bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical practices underlie COVID-19 patient respiratory microbiome composition and its interactions with the host
Authors: Lloréns-Rico Verónica , Gregory Ann C. , Van Weyenbergh Johan , Jansen Sander , Van Buyten Tina , Qian Junbin , Braz Marcos , Menezes Soraya Maria , Van Mol Pierre , Vanderbeke Lore , Dooms Christophe , Gunst Jan , Hermans Greet , Meersseman Philippe ,   CONTAGIOUS collaborators, Wauters Els , Neyts Johan , Lambrechts Diether , Wauters Joost , Raes Jeroen 
Published: December 2020

AbstractUnderstanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n=58) and lower (n=35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We found that time in the intensive care unit and the type of oxygen support, both of which are associated to additional treatments such as antibiotic usage, explained the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load had a reduced impact. Specifically, mechanical ventilation was linked to altered community structure, lower species- and higher strain-level diversity, and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomic analysis of the lower respiratory tract of mechanically ventilated COVID-19 patients identified specific oral bacteria, different to those observed in controls. These oral taxa were found physically associated with proinflammatory immune cells, which showed higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients.
Association between Use of Qingfei Paidu Tang and Mortality in Hospitalized Patients with COVID-19: A national retrospective registry study
Authors: Zhang Lihua , Zheng Xin , Bai Xueke , Wang Qing , Chen Bowang , Wang Haibo , Lu Jiapeng , Hu Shuang , Zhang Xiaoyan , Zhang Haibo , Liu Jiamin , Shi Ying , Zhou Zhiye , Gan Lanxia , Li Xi , Li Jing 
Published: December 2020

ABSTRACTBackgroundQingfei Paidu Tang (QPT), a formula of traditional Chinese medicine, which was suggested to be able to ease symptoms in patients with Coronavirus Disease 2019 (COVID-19), has been recommended by clinical guidelines and widely used to treat COVID-19 in China. However, whether it decreases mortality remains unknown.PurposeWe aimed to explore the association between QPT use and in-hospital mortality among patients hospitalized for COVID-19.Study designA retrospective study based on a real-world database was conducted.MethodsWe identified patients consecutively hospitalized with COVID-19 in 15 hospitals from a national retrospective registry in China, from January through May 2020. Data on patients’ characteristics, treatments, and outcomes were extracted from the electronic medical records. The association of QPT use with mortality was evaluated using Cox proportional hazards models based on propensity score analysis.ResultsOf the 8939 patients included, 28.7% received QPT. The crude mortality was 1.2% (95% confidence interval [CI] 0.8% to 1.7%) among the patients receiving QPT and 4.8% (95% CI 4.3% to 5.3%) among those not receiving QPT. After adjustment for patient characteristics and concomitant treatments, QPT use was associated with a relative reduction of 50% in in-hospital mortality (hazard ratio, 0.50; 95% CI, 0.37 to 0.66 P <0.001). This association was consistent across subgroups by sex and age. Meanwhile, the incidence of acute liver injury (8.9% [95% CI, 7.8% to 10.1%]vs. 9.9% [95% CI, 9.2% to 10.7%]; odds ratio, 0.96 [95% CI, 0.81% to 1.14%], P =0.658) and acute kidney injury (1.6% [95% CI, 1.2% to 2.2%] vs. 3.0% [95% CI, 2.6% to 3.5%]; odds ratio, 0.85 [95% CI, 0.62 to 1.17], P =0.318) was comparable between patients receiving QPT and those not receiving QPT. The major study limitations included that the study was an observational study based on real-world data rather than a randomized control trial, and the quality of data could be affected by the accuracy and completeness of medical records.ConclusionsQPT was associated with a substantially lower risk of in-hospital mortality, without extra risk of acute liver injury or acute kidney injury among patients hospitalized with COVID-19.
Motion prediction using electromyography and sonomyography for an individual with transhumeral limb loss
Authors: Engdahl Susannah , Dhawan Ananya , Lévay György , Bashatah Ahmed , Kaliki Rahul , Sikdar Siddhartha 
Published: December 2020

