bluuebunny/crossref_metadata_2025_split huggingface dataset:
Updates to HCOP: the HGNC comparison of orthology predictions tool
Authors: Yates Bethan , Gray Kristian A , Jones Tamsin E M , Bruford Elspeth A 
Published: April 2021

AbstractMultiple resources currently exist that predict orthologous relationships between genes. These resources differ both in the methodologies used and in the species they make predictions for. The HGNC Comparison of Orthology Predictions (HCOP) search tool integrates and displays data from multiple ortholog prediction resources for a specified human gene or set of genes. An indication of the reliability of a prediction is provided by the number of resources that support it. HCOP was originally designed to show orthology predictions between human and mouse but has been expanded to include data from a current total of 20 selected vertebrate and model organism species. The HCOP pipeline used to fetch and integrate the information from the disparate ortholog and nomenclature data resources has recently been rewritten, both to enable the inclusion of new data and to take advantage of modern web technologies. Data from HCOP are used extensively in our work naming genes as the Vertebrate Gene Nomenclature Committee (https://vertebrate.genenames.org).
A novel systematic approach for cancer treatment prognosis and its applications in oropharyngeal cancer with microRNA biomarkers
Authors: He Shenghua , Lian Chunfeng , Thorstad Wade , Gay Hiram , Zhao Yujie , Ruan Su , Wang Xiaowei , Li Hua 
Published: April 2021

Abstract

Motivation
Predicting early in treatment whether a tumor is likely to respond to treatment is one of the most difficult yet important tasks in providing personalized cancer care. Most oropharyngeal squamous cell carcinoma (OPSCC) patients receive standard cancer therapy. However, the treatment outcomes vary significantly and are difficult to predict. Multiple studies indicate that microRNAs (miRNAs) are promising cancer biomarkers for the prognosis of oropharyngeal cancer. The reliable and efficient use of miRNAs for patient stratification and treatment outcome prognosis is still a very challenging task, mainly due to the relatively high dimensionality of miRNAs compared to the small number of observation sets; the redundancy, irrelevancy and uncertainty in the large amount of miRNAs; and the imbalanced observation patient samples.

Results
In this study, a new machine learning-based prognosis model was proposed to stratify subsets of OPSCC patients with low and high risks for treatment failure. The model cascaded a two-stage prognostic biomarker selection method and an evidential K-nearest neighbors classifier to address the challenges and improve the accuracy of patient stratification. The model has been evaluated on miRNA expression profiling of 150 oropharyngeal tumors by use of overall survival and disease-specific survival as the end points of disease treatment outcomes, respectively. The proposed method showed superior performance compared to other advanced machine-learning methods in terms of common performance quantification metrics. The proposed prognosis model can be employed as a supporting tool to identify patients who are likely to fail standard therapy and potentially benefit from alternative targeted treatments.

Availability and implementation: Code is available in https://github.com/shenghh2015/mRMR-BFT-outcome-prediction.
Territorial and institutional obduracy in regional transition: politicising the case of Flanders’ energy distribution system
Authors: Juwet Griet , Deruytter Laura 
Published: April 2021

Abstract
This case study unravels the ambiguous position of public energy distributor Fluvius in dealing with strategic regional transition challenges. It enriches current understandings of spatial transition dimensions and of public regime actors’ role in transitions, by unravelling the territorial and institutional embeddedness of regional energy distribution systems. We disentangle three controversies in Flemish energy distribution, centred around the spatial concepts of density, spatial selectivity and socio-spatial redistribution. This spatial lens reveals the implicit spatial logics and inherently political character of transforming regional distribution systems. We conclude that a fundamental energy transition requires more inclusive governance, and an ambitious spatial transition vision.
Kidney involvement in multisystem inflammatory syndrome in children: a pediatric nephrologist’s perspective
Authors: Sethi Sidharth Kumar , Rana Abhyuday , Adnani Harsha , McCulloch Mignon , Alhasan Khalid , Sultana Azmeri , Safadi Rama , Agrawal Nirav , Raina Rupesh 
Published: April 2021

