , D’Auria Enza , Zuccotti Gianvincenzo , Comandatore Francesco 
Published: June 2024

AbstractCulture-independent approaches are commonly used to characterise the taxonomic composition of bacterial communities. Among these approaches, the amplicon-based metagenomics relies on specific genetic markers, such as the 16S rRNA gene, while the shotgun metagenomics annotates the whole bacterial DNA. Despite the 16S being the gold standard marker, studies highlighted its inefficiency in characterising and quantifying divergent bacterial groups such as the Candidate Phyla Radiation. On the other hand, shotgun metagenomics is highly informative and accurate but it is more expensive and requires computational resources and time. In this study, we propose RecA as a pan-bacterial genetic marker, particularly suitable for the Candidate Phyla Radiation. Indeed, we found that applying a Random Forest machine learning model on RecA amino acid sequences provides an accurate and fast taxonomic annotation across the whole bacterial tree of life. Ultimately, we produced Forestax, a tool for the characterisation and quantification of bacterial communities in metagenomics data, on the basis of RecA sequences. The analyses showed that RecA-based metagenomics has a taxonomic accuracy comparable to other multi-gene approaches, reinforcing RecA as a powerful marker for taxonomic annotation in bacteria. In perspective, RecA could be considered as a broad-spectrum marker for amplicon-based studies to overcome the limits of 16S rRNA.
Single-stranded DNA binding protein hitches a ride with theEscherichia coliYoaA-χ helicase
Authors: Weeks-Pollenz Savannah J. , Petrides Matthew J. , Davis Robert , Harris Kathryn K. , Bloom Linda B. 
Published: June 2024

AbstractTheEscherichia coliXPD/Rad3-like helicase, YoaA, and DNA polymerase III subunit, χ, are involved inE. coliDNA damage tolerance and repair. YoaA and χ promote tolerance to the DNA chain-terminator, 3□-azidothymidine (AZT), and together form the functional helicase complex, YoaA-χ. How YoaA-χ contributes to DNA damage tolerance is not well understood.E. colisingle-stranded DNA binding protein (SSB) accumulates at stalled replication forks, and the SSB-χ interaction is required to promote AZT tolerance via an unknown mechanism. YoaA-χ and SSB interactions were investigatedin vitroto better understand this DNA damage tolerance mechanism, and we discovered YoaA-χ and SSB have a functional interaction. SSB confers a substrate-specific effect on the helicase activity of YoaA-χ, barely affecting YoaA-χ on an overhang DNA substrate but inhibiting YoaA-χ on forked DNA. A paralog helicase, DinG, unwinds SSB-bound DNA in a similar manner to YoaA-χ on the substrates tested. Through use of ensemble experiments, we believe SSB binds behind YoaA-χ relative to the DNA ds/ss junction and show via single-molecule assays that SSB translocates along ssDNA with YoaA-χ. This is, to our knowledge, the first demonstration of a mechanoenzyme pulling SSB along ssDNA.
Architecture matters: exploring audiences’ holistic theatrical experience through social media reviews
Authors: Jiang Shan , Kinney Marcene , Yost Christopher 
Published: June 2024

PurposeAssessing performance art has shifted toward an audience-centric approach, with various factors impacting audiences’ holistic experiences in a theater. Existing theater marketing research has predominantly focused on servicescapes, leaving a research gap regarding audiences’ spatial experience within theater buildings.Design/methodology/approachTo address this gap, this case study collected crowdsourced data from mainstream social media platforms, including rating scores, textual reviews and reviewer-uploaded photos. The aim was to explore to what extent the theater architecture design impacted audiences’ theatrical experience. The old and new facilities of the case study theater were compared, and a series of quantitative and qualitative techniques were applied for data analysis, including statistics, content analysis, sentiment analysis and thematic analysis.FindingsThe study identified five major themes in social media review: the show, architectural design and attributes, staff and service, neighborhood and amenities, and financial consideration. Comments about theater architecture constituted a substantial portion of reviews, with seating comfort, intimacy and stage visibility being frequently discussed features. Seven subthemes related to architectural design emerged as key contributors to audiences’ spatial experiences, including aesthetics, design and spatial configuration; the bar and lobby; the new facility; seats; sets and stage; acoustics; and intimacy and atmosphere.Originality/valueThe study places the individual experiences of audience members as central and uses an inductive approach to analyze their self-generated data. The research results offer valuable insights into theater design and confirm the belief that architectural design has a significant impact on the overall theatrical experience of audiences.
How do live-streamers attract their consumers: insights from a multi-group analysis
Authors: Xiong Jie , Li Feng 
Published: June 2024