AbstractControlling multi-articulated prosthetic hands with surface electromyography can be challenging for users. Sonomyography, or ultrasound-based sensing of muscle deformation, avoids some of the problems of electromyography and enables classification of multiple motion patterns in individuals with upper limb loss. Because sonomyography has been previously studied only in individuals with transradial limb loss, the purpose of this study was to assess the feasibility of an individual with transhumeral limb loss using this modality for motion classification. A secondary aim was to compare motion classification performance between electromyography and sonomyography. A single individual with transhumeral limb loss created two datasets containing 11 motions each (individual flexion of each finger, thumb abduction, power grasp, key grasp, tripod, point, pinch, wrist pronation). Electromyography or sonomyography signals associated with every motion were acquired and cross-validation accuracy was computed for each dataset. While all motions were usually predicted successfully with both electromyography and sonomyography, the cross-validation accuracies were typically higher for sonomyography. Although this was an exploratory study, the results suggest that controlling an upper limb prosthesis using sonomyography may be feasible for individuals with transhumeral limb loss.
Association of MRI-measured cerebral ventricular volume with APOE ε4 genotype, cerebrospinal fluid biomarkers (Aβ42 and Tau) and neuropsychological measures in Alzheimer’s disease: A Systematic Review
Authors: Piersson Albert Dayor , Mohamad Mazlyfarina , Rajab Fadilah , Suppiah Subapriya 
Published: December 2020

AbstractRationale and ObjectivesAlthough neuroimaging studies suggest that the cerebral ventricle is independently associated with APOE ε4, cerebrospinal fluid (CSF) biomarkers, and neuropsychological scores in aging and Alzheimer’s disease (AD), there is no formal synthesis of these findings. We summarized the association of ventricular changes with APOE ε4, CSF biomarkers, and neuropsychological measures.Materials and MethodsThe Preferred Reporting Items for Systematic reviews and Meta-Analyses guideline was used. PubMed, Scopus, Ovid, Cochrane, and grey literature were searched, and assessment of eligible articles was conducted using the Newcastle-Ottawa Scale.Results24 studies met the inclusion criteria. Progressive ventricular volume is increased in AD patients at an average volume of 4.4 – 4.7 cm3/ year compared to average volumes of 2.7 – 2.9 cm3/ year and 1.1 – 1.4 cm3/year for patients with MCI and healthy controls (HCs) respectively. The ventricular volume is estimated to increase by 1.7 cm3/year for progression from MCI to AD. APOE ε4 is an independent risk factor for ventricular enlargement in aging and dementia, with AD patients most affected. The combination of CSF Aβ42 with ventricular volume compared to tau is more robust, for tracking the progression of the AD continuum. Further, the combination of ventricular volume with mini-mental state examination (MMSE) scores is the most robust for differentiating AD and MCI from HCs and tracking the progression of the disease.ConclusionThe combination of ventricular volume with APOE ε4, CSF Aβ42, and MMSE scores independently may be potentially useful biomarkers for differentiating and tracking the progression of AD.
The importance of continued non-pharmaceutical interventions during the upcoming SARS-COV-2 vaccination campaign
Authors: Galanti Marta , Pei Sen , Yamana Teresa K. , Angulo Frederick J. , Charos Apostolos , Swerdlow David L. , Shaman Jeffrey 
Published: December 2020

AbstractIn this communication we assess the potential benefit of SARS-COV-2 pandemic vaccination in the US and show how continued use of non-pharmaceutical interventions (NPIs) will be crucial during implementation.
Support and follow-up needs of patients discharged from Intensive Care after severe COVID-19: a mixed-methods study of the views of UK general practitioners and intensive care staff during the pandemic’s first wave
Authors: Castro-Avila Ana , Jefferson Laura , Dale Veronica , Bloor Karen 
Published: December 2020

AbstractBackgroundAfter discharge from an intensive care unit(ICU), over 50% of patients face significant physical, mental and cognitive problems. The COVID-19 pandemic has resulted in a large cohort of these patients who will need follow-up services that can address their support needs.ObjectivesTo identify follow-up services planned for COVID-19 patients discharged from ICU, and to explore the views of ICU staff and General Practitioners(GPs) regarding these patients’ future needs and care coordination.DesignSequential mixed-methods UK study. We explored usual follow-up practice after ICU discharge and changes in follow-up during the pandemic through a survey of ICU staff, and GP awareness of follow-up and support needs of patients discharged from ICU through a survey of GPs. Through these surveys, we identified participants for semi-structured interviews with both groups.ResultsWe obtained 170 survey responses and conducted 23 interviews. Over 60% of GPs were unaware of the follow-up services generally provided by their local hospitals, and whether or not these were functioning during the pandemic. Eighty percent of ICUs reported some form of follow-up services, with 25% of these suspending provision during the peak of the pandemic, and over half modifying their provision (usually to provide the service remotely). Complex funding streams, poor communication between primary and secondary care, and lack of clarity about who was responsible for referrals and follow-up were the most common problems identified. Discharge documentation was described as poor and lacking key information. Both groups mentioned difficulties accessing services in the community.ConclusionsThe pandemic has highlighted long-standing issues of continuity of care and complex funding streams for post-ICU follow-up care. The large cohort of ICU patients admitted due to COVID-19 highlights the need for improved follow-up services and communication between specialists and GPs, not only for COVID-19 patients, but for all those discharged from ICU.Article SummaryStrengths and limitations of this studyThis is the first study exploring NHS staff views of post-ICU follow-up services to support patients recovering from severe COVID-19.Responses to our survey had good geographic spread but were limited in number and relied on volunteers.GP interviews were small in number, but our findings align with those of larger studies conducted before the pandemic.
Pseudomonas putidagroup species serve as reservoirs of conjugative plasmids disseminating Tn402-like class 1 integrons carryingblaVIM-2metallo-β-lactamase genes
Authors: Brovedan Marco A. , Marchiaro Patricia M. , Díaz María S. , Faccone Diego , Corso Alejandra , Pasteran Fernando , Viale Alejandro M. , Limansky Adriana S. 
Published: December 2020

