bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sneathiella aquimaris sp. nov., isolated from aquaculture seawater
Authors: Li Guizhen , Lai Qiliang , Yan Peisheng , Gu Li , Shao Zongze 
Published: May 2020

A novel marine bacterium, designated strain 216LB-ZA1-12T, was isolated from a Penaeus vannamei aquaculture seawater sample. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 216LB-ZA1-12T belonged to the genus

Sneathiella

, with the highest sequence similarity to

Sneathiella glossodoripedis

MKT133T (97.7 %), followed by

Sneathiella limimaris

GH1-24T (97.0 %),

Sneathiella chungangensis

CAU 1294T (96.6 %) and

Sneathiella chinensis

LMG 23452T (96.1 %). The average nucleotide identity and the DNA–DNA hybridization estimate values between strain 216LB-ZA1-12T and four close type strains were between 69.2–71.3% and 16.7–17.8 %, respectively. The bacterium was Gram-stain-negative, facultatively anaerobic, oxidase and catalase positive, oval- to rod-shaped, and motile. Growth was observed at pH 7–9, salinities of 1–15% and temperatures of 4–42 °C. The G+C content of the chromosomal DNA was 48.50 mol%. The major respiratory quinone was determined to be Q-10. The principal fatty acids were summed feature 8 (C18 : 1
ω7c/ω6c) and C16 : 0. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and aminophospholipid. The combined genotypic and phenotypic data show that strain 216LB-ZA1-12T represents a novel species within the genus

Sneathiella

, for which the name Sneathiella aquimaris sp. nov. is proposed, with the type strain 216LB-ZA1-12T (=MCCC 1A14570T=KCTC 72144T).
The antidepressant sertraline provides a novel host directed therapy module for augmenting TB therapy
Authors: Shankaran Deepthi , Singh Anjali , Dawa Stanzin , Prabhakar A , Gandotra Sheetal , Rao Vivek 
Published: May 2020

ABSTRACTA prolonged therapy, primarily responsible for development of drug resistance byMycobacterium tuberculosis(Mtb), obligates any new TB regimen to not only reduce treatment duration but also escape pathogen resistance mechanisms. With the aim of harnessing the host response in providing support to existing regimens, we used sertraline (SRT) to stunt the pro-pathogenic type I IFN response of macrophages to infection. While SRT alone could only arrest bacterial growth, it effectively escalated the bactericidal activities of Isoniazid (H) and Rifampicin (R) in macrophages. This strengthening of antibiotic potencies by SRT was more evident in conditions of ineffective control by these frontline TB drug, against tolerant strains or dormant Mtb. SRT, could significantly combine with standard TB drugs to enhance early pathogen clearance from tissues of mice infected with either drug sensitive/ tolerant strains of Mtb. Further, we demonstrate an enhanced protection in acute TB infection of the highly susceptible C3HeB/FeJ mice with the combination therapy signifying the use of SRT as a potent adjunct to standard TB therapeutic regimens against bacterial populations of diverse physiology. This study advocates a novel host directed adjunct therapy regimen for TB with a clinically approved anti-depressant to achieve quicker and greater control of infection.
Sponges as bioindicators for microparticulate pollutants
Authors: Girard Elsa B. , Fuchs Adrian , Kaliwoda Melanie , Lasut Markus , Ploetz Evelyn , Schmahl Wolfgang W. , Wörheide Gert 
Published: May 2020

