bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of multiple freeze-thaw cycles on detection of anti-SARS-CoV-2 IgG antibodies
Authors: Shurrab Farah M. , Al-Sadeq Duaa W. , Amanullah Fathima , Younes Salma N. , Al-Jighefee Hadeel , Younes Nadin , Dargham Soha R. , Yassine Hadi M. , Raddad Laith J. Abu , Nasrallah Gheyath K. 
Published: April 2021

AbstractSeveral studies have investigated the effect of repeated freeze-thaw (F/T) cycles on RNA detection for SARS-CoV-2. However, no data is available regarding the effect of repeated F/T cycles on SARS-CoV-2 antibody detection in serum. We investigated the effect of multiple F/T cycles on anti-SARS-CoV-2 IgG detection using an ELISA test targeting the nucleocapsid antibodies. Ten positive and one negative SARS-CoV-2 IgG sera from 11 participants, in replicates of five were subjected to a total of 16 F/T cycles and stored at 4°C until tested by ELISA. Statistical analysis was done to test for F/T cycle effect. Non-of the 10 positive sera turned into negative after 16 F/T cycles. There was no significant difference in the OD average reading between the first and last F/T cycles, except for one serum with a minimal decline in the OD. The random-effect linear regression of log (OD) on the number of cycles showed no significant trend with a slope consistent with zero (B=-0.0001; 95% CI −0.0008; 0.0006; p-value=0.781). These results suggest that multiple F/T cycles had no effect on the ability of the ELISA assay to detect the SARS-CoV-2 IgG antibodies.
Association of cerebral small vessel disease burden with brain structure and cognitive and vascular risk trajectories in mid-to-late life
Authors: Jansen Michelle G , Griffanti Ludovica , Mackay Clare E , Anatürk Melis , Melazzini Luca , de Lange Ann-Marie G , Filippini Nicola , Zsoldos Enikő , Wiegertjes Kim , de Leeuw Frank-Erik , Singh-Manoux Archana , Kivimäki Mika , Ebmeier Klaus P , Suri Sana 
Published: April 2021

AbstractWe characterize the associations of total cerebral small vessel disease (SVD) burden with brain structure, trajectories of vascular risk factors, and cognitive functions in mid-to-late life. Participants were 623 community-dwelling adults from the Whitehall II Imaging Sub-study with multi-modal MRI (mean age 69.96 SD=5.18, 79% men). We used linear mixed-effects models to investigate associations of SVD burden with up to 25-year retrospective trajectories of vascular risk and cognitive performance. General linear modelling was used to investigate concurrent associations with grey matter (GM) density and white matter (WM) microstructure, and whether these associations were modified by cognitive status (Montreal Cognitive Assessment, MoCA). Severe SVD burden in older age was associated with higher mean arterial pressure throughout midlife (β=3.36, 95% CI [0.42-6.30]), and faster 25-year cognitive decline in letter fluency (β=-0.07, 95% CI [-0.13–-0.01]), and verbal reasoning (β=-0.05, 95% CI [-0.11–-0.001]). Moreover, SVD burden was related to lower GM volumes in 9.7% of total GM, and widespread WM microstructural decline (FWE-corrected p<0.05). The latter association was most pronounced in individuals with cognitive impairments on MoCA (F3,608=2.14, p=0.007). These findings highlight the importance of managing midlife vascular health to preserve brain structure and cognitive function in old age.
Survival analysis methods for analysis of hospitalization data: Application to COVID-19 patient hospitalization experience
Authors: Rathouz Paul J. , Valencia Victoria , Chang Patrick , Morton David , Yang Haoxiang , Surer Ozge , Fox Spencer , Meyers Lauren Ancel , Matsui Elizabeth C. , Haynes Alex B. 
Published: April 2021

