bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prehospital cardiopulmonary resuscitation duration and neurological outcome after adult out-of-hospital cardiac arrest by location of arrest
Authors: Kishimori Takefumi , Matsuyama Tasuku , Kiyohara Kosuke , Kitamura Tetsuhisa , Shida Haruka , Kiguchi Takeyuki , Nishiyama Chika , Kobayashi Daisuke , Okabayashi Satoe , Shimamoto Tomonari , Sado Junya , Kawamura Takashi , Iwami Taku 
Published: April 2020

Background
Little is known about the association between prehospital cardiopulmonary resuscitation duration for adults with out-of-hospital cardiac arrest and outcome by the location of arrests. This study aimed to investigate the association between prehospital cardiopulmonary resuscitation duration and one-month survival with favourable neurological outcome.

Methods
We analysed 276,391 adults aged 18 years and older with out-of-hospital cardiac arrest of medical origin before emergency medical service arrival. Prehospital cardiopulmonary resuscitation duration was defined as the time from emergency medical service-initiated cardiopulmonary resuscitation to prehospital return of spontaneous circulation or to hospital arrival. The primary outcome was one-month survival with favourable neurological outcome (cerebral performance category 1 or 2). The association between prehospital cardiopulmonary resuscitation duration and favourable neurological outcome was assessed using univariable and multivariable logistic regression analyses.

Results
The proportion of favourable neurological outcomes was 2.3% in total, 7.6% in public locations, 1.5% in residential locations and 0.7% in nursing homes (P &lt; 0.001). In univariable and multivariable logistic regression analyses, longer prehospital cardiopulmonary resuscitation duration was associated with poor neurological outcome, regardless of arrest location (P for trend &lt; 0.001). Patients with shockable rhythm in both public and residential locations had better neurological outcome than those in nursing homes at any time point, and residential and public locations had a similar neurological outcome tendency among patients with shockable rhythm.

Conclusions
Longer prehospital cardiopulmonary resuscitation duration was independently associated with a lower proportion of patients with favourable neurological outcomes. Moreover, the association between prehospital cardiopulmonary resuscitation duration and neurological outcome differed according to the location of arrest and the first documented rhythm.
Effect of dimethyl fumarate on lymphocyte subsets in patients with relapsing multiple sclerosis
Authors: Buckle Guy , Bandari Daniel , Greenstein Jeffrey , Gudesblatt Mark , Khatri Bhupendra , Kita Mariko , Repovic Pavle , Riser Emily , Weinstock-Guttman Bianca , Thrower Ben , Loring Sherrill , Riester Katherine , Everage Nick , Prada Claudia , Koulinska Irene , Mann Monica 
Published: April 2020

Background In patients treated with dimethyl fumarate, absolute lymphocyte count decline typically occurs during the first year and then plateaus; early drops have been associated with the development of severe prolonged lymphopenia. Objective We investigated the effect of dimethyl fumarate on absolute lymphocyte counts and CD4+/CD8+ T cells in patients with relapsing–remitting multiple sclerosis treated with dimethyl fumarate in routine practice. Methods Lymphocyte data were collected via medical chart abstraction. Primary endpoint: change from baseline in absolute lymphocyte count and CD4+/CD8+ counts at 6‐month intervals following dimethyl fumarate initiation. Results Charts of 483 patients were abstracted and 476 patients included in the analysis. Mean baseline absolute lymphocyte count (2.23 × 109/l) decreased by ∼39% (95% confidence interval: –41.1 to –37.2) by month 6 and 44% (95% confidence interval: –46.6 to –42.1) by month 12. CD4+ and CD8+ T-cell subsets strongly correlated with absolute lymphocyte count, with greater decreases from baseline to 6 months vs 6–12 months, and in CD8+ vs CD4+ T cells. Prior natalizumab was not a risk factor for lymphopenia. Conclusion Dimethyl fumarate-associated decline in absolute lymphocyte count in the first 12 months correlated with decline in CD4+ and CD8+ T cells and was independent of prior natalizumab. Absolute lymphocyte count monitoring continues to be an effective strategy to identify patients at risk of prolonged lymphopenia.
The efficacy of spinal anaesthesia with fentanyl supplementation for arthroscopic knee surgery: A meta-analysis of randomized controlled studies
Authors: Chen Jianfeng , Yan Chao , Luo Chaosong , Li Guizhen , Yang Zong 
Published: April 2020

