bluuebunny/crossref_metadata_2025_split huggingface dataset:
DIETARY RESCUE OF ADULT BEHAVIORAL DEFICITS IN THEFMR1KNOCKOUT MOUSE
Authors: Nolan Suzanne O. , Hodges Samantha L. , Binder Matthew S. , Smith Gregory D. , Okoh James T. , Jefferson Taylor S. , Escobar Brianna , Lugo Joaquin N. 
Published: April 2021

ABSTRACTThe current study aimed to further address important questions regarding the therapeutic efficacy of omega-3 fatty acids for various behavioral and neuroimmune aspects of theFmr1phenotype. To address these questions, our experimental design utilized two different omega-3 fatty acid administration timepoints, compared to both standard laboratory chow controls (“Standard”) and a diet controlling for the increase in fat content (“Control Fat”). In the first paradigm, post-weaning supplementation (after postnatal day 21) with the omega-3 fatty acid diet (“Omega-3”) reversed deficits in startle threshold, but not deficits in prepulse inhibition, and the effect on startle threshold was not specific to the Omega-3 diet. However, post-weaning supplementation with both experimental diets also impaired acquisition of a fear response, recall of the fear memory and contextual fear conditioning compared to the Standard diet. The post-weaning Omega-3 diet reduced hippocampal expression of IL-6 and this reduction of IL-6 was significantly associated with diminished performance in the fear conditioning task. In the prenatal experimental paradigm, the Omega-3 diet attenuated hyperactivity and acquisition of a fear response. Additionally, prenatal exposure to the Control Fat diet (similar to a “Western” diet) further diminished nonsocial anxiety in theFmr1knockout. This study provides significant evidence that dietary fatty acids throughout the lifespan can significantly impact the behavioral and neuroimmune phenotype of theFmr1knockout model.
Feasibility and diagnostic accuracy of saliva-based SARS-CoV-2 screening in educational settings and children aged < 12 years
Authors: Hoch Martin , Vogel Sebastian , Eberle Ute , Kolberg Laura , Gruenthaler Valerie , Fingerle Volker , Ackermann Nikolaus , Sing Andreas , Liebl Bernhard , Huebner Johannes , Kuttiadan Simone , Rack-Hoch Anita , Meyer-Buehn Melanie , Schober Tilmann , Both Ulrich von 
Published: April 2021

AbstractChildren have been disproportionately affected during the COVID-19 pandemic. We aimed to assess a saliva-based algorithm for SARS-CoV-2 testing to be used in schools and childcare institutions under pandemic conditions. A weekly SARS-CoV-2 sentinel study in primary schools, kindergartens and childcare facilities was conducted over a 12-week-period. In a sub-study covering 7 weeks, 1895 paired oropharyngeal and saliva samples were processed for SARS-CoV-2 rRT-PCR testing in both asymptomatic children (n=1243) and staff (n=652). Forty-nine additional concurrent swab and saliva samples were collected from SARS-CoV-2 infected patients (patient cohort). The Salivette® system was used for saliva collection and assessed for feasibility and diagnostic performance. For children a mean of 1.18 ml saliva could be obtained. Based on results from both cohorts, the Salivette® testing algorithm demonstrated specificity of 100% (95% CI 99.7 - 100) and sensitivity of 94.9% (95% CI 81.4 - 99.1) with oropharyngeal swabs as reference. Agreement between sampling systems was 100% for moderate to high viral load situations (defined as Ct-values < 33 from oropharyngeal swabs). Comparative analysis of Ct-values derived from saliva vs. oropharyngeal swabs demonstrated a significant difference (mean 4.23; 95% CI 2.48–6.00). In conclusion, the Salivette® system proved to be an easy-to-use, safe and feasible saliva collection method and a more pleasant alternative to oropharyngeal swabs for SARS-CoV-2 testing in children aged 3 years and above.
Identification of unknown proteins in X-ray crystallography and cryo-EM
Authors: Chojnowski Grzegorz , Simpkin Adam J. , Leonardo Diego A. , Seifert-Davila Wolfram , Vivas-Ruiz Dan E. , Keegan Ronan M. , Rigden Daniel J. 
Published: April 2021

