bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of tools for taxonomic classification of viruses
Authors: Cadenas-Castrejón Elizabeth , Verleyen Jérôme , Boukadida Celia , Díaz-González Lorena , Taboada Blanca 
Published: November 2022

Abstract
Viruses are the most abundant infectious agents on earth, and they infect living organisms such as bacteria, plants and animals, among others. They play an important role in the balance of different ecosystems by modulating microbial populations. In humans, they are responsible for some common diseases and may cause severe illnesses. Viral metagenomic studies have become essential and offer the possibility to understand and extend the knowledge of virus diversity and functionality. For these approaches, an essential step is the classification of viral sequences. In this work, 11 taxonomic classification tools were compared by analysing their performances, in terms of sensitivity and precision, to classify reads at the species and family levels using the same (viral and nonviral) datasets and evaluation metrics, as well as their processing times and memory requirements. The results showed that factors such as richness (numbers of viral species in samples), taxonomic level in the classification and read length influence tool performance. High values of viral richness in samples decreased the performances of most tools. Additionally, the classifications were better at higher taxonomic levels, such as families, compared to lower taxonomic levels, such as species, and were more evident in short reads. The results also indicated that BLAST and Kraken2 were the best tools for classifying all types of reads, while FastViromeExplorer and VirusFinder were only good when used for long reads and Centrifuge, DIAMOND, and One Codex when used for short reads. Regarding nonviral datasets (human and bacterial), all tools correctly classified them as nonviral.
Selective attention sharpens population receptive fields in human auditory cortex
Authors: Lage-Castellanos Agustin , De Martino Federico , Ghose Geoffrey M , Gulban Omer Faruk , Moerel Michelle 
Published: November 2022

Abstract
Selective attention enables the preferential processing of relevant stimulus aspects. Invasive animal studies have shown that attending a sound feature rapidly modifies neuronal tuning throughout the auditory cortex. Human neuroimaging studies have reported enhanced auditory cortical responses with selective attention. To date, it remains unclear how the results obtained with functional magnetic resonance imaging (fMRI) in humans relate to the electrophysiological findings in animal models. Here we aim to narrow the gap between animal and human research by combining a selective attention task similar in design to those used in animal electrophysiology with high spatial resolution ultra-high field fMRI at 7 Tesla. Specifically, human participants perform a detection task, whereas the probability of target occurrence varies with sound frequency. Contrary to previous fMRI studies, we show that selective attention resulted in population receptive field sharpening, and consequently reduced responses, at the attended sound frequencies. The difference between our results to those of previous fMRI studies supports the notion that the influence of selective attention on auditory cortex is diverse and may depend on context, stimulus, and task.
The effects of bilateral posterior parietal cortex tRNS on reading performance
Authors: Bertoni Sara , Franceschini Sandro , Campana Gianluca , Facoetti Andrea 
Published: November 2022

AbstractAccording to established cognitive neuroscience knowledge based on studies on disabled and typically developing readers, reading is based on a dual-stream model in which a phonological-dorsal stream (left temporo-parietal and inferior frontal areas) processes unfamiliar words and pseudowords, whereas an orthographic-ventral stream (left occipito-temporal and inferior frontal areas) processes known words. However, correlational neuroimaging, causal longitudinal, training, and pharmacological studies have suggested the critical role of visuo-spatial attention in reading development. In a double blind, crossover within-subjects experiment, we manipulated the neuromodulatory effect of a short-term bilateral stimulation of posterior parietal cortex (PPC) by using active and sham tRNS during reading tasks in a large sample of young adults. In contrast to the dual-stream model predicting either no effect or a selective effect on the stimulated phonological-dorsal stream (as well as to a general multisensory effect on both reading streams), we found that only word-reading performance improved after active bilateral PPC tRNS. These findings demonstrate a direct neural connectivity between the PPC, controlling visuo-spatial attention, and the ventral stream for visual word recognition. These results support a neurobiological model of reading where performance of the orthographic-ventral stream is boosted by an efficient deployment of visuo-spatial attention from bilateral PPC stimulation.
Dopamine D2 receptors in the dorsomedial prefrontal cortex modulate social hierarchy in male mice
Authors: Li Lai-Fu , Li Zi-Lin , Song Bai-Lin , Jiang Yi , Wang Yan , Zou Hua-Wei , Yao Lun-Guang , Liu Ying-Juan 
Published: November 2022

