bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scar border zone mass and presence of border zone channels assessed with cardiac magnetic resonance imaging are associated with ventricular arrhythmia in patients with ST-segment elevation myocardial infarction
Authors: Thomsen Anna F , Bertelsen Litten , Jøns Christian , Jabbari Reza , Lønborg Jacob , Kyhl Kasper , Göransson Christoffer , Nepper-Christensen Lars , Atharovski Kiril , Ekström Kathrine , Tilsted Hans-Henrik , Pedersen Frants , Køber Lars , Engstrøm Thomas , Vejlstrup Niels , Jacobsen Peter Karl 
Published: December 2022

AbstractAimsLate gadolinium enhancement cardiac magnetic resonance (CMR) permits characterization of left ventricular ischaemic scars. We aimed to evaluate if scar core mass, border zone (BZ) mass, and BZ channels are risk markers for subsequent ventricular arrhythmia (VA) in ST-segment elevation myocardial infarction (STEMI).Methods and resultsA sub-study of the DANish Acute Myocardial Infarction-3 multi-centre trial and Danegaptide phase II proof-of-concept clinical trial in which a total of 843 STEMI patients had a 3-month follow-up CMR. Of these, 21 patients subsequently experienced VA during 100 months of follow-up and were randomly matched 1:5 with 105 controls. A VA event was defined as: ventricular tachycardia, ventricular fibrillation, or sudden cardiac death. Ischaemic scar characteristics were automatically detected by specialized software. We included 126 patients with a median left ventricular ejection fraction of 51.0 ± 11.6% in cases with VA vs. 55.5 ± 8.5% in controls (P = 0.10). Cases had a larger mean BZ mass and more often BZ channels compared to controls [BZ mass: 17.2 ± 10.3 g vs. 10.3 ± 6.0 g; P = 0.0002; BZ channels: 17 (80%) vs. 44 (42%); P = 0.001]. A combination of ≥17.2 g BZ mass and the presence of BZ channels was five times more prevalent in cases vs. controls (P ≤ 0.00001) with an odds ratio of 9.40 (95% confidence interval 3.26–27.13; P ≤ 0.0001) for VA. This identified cases with 52% sensitivity and 90% specificity.Conclusion(s)Scar characterization with CMR indicates that a combination of ≥17.2 g BZ mass and the presence of BZ channels had the strongest association with subsequent VA in STEMI patients.ClinicalTrials.govUnique identifier: NCT01435408 (DANAMI 3-iPOST and DANAMI 3-DEFER), NCT01960933 (DANAMI 3-PRIMULTI), and NCT01977755 (Danegaptide).
Grad-seq analysis ofEnterococcus faecalisandEnterococcus faeciumprovides a global view of RNA and protein complexes in these two opportunistic pathogens
Authors: Michaux Charlotte , Gerovac Milan , Hansen Elisabeth E , Barquist Lars , Vogel Jörg 
Published: December 2022

AbstractEnterococcus faecalis and Enterococcus faecium are major nosocomial pathogens. Despite their relevance to public health and their role in the development of bacterial antibiotic resistance, relatively little is known about gene regulation in these species. RNA–protein complexes serve crucial functions in all cellular processes associated with gene expression, including post-transcriptional control mediated by small regulatory RNAs (sRNAs). Here, we present a new resource for the study of enterococcal RNA biology, employing the Grad-seq technique to comprehensively predict complexes formed by RNA and proteins in E. faecalis V583 and E. faecium AUS0004. Analysis of the generated global RNA and protein sedimentation profiles led to the identification of RNA–protein complexes and putative novel sRNAs. Validating our data sets, we observe well-established cellular RNA–protein complexes such as the 6S RNA–RNA polymerase complex, suggesting that 6S RNA-mediated global control of transcription is conserved in enterococci. Focusing on the largely uncharacterized RNA-binding protein KhpB, we use the RIP-seq technique to predict that KhpB interacts with sRNAs, tRNAs, and untranslated regions of mRNAs, and might be involved in the processing of specific tRNAs. Collectively, these datasets provide departure points for in-depth studies of the cellular interactome of enterococci that should facilitate functional discovery in these and related Gram-positive species. Our data are available to the community through a user-friendly Grad-seq browser that allows interactive searches of the sedimentation profiles (https://resources.helmholtz-hiri.de/gradseqef/).
Accurate and fast clade assignment via deep learning and frequency chaos game representation
Authors: Avila Cartes Jorge , Anand Santosh , Ciccolella Simone , Bonizzoni Paola , Della Vedova Gianluca 
Published: December 2022

