bluuebunny/crossref_metadata_2025_split huggingface dataset:
Superior Labral Anterior Posterior Repair and Biceps Tenodesis Surgery: Trends of the American Board of Orthopaedic Surgery Database
Authors: Cvetanovich Gregory L. , Gowd Anirudh K. , Frantz Travis L. , Erickson Brandon J. , Romeo Anthony A. 
Published: April 2020

Background: Recent evidence has specified indications for performing superior labral anterior posterior (SLAP) repair and biceps tenodesis (BT) for the treatment of bicipital-labral lesions in the shoulder. Trends in performance of these procedures are expected to reflect the growing body of research regarding this topic. Purpose: To report practice trends for the surgical treatment of SLAP lesions utilizing the American Board of Orthopaedic Surgery (ABOS) database, particularly in older patients. Study Design: Cohort study; Level of evidence, 3. Methods: The ABOS database was retrospectively queried between 2012 and 2017 by Current Procedural Terminology (CPT) codes for SLAP repair (29807), open BT (23430), and arthroscopic BT (29828). The patient population was excluded if any concomitant open shoulder procedure was performed. Trends over time were evaluated with respect to case volume, patient age, surgeon subspecialty, and whether a concomitant arthroscopic rotator cuff repair (RCR) was performed (CPT 29827). Results: A total of 9908 cases met inclusion/exclusion criteria: 4632 performed with RCR and 5276 performed without. The mean age of patients without RCR was 40.8 ± 13.8 years, while for those receiving RCR it was 55.0 ± 9.9 years ( P < .001). In patients without RCR, there was a significant decline in rate of SLAP repairs performed over this period ( P < .001). A significantly greater proportion of patients receiving open and arthroscopic BT were older than 35 years of age, compared with those receiving SLAP repair ( P < .001). Within the RCR cohort, there was also a significant decline in concomitant SLAP repairs performed ( P < .001) over the study period. With respect to BT, open BT was performed more frequently in the cohort without RCR (74.5%) than in the cohort with RCR (52.1%) ( P < .001). Similarly, arthroscopic BT was performed more commonly in the cohort with RCR (47.9%) than in the cohort without RCR (25.5%) ( P < .001). Conclusion: The ABOS database revealed significantly reduced rates of SLAP repairs performed in recent times. Trends with age remained consistent over time, in that SLAP repairs were predominantly performed in younger patients. Open BT was performed more frequently overall, but with an increased proportion of arthroscopic BT occurring with RCR. Arthroscopic BT was performed much more frequently with RCR than without.
Effect of a Law Requiring Prescription Drug Monitoring Program Use on Emergency Department Opioid Prescribing: A Single-Center Analysis
Authors: Zeiner Abigail L. , Burak Michelle A. , O’Sullivan David M. , Laskey Dayne 
Published: April 2020

Objective: To compare opioid prescribing behavior of emergency medicine providers following the enactment of Connecticut Public Act (PA) 15-198 at a large academic tertiary medical center. Methods: This study is a single-center pre and postlaw retrospective cohort of ED patients discharged with opioid prescriptions. Patients discharged from January 1, 2015, to June 30, 2015, were analyzed as the prelaw cohort, and patients discharged from January 1, 2016, to June 30, 2016, were analyzed as the postlaw cohort. The primary outcome was the cumulative dose of solid dosage forms of opioids per prescription, calculated in morphine milligram equivalents (MME). Results: A total of 10,307 prescriptions included in the final analysis. A statistically significant decrease in the primary outcome was seen in the postlaw cohort compared with the prelaw cohort, respectively (75 MME [interquartile range, IQR: 60-100) vs 80 MME [IQR: 75-150]; P < .001). The postlaw cohort also saw 1289 (22.2%) fewer opioid prescriptions, primarily driven by a reduction in the number of schedule II opioids prescribed. In a posthoc analysis, the primary outcome remained statistically significant even when opioid prescriptions were only included if their prebuilt settings were unchanged between pre and postlaw cohorts, respectively (85.1%; 95.6 MME (±56.0); n = 5041 vs 86.7 MME (±39.6); n = 3713; P < .001). Conclusions: The passage of PA 15-198 was associated with a decrease in the cumulative dose of opioids per prescription of solid dosage form products. This drop was precipitated by a transition from using opioids in schedule II to opioids in schedule IV and a modest decrease in prescribed opioid quantity.
Electroacupuncture combined with acarbose improves insulin sensitivity via peroxisome proliferator–activated receptor γ activation and produces a stronger glucose-lowering effect than acarbose alone in a rat model of steroid-induced insulin resistance
Authors: Chung Yuan-Chiang , Chen Ying-I , Lin Chih-Ming , Chang Su-Wei , Hsu Tai-Hao , Ho Wai-Jane , Lin Jaug-Geng , Chang Shih-Liang , Tzeng Chung-Yuh 
Published: April 2020