Abstract
Social hierarchy greatly influences behavior and health. Both human and animal studies have signaled the medial prefrontal cortex (mPFC) as specifically related to social hierarchy. Dopamine D1 receptors (D1Rs) and D2 receptors (D2Rs) are abundantly expressed in the mPFC, modulating its functions. However, it is unclear how DR-expressing neurons in the mPFC regulate social hierarchy. Here, using a confrontation tube test, we found that most adult C57BL/6J male mice could establish a linear social rank after 1 week of cohabitation. Lower rank individuals showed social anxiety together with decreased serum testosterone levels. D2R expression was significantly downregulated in the dorsal part of mPFC (dmPFC) in lower rank individuals, whereas D1R expression showed no significant difference among the rank groups in the whole mPFC. Virus knockdown of D2Rs in the dmPFC led to mice being particularly prone to lose the contests in the confrontation tube test. Finally, simultaneous D2R activation in the subordinates and D2R inhibition in the dominants in a pair switched their dominant–subordinate relationship. The above results indicate that D2Rs in the dmPFC play an important role in social dominance. Our findings provide novel insights into the divergent functions of prefrontal D1Rs and D2Rs in social dominance, which may contribute to ameliorating social dysfunctions along with abnormal social hierarchy.
Morphological characteristics of lesions with thin cap fibroatheroma—a substudy from the COMBINE (OCT-FFR) trial
Authors: Roleder-Dylewska Magda , Gasior Pawel , Hommels Tobias M , Roleder Tomasz , Berta Balasz , Ang Hui Ying , Ng Jaryl Chen Koon , Hermanides Renicus S , Fabris Enrico , IJsselmuiden Alexander J J , Kauer Floris , Alfonso Fernando , von Birgelen Clemens , Escaned Javier , Camaro Cyril , Kennedy Mark W , Pereira Bruno , Magro Michael , Nef Holger , Reith Sebastian , Malinowski Krzysztof , De Luca Giuseppe , Garcia Garcia Hector M , Granada Juan F , Wojakowski Wojciech , Kedhi Elvin 
Published: November 2022

Abstract

Aims
To study if any qualitative or quantitative optical coherence tomography (OCT) variables in combination with thin cap fibroatheroma (TCFA) patients could improve the identification of lesions at risk for future major adverse cardiac events (MACEs).

Methods and results
From the combined optical coherence tomography morphologic and fractional flow reserve hemodynamic assessment of non- culprit lesions to better predict adverse event outcomes in diabetes mellitus patients: COMBINE (OCT-FFR) trial database (NCT02989740), we performed a detailed assessment OCT qualitative and quantitative variables in TCFA carrying diabetes mellitus (DM) patients with vs. without MACE during follow-up. MACEs were defined as a composite of cardiac death, target vessel myocardial infarction, clinically driven target lesion revascularization, and hospitalization for unstable angina. From the 390 fractional flow reserve (FFR)-negative DM patients, 98 (25.2%) had ≥1 OCT-detected TCFA, of which 13 (13.3%) had MACE and 85 (86.7%) were event-free (non-MACE). The baseline characteristics were similar between both groups; however, a smaller minimal lumen area (MLA) and lower mean FFR value were observed in MACE group (1.80 vs. 2.50 mm2, P = 0.01, and 0.85 vs. 0.89, P = 0.02, respectively). Prevalence of healed plaque (HP) was higher in the MACE group (53.85 vs. 21.18%, P = 0.01). TCFA were predominantly located proximal to the MLA. TCFA area was smaller in the MACE group, while no difference was observed regarding the lesion area.

Conclusion
Within TCFA carrying patients, a smaller MLA, lower FFR values, and TCFA location adjacent to a HP were associated with future MACE. Carpet-like measured lesion area surface was similar, while the TCFA area was smaller in the MACE arm, and predominantly located proximal to the MLA.
Discrimination driven by variation in social and economic conservatism: evidence from a nationwide field experiment
Authors: Lacroix Julie , Ruedin Didier , Zschirnt Eva 
Published: November 2022

