bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transplant outcomes in kidney recipients with lupus nephritis, and systematic review
Authors: Kim J E , Kim Y C , Min S-l , Lee H , Ha J , Chin H J , Kim Y S , Han S S 
Published: January 2020

Background Despite improved survival of patients with lupus nephritis (LN), some require kidney transplantation because of progression to end-stage renal disease (ESRD). However, the transplant outcomes of these patients and other recipients have not been thoroughly compared. Methods In total, 1848 Korean kidney recipients who underwent transplantation from 1998 to 2017 at two tertiary referral centers were evaluated retrospectively. Among them, 28 recipients with LN, and 50 control recipients matched by age, sex, and donor type, were compared with respect to graft and patient survival. We pooled our data with 17 previous cohort studies in which the graft survival of recipients with LN was described in detail. Results During the median follow-up period of 9.5 years (maximum 21 years), graft failure (GF) occurred in 10.7% and 16.0% of LN and control recipients, respectively. No differences were found in the rates of GF and death-censored graft failure or patient survival between the two groups. The risks of acute T cell-mediated and antibody-mediated rejection were also similar between the two groups. The pooled analysis showed similar 1- and 5-year graft survival rates between LN and control recipients. Conclusions Kidney transplantation is an acceptable option in patients with concurrent LN and ESRD.
Axial Rotational Alignment in Mobile-Bearing Total Ankle Arthroplasty
Authors: Hintermann Beat , Susdorf Roman , Krähenbühl Nicola , Ruiz Roxa 
Published: January 2020

Background: The presence of an interface between the tibial component and the polyethylene insert (PI) in mobile-bearing total ankle arthroplasty (TAA) may allow the talus to adapt its axial position according to the patient’s anatomy. However, little is known about differences of the axial talar rotation between patients following mobile-bearing TAA. Therefore, the aim of this study was to assess the relative axial rotation between the talar and tibial component intraoperatively and after a minimum follow-up of 3 years following mobile-bearing TAA. Methods: The relative axial rotation between the talar and the tibial component was measured intraoperatively in a cohort of 58 patients who underwent mobile-bearing TAA. In addition, it was measured on weightbearing computed tomography (CT) scans in 48 patients after a mean of 6.3 (3.0-16.3) years following mobile-bearing TAA. The pre- and postoperative alignment of the ankle joint/tibial component and hindfoot assessed on conventional radiographs was correlated with the intra- and postoperatively determined relative axial rotation of the talar and tibial component. Results: The mean intra- and postoperative axial talar component position was 1.7 (range, 14 internal to 14 external) and 1.4 (range, 12 internal to 20 external) degrees toward internal when compared to the tibial component ( P = .960). The preoperative sagittal alignment of the distal tibia correlated with the intraoperatively determined relative axial rotation between the talar and the tibial component ( P = .019). Conclusion: The wide range of the relative axial rotation between the tibial and talar component suggests that it is crucial to allow the talus to intraoperatively find a position that corresponds to the patient’s individual anatomy. The fact that the range of axial rotation was similar after a minimum of 3 years measured under weightbearing conditions suggests that structural changes of the osteoarthritic ankle may be the main determining factors for the axial rotational position of the talus. Our findings improve current understanding of proper implant position during TAA. In addition, the current study provides a reliable method to assess the postoperative axial position of the prosthesis components. The high interindividual variability of the relative rotation between the tibial and talar component in the axial plane suggests that axial malpositioning following TAA may be a more common issue than currently expected. Our findings may help to improve the assessment of patients with persistent pain following TAA. Level of Evidence: Level III, comparative series.
The crosstalk between hypoxia-inducible factor-1α and microRNAs in acute kidney injury
Authors: Wang Zhiyu , Zhang Wen 
Published: January 2020