Background: Previous studies have reported that electroacupuncture (EA) induces a glucose-lowering effect by improving insulin resistance (IR) and reduces plasma free fatty acid (FFA) levels in rats with steroid-induced insulin resistance (SIIR). In addition, EA can activate cholinergic nerves and stimulate endogenous opioid peptides to lower plasma glucose in streptozotocin-induced hyperglycemic rats. The aim of this study was to investigate the glucose-lowering effects of 15 Hz EA at bilateral ST36 in combination with acarbose (ACA). We hypothesized that EA combined with ACA would produce a stronger glucose-lowering effect than ACA alone. Methods: In this study, normal Wistar rats and SIIR rats were randomly divided into two groups: ACA and ACA + EA. To explore the potential mechanisms underlying the glucose-lowering effect, plasma FFA/insulin and insulin transduction signal pathway proteins were assayed. Results: Combined ACA + EA treatment had a greater glucose-lowering effect than ACA alone in normal Wistar rats (−45% ± 3% vs −19% ± 3%, p < 0.001) and SIIR model rats (−43% ± 2% vs −16% ± 6%, p < 0.001). A significant reduction in plasma FFA levels, improvement in homeostatic model assessment of IR (HOMA-IR) index (−48.9% ± 4.0%, p < 0.001) and insulin sensitivity index (102% ± 16.9%, p < 0.001), and significant increases in insulin receptor substrate 1, glucose transporter 4, and peroxisome proliferator–activated receptor γ protein expressions in skeletal muscle, were also observed in the ACA + EA group of SIIR rats. Conclusion: Combined EA and ACA therapy had a greater glucose-lowering effect than ACA monotherapy; this combined therapy could be more effective at improving IR in SIIR rats, which may be related to a reduction in plasma FFA levels and an elevation of insulin signaling proteins. Whether this combined therapy has an effect in type 2 diabetes mellitus (T2DM) patients still needs to be explored.
Attitudes to Palliative Care in Patients With Neck-of-Femur Fracture—A Multicenter Survey
Authors: Harries Luke , Moore Andrew , Kendall Clare , Stanger Sophie , Stringfellow Thomas D. , Davies Andrew , Kelly Mike 
Published: April 2020

Introduction: The mortality of patients with neck-of-femur (NOF) fractures remains high, with increasing recognition of a subgroup of patients with predictable mortality. The role of palliative care in this group is poorly understood and underdeveloped. This research aims to investigate current clinician attitudes toward palliative care for patients with NOF fracture, and explore processes in place for early identification for patients nearing the end of life. Materials and Methods: An online survey was constructed with reference to National Institute for Health and Clinical Excellence end-of-life guidelines (CG13) and distributed to multidisciplinary teams involved in the care of NOF fracture patients in 4 hospitals of contrasting size and location in the United Kingdom. Results: Forty health-care professionals with a broad range of seniority and roles responded. The palliative care team was felt to have several potential roles in the care of NOF fracture patients, but there was difference of opinion between specialties about what these were. A number of barriers to palliative referral were identified, including stigma and active surgical management. The majority (75%) felt that all NOF fracture patients should have a discussion about ceiling of care, with difference of opinion about who should do so, and when. Discussion: As the elderly population has grown, so too has the volume of NOF fracture patients. It is increasingly important to identify and escalate patients who have poor prognosis following hip fracture and ensure they benefit from palliative care where appropriate. This survey demonstrates a barrier to addressing the care of these patients and a lack of consensus on identification and referral to appropriate palliative care planning. Conclusions: There should be close communication between specialties with regard to requirements for palliative care in NOF fracture patients, with ongoing education and clear local and national guidance to ensure they receive the right care at the right time.
Occult primary brain cancers manifesting in the aftermath of ischaemic and haemorrhagic stroke
Authors: Andersen Klaus Kaae , Tybjerg Anne Julie , Babore Alejandro Daniel , Olsen Tom Skyhøj 
Published: April 2020