Introduction: The efficacy of spinal anaesthesia with fentanyl supplementation for arthroscopic knee surgery remains controversial. We conducted a systematic review and meta-analysis to explore the influence of fentanyl supplementation for arthroscopic knee surgery. Methods: We searched PubMed, Embase, Web of Science, EBSCO and Cochrane Library databases through May 2019 for randomized controlled trials (RCTs) assessing the efficacy and safety of fentanyl supplementation for arthroscopic knee surgery. This meta-analysis is performed using the random-effects model. Results: Five RCTs are included in the meta-analysis. Overall, compared with the control group for knee arthroscopy, fentanyl supplementation is associated with decreased time for sensory block regression to S1 (mean difference (MD) = −47.38; 95% confidence interval (CI) = −56.74 to −38.02; p < 0.00001), first ambulation (MD = −41.65; 95% CI = −65.11 to −18.19; p = 0.0005), first urination (MD = −23.45; 95% CI = −32.16 to −14.74; p < 0.00001) and hospital discharge (MD = −29.39; 95% CI = −44.73 to −14.06; p = 0.0002) but has no substantial influence on onset time of anaesthesia (MD = 0.50; 95% CI = −1.71 to 2.70; p = 0.66), duration for motor blockade (MD = −42.56; 95% CI = −119.18 to 34.07; p = 0.28), pruritus (risk ratio (RR) = 2.17; 95% CI = 0.28 to 16.90; p = 0.46) or nausea (RR = 0.42; 95% CI = 0.10 to 1.81; p = 0.25). Conclusions: Fentanyl supplementation benefits postoperative recovery after knee arthroscopy.
Femoral Tunnel Placement Analysis in ACL Reconstruction Through Use of a Novel 3-Dimensional Reference With Biplanar Stereoradiographic Imaging
Authors: Montreuil Julien , Saleh Joseph , Cresson Thierry , De Guise Jacques A. , Lavoie Frédéric 
Published: April 2020

Background: The femoral-sided anatomic footprint of the anterior cruciate ligament (ACL) has been widely studied during the past decades. Nonanatomic placement is an important cause of ACL reconstruction (ACLR) failure. Purpose: To describe femoral tunnel placement in ACLR through use of a comprehensive 3-dimensional (3D) cylindrical coordinate system combining both the traditional clockface technique and the quadrant method. Our objective was to validate this technique and evaluate its reproducibility. Study Design: Descriptive laboratory study. Methods: The EOS Imaging System was used to make 3D models of the knee for 37 patients who had undergone ACLR. We designed an automated cylindrical reference software program individualized to the distal femoral morphology of each patient. Cylinder parameters were collected from 2 observers’ series of 3D models. Each independent observer also manually measured the corresponding parameters using a lateral view of the 3D contours and a 2-dimensional stereoradiographic image for the corresponding patient. Results: The average cylinder produced from the first observer’s EOS 3D models had a 30.0° orientation (95% CI, 28.4°-31.5°), 40.4 mm length (95% CI, 39.3-41.4 mm), and 19.3 mm diameter (95% CI, 18.6-20.0 mm). For the second observer, these measurements were 29.7° (95% CI, 28.1°-31.3°), 40.7 mm (95% CI, 39.7-41.8 mm), and 19.7 mm (95% CI, 18.8-20.6 mm), respectively. Our method showed moderate intertest intraclass correlation among all 3 measuring techniques for both length ( r = 0.68) and diameter ( r = 0.63) but poor correlation for orientation ( r = 0.44). In terms of interobserver reproducibility of the automated EOS 3D method, similar results were obtained: moderate to excellent correlations for length ( r = 0.95; P < .001) and diameter ( r = 0.66; P < .001) but poor correlation for orientation ( r = 0.29; P < .08). With this reference system, we were able to describe the placement of each individual femoral tunnel aperture, averaging a difference of less than 10 mm from the historical anatomic description by Bernard et al. Conclusion: This novel 3D cylindrical coordinate system using biplanar, stereoradiographic, low-irradiation imaging showed a precision comparable with standard manual measurements for ACLR femoral tunnel placement. Our results also suggest that automated cylinders issued from EOS 3D models show adequate accuracy and reproducibility. Clinical Relevance: This technique will open multiple possibilities in ACLR femoral tunnel placement in terms of preoperative planning, postoperative feedback, and even intraoperative guidance with augmented reality.
Intrinsic limitations in mainstream methods of identifying network motifs in biology
Authors: Fodor James , Brand Michael , Stones Rebecca J. , Buckle Ashley M. 
Published: April 2020

