bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corynebacterium zhongnanshanii sp. nov. isolated from trachea of Marmota himalayana, Corynebacterium lujinxingii sp. nov. and Corynebacterium wankanglinii sp. nov. from human faeces
Authors: Zhang Gui , Yang Jing , Lai Xin-He , Jin Dong , Lu Shan , Ren Zhihong , Qin Tian , Pu Ji , Ge Yajun , Cheng Yanpeng , Yang Caixin , Lv Xianglian , Jiao Yifan , Huang Ying , Xu Jianguo 
Published: November 2021

Six novel facultatively anaerobic, Gram-stain-positive, rod-shaped, non-haemolytic bacteria (zg-320T/zg-336, zg-917T/zg-910 and zg-913T/zg-915) isolated from animal tissues and human faeces were found to belong to the genus

Corynebacterium

based on the phylogenetic analyses of 16S rRNA gene and 262 core genes set. Based on the greatest degree of 16S rRNA similarity, zg-320T/zg-336 had the highest 16S rRNA gene similarity to

Corynebacterium falsenii

DSM 44353T (97.51 %), zg-917T/zg-910 to

Corynebacterium coyleae

DSM 44184T (98.68 %), and zg-913T/zg-915 to

Corynebacterium afermentans

subsp.

lipophilum

CIP 103500T (98.79 %). The three novel type strains had a relatively high DNA G+C content (61.2–64.4 mol%), low DNA relatedness and ANI values with their respective neighbours: 23.5/72.7 %, 25.0/72.3%and 22.6/73.1 % (zg-320T vs.

Corynebacterium auriscanis

CIP 106629T,

Corynebacterium resistens

DSM 45100T and

Corynebacterium suicordis

DSM 45110T); 24.4/82.3% and 23.7/81.3 % (zg-917T vs.

C. coyleae

DSM 44184T and

Corynebacterium jeddahense

JCBT); 26.8/83.7% and 27.7/84.4 % (zg-913T vs.

Corynebacterium mucifaciens

ATCC 700355T and

C. afermentans

subsp.

lipophilum

CCUG 32105T). The three novel species had C16 : 0, C18 : 0, C18 : 1
ω9c and C18 : 0 ante/C18 : 2
ω6,9c as the major cellular fatty acids; MK-8(H2) in strain zg-917T and MK-9(H2) in strains zg-320T and zg-913T were found to be the major respiratory quinones. For the three novel species, the detected major polar lipids included diphosphatidylglycerol, phosphatidyl inositol mannoside, phosphatidylglycerol and phosphatidylinositol, the cell-wall peptidoglycan was based on meso-DAP, and the whole-cell sugars mainly included ribose, arabinose and galactose. The three novel species grew optimally at 35–37 °C, 0.5 % (w/v) NaCl and pH 7.0–8.0; notably, they were tolerant of 10.5 % (w/v) NaCl. Based on the results of these comprehensive analyses, three novel species in the genus

Corynebacterium

are proposed, aptly named Corynebacterium zhongnanshanii sp. nov. (zg-320T = GDMCC 1.1719T = JCM 34106T), Corynebacterium lujinxingii sp. nov. (zg-917T = GDMCC 1.1707T = JCM 34094T) and Corynebacterium wankanglinii sp. nov. (zg-913T = GDMCC 1.1706T = JCM 34398T).
Dyadobacter sandarakinus sp. nov., isolated from Arctic tundra soil, and emended descriptions of Dyadobacter alkalitolerans, Dyadobacter koreensis and Dyadobacter psychrophilus
Authors: Zhang Yongping , Peng Xiaoya , Qin Kun , Liu Jia , Xu Qiang , Niu Jingjing , Zheng Yanyan , Peng Fang 
Published: November 2021

Strain Q3-56T, isolated from Arctic tundra soil, was found to be a Gram-stain-negative, yellow-pigmented, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and aerobic bacterium. Strain Q3-56T grew optimally at pH 7.0 and 28 °C. The strain could tolerate up to 1 % (w/v) NaCl with optimum growth in the absence of NaCl. The strain was not sensitive to oxacillin and ceftazidime. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain Q3-56T belonged to the genus