Introduction Symptoms of occult brain cancer may mimic stroke. Misdiagnosis may lead to improper treatment and delayed diagnosis. We characterised strokes associated with occult primary brain cancer and determined risk that ischaemic and haemorrhagic strokes are associated with occult primary brain cancer. Patients and methods All patients with incident stroke in Denmark 2003–2015 were identified through the Danish Stroke Registry (n = 85,893) and matched 1:10 on age and sex to the Danish background population without a stroke history (n = 858,740). This cohort was linked to the Danish Cancer Registry and prevalence of occult primary brain cancer defined as the event of previously unknown primary brain cancer during a one-year follow-up was estimated. We used Cox regression models to study risk of occult primary brain cancer in comparison to the background population. Results Of 77,484 patients with ischaemic strokes, 39 (1 in 2000) were associated with primary brain cancer; of 8409 with haemorrhagic strokes, it was 126 (1 in 66). In the background cohort, 205 (1 in 4000) had occult primary brain cancer. The multivariate stroke risk factor analysis showed that patients with occult primary brain cancer differed significantly from those without occult primary brain cancer indicating they might have stroke mimics rather than true strokes. Discussion and conclusions: Strokes associated with occult primary brain cancer tend to be stroke mimics rather than true strokes. Primary brain cancer is rare in patients with ischaemic stroke (1 in 2000); risk that misdiagnosis results in maltreatment is, therefore, very low. Occult primary brain cancers are mainly found among patients with haemorrhagic stroke; they are not uncommon (1 in 66) and should always be kept in mind.
Patient perspectives and experiences with in vitro fertilization and genetic testing options
Authors: Rothwell Erin , Lamb Brandy , Johnson Erin , Gurtcheff Shawn , Riches Naomi , Fagan Melinda , Sabatello Maya , Johnstone Erica 
Published: April 2020

Objective: Decision-making and patient experiences with embryo selection during in vitro fertilization often include genetic testing options. The purpose of this study was to gain insight about the experiences and perspectives of women using in vitro fertilization and genetic technologies. Methods: Interviews ( n = 37) were conducted among female patients who had undergone in vitro fertilization, underwent expanded carrier screening, and were offered pre-implantation genetic testing for aneuploidy between July 2016 and July 2017. The interviews were transcribed and a content analysis was conducted on the transcripts. Results: Categories that emerged from the data analysis included unexpected outcomes, uncertainty, unanticipated emotional consequences, too much emphasis on the woman’s contributions and questions about embryo viability. Patient experiences with genetic technologies during in vitro fertilization played a significant role within these results. Conclusion: The emotional and psychological impacts of infertility during in vitro fertilization were the primary concerns discussed by participants. Future research is needed to identify ways to help manage unexpected outcomes and continuous uncertainty, including the increasing use of genetic technologies, to not add to the psychological burden of infertility. There is a need to explore more support options or counseling services for patients struggling with infertility during in vitro fertilization treatment.
Effect of temperature on the mechanical performance of plywood used in membrane-type LNG carrier insulation systems
Authors: Cha Seung-Joo , Kim Jeong-Dae , Kim Seul-Kee , Kim Jeong-Hyeon , Oh Hoon-Kyu , Kim Yong-Tai , Park Seong-Bo , Lee Jae-Myung 
Published: April 2020

