bluuebunny/crossref_metadata_2025_split huggingface dataset:
Revision shock in Pacific oysters taxonomy: the genusMagallana(formerlyCrassostreain part) is well-founded and necessary
Authors: Salvi Daniele , Mariottini Paolo 
Published: August 2020

AbstractThe description of the genus Magallana provoked taxonomic ‘revision shock’ among Bayne and colleagues, who criticised: (1) the supporting evidence for this taxonomic change, (2) the procedure used and (3) its impact on the nomenclatural stability of oysters. Here, we demonstrate that the description of the genus Magallana fulfils the norms of taxonomic and indexing revisions, and is well-founded on a scientific basis. The clade named Magallana is supported by a robust phylogeny based on comprehensive taxon sampling, independent datasets and varied analytical methods. A new maximum likelihood phylogenetic analysis of oysters, based on mitochondrial gene order data (representing molecular phenotypes above the sequence level), has provided additional support for this classification. These results are fully consistent with all previously published phylogenetic studies, thus providing an unambiguous indication of the stability of the clade that meets all the currently accepted criteria for naming clades as taxa. We show that, while the criterion of ‘morphological diagnosability’ is not applicable at any level of oyster classification, several striking molecular phenotypes are diagnostic of Magallana, both at the nuclear and the mitochondrial genome level. The classification with three genera Magallana, Crassostrea and Talonostrea reflects the evolutionary diversity of Crassostreinae and is consistent with taxonomic ranking criteria adopted for other oyster subfamilies.
CE: Trauma-Related Hemorrhagic Shock: A Clinical Review
Authors: Caldwell Nicole W. , Suresh Mithun , Garcia-Choudary Tricia , VanFosson Christopher A. 
Published: August 2020

ABSTRACT:
Optimal management of trauma-related hemorrhagic shock begins at the point of injury and continues throughout all hospital settings. Several procedures developed on the battlefield to treat this condition have been adopted by civilian health care systems and are now used in a number of nonmilitary hospitals. Despite the important role nurses play in caring for patients with trauma-related hemorrhagic shock, much of the literature on this condition is directed toward paramedics and physicians. This article discusses the general principles underlying the pathophysiology and clinical management of trauma-related hemorrhagic shock and updates readers on nursing practices used in its management.
Can Pediatric Orthopaedic Surgery be Done Safely in a Freestanding Ambulatory Surgery Center? Review of 3780 Cases
Authors: Sheffer Benjamin W. , Kelly Derek M. , Spence David D. , Walker Kent L. , Westbrooks Timothy J. , Palm Preston H. , Nolan Vikki G. , Sawyer Jeffrey R. 
Published: August 2020

Background:
The purpose of this study was to determine the intraoperative and 30-day postoperative complication rates in a large consecutive cohort of pediatric patients who had orthopaedic surgery at a freestanding ambulatory surgery center (ASC). The authors also wanted to identify the rates of same-day, urgent hospital transfers, and 30-day hospital admissions. The authors hypothesized that pediatric orthopaedic procedures at a freestanding ASC can be done safely with a low rate of complications.

Methods:
A retrospective review identified patients aged 17 years or younger who had surgery at a freestanding ASC over a 9-year period. Adverse outcomes were divided into intraoperative complications, postoperative complications, need for the secondary procedure, unexpected hospital admission on the same day of the procedure, and unexpected hospital admission within 30 days of the index procedure. Complications were graded as grade 1, the complication could be treated without additional surgery or hospitalization; grade 2, the complication resulted in an unplanned return to the operating room (OR) or hospital admission; or grade 3, the complication resulted in an unplanned return to the OR or hospitalization with a change in the overall treatment plan.

Results:
Adequate follow-up was available for 3780 (86.1%) surgical procedures. Overall, there were 9 (0.24%) intraoperative complications, 2 (0.08%) urgent hospital transfers, 114 (3%) complications, and 16 (0.42%) readmissions. Seven of the 9 intraoperative complications resolved before leaving the OR, and 2 required return to the OR.
Neither complications nor hospitalizations correlated with age, race, gender, or length or type of surgery. There was no correlation between the presence of medical comorbidities, body mass index, or American Society of Anesthesiologists score and complication or hospitalization.

Conclusions:
Pediatric orthopaedic surgical procedures can be performed safely in an ASC because of multiple factors that include dedicated surgical teams, single-purpose ORs, and strict preoperative screening criteria. The rates of an emergency hospital transfer, surgical complications, and 30-day readmission, even by stringent criteria, are lower than those reported for outpatient procedures performed in the hospital setting.

