bluuebunny/crossref_metadata_2025_split huggingface dataset:
LanceOtron: a deep learning peak caller for genome sequencing experiments
Authors: Hentges Lance D , Sergeant Martin J , Cole Christopher B , Downes Damien J , Hughes Jim R , Taylor Stephen 
Published: July 2022

Abstract

Motivation
Genome sequencing experiments have revolutionized molecular biology by allowing researchers to identify important DNA-encoded elements genome wide. Regions where these elements are found appear as peaks in the analog signal of an assay’s coverage track, and despite the ease with which humans can visually categorize these patterns, the size of many genomes necessitates algorithmic implementations. Commonly used methods focus on statistical tests to classify peaks, discounting that the background signal does not completely follow any known probability distribution and reducing the information-dense peak shapes to simply maximum height. Deep learning has been shown to be highly accurate for many pattern recognition tasks, on par or even exceeding human capabilities, providing an opportunity to reimagine and improve peak calling.

Results
We present the peak calling framework LanceOtron, which combines deep learning for recognizing peak shape with multifaceted enrichment calculations for assessing significance. In benchmarking ATAC-seq, ChIP-seq and DNase-seq, LanceOtron outperforms long-standing, gold-standard peak callers through its improved selectivity and near-perfect sensitivity.

Availability and implementation
A fully featured web application is freely available from LanceOtron.molbiol.ox.ac.uk, command line interface via python is pip installable from PyPI at https://pypi.org/project/lanceotron/, and source code and benchmarking tests are available at https://github.com/LHentges/LanceOtron.

Supplementary information
Supplementary data are available at Bioinformatics online.
Preclinical Alzheimer’s disease biomarkers accurately predict cognitive and neuropathological outcomes
Authors: Long Justin M , Coble Dean W , Xiong Chengjie , Schindler Suzanne E , Perrin Richard J , Gordon Brian A , Benzinger Tammie L S , Grant Elizabeth , Fagan Anne M , Harari Oscar , Cruchaga Carlos , Holtzman David M , Morris John C 
Published: July 2022

Abstract
Alzheimer’s disease biomarkers are widely accepted as surrogate markers of underlying neuropathological changes. However, few studies have evaluated whether preclinical Alzheimer’s disease biomarkers predict Alzheimer’s neuropathology at autopsy. We sought to determine whether amyloid PET imaging or CSF biomarkers accurately predict cognitive outcomes and Alzheimer’s disease neuropathological findings.
This study included 720 participants, 42–91 years of age, who were enrolled in longitudinal studies of memory and aging in the Washington University Knight Alzheimer Disease Research Center and were cognitively normal at baseline, underwent amyloid PET imaging and/or CSF collection within 1 year of baseline clinical assessment, and had subsequent clinical follow-up. Cognitive status was assessed longitudinally by Clinical Dementia Rating®. Biomarker status was assessed using predefined cut-offs for amyloid PET imaging or CSF p-tau181/amyloid-β42. Subsequently, 57 participants died and underwent neuropathologic examination. Alzheimer’s disease neuropathological changes were assessed using standard criteria. We assessed the predictive value of Alzheimer’s disease biomarker status on progression to cognitive impairment and for presence of Alzheimer’s disease neuropathological changes.
Among cognitively normal participants with positive biomarkers, 34.4% developed cognitive impairment (Clinical Dementia Rating &gt; 0) as compared to 8.4% of those with negative biomarkers. Cox proportional hazards modelling indicated that preclinical Alzheimer's disease biomarker status, APOE ɛ4 carrier status, polygenic risk score and centred age influenced risk of developing cognitive impairment. Among autopsied participants, 90.9% of biomarker-positive participants and 8.6% of biomarker-negative participants had Alzheimer's disease neuropathological changes. Sensitivity was 87.0%, specificity 94.1%, positive predictive value 90.9% and negative predictive value 91.4% for detection of Alzheimer's disease neuropathological changes by preclinical biomarkers. Single CSF and amyloid PET baseline biomarkers were also predictive of Alzheimer’s disease neuropathological changes, as well as Thal phase and Braak stage of pathology at autopsy. Biomarker-negative participants who developed cognitive impairment were more likely to exhibit non-Alzheimer's disease pathology at autopsy.
The detection of preclinical Alzheimer's disease biomarkers is strongly predictive of future cognitive impairment and accurately predicts presence of Alzheimer's disease neuropathology at autopsy.
Glaucoma Detection Using Multiple Feature Set With Recurrent Neural Network
Authors: Shyla N S Jeya , Emmanuel W R Sam 
Published: July 2022