Abstract
Background
Network motifs are connectivity structures that occur with significantly higher frequency than chance, and are thought to play important roles in complex biological networks, for example in gene regulation, interactomes, and metabolomes. Network motifs may also become pivotal in the rational design and engineering of complex biological systems underpinning the field of synthetic biology. Distinguishing true motifs from arbitrary substructures, however, remains a challenge.

Results
Here we demonstrate both theoretically and empirically that implicit assumptions present in mainstream methods for motif identification do not necessarily hold, with the ramification that motif studies using these mainstream methods are less able to effectively differentiate between spurious results and events of true statistical significance than is often presented. We show that these difficulties cannot be overcome without revising the methods of statistical analysis used to identify motifs.

Conclusions
Present-day methods for the discovery of network motifs, and, indeed, even the methods for defining what they are, are critically reliant on a set of incorrect assumptions, casting a doubt on the scientific validity of motif-driven discoveries. The implications of these findings are therefore far-reaching across diverse areas of biology.
SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
Authors: Bergenstråhle Joseph , Bergenstråhle Ludvig , Lundeberg Joakim 
Published: April 2020

AbstractBackgroundTechnological developments in the emerging field of spatial transcriptomics have opened up an unexplored landscape where transcript information is put in a spatial context. Clustering commonly constitutes a central component in analyzing this type of data. However, deciding on the number of clusters to use and interpreting their relationships can be difficult.ResultsWe introduce SpatialCPie, an R package designed to facilitate cluster evaluation for spatial transcriptomics data. SpatialCPie clusters the data at multiple resolutions. The results are visualized with pie charts that indicate the similarity between spatial regions and clusters and a cluster graph that shows the relationships between clusters at different resolutions. We demonstrate SpatialCPie on several publicly available datasets.ConclusionsSpatialCPie provides intuitive visualizations of cluster relationships when dealing with Spatial Transcriptomics data.
Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes
Authors: Mih Nathan , Monk Jonathan M. , Fang Xin , Catoiu Edward , Heckmann David , Yang Laurence , Palsson Bernhard O. 
Published: April 2020

AbstractBackgroundThe reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studiedEscherichia coliK-12 MG1655 strain. The combination of the two leads to the formation of a structural systems biology framework, which we have used to analyze differences between the reactive oxygen species (ROS) sensitivity of the proteomes of sequenced strains ofE. coli. As proteins are one of the main targets of oxidative damage, understanding how the genetic changes of different strains of a species relates to its oxidative environment can reveal hypotheses as to why these variations arise and suggest directions of future experimental work.ResultsCreating a reference structural proteome forE. coliallows us to comprehensively map genetic changes in 1764 different strains to their locations on 4118 3D protein structures. We use metabolic modeling to predict basal ROS production levels (ROStype) for 695 of these strains, finding that strains with both higher and lower basal levels tend to enrich their proteomes with antioxidative properties, and speculate as to why that is. We computationally assess a strain’s sensitivity to an oxidative environment, based on known chemical mechanisms of oxidative damage to protein groups, defined by their localization and functionality. Two general groups - metalloproteins and periplasmic proteins - show enrichment of their antioxidative properties between the 695 strains with a predicted ROStype as well as 116 strains with an assigned pathotype. Specifically, proteins that a) utilize a molybdenum ion as a cofactor and b) are involved in the biogenesis of fimbriae show intriguing protective properties to resist oxidative damage. Overall, these findings indicate that a strain’s sensitivity to oxidative damage can be elucidated from the structural proteome, though future experimental work is needed to validate our model assumptions and findings.ConclusionWe thus demonstrate that structural systems biology enables a proteome-wide, computational assessment of changes to atomic-level physicochemical properties and of oxidative damage mechanisms for multiple strains in a species. This integrative approach opens new avenues to study adaptation to a particular environment based on physiological properties predicted from sequence alone.
The genetic basis of hybrid male sterility in sympatric Primulina species
Authors: Feng Chen , Yi Huiqin , Yang Lihua , Kang Ming 
Published: April 2020