AbstractAlthough experimental protein structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or as a contaminant. Regardless of the source of the problem, the unknown protein always requires tedious characterization. Here we present an automated pipeline for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. We present the method’s application to characterize the crystal structure of an unknown protein purified from a snake venom. We also show that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.
Rapid decay of host basal mRNAs during SARS-CoV-2 infection perturbs host antiviral mRNA biogenesis and export
Authors: Burke James M. , St Clair Laura A. , Perera Rushika , Parker Roy 
Published: April 2021

AbstractA key feature of the mammalian innate immune response to viral infection is the transcriptional induction of interferon (IFN) genes, which encode for secreted proteins that prime the antiviral response and limit viral replication and dissemination. A hallmark of severe COVID-19 disease caused by SARS-CoV-2 is the low presence of IFN proteins in patient serum despite elevated levels ofIFN-encoding mRNAs, indicative of post-transcriptional inhibition of IFN protein production. Herein, we show SARS-CoV-2 infection limits type I and type III IFN biogenesis by preventing the release of mRNA from their sites of transcription and/or triggering their nuclear degradation. In addition, SARS-CoV-2 infection inhibits nuclear-cytoplasmic transport ofIFNmRNAs as a consequence of widespread cytosolic mRNA degradation mediated by both activation of the host antiviral endoribonuclease, RNase L, and by the SARS-CoV-2 protein, Nsp1. These findings argue that inhibition of host and/or viral Nsp1-mediated mRNA decay, as well as IFN treatments, may reduce viral-associated pathogenesis by promoting the innate immune response.
Organic management and landscape heterogeneity combine to sustain multifunctional bird communities in European vineyards
Authors: Barbaro Luc , Assandri Giacomo , Brambilla Mattia , Castagneyrol Bastien , Froidevaux Jérémy , Giffard Brice , Pithon Joséphine , Puig‐Montserrat Xavier , Torre Ignasi , Calatayud François , Gaüzère Pierre , Guenser Josépha , Macià‐Valverde Francesc‐Xavier , Mary Séverine , Raison Laurent , Sirami Clélia , Rusch Adrien 
Published: April 2021

Abstract

Conserving functionally diverse bird communities in European farmland is becoming critical, with no exception for regions of wine production. Management intensification combined with the loss of semi‐natural habitats in wine‐growing landscapes has led to a long‐term decline not only in birds of conservation concern but also in once common insectivores and seed eaters. These declines are expected not only to threaten key ecological services provided by vineyard birds, such as pest or weed control, but also their cultural significance.

We analysed how organic management and landscape heterogeneity affected taxonomic and functional diversity of 334 bird communities from 12 regions of the three main wine‐producing European countries (France, Italy and Spain). We further modelled the responses of community‐level metrics measuring mean habitat specialization and bird song attractiveness to humans, as well as cumulative abundances of functional insectivores, seed and grape eaters to account for individual avian functions.

We found that organic viticulture enhanced bird functional diversity and individual functions, but that its positive effect partially depended on grass cover management in the inter‐rows and landscape heterogeneity. Woodland cover and landscape compositional heterogeneity increased both taxonomic and functional diversity of bird communities, as well as functional insectivory. Landscape configurational heterogeneity also increased functional diversity and mean song attractiveness of bird communities.

Overall, both bird diversity and functions were enhanced by higher landscape heterogeneity, especially in organic vineyards. However, mean habitat specialization decreased with woodland cover and configurational heterogeneity, meaning that open habitat specialists preferred more even landscapes with high vineyard cover.

Synthesis and applications. Our study highlights the benefits of combining organic management and partial grass cover at the field level and promoting interfaces between vineyards and semi‐natural habitats at the landscape level to sustain multifunctional bird communities in wine‐producing European countries.
Long‐term surveys support declines in early season forest plants used by bumblebees
Authors: Mola John M. , Richardson Leif L. , Spyreas Greg , Zaya David N. , Pearse Ian S. 
Published: April 2021

Abstract

Populations of bumblebees and other pollinators have declined over the past several decades due to numerous threats, including habitat loss and degradation. However, we can rarely investigate the role of resource loss due to a lack of detailed long‐term records of forage plants and habitats.

We used 22‐year repeated surveys of more than 262 sites located in grassland, forest, and wetland habitats across Illinois, USA to explore how the abundance and richness of bumblebee food plants have changed over the period of decline of the endangered rusty patched bumblebee Bombus affinis.