Abstract

Background
Since the beginning of the coronavirus disease 2019 pandemic, there has been an explosion of sequencing of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, making it the most widely sequenced virus in the history. Several databases and tools have been created to keep track of genome sequences and variants of the virus; most notably, the GISAID platform hosts millions of complete genome sequences, and it is continuously expanding every day. A challenging task is the development of fast and accurate tools that are able to distinguish between the different SARS-CoV-2 variants and assign them to a clade.

Results
In this article, we leverage the frequency chaos game representation (FCGR) and convolutional neural networks (CNNs) to develop an original method that learns how to classify genome sequences that we implement into CouGaR-g, a tool for the clade assignment problem on SARS-CoV-2 sequences. On a testing subset of the GISAID, CouGaR-g achieved an $96.29\%$ overall accuracy, while a similar tool, Covidex, obtained a $77,12\%$ overall accuracy. As far as we know, our method is the first using deep learning and FCGR for intraspecies classification. Furthermore, by using some feature importance methods, CouGaR-g allows to identify k-mers that match SARS-CoV-2 marker variants.

Conclusions
By combining FCGR and CNNs, we develop a method that achieves a better accuracy than Covidex (which is based on random forest) for clade assignment of SARS-CoV-2 genome sequences, also thanks to our training on a much larger dataset, with comparable running times. Our method implemented in CouGaR-g is able to detect k-mers that capture relevant biological information that distinguishes the clades, known as marker variants.

Availability
The trained models can be tested online providing a FASTA file (with 1 or multiple sequences) at https://huggingface.co/spaces/BIASLab/sars-cov-2-classification-fcgr. CouGaR-g is also available at https://github.com/AlgoLab/CouGaR-g under the GPL.
Antigen Discovery for Next-Generation Pertussis Vaccines Using Immunoproteomics and Transposon-Directed Insertion Sequencing
Authors: Gregg Kelsey A , Wang Yihui , Warfel Jason , Schoenfeld Elizabeth , Jankowska Ewa , Cipollo John F , Mayho Matthew , Boinett Christine , Prasad Deepika , Brickman Timothy J , Armstrong Sandra K , Parkhill Julian , Da Silva Antunes Ricardo , Sette Alessandro , Papin James F , Wolf Roman , Merkel Tod J 
Published: December 2022

Abstract

Background
Despite high vaccination rates, the United States has experienced a resurgence in reported cases of pertussis after switching to the acellular pertussis vaccine, indicating a need for improved vaccines that enhance infection control.

Methods
Bordetella pertussis antigens recognized by convalescent-baboon serum and nasopharyngeal wash were identified by immunoproteomics and their subcellular localization predicted. Genes essential or important for persistence in the baboon airway were identified by transposon-directed insertion-site sequencing (TraDIS) analysis.

Results
In total, 314 B. pertussis antigens were identified by convalescent baboon serum and 748 by nasopharyngeal wash. Thirteen antigens were identified as immunogenic in baboons, essential for persistence in the airway by TraDIS, and membrane-localized: BP0840 (OmpP), Pal, OmpA2, BP1485, BamA, Pcp, MlaA, YfgL, BP2197, BP1569, MlaD, ComL, and BP0183.

Conclusions
The B. pertussis antigens identified as immunogenic, essential for persistence in the airway, and membrane-localized warrant further investigation for inclusion in vaccines designed to reduce or prevent carriage of bacteria in the airway of vaccinated individuals.
Antimicrobial activity of antibiotics on biofilm formed byStaphylococcus aureusandPseudomonas aeruginosain an open microfluidic model mimicking the diabetic foot environment
Authors: Pouget Cassandra , Pantel Alix , Dunyach-Remy Catherine , Magnan Chloé , Sotto Albert , Lavigne Jean-Philippe 
Published: December 2022