Acute kidney injury (AKI) is a common critical clinical disease that is characterized by a rapid decline in renal function and reduced urine output. Ischemia and hypoxia are dominant pathophysiological changes in AKI that are induced by many factors, and the role of the “master” regulator hypoxia-inducible factor-1α (HIF-1α) is well recognized in AKI-related studies. MicroRNAs have been found to act as critical regulators of AKI pathophysiological process. More studies now have reported mutual interactions between HIF-1α and microRNAs in AKI. Therefore, in this brief review, we look into the mutual regulatory mechanisms between HIF-1α and microRNAs and discuss their function in the process of AKI. Recent studies demonstrated that HIF-1α is involved in the regulation of multiple functional microRNAs in AKI, and in turn, the level of HIF-1α is regulated by specific microRNAs. However, the role of the interactions between HIF-1α and microRNAs in AKI are controversial, and whether interventions targeting relevant mechanisms could achieve clinical benefits is not clear. Much work remains to further explore the value of targeting the HIF-1α-microRNA pathway in AKI treatment. Impact statement At first, we have discussed the role of hypoxia-inducible factor-1α (HIF-1α) and microRNAs in the acute kidney injury (AKI) pathophysiology. Then we have summarized the interactions between HIF-1α and microRNAs reported by AKI-related studies and concluded their regulatory effects in AKI process. Finally, we have made a vision of HIF-1α/microRNAs pathway’s potential as the intervention target in AKI. The mini review provides a systematic understanding of the crosstalk between HIF-1α and microRNAs in AKI and their effects on AKI pathophysiology and treatment.
Validation of prognostic accuracy of MESH, HKLC, and BCLC classifications in a large German cohort of hepatocellular carcinoma patients
Authors: Heinrich Sophia , Sprinzl Martin , Schmidtmann Irene , Heil Elena , Koch Sandra , Czauderna Carolin , Heinrich Bernd , Philippe P Diggs Laurence , Wörns Marcus‐Alexander , Kloeckner Roman , Galle Peter R , Marquardt Jens U , Weinmann Arndt 
Published: January 2020

Background and aimThe Barcelona Clinic Liver Cancer (BCLC) staging system is commonly used to classify hepatocellular carcinoma (HCC) patients. However, other staging classification schemes have been proposed. We aimed to compare the prognostic accuracy of the Hong Kong Liver Cancer Staging (HKLC), the Model to Estimate Survival for HCC (MESH), and the BCLC staging systems using a Western cohort of HCC patients.MethodsWe retrospectively analyzed 918 patients diagnosed with HCC treated at the University Medical Center of Mainz between 2005 and 2014. We compared the predictive power of survival time of the BCLC, HKLC, and MESH. Predictive ability was tested using the integrated Brier score (IBS) and Harrell’s C index.ResultsKaplan–Meier analyses showed significant differences in survival between stages defined by the BCLC, HKLC, and MESH. The HKLC classification demonstrated a more robust classification concordance and lower prediction error compared to the BCLC and MESH. In addition, we found that the BCLC offers superior predictive ability to the MESH in the first four years, whereas the MESH is superior for long‐term predictions.ConclusionOur analyses confirm the prognostic value of three different HCC scoring systems. When compared, the HKLC provides superior prognostication ability.
Neuromuscular Exercises Improve Shoulder Function More Than Standard Care Exercises in Patients With a Traumatic Anterior Shoulder Dislocation: A Randomized Controlled Trial
Authors: Eshoj Henrik Rode , Rasmussen Sten , Frich Lars Henrik , Hvass Inge , Christensen Robin , Boyle Eleanor , Jensen Steen Lund , Søndergaard Jens , Søgaard Karen , Juul-Kristensen Birgit 
Published: January 2020