SummaryDuring most of 2020, the COVID-19 pandemic gave rise to considerable and growing numbers of hospitalizations across most of the U.S. Typical COVID-19 hospitalization data, including length of stay, intensive care unit (ICU) use, mechanical ventilation (Vent), and in-hospital mortality provide clearly interpretable health care endpoints that can be compared across population strata. They capture the resources consumed for the care of COVID-19 patients, and analysis of these endpoints can be used for resource planning at the local level. Yet, hospitalization data embody novel features that require careful statistical treatment to be useful in this context. Specifically, statistical models must meet three goals: (i) They should mesh with and inform mathematical epidemiologic or agent-based models of the COVID-19 experience in the population. (ii) They need to handle administrative censoring of hospitalization experience when data are extracted and downloaded for a given patient before that patient’s hospitalization experience has terminated. And, (iii) models need to handle risks for competing events, the occurrence of one blocking the possibility of the other(s). For example, live discharge from the hospital “competes with” (i.e., blocks) in-hospital mortality. We have adapted approaches from the survival analysis literature to address these challenges in order to better understand and quantify the population experience in hospital with respect to length of stay, ICU, Vent use and so on. Using hospitalization data from a large U.S. metropolitan region, in this report, we show how standard techniques from survival analysis can be brought to bear to address these challenges and yield interpretable results. In the breakout/discussion, we will discuss formulation, estimation and inference, and interpretation of competing risks models.
Eating Disorders Spectrum during COVID Pandemic: a systematic review
Authors: Miniati Mario , Marzetti Francesca , Palagini Laura , Marazziti Donatella , Orrù Graziella , Conversano Ciro , Gemignani Angelo 
Published: April 2021

AbstractBackgroundSeveral data suggest that COVID-19 pandemic might exacerbate or trigger Eating Disorders (EDs). The aim of this paper was to summarize present literature on COVID pandemic and EDs.MethodsLiterature search, study selection, methods, and quality evaluation were performed following PRISMA Guidelines.ResultsThe systematic search permitted the identification of 91 studies; 21 papers were eligible and included in the review. Nine papers (42.9%) evaluated the effect of pandemic and associated protective and risk factors in EDs patients, ten (47.6%) explored the prevalence of disturbed eating behaviours and risk factors for exacerbating EDs in the general population, and the remaining two (9.5%) were qualitative studies describing the impact of lockdown and quarantine on EDs patients.Their analysis revealed five main findings: 1) changes in physical activities routines were related to a worsening of preoccupation on weight/body shape; 2) food access limitation during pandemic represented a risk factors for both triggering and exacerbating EDs; 3) restriction in healthcare facilities contributed to increase anxiety levels and modifies treatment compliance; 4) social isolation was related to symptoms’ exacerbation in EDs patients who are home-confined with family members; 5) conflicts and difficulties in relationships with ‘no way out’ were maintenance factors for EDs symptoms, especially in adolescents and young adults.ConclusionCOVID-19 pandemic had a negative impact on EDs that might be triggered or worsened by the exceptional conditions deriving from COVID-19-related stress in predisposed subjects. Patients already affected by EDs experienced a worsening of their clinical conditions and related quality of life.
Increased Transmissibility of SARS-CoV-2 Lineage B.1.1.7 by Age and Viral Load: Evidence from Danish Households
Authors: Lyngse Frederik Plesner , Mølbak Kåre , Skov Robert Leo , Christiansen Lasse Engbo , Mortensen Laust Hvas , Albertsen Mads , Møller Camilla Holten , Krause Tyra Grove , Rasmussen Morten , Michaelsen Thomas Yssing , Voldstedlund Marianne , Fonager Jannik , Steenhard Nina ,   The Danish Covid-19 Genome Consortium, Kirkeby Carsten 
Published: April 2021