Level of Evidence:
Level IV—case series.
Pooling of samples to optimize SARS-CoV-2 diagnosis by RT-qPCR: comparative analysis of two protocols
Authors: Volpato Fabiana , Lima-Morales Daiana , Wink Priscila Lamb , Willig Julia , Paris Fernanda , Ashton-Prolla Patricia , Barth Afonso Luís 
Published: August 2020

AbstractRT-qPCR for SARS-CoV-2 is the main diagnostic test used to identify the novel coronavirus. Several countries have used large scale SARS-CoV-2 RT-qPCR testing as one of the important strategies for combating the pandemic. In order to process the massive needs for coronavirus testing, the usual throughput of routine clinical laboratories has reached and often surpassed its limits and new approaches to cope with this challenge must be developed. This study has aimed to evaluate the use pool of samples as a strategy to optimize the diagnostic of SARS-CoV-2 by RT-qPCR in a general population. A total of 220 naso/orofaryngeal swab samples were collected and tested using two different protocols of sample pooling. In the first protocol (Protocol A); 10 clinical samples were pooled before RNA extraction. The second protocol (Protocol B) consisted of pooling the already extracted RNAs from 10 individual samples. Results from Protocol A were identical (100% agreement) with the individual results. However, for results from Protocol B, reduced agreement (91%) was observed in relation to results obtained by individual testing. Inconsistencies observed were related to RT-qPCR results with higher Cycle Thresholds (Ct > 32.73). Furthermore, in pools containing more than one positive individual, the Ct of the pool was equivalent to the lowest Ct among the individual results. These results provide additional evidence in favor of the clinical use of pooled samples for SARS-CoV-2 diagnosis by RT-qPCR and suggest that pooling of samples before RNA extraction is preferrable in terms of diagnostic yield.
MicroRNA variants and HLA-miRNA interactions are novel rheumatoid arthritis susceptibility factors
Authors: Guo Shicheng , Jin Yehua , Zhou Jieru , Zhu Qi , Jiang Ting , Bian Yanqin , Zhang Runrun , Chang Cen , Xu Lingxia , Shen Jie , Zheng Xinchun , Shen Yi , Qin Yingying , Chen Jihong , Tang Xiaorong , Cheng Peng , Ding Qin , Zhang Yuanyuan , Liu Jia , Cheng Qingqing , Guo Mengru , Liu Zhaoyi , Qiu Weifang , Qian Yi , Sun Yang , Shen Yu , Nie Hong , Schrodi Steven J , He Dongyi 
Published: August 2020

AbstractObjectiveAlthogh Genome-wide association studies have identified >100 variants for rheumatoid arthritis (RA),the reported genetic variants only explain <40% of RA heritability. We conducted a systemic association study between common East-Asian miRNA SNPs with RA in a large Han Chinese cohort to explain missing heritability and identify miRNA epistatic interactions.Methods4 HLA SNPs (HLA-DRB1, HLA-DRB9, HLA-DQB1 and TNFAIP3) and 225 common SNPs located in miRNA which might influence the miRNA target binding or pre-miRNA stability were genotyped in 1,607 rheumatoid arthritis and 1,580 matched normal individuals. A meta-analysis with previous GWAS studies (4,873 RA cases and 17,642 controls) was performed to discovery another novel miRNA RA-associated SNPs.Results2 novel SNPs including rs1414273 (miR-548ac, OR=0.84, P=8.26×10-4) and rs2620381 (miR-627, OR=0.77, P=2.55×10-3) conferred significant association with RA. Individuals carried 8 risk alleles showed 15.38 (95%CI: 4.69-50.49, P<1.0×10-6) times more risk to be affected by RA. In addition, rs5997893 (miR-3928) showed significant epistasis effect with rs4947332 (HLA-DRB1, OR=4.23, P=0.04) and rs2967897 (miR-5695) with rs7752903 (TNFAIP3, OR=4.43, P=0.03). Finally, we demonstrated targets of the significant miRNAs showed enrichment in immune related genes (P=2.0×10-5) and FDA approved drug target genes (P=0.014).Conclusions6 novel miRNA SNPs including rs1414273 (miR-548ac, P=8.26×10-4), rs2620381 (miR-627, P=2.55×10-3), rs4285314 (miR-3135b, P=1.10×10-13), rs28477407 (miR-4308, P=3.44×10-5), rs5997893 (miR-3928, P=5.9×10-3) and rs45596840 (miR-4482, P=6.6×10-3) were confirmed to be significantly associated with RA in a Chinese population. Our study suggests that miRNAs might be interesting targets to accelerate the understanding of the pathogenesis and drug development for rheumatoid arthritis.
Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay
Authors: Vanaerschot Manu , Mann Sabrina A. , Webber James T. , Kamm Jack , Bell Sidney M. , Bell John , Hong Si Noon , Nguyen Minh Phuong , Chan Lienna Y. , Bhatt Karan D. , Tan Michelle , Detweiler Angela M. , Espinosa Alex , Wu Wesley , Batson Joshua , Dynerman David ,   CLIAHUB Consortium, Wadford Debra A. , Puschnik Andreas S. , Neff Norma , Ahyong Vida , Miller Steve , Ayscue Patrick , Tato Cristina M. , Paul Simon , Kistler Amy , DeRisi Joseph L. , Crawford Emily D. 
Published: August 2020