AbstractBackgroundDiabetic foot infections (DFIs) represent a public health problem because of their frequency and the severity of their consequences, i.e. amputation and mortality. Polymicrobial biofilms on the skin surface of these ulcers complicate wound healing. Few in vitro models exist to study the antibiotics activity in this context.ObjectivesThis study evaluated the in vitro activity of antibiotics against the two main bacteria isolated in DFI, Staphylococcus aureus and Pseudomonas aeruginosa, using a dynamic system (BioFlux™ 200) and a chronic wound-like medium (CWM) that mimic the foot ulcer environment.MethodsReference strains and two pairs of clinical S. aureus and P. aeruginosa isolated together from a DFI were cultivated in brain heart infusion and CWM media during 72 h at 37°C, alone and combined in the BioFlux™ 200 system. Antibiotic activity was evaluated after a mechanical debridement. The activities were measured by the reduction of biofilm percentage of bacteria in the microfluidic system using microscopy.ResultsDaptomycin for S. aureus and ceftazidime for P. aeruginosa showed excellent activity to reduce biofilm biomass, whereas linezolid action was more mitigated and dalbavancin was ineffective. Ceftazidime + daptomycin presented the most potent in vitro activity on a mixed biofilm.ConclusionsThe combination of CWM and the BioFlux™ microfluidic system represents a valuable tool to screen the potential antimicrobial activity of antibiotics under conditions mimicking those encountered in DFI. It could help clinicians in their management of chronic wounds.
When national identity meets conspiracies: the contagion of national identity language in public engagement and discourse about COVID-19 conspiracy theories
Authors: Chen Anfan , Chen Kaiping , Zhang Jingwen , Meng Jingbo , Shen Cuihua 
Published: December 2022

AbstractThere are growing concerns about the role of identity narratives in spreading misinformation on social media, which threatens informed citizenship. Drawing on the social identity model of deindividualization effects (SIDE) and social identity theory, we investigate how the use of national identity language is associated with the diffusion and discourse of COVID-19 conspiracy theories on Weibo, a popular social media platform in China. Our results reveal a pattern of identity communication contagion in public conversations about conspiracies: national identity language usage in original posts is associated with more frequent use of such language in all subsequent conversations. Users who engaged in discussions about COVID-19 conspiracies used more national identity expressions in everyday social media conversations. By extending the SIDE model and social identity theory to misinformation studies, our article offers theoretical and empirical insight into how identity–contagious communication might exacerbate public engagement with misinformation on social media in non-Western contexts.
The Preference for Spontaneity in Entertainment
Authors: Rifkin Jacqueline R , Du Katherine M , Cutright Keisha M 
Published: December 2022

Abstract
Whether watching a movie, sports game, or musical performance, consumers often seek entertainment experiences that are produced by one or more individuals. And although consumers often witness producers acting spontaneously, little is known about the preference for spontaneity in entertainment. Six studies, including real consumer-relevant decisions and a Facebook field experiment, reveal that consumers prefer spontaneity (vs. planned behavior) across several entertainment contexts, as spontaneous producers seem more authentic than planned producers. At the same time, however, spontaneous actions are also believed to beget lower-quality outcomes, suggesting that consumers generally prefer spontaneity even despite the possibility of reduced quality. Subsequent experiments examine the characteristics of the entertainment context and the producer to provide further insight into how consumers manage the authenticity–quality tradeoff: by shaping when and why spontaneity is associated with increased authenticity and decreased quality expectations, as well as the relative importance of these dimensions, higher-stakes contexts (e.g., when consumers’ outcomes are enmeshed with the producer’s), negative inferences about spontaneity (e.g., laziness, lack of concern), and low-competence producers attenuate the effects. Together, this research advances knowledge about spontaneity and authenticity and has implications for those seeking to produce appealing entertainment experiences.
Influence of Wireworm Diet on its Susceptibility to and Control With the Entomopathogenic FungusMetarhizium brunneum(Hypocreales: Clavicipitaceae) in Laboratory and Field Settings
Authors: Reinbacher Lara , Praprotnik Eva , Razinger Jaka , Bacher Sven , Grabenweger Giselher 
Published: December 2022