ABSTRACTAmongst other threats, the world’s oceans are faced with man-made pollution, including an increasing number of microparticulate pollutants. Sponges, aquatic filter-feeding animals, are able to incorporate fine foreign particles, and thus may be a potential bioindicator for microparticulate pollutants. To address this question, 15 coral reef demosponges sampled around Bangka Island (North Sulawesi, Indonesia) were analyzed for the nature of their foreign particle content using traditional histological methods, advanced light microscopy, and Raman spectroscopy. Sampled sponges accumulated and embedded the very fine sediment fraction (< 200 µm), absent in the surrounding sand, in the ectosome (outer epithelia) and spongin fibers (skeletal elements), which was confirmed by two-photon microscopy. A total of 34 different particle types were identified, of which degraded man-made products, i.e., polystyrene, cotton, titanium dioxide and blue-pigmented particles, were incorporated by eight specimens at concentrations between 91 to 612 particle/g dry sponge tissue. As sponges can weigh several hundreds of grams, we conservatively extrapolate that sponges can incorporate on average 10,000 microparticulate pollutants in their tissue. The uptake of particles, however, appears independent of the material, which suggests that the fluctuation in material ratios is due to the spatial variation of surrounding microparticles. Therefore, sponges have a strong potential to biomonitor microparticulate pollutants, such as microplastics and other degraded industrial products.
“Select and retrieve via direct upsampling” network (SARDU-Net): a data-driven, model-free, deep learning approach for quantitative MRI protocol design
Authors: Grussu Francesco , Blumberg Stefano B. , Battiston Marco , Kakkar Lebina S. , Lin Hongxiang , Ianuş Andrada , Schneider Torben , Singh Saurabh , Bourne Roger , Punwani Shonit , Atkinson David , Gandini Wheeler-Kingshott Claudia A. M. , Panagiotaki Eleftheria , Mertzanidou Thomy , Alexander Daniel C. 
Published: May 2020

AbstractPurposeWe introduce“Select and retrieve via direct upsampling”network (SARDU-Net), a data-driven framework for model-free quantitative MRI (qMRI) protocol design, and demonstrate it onin vivobrain and prostate diffusion-relaxation imaging (DRI).MethodsSARDU-Net selects subsets of informative measurements within lengthy pilot scans, without the requirement to identify tissue parameters for which to optimise for. The algorithm consists of aselector, identifying measurement subsets, and apredictor, estimating fully-sampled signals from the subsets. We implement both using deep neural networks, which are trained jointly end-to-end. We demonstrate the algorithm on brain (32 diffusion-/T1-weightings) and prostate (16 diffusion-/T2-weightings) DRI scans acquired on 3 healthy volunteers on two separate 3T Philips systems each. We used SARDU-Net to identify sub-protocols of fixed size, assessing the reproducibility of the procedure and testing sub-protocols for their potential to inform multi-contrast analyses viaT1-weighted spherical mean diffusion tensor(T1-SMDT, brain) andhybrid multi-dimensionalMRI (HM-MRI, prostate) modelling.ResultsIn both brain and prostate, SARDU-Net identifies sub-protocols that maximise information content in a reproducible manner across training instantiations. The sub-protocols enable multi-contrast modelling for which they were not optimised explicitly, providing robust T1-SMDT and HM-MRI maps and goodness-of-fit in the top 5% against extensive sub-protocol comparisons.ConclusionsSARDU-Net gives new opportunities to identify economical but informative qMRI protocols from a subset of the pilot scans that can be used for acquisition-time-sensitive applications. The simple architecture makes the algorithm easy to train when exhaustive searches are intractable, and applicable to a variety of anatomical contexts.
NF45/NF90-mediated rDNA transcription provides a novel target for immunosuppressant development
Authors: Tsai Hsiang-i , Zeng Xiaobin , Liu Longshan , Xin Shengchang , Wu Yingyi , Xu Zhanxue , Zhang Huanxi , Liu Gan , Bi Zirong , Su Dandan , Yang Min , Tao Yijing , Wang Changxi , Zhao Jing , Eriksson John E. , Deng Wenbin , Cheng Fang , Chen Hongbo 
Published: May 2020

AbstractHerein, we demonstrate that NFAT, a key regulator of the immune response, translocates from cytoplasm to nucleolus and interacts with NF45/NF90 complex to collaboratively promote rDNA transcription via triggering the directly binding of NF45/NF90 to the ARRE2-like sequences in rDNA promoter upon T cell activationin vitro. The elevated pre-rRNA level of T cells is also observed in both mouse heart or skin transplantation models, and in kidney transplanted patients. Importantly, T cell activation can be significantly suppressed by inhibiting NF45/NF90-dependent rDNA transcription. Amazingly, CX5461, a rDNA transcription specific inhibitor, outperformed FK506, the most commonly used immunosuppressant, both in terms of potency and off-target activity (i.e. toxicity), as demonstrated by a series of skin and heart allograft models. Collectively, this reveals NF45/NF90-mediated rDNA transcription as a novel signaling pathway essential for T cell activation and as a new target for the development of safe and effective immunosuppressants.
Immune Response Drives Outcomes in Prostate Cancer: Implications for Immunotherapy
Authors: Meng Jialin , Zhou Yujie , Lu Xiaofan , Bian Zichen , Chen Yiding , Fan Song , Zhou Jun , Zhang Li , Hao Zongyao , Zhang Meng , Liang Chaozhao 
Published: May 2020

