bluuebunny/crossref_metadata_2025_split huggingface dataset:
Test-Retest Reliability and Known-Groups Validity of Trunk Muscle Tests in People With Multiple Sclerosis: A Cross-Sectional, Case-Control Study
Authors: Moreno-Navarro Pedro , Manca Andrea , Martinez Gianluca , Ventura Lucia , Barbado David , Vera-García Francisco J , Deriu Franca 
Published: February 2021

Abstract

Objective
Research on muscle performance testing reliability in people with multiple sclerosis (MS) has focused on limb performance while less is known about trunk strength and endurance. This work aims to 1) establish test–retest reliability of trunk flexion, lateral flexion, and extension strength tests, and plank, side bridge, and Biering-Sørensen endurance tests in people with MS and matched healthy controls (HCs); 2) analyze known-groups validity of these tests in people with MS and HCs; 3) to compare groups for side-to-side differences; and 4) to describe the relationships between trunk performance and functional mobility tests.

Methods
Fifteen people with MS (median Expanded Disability Status Scale = 3) and 15 HCs underwent 2 trunk isometric strength and endurance testing sessions. Mobility was evaluated by Timed Up-and-Go test. Intraclass correlation coefficient, SEM, and minimal detectable change (MDC) were calculated. Between-group differences in trunk performance were tested using the t test for independent measures. Between-group differences in an asymmetry index were analyzed by independent t test. Bivariate correlations between trunk tests and mobility were also examined.

Results
All trunk tests showed good-to-excellent relative reliability in both groups (intraclass correlation coefficient &gt; 0.71). Regarding absolute reliability, strength tests were associated with low intersession variability in both groups (MDC: MS, 11.23%–36.45%; HCs, 26.60%–31.98%). Conversely, endurance tests showed higher variability scores in people with MS (MDC: MS, 69.55%–116.50%; HCs, 29.57%–54.40%). People with MS displayed significantly lower trunk performance. Likewise, the asymmetry index showed significantly higher scores in people with MS for endurance assessment but not in strength tests. Significant correlations were detected in people with MS between Timed Up-and-Go and several trunk tests (r = 0.63–0.70).

Conclusions
SEM and MDC scores revealed similar consistency and variability between groups for strength tests, whereas higher variability was observed for endurance tests in people with MS. Trunk strength tests are reliable and present discriminant validity to distinguish mildly disabled people with MS from HCs. Conversely, the high measurement error and variability of the endurance tests may hinder their application in intervention programs.

Impact
Determining the reliability and validity of the tests currently used to assess trunk function is of the greatest importance for people with MS (who show not only impaired trunk function but also wide fluctuations in performance), as it requires consistent and accurate measurements that are sensitive enough to detect minimal changes induced by rehabilitation.
Maintaining Symbiotic Homeostasis: How Do Plants Engage With Beneficial Microorganisms While at the Same Time Restricting Pathogens?
Authors: Thoms David , Liang Yan , Haney Cara H. 
Published: February 2021

This article is part of the Top 10 Unanswered Questions in MPMI invited review series. That plants recruit beneficial microbes while simultaneously restricting pathogens is critical to their survival. Plants must exclude pathogens; however, most land plants are able to form mutualistic symbioses with arbuscular mycorrhizal fungi. Plants also associate with the complex microbial communities that form the microbiome. The outcome of each symbiotic interaction—whether a specific microbe is pathogenic, commensal, or mutualistic—relies on the specific interplay of host and microbial genetics and the environment. Here, we discuss how plants use metabolites as a gate to select which microbes can be symbiotic. Once present, we discuss how plants integrate multiple inputs to initiate programs of immunity or mutualistic symbiosis and how this paradigm may be expanded to the microbiome. Finally, we discuss how environmental signals are integrated with immunity to fine-tune a thermostat that determines whether a plant engages in mutualism, resistance to pathogens, and shapes associations with the microbiome. Collectively, we propose that the plant immune thermostat is set to select for and tolerate a largely nonharmful microbiome while receptor-mediated decision making allows plants to detect and dynamically respond to the presence of potential pathogens or mutualists. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Entomobacter blattae gen. nov., sp. nov., a new member of the Acetobacteraceae isolated from the gut of the cockroach Gromphadorhina portentosa
Authors: Guzman Juan , Sombolestani Atena Sadat , Poehlein Anja , Daniel Rolf , Cleenwerck Ilse , Vandamme Peter , Vilcinskas Andreas 
Published: February 2021

