bluuebunny/crossref_metadata_2025_split huggingface dataset:
The low dimensionality of post-stroke cognitive deficits: it’s the lesion anatomy!
Authors: Sperber Christoph , Gallucci Laura , Umarova Roza 
Published: November 2022

Abstract
For years, dissociation studies on neurological single-case patients with brain lesions were the dominant method to infer fundamental cognitive functions in neuropsychology. In contrast, the association between deficits was considered to be of less epistemological value. Still, associational computational methods for dimensionality reduction—such as principal component analysis or factor analysis—became popular for the identification of fundamental cognitive functions and to understand human cognitive brain architecture from post-stroke neuropsychological profiles. In the present in silico study with lesion imaging of 300 stroke patients, we investigated the dimensionality of artificial simulated neuropsychological profiles that exclusively contained independent fundamental cognitive functions without any underlying low-dimensional cognitive architecture. Still, the anatomy of stroke lesions alone was sufficient to create a dependence between variables that allowed a low-dimensional description of the data with principal component analysis. All criteria that we used to estimate the dimensionality of data, including the Kaiser criterion, were strongly affected by lesion anatomy, while the Joliffe criterion provided the least affected estimates. The dimensionality of profiles was reduced by 62–70% for the Kaiser criterion, up to the degree that is commonly found in neuropsychological studies on actual cognitive measures. The interpretability of such low-dimensional factors as deficits of fundamental cognitive functions and their provided insights into human cognitive architecture thus seem to be severely limited, and the heavy focus of current cognitive neuroscience on group studies and associations calls for improvements. We suggest that qualitative criteria and dissociation patterns could be used to refine estimates for the dimensionality of the cognitive architecture behind post-stroke deficits. Further, given the strong impact of lesion anatomy on the associational structure of data, we see the need for further optimization of interpretation strategies of computational factors in post-stroke lesion studies of cognitive deficits.
Association of Upper Respiratory Streptococcus pneumoniae Colonization With Severe Acute Respiratory Syndrome Coronavirus 2 Infection Among Adults
Authors: Parker Anna M , Jackson Nicole , Awasthi Shevya , Kim Hanna , Alwan Tess , Wyllie Anne L , Baldwin Alisha B , Brennick Nicole B , Moehle Erica A , Giannikopoulos Petros , Kogut Katherine , Holland Nina , Mora Ana M , Eskenazi Brenda , Riley Lee W , Lewnard Joseph A 
Published: November 2022

Abstract

Background
Streptococcus pneumoniae interacts with numerous viral respiratory pathogens in the upper airway. It is unclear whether similar interactions occur with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Methods
We collected saliva specimens from working-age adults undergoing SARS-CoV-2 molecular testing at outpatient clinics and via mobile community-outreach testing between July and November 2020 in Monterey County, California. After bacterial culture enrichment, we tested for pneumococci by means of quantitative polymerase chain reaction targeting the lytA and piaB genes, and we measured associations with SARS-CoV-2 infection using conditional logistic regression.

Results
Analyses included 1278 participants, with 564 enrolled in clinics and 714 enrolled through outreach-based testing. The prevalence of pneumococcal carriage was 9.2% (117 of 1278) among all participants (11.2% [63 of 564] in clinic-based testing and 7.6% [54 of 714] in outreach-based testing). The prevalence of SARS-CoV-2 infection was 27.4% (32 of 117) among pneumococcal carriers and 9.6% (112 of 1161) among noncarriers (adjusted odds ratio [aOR], 2.73 [95% confidence interval (CI): 1.58–4.69). Associations between SARS-CoV-2 infection and pneumococcal carriage were enhanced in the clinic-based sample (aOR, 4.01 [95% CI: 2.08–7.75]) and among symptomatic participants (3.38 [1.35–8.40]), compared with findings within the outreach-based sample and among asymptomatic participants. The adjusted odds of SARS-CoV-2 coinfection increased 1.24-fold (95% CI: 1.00–1.55-fold) for each 1-unit decrease in piaB quantitative polymerase chain reaction cycle threshold value among pneumococcal carriers. Finally, pneumococcal carriage modified the association of SARS-CoV-2 infection with recent exposure to a suspected coronavirus disease 2019 case (aOR, 7.64 [95% CI: 1.91–30.7] and 3.29 [1.94–5.59]) among pneumococcal carriers and noncarriers, respectively).