AbstractBackgroundThe heterogeneity of the immune microenvironment leads to the different response results of immune checkpoint blockade therapy. We aimed to propose a robust molecular classification of prostate cancer microenvironment to identify ideal patients for delivering effective immunotherapy.MethodsA total of 1,557 prostate cancer patients were enrolled in the current study, including 69 real-world samples from the AHMU-PC cohort. Non-negative matrix factorization algorithm was employed to virtually microdissect the patients to immune and non-immune subclasses. The patients in the immune class were dichotomized to immune activated and suppressed subtypes by the nearest template prediction of activated stroma signature. The curative effects of different immune subclasses in response to immunotherapy were also predicted.ResultsWe termed the newly identified molecular class of tumors as “immune class”, which was characterized by a high enrichment of T cell, B cell, NK cell, macrophage associated signatures,etc., compared with the non-immune class (all,P< 0.05). Subsequently, the immune class was subclassified into immune activated and suppressed subtypes determined by the activation status of WNT/TGF-β, TGF-β1, and C-ECM signatures. As a result, around 14.9% to 24.3% of overall patients belonged to the immune activated subgroup, and they were proved with the favorable recurrence-free survival outcomes than others and showed potential curative effects in response to the anti-PD-1/PD-L1 immunotherapy.ConclusionOur study identifies a novel immune class in prostate cancer, which is further described by active or exhausted immune responses. These findings provide novel insights into tailoring immunotherapeutic strategies for different prostate cancer subgroups.Highlights▪Immunotherapy could trigger a durable response in advanced prostate cancer, but it only benefits a minority of patients;▪Immune response drives recurrence-free survival outcomes in prostate cancer;▪The robust molecular classification system helps identify more ideal patients for delivering anti-PD-1/PD-L1 immunotherapy.
A Reference Genome from the symbiotic hydrozoan,Hydra viridissima
Authors: Hamada Mayuko , Satoh Noriyuki , Khalturin Konstantin 
Published: May 2020

ABSTRACTCnidarians are one of the oldest eumetazoan taxa, and are thought to be a sister group to all bilaterians. In spite of comparatively simple morphology, cnidarians exhibit diverse body forms and life histories. In addition, many cnidarian species establish symbiotic relationships with microalgae. VariousHydraspecies have been employed as model organisms since the 18th century. Introduction of transgenic and knock-down technologies made them ideal experimental systems for studying cellular and molecular mechanisms involved in regeneration, body-axis formation, senescence, symbiosis, and holobiosis. In order to provide an important reference for genetic studies, theHydra magnipapillatagenome was sequenced. However, the initial published version of theH. magnipapillatagenome did not achieve assembly continuity comparable to those of other model systems, due mainly to a large number of transposable elements. For almost a decade, the highly fragmented genome assembly ofH. magnipapillata(scaffold N50=128Kb) has remained the only genomic resource for this genus with several dozen species. Here we report a draft 280-Mbp genome assembly forHydra viridissimastrain A99, a symbiotic, early diverging member of theHydraclade, with a scaffold N50 of 1.1 Mbp. TheH. viridissimagenome contains an estimated 21,476 protein-coding genes. Comparative analysis of Pfam domains and orthologous proteins highlights characteristic features ofH. viridissima, such as diversification of innate immunity genes that are important for host-symbiont interactions. Thus, theHydra viridissimaassembly provides an important hydrozoan genome reference that will facilitate symbiosis research and better comparisons of metazoan genome architectures.
Belief in Conspiracy Theory about COVID-19 Predicts Mental Health and Well-being: A Study of Healthcare Staff in Ecuador
Authors: Chen Xi , Zhang Stephen X. , Jahanshahi Asghar Afshar , Alvarez-Risco Aldo , Dai Huiyang , Li Jizhen , Ibarra Verónica García 
Published: May 2020