AbstractEntomopathogenic fungi (EPF) represent promising control agents against wireworms but success in field experiments is inconsistent. The physiological condition of the targeted insect is crucial for its ability to withstand fungal infection. In particular, nutritional status is among the most important determinants of the insects’ immune defense. In this study, we investigated the effects of diet on the development of the wireworm Agriotes obscurus (L.) (Coleoptera: Elateridae) and its subsequent susceptibility to the fungal pathogen Metarhizium brunneum (Petch) (Hypocreales: Clavicipitaceae) in a pot experiment. After being reared on one of five plant diets for eight weeks, wireworms were exposed to an environment inoculated with the EPF and monitored for their susceptibility to fungal infection. We then performed a field experiment in which three plant diets (clover, radish, and a cover crop mix), selected according to the insects’ performance in the laboratory experiment, were grown as a cover crop with EPF application. Plant diet influenced growth and development of larvae, but there were no strong differences in susceptibility toward fungal infection in the laboratory experiment. Damage levels in EPF-treated plots in the field varied depending on the cover crop. Damage was highest in plots planted with a mix of cover crop species, whereas damage was lowest in plots with clover or radish alone. This agrees with the laboratory results where insect performance was inferior when fed on clover or radish. Cover crop effects on wireworm damage in the subsequent cash crop may thus vary depending on the cover crop species selected.
A reduction-based cut-free Gentzen calculus for dynamic epistemic logic
Authors: Wirsing Martin , Knapp Alexander 
Published: December 2022

Abstract
Dynamic epistemic logic (DEL) is a multi-modal logic for reasoning about the change of knowledge in multi-agent systems. It extends epistemic logic by a modal operator for actions which announce logical formulas to other agents. In Hilbert-style proof calculi for DEL, modal action formulas are reduced to epistemic logic, whereas current sequent calculi for DEL are labelled systems which internalize the semantic accessibility relation of the modal operators, as well as the accessibility relation underlying the semantics of the actions. We present a novel cut-free ordinary sequent calculus, called $ \textbf{G4}_{P,A}[] $, for propositional DEL. In contrast to the known sequent calculi, our calculus does not internalize the accessibility relations, but—similar to Hilbert style proof calculi—action formulas are reduced to epistemic formulas. Since no ordinary sequent calculus for full S5 modal logic is known, the proof rules for the knowledge operator and the Boolean operators are those of an underlying S4 modal calculus. We show the soundness and completeness of $ \textbf{G4}_{P,A}[] $ and prove also the admissibility of the cut-rule and of several other rules for introducing the action modality.
Circadian clock control of MRTF/SRF pathway suppresses beige adipocyte thermogenic recruitment
Authors: Xiong Xuekai , Li Weini , Liu Ruya , Saha Pradip , Yechoor Vijay , Ma Ke 
Published: December 2022

ABSTRACT
The morphological transformation of adipogenic progenitors into mature adipocytes requires dissolution of actin cytoskeleton with loss of myocardin-related transcription factor (MRTF)/serum response factor (SRF) activity. Circadian clock confers temporal control in adipogenic differentiation, while the actin cytoskeleton–MRTF/SRF signaling transduces extracellular physical niche cues. Here, we define a novel circadian transcriptional control involved in actin cytoskeleton–MRTF/SRF signaling cascade that modulates beige fat thermogenic function. Key components of actin dynamic–MRTF/SRF pathway display circadian regulation in beige fat depot. The core clock regulator, brain and muscle arnt-like 1 (Bmal1), exerts direct transcriptional control of genes within the actin dynamic–MRTF/SRF cascade that impacts actin cytoskeleton organization and SRF activity. Employing beige fat-selective gene-targeting models together with pharmacological rescues, we further demonstrate that Bmal1 inhibits beige adipogenesis and thermogenic capacity in vivo via the MRTF/SRF pathway. Selective ablation of Bmal1 induces beigeing with improved glucose homeostasis, whereas its targeted overexpression attenuates thermogenic induction resulting in obesity. Collectively, our findings identify the clock–MRTF/SRF regulatory axis as an inhibitory mechanism of beige fat thermogenic recruitment with significant contribution to systemic metabolic homeostasis.
Gender differences and similarities in news media effects on political candidate evaluations: a meta-analysis
Authors: Rohrbach Tobias , Aaldering Loes , Van der Pas Daphne Joanna 
Published: December 2022

AbstractHow do different types of media coverage shape—and potentially bias—voter evaluations of women and men politicians? Theoretically reviewing 50 experimental studies and statistically synthesizing 671 evaluation outcomes from more than 23,000 participants, this meta-analytic review shows that gender bias in media-induced voter evaluations is conditional rather than universal. Our findings suggest that voters respond similarly to most media messages about women and men candidates. When gender-differentiated media effects are found, for instance, based on trait, appearance, or family coverage of politicians, this is mostly harmful for women candidates as it reaffirms gender stereotypical beliefs and lowers their viability ratings and vote preferences. Shedding light on the conditional nature of media-driven voter bias, this study adds to a better understanding of how the mediation of gender stereotypes sustains the underrepresentation of women in politics.
The nonlinear change in pollinator assemblages and self-mating syndromes ofPrimula atrodentataalong elevation gradients
Authors: Ma Yin-Mei , Cha Yong-Peng , Tong Zhao-Li , Zhang Jie , Li Qing-Jun 
Published: December 2022