Background: There is an important gap in knowledge about the effectiveness of nonoperative treatment (exercise) for patients with traumatic primary and recurrent anterior shoulder dislocations (ASDs). Purpose/Hypothesis: The purpose of this study was to assess the efficacy and safety of physical therapist–supervised, shoulder instability neuromuscular exercise (SINEX) versus self-managed, home-based, standard care shoulder exercise (HOMEX) in patients with traumatic ASDs. The hypothesis was that SINEX would have a larger effect and fewer adverse events compared with HOMEX. Study Design: Randomized controlled trial; Level of evidence, 2. Methods: A total of 56 participants with radiographically verified, trauma-initiated primary or recurrent ASDs and self-reported decreased shoulder function were randomized to 12 weeks of either SINEX or HOMEX. The SINEX program consisted of 7 exercises, individually progressing from basic (2 × 20 repetitions each day) to elite (2 × 10 repetitions, 3 times weekly). The HOMEX program included 5 shoulder exercises performed 3 times weekly (2 × 10 repetitions). The primary outcome was the Western Ontario Shoulder Instability Index (WOSI) score, ranging from 0 (best possible) to 2100. The between-group minimal clinically important difference at 12 weeks was 250 points. Secondary outcomes included WOSI subdomain scores, patient-reported ratings of kinesiophobia and pain, objective shoulder function, patient satisfaction, and number of adverse events. Results: The between-group mean difference in the WOSI total score at 12 weeks significantly favored SINEX over HOMEX (–228.1 [95% CI, –430.5 to –25.6]). SINEX was furthermore superior to HOMEX in most of the secondary outcomes (3/4 subdomains of the WOSI and pain level during the past 7 days as well as clinical signs of anterior shoulder instability). Also, although not statistically significant, less than half the proportion of the SINEX patients compared with the HOMEX patients (3/27 [11%] vs 6/24 [25%], respectively; P = .204) underwent or were referred for shoulder stabilizing surgery. Satisfaction with both exercise programs was high, and no serious adverse events were reported. Conclusion: Neuromuscular shoulder exercise (SINEX) was superior to standard care exercise (HOMEX) in patients with traumatic ASDs. Further long-term follow-ups on treatment effects are needed. Registration: NCT02371928 ( ClinicalTrials.gov identifier).
A cryptic imatinib-sensitive G3BP1-PDGFRB rearrangement in a myeloid neoplasm with eosinophilia
Authors: Jan Max , Grinshpun Daniel E. , Villalba Julian A. , Dal Cin Paola , Sykes David B. , Iafrate A. John , Ebert Benjamin L. , Hobbs Gabriela S. , Nardi Valentina 
Published: January 2020

Key Points
Targeted RNA sequencing detected a cryptic G3BP1-PDGFRB rearrangement in a myeloid neoplasm with eosinophilia and normal FISH studies. Consistent with the patient’s response to imatinib, we demonstrate this rearrangement is oncogenic and sensitive to TKI in cell culture.
Expression of Concern to: Diet restriction inhibits apoptosis and HMGB1 oxidation and promotes inflammatory cell recruitment during acetaminophen hepatoxicity
Authors: Antoine Daniel James , Williams Dominic P. , Kipar Anja , Laverty Hugh , Park B. Kevin 
Published: January 2020

AbstractThe Editors-in-Chief would like to alert readers that this article [1] is part of an investigation being conducted by the journal following the conclusions of an institutional enquiry at the University of Liverpool with respect to the quantitative mass spectrometry-generated results regarding acetylated and redox-modified HMGB1.
Detection of suspicious interactions of spiking covariates in methylation data
Authors: Sieg Miriam , Richter Gesa , Schaefer Arne S. , Kruppa Jochen 
Published: January 2020

Abstract
Background
In methylation analyses like epigenome-wide association studies, a high amount of biomarkers is tested for an association between the measured continuous outcome and different covariates. In the case of a continuous covariate like smoking pack years (SPY), a measure of lifetime exposure to tobacco toxins, a spike at zero can occur. Hence, all non-smokers are generating a peak at zero, while the smoking patients are distributed over the other SPY values. Additionally, the spike might also occur on the right side of the covariate distribution, if a category “heavy smoker” is designed. Here, we will focus on methylation data with a spike at the left or the right of the distribution of a continuous covariate. After the methylation data is generated, analysis is usually performed by preprocessing, quality control, and determination of differentially methylated sites, often performed in pipeline fashion. Hence, the data is processed in a string of methods, which are available in one software package. The pipelines can distinguish between categorical covariates, i.e. for group comparisons or continuous covariates, i.e. for linear regression. The differential methylation analysis is often done internally by a linear regression without checking its inherent assumptions. A spike in the continuous covariate is ignored and can cause biased results.