AbstractBackgroundSocial media are becoming hotbeds of conspiracy theories, which aim to give resolute explanations on the cause of COVID-19 pandemic. Yet, no research has investigated whether individuals’ belief in conspiracy theory about COVID-19 is associated with mental health and well-being issues. This association enables an assessable channel to identify and reach people with mental health and well-being issues during the pandemic.ObjectiveWe aim to provide the first evidence of belief in conspiracy theory regarding the COVID-19 virus as a predictor of the mental health and well-being of healthcare workers.MethodsWe conducted a survey of 252 healthcare workers in Ecuador from April 10 to May 2, 2020. We analyzed the data of distress and anxiety caseness with logistic regression and life and job satisfaction with linear regression.ResultsAmong the sampled healthcare workers in Ecuador, 24.2% believed that the virus was developed intentionally in a lab; 32.54% experienced distress disorder, and 28.17% had anxiety disorder. Compared to healthcare workers who were not sure where the virus originated, those who believed the virus was developed intentionally in a lab were more likely to have distress disorder and anxiety disorder and had lower levels of job satisfaction and life satisfaction.ConclusionsThis paper identifies belief in a COVID-19 conspiracy theory as an important predictor of distress, anxiety, and job and life satisfaction of healthcare workers. It enables mental health services to better target and help mentally vulnerable healthcare workers during the ongoing COVID-19 pandemic.
Modelling the thermal inactivation of viruses from the Coronaviridae family in suspensions or on surfaces with various relative humidities
Authors: Guillier Laurent , Martin-Latil Sandra , Chaix Estelle , Thébault Anne , Pavio Nicole , Poder Sophie Le , Batéjat Christophe , Biot Fabrice , Koch Lionel , Schaffner Don , Sanaa Moez 
Published: May 2020

AbstractTemperature and relative humidity are major factors determining virus inactivation in the environment. This article reviews inactivation data of coronaviruses on surfaces and in liquids from published studies and develops secondary models to predict coronaviruses inactivation as a function of temperature and relative humidity. A total of 102 D-values (time to obtain a log10 reduction of virus infectivity), including values for SARS-CoV-2, were collected from 26 published studies. The values obtained from the different coronaviruses and studies were found to be generally consistent. Five different models were fitted to the global dataset of D-values. The most appropriate model considered temperature and relative humidity. A spreadsheet predicting the inactivation of coronaviruses and the associated uncertainty is presented and can be used to predict virus inactivation for untested temperatures, time points or new coronavirus strains.ImportanceThe prediction of the persistence of SARS-CoV-2 on fomites is essential to investigate the importance of contact transmission. This study collects available information on inactivation kinetics of coronaviruses in both solid and liquid fomites and creates a mathematical model for the impact of temperature and relative humidity on virus persistence. The predictions of the model can support more robust decision-making and could be useful in various public health contexts. Having a calculator for the natural clearance of SARS-CoV-2 depending on temperature and relative humidity could be a valuable operational tool for public authorities.
Analysis of Rapidly Emerging Variants in Structured Regions of the SARS-CoV-2 Genome
Authors: Ryder Sean P. , Morgan Brittany R. , Massi Francesca 
Published: May 2020

AbstractThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has motivated a widespread effort to understand its epidemiology and pathogenic mechanisms. Modern high-throughput sequencing technology has led to the deposition of vast numbers of SARS-CoV-2 genome sequences in curated repositories, which have been useful in mapping the spread of the virus around the globe. They also provide a unique opportunity to observe virus evolution in real time. Here, we evaluate two cohorts of SARS-CoV-2 genomic sequences to identify rapidly emerging variants within structured cis-regulatory elements of the SARS-CoV-2 genome. Overall, twenty variants are present at a minor allele frequency of at least 0.5%. Several enhance the stability of Stem Loop 1 in the 5’UTR, including a set of co-occurring variants that extend its length. One appears to modulate the stability of the frameshifting pseudoknot between ORF1a and ORF1b, and another perturbs a bi-stable molecular switch in the 3’UTR. Finally, five variants destabilize structured elements within the 3’UTR hypervariable region, including the S2M stem loop, raising questions as to the functional relevance of these structures in viral replication. Two of the most abundant variants appear to be caused by RNA editing, suggesting host-viral defense contributes to SARS-CoV-2 genome heterogeneity. This analysis has implications for the development of therapeutics that target viral cis-regulatory RNA structures or sequences, as rapidly emerging variations in these regions could lead to drug resistance.
Evidence for anti-viral effects of complete Freund’s adjuvant in the mouse model of enterovirus infection
Authors: Gangaplara Arunakumar , Massilamany Chandirasegaran , Lasrado Ninaad , Steffen David , Reddy Jay 
Published: May 2020