AbstractWe identify a mutation in the N gene of SARS-CoV-2 that adversely affects annealing of a commonly used RT-PCR primer; epidemiologic evidence suggests the virus retains pathogenicity and competence for spread. This reinforces the importance of using multiple targets, preferably in at least 2 genes, for robust SARS-CoV-2 detection.Article Summary LineA SARS-CoV-2 variant that occurs worldwide and has spread in California significantly affects diagnostic sensitivity of an N gene assay, highlighting the need to employ multiple viral targets for detection.
Multi-omics phenotyping of the gut-liver axis allows health risk predictability fromin vivosubchronic toxicity tests of a low-dose pesticide mixture
Authors: Mesnage Robin , Teixeira Maxime , Mandrioli Daniele , Falcioni Laura , Ducarmon Quinten Raymond , Zwittink Romy Daniëlle , Amiel Caroline , Panoff Jean-Michel , Bourne Emma , Savage Emanuel , Mein Charles A , Belpoggi Fiorella , Antoniou Michael N 
Published: August 2020

AbstractHuman health effects from chronic exposure to mixtures of pesticide residues are little investigated. We compared standard histopathology and serum biochemistry measures and multi-omics analyses in anin vivosubchronic toxicity test of a mixture of six pesticide active ingredients frequently detected in foodstuffs (azoxystrobin, boscalid, chlorpyrifos, glyphosate, imidacloprid and thiabendazole). Sprague-Dawley rats were administered with the pesticide mixture with each ingredient at its regulatory permitted acceptable daily intake. Analysis of water and feed consumption, body weight, histopathology and serum biochemistry showed little or no physiological effects from exposure to the pesticide mixture. In marked contrast, analysis of the host-gut microbiome axis using serum and caecum metabolomics revealed that nicotinamide and tryptophan metabolism were affected, which suggested the initiation of a cell danger response, including adaptation to oxidative stress. Only limited effects were detected on the caecum microbiota by shotgun metagenomics. Further analyses ofin vitrobacterial cultures showed that growth ofLactobacillus rhamnosusandEscherichia colistrains was negatively impacted by the pesticide mixture at concentrations that were not inhibitory when exposure was to a single agent. Transcriptomics of the liver showed that 257 genes had their expression changed. Gene functions affected included those involved in the regulation of response to hormones and correlated with previously reported transcriptome changes following administration of nicotinamide. Genome-wide DNA methylation analysis of the same liver samples showed that 4255 CpG sites were differentially methylated (> 10% difference). Overall, we demonstrated that unlike standard blood biochemical and organ histological analysis, in-depth molecular profiling using a combination of high-throughput ‘-omics’ methods in laboratory animals exposed to low concentrations of pesticides reveals metabolic effects on the gut-liver axis, which can potentially be used as biomarkers for the prediction of future negative health outcomes. Our data suggest that adoption of multi-omics as part of regulatory risk assessment procedures will result in more accurate outcome measures, with positive public health implications.
PieParty: Visualizing cells from scRNA-seq data as pie charts
Authors: Kurtenbach Stefan , Dollar James J. , Cruz Anthony M. , Durante Michael A. , Harbour J. William 
Published: August 2020