Abstract
The initial report of the multisystem inflammatory syndrome in children (MIS-C) was from the UK in April 2020; since then, cases have been reported worldwide. Renal involvement has been seen commonly, ranging from 10% to 46%. Kidney involvement following severe acute respiratory syndrome coronavirus 2 infection in children with MIS-C is more common than initially thought and is associated with higher morbidity and mortality. There are several reports of a direct viral tropism of coronavirus disease 2019 and MIS-C-associated renal damage. This study’s objective was to systematically review the current understanding of kidney involvement in children suffering from MIS-C. Based on our systemic literature search, 19 studies have either partially or fully discussed kidney involvement in MIS-C patients. Furthermore, we discuss the multifactorial pathogenesis contributing to acute kidney injury (AKI) development in MIS-C. The current review gives a pediatric nephrologist’s perspective of the renal involvement in MIS-C, the incidence of AKI, the pathophysiology of AKI in MIS-C and the proposed therapeutic regimens available, including the need for kidney replacement therapy for a child with AKI associated with MIS-C. As the disease is rapidly evolving, more detailed clinical prospective studies are required to understand MIS-C and its role in AKI better.
High-Sensitivity Cardiac Troponin T for the Detection of Myocardial Injury and Risk Stratification in COVID-19
Authors: De Michieli Laura , Ola Olatunde , Knott Jonathan D , Akula Ashok , Mehta Ramila A , Hodge David O , Dworak Marshall , Yang Eric H , Gharacholou Michael , Singh Gurpreet , Singh Ripudamanjit , Gulati Rajiv , Jaffe Allan S , Sandoval Yader 
Published: April 2021

Abstract

Background
Limited data exist on high-sensitivity cardiac troponin (hs-cTn) for risk-stratification in COVID-19.

Methods
We conducted a multicenter, retrospective, observational, US-based study of COVID-19 patients undergoing hs-cTnT. Outcomes included short-term mortality (in-hospital and 30-days post-discharge) and a composite of major adverse events, including respiratory failure requiring mechanical ventilation, cardiac arrest, and shock within the index presentation and/or mortality during the index hospitalization or within 30-days post-discharge.

Results
Among 367 COVID-19 patients undergoing hs-cTnT, myocardial injury was identified in 46%. They had a higher risk for mortality (20% vs 12%, P &lt; 0.0001; unadjusted HR 4.44, 95% CI 2.13–9.25, P &lt; 0.001) and major adverse events (35% vs. 11%, P &lt; 0.0001; unadjusted OR 4.29, 95% CI 2.50–7.40, P &lt; 0.0001). Myocardial injury was associated with major adverse events (adjusted OR 3.84, 95% CI 2.00–7.36, P &lt; 0.0001) but not mortality. Baseline (adjusted OR 1.003, 95% CI 1.00–1.007, P = 0.047) and maximum (adjusted OR 1.005, 95% CI 1.001–1.009, P = 0.0012) hs-cTnT were independent predictors of major adverse events. Most (95%) increases were due to myocardial injury, with 5% (n = 8) classified as type 1 or 2 myocardial infarction. A single hs-cTnT &lt;6 ng/L identified 26% of patients without mortality, with a 94.9% (95% CI 87.5–98.6) negative predictive value and 93.1% sensitivity (95% CI 83.3–98.1) for major adverse events in those presenting to the ED.

Conclusions
Myocardial injury is frequent and prognostic in COVID-19. While most hs-cTnT increases are modest and due to myocardial injury, they have important prognostic implications. A single hs-cTnT &lt;6 ng/L at presentation may facilitate the identification of patients with a favorable prognosis.
Failing systemic right ventricle in a patient with dextrocardia and complex congenitally corrected transposition of the great arteries: a case report of successful transvenous cardiac resynchronization therapy
Authors: Nederend Marieke , van Erven Lieselot , Zeppenfeld Katja , Vliegen Hubert W , Egorova Anastasia D 
Published: April 2021

Abstract

Background
Patients with congenitally corrected transposition of the great arteries (ccTGA) are prone to the development of advanced atrio-ventricular block requiring chronic ventricular pacing. The morphological right ventricle (RV) often develops systolic dysfunction as it is unable to withstand the chronic pressure overload it is exposed to when supporting the systemic circulation.