A novel bacterium designated G55GPT and pertaining to the family

Acetobacteraceae

was isolated from the gut of the Madagascar hissing cockroach Gromphadorhina portentosa. The Gram-negative cells were rod-shaped and non-motile. The complete 16S rRNA sequence of the strain G55GPT showed the highest pairwise similarity to

Gluconacetobacter johannae

CFN-Cf-55T (95.35 %), suggesting it represents a potential new genus of the family

Acetobacteraceae

. Phylogenetic analysis based on 16S rRNA gene and 106 orthologous housekeeping protein sequences revealed that G55GPT forms a monophyletic clade with the genus

Commensalibacter

, which thus far has also been isolated exclusively from insects. The G55GPT genome size was 2.70 Mbp, and the G+C content was 45.4 mol%, which is lower than most acetic acid bacteria (51–68 mol%) but comparable to

Swingsia samuiensis

AH83T (45.1 mol%) and higher than

Commensalibacter intestini

A911T (36.8 mol%). Overall genome relatedness indices based on gene and protein sequences strongly supported the assignment of G55GPT to a new genus within the family

Acetobacteraceae

. The percentage of conserved proteins, which is a useful metric for genus differentiation, was below 54 % when comparing G55GPT to type strains of acetic acid bacteria, thus strongly supporting our hypothesis that G55GPT is a member of a yet-undescribed genus. The fatty acid composition of G55GPT differed from that of closely related acetic acid bacteria, particularly given the presence of C19 : 1
ω9c/ω11c and the absence of C14 : 0 and C14 : 0 2-OH fatty acids. Strain G55GPT also differed in terms of metabolic features such as its ability to produce acid from d-mannitol, and its inability to produce acetic acid from ethanol or to oxidize glycerol to dihydroxyacetone. Based on the results of combined genomic, phenotypic and phylogenetic characterizations, isolate G55GPT (=LMG 31394T=DSM 111244T) is considered to represent a new species in a new genus, for which we propose the name Entomobacter blattae gen. nov., sp. nov.
Tsuneonella suprasediminis sp. nov., isolated from the Pacific Ocean
Authors: Gao Yan , Li Guangyu , Fang Chen , Shao Zongze , Wu Yue-Hong , Xu Xue-Wei 
Published: February 2021

A Gram-stain-negative, rod-shaped and aerobic bacterial strain, named Ery12T, was isolated from the overlying water of the Lau Basin in the Southwest Pacific Ocean. Strain Ery12T showed high 16S rRNA gene sequences similarity to

Tsuneonella flava

MS1-4T (99.9 %),

T. mangrovi

MCCC 1K03311T (98.1 %),

Altererythrobacter ishigakiensis

NBRC 107699T (97.3 %) and exhibited ≤97.0 % sequence similarity with other type strains of species with validly published names. Growth was observed in media with 0–10.0 % NaCl (optimum 0–1.0 %, w/v), pH 5.0–9.5 (optimum 6.0–7.0) and 10–42 °C (optimum 30–37 °C). The predominant respiratory quinone was ubiquinone 10 (Q-10). The major cellular fatty acid was summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c). The major polar lipids were sphingoglycolipid, phosphatidyglycerol, diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, three unidentified glycolipids, one unidentified aminoglycolipid and one unidentified lipid. The DNA G+C content was 60.8 %. The ANI and in silico DDH values between strain Ery12T and the type strains of its closely related species were 71.0- 91.8 % and 19.5- 44.6 %, respectively. According to the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain Ery12T represents a novel species of the genus

Tsuneonella

, for which the name Tsuneonella suprasediminis is proposed. The type strain is Ery12T (=CGMCC 1.16500 T=MCCC 1A04421T=KCTC 62388T). We further propose to reclassify

