bluuebunny/crossref_metadata_2025_split huggingface dataset:
Segregation of children into small groups for in-person learning during the COVID-19 pandemic
Authors: Muñoz-Nava Luis Manuel , Nahmad Marcos 
Published: August 2021

AbstractThe COVID-19 pandemic affected in-person learning worldwide due to fears that schools could contribute to the propagation of the virus within their communities. Using computational modeling, we compare the reopening of schools with mitigation measures with a strategy in which schoolchildren are segregated into small isolated groups or “bubbles,” where children physically interact without restrictions while receiving remote instruction from their teachers. This strategy is robust to common perturbations and is more flexible and stable than reopening of schools. Our modeling results and a real-world implementation of a bubbles program in an elementary school in Mexico City support that this strategy is an effective transition alternative, especially in communities with low vaccination rates or where operational costs associated to safely reopening schools cannot be afforded.
Classifying Refugee Status Using Common Features in EMR
Authors: Morrison Malia , Nobles Vanessa , Johnson-Agbakwu Crista E. , Bailey Celeste , Liu Li 
Published: August 2021

ABSTRACTObjectiveAutomated and accurate identification of refugees in healthcare databases is a critical first step to investigate healthcare needs of this vulnerable population and improve health disparities. This study developed a machine-learning method, named refugee identification system (RIS) that uses features commonly collected in healthcare databases to classify refugees and non-refugees.Materials and MethodsWe compiled a curated data set consisting of 103 refugees and 930 non-refugees in Arizona. For each person in the curated data set, we collected age, primary language, and noise-masked home address. We supplemented de-identified individual-level data with state-level refugee resettlement statistics and world language statistics, then performed feature engineering to convert primary language and masked address into quantitative features. Finally, we built a random forest model to classify refugee status.ResultsEvaluated on holdout testing data, RIS achieved a high classification accuracy of 0.97, specificity of 0.99, sensitivity of 0.85, positive predictive value of 0.88, and negative predictive value of 0.98. The receiver operating characteristic curve had an area under the curve value of 0.98. The source code is available at GitHub (https://github.com/liliulab/ris).Discussion and ConclusionRIS is an automated, accurate, and scalable method to predict refugee status. It uses only de-identified information to protect patient privacy. The computational framework is adaptable to address similar challenges in other States. Its application enables large-scale investigation of refugee healthcare needs and improvement of health disparities.
Changing incidence of invasive pneumococcal disease in infants less than 90 days of age before and after introduction of the 13-valent Pneumococcal Conjugate Vaccine in Blantyre, Malawi: a 14-year hospital based surveillance study
Authors: Koenraads Marianne , Swarthout Todd D. , Bar-Zeev Naor , Brown Comfort , Msefula Jacquline , Denis Brigitte , Dube Queen , Gordon Stephen B. , Heyderman Robert S. , Gladstone Melissa , French Neil 
Published: August 2021

AbstractBackgroundInvasive pneumococcal disease (IPD) in young infants is uncommon but associated with high morbidity and mortality. Accurate data on the burden of IPD in young infants in low-income countries are lacking. We examined the burden of IPD in infants aged <90 days in Blantyre, Malawi over a 14 year period and evaluated the impact of the 12 November 2011 introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) on vaccine-serotype IPD (VT-IPD) in this population.MethodsWe conducted laboratory-based prospective IPD surveillance in infants aged <90 days admitted to Queen Elizabeth Central Hospital (QECH) in Blantyre between 2005 and 2018, including 7 years pre- and 7 years post-PCV13 introduction. IPD was defined as Streptococcus pneumoniae identified by culture from blood or cerebrospinal fluid. Serotypes were determined by multiplex PCR and latex agglutination testing.ResultsWe identified 130 cases of culture-confirmed IPD in infants <90 days old between 2005-2018. Total IPD incidence was declining prior to PCV13 introduction. The mean incidence of IPD was significantly lower in the post-PCV era. Serotypes 5 (27.8%) and 1(15.6%), were most prevalent. Even after PCV13 introduction, VT-IPD remained dominant with serotype 5 accounting for 17.4% and serotype 1 for 13% of cases in young infants.ConclusionVaccine serotypes were the main cause of IPD in neonates and young infants, both before and after PCV13 introduction. Further strategies need to be considered to protect this vulnerable population, including maternal or neonatal immunization and implementation of an alternative PCV schedule with a booster dose.SummaryThe incidence of invasive pneumococcal disease in infants in Blantyre, Malawi has declined over the past decade and more significantly after introduction of the pneumococcal conjugate vaccine. Vaccine serotypes have remained the main cause of disease in this population.
Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK
Authors: Pouwels Koen B. , Pritchard Emma , Matthews Philippa C. , Stoesser Nicole , Eyre David W. , Vihta Karina-Doris , House Thomas , Hay Jodie , Bell John I , Newton John N , Farrar Jeremy , Crook Derrick , Cook Duncan , Rourke Emma , Studley Ruth , Peto Tim , Diamond Ian , Walker A. Sarah ,   the COVID-19 Infection Survey Team
Published: August 2021