Conclusions
Associations of pneumococcal carriage detection and density with SARS-CoV-2 suggest a synergistic relationship in the upper airway. Longitudinal studies are needed to determine interaction mechanisms between pneumococci and SARS-CoV-2.
Key Node Identification Method Integrating Information Transmission Probability and Path Diversity in Complex Network
Authors: Liu Xiaoyang , Gao Luyuan , Fiumara Giacomo , De Meo Pasquale 
Published: November 2022

AbstractPrevious key node identification approaches assume that the transmission of information on a path always ends positively, which is not necessarily true. In this paper, we propose a new centrality index called Information Rank (IR for short) that associates each path with a score specifying the probability that such path successfully conveys a message. The IR method generates all the shortest paths of any arbitrary length coming out from a node $u$ and defines the centrality of u as the sum of the scores of all the shortest paths exiting $u$. The IR algorithm is more robust than other centrality indexes based on shortest paths because it uses alternative paths in its computation, and it is computationally efficient because it relies on a Beadth First Search-BFS to generate all shortest paths. We validated the IR algorithm on nine real networks and compared its ability to identify super-spreaders (i.e. nodes capable of spreading an infection in a real network better than others) with five popular centrality indices such as Degree, Betweenness, K-Shell, DynamicRank and PageRank. Experimental results highlight the clear superiority of IR over all considered competitors.
Paternal transmission of behavioural and metabolic traits induced by postnatal stress to the 5th generation in mice
Authors: Boscardin Chiara , Manuella Francesca , Mansuy Isabelle M 
Published: November 2022

AbstractLife experiences and environmental conditions in childhood can change the physiology and behaviour of exposed individuals and, in some cases, of their offspring. In rodent models, stress/trauma, poor diet, and endocrine disruptors in a parent have been shown to cause phenotypes in the direct progeny, suggesting intergenerational inheritance. A few models also examined transmission to further offspring and suggested transgenerational inheritance, but such multigenerational inheritance is not well characterized. Our previous work on a mouse model of early postnatal stress showed that behaviour and metabolism are altered in the offspring of exposed males up to the 4th generation in the patriline and up to the 2nd generation in the matriline. The present study examined if symptoms can be transmitted beyond the 4th generation in the patriline. Analyses of the 5th and 6th generations of mice revealed that altered risk-taking and glucose regulation caused by postnatal stress are still manifested in the 5th generation but are attenuated in the 6th generation. Some of the symptoms are expressed in both males and females, but some are sex-dependent and sometimes opposite. These results indicate that postnatal trauma can affect behaviour and metabolism over many generations, suggesting epigenetic mechanisms of transmission.
Proton Pump Inhibitor Use and Cognitive Function in the Boston Puerto Rican Health Study
Authors: Dinesh Deepika , Lee Jong Soo , Scott Tammy M , Tucker Katherine L , Palacios Natalia 
Published: November 2022

Abstract

Background
There is a lack of consensus among studies on the association between proton pump inhibitor (PPI) use and cognitive impairment. This association is not well studied among minority populations, including among Puerto Ricans. Therefore, we sought to examine this association among Boston-area Puerto Ricans.

Methods
The Boston Puerto Rican Health Study is an ongoing longitudinal cohort that enrolled 1499 Boston-area Puerto Rican adults, aged 45–75 years at baseline. Complete outcome and exposure data was available for 1290 baseline participants. Covariate-adjusted linear regression and linear mixed effects models were used to examine the association between PPI use, and global cognition, executive function, and memory cross-sectionally and longitudinally over ~12.7 years of follow-up. Furthermore, we examined the cross-sectional association between long-term PPI use (continuous use of ~6.2 years) and global cognition, executive function, and memory.

Results
Among 1 290 participants at baseline, 313 (24.3%) self-reported PPI use. Baseline PPI use was not associated with baseline global cognition, executive function, or memory. Baseline PPI use also did not alter the trajectory of global cognition, executive function, or memory over ~12.7 years of follow-up. Long-term PPI use was not associated with global cognition, executive function, or memory over ~12.7 years of follow-up.