Altererythrobacter rhizovicinus

and

Altererythrobacter spongiae

as Pelagerythrobacter rhizovicinus comb. nov. and Altericroceibacterium spongiae comb. nov., respectively.
IgG1 pan-neurofascin antibodies identify a severe yet treatable neuropathy with a high mortality
Authors: Fehmi Janev , Davies Alexander J. , Walters R. Jon , Lavin Tim , Keh Ryan , Rossor Alexander M. , Munteanu Tudor , Delanty Norman , Roberts Rhys , B□umer Dirk , Lennox Graham , Rinaldi Simon 
Published: February 2021

AbstractGuillain-Barré syndrome and chronic inflammatory demyelinating polyneuropathy are umbrella terms for a number of pathologically distinct diseases involving disabling, immune-mediated injury to peripheral nerves. Current treatments involve non-specific immunomodulation. Prospective identification of patients with specific disease mechanisms should increasingly inform the use of more targeted disease modifying therapies and may lead to improved outcomes. In this cohort study, we tested serum for antibodies directed against nodal/paranodal protein antigens. The clinical characteristics of antibody positive and seronegative patients were then compared. Eight patients with IgG1-subclass antibodies directed against both isoforms of the nodal/paranodal cell-adhesion molecule neurofascin were identified. All developed rapidly progressive tetraplegia. Cranial nerve deficits (100% versus 26%), autonomic dysfunction (75% versus 13%) and respiratory involvement (88% versus 14%) were more common than in seronegative patients. The response to intravenous immunoglobulin, steroids and/or plasmapheresis was poor. Four patients received the B-cell-depleting therapy rituximab. After several weeks, these patients began to show progressive functional improvements, became seronegative, and were ultimately discharged home. Four patients who did not receive rituximab did not improve and died following the development of infectious complications and/or withdrawal of intensive care support. IgG1 panneurofascin antibodies define a very severe autoimmune neuropathy. We urgently recommend trials of targeted immunotherapy for this serologically-classified patient group.
COVID-19 spread and Weather in U.S. states: a cross-correlative study on summer-autumn 2020
Authors: de Margerie Emmanuel 
Published: February 2021

AbstractAn effect of weather on sars-cov-2 transmission is regularly proposed as a putative cause of unexplained fluctuations of covid-19 new cases, but clear data supporting this hypothesis remains to be presented. Here I measured longitudinal time-series correlations between outdoor temperature, humidity and covid-19 reproduction number (Rt) in the 50 U.S. states (+DC). In order to mitigate the confounding influence of varying social restriction measures, the analysis spans a 5-month period during summer and autumn 2020 when restrictions were comparatively lower and more stable. I used a cross-covariance approach to account for a variable delay between infection and case report. For a delay near 11 days, most U.S. states exhibited a negative correlation between outdoor temperature and Rt, as well as between absolute humidity and Rt (mean r = −0.35). In 21 states, the correlation was strong (r < −0.5). Individual state data are presented, and associations between cold and/or dry weather episodes and short-term new case surges are proposed. After identifying potential confounding factors, I discuss 3 possible causal mechanisms that could explain a correlation between outdoor weather and indoor disease transmission: behavioral adaptations to cold weather, respiratory tract temperature, and the importing of outdoor absolute humidity to indoor spaces.
Cohort-based association study of germline genetic variants with acute and chronic health complications of childhood cancer and its treatment: Genetic risks for childhood cancer complications Switzerland (GECCOS) study protocol
Authors: Waespe Nicolas , Strebel Sven , Nava Tiago , Uppugunduri Chakradhara Rao S. , Marino Denis , Mattiello Veneranda , Otth Maria , Gumy-Pause Fabienne , von Bueren André O. , Baleydier Frederic , Mader Luzius , Spoerri Adrian , Kuehni Claudia E. , Ansari Marc 
Published: February 2021