ABSTRACTThePseudomonas putidagroup (P. putidaG) is composed of at least 21 species associated to a wide range of environments, including the clinical setting. Here, we characterized 13 carbapenem-resistantP. putidaG clinical isolates carryingblaVIM-2from different hospitals of Argentina. Multilocus sequencing (MLSA) and phylogenetic analyses based on the 16S rDNA,gyrBandrpoDsequences comparison allowed us to assign them to 7 well-differentiated species. Sequencing analysis revealed thatblaVIM-2genes were carried in these isolates by three different class 1 integrons (In41, In899and In528) embedded into Tn402-like transposons. Those harboring In41and In899were designated Tn6335and Tn6336, respectively, with the former found among 10 isolates. Both encompassed complete transposition modules and inverted repeats boundaries characteristic of the Tn5053/Tn402family, whereas the third, bearing In528, exhibited a defectivetnimodule. Tn6335and Tn6336were located in conjugative pLD209-type plasmids inP. asiatica, P. juntendi, P. putidaG/II, andP. putidaG/V isolates, and could be mobilized toEscherichia coliandP. aeruginosaindicating a relevant mechanism ofblaVIM-2dissemination. In otherP. asiaticaandP. putidaG/II isolates, Tn6335was found inserted into the Tn21subgroup transposons-resregion, indicating capability for intragenomic mobilization and further dissemination associated to Tn3family transposons. The Tn402-like defective element was also found inserted into theresregion of another Tn3family transposon in aP. monteiliiisolate, but in an atypical orientation. Overall findings shed light on the mechanisms by which resistance genes move through environmental and opportunistPseudomonasspecies.
Single point mutations can potentially enhance infectivity of SARS-CoV-2 revealed by in silico affinity maturation and SPR assay
Authors: Xue Ting , Wu Weikun , Guo Ning , Wu Chengyong , Huang Jian , Lai Lipeng , Liu Hong , Li Yalun , Wang Tianyuan , Wang Yuxi 
Published: December 2020

AbstractThe RBD (receptor binding domain) of the SARS-CoV-2 virus S (spike) protein mediates the viral cell attachment and serves as a promising target for therapeutics development. Mutations on the S-RBD may alter its affinity to cell receptor and affect the potency of vaccines and antibodies. Here we used an in-silico approach to predict how mutations on RBD affect its binding affinity to hACE2 (human angiotensin-converting enzyme2). The effect of all single point mutations on the interface was predicted. SPR assay result shows that 6 out of 9 selected mutations can strengthen binding affinity. Our prediction has reasonable agreement with the previous deep mutational scan results and recently reported mutants. Our work demonstrated in silico method as a powerful tool to forecast more powerful virus mutants, which will significantly benefit for the development of broadly neutralizing vaccine and antibody.
TCR meta-clonotypes for biomarker discovery with tcrdist3: identification of public, HLA-restricted SARS-CoV-2 associated TCR features
Authors: Mayer-Blackwell Koshlan , Schattgen Stefan , Cohen-Lavi Liel , Crawford Jeremy Chase , Souquette Aisha , Gaevert Jessica A. , Hertz Tomer , Thomas Paul G. , Bradley Philip , Fiore-Gartland Andrew 
Published: December 2020

ABSTRACTAs the mechanistic basis of adaptive cellular antigen recognition, T cell receptors (TCRs) encode clinically valuable information that reflects prior antigen exposure and potential future response. However, despite advances in deep repertoire sequencing, enormous TCR diversity complicates the use of TCR clonotypes as clinical biomarkers. We propose a new framework that leverages antigen-enriched repertoires to form meta-clonotypes – groups of biochemically similar TCRs – that can be used to robustly identify and quantify functionally similar TCRs in bulk repertoires. We apply the framework to TCR data from COVID-19 patients, generating 1831 public TCR meta-clonotypes from the 17 SARS-CoV-2 antigen-enriched repertoires with the strongest evidence of HLA-restriction. Applied to independent cohorts, meta-clonotypes targeting these specific epitopes were more frequently detected in bulk repertoires compared to exact amino acid matches, and 59.7% (1093/1831) were more abundant among COVID-19 patients that expressed the putative restricting HLA allele (FDR < 0.01), demonstrating the potential utility of meta-clonotypes as antigen-specific features for biomarker development. To enable further applications, we developed an open-source software package, tcrdist3, that implements this framework and facilitates flexible workflows for distance-based TCR repertoire analysis.
Influence of HLA class II polymorphism on predicted cellular immunity against SARS-CoV-2 at the population and individual level
Authors: Copley Hannah C , Gragert Loren , Leach Andrew R , Kosmoliaptsis Vasilis 
Published: December 2020