Dyadobacter

. Strain Q3-56T showed the highest sequence similarities to

Dyadobacter luticola

T17T (96.58 %),

Dyadobacter ginsengisoli

Gsoil 043T (96.50 %),

Dyadobacter flavalbus

NS28T (96.43 %) and

Dyadobacter bucti

QTA69T (96.43 %). The predominant respiratory isoprenoid quinone was identified as MK-7, The polar lipid profile of strain Q3-56T was found to contain one phosphatidylethanolamine, three unidentified aminolipids, three unidentified lipids and one unidentified phospholipid. The G+C content of the genomic DNA was determined to be 49.1 mol%. The main fatty acids were summed feature 3 (comprising C16 : 1
ω7c/C16 : 1
ω6c), iso-C15 : 0, C16 : 1
ω5c and iso-C16 : 1 3-OH. On the basis of the evidence presented in this study, a novel species of the genus

Dyadobacter

, Dyadobacter sandarakinus sp. nov., is proposed, with the type strain Q3-56T (=CCTCC AB 2019271T=KCTC 72739T). Emended descriptions of

Dyadobacter alkalitolerans

,

Dyadobacter koreensis

and

Dyadobacter psychrophilus

are also provided.
Problems with comparative analyses of avian brain size
Authors: Hooper Rebecca , Brett Becky , Thornton Alex 
Published: November 2021

AbstractThere are multiple hypotheses for the evolution of cognition. The most prominent hypotheses are the Social Intelligence Hypothesis (SIH) and the Ecological Intelligence Hypothesis (EIH), which are often pitted against one another. These hypotheses tend to be tested using broad-scale comparative studies of brain size, where brain size is used as a proxy of cognitive ability, and various social and/or ecological variables are included as predictors. Here, we test how methodologically robust such analyses are. First, we investigate variation in brain and body size measurements across >1000 species of bird. We demonstrate that there is substantial variation in brain and body size estimates across datasets, indicating that conclusions drawn from comparative brain size models are likely to differ depending on the source of the data. Following this, we subset our data to the Corvides infraorder and interrogate how modelling decisions impact results. We show that model results change substantially depending on variable inclusion, source and classification. Indeed, we could have drawn multiple contradictory conclusions about the principal drivers of brain size evolution. These results reflect recent concerns that current methods in comparative brain size studies are not robust. We add our voices to a growing community of researchers suggesting that we move on from using such methods to investigate cognitive evolution. We suggest that a more fruitful way forward is to instead use direct measures of cognitive performance to interrogate why variation in cognition arises within species and between closely related taxa.
Potent neutralizing anti-SARS-CoV-2 human antibodies cure infection with SARS-CoV-2 variants in hamster model
Authors: Imbrechts Maya , Maes Wim , Ampofo Louanne , Van den Berghe Nathalie , Calcoen Bas , Van Looveren Dominique , Noppen Sam , Hollevoet Kevin , Vercruysse Thomas , Zhang Xin , Abdelnabi Rana , Foo Caroline , Jan Thibaut Hendrik , Jochmans Dirk , Ven Karen , Lammertyn Jeroen , Vanhoorelbeke Karen , Callewaert Nico , De Munter Paul , Schols Dominique , Neyts Johan , Declerck Paul , Geukens Nick 
Published: November 2021

AbstractTreatment with neutralizing monoclonal antibodies (mAbs) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contributes to COVID-19 management. Unfortunately, SARS-CoV-2 variants can escape several of these recently approved mAbs, highlighting the need for additional discovery and development. In a convalescent COVID-19 patient, we identified six mAbs, classified in four epitope groups, that potently neutralized SARS-CoV-2 Wuhan, alpha, beta, gamma and delta infection in vitro. In hamsters, mAbs 3E6 and 3B8 potently cured infection with SARS-CoV-2 Wuhan, beta and delta when administered post-viral infection at 5 mg/kg. Even at 0.2 mg/kg, 3B8 still reduced viral titers. Intramuscular delivery of DNA-encoded 3B8 resulted in in vivo mAb production of median serum levels up to 90 μg/ml, and protected hamsters against delta infection. Overall, our data mark 3B8 as a promising candidate against COVID-19, and highlight advances in both the identification and gene-based delivery of potent human mAbs.
Interactions of host defense and hyper-keratinization in psoriasis
Authors: Deng Jingwen , Leijten Emmerik , Nordkamp Michel Olde , Hartgring Sarita , Tao Weiyang , Pouw Juliette , Balak Deepak , Rijken Rianne , Huang Runyue , Radstake Timothy , Lu Chuanjian , Pandit Aridaman 
Published: November 2021