BackgroundChildhood cancer and its treatment may lead to many acute and chronic health complications. Related impairment in quality of life, excess in deaths, and accumulated health care costs are relevant. There is a wide inter-individual variability in the type and severity of health complications. Genetic variations are suggested to contribute to individual susceptibility. So far, only few genetic variants have been used to risk-stratify treatment and follow-up care. This study platform aims to identify germline genetic variants associated with acute and late complications of childhood cancer.MethodsThe Genetic Risks for Childhood Cancer Complications Switzerland (GECCOS) study is a nationwide cohort study. It includes patients and survivors who were diagnosed with childhood cancers or Langerhans cell histiocytosis before age 21 years, were registered in the Swiss Childhood Cancer Registry (SCCR) since 1976 and have consented to the Pediatric Biobank for Research in Hematology and Oncology (BaHOP), Geneva, host of the Germline DNA Biobank Switzerland for Childhood Cancer and Blood Disorders (BISKIDS). BISKIDS is a national biobank for the collection of germline DNA in childhood cancer patients and survivors.GECCOS uses demographic and clinical data from the SCCR and the associated Swiss Childhood Cancer Survivor Study (SCCSS), which contains health-related data of survivors. Phenotypic data consist of objective measurements, health conditions diagnosed by physicians, second primary neoplasms, self-reported and health-related information from participants. Germline genetic samples and sequencing data have been collected in BISKIDS. We will perform gene panel sequencing, whole-exome sequencing, or whole-genome sequencing depending on the research questions. We will perform association analyses to identify genetic variants associated with specified health conditions. We will use clustering and machine-learning techniques and assess multiple health conditions in different models.DiscussionGECCOS will serve as an overarching platform to enable genotype-phenotype association analyses on complications associated with childhood cancer and its treatments. Knowledge of germline genetic variants associated with childhood cancer-associated health conditions will help to further individualize cancer treatment and follow-up care, potentially resulting in improved efficacy and reduced side effects, for personalized cancer care.Trial registrationClinicaltrials.gov: NCT04702321
Comparing the impact of vaccination strategies on spread of COVID-19, including a novel household-targeted vaccination strategy
Authors: Voigt André , Omholt Stig , Almaas Eivind 
Published: February 2021

AbstractWith limited availability of vaccines, an efficient use of the limited supply of vaccines in order to achieve herd immunity will be an important tool to combat the wide-spread prevalence of COVID-19. Here, we compare a selection of strategies for vaccine distribution, including a novel targeted vaccination approach (EHR) that provides a noticeable increase in vaccine impact on disease spread compared to age-prioritized and random selection vaccination schemes. Using high-fidelity individual-based computer simulations with Oslo, Norway as an example, we find that for a community reproductive number in a setting where the base pre-vaccination reproduction number R = 2.1 without population immunity, the EHR method reaches herd immunity at 48% of the population vaccinated with 90% efficiency, whereas the common age-prioritized approach needs 89%, and a population-wide random selection approach requires 61%. We find that age-based strategies have a substantially weaker impact on epidemic spread and struggle to achieve herd immunity under the majority of conditions. Furthermore, the vaccination of minors is essential to achieving herd immunity, even for ideal vaccines providing 100% protection.
Estimated SARS-CoV-2 Seroprevalence in Healthy Children and Those with Chronic Illnesses in The Washington Metropolitan Area as of October 2020
Authors: Bahar Burak , Simpson Joelle N. , Biddle Cara , Campbell Andrew , Dome Jeffrey S. , DeBiasi Roberta L. , Mowbray Catriona , Marguilies Stefanie , Sherman Adrienne , Reuben Jacqueline , Delaney Meghan 
Published: February 2021

AbstractThe estimated SARS-CoV-2 seroprevalence in children was found to be 9.46% for the Washington Metropolitan area. Hispanic/Latinx individuals were found to have higher odds of seropositivity. While chronic medical conditions were not associated with having antibodies, previous fever and body aches were predictive symptoms.
Prefrontal-motor and somatosensory-motor cortical network interactions during reactive balance are associated with distinct aspects of balance behavior in older adults
Authors: Palmer Jacqueline A. , Payne Aiden M. , Ting Lena H. , Borich Michael R. 
Published: February 2021