AbstractThe effectiveness of BNT162b2, ChAdOx1, and mRNA-1273 vaccines against new SARS-CoV-2 infections requires continuous re-evaluation, given the increasingly dominant Delta variant. We investigated the effectiveness of the vaccines in a large community-based survey of randomly selected households across the UK. We found that the effectiveness of BNT162b2 and ChAd0x1 against any infections (new PCR positives) and infections with symptoms or high viral burden is reduced with the Delta variant. A single dose of the mRNA-1273 vaccine had similar or greater effectiveness compared to a single dose of BNT162b2 or ChAdOx1. Effectiveness of two doses remains at least as great as protection afforded by prior natural infection. The dynamics of immunity following second doses differed significantly between BNT162b2 and ChAdOx1, with greater initial effectiveness against new PCR-positives but faster declines in protection against high viral burden and symptomatic infection with BNT162b2. There was no evidence that effectiveness varied by dosing interval, but protection was higher among those vaccinated following a prior infection and younger adults. With Delta, infections occurring following two vaccinations had similar peak viral burden to those in unvaccinated individuals. SARS-CoV-2 vaccination still reduces new infections, but effectiveness and attenuation of peak viral burden are reduced with Delta.
Symptoms and SARS-CoV-2 positivity in the general population in the UK
Authors: Vihta Karina-Doris , Pouwels Koen B. , Peto Tim , Pritchard Emma , Eyre David W. , House Thomas , Gethings Owen , Studley Ruth , Rourke Emma , Cook Duncan , Diamond Ian , Crook Derrick , Matthews Philippa C. , Stoesser Nicole , Walker Ann Sarah ,   the COVID-19 Infection Survey team
Published: August 2021

ABSTRACTBackgroundSeveral community-based studies have assessed the ability of different symptoms to identify COVID-19 infections, but few have compared symptoms over time (reflecting SARS-CoV-2 variants) and by vaccination status.MethodsUsing data and samples collected by the COVID-19 Infection Survey at regular visits to representative households across the UK, we compared symptoms in new PCR-positives and comparator test-negative controls.ResultsFrom 26/4/2020-7/8/2021, 27,869 SARS-CoV-2 PCR-positive episodes occurred in 27,692 participants (median 42 years (IQR 22-58)); 13,427 (48%) self-reported symptoms (“symptomatic positive episodes”). The comparator group comprised 3,806,692 test-negative visits (457,215 participants); 130,612 (3%) self-reported symptoms (“symptomatic negative visit”). Reporting of any symptoms in positive episodes varied over calendar time, reflecting changes in prevalence of variants, incidental changes (e.g. seasonal pathogens, schools re-opening) and vaccination roll-out. There was a small increase in sore throat reporting in symptomatic positive episodes and negative visits from April-2021. After May-2021 when Delta emerged there were substantial increases in headache and fever in positives, but not in negatives. Although specific symptom reporting in symptomatic positive episodes vs. negative visits varied by age, sex, and ethnicity, only small improvements in symptom-based infection detection were obtained; e.g. adding fatigue/weakness or all eight symptoms to the classic four symptoms (cough, fever, loss of taste/smell) increased sensitivity from 74% to 81% to 90% but tests per positive from 4.6 to 5.3 to 8.7.ConclusionsWhilst SARS-CoV-2-associated symptoms vary by variant, vaccination status and demographics, differences are modest and do not warrant large-scale changes to targeted testing approaches given resource implications.SummaryWithin the COVID-19 Infection Survey, recruiting representative households across the UK general population, SARS-CoV-2-associated symptoms varied by viral variant, vaccination status and demographics. However, differences are modest and do not currently warrant large-scale changes to targeted testing approaches.
Long-Term Effectiveness of a Digital Therapeutic Intervention for Smoking Cessation: A Randomized Controlled Trial
Authors: Webb Jamie , Peerbux Sarrah , Ang Alfonso , Siddiq Sarim , Sherwani Yusuf , Ahmed Maroof , MacRae Hannah , Puri Hannah , Majeed Azeem , Glasner Suzette 
Published: August 2021