1AbstractAimThe aim of this study was to estimate the household transmissibility of SARS-CoV-2 for lineage B.1.1.7 compared with other lineages, by age and viral load. Further-more, we wanted to estimate whether there is a multiplicative or additive effect of the increased transmissibility of B.1.1.7 compared with other lineages.BackgroundNew lineages of SARS-CoV-2 are of potential concern due to higher transmissibility, risk of severe outcomes, and/or escape from neutralizing antibodies. Lineage B.1.1.7 has been estimated to be more transmissible than other previously known lineages, but the association between transmissibility and risk factors, such as age of primary case and viral load is still unknown.MethodsWe used comprehensive administrative data from Denmark, comprising the full population, all SARS-CoV-2 RT-PCR tests, and all WGS lineage data (January 11 to February 7, 2021), to estimate household transmissibility stratified by lineage B.1.1.7 and other lineages.ResultsWe included 5,241 households with primary cases; 808 were infected with SARS-CoV-2 lineage B.1.1.7 and 4,433 were infected with other lineages. The attack rate was 38% in households with a primary case infected with B.1.1.7 and 27% in households with a primary case infected with other lineages. Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5-1.7 times that of primary cases infected with other lineages. The increased transmissibility of B.1.1.7 was multiplicative across age and viral load.ConclusionsThe results found in this study add new knowledge that can be used to mitigate the further spread of SARS-CoV-2 lineage B.1.1.7, which is becoming increasingly widespread in numerous countries. Our results clarify that the transmissibility of B.1.1.7 should be included as a multiplicative effect in mathematical models used as a tool for decision makers. The results may have important public health implications, as household transmission may serve as a bridge between otherwise separate transmission domains, such as schools and physical workplaces, despite implemented non-pharmaceutical interventions.
Genetics and Epigenetics of Aldehyde Dehydrogenase (ALDH2) in Alcohol Related Liver Disease
Authors: Shankarappa Bhagyalakshmi , Mahadevan Jayant , Murthy Pratima , Purushottam Meera , Viswanath Biju , Jain Sanjeev , Devarbhavi Harshad , Mysore Ashok V. 
Published: April 2021

AbstractAlcohol dependence and cirrhosis are key outcomes of excessive alcohol use. We studied the interaction between genetics and epigenetics at the aldehyde dehydrogenase (ALDH2) locus to understand differences in vulnerability to cirrhosis. Individuals were selected according to ICD 10 criteria for Alcohol dependence with Cirrhosis (AUDC+ve, N=116) and Alcohol dependence but without Cirrhosis; (AUDC-ve, N=123) from the clinical services of Gastroenterology and Psychiatry at the St John’s Medical College Hospital (SJMCH). Fibroscan/sonographic evidence was used to rule out fibrosis for the AUDC-ve group. Genomic DNA from blood was used for genotyping at ALDH2 (rs2238151) locus. A subset of the samples was assessed for DNA methylation (AUDC+ve, N=50; AUDC-ve, N=50) at the LINE-1 and ALDH2 CpG loci by pyrosequencing on a PyroMark Q24.LINE1 DNA methylation did not differ between the groups. ALDH2 DNA methylation was significantly lower in AUDC+ve group compared to AUDC-ve group (P <0.001). Lower methylation in T-allele carriers compared to T-allele non-carriers of the ALDH2 locus (rs2238151) was observed in AUDC+ve subjects (P=0.009). Compromised methylation in blood DNA at candidate loci, in those with liver disease in the context of prolonged severe alcohol abuse, could be explored as a biomarker for current pathology, and further progression.
Prevalence and Transmission of SARS-CoV-2 in Childcare Facilities: A Longitudinal Study
Authors: Haag Luise , Blankenburg Judith , Unrath Manja , Grabietz Johanna , Kahre Elisabeth , Galow Lukas , Schneider Josephine , Dalpke Alexander H. , Lück Christian , Büttner Leo , Berner Reinhard , Armann Jakob P. 
Published: April 2021

AbstractObjectivesPrevious data indicate that children might play a less crucial role in SARS-CoV-2 transmission than initially assumed. We conducted a study to gain further knowledge on prevalence, transmission and spread of SARS-CoV-2 among preschool children, their parents and caretakers.MethodsChildren, their parents and care givers in 14 childcare facilities in Dresden, Saxony/ Germany were invited to participate in the KiTaCoviDD19-study between July 2020 and January 2021. Seroprevalence of SARS-CoV-2 antibodies was assessed up to 4 times during the study period in all participating adults and personal characteristics as well as epidemiological information of personal SARS-CoV-2 history were obtained. Stool viral shedding of SARS-CoV-2 was analyzed every 2-4 weeks in all participating children.ResultsIn total, 318 children, 299 parents and 233 childcare workers were enrolled. The percentage of seropositive adults and SARS-CoV-2 positive detected children rose considerably by January 2021. However, the rate of SARS-CoV-2 positive children was considerably lower than the rate of seropositive adults. Overall, we detected a maximum of three connected cases in children. About 50% of SARS-CoV-2 infections in children could not be connected to a secondary case within our study population.ConclusionThe study could not provide evidence for a relevant asymptomatic (“silent”) spread of SARS-CoV-2 in childcare facilities, neither in a low nor a high prevalence setting. This finding adds to the evidence that childcare and educational settings do not play a crucial role in driving the SARS-CoV-2 pandemic.Table of Contents SummaryThis longitudinal study among children, parents and childcare workers provides further insight on SARS-CoV-2 prevalence and transmission within childcare facilities.What’s Known on This SubjectBased on age distribution of SARS-CoV-2 infections and previous data of very limited spread of COVID-19 among primary and secondary schools there is reason to believe that children play a less crucial role in SARS-CoV-2 transmission than initially assumed.What This Study AddsPreviously published studies focus mainly on SARS-CoV-2 transmission in schools. This longitudinal study provides information on prevalence, transmission and spread of SARS-CoV-2 within childcare facilities during low- and high-prevalence settings.
Modeling drug combination effects via latent tensor reconstruction
Authors: Wang Tianduanyi , Szedmak Sandor , Wang Haishan , Aittokallio Tero , Pahikkala Tapio , Cichonska Anna , Rousu Juho 
Published: April 2021