Abstract
One of the most widespread illnesses of blindness is glaucoma. Optic nerve are essentialfor clear vision, but glaucoma effects the optic nerves and results blurred vision. This condition is often exacerbated by abnormally high intra-ocular pressure. Accurate early identification and continuous screening can help to minimize loss of vision. A non-invasive computer-aided diagnosis treatment uses optical fundus images to detect glaucoma in its early stages. This work includes image preprocessing, optic disk (OD) segmentation, feature extraction from the OD and recurrent neural network classification to identify glaucoma. The performance of the proposed system is tested using fundus image datasets such as DRISHTI-GS and Large-Scale Attention-Based Glaucoma (LAG). By this method, glaucoma detection accuracyof 96.1% is obtained for DRISHTI-GS and 92.73% for LAG dataset, which is higher thanthe existing state of arts. Proposed procedure can help ophthalmologists diagnose glaucomawith good performance.
Impacts of ocean warming and acidification on the energy budget of three commercially important fish species
Authors: Moreira José M , Mendes Ana Candeias , Maulvault Ana Luísa , Marques António , Rosa Rui , Pousão-Ferreira Pedro , Sousa Tânia , Anacleto Patrícia , Marques Gonçalo M 
Published: July 2022

Abstract
A mechanistic model based on Dynamic Energy Budget (DEB) theory was developed to predict the combined effects of ocean warming, acidification and decreased food availability on growth and reproduction of three commercially important marine fish species: white seabream (Diplodus sargus), zebra seabream (Diplodus cervinus) and Senegalese sole (Solea senegalensis). Model simulations used a parameter set for each species, estimated by the Add-my-Pet method using data from laboratory experiments complemented with bibliographic sources. An acidification stress factor was added as a modifier of the somatic maintenance costs and estimated for each species to quantify the effect of a decrease in pH from 8.0 to 7.4 (white seabream) or 7.7 (zebra seabream and Senegalese sole). The model was used to project total length of individuals along their usual lifespan and number of eggs produced by an adult individual within one year, under different climate change scenarios for the end of the 21st century. For the Intergovernmental Panel on Climate Change SSP5–8.5, ocean warming led to higher growth rates during the first years of development, as well as an increase of 32–34% in egg production, for the three species. Ocean acidification contributed to reduced growth for white seabream and Senegalese sole and a small increase for zebra seabream, as well as a decrease in egg production of 48–52% and 14–33% for white seabream and Senegalese sole, respectively, and an increase of 4–5% for zebra seabream. The combined effect of ocean warming and acidification is strongly dependent on the decrease of food availability, which leads to significant reduction in growth and egg production. This is the first study to assess the combined effects of ocean warming and acidification using DEB models on fish, therefore, further research is needed for a better understanding of these climate change-related effects among different taxonomic groups and species.
Bubble testing under polynomial trends
Authors: Wang Xiaohu , Yu Jun 
Published: July 2022

Summary
This paper develops the asymptotic theory of the least squares estimator of the autoregressive (AR) coefficient in an AR(1) regression with intercept when data is generated from a polynomial trend model in different forms. It is shown that the commonly used right-tailed unit root tests tend to favour the explosive alternative. A new procedure, which implements the right-tailed unit root tests in an AR(2) regression, is proposed. It is shown that, when the data generating process has a polynomial trend, the test statistics based on the new procedure cannot find evidence of explosiveness. Whereas, when the data generating process is mildly explosive, the new procedure finds evidence of explosiveness. Hence, it enables robust bubble testing under polynomial trends. Empirical application of the proposed procedure using data from the US real estate market reveals some interesting findings. In particular, all the negative bubble episodes flagged by the traditional method are no longer regarded as bubbles by the new procedure.
Novel ACTN2 missense variant is associated with idiopathic ventricular fibrillation: a case report
Authors: Hou Cody R , Cortez Daniel 
Published: July 2022

Abstract

Background
Idiopathic ventricular fibrillation (VF) is a diagnosis of exclusion made in patients who experience VF without an attributable cause. Pathogenic variants of the ACTN2 gene encoding the sarcomeric protein alpha-actinin-2 are known to cause hypertrophic and dilated cardiomyopathy. We show that ACTN2 variants may also be associated with malignant arrhythmias in the absence of overt structural heart disease.