Abstract
Background
Sympatric sister species provide an opportunity to investigate the genetic mechanisms and evolutionary forces that maintain species boundaries. The persistence of morphologically and genetically distinct populations in sympatry can only occur if some degree of reproductive isolation exists. A pair of sympatric sister species of Primulina (P. depressa and P. danxiaensis) was used to explore the genetic architecture of hybrid male sterility.

Results
We mapped one major- and seven minor-effect quantitative trait loci (QTLs) that underlie pollen fertility rate (PFR). These loci jointly explained 55.4% of the phenotypic variation in the F2 population. A Bateson–Dobzhansky–Muller (BDM) model involving three loci was observed in this system. We found genotypic correlations between hybrid male sterility and flower morphology, consistent with the weak but significant phenotypic correlations between PFR and floral traits.

Conclusions
Hybrid male sterility in Primulina is controlled by a polygenic genetic basis with a complex pattern. The genetic incompatibility involves a three-locus BDM model. Hybrid male sterility is genetically correlated with floral morphology and divergence hitchhiking may occur between them.
Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23
Authors: Taslima Khanam , Wehner Stefanie , Taggart John B. , de Verdal Hugues , Benzie John A. H. , Bekaert Michaël , McAndrew Brendan J. , Penman David J. 
Published: April 2020

AbstractBackgroundTilapias (Family Cichlidae) are the second most important group of aquaculture species in the world. They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Different sex-determining loci (linkage group 1, 20 and 23) have been detected in various tilapia stocks. The ‘genetically improved farmed tilapia’ (GIFT) stock, founded from multiple Nile tilapia (Oreochromis niloticus) populations, with some likely to have been introgressed withO. mossambicus, is a key resource for tilapia aquaculture. The sex-determining mechanism in the GIFT stock was unknown, but potentially complicated due to its multiple origins.ResultsA bulk segregant analysis (BSA) version of double-digest restriction-site associated DNA sequencing (BSA-ddRADseq) was developed and used to detect and position sex-linked single nucleotide polymorphism (SNP) markers in 19 families from the GIFT strain breeding nucleus and two Stirling families as controls (a single XY locus had been previously mapped to LG1 in the latter). About 1500 SNPs per family were detected across the genome. Phenotypic sex in Stirling families showed strong association with LG1, whereas only SNPs located in LG23 showed clear association with sex in the majority of the GIFT families. No other genomic regions linked to sex determination were apparent. This region was validated using a series of LG23-specific DNA markers (five SNPs with highest association to sex from this study, the LG23 sex-associated microsatelliteUNH898andARO172,and the recently isolatedamhymarker for individual fish (n = 284).ConclusionsPerhaps surprisingly given its multiple origins, sex determination in the GIFT strain breeding nucleus was associated only with a locus in LG23. BSA-ddRADseq allowed cost-effective analysis of multiple families, strengthening this conclusion. This technique has potential to be applied to other complex traits. The sex-linked SNP markers identified will be useful for potential marker-assisted selection (MAS) to control sex-ratio in GIFT tilapia to suppress unwanted reproduction during growout.
P finder: genomic and metagenomic annotation of RNase P RNA gene (rnpB)
Authors: Ellis J. Christopher 
Published: April 2020

Abstract
Background
The rnpB gene encodes for an essential catalytic RNA (RNase P). Like other essential RNAs, RNase P’s sequence is highly variable. However, unlike other essential RNAs (i.e. tRNA, 16 S, 6 S,...) its structure is also variable with at least 5 distinct structure types observed in prokaryotes. This structural variability makes it labor intensive and challenging to create and maintain covariance models for the detection of RNase P RNA in genomic and metagenomic sequences. The lack of a facile and rapid annotation algorithm has led to the rnpB gene being the most grossly under annotated essential gene in completed prokaryotic genomes with only a 24% annotation rate. Here we describe the coupling of the largest RNase P RNA database with the local alignment scoring algorithm to create the most sensitive and rapid prokaryote rnpB gene identification and annotation algorithm to date.