AbstractHeightened reliance on the cerebral cortex for postural stability with aging is well-known, yet the cortical dynamics of balance control, particularly in relationship to balance function, is unclear. Here we aimed to investigate motor cortical activity in relationship to the level of balance challenge presented during reactive balance recovery, and identify circuit-specific interactions between motor cortex and prefrontal or somatosensory regions to metrics of balance function that predict fall risk. Using electroencephalography, we assessed motor cortical beta power, and beta coherence during balance reactions to perturbations in older adults. We found that individuals with greater somatosensory-motor beta coherence at baseline and lower beta power evoked over motor regions following perturbations demonstrated higher general clinical balance function. At the group-level, beta coherence between prefrontal-motor regions reduced during balance reactions. Older adults with the highest post-perturbation prefrontal-motor coherence showed greater cognitive dual-task interference and elicited stepping reactions at lower perturbation magnitudes. Our results support motor cortical beta activity as a potential biomarker for individual level of balance challenge and implicate prefrontal-and somatosensory-motor cortical networks in different aspects of balance control in older adults. Cortical network activity during balance may provide a neural target for precision-medicine efforts aimed at fall-prevention with aging.
CDSeqR: fast complete deconvolution for gene expression data from bulk tissues
Authors: Kang Kai , Huang Caizhi David , Li Yuanyuan , Umbach David M. , Li Leping 
Published: February 2021

AbstractBackgroundBiological tissues consist of heterogenous populations of cells. Because gene expression patterns from bulk tissue samples reflect the contributions from all cells in the tissue, understanding the contribution of individual cell types to the overall gene expression in the tissue is fundamentally important. We recently developed a computational method, CDSeq, that can simultaneously estimate both sample-specific cell-type proportions and cell-type-specific gene expression profiles using only bulk RNA-Seq counts from multiple samples. Here we present an R implementation of CDSeq (CDSeqR) with significant performance improvement over the original implementation in MATLAB and an added new function to aid cell type annotation. The R package would be of interest for the broader R community.ResultWe developed a novel strategy to substantially improve computational efficiency in both speed and memory usage. In addition, we designed and implemented a new function for annotating the CDSeq estimated cell types using single-cell RNA sequencing (scRNA-seq) data. This function allows users to readily interpret and visualize the CDSeq estimated cell types. In addition, this new function further allows the users to annotate CDSeq-estimated cell types using marker genes. We carried out additional validations of the CDSeqR software using synthetic, real cell mixtures, and real bulk RNA-seq data from the Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) project.ConclusionsThe existing bulk RNA-seq repositories, such as TCGA and GTEx, provide enormous resources for better understanding changes in transcriptomics and human diseases. They are also potentially useful for studying cell-cell interactions in the tissue microenvironment. Bulk level analyses neglect tissue heterogeneity, however, and hinder investigation of a cell-type-specific expression. The CDSeqR package may aidin silicodissection of bulk expression data, enabling researchers to recover cell-type-specific information.
7-Dehydrocholesterol-derived oxysterols cause neurogenic defects in Smith-Lemli-Opitz syndrome
Authors: Tomita Hideaki , Hines Kelly M. , Herron Josi M. , Li Amy , Baggett David W. , Xu Libin 
Published: February 2021

AbstractDefective 3β-hydroxysterol-Δ7-reductase (DHCR7) in the developmental disorder, Smith-Lemli-Opitz syndrome (SLOS), results in deficiency in cholesterol and accumulation of its precursor, 7-dehydrocholesterol (7-DHC). Here, we show that loss ofDHCR7causes accumulation of 7-DHC-derived oxysterol metabolites, premature neurogenesis, and perturbation of neuronal localization in developing murine or human cortical neural precursors, bothin vitroandin vivo. We found that a major oxysterol, 3β,5α-dihydroxycholest-7-en-6-one (DHCEO), mediates these effects by initiating crosstalk between glucocorticoid receptor (GR) and neurotrophin receptor kinase TrkB. Either loss ofDHCR7or direct exposure to DHCEO causes hyperactivation of GR and TrkB and their downstream MEK-ERK-C/EBP signaling pathway in cortical neural precursors. Moreover, direct inhibition of GR activation with an antagonist or inhibition of DHCEO accumulation with antioxidants rescues the premature neurogenesis phenotype caused by the loss ofDHCR7. These results suggest that GR could be a new therapeutic target against the neurological defects observed in SLOS.