AbstractWe examine how contextual variation in aggregated political attitudes shapes ethnic discrimination. Using a field experiment with national coverage we identify ethnic discrimination in the Swiss housing market (N = 7,533 queries for viewings from fictitious persons who vary by name to signal ethnic origin). We use referendums and popular initiatives to identify the aggregated political attitudes at the municipality level in two dimensions: social conservatism and economic conservatism. We show that although aggregated levels of discrimination are low, discrimination varies spatially – higher levels of discrimination are found in municipalities that are both socially and economically conservative. Municipalities that are economically conservative, but socially liberal also tend to exhibit ethnic discrimination. By contrast, we find no evidence of ethnic discrimination in municipalities that are socially conservative, but economically liberal. Considering how the literature highlights social conservatism when discussing the role of political ideology on attitudes and ethnic discrimination, this result highlights how differentiating different forms of conservatism helps better understand the relationship between ideology and behaviour – in this case ethnic discrimination.
Coronary microvascular dysfunction is associated with impaired cognitive function: the Cerebral-Coronary Connection study (C3 study)
Authors: Mejia-Renteria Hernan , Travieso Alejandro , Matías-Guiu Jordi A , Yus Miguel , Espejo-Paeres Carolina , Finocchiaro Francesca , Fernández Sara , Gomez-Escalonilla Carlos Ignacio , Reneses-Prieto Blanca , Gómez-Garré Maria Dulcenombre , Delgado-Alvarez Alfonso , Bustos Ana , Perez de Isla Leopoldo , de Diego Jose Juan Gomez , Modrego-Martin Javier , Ortega-Hernandez Adriana , Papadopoulos Petros , Arrazola-García Juan , Matías-Guiu Jorge , Escaned Javier 
Published: November 2022

Abstract

Background
It remains unknown whether the presence of coronary microcirculatory dysfunction (CMD) correlates with its equivalent condition in the brain, cerebral small vessel disease (CSVD). The cerebral-coronary connection (C3), a prospective blinded study, investigated the prevalence of CMD in patients with coronary artery disease (CAD) and its association with CSVD and cognitive function.

Methods and results
Patients with documented CAD fulfilling inclusion criteria underwent physiological assessment of epicardial vessels and the microcirculation using intracoronary pressure and Doppler. Coronary microcirculation-related indices included coronary flow reserve (CFR) and hyperaemic microvascular resistance. Brain magnetic resonance imaging, transcranial Doppler (TCD), and neurocognitive examination were performed. Overall, 67 patients were included in the study (mean age 66 years, 73% female). Patients with abnormal CFR (&lt;2.0) (55.2%) showed higher burden of white-matter hyperintensities: 43.2 vs. 20.0% (P = 0.044). After statistical adjustment, low CFR was associated with lower grey matter volume (P = 0.024) and with parameters of white-matter microstructural damage in diffusion-tensor imaging (lower fractional anisotropy and higher mean diffusivity, P = 0.029 and P = 0.032, respectively). Low CFR was associated with higher resistive (P = 0.027) and pulsatility (P = 0.043) values on TCD, and worse neurocognitive test scores (lower mini mental state examination, P = 0.025, and slower Trail Making Test A, P = 0.034).

Conclusions
Coronary microcirculatory dysfunction is frequent in patients with CAD and correlates with CSVD, abnormal cerebral flow haemodynamics, and significant cognitive impairment. These findings support the hypothesis that microvascular dysfunction in the heart and the brain are part of a single pathological process affecting microcirculation in patients with CAD.

Clinical Trial Registration
ClinicalTrials.gov NCT04131075.
Cardiac troponin release following coronary artery bypass grafting: mechanisms and clinical implications
Authors: Heuts Samuel , Gollmann-Tepeköylü Can , Denessen Ellen J S , Olsthoorn Jules R , Romeo Jamie L R , Maessen Jos G , van ‘t Hof Arnoud W J , Bekers Otto , Hammarsten Ola , Pölzl Leo , Holfeld Johannes , Bonaros Nikolaos , van der Horst Iwan C C , Davidson Sean M , Thielmann Matthias , Mingels Alma M A 
Published: November 2022

Abstract
The use of biomarkers is undisputed in the diagnosis of primary myocardial infarction (MI), but their value for identifying MI is less well studied in the postoperative phase following coronary artery bypass grafting (CABG). To identify patients with periprocedural MI (PMI), several conflicting definitions of PMI have been proposed, relying either on cardiac troponin (cTn) or the MB isoenzyme of creatine kinase, with or without supporting evidence of ischaemia. However, CABG inherently induces the release of cardiac biomarkers, as reflected by significant cTn concentrations in patients with uncomplicated postoperative courses. Still, the underlying (patho)physiological release mechanisms of cTn are incompletely understood, complicating adequate interpretation of postoperative increases in cTn concentrations. Therefore, the aim of the current review is to present these potential underlying mechanisms of cTn release in general, and following CABG in particular (Graphical Abstract). Based on these mechanisms, dissimilarities in the release of cTnI and cTnT are discussed, with potentially important implications for clinical practice. Consequently, currently proposed cTn biomarker cut-offs by the prevailing definitions of PMI might warrant re-assessment, with differentiation in cut-offs for the separate available assays and surgical strategies. To resolve these issues, future prospective studies are warranted to determine the prognostic influence of biomarker release in general and PMI in particular.
High-density lipoprotein revisited: biological functions and clinical relevance
Authors: von Eckardstein Arnold , Nordestgaard Børge G , Remaley Alan T , Catapano Alberico L 
Published: November 2022