Conclusion
In this study of Boston-area Puerto Ricans, we did not observe an association between PPI use and global cognition, executive function, or memory either cross-sectionally or over 12.7 years of follow-up.
Immunogenicity of an Additional mRNA-1273 SARS-CoV-2 Vaccination in People With HIV With Hyporesponse After Primary Vaccination
Authors: Jongkees Marlou J , Geers Daryl , Hensley Kathryn S , Huisman Wesley , GeurtsvanKessel Corine H , Bogers Susanne , Gommers Lennert , Papageorgiou Grigorios , Jochems Simon P , den Hollander Jan G , Schippers Emile F , Ammerlaan Heidi S M , Bierman Wouter F W , van der Valk Marc , Berrevoets Marvin A H , Soetekouw Robert , Langebeek Nienke , Bruns Anke H W , Leyten Eliane M S , Sigaloff Kim C E , van Vonderen Marit G A , Delsing Corine E , Branger Judith , Katsikis Peter D , Mueller Yvonne M , de Vries Rory D , Rijnders Bart J A , Brinkman Kees , Rokx Casper , Roukens Anna H E 
Published: November 2022

AbstractBackgroundThe COVIH study is a prospective coronavirus disease 2019 (COVID-19) vaccination study in 1154 people with HIV (PWH), of whom 14% showed reduced antibody levels after primary vaccination. We evaluated whether an additional vaccination boosts immune responses in these hyporesponders.MethodsThe primary end point was the increase in antibodies 28 days after additional mRNA-1273 vaccination. Secondary end points included neutralizing antibodies, S-specific T-cell and B-cell responses, and reactogenicity.ResultsOf the 66 participants, 40 previously received 2 doses ChAdOx1-S, 22 received 2 doses BNT162b2, and 4 received a single dose Ad26.COV2.S. The median age was 63 years (interquartile range [IQR], 60–66), 86% were male, and median CD4+ T-cell count was 650/μL (IQR, 423–941). The mean S1-specific antibody level increased from 35 binding antibody units (BAU)/mL (95% confidence interval [CI], 24–46) to 4317 BAU/mL (95% CI, 3275–5360) (P &lt; .0001). Of all participants, 97% showed an adequate response and the 45 antibody-negative participants all seroconverted. A significant increase in the proportion of PWH with ancestral S-specific CD4+ T cells (P = .04) and S-specific B cells (P = .02) was observed.ConclusionsAn additional mRNA-1273 vaccination induced a robust serological response in 97% of PWH with a hyporesponse after primary vaccination.Clinical Trials Registration. EUCTR2021-001054-57-N.
Environmental Concern Leads to Trade Skepticism on the Political Left and Right
Authors: Rudolph Lukas , Quoß Franziska , Buchs Romain , Bernauer Thomas 
Published: November 2022

Abstract
The environmental implications of international trade appear to be associated with public backlash against trade liberalization and efforts at greening international trade. Because public support is essential to environmental and trade policy-making alike, we examine the trade–environment nexus from a public opinion perspective. We investigate whether negative attitudes toward trade are in fact fueled by concern over its environmental consequences. We argue that environmental concern affects how citizens evaluate the costs and benefits of trade, and that such evaluation is moderated by political ideology. The empirical analysis relies on a large representative survey and a population-based survey experiment in Switzerland, a small open economy. We show that environmental concern leads to decreasing appreciation of and support for international trade, with different manifestations of trade skepticism on the political left and right. This suggests (i) that policy-makers should focus more on greening global supply chains, and thus trade, if they wish to sustain public support for liberal international trade policy; and (ii) that the public follows informational cues on the environmental impacts of trade.
X-ray from outflow-cloud interaction and its application in tidal disruption events
Authors: Chen Jiashi , Wang Wei 
Published: November 2022