AbstractDevelopment of effective adaptive immune responses after coronavirus disease 2019 (COVID-19) and after vaccination against SARS-CoV-2 is predicated on recognition of viral peptides, presented in the context of HLA class II molecules, by CD4+T-cells. We capitalised on extensive high resolution HLA data deposited in the National Marrow Donor Program registry to obtain detailed information on human HLA haplotype frequencies of twenty five human populations and used a bioinformatics approach to investigate the role of HLA polymorphism on SARS-CoV-2 immunogenicity at the population and at the individual level. Within populations, we identify wide inter-individual variability in predicted CD4+T-cell reactivity against structural, non-structural and accessory SARS-CoV-2 proteins, according to expressed HLA genotype. However, we find similar potential for anti-SARS-CoV-2 cellular immunity at the population level, across all ethnic groups examined, suggesting that HLA polymorphism is unlikely to account for observed disparities in clinical outcomes after COVID-19 among different race and ethnic groups. We predict robust immune reactivity against SARS-CoV-2 Spike protein, the basis for the majority of current vaccination efforts, both at the population and individual level, despite significant variation in Spike-derived peptide presentation by individual HLA genotypes. Finally, we provide comprehensive maps of SARS-CoV-2 proteome immunogenicity accounting for population coverage in major ethnic groups. Our findings provide important insight on the potential role of HLA polymorphism on development of protective immunity after SARS-CoV-2 infection and after vaccination and a firm basis for further experimental studies in this field.
The root of the transmissible cancer: first description of a widespreadMytilus trossulus-derived cancer lineage inM. trossulus
Authors: Skazina Maria , Odintsova Nelly , Maiorova Maria , Ivanova Angelina , Väinölä Risto , Strelkov Petr 
Published: December 2020

AbstractTwo lineages of bivalve transmissible neoplasia (BTN), BTN1 and BTN2, are known in blue musselsMytilus. Both lineages derive from the Pacific musselM. trossulusand are identified primarily by the unique genotypes of the nuclear gene EF1α. BTN1 is found in populations ofM. trossulusfrom the Northeast Pacific, while BTN2 has been detected in populations of otherMytilusspecies worldwide but not inM. trossulusitself. The aim of our study was to examine musselsM. trossulusfrom the Sea of Japan (Northwest Pacific) for the presence of BTN. Using hemocytology and flow cytometry of the hemolymph, we confirmed disseminated neoplasia in our specimens. Cancerous mussels possessed the unique BTN2 EF1α genotype and two mitochondrial haplotypes with different recombinant control regions, similar to that of common BTN2 lineages. This is the first report of BTN2 in its original host speciesM. trossuluspopulations in West Pacific may be the birthplace of BTN2 and a natural reservoir where it is maintained and whence it spreads worldwide. A comparison of all available BTN andM. trossulusCOI sequences suggests a common and recent, though presumably prehistoric origin of BTN2 diversity in populations ofM. trossulusoutside the Northeast Pacific.
Neural correlates of beauty retouching to enhance attractiveness of self-depictions in women
Authors: Ota Chisa , Nakano Tamami 
Published: December 2020

AbstractBeauty filters, while often employed for retouching photos to appear more attractive on social media, when used in excess cause images to give a distorted impression. The neural mechanisms underlying this change in facial attractiveness according to beauty retouching level remain unknown. The present study used functional magnetic resonance imaging in women as they viewed photos of their own face or unknown faces that had been retouched at three levels: no, mild, and extreme. The activity in the nucleus accumbens (NA) exhibited a positive correlation with facial attractiveness, whereas amygdala activity showed a negative correlation with attractiveness. Even though the participants rated others’ faces as more attractive than their own, the NA showed increased activity only for their mildly retouched own face and the amygdala exhibited greater activation in the others’ faces condition than the own face condition. Moreover, amygdala activity was greater for extremely retouched faces than for unretouched or mildly retouched faces for both conditions. Frontotemporal and cortical midline areas showed greater activation for one’s own than others’ faces, but such self-related activation was absent when extremely retouched. These results suggest that neural activity dynamically switches between the NA and amygdala according to perceived attractiveness of one’s face.