ObjectivesTo understand the crosstalk between the host and microbiota in psoriatic skin, using a systems biology approach based on transcriptomics and microbiome profiling.MethodsWe collected the skin tissue biopsies and swabs in both lesion and non-lesion skin of 13 patients with psoriasis (PsO), 15 patients with psoriatic arthritis (PsA), and healthy skin from 12 patients with ankylosing spondylitis (AS). We performed transcriptome sequencing and metagenomics profiling on the local skin sites to study the similarities and differences in the molecular profiles between the three conditions, and the associations between the host defense and microbiota dynamic.ResultsWe found that lesion and non-lesional samples were remarkably different in terms of their transcriptome profiles. Functional annotation of differentially expressed genes (DEGs) showed a major enrichment in neutrophil activation. By using coexpression gene networks, we identified a gene module that was associated with local psoriasis severity at the site of biopsy. From this module, we extracted a “core” set of genes that were functionally involved in neutrophil activation, epidermal cell differentiation and response to bacteria. Skin microbiome analysis revealed that the abundance of Enhydrobacter, Micrococcus and Leptotrichia were significantly correlated with the “core network” of genes.ConclusionsWe identified a core network that regulates inflammation and hyper-keratinization in psoriatic skin, and is associated with local disease severity and microbiome composition.
A large-scale systematic survey of SARS-CoV-2 antibodies reveals recurring molecular features
Authors: Wang Yiquan , Yuan Meng , Peng Jian , Wilson Ian A. , Wu Nicholas C. 
Published: November 2021

ABSTRACTIn the past two years, the global research in combating COVID-19 pandemic has led to isolation and characterization of numerous human antibodies to the SARS-CoV-2 spike. This enormous collection of antibodies provides an unprecedented opportunity to study the antibody response to a single antigen. From mining information derived from 88 research publications and 13 patents, we have assembled a dataset of ∼8,000 human antibodies to the SARS-CoV-2 spike from >200 donors. Analysis of antibody targeting of different domains of the spike protein reveals a number of common (public) responses to SARS-CoV-2, exemplified via recurring IGHV/IGK(L)V pairs, CDR H3 sequences, IGHD usage, and somatic hypermutation. We further present a proof-of-concept for prediction of antigen specificity using deep learning to differentiate sequences of antibodies to SARS-CoV-2 spike and to influenza hemagglutinin. Overall, this study not only provides an informative resource for antibody and vaccine research, but fundamentally advances our molecular understanding of public antibody responses to a viral pathogen.
Effectiveness of a third dose of BNT162b2 or mRNA-1273 vaccine for preventing post-vaccination COVID-19 infection: an observational study
Authors: Sharma Aditya , Oda Gina , Holodniy Mark 
Published: November 2021

BackgroundBNT162b2 and mRNA-1273 vaccines are highly protective against COVID-19. Concern about waning immunity and reduced effectiveness against SARS-COV-2 variants led to use of a third dose six months after completing the primary series. We used data from the Veterans Health Administration to evaluate the effectiveness of a third dose of BNT162b2 or mRNA-1273 compared to the primary series in preventing post-vaccination COVID-19.MethodsDuring January 1 - November 25, 2021, third dose recipients were matched (1:1) to demographically similar controls who did not receive a third dose. Eligible participants had completed the primary series at least six months (180 days) before recruitment date and had received at least one SARS-CoV-2 PCR test. Long-term care residents were excluded. Primary outcomes were documented SARS-CoV-2 infection and COVID-19 hospitalization. Effectiveness was estimated as 1-incidence rate ratio.FindingsFollowing matching, the BNT162b2 group included 74,032 pairs and the mRNA-1273 group included 55,098 pairs. In BNT162b2 and mRNA-1273 groups, median age was 72 (interquartile range [IQR]: 64-75) and 72 (IQR: 66-77) years, 69,426 (93.8%) and 52,241 (94.8%) were male, and 43,039 (58.1%) and 37,218 (67.5%) were non-Hispanic White, respectively. Effectiveness of a third dose of BNT162b2 or mRNA-1273 compared to the primary series was 45.7% (95% confidence interval [CI]: 37.9-52.5%) and 46.6% (95% CI: 36.4-55.3%) for documented SARS-CoV-2 infection and 44.8% (95% CI: 26.6-58.4%) and 50.0% (95% CI: 26.2-66.1%) for COVID-19 hospitalization, respectively.InterpretationA third dose of BNT162b2 or mRNA-1273 is moderately effective against post-vaccination COVID-19 infection compared to the primary series.FundingNone.
SARS-CoV-2 genomic monitoring in the São Paulo State unveils new sublineages of the AY.43 strain
Authors: Lima Alex Ranieri Jerônimo , Ribeiro Gabriela , Viala Vincent Louis , de Lima Loyze Paola Oliveira , Martins Antonio Jorge , Santos Barros Claudia Renata dos , Marqueze Elaine Cristina , de Souza Todao Bernardino Jardelina , Moretti Debora Botequio , Rodrigues Evandra Strazza , Santos Elaine Vieira , Brassaloti Ricardo Augusto , de Lello Rocha Campos Cassano Raquel , Mariani Pilar Drummond Sampaio Corrêa , Clemente Luan Gaspar , Assato Patricia Akemi , Silva da Costa Felipe Allan da , Poleti Mirele Daiana , Lesbon Jessika Cristina Chagas , Mattos Elisangela Chicaroni , Banho Cecilia Artico , Sacchetto Lívia , Moraes Marília Mazzi , Palmieri Melissa , da Silva Fabiana Erica Vilanova , Grotto Rejane Maria Tommasini , Souza-Neto Jayme A. , Giovanetti Marta , de Alcantara Luiz Carlos Junior , Nogueira Maurício Lacerda , Fukumasu Heidge , Coutinho Luiz Lehmann , Kashima Simone , Neto Raul Machado , Covas Dimas Tadeu , Slavov Svetoslav Nanev , Elias Maria Carolina , Sampaio Sandra Coccuzzo 
Published: November 2021