AbstractPrevious interest in high-density lipoproteins (HDLs) focused on their possible protective role in atherosclerotic cardiovascular disease (ASCVD). Evidence from genetic studies and randomized trials, however, questioned that the inverse association of HDL-cholesterol (HDL-C) is causal. This review aims to provide an update on the role of HDL in health and disease, also beyond ASCVD. Through evolution from invertebrates, HDLs are the principal lipoproteins, while apolipoprotein B-containing lipoproteins first developed in vertebrates. HDLs transport cholesterol and other lipids between different cells like a reusable ferry, but serve many other functions including communication with cells and the inactivation of biohazards like bacterial lipopolysaccharides. These functions are exerted by entire HDL particles or distinct proteins or lipids carried by HDL rather than by its cholesterol cargo measured as HDL-C. Neither does HDL-C measurement reflect the efficiency of reverse cholesterol transport. Recent studies indicate that functional measures of HDL, notably cholesterol efflux capacity, numbers of HDL particles, or distinct HDL proteins are better predictors of ASCVD events than HDL-C. Low HDL-C levels are related observationally, but also genetically, to increased risks of infectious diseases, death during sepsis, diabetes mellitus, and chronic kidney disease. Additional, but only observational, data indicate associations of low HDL-C with various autoimmune diseases, and cancers, as well as all-cause mortality. Conversely, extremely high HDL-C levels are associated with an increased risk of age-related macular degeneration (also genetically), infectious disease, and all-cause mortality. HDL encompasses dynamic multimolecular and multifunctional lipoproteins that likely emerged during evolution to serve several physiological roles and prevent or heal pathologies beyond ASCVD. For any clinical exploitation of HDL, the indirect marker HDL-C must be replaced by direct biomarkers reflecting the causal role of HDL in the respective disease.
Prevalence, trends, and outcomes of cardiovascular diseases in pregnant patients in the USA: 2010–19
Authors: Majmundar Monil , Doshi Rajkumar , Patel Kunal N , Zala Harshvardhan , Kumar Ashish , Kalra Ankur 
Published: November 2022

AbstractAimsContemporary data on the prevalence, trends, and outcomes of cardiovascular diseases (CVDs) in pregnant patients are limited. This study aimed to analyse the prevalence, trends, and outcomes of CVD and their subtypes in hospitalized pregnant patients in the USA.Methods and resultsThis retrospective population-based cohort study used the Nationwide Readmission Database to identify all hospitalized pregnant patients from 1 January 2010, to 31 December 2019. Data analyses were conducted from January to February 2022. Pregnancy-associated hospitalizations were identified. The main outcomes were the prevalence and trend of CVD in pregnant patients. 39 212 104 hospitalized pregnant patients were identified: 4 409 924 with CVD (11.3%) and 34 802 180 without CVD (88.8%). The annual age-adjusted CVD prevalence increased from 9.2% in 2010 to 14.8% in 2019 (P &lt; 0.001). Hypertensive disorder of pregnancy (1069/10 000) was the most common, and aortic dissection (0.1/10 000) was the least common CVD. The trends of all CVD subtypes increased; however, the trend of valvular heart disease decreased. Age-adjusted in-hospital all-cause mortality was 8.2/10 000 in CVD, but its trend decreased from 8.1/10 000 in 2010 to 6.5/10 000 in 2019 (P &lt; 0.001). CVD was associated with 15.51 times higher odds of in-hospital all-cause mortality compared with non-CVD patients [odds ratio (OR): 15.51, 95% confidence interval (CI)13.22–18.20, P &lt; 0.001]. CVD was associated with higher 6-week postpartum readmission (OR: 1.97, 95% CI: 1.95–1.99), myocardial infarction (OR: 3.04, 95% CI: 2.57–3.59), and stroke (OR: 2.66, 95% CI: 2.41–2.94)(P &lt; 0.001 for all).ConclusionThere is an increasing age-adjusted trend in overall CVD and its subtypes among pregnant patients in the USA from 2010 to 2019. Pregnant patients with CVD had higher odds of in-hospital mortality than those without CVD. However, in-hospital all-cause mortality among patients with and without CVD has decreased over the past 10 years. CVD was associated with higher 6-week postpartum all-cause readmission, myocardial infarction, and stroke rates.
Surgical or percutaneous coronary revascularization for heart failure: an in silico model using routinely collected health data to emulate a clinical trial
Authors: Pathak Suraj , Lai Florence Y , Miksza Joanne , Petrie Mark C , Roman Marius , Murray Sarah , Dearling Jeremy , Perera Divaka , Murphy Gavin J 
Published: November 2022