We documented a decline in abundance of bumblebee forage plants in forest understories, which our phenology analysis suggests provide the primary nectar and pollen sources for foundress queens in spring, a critical life stage in bumblebee demography. By contrast, the per‐unit area abundance of food plants in primarily midsummer‐flowering grassland and wetland habitats had not declined. However, the total area of grasslands had declined across the region resulting in a net loss of grassland resources.

Synthesis and applications. Our results suggest a decline in spring‐flowering forest understorey plants is a previously unappreciated bumblebee stressor, compounding factors like agricultural intensification, novel pathogen exposure and grassland habitat loss. These findings emphasize the need for greater consideration of habitat complementarity in bumblebee conservation. We conclude that the continued loss of early season floral resources may add additional stress to critical life stages of bumblebees and limit restoration efforts if not explicitly considered in pollinator conservation.
Extracellular sulfite is protective against reactive oxygen species and antibiotic stress in Shewanella oneidensis MR‐1
Authors: Goff Jennifer L. , Schaefer Jeffra K. , Yee Nathan 
Published: April 2021

SummaryIn this study, we investigated the extracellular reactive sulfur species produced by Shewanella oneidensis MR‐1 during growth. The results showed that sulfite is the major extracellular sulfur metabolite released to the growth medium under both aerobic and anaerobic growth conditions. Exogenous sulfite at physiological concentrations protected S. oneidensis MR‐1 from hydrogen peroxide toxicity and enhanced tolerance to the beta‐lactam antibiotics cefazolin, meropenem, doripenem and ertapenem. These findings suggest that the release of extracellular sulfite is a bacterial defence mechanism that plays a role in the mitigation of environmental stress.
Meeting unique requirements: Community consultation and public disclosure for research in emergency setting using exception from informed consent
Authors: Dickert Neal W. , Metz Kathleen , Fetters Michael D. , Haggins Adrianne N. , Harney Deneil K. , Speight Candace D. , Silbergleit Robert 
Published: April 2021

AbstractBackgroundException from informed consent (EFIC) regulations for research in emergency settings contain unique requirements for community consultation and public disclosure. These requirements address ethical challenges intrinsic to this research context. Multiple approaches have evolved to accomplish these activities that may reflect and advance different aims. This scoping review was designed to identify areas of consensus and lingering uncertainty in the literature.MethodsScoping review methodology was used. Conceptual and empirical literature related to community consultation and public disclosure for EFIC research was included and identified through a structured search using Embase, HEIN Online, PubMed, and Web of Science. Data were extracted using a standardized tool with domains for major literature categories.ResultsAmong 84 manuscripts, major domains included conceptual or policy issues, reports of community consultation processes and results, and reports of public disclosure processes and results. Areas of consensus related to community consultation included the need for a two‐way exchange of information and use of multiple methods. Public acceptance of personal EFIC enrollment is commonly 64% to 85%. There is less consensus regarding how to assess attitudes, what “communities” to prioritize, and how to determine adequacy for individual projects. Core goals of public disclosure are less well developed; no metrics exist for assessing adequacy.ConclusionsMultiple methods are used to meet community consultation and public disclosure requirements. There remain no settled norms for assessing adequacy of public disclosure, and there is lingering debate about needed breadth and depth of community consultation.
Quantifying direct and indirect effect for longitudinal mediator and survival outcome using joint modeling approach
Authors: Zheng Cheng , Liu Lei 
Published: April 2021

AbstractLongitudinal biomarkers are widely used in biomedical and translational researches to monitor the progressions of diseases. Methods have been proposed to jointly model longitudinal data and survival data, but its causal mechanism is yet to be investigated rigorously. Understanding how much of the total treatment effect is through the biomarker is important in understanding the treatment mechanism and evaluating the biomarker. In this work, we propose a causal mediation analysis method to compute the direct and indirect effects, when a joint modeling approach is used to take the longitudinal biomarker as the mediator and the survival endpoint as the outcome. Such a joint modeling approach allows us to relax the commonly used “sequential ignorability” assumption. We demonstrate how to evaluate longitudinally measured biomarkers using our method with two case studies, an AIDS study and a liver cirrhosis study.
ENT from afar: Opportunities for remote patient assessment, clinical management, teaching and learning
Authors: Bhutta Mahmood F. , Swanepoel De Wet , Fagan Johan 
Published: April 2021