ABSTRACT
Tidal disruption events (TDEs) may occur in supermassive black holes (SMBHs) surrounded by clouds. TDEs can generate ultrafast and large opening-angle outflow with a velocity of ∼0.01–0.2 c, which will collide with clouds with time lags depending on outflow velocity and cloud distances. Since the fraction of the outflow energy transferred into cloud’s radiation is anticorrelated with the cloud density, high-density clouds was thought to be inefficient in generating radiation. In this work, we studied the radiation from the outflow-cloud interactions for high-density clouds, and found that thermal conduction plays crucial roles in increasing the cloud’s radiation. Up to 10 per cent of the bow shock energy can be transferred into clouds and gives rise to X-ray emission with equivalent temperature of 105–6 K due to the cooling catastrophe. The inverse Compton scattering of TDE UV/optical photons by relativistic electrons at bow shock generates power-law X-ray spectra with photon indices Γ ∼ 2–3. This mechanism may account for some TDE candidates with delayed X-ray emission, and can be examined by delayed radio and gamma-ray emissions.
LazySampling and LinearSampling: fast stochastic sampling of RNA secondary structure with applications to SARS-CoV-2
Authors: Zhang He , Li Sizhen , Zhang Liang , Mathews David H , Huang Liang 
Published: November 2022

Abstract
Many RNAs fold into multiple structures at equilibrium, and there is a need to sample these structures according to their probabilities in the ensemble. The conventional sampling algorithm suffers from two limitations: (i) the sampling phase is slow due to many repeated calculations; and (ii) the end-to-end runtime scales cubically with the sequence length. These issues make it difficult to be applied to long RNAs, such as the full genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To address these problems, we devise a new sampling algorithm, LazySampling, which eliminates redundant work via on-demand caching. Based on LazySampling, we further derive LinearSampling, an end-to-end linear time sampling algorithm. Benchmarking on nine diverse RNA families, the sampled structures from LinearSampling correlate better with the well-established secondary structures than Vienna RNAsubopt and RNAplfold. More importantly, LinearSampling is orders of magnitude faster than standard tools, being 428× faster (72 s versus 8.6 h) than RNAsubopt on the full genome of SARS-CoV-2 (29 903 nt). The resulting sample landscape correlates well with the experimentally guided secondary structure models, and is closer to the alternative conformations revealed by experimentally driven analysis. Finally, LinearSampling finds 23 regions of 15 nt with high accessibilities in the SARS-CoV-2 genome, which are potential targets for COVID-19 diagnostics and therapeutics.
TOXRIC: a comprehensive database of toxicological data and benchmarks
Authors: Wu Lianlian , Yan Bowei , Han Junshan , Li Ruijiang , Xiao Jian , He Song , Bo Xiaochen 
Published: November 2022

Abstract
The toxic effects of compounds on environment, humans, and other organisms have been a major focus of many research areas, including drug discovery and ecological research. Identifying the potential toxicity in the early stage of compound/drug discovery is critical. The rapid development of computational methods for evaluating various toxicity categories has increased the need for comprehensive and system-level collection of toxicological data, associated attributes, and benchmarks. To contribute toward this goal, we proposed TOXRIC (https://toxric.bioinforai.tech/), a database with comprehensive toxicological data, standardized attribute data, practical benchmarks, informative visualization of molecular representations, and an intuitive function interface. The data stored in TOXRIC contains 113 372 compounds, 13 toxicity categories, 1474 toxicity endpoints covering in vivo/in vitro endpoints and 39 feature types, covering structural, target, transcriptome, metabolic data, and other descriptors. All the curated datasets of endpoints and features can be retrieved, downloaded and directly used as output or input to Machine Learning (ML)-based prediction models. In addition to serving as a data repository, TOXRIC also provides visualization of benchmarks and molecular representations for all endpoint datasets. Based on these results, researchers can better understand and select optimal feature types, molecular representations, and baseline algorithms for each endpoint prediction task. We believe that the rich information on compound toxicology, ML-ready datasets, benchmarks and molecular representation distribution can greatly facilitate toxicological investigations, interpretation of toxicological mechanisms, compound/drug discovery and the development of computational methods.
Structural and dynamic basis of DNA capture and translocation by mitochondrial Twinkle helicase
Authors: Li Zhuo , Kaur Parminder , Lo Chen-Yu , Chopra Neil , Smith Jamie , Wang Hong , Gao Yang 
Published: November 2022