Results
We have reanalysed five data sets, four freely available from ArrayExpress, including methylation data and smoking habits reported by smoking pack years. Therefore, we generated an algorithm to check for the occurrences of suspicious interactions between the values associated with the spike position and the non-spike positions of the covariate. Our algorithm helps to decide if a suspicious interaction can be found and further investigations should be carried out. This is mostly important, because the information on the differentially methylated sites will be used for post-hoc analyses like pathway analyses.

Conclusions
We help to check for the validation of the linear regression assumptions in a methylation analysis pipeline. These assumptions should also be considered for machine learning approaches. In addition, we are able to detect outliers in the continuous covariate. Therefore, more statistical robust results should be produced in methylation analysis using our algorithm as a preprocessing step.
Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes
Authors: Zhou Huiwei , Ning Shixian , Liu Zhe , Lang Chengkun , Liu Zhuang , Lei Bizun 
Published: January 2020

Abstract
Background
Automated biomedical named entity recognition and normalization serves as the basis for many downstream applications in information management. However, this task is challenging due to name variations and entity ambiguity. A biomedical entity may have multiple variants and a variant could denote several different entity identifiers.

Results
To remedy the above issues, we present a novel knowledge-enhanced system for protein/gene named entity recognition (PNER) and normalization (PNEN). On one hand, a large amount of entity name knowledge extracted from biomedical knowledge bases is used to recognize more entity variants. On the other hand, structural knowledge of entities is extracted and encoded as identifier (ID) embeddings, which are then used for better entity normalization. Moreover, deep contextualized word representations generated by pre-trained language models are also incorporated into our knowledge-enhanced system for modeling multi-sense information of entities. Experimental results on the BioCreative VI Bio-ID corpus show that our proposed knowledge-enhanced system achieves 0.871 F1-score for PNER and 0.445 F1-score for PNEN, respectively, leading to a new state-of-the-art performance.

Conclusions
We propose a knowledge-enhanced system that combines both entity knowledge and deep contextualized word representations. Comparison results show that entity knowledge is beneficial to the PNER and PNEN task and can be well combined with contextualized information in our system for further improvement.
Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon
Authors: Kleppe Lene , Edvardsen Rolf Brudvik , Furmanek Tomasz , Andersson Eva , Skaftnesmo Kai Ove , Thyri Segafredo Frida , Wargelius Anna 
Published: January 2020

Abstract
Background
Sustainability challenges are currently hampering an increase in salmon production. Using sterile salmon can solve problems with precocious puberty and genetic introgression from farmed escapees to wild populations. Recently sterile salmon was produced by knocking out the germ cell-specific dead end (dnd). Several approaches may be applied to inhibit Dnd function, including gene knockout, knockdown or immunization. Since it is challenging to develop a successful treatment against a gene product already existing in the body, alternative targets are being explored. Germ cells are surrounded by, and dependent on, gonadal somatic cells. Targeting genes essential for the survival of gonadal somatic cells may be good alternative targets for sterility treatments. Our aim was to identify and characterize novel germ cell and gonadal somatic factors in Atlantic salmon.

Results
We have for the first time analysed RNA-sequencing data from germ cell-free (GCF)/dnd knockout and wild type (WT) salmon testis and searched for genes preferentially expressed in either germ cells or gonadal somatic cells. To exclude genes with extra-gonadal expression, our dataset was merged with available multi-tissue transcriptome data. We identified 389 gonad specific genes, of which 194 were preferentially expressed within germ cells, and 11 were confined to gonadal somatic cells. Interestingly, 5 of the 11 gonadal somatic transcripts represented genes encoding secreted TGF-β factors; gsdf, inha, nodal and two bmp6-like genes, all representative vaccine targets. Of these, gsdf and inha had the highest transcript levels. Expression of gsdf and inha was further confirmed to be gonad specific, and their spatial expression was restricted to granulosa and Sertoli cells of the ovary and testis, respectively. Finally, we show that inha expression increases with puberty in both ovary and testis tissue, while gsdf expression does not change or decreases during puberty in ovary and testis tissue, respectively.