AbstractMotivationCombination therapies have emerged as a powerful treatment modality to overcome drug resistance and improve treatment efficacy. However, the number of possible drug combinations increases very rapidly with the number of individual drugs in consideration which makes the comprehensive experimental screening infeasible in practice. Machine learning models offer time- and cost-efficient means to aid this process by prioritising the most effective drug combinations for further pre-clinical and clinical validation. However, the complexity of the underlying interaction patterns across multiple drug doses and in different cellular contexts poses challenges to the predictive modelling of drug combination effects.ResultsWe introducecomboLTR, highly time-efficient method for learning complex, nonlinear target functions for describing the responses of therapeutic agent combinations in various doses and cancer cell-contexts. The method is based on a polynomial regression via powerful latent tensor reconstruction. It uses a combination of recommender system-style features indexing the data tensor of response values in different contexts, and chemical and multi-omics features as inputs. We demonstrate thatcomboLTRoutperforms state-of-the-art methods in terms of predictive performance and running time, and produces highly accurate results even in the challenging and practical inference scenario where full dose-response matrices are predicted for completely new drug combinations with no available combination and monotherapy response measurements in any training cell line.Availability and implementationcomboLTRcode is available athttps://github.com/aalto-ics-kepaco/ComboLTRContacttianduanyi.wang@aalto.fi;juho.rousu@aalto.fi
An Artificial Intelligence and Telemedicine Based Screening Tool to Identify Glaucoma Suspects from Color Fundus Imaging
Authors: Bhuiyan Alauddin , Govindaiah Arun , Smith R Theodore 
Published: April 2021

AbstractBackgrounds & ObjectiveGlaucomatous vision loss may be preceded by an enlargement of the cup-to-disc ratio (CDR). We propose to develop and validate an artificial intelligence based CDR grading system that may aid in effective glaucoma-suspect screening.Design, Setting & Participants1546 disc-centered fundus images were selected including all 457 images from the Retinal Image Database for Optic Nerve Evaluation dataset, and images randomly selected from the Age-Related EyeDisease Study, and Singapore Malay Eye Study to develop the system. First, a proprietary semi-automated software was used by an expert grader to quantify vertical CDR. Then, using CDR below 0.5 (not suspect) and CDR above 0.5 (glaucoma-suspect), deep learning architectures were used to train and test a binary classifier system.MeasurementsThe binary classifier, with glaucoma-suspect as positive, is measured using sensitivity, specificity, accuracy, and AUC.ResultsThe system achieved an accuracy of 89.67% (sensitivity, 83.33%; specificity, 93.89%; AUC, 0.93). For external validation, the Retinal Fundus Image database for Glaucoma Analysis dataset, which has 638 gradable quality images, was used. Here the model achieved an accuracy of 83.54% (sensitivity, 80.11%; specificity, 84.96%; AUC, 0.85).ConclusionsHaving demonstrated an accurate and fully automated glaucoma-suspect screening system that can be deployed on telemedicine platforms, we plan prospective trials to determine the feasibility of the system in primary care settings.
Evidence for a general neural signature of face familiarity
Authors: Dalski Alexia , Kovács Gyula , Ambrus Géza Gergely 
Published: April 2021