AbstractIn this study, the mechanical performance of melamine–urea–formaldehyde (MUF) resin plywood composed of an orthotropic material, which is used as a structural material in liquefied natural gas (LNG) cargo containment systems (CCSs), is evaluated. With a decrease in temperature, the plywood changes from ductile to brittle under compressive loads; thus, it may fail to distribute the compressive loads caused by sloshing impact as well as lose its stiffness, which helps maintain the shape of the structure. However, only a few studies investigated the mechanical characteristics of MUF resin plywood under compressive loads caused by sloshing impact as well as the crack propagation and change in material features with decreasing temperatures. Therefore, the present study investigated the mechanical performance of MUF plywoods of different thicknesses under different temperatures and grain orientation parameters. The results indicate the mechanical properties of MUF plywood for compression with decreasing temperatures. Furthermore, based on thermomechanical analysis, this study shows that the critical temperature at which the plywood material tends to transition from ductile to brittle behavior is − 110 °C. This finding will help in the design of MUF plywood-based LNG CCSs considering its low-temperature brittleness.
PathME: pathway based multi-modal sparse autoencoders for clustering of patient-level multi-omics data
Authors: Lemsara Amina , Ouadfel Salima , Fröhlich Holger 
Published: April 2020

AbstractBackgroundRecent years have witnessed an increasing interest in multi-omics data, because these data allow for better understanding complex diseases such as cancer on a molecular system level. In addition, multi-omics data increase the chance to robustly identify molecular patient sub-groups and hence open the door towards a better personalized treatment of diseases. Several methods have been proposed for unsupervised clustering of multi-omics data. However, a number of challenges remain, such as the magnitude of features and the large difference in dimensionality across different omics data sources.ResultsWe propose a multi-modal sparse denoising autoencoder framework coupled with sparse non-negative matrix factorization to robustly cluster patients based on multi-omics data. The proposed model specifically leverages pathway information to effectively reduce the dimensionality of omics data into a pathway and patient specific score profile. In consequence, our method allows us to understand, which pathway is a feature of which particular patient cluster. Moreover, recently proposed machine learning techniques allow us to disentangle the specific impact of each individual omics feature on a pathway score. We applied our method to cluster patients in several cancer datasets using gene expression, miRNA expression, DNA methylation and CNVs, demonstrating the possibility to obtain biologically plausible disease subtypes characterized by specific molecular features. Comparison against several competing methods showed a competitive clustering performance. In addition, post-hoc analysis of somatic mutations and clinical data provided supporting evidence and interpretation of the identified clusters.ConclusionsOur suggested multi-modal sparse denoising autoencoder approach allows for an effective and interpretable integration of multi-omics data on pathway level while addressing the high dimensional character of omics data. Patient specific pathway score profiles derived from our model allow for a robust identification of disease subgroups.
Assessing breed integrity of Göttingen Minipigs
Authors: Reimer Christian , Ha Ngoc-Thuy , Sharifi Ahmad Reza , Geibel Johannes , Mikkelsen Lars Friis , Schlather Martin , Weigend Steffen , Simianer Henner 
Published: April 2020

AbstractBackgroundGöttingen Minipigs (GMP) is the smallest commercially available minipig breed under a controlled breeding scheme and is globally bred in five isolated colonies. The genetic isolation harbors the risk of stratification which might compromise the identity of the breed and its usability as an animal model for biomedical and human disease. We conducted whole genome re-sequencing of two DNA-pools per colony to assess genomic differentiation within and between colonies. We added publicly available samples from 13 various pig breeds and discovered overall about 32 M loci, ~ 16 M. thereof variable in GMPs. Individual samples were virtually pooled breed-wise. FSTbetween virtual and DNA pools, a phylogenetic tree, principal component analysis (PCA) and evaluation of functional SNP classes were conducted. An F-test was performed to reveal significantly differentiated allele frequencies between colonies. Variation within a colony was quantified as expected heterozygosity.ResultsPhylogeny and PCA showed that the GMP is easily discriminable from all other breads, but that there is also differentiation between the GMP colonies. Dependent on the contrast between GMP colonies, 4 to 8% of all loci had significantly different allele frequencies. Functional annotation revealed that functionally non-neutral loci are less prone to differentiation. Annotation of highly differentiated loci revealed a couple of deleterious mutations in genes with putative effects in the GMPs .ConclusionDifferentiation and annotation results suggest that the underlying mechanisms are rather drift events than directed selection and limited to neutral genome regions. Animal exchange seems not yet necessary. The Relliehausen colony appears to be the genetically most unique GMP sub-population and could be a valuable resource if animal exchange is required to maintain uniformity of the GMP.
Integrated likelihood for phylogenomics under a no-common-mechanism model
Authors: Tidwell Hunter , Nakhleh Luay 
Published: April 2020

Abstract
Background
Multi-locus species phylogeny inference is based on models of sequence evolution on gene trees as well as models of gene tree evolution within the branches of species phylogenies. Almost all statistical methods for this inference task assume a common mechanism across all loci as captured by a single value of each branch length of the species phylogeny.