AbstractDelta VOC is highly diverse and more than 120 sublineages have been identified in Pango lineages with the continuous description of emerging ones. Brazil is now one of the most vaccinated countries against SARS-CoV-2 in the world which can enhance the emergence of viral mutations related to improved viral fitness. In this study, we identified two novel sublineages of the AY.43 lineage which were classified as AY.43.1 and AY.43.2 as observed on the specific clustering on the obtained phylogenetic tree. The novel sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2. The majority of the analyzed sequences of both lineages were Brazilian, which shows that probably these two emerging sublineages have Brazilian origin. It is still unknown how these two sublineages are disseminated in São Paulo State and Brazil and their potential impact on the ongoing vaccination process. However, the performed study reinforces the importance of the SARS-CoV-2 genome monitoring for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.
Population level impact of a pulse oximetry remote monitoring programme on mortality and healthcare utilisation in the people with covid-19 in England: a national analysis using a stepped wedge design
Authors: Beaney T , Clarke J , Alboksmaty A , Flott K , Fowler A , Benger JR , Aylin P , Elkin S , Neves AL , Darzi A 
Published: November 2021

AbstractObjectivesTo identify the population level impact of a national pulse oximetry remote monitoring programme for covid-19 (COVID Oximetry @home; CO@h) in England on mortality and health service use.DesignRetrospective cohort study using a stepped wedge pre- and post-implementation design.SettingAll Clinical Commissioning Groups (CCGs) in England implementing a local CO@h programme.Participants217,650 people with a positive covid-19 polymerase chain reaction test result and symptomatic, from 1st October 2020 to 3rd May 2021, aged ≥65 years or identified as clinically extremely vulnerable. Care home residents were excluded.InterventionsA pre-intervention period before implementation of the CO@h programme in each CCG was compared to a post-intervention period after implementation.Main outcome measuresFive outcome measures within 28 days of a positive covid-19 test: i) death from any cause; ii) any A&E attendance; iii) any emergency hospital admission; iv) critical care admission; and v) total length of hospital stay.ResultsImplementation of the programme was not associated with mortality or length of hospital stay. Implementation was associated with increased health service utilisation with a 12% increase in the odds of A&E attendance (95% CI: 6%-18%) and emergency hospital admission (95% CI: 5%-20%) and a 24% increase in the odds of critical care admission in those admitted (95% CI: 5%-47%). In a secondary analysis of CO@h sites with at least 10% or 20% of eligible people enrolled, there was no significant association with any outcome measure. However, uptake of the programme was low, with enrolment data received for only 5,527 (2.5%) of the eligible population.ConclusionsAt a population level, there was no association with mortality following implementation of the CO@h programme, and small increases in health service utilisation were observed. Low enrolment of eligible people may have diluted the effects of the programme at a population level.
SARS-CoV-2 Delta variant saliva viral load is 15-fold higher than wild-type strains
Authors: Imai Kenichi , Ikeno Ryo , Tanaka Hajime , Takada Norio 
Published: November 2021