AbstractRemote communication in ENT has been expanding, spurred by the COVID‐19 pandemic. Conferences and teaching have moved online, enabling easier participation and reducing financial and environmental costs. Online multi‐disciplinary meetings have recently been instigated in Africa to discuss management of cases in head and neck cancer, or cochlear implantation, expanding access and enhancing patient care. Remote patient consultation has also seen an explosion, but existing literature suggests some caution, particularly because many patients in ENT need an examination to enable definitive diagnosis. Ongoing experience will help us to better understand how remote communication will fit into our future working lives, and also where face‐to‐face interaction may still be preferable.
Endoscopic features of isolated and traditional serrated adenoma‐associated superficially serrated adenomas of the colorectum
Authors: Mizuguchi Yasuhiko , Tanaka Yusaku , Cho Hourin , Sekiguchi Masau , Takamaru Hiroyuki , Yamada Masayoshi , Sakamoto Taku , Matsuda Takahisa , Hashimoto Taiki , Sekine Shigeki , Saito Yutaka 
Published: April 2021

Background and AimSuperficially serrated adenoma (SuSA) is a recently proposed subtype of colorectal serrated lesions. It is characterized by distinct clinicopathological and molecular features, including mixed serrated and adenomatous histology and frequent genetic alterations involving KRAS and RSPO. This study aimed to characterize the endoscopic features of isolated and traditional serrated adenoma (TSA)‐associated SuSAs.MethodsWe retrospectively evaluated the endoscopic findings of 25 isolated SuSAs and 21 TSA‐associated SuSAs that were histologically and molecularly characterized.ResultsSuSAs appeared as a sessile polyp or slightly elevated lesion located mostly in the sigmoid colon and rectum (88%). The size was between 3 and 20 mm (median, 6 mm). Most of them exhibited KRAS mutations (96%) and RSPO fusions/overexpression (92%). Endoscopically, many lesions had a whitish color (84%), a distinct border (96%), an irregular border (76%), and a lobulated surface (72%). However, diminutive lesions exhibited overlapping features with hyperplastic polyps. On narrow‐band imaging, vessel patterns were invisible or appeared as lacy microvessels in most lesions (80%). Chromoendoscopy invariably showed stellar or elongated/branched stellar pits, indicating a serrated microarchitecture. Most TSA‐associated SuSAs typically presented as polyps with a two‐tier raised appearance, consisting of whitish lower and reddish higher components corresponding to a SuSA and a TSA, respectively.ConclusionsSuSAs exhibit several characteristic endoscopic features on white‐light and image‐enhanced endoscopy. Diminutive lesions exhibit endoscopic features overlapping with hyperplastic polyps. Nonetheless, the endoscopic diagnosis of larger and TSA‐associated SuSAs may be feasible.
Comparative analysis of the diagnostic value of several methods for the diagnosis of patent foramen ovale
Authors: Liu Fangfang , Kong Qingyu , Zhang Xiaojun , Li Yan , Liang Shimin , Han Shuang , Li Guishuang 
Published: April 2021

AbstractThe aim of this research was to compare the sensitivity and positive predictive value of contrast transcranial Doppler (c‐TCD), contrast transthoracic echocardiography (c‐TTE), and contrast transesophageal echocardiography (c‐TEE), to determine the best method for diagnosing patent foramen ovale (PFO) and to provide a reference for the further improvement of clinical practice. We investigated 161 patients who suffered from migraines, cryptogenic stroke, TIA, and cerebral infarction of unknown cause. All patients underwent transcatheter examination, and the results of the right heart catheterization (RHC) were considered the gold standard for PFO diagnosis. The present study revealed that c‐TTE with the Valsalva maneuver had a higher sensitivity in detecting PFO related right‐to‐left shunt (PFO‐RLS), c‐TCD performed similarly to c‐TEE but maybe produce more false positives. Moreover, when we observed color shunt from the slit‐like channel between the septum primum and the septum secundum on TEE, the positive predictive value was the highest. Patients with suspected PFO should be examined with c‐TTE and c‐TEE for confirmation. When there were a large number of bubbles in the left heart, especially in the presence of color shunt, the positive predictive value was the highest. The positive results of c‐TCD only point out the presence of right‐to‐left shunt and cannot exclude extracardiac shunt, so c‐TCD should not be used as a screen for PFO, additional measures such as c‐TTE and c‐TEE should be used.
ClimPlant: Realized climatic niches of vascular plants in European forest understoreys
Authors: Vangansbeke Pieter , Máliš František , Hédl Radim , Chudomelová Markéta , Vild Ondřej , Wulf Monika , Jahn Ute , Welk Erik , Rodríguez‐Sánchez Francisco , De Frenne Pieter 
Published: April 2021