Abstract
Twinkle is a mitochondrial replicative helicase which can self-load onto and unwind mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human mitochondrial diseases. Using cryo-electron microscopy (cryo-EM) and high-speed atomic force microscopy (HS-AFM), we obtained the atomic-resolution structure of a vertebrate Twinkle homolog with DNA and captured in real-time how Twinkle is self-loaded onto DNA. Our data highlight the important role of the non-catalytic N-terminal domain of Twinkle. The N-terminal domain directly contacts the C-terminal helicase domain, and the contact interface is a hotspot for disease-related mutations. Mutations at the interface destabilize Twinkle hexamer and reduce helicase activity. With HS-AFM, we observed that a highly dynamic Twinkle domain, which is likely to be the N-terminal domain, can protrude ∼5 nm to transiently capture nearby DNA and initialize Twinkle loading onto DNA. Moreover, structural analysis and subunit doping experiments suggest that Twinkle hydrolyzes ATP stochastically, which is distinct from related helicases from bacteriophages.
Efficacy of Duloxetine in Patients with Central Post-stroke Pain: A Randomized Double Blind Placebo Controlled Trial
Authors: Mahesh Bandari , Singh Varun Kumar , Pathak Abhishek , Kumar Anand , Mishra Vijaya Nath , Joshi Deepika , Chaurasia Rameshwar Nath 
Published: November 2022

Abstract

Objective
Central post-stroke pain (CPSP) refers to neuropathic pain in areas of the body corresponding to stroke lesions. Duloxetine, a serotonin-norepinephrine reuptake inhibitor, is safe and effective against neuropathic pain. In this randomized double-blind placebo-controlled study, we studied the effect of duloxetine in CPSP patients.

Methods
Consecutive patients satisfying the inclusion criteria were enrolled in the study and were randomized in a simple 1:1 randomization to duloxetine and placebo groups. Baseline demographic, clinical and imaging data were obtained. Prespecified primary outcome was comparison of change in pain intensity from baseline to 4 weeks, as assessed on Numeric Rating Scale (NRS) in both groups. Prespecified secondary outcomes were comparison of change in average pain severity from baseline to 4 weeks as measured on Short-form McGill Pain Questionnaire-2 (SFMPQ-2) score and Pain Disability Index (PDI) score and comparison of Patient Global Impression of Change (PGIC) score at the end of 4 weeks of treatment in both groups. Duloxetine at doses of 30 mg and similarly appearing placebo tablets were given and the dose was doubled if there was no response at the end of 2 weeks. Response to treatment was defined as ≥2 points reduction of NRS pain score.

Results
In total, 82 patients were enrolled in the study, 41 in each group. There was a significant difference in reduction in NRS score between duloxetine and placebo group from baseline (6.51 ± 1.03 vs 6.37 ± 1.41) to 4 weeks (3.02 ± 1.70 vs 4.40 ± 1.77, P = .02 for difference in reduction between groups). SFMPQ-2 score (P = .032) and Pain Disability Index score (P = .005) also differ significantly from baseline to 4 weeks between the two groups. PGIC score at the end of 4 weeks was significantly different between the two groups (5.15 ± 1.54 vs 3.89 ± 1.51; P &lt; .001). Responder rate (defined as % of patients with ≥ 2 points reduction on NRS pain score from baseline to end of 4 weeks), on post hoc analysis was found to be significantly higher in duloxetine group (80.5%) than placebo group (43.9%) (P = .042).

Conclusions
Duloxetine can be an effective treatment option for patients with moderate to severe central post-stroke pain.
De-policing, police stops, and crime
Authors: Powell Zachary A 
Published: November 2022

Abstract
Contemporary discussions on policing focus on the impact of intense external scrutiny on proactive policing practices. Some commentators suggest negative feedback directed at law enforcement inhibits police willingness to engage in proactive police practices. This effect, known as ‘de-policing’, endangers communities due to officer disengagement in crime prevention techniques. To examine this effect, previous research relies on crime data to examine de-policing; few studies explore how officer-initiated actions, such as a stop, shift in the wake of a de-policing effect. Using data from the Stanford Open Policing Project, this paper examines how officer-initiated behaviour (vehicle and pedestrian stops) changes after a negative public scrutiny shock (in this case, the shooting of Michael Brown). Further, the study examines how crime rates changed after Brown’s death. The findings of this paper suggest police proactivity declined and crime increased after Michael Brown’s death in Ferguson, Missouri. Policy implications, future research avenues, and theoretical enhancements to de-policing are discussed.