Conclusions
This study contributes with transcriptome data on salmon testis tissue with and without germ cells. We provide a list of novel and known germ cell- and gonad somatic specific transcripts, and show that the expression of two highly active gonadal somatic secreted TGF-β factors, gsdf and inha, are located within granulosa and Sertoli cells.
Transcriptomics supports local sensory regulation in the antenna of the kissing-bug Rhodnius prolixus
Authors: Latorre-Estivalis Jose Manuel , Sterkel Marcos , Ons Sheila , Lorenzo Marcelo Gustavo 
Published: January 2020

AbstractBackgroundRhodnius prolixushas become a model for revealing the molecular bases of insect sensory biology due to the publication of its genome and its well-characterized behavioural repertoire. Gene expression modulation underlies behaviour-triggering processes at peripheral and central levels. Still, the regulation of sensory-related gene transcription in sensory organs is poorly understood. Here we study the genetic bases of plasticity in antennal sensory function, usingR. prolixusas an insect model.ResultsAntennal expression of neuromodulatory genes such as those coding for neuropeptides, neurohormones and their receptors was characterized in fifth instar larvae and female and male adults by means of RNA-Sequencing (RNA-Seq). New nuclear receptor andtakeoutgene sequences were identified for this species, as well as those of enzymes involved in the biosynthesis and processing of neuropeptides and biogenic amines.ConclusionsWe report a broad repertoire of neuromodulatory and neuroendocrine-related genes expressed in the antennae ofR. prolixusand suggest that they may serve as the local basis for modulation of sensory neuron physiology. Diverse neuropeptide precursor genes showed consistent expression in the antennae of all stages studied. Future studies should characterize the role of these modulatory components acting over antennal sensory processes to assess the relative contribution of peripheral and central regulatory systems on the plastic expression of insect behaviour.
The effects of common structural variants on 3D chromatin structure
Authors:   Human Genome Structural Variation Consortium (HGSVC), Shanta Omar , Noor Amina , Sebat Jonathan 
Published: January 2020

Abstract
Background
Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1–1 Mb in size termed Topological Associating Domains (TADs). Genetic factors that explain dynamic variation in TAD structure are not understood. We hypothesize that common structural variation (SV) in the human population can disrupt regulatory sequences and thereby influence TAD formation. To determine the effects of SVs on 3D chromatin organization, we performed chromosome conformation capture sequencing (Hi-C) of lymphoblastoid cell lines from 19 subjects for which SVs had been previously characterized in the 1000 genomes project. We tested the effects of common deletion polymorphisms on TAD structure by linear regression analysis of nearby quantitative chromatin interactions (contacts) within 240 kb of the deletion, and we specifically tested the hypothesis that deletions at TAD boundaries (TBs) could result in large-scale alterations in chromatin conformation.

Results
Large (> 10 kb) deletions had significant effects on long-range chromatin interactions. Deletions were associated with increased contacts that span the deleted region and this effect was driven by large deletions that were not located within a TAD boundary (nonTB). Some deletions at TBs, including a 80 kb deletion of the genes CFHR1 and CFHR3, had detectable effects on chromatin contacts. However for TB deletions overall, we did not detect a pattern of effects that was consistent in magnitude or direction. Large inversions in the population had a distinguishable signature characterized by a rearrangement of contacts that span its breakpoints.

Conclusions
Our study demonstrates that common SVs in the population impact long-range chromatin structure, and deletions and inversions have distinct signatures. However, the effects that we observe are subtle and variable between loci. Genome-wide analysis of chromatin conformation in large cohorts will be needed to quantify the influence of common SVs on chromatin structure.