AbstractWe explored the neural signatures of face familiarity using cross-participant and cross-experiment decoding of event-related potentials, evoked by unknown and experimentally familiarized faces from a set of experiments with different participants, stimuli, and familiarization-types. Participants were either familiarized perceptually, via media exposure, or by personal interaction. We observed significant cross-experiment familiarity decoding involving all three experiments, predominantly over posterior and central regions of the right hemisphere in the 270 – 630 ms time window. This shared face familiarity effect was most prominent between the Media and Personal, as well as between the Perceptual and Personal experiments. Cross-experiment decodability makes this signal a strong candidate for a general neural indicator of face familiarity, independent of familiarization methods and stimuli. Furthermore, the sustained pattern of temporal generalization suggests that it reflects a single automatic processing cascade that is maintained over time.HighlightsWe investigated if a general neural signature of face familiarity existA cross-experiment decoding analysis of EEG data was usedThe analysis involved perceptual, media and personal familiarization methodsWe found a preserved pattern of familiarity decoding across experiments between 270 and 630 ms post-stimulusThis signature is consistent with previous reports on face familiarity effects
Ubiquity of the SymbiontSerratia symbioticain the Aphid Natural Environment: Distribution, Diversity and Evolution at a Multitrophic Level
Authors: Pons Inès , Scieur Nora , Dhondt Linda , Renard Marie-Eve , Renoz François , Hance Thierry 
Published: April 2021

ABSTRACTBacterial symbioses are significant drivers of insect evolutionary ecology. However, despite recent findings that these associations can emerge from environmentally derived bacterial precursors, there is still little information on how these potential progenitors of insect symbionts circulates in the trophic systems. The aphid symbiontSerratia symbioticarepresents a valuable model for deciphering evolutionary scenarios of bacterial acquisition by insects, as its diversity includes intracellular host-dependent strains as well as gut-associated strains that have retained some ability to live independently of their hosts and circulate in plant phloem sap. These strains represent a potential reservoir for the emergence of new and more intimate symbioses. Here, we conducted a field study to examine the distribution and diversity ofS. symbioticafound in aphid populations, as well as in different compartments of their surrounding environment. A total of 250 aphid colonies, 203 associated insects, and 161 plant samples associated with aphid colonies were screened forS. symbiotica. Twenty percent of aphids were infected withS. symbiotica, and the symbiont includes a wide diversity of strains with varied tissue tropism corresponding to different lifestyle. We also showed that the prevalence ofS. symbioticais influenced by seasonal temperatures. For the first time, we found thatS. symbioticawas present in non aphid species and in host plants, and that the prevalence of the bacterium in these samples was higher when associated aphid colonies were infected. Furthermore, phylogenetic analyses suggest the existence of horizontal transfers between the different trophic levels examined. These results provide a completely new picture of the ubiquity of an insect symbiont in nature. They suggest that ecological interactions promote the dissemination of strains that are still free-living and poorly specialized, and for which plants are a proabable reservoir for the acquisition of new bacterial partners in insects.
Chemical phylogenetics of the staphylococcal quorum sensing landscape
Authors: Gless Bengt H. , Bejder Benjamin S. , Vitolo Ludovica , Marques Leonor , Andersen Paal S. , Bojer Martin S. , Ingmer Hanne , Olsen Christian A. 
Published: April 2021

AbstractStaphylococci utilize secreted autoinducing peptides (AIPs) to regulate group behaviour through a process called quorum sensing (QS). Here, we survey the QS interaction landscape within theStaphylococcusgenus by assembling a unique compound collection, comprising all the currently known AIPs. These ribosomally synthesized and posttranslationally modified peptides (RiPPs) were obtained by chemical synthesis and mapping of their ability to modulate QS was evaluated using reporter strains of common human and animal colonizing pathogens (S. aureus, S. epidermidis, S. lugdunensis). The resulting map of >200 native QS interactions provides a holistic view of nodes that contribute to the complex signalling network within theStaphylococcusgenus. This overview reveals surprising cross-species QS induction and identify the first pan-inhibitory AIP, which is then shown to attenuate MRSA induced skin infection in a mouse model. Our results expose a complex universe of possible staphylococcal interactions and provide further impetus for development of therapeutics based on QS modulators targeting antibiotic resistant pathogens.