AbstractGroup B Coxsackieviruses belonging to the genus, Enterovirus, contain six serotypes that induce various diseases, whose occurrence may involve the mediation of more than one serotype. We recently identified immunogenic epitopes within CVB3 viral protein 1 that induce anti-viral T cell responses in mouse models of CVB infections. In our investigations to determine the protective responses of the viral epitopes, we unexpectedly noted that animals immunized with complete Freund’s adjuvant (CFA) alone and later challenged with CVB3 were completely protected against myocarditis. Similarly, the pancreatitis-inducing ability of CVB3 was remarkably reduced to only 10% in the CFA group as opposed to 73.3% in the control group that received no CFA. Additionally, no mortalities were noted in the CFA group, whereas 40% of control animals died during the course of 21 days post-infection with CVB3. Taken together, our data suggest that the adjuvant effects of CFA may be sufficient for protection against CVB infections. These observations may provide new insights into our understanding of the occurrence of viral infections. One example is Coronavirus disease-19 (COVID-19) as individuals suffering from COVID-19 who have been vaccinated with Bacillus Calmette–Guérin appear to have fewer morbidities and mortalities than unvaccinated individuals.
“The expediency of local modelling to aid national responses to SARS-CoV-2.”
Authors: Groen Bernard M. , Turner Paul , Lacey Peter 
Published: May 2020

AbstractBackgroundWith the SARS-CoV-2 pandemic gripping most of the globe, healthcare and economic recovery strategies are being explored currently as a matter of urgency. The underpinning rationale of this paper is that we believe that health and care services are provided locally, therefore, local implications of national policy need to be reflected when informing national responses to the SARS-CoV-2 pandemic.MethodsWe adopted the assumptions underlying the United Kingdom government’s national epidemiological model which influences the national policy response to the SARS-CoV-2 pandemic. We used these in a local context and show projections in terms of presentations of symptomatic patients differ in a variety of settings. Setting:North of England, United Kingdom, population modelled at four local constituent levels which aggregated gives a total population of 3.2m.ResultsWe clearly demonstrate that there is significant difference in the way the national modelling outputs are replicated at local levels. Specifically, in terms of projected increased levels of demand for services on the local health and care systems.ConclusionsWe present significant evidence of differing timelines specifically in terms of subsequent projected peak demands. Additionally, it clearly indicates varying levels of such demand throughout the four modelled localities. These idiosyncrasies are ‘masked’ by both regional and national approaches to modelling. We urge readers to ensure that any national policy is appropriately adopted through the use of complementary bottom up approach, to suit local health and care systems. Finally, we share our methodology to ensure other professionals could replicate this study elsewhere.
A Gynecology-Led Transgender Clinic: Retrospective Review of Referral Patterns and Quality Indicators
Authors: McCall Jennifer , She Jennifer , Pudwell Jessica , Kielly Maria , Waddington Ashley 
Published: May 2020

AbstractBackgroundThe Transgender Clinic at the Kingston Health Sciences Centre (KTC) was created in 2017 to meet the needs of transgender patients.MethodsA retrospective review of all KTC patient charts was completed. The primary outcomes were the referral pattern to, and services provided by KTC. The secondary outcomes were the quality indicators i) rates of cervical screening and ii) offers of fertility preservation.Results108 patients were referred and 92 were seen; the median age was 20 years old. 77.2% of all patients sought, and 72.8% ultimately received, hormone therapy. Cervical cancer screening was documented as up to date for 69.8% of eligible people. 81.7% of eligible patients had documented fertility preservation offers.ConclusionAccessible local transgender care is a standard that can and should be met in Canada and internationally.77.2% of patients sought hormone therapy, which is in the scope of providers from many specialtiesAccessible local transgender care is a standard than can and should be met in Canada and internationallyGynecologists, pediatricians, and primary care providers are well-suited to provide transgender care