AbstractSingle cell RNA sequencing (scRNA-seq) has been a transformative technology in many research fields. Dimensional reduction techniques such as UMAP and tSNE are used to visualize scRNA-seq data in two or three dimensions in order for cells to be clustered in biologically meaningful ways. Subsequently, gene expression is frequently mapped onto these plots to show the distribution of gene expression across the plots, for instance to distinguish cell types. However, plotting each cell with only one color leads to repetitive and unintuitive representations. Here, we present Pie Party, which allows scRNA-seq data to be plotted such that every cell is represented as a pie chart, and every slice in the pie charts corresponds to the gene expression of individual genes. This allows for the simultaneous visualization of the expression of multiple genes and gene networks. The resulting figures are information dense, space efficient and highly intuitive. PieParty is publicly available on GitHub athttps://github.com/harbourlab/PieParty.
Optimization and scaling of patient-derived brain organoids uncovers deep phenotypes of disease
Authors: Shah Kevan , Bedi Rishi , Rogozhnikov Alex , Ramkumar Pavan , Tong Zhixiang , Rash Brian , Stanton Morgan , Sorokin Jordan , Apaydin Cagsar , Batarse Anthony , Bergamaschi Julia , Blattner Robert , Brown Spencer , Bosshardt Anthony , Castrillo Carlos , Dang Brenda , Drusinsky Shiron , Enriquez Luigi , Grayson David , Hilliard Juliana , Hsu Pei-Ken , Johnson Chili , Jones Ryan , Lash Andy , Lee Chia-Yao , Li Kelly , McKay Austin , Mount Elliot , Nicola Justin , Oumzil Ismael , Paek Justin , Pascoe Deborah , Piepho Arden , Poust Sean , Quang Daphne , Schultz Matthew , Sims Jessica , Taylor Patrick , Treiman Geffen , Wueseke Oliver , Young Noah , Pollen Alex , Flanzer Doug , Chao Daniel , Skibinski Gaia , Kato Saul , Escola G. Sean 
Published: August 2020

AbstractCerebral organoids provide unparalleled access to human brain development in vitro. However, variability induced by current culture methodologies precludes using organoids as robust disease models. To address this, we developed an automated Organoid Culture and Assay (ORCA) system to support longitudinal unbiased phenotyping of organoids at scale across multiple patient lines. We then characterized organoid variability using novel machine learning methods and found that the contribution of donor, clone, and batch is significant and remarkably consistent over gene expression, morphology, and cell-type composition. Next, we performed multi-factorial protocol optimization, producing a directed forebrain protocol compatible with 96-well culture that exhibits low variability while preserving tissue complexity. Finally, we used ORCA to study tuberous sclerosis, a disease with known genetics but poorly representative animal models. For the first time, we report highly reproducible early morphological and molecular signatures of disease in heterozygous TSC+/− forebrain organoids, demonstrating the benefit of a scaled organoid system for phenotype discovery in human disease models.
Network asynchrony underlying increased broadband gamma power
Authors: Guyon Nicolas , Zacharias Leonardo Rakauskas , de Oliveira Eliezyer Fermino , Kim Hoseok , Leite João Pereira , Lopes-Aguiar Cleiton , Carlén Marie 
Published: August 2020

AbstractSynchronous activity of cortical inhibitory interneurons expressing parvalbumin (PV) underlies the expression of cortical gamma rhythms. Paradoxically, deficient PV inhibition is associated with increased broadband gamma power. Increased baseline broadband gamma is also a prominent characteristic in schizophrenia, and a hallmark of network alterations induced by N-methyl-D-aspartate receptor (NMDAR) antagonists such as ketamine. It has been questioned if enhanced broadband gamma power is a true rhythm, and if rhythmic PV inhibition is involved or not. It has been suggested that asynchronous and increased firing activities underlie broadband power increases spanning the gamma band. Using mice lacking NMDAR activity specifically in PV neurons to model deficient PV inhibition, we here show that local LFP (local field potential) oscillations and neuronal activity with decreased synchronicity generate increases in prefrontal broadband gamma power. Specifically, reduced spike time precision of both local PV interneurons and wide-spiking (WS) excitatory neurons contribute to increased firing rates, and spectral leakage of spiking activity (spike “contamination”) affecting the broadband gamma band. Desynchronization was evident at multiple time scales, with reduced spike-LFP entrainment, reduced cross-frequency coupling, and fragmentation of brain states. While local application of S(+)-ketamine in wildtype mice triggered network desynchronization and increases in broadband gamma power, our investigations suggest that disparate mechanisms underlie increased power of broadband gamma caused by genetic alteration of PV interneurons, and ketamine-induced power increases in broadband gamma. Our studies, thus, confirm that broadband gamma increases can arise from asynchronous activities, and demonstrate that long-term deficiency of PV inhibition can be a contributor.
Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome
Authors: Ehrenbolger Kai , Jespersen Nathan , Sharma Himanshu , Sokolova Yuliya Y. , Tokarev Yuri S. , Vossbrinck Charles R. , Barandun Jonas 
Published: August 2020

AbstractAssembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic microsporidia, conservation of energy via ribosomal hibernation and recycling is critical. The mechanisms by which hibernation is achieved in microsporidia, however, remain poorly understood. Here, we present the cryo-EM structure of the ribosome from Paranosema locustae spores, bound by the conserved eukaryotic hibernation and recycling factor Lso2. The microsporidian Lso2 homolog adopts a V-shaped conformation to bridge the mRNA decoding site and the large subunit tRNA binding sites, providing a reversible ribosome inactivation mechanism. Although microsporidian ribosomes are universally highly compacted, the P. locustae ribosome retains several rRNA segments absent in other microsporidia, and represents an intermediate state of rRNA reduction. In one case, the near complete reduction of an expansion segment has resulted in a single bound nucleotide, which acts as an architectural co-factor to stabilize a protein-protein interface. The presented structure highlights the reductive evolution in these emerging pathogens and sheds light on a conserved mechanism for eukaryotic ribosome hibernation.
Multi-species ELISA for the detection of antibodies against SARS-CoV-2 in animals
Authors: Wernike Kerstin , Aebischer Andrea , Michelitsch Anna , Hoffmann Donata , Freuling Conrad , Balkema-Buschmann Anne , Graaf Annika , Müller Thomas , Osterrieder Nikolaus , Rissmann Melanie , Rubbenstroth Dennis , Schön Jacob , Schulz Claudia , Trimpert Jakob , Ulrich Lorenz , Volz Asisa , Mettenleiter Thomas , Beer Martin 
Published: August 2020

SummarySevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic with millions of infected humans and hundreds of thousands of fatalities. As the novel disease - referred to as COVID-19 - unfolded, occasional anthropozoonotic infections of animals by owners or caretakers were reported in dogs, felid species and farmed mink. Further species were shown to be susceptible under experimental conditions. The extent of natural infections of animals, however, is still largely unknown. Serological methods will be useful tools for tracing SARS-CoV-2 infections in animals once test systems are validated for use in different species. Here, we developed an indirect multi-species ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The newly established ELISA was validated using 59 sera of infected or vaccinated animals including ferrets, raccoon dogs, hamsters, rabbits, chickens, cattle and a cat, and a total of 220 antibody-negative sera of the same animal species. Overall, a diagnostic specificity of 100.0% and sensitivity of 98.31% was achieved, and the functionality with every species included in this study could be demonstrated. Hence, a versatile and reliable ELISA protocol was established that enables high-throughput antibody detection in a broad range of animal species, which may be used for outbreak investigations, to assess the seroprevalence in susceptible species or to screen for reservoir or intermediate hosts.
Production of biopolymer precursors beta-alanine and L-lactic acid from CO2with metabolically versatileRhodococcus opacusDSM 43205
Authors: Salusjärvi Laura , Ojala Leo , Peddinti Gopal , Lienemann Michael , Jouhten Paula , Pitkänen Juha-Pekka , Toivari Mervi 
Published: August 2020

AbstractHydrogen oxidizing autotrophic bacteria are promising hosts for CO2conversion into chemicals. In this work, we engineered the metabolically versatile lithoautotrophic bacteriumRhodococcus opacusstrain DSM 43205 for synthesis of polymer precursors. Aspartate decarboxylase (panD) or lactate dehydrogenase (ldh) were expressed for beta-alanine or L-lactic acid production, respectively. The heterotrophic cultivations on glucose produced 25 mg L-1beta-alanine and 742 mg L-1L-lactic acid, while autotrophic cultivations with CO2, H2and O2resulted in the production of 1.8 mg L-1beta-alanine and 146 mg L-1L-lactic acid. Beta-alanine was also produced at 345 µg L-1from CO2in electrobioreactors, where H2and O2were provided by water electrolysis. This work demonstrates thatR. opacusDSM 43205 can be readily engineered to produce chemicals from CO2and provides base for its further metabolic engineering.