AbstractThe reproductive strategies of alpine plants are often altered by environmental changes caused by changes in the spatial distribution of the gradient. However, few studies have investigated whether reproductive patterns of the same species vary with elevation. Three natural populations of Primula atrodentata, which are distributed in the eastern Himalayas and have a long flowering period, were selected along the elevation gradients in Shergyla Mountain, Tibet, China. Morph ratio investigation, floral trait measurement, pollinator observation and manipulated pollination experiments were conducted to explore the changes in self-compatibility and floral traits associated with the selfing syndrome along elevation gradients. We found that the breeding system of the S-morph is facultative outcrossing, and that of the L-morph is obligatory outcrossing. We further found that with increasing elevation, the number of pollen and ovules, anther–stigma distance, and inbreeding depression index first increased and then decreased, whereas the seeds per fruit and seed-setting rate under hand self-pollination, pollen limitation and self-incompatibility index tended to decrease first, but then increased. In addition, pollinator diversity and visiting frequency were the highest at the middle elevation (4050 population), which can better explain the nonlinear change in self-fertility with elevation. Our findings provide insights into the evolutionary pattern of self-compatibility in alpine plants along elevational gradients.
Cumulative Human Immunodeficiency Virus (HIV)-1 Viremia Is Associated With Increased Risk of Multimorbidity Among US Women With HIV, 1997–2019
Authors: Morton Zoey P , Christina Mehta C , Wang Tingyu , Palella Frank J , Naggie Susanna , Golub Elizabeth T , Anastos Kathryn , French Audrey L , Kassaye Seble , Taylor Tonya N , Fischl Margaret A , Adimora Adaora A , Kempf Mirjam-Colette , Tien Phyllis C , Ofotokun Ighovwerha , Sheth Anandi N , Collins Lauren F 
Published: December 2022

Abstract

Background
To evaluate the effect of cumulative human immunodeficiency virus (HIV)-1 viremia on aging-related multimorbidity among women with HIV (WWH), we analyzed data collected prospectively among women who achieved viral suppression after antiretroviral therapy (ART) initiation (1997–2019).

Methods
We included WWH with ≥2 plasma HIV-1 viral loads (VL) &lt;200 copies/mL within a 2-year period (baseline) following self-reported ART use. Primary outcome was multimorbidity (≥2 nonacquired immune deficiency syndrome comorbidities [NACM] of 5 total assessed). The trapezoidal rule calculated viremia copy-years (VCY) as area-under-the-VL-curve. Cox proportional hazard models estimated the association of time-updated cumulative VCY with incident multimorbidity and with incidence of each NACM, adjusting for important covariates (eg, age, CD4 count, etc).

Results
Eight hundred six WWH contributed 6368 women-years, with median 12 (Q1–Q3, 7–23) VL per participant. At baseline, median age was 39 years, 56% were Black, and median CD4 was 534 cells/mm3. Median time-updated cumulative VCY was 5.4 (Q1–Q3, 4.7–6.9) log10 copy-years/mL. Of 211 (26%) WWH who developed multimorbidity, 162 (77%) had incident hypertension, 133 (63%) had dyslipidemia, 60 (28%) had diabetes, 52 (25%) had cardiovascular disease, and 32 (15%) had kidney disease. Compared with WWH who had time-updated cumulative VCY &lt;5 log10, the adjusted hazard ratio of multimorbidity was 1.99 (95% confidence interval [CI], 1.29–3.08) and 3.78 (95% CI, 2.17–6.58) for those with VCY 5–6.9 and ≥7 log10 copy-years/mL, respectively (P &lt; .0001). Higher time-updated cumulative VCY increased the risk of each NACM.

Conclusions
Among ART-treated WWH, greater cumulative viremia increased the risk of multimorbidity and of developing each NACM, and hence this may be a prognostically useful biomarker for NACM risk assessment in this population.