Abstract

Aims
The choice of revascularization with coronary artery bypass grafting (CABG) vs. percutaneous coronary intervention (PCI) in people with ischaemic left ventricular dysfunction is not guided by high-quality evidence.

Methods and results
A trial of CABG vs. PCI in people with heart failure (HF) was modelled in silico using routinely collected healthcare data. The in silico trial cohort was selected by matching the target trial cohort, identified from Hospital Episode Statistics in England, with individual patient data from the Surgical Treatment for Ischemic Heart Failure (STICH) trial. Allocation to CABG vs. complex PCI demonstrated random variation across administrative regions in England and was a valid statistical instrument. The primary outcome was 5-year all-cause mortality or cardiovascular hospitalization. Instrumental variable analysis (IVA) was used for the primary analysis. Results were expressed as average treatment effects (ATEs) with 95% confidence intervals (CIs). The target population included 13 519 HF patients undergoing CABG or complex PCI between April 2009 and March 2015. After matching, the emulated trial cohort included 2046 patients. The unadjusted primary outcome rate was 51.1% in the CABG group and 70.0% in the PCI group. IVA of the emulated cohort showed that CABG was associated with a lower risk of the primary outcome (ATE −16.2%, 95% CI −20.6% to −11.8%), with comparable estimates in the unmatched target population (ATE −15.5%, 95% CI −17.5% to −13.5%).

Conclusion
In people with HF, in silico modelling suggests that CABG is associated with fewer deaths or cardiovascular hospitalizations at 5 years vs. complex PCI. A pragmatic clinical trial is needed to test this hypothesis and this trial would be feasible.
Assessment of Safety and Efficacy of Tofacitinib, Stratified by Age, in Patients from the Ulcerative Colitis Clinical Program
Authors: Lichtenstein Gary R , Bressler Brian , Francisconi Carlos , Vermeire Severine , Lawendy Nervin , Salese Leonardo , Sawyerr Gosford , Shi Hongjiong , Su Chinyu , Judd Donna T , Jones Thomas , Loftus Edward V 
Published: November 2022

Abstract

Background
In patients with ulcerative colitis (UC), risks of infection and malignancies increase with age. Tofacitinib is an oral, small molecule Janus kinase inhibitor for the treatment of UC. This analysis assessed age as a risk factor for adverse events of special interest (AESI) in the tofacitinib UC clinical program.

Methods
Data were from phase 2 and 3 induction studies, a phase 3 maintenance study, and an open-label, long-term extension study. Efficacy and/or safety outcomes were analyzed in the Induction, Maintenance, and Overall Cohorts (patients who received ≥ 1 dose of tofacitinib), stratified by age. The effects of baseline demographic and disease-related factors on AESI incidence were assessed by Cox proportional-hazards regression analysis.

Results
In the Overall Cohort (1157 patients with ≤ 6.8 years’ tofacitinib treatment), age was a statistically significant predictor of herpes zoster (HZ), malignancies excluding nonmelanoma skin cancer (NMSC), and NMSC. Other statistically significant predictors included prior tumor necrosis factor inhibitor failure for HZ, NMSC, and opportunistic infection events, and prior duration of UC for malignancies excluding NMSC. In the Induction and Maintenance Cohorts, a higher proportion of tofacitinib-treated than placebo-treated patients (numerical difference) achieved the efficacy endpoints (endoscopic improvement, clinical remission, clinical response) across all age groups.

Conclusions
Older individuals receiving tofacitinib as induction and maintenance therapy to treat UC may have an increased risk of HZ, malignancies (excluding NMSC), and NMSC versus similarly treated younger patients, consistent with findings from the general population. Across all age groups, tofacitinib demonstrated greater efficacy than placebo as an induction and maintenance therapy.

ClinicalTrials.gov Registration Numbers
NCT00787202; NCT01465763; NCT01458951; NCT01458574; NCT01470612.