AbstractIntroductionThe present study evaluated the long-term effectiveness of Quit Genius (QG), an extended digital smoking cessation intervention.MethodsParticipants were adult smokers (N=556) recruited between January and November of 2019 via social media and referrals from primary care practices who were given nicotine replacement therapy and randomly assigned to Quit Genius (QG) (n=277), a cognitive behavioral therapy (CBT) based digital intervention or Very Brief Advice (VBA) (n=279), a face-to-face control intervention. Primary analyses (N=530), by intention-to-treat, compared QG and VBA on biochemically verified continuous 7-day abstinence at 4, 26, and 52 weeks post-quit date. Secondary outcomes included sustained abstinence, quit attempts, self-efficacy and mental well-being.ResultsSeven-day point prevalence abstinence from weeks 4 through 52 ranged from 27% to nearly 45% among those who received QG, and from 13% to 29% for those in VBA. Continuous 7-day abstinence at 26 and 52 weeks occurred in 27.2% and 22.6% of QG participants, respectively, relative to 16.6% and 13.2% of VBA participants; QG participants were more likely to remain abstinent than those in VBA (Relative Risk [RR]= 1.71, 95% CI 1.17-2.50; p=0.005).ConclusionsThis study provides evidence for the long-term effectiveness of an extended digital therapeutic intervention.ImplicationsThe long-term effectiveness of digital smoking cessation interventions has not been well-studied. This study established the long-term effectiveness of an extended CBT-based intervention; results may inform implementation of scalable, cost-effective approaches to smoking cessation in the health system.
Cytotoxic T cells are silenced to induce disease tolerance in human malaria
Authors: Sandoval Diana Muñoz , Bach Florian A. , Ivens Alasdair , Harding Adam C. , Smith Natasha L. , Mazurczyk Michalina , Themistocleous Yrene , Edwards Nick J. , Silk Sarah E. , Barrett Jordan R. , Cowan Graeme J.M. , Napolitani Giorgio , Savill Nicholas J. , Draper Simon J. , Minassian Angela M. , Nahrendorf Wiebke , Spence Philip J. 
Published: August 2021

AbstractImmunity to severe malaria is acquired quickly, operates independently of pathogen load and represents a highly effective form of disease tolerance. The mechanism that underpins tolerance remains unknown. We developed a human re-challenge model of falciparum malaria in which healthy adult volunteers were infected three times over a 12 month period to track the development of disease tolerance in real-time. We found that parasitemia triggered a hardwired emergency host response that led to systemic inflammation, pyrexia and hallmark symptoms of clinical malaria across the first three infections of life. In contrast, a single infection was sufficient to reprogramme T cell activation and reduce the number and diversity of effector cells upon re-challenge. Crucially, this did not silence stem-like memory cells but instead prevented the generation of cytotoxic effectors associated with autoinflammatory disease. Tolerised hosts were thus able to prevent collateral tissue damage in the absence of anti-parasite immunity.
An ultra-low dose of Δ9-tetrahydrocannabinol improves Alzheimer’s Disease-related cognitive deficits
Authors: Nitzan K. , Ellenbogen L. , Beniamin T. , Sarne Y. , Doron R 
Published: August 2021