PurposeThe rapid development of e-commerce live streaming is inseparable from the important role of live-streamer. However, research exploring the impacts of live-streamers’ characteristics on customer engagement in different types of live streaming rooms remains limited. This study aims to examine the impacts of live-streamers’ characteristics (i.e. expertise, moral reputation, popularity, responsiveness) on consumer engagement in e-commerce live streaming, and verify whether there are differences in the impact of live-streamers’ characteristics on consumer experience for different types of live-streamers.Design/methodology/approachData were gathered from 266 Chinese adults who have experience watching e-commerce live streaming. Partial least squares techniques were used to verify the model.FindingsThe results show that expertise, moral reputation, popularity, and responsiveness of live-streamers have positive impacts on consumer engagement through perceived trust and perceived pleasure. Moreover, through multi-group analysis, this study found that compared with enterprise live-streamers, the moral reputation of individual live-streamers exerts a stronger effect on consumers’ perceived trust, and the popularity of individual live-streamers exerts a stronger effect on consumers’ perceived pleasure. Compared with individual live-streamers, the responsiveness of enterprise live-streamers exerts a stronger effect on consumers’ perceived pleasure.Originality/valueThis study contributes to e-commerce live streaming research by categorizing live-streamers into two types: individual live-streamers and enterprise live-streamers, and verifying the specific difference in the impacts of live-streamers’ characteristics on consumer experience for the two types of live-streamers.
Navigating the adoption landscape of blockchain in food delivery: a UTAUT perspective
Authors: Shukla Vishal , Kumar Jitender , Rana Sudhir , Prashar Sanjeev 
Published: June 2024

PurposeThis study explores the factors impacting user adoption and trust in blockchain-based food delivery systems, with a spotlight on the Open Network for Digital Commerce (ONDC). In the evolving food delivery sector, blockchain offers transparency and efficiency. Through the Unified Theory of Acceptance and Use of Technology (UTAUT) lens, this research provides insights for businesses and policymakers, highlighting the importance of blockchain’s integration into food delivery.Design/methodology/approachThe research employed the UTAUT and its extensions as the theoretical framework. A structured questionnaire was developed and disseminated to users of the ONDC platform, and responses were collected on a seven-point extended Likert scale. The analyses were undertaken employing the partial least squares (PLS) methodology and structural equation modelling (SEM).FindingsKey factors like performance expectancy, effort expectancy and social influence were found influential for adoption. Trust played a central role, while perceived risk didn’t significantly mediate the adoption process. Digital culture didn’t significantly moderate the adoption intention.Originality/valueThis research adds to the existing body of knowledge by providing empirical insights into user adoption and trust in blockchain-based food delivery platforms. It is among the pioneer studies to apply the UTAUT model in the realm of blockchain-based food delivery platforms, thereby offering a unique perspective on the dynamics of user behaviour in this emerging field.
Visual portrayal of Monkeypox outbreak on BBC: is Western media biased against Africa?
Authors: Shodipe Oluwafunmilayo Abimbola , Arowolo Olasunkanmi , Oloyede Isikilu Bayo , Alade Moyosore , Fadeyi Isaac Olajide , Oko-Epelle Lydia 
Published: June 2024

Purpose
This paper aims to examine the British Broadcasting Corporation’s (BBC) portrayal of the May 2022 Monkeypox outbreak in the West. The Monkeypox outbreak and the outcry from African journalists on some Western media outlets’ use of black people to portray the Monkeypox outbreak informed the present study to investigate, through empirical evidence, whether Western media portrays Africa negatively.

Design/methodology/approach
The paper opted for the content analysis method. The news recordings from BBC News analysed for this study were archived videos on Monkeypox retrieved from Blob of Broadcast, an on-demand audio and video streaming service in the UK.

Findings
Findings indicated that videos were the most used visuals by the BBC to depict the Monkeypox outbreak in the observed period. Findings also revealed that Black was the prevalent skin tone used in depicting those affected by the outbreak, while White was the prevalent skin tone used in depicting the scientists interviewed for their expert knowledge and at the forefront of the Monkeypox outbreak.

Practical implications
The paper includes implications for Western media outlets on how to portray Africa and its people.

Originality/value
This paper fulfils an identified need to investigate how Africa is portrayed in Western media through empirical evidence.