Case summary
A 48-year-old female presented with cardiac arrest due to VF without any history of cardiovascular disease or family history of sudden cardiac death. Troponin I was elevated at 0.698 ng/mL, but coronary angiography showed no significant coronary artery disease. Substance abuse testing showed elevated benzodiazepine and sertraline levels, which she was taking for anxiety. Electrocardiogram showed normal QRS complexes without prolonged PR or QTc intervals. She underwent therapeutic hypothermia. Cardiac magnetic resonance imaging at 2 weeks showed normal biventricular function without structural abnormalities, fibrosis, or evidence of myocardial infarction. A targeted gene panel revealed a heterozygous missense variant of unknown significance (VUS) in exon 18 of the ACTN2 gene (c.2162G &gt; A/p.R721H).

Discussion
The identified VUS is located in a highly conserved residue of a spectrin-like repeat domain of alpha-actinin-2. Spectrin-like domains of alpha-actinin-2 bind and regulate the ion channels Nav1.5, Kv1.4, and Kv1.5, which contribute to the myocardial action potential. The VUS was predicted as pathogenic by MutationTaster, Polymorphism Phenotyping v2, and Sorting Intolerant From Tolerant in silico missense prediction tools. The c.2162G &gt; A/p.R721H alpha-actinin-2 variant may result in dysregulation of cardiac ion channels, leading to arrhythmias.
The Rattlesnake W Chromosome: A GC-Rich Retroelement Refugium with Retained Gene Function Across Ancient Evolutionary Strata
Authors: Schield Drew R , Perry Blair W , Card Daren C , Pasquesi Giulia I M , Westfall Aundrea K , Mackessy Stephen P , Castoe Todd A 
Published: July 2022

Abstract
Sex chromosomes diverge after the establishment of recombination suppression, resulting in differential sex-linkage of genes involved in genetic sex determination and dimorphic traits. This process produces systems of male or female heterogamety wherein the Y and W chromosomes are only present in one sex and are often highly degenerated. Sex-limited Y and W chromosomes contain valuable information about the evolutionary transition from autosomes to sex chromosomes, yet detailed characterizations of the structure, composition, and gene content of sex-limited chromosomes are lacking for many species. In this study, we characterize the female-specific W chromosome of the prairie rattlesnake (Crotalus viridis) and evaluate how recombination suppression and other processes have shaped sex chromosome evolution in ZW snakes. Our analyses indicate that the rattlesnake W chromosome is over 80% repetitive and that an abundance of GC-rich mdg4 elements has driven an overall high degree of GC-richness despite a lack of recombination. The W chromosome is also highly enriched for repeat sequences derived from endogenous retroviruses and likely acts as a “refugium” for these and other retroelements. We annotated 219 putatively functional W-linked genes across at least two evolutionary strata identified based on estimates of sequence divergence between Z and W gametologs. The youngest of these strata is relatively gene-rich, however gene expression across strata suggests retained gene function amidst a greater degree of degeneration following ancient recombination suppression. Functional annotation of W-linked genes indicates a specialization of the W chromosome for reproductive and developmental function since recombination suppression from the Z chromosome.
Productivity within the epidemic-type seismicity model
Authors: Molchan G , Varini E , Peresan A 
Published: July 2022

SUMMARY
The productivity of a magnitude m event can be characterized in term of triggered events of magnitude above m − Δ: it is the number of direct ‘descendants’ $\nu _\Delta$ and the number of all ‘descendants’ $V_\Delta$. There is evidence in favour of the discrete exponential distribution for both $\nu _\Delta$ and $V_\Delta$ with a dominant initial magnitude m (the case of aftershock cluster). We consider the general Epidemic Type Aftershock Sequence model adapted to any distribution of $\nu _\Delta$. Our first result shows that models with branching aftershock structure do not allow for the coincidence of distribution types of $\nu _\Delta$ and $V_\Delta$ (say, the discrete exponential, as in the scientific literature). The second problem is related to the tail behaviour of the $V_\Delta$ distribution. We show the fundamental difference in tail behaviour of the $V_\Delta$-distributions for general-type clusters and clusters with a dominant initial magnitude: the tail is heavy in the former case and light in the latter. The real data demonstrate the possibilities of this kind. This result provides theoretical and practical constraints for distributional analysis of $V_\Delta$.
Functional analysis of GCNT3 for cell migration and EMT of castration-resistant prostate cancer cells
Authors: Yamamoto Daiki , Sasaki Katsumasa , Kosaka Takeo , Oya Mototsugu , Sato Toshinori 
Published: July 2022