Case summary
A 56-year-old woman with dextrocardia and complex ccTGA with a history of dual-chamber implantable cardioverter-defibrillator (DDD-ICD, high degree atrio-ventricular-block and syncopal ventricular tachycardia), presented with progressive heart failure and symptomatic atrial arrhythmias. She underwent a successful ablation and concomitant invasive haemodynamic evaluation of potential alternative/biventricular pacing modalities. During biventricular pacing, the QRS narrowed and the systemic RV intraventricular pressure (Dp/Dt) increased with 30%. She underwent a successful transvenous upgrade to cardiac resynchronization therapy (CRT). The electrocardiogram post-implantation showed biventricular capture and patient showed subjective and objective clinical improvement.

Discussion
Systemic RV dysfunction in ccTGA can be aggravated by chronic pacing-induced dyssynchrony, contributing to progression of heart failure in this patient group. Transvenous CRT is feasible in ccTGA anatomy and may be pursued in order to improve or preserve the functional status of pacing-dependent ccTGA patients. Invasive haemodynamic contractility evaluation can help assess the potential benefit of CRT in patients with complex anatomy.
A case report: Amplatzer occluder device closure of an iatrogenic ventricular septal defect following radiofrequency ablation
Authors: Michaelis Anna , Dähnert Ingo , Riede Frank-Thomas , Paetsch Ingo , Jahnke Cosima , Paech Christian 
Published: April 2021

Abstract

Background
Interventricular septal perforation is an extremely rare complication of radiofrequency ablation (RFA), with an incidence of 1%. The most common mechanism is a ‘steam pop’, which can be described as ‘mini-explosions’ of gas bubbles. Data for percutaneous repair of cardiac perforations due to RFA are limited.

Case summary
A 78-year-old female patient was referred to our department for the treatment of two iatrogenic ventricular septal defects (VSDs) following radiofrequency ablation (RFA) of premature ventricular contractions. One week post-ablation, chest pain and progressive dyspnoea occurred. Transthoracic echocardiography detected a VSD, diameter 10 mm. Hence, iatrogenic, RFA-related myocardial injury was considered the most likely cause of VSD, and the patient was referred to our tertiary care centre for surgical repair. Cardiovascular magnetic resonance (CMR) imaging demonstrated border-zone oedema of the VSD only and confirmed the absence of necrotic tissue boundaries, and the patient was deemed suitable for percutaneous device closure. Laevocardiography identified an additional, smaller muscular defect that cannot be explained by analysing the Carto-Map. Both defects could be successfully closed percutaneously using two Amplatzer VSD occluder devices.

Discussion
In conclusion, this case demonstrates a successful percutaneous closure of a VSD resulting from RFA using an Amplatzer septal occluder device. CMR might improve tissue characterization of the VSD borders and support the decision if to opt for interventional or surgical closure.
Suction thrombectomy of a massive, hypermobile (type C) right atrial thrombus: a case report
Authors: Reddy Pavan K V , Kwan Tak , Latouff Omar , Patel Apurva 
Published: April 2021

Abstract

Background
Right atrial thrombus (RAT) may be managed according to morphology and aetiology, i.e. Type A thrombi (‘clot-in-transit’, hypermobile) are managed with thrombolytics and surgical embolectomy due to high risk of embolization; Type B thrombi (broad-based, globular) may be managed medically as they will very likely maintain a benign course. Experience with management of a Type C thrombus (hypermobile but also broad-based) has not been explicitly described in the literature.

Case summary
A 25-year-old man with history of leukaemia with prior right subclavian vein chemoport is found to have massive RAT. Multimodal imaging shows a hypermobile mass attached to the right atrial lateral wall inferior to superior vena cava and prolapsing into right ventricle in diastole. Given the thrombus morphology and likely propagation from subclavian port, risk of catastrophic embolization was deemed high and as such, intervention was indicated. Systemic anticoagulation was considered but deferred due to theoretical risk of dissolving the thrombus stalk leading to embolization. Surgical thrombectomy was offered but the patient declined. Due to evidence for success in RAT, the AngioVac System: Generation 3 (Angiodynamics, Inc., Latham, NY, USA) was chosen for intervention. The RAT was successfully removed without any complication.

Discussion
AngioVac suction thrombectomy is a safe alternative option for removal of a Type C, massive, hypermobile RAT.
Do patients who have newly identified prediabetes lose weight in the following year?
Authors: Varghai Nayyer Homa , Rothberg Michael B , Nathan Cassandra , Pfoh Elizabeth R 
Published: April 2021

Abstract

Background
Identifying a window of opportunity when patients are motivated to lose weight might improve the effectiveness of weight loss counseling. The onset of chronic disease could create such a window.