AbstractMotivationDetailed knowledge on the climatic tolerances of species is crucial to understand, quantify and predict the impact of climate change on biodiversity and ecosystem functions. However, quantitative data are limited; often, only expert‐based qualitative estimates are available. With the ClimPlant database, we capitalize on the link between species distribution ranges and macroclimate to infer the realized climatic niches of 968 European forest plant species.Main types of variables containedThe ClimPlant database contains information on the distribution of monthly, growing‐season and annual mean, minimum and maximum temperature and total precipitation within the distribution range of 968 European forest plants.Spatial location and grainEurope in 10 arc‐min grid cells; the study area has been cropped rectangularly at 15° W (Atlantic Ocean), 60° E (Ural Mountains), 25° N (Sahara) and 75° N (Arctic Ocean).Time period and grainThe distribution ranges of forest plant species are based on two renowned distribution atlases. The monthly mean, minimum and maximum temperature and precipitation between 1970 and 2000 were extracted from WorldClim v.2.Major taxa and level of measurementNine hundred and sixty‐eight vascular plant species of European forests, with taxonomy following the Euro+Med PlantBase nomenclature .Software formatData in 56 CSV files, with 1,000 values for monthly, growing season and annual observations of mean, minimum and maximum temperature and precipitation in the distribution range for every species. One summary CSV file with summary statistics (mean, median, fifth and 95th percentile), for every species, of each climatic variable, together with seven key geographical descriptors: area of the distribution range, latitude and longitude of the centroid, and northern, eastern, western and southern range limits within the study area.
Lynch syndrome screening in colorectal cancer: results of a prospective 2‐year regional programme validating the NICE diagnostics guidance pathway throughout a 5.2‐million population
Authors: West Nicholas P , Gallop Niall , Kaye Danny , Glover Amy , Young Caroline , Hutchins Gordon G A , Brockmoeller Scarlet F , Westwood Alice C , Rossington Hannah , Quirke Philip ,   the Yorkshire Cancer Research Bowel Cancer Improvement Programme Group
Published: April 2021

AimsScreening all patients newly diagnosed with colorectal cancer (CRC) for possible Lynch syndrome (LS) has been recommended in the United Kingdom since the National Institute for Health and Care Excellence (NICE) released new diagnostics guidance in February 2017. We sought to validate the NICE screening pathway through a prospective regional programme throughout a 5.2‐million population during a 2‐year period.Methods and resultsPathology departments at 14 hospital trusts in the Yorkshire and Humber region of the United Kingdom were invited to refer material from patients with newly diagnosed CRC aged 50 years or over between 1 April 2017 and 31 March 2019 for LS screening. Testing consisted of immunohistochemistry for MLH1, PMS2, MSH2 and MSH6 followed by BRAF mutation analysis ± MLH1 promoter methylation testing in cases showing MLH1 loss. A total of 3141 individual specimens were submitted for testing from 12 departments consisting of 3061 unique tumours and 2791 prospectively acquired patients with CRC. Defective mismatch repair (dMMR) was observed in 15% of cases. In cases showing MLH1 loss, 76% contained a detectable BRAF mutation and, of the remainder, 77% showed MLH1 promoter hypermethylation. Of the patients included in the final analysis, 81 (2.9%) had an indication for germline testing.ConclusionLS screening using the NICE diagnostics guidance pathway is deliverable at scale identifying significant numbers of patients with dMMR. This information is used to refer patients to regional clinical genetics services in addition to informing treatment pathways including the use of adjuvant/neoadjuvant chemotherapy and immunotherapy.