AbstractAlzheimer’s disease (AD) is the most common form of dementia. AD has a physical, emotional, and economic impact on the patients and their families and society at large. More than a decade since its discovery, there is still no available treatment. Δ9-tetrahydrocannabinol (THC) is emerging as a promising therapeutic agent. Using THC in conventional-high doses may have deleterious effects. Therefore, we propose to use an ultra-low dose of THC (ULD-THC). We previously published that a single injection of ULD-THC elevated Sirtuin-1 (Sirt-1) levels in the brain and ameliorated cognitive functioning in several models of brain injuries as well as in naturally aging mice. Our working hypothesis suggests that ULD-THC can prevent and even reverse AD pathology. In this preliminary study, we saw that a single injection of ULD-THC alleviated cognitive impairments of a mice model for AD, 5xFAD mice. Our work may establish the foundations for the development of a pharmaceutical preparation for the treatment of AD patients, thus, bringing the ULD-THC treatment closer to clinical application.
Self-assembly of pericentriolar material in interphase cells lacking centrioles
Authors: Chen Fangrui , Wu Jingchao , Iwanski Malina K. , Jurriens Daphne , Sandron Arianna , Pasolli Milena , Puma Gianmarco , Kromhout Jannes Z. , Yang Chao , Nijenhuis Wilco , Kapitein Lukas C. , Berger Florian , Akhmanova Anna 
Published: August 2021

AbstractThe major microtubule-organizing center (MTOC) in animal cells, the centrosome, comprises a pair of centrioles surrounded by pericentriolar material (PCM), which nucleates and anchors microtubules. Centrosome assembly depends on PCM binding to centrioles, PCM self-association and dynein­mediated PCM transport, but the self-assembly properties of PCM in interphase cells are poorly understood. Here, we used experiments and modeling to study centriole-independent features of interphase PCM assembly. We showed that when centrioles are lost due to PLK4 depletion or inhibition, dynein-based PCM transport and PCM self-clustering are sufficient to form a single compact MTOC, which generates a dense radial microtubule array. Interphase PCM self-assembly depends on γ-tubulin, pericentrin, CDK5RAP2 and ninein, but not NEDD1, CEP152 or CEP192. Formation of a compact acentriolar MTOC is inhibited by AKAP450-dependent PCM recruitment to the Golgi or by randomly organized CAMSAP2-stabilized microtubules, which keep PCM mobile and prevent its coalescence. Linking of CAMSAP2 to a minus-end-directed motor leads to the formation of an MTOC, but MTOC compaction requires cooperation with pericentrin-containing self-clustering PCM. Our data reveal that interphase PCM contains a set of components that can self-assemble into a compact structure and organize microtubules, but PCM self-organization is sensitive to motor-and microtubule-based rearrangement.
Environment symmetry drives a multidirectional code in rat retrosplenial cortex
Authors: Zhang Ningyu , Grieves Roddy M. , Jeffery Kate J. 
Published: August 2021

AbstractA class of neurons showing bidirectional tuning in a two-compartment environment was recently discovered in dysgranular retrosplenial cortex (dRSC). We investigated here whether these neurons possess a more general environmental symmetry-encoding property, potentially useful in representing complex spatial structure. We report that directional tuning of dRSC neurons reflected environment symmetry in onefold, twofold and fourfold-symmetric environments: this was the case not just globally, but also locally within each sub-compartment. Thus, these cells use environmental cues to organize multiple directional tuning curves, which perhaps sometimes combine via interaction with classic head direction cells. A consequence is that both local and global environmental symmetry are simultaneously encoded even within local sub-compartments, which may be important for cognitive mapping of the space beyond immediate perceptual reach.One Sentence SummaryRetrosplenial directionally tuned neurons encode global environment symmetry even in local sub-compartments.
FEDERATED MORPHOMETRY FEATURE SELECTION FOR HIPPOCAMPAL MORPHOMETRY ASSOCIATED BETA-AMYLOID AND TAU PATHOLOGY
Authors: Wu Jianfeng , Dong Qunxi , Zhang Jie , Su Yi , Wu Teresa , Caselli Richard J. , Reiman Eric M. , Ye Jieping , Lepore Natasha , Chen Kewei , Thompson Paul M. , Wang Yalin ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: August 2021