Objective
To determine whether identifying prediabetes was associated with subsequent weight loss.

Methods
Our retrospective cohort study included adults with obesity and a primary care visit between 2015 and 2017. Data were collected and analysed in 2019/2020. We compared patients who developed prediabetes [haemoglobin A1c (HbA1c) ≥5.7 and &lt;6.5] to patients with a normal HbA1c (&lt;5.7). We ran linear regression models to identify the association between identifying prediabetes and percent body mass index (BMI) change at 6 and 12 months. The adjusted model controlled for demographic characteristics at baseline, Charlson comorbidity score, and metformin, antipsychotic, antidepressant and antiobesity medication prescribed in either the first 3 months (for the 6-month outcome) or first 9 months (for 12-month outcome) and clustering within physician.

Results
Of 11 290 participants, 43% developed prediabetes. At 6 months, 15% of the prediabetes group lost ≥5% of their BMI compared with 13% of the comparison group. The results were similar at 12 months with 18% of the prediabetes group losing ≥5% of their BMI compared with 17%. The prediabetes group lost a higher percentage of their BMI (β = −0.7% versus −0.3% at 6 months and β = −0.5% versus 0.01% at 12 months).

Conclusions
While the percent of BMI change was small, patients with newly identified prediabetes lost more weight than a comparison group.
Evolutionary Perspectives on Germline-Restricted Chromosomes in Flies (Diptera)
Authors: Hodson Christina N , Ross Laura 
Published: April 2021

Abstract
In some eukaryotes, germline soma differentiation involves elimination of parts of the genome from somatic cells. The portions of the genome restricted to the germline often contain genes that play a role in development and function of the germline. Lineages with germline-restricted DNA are taxonomically diverse, and the size of the germline-restricted genome varies substantially. Unfortunately, few of these lineages have been studied in detail. As a result, we understand little about the general evolutionary forces that drive the origin and maintenance of germline-restricted DNA. One of the taxonomic groups where germline-restricted DNA has been poorly studied are the flies (Diptera). In three Dipteran families, Chironomidae, Cecidomyiidae, and Sciaridae, entire chromosomes are eliminated from somatic cells early in embryonic development. Germline-restricted chromosomes are thought to have evolved independently in the Dipteran families and their size, number, and transmission patterns vary between families. Although there is a wealth of cytological studies on these chromosomes in flies, almost no genomic studies have been undertaken. As a result, very little is known about how and why they evolved and what genes they encode. This review summarizes the literature on germline-restricted chromosomes in Diptera, discusses hypotheses for their origin and function, and compares germline-restricted DNA in Diptera to other eukaryotes. Finally, we discuss why Dipteran lineages represent a promising system for the study of germline-restricted chromosomes and propose future avenues of research on this topic.
Functional Analysis of the PUT3 Transcriptional Activator of the Proline Utilization Pathway in Saccharomyces cerevisiae
Authors: Etages Shelley Ann G des , Fahey Darlene A , Reece Richard J , Brandriss Marjorie C 
Published: April 2021

Abstract
Proline can serve as a nitrogen source for the yeast Saccharomyces cerevisiae when preferred sources of nitrogen are absent from the growth medium. PUT3, the activator of the proline utilization pathway, is required for the transcription of the genes encoding the enzymes that convert proline to glutamate. PUT3 is a 979 amino acid protein that constitutively binds a short DNA sequence in the promoters of its target genes, but does not activate their expression in the absence of induction by proline and in the presence of preferred sources of nitrogen. To understand how PUT3 is converted from an inactive to an active state, a dissection of its functional domains has been undertaken. Biochemical and molecular tests, domain swapping experiments, and an analysis of activator-constitutive and activator-defective mutant proteins indicate that PUT3 is dimeric and activates transcription with its negatively charged carboxyterminus, which does not appear to contain a proline-responsive domain. A mutation in the conserved central domain found in many fungal activators interferes with activation without affecting DNA binding or protein stability. Intragenic suppressors of the central domain mutation have been isolated and analyzed.
Centromere-Linkage Analysis and Consolidation of the Zebrafish Genetic Map
Authors: Johnson Stephen L , Gates Michael A , Johnson Michele , Talbot William S , Horne Sally , Baik Kris , Rude Sunny , Wong Jamie R , Postlethwait John H 
Published: April 2021