ABSTRACTThe emergence of SARS-CoV-2 Delta variants has escalated COVID-19 cases globally due to their high transmissibility. Since saliva is crucial for SARS-CoV-2 transmission, we hypothesized that a higher viral load of Delta variants in saliva than their parental wild-type strains contributed to the high transmissibility in the first place. However, studies have not reported this particular comparison done with viral copy numbers. Twenty-two genetically confirmed -positive saliva samples for wild-type strain and 32 Delta variants were statistically compared for viral copy number per milliliter determined by real-time qPCR combined with synthesized viral RNA and Poisson’s null distribution equation between the groups of wild and variant strains and between whole saliva and centrifugal supernatant in each group. We found that the copy number of the Delta variants was 15.1 times higher than wild-type strains of the whole saliva. In addition, the viral load of both strains in the whole saliva was higher than the pertinent supernatant, indicating that most viruses in the whole saliva are associated with host cells. Meanwhile, more than a million virions per milliliter of the viral load of the variants in the supernatants were 4.0 times higher but not significant than wild-type strains. Humanity must share our findings; the simple but concrete note that Delta variant viral load is abundant in the saliva is critical for preventing the spread of infection.
Donor Age and Time in Culture Affect Dermal Fibroblast Contraction in a Hydrogel Skin Graft Model
Authors: Detwiler Amber , Polkoff Kathryn , Gaffney Lewis , Freytes Donald , Piedrahita Jorge 
Published: November 2021

ABSTRACTRegenerating functional skin without the formation of scar tissue remains an important goal for Tissue Engineering. Current hydrogel-based grafts minimize contraction of full-thickness skin wounds and support skin regeneration using adult or neonatal foreskin dermal fibroblasts, which are often expanded in vitro and used after multiple passages. Based on the known effects of 2D tissue culture expansion on cellular proliferation and gene expression, we hypothesized that differences in donor age and time in culture may also influence the functionality of 3D skin constructs by affecting fibroblast-mediated graft contraction. To validate these predicted differences in fibroblast phenotype and resulting 3D graft model contraction, we isolated porcine dermal fibroblasts of varying donor age for use in a 2D proliferation assay and a 3D cell-populated collagen matrix contractility assay. In 2D cell culture, doubling time remained relatively consistent between all age groups from passage 1 to 6. In the contractility assays, fetal and neonatal groups contracted faster and generated more contractile force than the adult group at passage 1. However, after 5 passages in culture, there was no difference in contractility between groups. These results show how cellular responses differ based on donor age and time in culture, which could account for important differences in biomanufacturing of 3D hydrogel-based skin grafts. Future research and therapies using bioengineered skin grafts should consider how results may vary based on donor age and time in culture before seeding.IMPACT STATEMENTLittle is known about the impact of donor age and time in culture on the contraction of the 3D hydrogel-based graft. These results show how cellular phenotypes differ based on donor age and time in culture, which could account for important inconsistencies in biomanufacturing of skin grafts and in vitro models. These findings are relevant to research and therapies using bioengineered skin graft models and the results can be used to increase reproducibility and consistency during the production of bioengineered skin constructs. Future in vivo studies could help determine the best donor age and time in culture for improved wound healing outcomes or more reproducible in vitro testing constructs.
Asymmetrical dose-responses shape the evolutionary trade-off between antifungal resistance and nutrient use
Authors: Després Philippe C , Cisneros Angel F , Alexander Emilie MM , Sonigara Ria , Gagné-Thivierge Cynthia , Dubé Alexandre K , Landry Christian R 
Published: November 2021

AbstractAntimicrobial resistance is an emerging threat for public health. The success of resistance mutations depends on the trade-off between the benefits and costs they incur. This trade-off is largely unknown and uncharacterized for antifungals. Here, we systematically measure the effect of all amino acid substitutions in the yeast cytosine deaminase Fcy1, the target of the antifungal 5-FC (flucytosine). We identify over 900 missense mutations granting resistance to 5-FC, a large fraction of which appear to act through destabilisation of the protein. The relationship between 5-FC resistance and growth sustained by cytosine deamination is characterized by a sharp trade-off, such that small gains in resistance universally lead to large losses in canonical enzyme function. We show that this steep relationship can be explained by differences in the dose-response functions of 5-FC and cytosine. Finally, we observe the same trade-off shape for the ortholog ofFCY1inCryptoccocus neoformans, a human pathogen. Our results provide a powerful resource and platform for interpreting drug target variants in fungal pathogens as well as unprecedented insights into resistance-function trade-offs.