ABSTRACTAmyloid-β (Aβ) plaques and tau protein tangles in the brain are now widely recognized as the defining hallmarks of Alzheimer’s disease (AD), followed by structural atrophy detectable on brain magnetic resonance imaging (MRI) scans. One of the particular neurodegenerative regions is the hippocampus to which the influence of Aβ/tau on has been one of the research focuses in the AD pathophysiological progress. This work proposes a novel framework, Federated Morphometry Feature Selection (FMFS) model, to examine subtle aspects of hippocampal morphometry that are associated with Aβ/tau burden in the brain, measured using positron emission tomography (PET). FMFS is comprised of hippocampal surface-based feature calculation, patch-based feature selection, federated group LASSO regression, federated screening rule-based stability selection, and region of interest (ROI) identification. FMFS was tested on two ADNI cohorts to understand hippocampal alterations that relate to Aβ/tau depositions. Each cohort included pairs of MRI and PET for AD, mild cognitive impairment (MCI) and cognitively unimpaired (CU) subjects. Experimental results demonstrated that FMFS achieves an 89x speedup compared to other published state-of-the-art methods under five independent hypothetical institutions. In addition, the subiculum andcornu ammonis1 (CA1 subfield) were identified as hippocampal subregions where atrophy is strongly associated with abnormal Aβ/tau. As potential biomarkers for Aβ/tau pathology, the features from the identified ROIs had greater power for predicting cognitive assessment and for survival analysis than five other imaging biomarkers. All the results indicate that FMFS is an efficient and effective tool to reveal associations between Aβ/tau burden and hippocampal morphometry.
Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids
Authors: Cheng Lauren Y. , Dai Peng , Wu Lucia R. , Zhang David Yu 
Published: August 2021

AbstractDirect capture and sequencing revealed a new DNA population in biofluids, named ultra-short single-stranded DNA (ussDNA), which was neglected by conventional DNA extraction and sequencing approaches. Evaluation of the size distribution and abundance of ussDNA in biofluids manifested generality of its presence in human, animal, and plants. Red blood cells were found to contain abundant ussDNA with enriched functional elements, and thus possesses great potential as a novel DNA biomarker.
Monodopsis and Vischeria genomes elucidate the biology of eustigmatophyte algae
Authors: Yang Hsiao-Pei , Wenzel Marius , Hauser Duncan A. , Nelson Jessica M. , Xu Xia , Eliáš Marek , Li Fay-Wei 
Published: August 2021

AbstractMembers of eustigmatophyte algae, especially Nannochloropsis, have been tapped for biofuel production owing to their exceptionally high lipid content. While extensive genomic, transcriptomic, and synthetic biology toolkits have been made available for Nannochloropsis, very little is known about other eustigmatophytes. Here we present three near-chromosomal and gapless genome assemblies of Monodopsis (60 Mb) and Vischeria (106 Mb), which are the sister groups to Nannochloropsis. These genomes contain unusually high percentages of simple repeats, ranging from 12% to 21% of the total assembly size. Unlike Nannochloropsis, LINE repeats are abundant in Monodopsis and Vischeria and might constitute the centromeric regions. We found that both mevalonate and non-mevalonate pathways for terpenoid biosynthesis are present in Monodopsis and Vischeria, which is different from Nannochloropsis that has only the latter. Our analysis further revealed extensive spliced leader trans-splicing in Monodopsis and Vischeria at 36-61% of genes. Altogether, the high-quality genomes of Monodopsis and Vischeria not only serve as the much-needed outgroups to advance Nannochloropsis research, but also shed new light on the biology and evolution of eustigmatophyte algae.
Integrative Genome Modeling Platform reveals essentiality of rare contact events in 3D genome organizations
Authors: Boninsegna Lorenzo , Yildirim Asli , Polles Guido , Quinodoz Sofia A. , Finn Elizabeth , Guttman Mitchell , Zhou Xianghong Jasmine , Alber Frank 
Published: August 2021

AbstractA multitude of sequencing-based and microscopy technologies provide the means to unravel the relationship between the three-dimensional (3D) organization of genomes and key regulatory processes of genome function. However, it remains a major challenge to systematically integrate all available data sources to characterize the nuclear organization of genomes across different spatial scales. Here, we develop a multi-modal data integration approach to produce genome structures that are highly predictive for nuclear locations of genes and nuclear bodies, local chromatin compaction, and spatial segregation of functionally related chromatin.By performing a quantitative assessment of the predictive power of genome structures generated from different data combinations, we demonstrate that multimodal data integration can compensate for systematic errors and missing values in some of the data and thus, greatly increases accuracy and coverage of genome structure models. We also show that alternative combinations of different orthogonal data sources can converge to models with similar predictive power. Moreover, our study reveals the key contributions of low-frequency inter-chromosomal contacts (e.g., “rare” contact events) to accurately predicting the global nuclear architecture, including the positioning of genes and chromosomes. Overall, our results highlight the benefits of multi-modal data integration for genome structure analysis, available through the Integrative Genome structure Modeling (IGM) software package that we introduce here.