Abstract
The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.
Transmission-Ratio Distortion Through F1 Females at Chromosome 11 Loci Linked to Om in the Mouse DDK Syndrome
Authors: de Villena F Pardo-Manuel , Slamka C , Fonseca M , Naumova A K , Paquette J , Pannunzio P , Smith M , Verner A , Morgan K , Sapienza C 
Published: April 2021

Abstract
We determined the genotypes of &gt;200 offspring that are survivors of matings between female reciprocal F1 hybrids (between the DDK and C57BL/6J inbred mouse strains) and C57BL/6J males at markers linked to the Ovum mutant (Om) locus on chromosome 11. In contrast to the expectations of our previous genetic model to explain the “DDK syndrome,” the genotypes of these offspring do not reflect preferential survival of individuals that receive C57BL/6J alleles from the F1 females in the region of chromosome 11 to which the Om locus has been mapped. In fact, we observe significant transmission-ratio distortion in favor of DDK alleles in this region. These results are also in contrast to the expectations of Wakasugi's genetic model for the inheritance of Om, in which he proposed equal transmission of DDK and non-DDK alleles from F1 females. We propose that the results of these experiments may be explained by reduced expression of the maternal DDK Om allele or expression of the maternal DDK Om allele in only a portion of the ova of F1 females
Vegetative Incompatibility in the het-6 Region of Neurospora crassa Is Mediated by Two Linked Genes
Authors: Smith M L , Micali O C , Hubbard S P , Mir-Rashed N , Jacobson D J , Glass N Louise 
Published: April 2021

Abstract
Non-self-recognition during asexual growth of Neurospora crassa involves restriction of heterokaryon formation via genetic differences at 11 het loci, including mating type. The het-6 locus maps to a 250-kbp region of LGIIL. We used restriction fragment length polymorphisms in progeny with crossovers in the het-6 region and a DNA transformation assay to identify two genes in a 25-kbp region that have vegetative incompatibility activity. The predicted product of one of these genes, which we designate het-6OR, has three regions of amino acid sequence similarity to the predicted product of the het-e vegetative incompatibility gene in Podospora anserina and to the predicted product of tol, which mediates mating-type vegetative incompatibility in N. crassa. The predicted product of the alternative het-6 allele, HET-6PA, shares only 68% amino acid identity with HET-6OR. The second incompatibility gene, un-24OR, encodes the large subunit of ribonucleotide reductase, which is essential for de novo synthesis of DNA. A region in the carboxylterminal portion of UN-24 is associated with incompatibility and is variable between un-24OR and the alternative allele un-24PA. Linkage analysis indicates that the 25-kbp un-24-het-6 region is inherited as a block, suggesting that a nonallelic interaction may occur between un-24 and het-6 and possibly other loci within this region to mediate vegetative incompatibility in the het-6 region of N. crassa.
The Cloning and Molecular Analysis of pawn-B in Paramecium tetraurelia
Authors: Haynes W John , Ling Kit-Yin , Preston Robin R , Saimi Yoshiro , Kung Ching 
Published: April 2021

Abstract
Pawn mutants of Paramecium tetraurelia lack a depolarization-activated Ca2+ current and do not swim backward. Using the method of microinjection and sorting a genomic library, we have cloned a DNA fragment that complements pawn-B (pwB/pwB). The minimal complementing fragment is a 798-bp open reading frame (ORF) that restores the Ca2+ current and the backward swimming when expressed. This ORF contains a 29-bp intron and is transcribed and translated. The translated product has two putative transmembrane domains but no clear matches in current databases. Mutations in the available pwB alleles were found within this ORF. The d4-95 and d4-96 alleles are single base substitutions, while d4-662 (previously pawn-D) harbors a 44-bp insertion that matches an internal eliminated sequence (IES) found in the wild-type germline DNA except for a single C-to-T transition. Northern hybridizations and RT-PCR indicate that d4-662 transcripts are rapidly degraded or not produced. A second 155-bp IES in the wild-type germline ORF excises at two alternative sites spanning three asparagine codons. The pwB ORF appears to be separated from a 5′ neighboring ORF by only 36 bp. The close proximity of the two ORFs and the location of the pwB protein as indicated by GFP-fusion constructs are discussed.