Abstract
Castration-resistant prostate cancer (CRPC) is a malignant tumor that is resistant to androgen deprivation therapy. Treatments for CRPC are limited, and no diagnostic markers are currently available. O-glycans are known to play an important role in cell proliferation, migration, invasion, and metastasis of cancer cells. However, the differences in the O-glycan expression profiles for normal prostate cancer (PCa) cells compared with CRPC cells have not yet been investigated. In this study, the saccharide primer method was employed to analyze the O-glycans expressed in CRPC cells. Expression levels of core 4-type O-glycans were significantly increased in CRPC cells. Furthermore, the expression level of N-Acetylglucosaminyltransferase 3 (GCNT3), a core 4-type O-glycan synthase gene, was increased in CRPC cells. The expression of core 4-type O-glycans and GCNT3 was presumed to be regulated by androgen deprivation. GCNT3 knockdown induced cell migration and epithelial-mesenchymal transition. These observations elucidate the mechanism of acquisition of castration resistance in PCa and offer new possibilities for the development of diagnostic markers and therapeutic targets in the treatment of PCa.
The Value of a Dedicated IBD Flare Clinic to Effectively Manage Exacerbations of Inflammatory Bowel Disease: The Edinburgh IBD Unit
Authors: Grant Rebecca K , Brindle William M , Arnott Ian D R 
Published: July 2022

Lay SummaryWe assessed the impact of a dedicated inflammatory bowel disease flare clinic. Attenders had more changes to maintenance medications made and less steroid use than inflammatory bowel disease patients reviewed at the Acute Receiving Unit. This model of care may potentially reduce hospital admissions.
Femoral de-rotation osteotomy versus hip arthroscopy for management of femoroacetabular impingement in adult patients with decreased femoral anteversion: a matched retrospective cohort study
Authors: Mastel Matthew S , Federico Alyssa , Desy Nicholas M , Johnston Kelly D 
Published: July 2022

ABSTRACTFemoral de-rotation osteotomy (FDO) and hip arthroscopy are both recognized surgical options for the management of femoroacetabular impingement (FAI) in the setting of decreased femoral anteversion (&lt;5°). Minimal comparative data exist regarding the difference in outcomes between these two techniques, and we believe this is the first study to provide that comparison. This retrospective cohort study included a total of 20 patients with such pathology, matched for age, gender and body mass index. A total of 10 patients were included in the FDO group [median anteversion −0.5° (true retroversion); average follow-up 17.9 months]. In total, 10 patients were included in the hip arthroscopy group [median anteversion −0.5° (true retroversion); average follow-up 28.5 months]. Both groups demonstrated statistically and clinically significant improvement in the post-operative International Hip Outcome Tool (iHOT-33) scores [median improvement: FDO group, 37.7 points (r 14–58.8; P &lt; 0.041); hip arthroscopy group, 35.9 points (r 11.1–81; P &lt; 0.05)], noting that the minimal clinically important difference for the iHOT-33 is 6.1 points. However, the study was not adequately powered to delineate a difference in improvement between the two groups. The findings suggest significant improvement in patient-reported outcomes, and clinical findings can be achieved with either FDO or hip arthroscopy for FAI in the setting of decreased femoral anteversion. However, selection of the most suitable surgical procedure using a patient-specific approach may optimize outcomes in this challenging population.
Minimally invasive treatment of an amebic empyema secondary to the transdiaphragmatic rupture of a liver abscess: a case report
Authors: Abello Vaamonde Jorge A , White Elizabeth Gil , López Alfredo Muñoz , Lorenzo Silva José M 
Published: July 2022