Results
Of the 2772 completed microbial genomes downloaded from GenBank only 665 genomes had an annotated rnpB gene. We applied P Finder to these genomes and were able to identify 2733 or nearly 99% of the 2772 microbial genomes examined. From these results four new rnpB genes that encode the minimal T-type P RNase P RNAs were identified computationally for the first time. In addition, only the second C-type RNase P RNA was identified in Sphaerobacter thermophilus. Of special note, no RNase P RNAs were detected in several obligate endosymbionts of sap sucking insects suggesting a novel evolutionary adaptation.

Conclusions
The coupling of the largest RNase P RNA database and associated structure class identification with the P Finder algorithm is both sensitive and rapid, yielding high quality results to aid researchers annotating either genomic or metagenomic data. It is the only algorithm to date that can identify challenging RNAse P classes such as C-type and the minimal T-type RNase P RNAs. P Finder is written in C# and has a user-friendly GUI that can run on multiple 64-bit windows platforms (Windows Vista/7/8/10). P Finder is free available for download at https://github.com/JChristopherEllis/P-Finder as well as a small sample RNase P RNA file for testing.
Genomic characterization of Lactobacillus fermentum DSM 20052
Authors: Brandt Katelyn , Nethery Matthew A. , O’Flaherty Sarah , Barrangou Rodolphe 
Published: April 2020

Abstract
Background
Lactobacillus fermentum, a member of the lactic acid bacteria complex, has recently garnered increased attention due to documented antagonistic properties and interest in assessing the probiotic potential of select strains that may provide human health benefits. Here, we genomically characterize L. fermentum using the type strain DSM 20052 as a canonical representative of this species.

Results
We determined the polished whole genome sequence of this type strain and compared it to 37 available genome sequences within this species. Results reveal genetic diversity across nine clades, with variable content encompassing mobile genetic elements, CRISPR-Cas immune systems and genomic islands, as well as numerous genome rearrangements. Interestingly, we determined a high frequency of occurrence of diverse Type I, II, and III CRISPR-Cas systems in 72% of the genomes, with a high level of strain hypervariability.

Conclusions
These findings provide a basis for the genetic characterization of L. fermentum strains of scientific and commercial interest. Furthermore, our study enables genomic-informed selection of strains with specific traits for commercial product formulation, and establishes a framework for the functional characterization of features of interest.
Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches
Authors: Babenko Vladislav V. , Podgorny Oleg V. , Manuvera Valentin A. , Kasianov Artem S. , Manolov Alexander I. , Grafskaia Ekaterina N. , Shirokov Dmitriy A. , Kurdyumov Alexey S. , Vinogradov Dmitriy V. , Nikitina Anastasia S. , Kovalchuk Sergey I. , Anikanov Nickolay A. , Butenko Ivan O. , Pobeguts Olga V. , Matyushkina Daria S. , Rakitina Daria V. , Kostryukova Elena S. , Zgoda Victor G. , Baskova Isolda P. , Trukhan Vladimir M. , Gelfand Mikhail S. , Govorun Vadim M. , Schiöth Helgi B. , Lazarev Vassili N. 
Published: April 2020

Abstract
Background
Salivary cell secretion (SCS) plays a critical role in blood feeding by medicinal leeches, making them of use for certain medical purposes even today.

Results
We annotated the Hirudo medicinalis genome and performed RNA-seq on salivary cells isolated from three closely related leech species, H. medicinalis, Hirudo orientalis, and Hirudo verbana. Differential expression analysis verified by proteomics identified salivary cell-specific gene expression, many of which encode previously unknown salivary components. However, the genes encoding known anticoagulants have been found to be expressed not only in salivary cells. The function-related analysis of the unique salivary cell genes enabled an update of the concept of interactions between salivary proteins and components of haemostasis.

Conclusions
Here we report a genome draft of Hirudo medicinalis and describe identification of novel salivary proteins and new homologs of genes encoding known anticoagulants in transcriptomes of three medicinal leech species. Our data provide new insights in genetics of blood-feeding lifestyle in leeches.