Results
In this paper, we pursue a “no common mechanism" (NCM) model, where every gene tree evolves according to its own parameters of the species phylogeny. Based on this model, we derive an analytically integrated likelihood of both species trees and networks given the gene trees of multiple loci under an NCM model. We demonstrate the performance of inference under this integrated likelihood on both simulated and biological data.

Conclusions
The model presented here will afford opportunities for exploring connections among various criteria for estimating species phylogenies from multiple, independent loci. Furthermore, further development of this model could potentially result in more efficient methods for searching the space of species phylogenies by focusing solely on the topology of the phylogeny.
Getting insight into the pan-genome structure with PangTree
Authors: Dziadkiewicz Paulina , Dojer Norbert 
Published: April 2020

Abstract
Background
The term pan-genome was proposed to denominate collections of genomic sequences jointly analyzed or used as a reference. The constant growth of genomic data intensifies development of data structures and algorithms to investigate pan-genomes efficiently.

Results
This work focuses on providing a tool for discovering and visualizing the relationships between the sequences constituting a pan-genome. A new structure to represent such relationships – called affinity tree – is proposed. Each node of this tree has assigned a subset of genomes, as well as their homogeneity level and averaged consensus sequence. Moreover, subsets assigned to sibling nodes form a partition of the genomes assigned to their parent.

Conclusions
Functionality of affinity tree is demonstrated on simulated data and on the Ebola virus pan-genome. Furthermore, two software packages are provided: PangTreeBuild constructs affinity tree, while PangTreeVis presents its result.
Transcriptomic analysis of sea cucumber (Holothuria leucospilota) coelomocytes revealed the echinoderm cytokine response during immune challenge
Authors: Wu Xiaofen , Chen Ting , Huo Da , Yu Zonghe , Ruan Yao , Cheng Chuhang , Jiang Xiao , Ren Chunhua 
Published: April 2020

AbstractBackgroundThe sea cucumberHolothuria leucospilotabelongs to echinoderm, which is evolutionally the most primitive group of deuterostomes. Sea cucumber has a cavity between its digestive tract and the body wall that is filled with fluid and suspended coelomic cells similar to blood cells. The humoral immune response of the sea cucumber is based on the secretion of various immune factors from coelomocytes into the coelomic cavity. The aim of this study is to lay out a foundation for the immune mechanisms in echinoderms and their origins in chordates by using RNA-seq.ResultsSea cucumber primary coelomocytes were isolated from healthyH. leucospilotaand incubated with lipopolysaccharide (LPS, 10 μg/ml), polyinosinic-polycytidylic acid [Poly (I:C), 10 μg/ml] and heat-inactivedVibrio harveyi(107cell/ml) for 24 h, respectively. After high-throughput mRNA sequencing on an Illumina HiSeq2500, a de novo transcriptome was assembled and the Unigenes were annotated. Thirteen differentially expressed genes (DEGs) were selected randomly from our data and subsequently verified by using RT-qPCR. The results of RT-qPCR were consistent with those of the RNA-seq (R2 = 0.61). The top 10 significantly enriched signaling pathways and immune-related pathways of the common and unique DEGs were screened from the transcriptome data. Twenty-one cytokine candidate DEGs were identified, which belong to 4 cytokine families, namely, BCL/CLL, EPRF1, IL-17 and TSP/TPO. Gene expression in response to LPS dose-increased treatment (0, 10, 20 and 50 μg/ml) showed that IL-17 family cytokines were significantly upregulated after 10 μg/ml LPS challenge for 24 h.ConclusionA de novo transcriptome was sequenced and assembled to generate the gene expression profiling across the sea cucumber coelomocytes treated with LPS, Poly (I:C) andV. harveyi. The cytokine genes identified in DEGs could be classified into 4 cytokine families, in which the expression of IL-17 family cytokines was most significantly induced after 10 μg/ml LPS challenge for 24 h. Our findings have laid the foundation not only for the research of molecular mechanisms related to the immune response in echinoderms but also for their origins in chordates, particularly in higher vertebrates.