Abstract
Liver abscesses are a common complication in patients with amebiasis. Rarely, these will rupture across the diaphragm causing life-threatening empyemas. Evidence justifies performing surgical debridement or decortication for their treatment, given the better overall performance in comparison to open surgeries. However, no current guideline specifies which is the best approach. This report presents the case of a 39-year-old male with clinical, radiographical and microbiological evidence of an amebic empyema secondary to an amebic liver abscess, who received treatment by video-assisted thoracoscopy. The case description highlights the surgical technique, findings and operative outcomes that could be taken into consideration by other physicians to timely manage similar cases. The latter is especially relevant in underdeveloped and developing countries, where the burden of amebiasis appears to be greater. To the best of the authors’ knowledge, this is the first description of a transdiaphragmatic amebic infection treated in a minimally invasive fashion.
Laparoscopic Roux-en-Y gastric bypass in a patient with situs inversus totalis: case report
Authors: Zorrilla-Blanco Pablo Gerardo , Muñoz-Maldonado Gerardo , Zorrilla-Nuñez Luis Fernando , Núñez-Jasso Noé , González-Zorrilla Fernando , Mata-De Anda Lilia Andrea , de la O-Escamilla Manuel 
Published: July 2022

Abstract
The purpose of this report is to present the case of a patient with situs inversus totalis (SIT) who underwent laparoscopic gastric bypass and review of the literature. Situs inversus is a rare congenital abnormality that occurs in ~0.01% of the population and is characterized by transposition of the abdominal viscera1. When associated with dextrocardia, it is known as SIT. Electrocardiography reveals a reversal of the electrical waves of the heart and is the diagnostic measure of choice. Roux-en-Y laparoscopic gastric bypass for morbid obesity is one of the most effective bariatric procedures currently considered as the gold standard in bariatric surgery. We present the case of a 19-year-old male with morbid obesity and diagnosis of SIT, who underwent a laparoscopic gastric bypass adjusting the technique to the anatomical changes typical of this variant. It can be concluded, based on the previously compared cases and what was reported in ours, that in patients who have an indication to perform bariatric surgery and present SIT, surgery is not contraindicated, obtaining favorable results.
The authorship of George a Greene, the Pinner of Wakefield
Authors: Ilsemann Hartmut 
Published: July 2022

AbstractEstablishing the authorship of George a Greene, the Pinner of Wakefield can be seen within the wider context of detecting a collaborative or single-authored canon of early Shakespeare plays which, perhaps, he did not want to see as part of his dramatic work if we are to trust Heminges’ and Condell’s references to ‘surrepetitious copies, maimed, and deformed by the frauds and stealthes of injurious imposters, that expos’d them’ (First Folio preface). The fact that the remaining plays of the First Folio [are] ‘absolute in their numbers as he [Shakespeare] conceived them,’ has in some way a ring of self-amputation. The conclusion of the present study, based on the acknowledged methodological advances in non-traditional stylometric tools, contained in the R Stylo suite, is that George a Greene, the Pinner of Wakefield was originally written by William Shakespeare, even though the play may have been shortened for performances outside London with a reduced company of players during the plague years of 1592 and 1593.
Transcriptional profiles of genes related to mitochondrial aging in placental pathologies
Authors: Bartho Lucy A , McKeating Daniel R , Hannan Natalie J , Kaitu’u-Lino Tu’uhevaha J , Perkins Anthony V 
Published: July 2022

Abstract
As the placenta develops across gestation, the mitochondria and other organelles like the endoplasmic reticulum (ER) must continue to adapt to stressors such as oxidative stress. As pregnancy approaches term, these stressors may contribute to placental aging, including mitochondrial changes leading to cellular senescence. When these processes are exacerbated, pregnancy pathologies arise. This study aimed to identify correlations between genes related to mitochondria, ER and cellular senescence in placentae complicated by pregnancy complications. Placental samples from pregnancies classified as preterm, term, post-term, preterm with foetal growth restriction (FGR), preterm with preeclampsia (PE) and preterm with PE and FGR were used to measure gene expression of TOMM20, MFN1, TFAM, MFN2, PARK2, PINK1, EIF2AK3, TP53 and ERN1. MetaboAnalyst 5.0 was used to generate heatmaps, principal component analysis plots, correlation graphs and receiver operating characteristic analysis. This study found that genes-related mitochondrial dynamics and aging undergo changes in placentae affected by pregnancy pathologies. The TOMM20/PARK2 ratio may be a promising marker to discriminate between healthy and unhealthy placental tissue. Future studies should explore circulating biomarkers of mitochondrial aging and dysfunction as indicators of placental health.