bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling
Authors: Bang Ina , Lee Sang-Mok , Park Seojoung , Park Joon Young , Nong Linh Khanh , Gao Ye , Palsson Bernhard O , Kim Donghyuk 
Published: January 2023

AbstractRecognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair resolution. However, the peak calling step hinders ChIP-exo application since the published algorithms tend to generate false-positive and false-negative predictions. Here, we report the development of DEOCSU (DEep-learning Optimized ChIP-exo peak calling SUite), a novel machine learning-based ChIP-exo peak calling suite. DEOCSU entails the deep convolutional neural network model which was trained with curated ChIP-exo peak data to distinguish the visualized data of bona fide peaks from false ones. Performance validation of the trained deep-learning model indicated its high accuracy, high precision and high recall of over 95%. Applying the new suite to both in-house and publicly available ChIP-exo datasets obtained from bacteria, eukaryotes and archaea revealed an accurate prediction of peaks containing canonical motifs, highlighting the versatility and efficiency of DEOCSU. Furthermore, DEOCSU can be executed on a cloud computing platform or the local environment. With visualization software included in the suite, adjustable options such as the threshold of peak probability, and iterable updating of the pre-trained model, DEOCSU can be optimized for users’ specific needs.
Subtype-DCC: decoupled contrastive clustering method for cancer subtype identification based on multi-omics data
Authors: Zhao Jing , Zhao Bowen , Song Xiaotong , Lyu Chujun , Chen Weizhi , Xiong Yi , Wei Dong-Qing 
Published: January 2023

AbstractDue to the high heterogeneity and complexity of cancers, patients with different cancer subtypes often have distinct groups of genomic and clinical characteristics. Therefore, the discovery and identification of cancer subtypes are crucial to cancer diagnosis, prognosis and treatment. Recent technological advances have accelerated the increasing availability of multi-omics data for cancer subtyping. To take advantage of the complementary information from multi-omics data, it is necessary to develop computational models that can represent and integrate different layers of data into a single framework. Here, we propose a decoupled contrastive clustering method (Subtype-DCC) based on multi-omics data integration for clustering to identify cancer subtypes. The idea of contrastive learning is introduced into deep clustering based on deep neural networks to learn clustering-friendly representations. Experimental results demonstrate the superior performance of the proposed Subtype-DCC model in identifying cancer subtypes over the currently available state-of-the-art clustering methods. The strength of Subtype-DCC is also supported by the survival and clinical analysis.
MS1Connect: a mass spectrometry run similarity measure
Authors: Lin Andy , Deatherage Kaiser Brooke L , Hutchison Janine R , Bilmes Jeffrey A , Noble William Stafford 
Published: January 2023

Abstract

Motivation
Interpretation of newly acquired mass spectrometry data can be improved by identifying, from an online repository, previous mass spectrometry runs that resemble the new data. However, this retrieval task requires computing the similarity between an arbitrary pair of mass spectrometry runs. This is particularly challenging for runs acquired using different experimental protocols.

Results
We propose a method, MS1Connect, that calculates the similarity between a pair of runs by examining only the intact peptide (MS1) scans, and we show evidence that the MS1Connect score is accurate. Specifically, we show that MS1Connect outperforms several baseline methods on the task of predicting the species from which a given proteomics sample originated. In addition, we show that MS1Connect scores are highly correlated with similarities computed from fragment (MS2) scans, even though these data are not used by MS1Connect.

Availability and implementation
The MS1Connect software is available at https://github.com/bmx8177/MS1Connect.

Supplementary information
Supplementary data are available at Bioinformatics online.
Obesity partially potentiates dimethylbenz[a]anthracene-exposed ovotoxicity by altering the DNA damage repair response in mice
Authors: Rishi Jaspreet K , Timme Kelsey , White Hunter E , Kerns Karl C , Keating Aileen F 
Published: January 2023

AbstractObesity adversely affects reproduction, impairing oocyte quality, fecundity, conception, and implantation. The ovotoxicant, dimethylbenz[a]anthracene, is biotransformed into a genotoxic metabolite to which the ovary responds by activating the ataxia telangiectasia mutated DNA repair pathway. Basal ovarian DNA damage coupled with a blunted response to genotoxicant exposure occurs in obese females, leading to the hypothesis that obesity potentiates ovotoxicity through ineffective DNA damage repair. Female KK.Cg-a/a (lean) and KK.Cg-Ay/J (obese) mice received corn oil or dimethylbenz[a]anthracene (1 mg/kg) at 9 weeks of age for 7 days via intraperitoneal injection (n = 10/treatment). Obesity increased liver weight (P &lt; 0.001) and reduced (P &lt; 0.05) primary, preantral, and corpora lutea number. In lean mice, dimethylbenz[a]anthracene exposure tended (P &lt; 0.1) to increase proestrus duration and reduced (P = 0.07) primordial follicle number. Dimethylbenz[a]anthracene exposure decreased (P &lt; 0.05) uterine weight and increased (P &lt; 0.05) primary follicle number in obese mice. Total ovarian abundance of BRCA1, γH2AX, H3K4me, H4K5ac, H4K12ac, and H4K16ac (P &gt; 0.05) was unchanged by obesity or dimethylbenz[a]anthracene exposure. Immunofluorescence staining demonstrated decreased (P &lt; 0.05) abundance of γH2AX foci in antral follicles of obese mice. In primary follicle oocytes, BRCA1 protein was reduced (P &lt; 0.05) by dimethylbenz[a]anthracene exposure in lean mice. Obesity also decreased (P &lt; 0.05) BRCA1 protein in primary follicle oocytes. These findings support both a follicle stage-specific ovarian response to dimethylbenz[a]anthracene exposure and an impact of obesity on this ovarian response.
Core outcome domains for lichen sclerosus: a CORALS initiative consensus statement
Authors: Simpson Rosalind C , Kirtschig Gudula , Selk Amanda , von Seitzberg Suzanne , Vittrup Gitte , Bissonnette Ione , Kottner Jan , Lanthier Jaclyn , Stanton Chris , Foster David , Promm Martin , Augenti Angelo , Lauretti Stefano , Thomas Kim S ,   the Core Outcomes for Research in Lichen Sclerosus (CORALS) initiative steering group
Published: January 2023

Abstract

Background
Lichen sclerosus (LS) is a chronic inflammatory condition mainly affecting genital skin. It causes distressing symptoms that impact daily quality of life (QoL). It causes progressive anatomical changes and a potential risk of cancer. Published randomized controlled trials are of varying methodological quality and difficult to combine in meta-analyses. This is partly due to lack of agreed outcome measures to assess treatment response. Identification of core outcome sets (COSs), which standardize key outcomes to be measured in all future trials, is a solution to this problem.

Objectives
To obtain international agreement on which outcome domains should be measured in interventional trials of genital LS.

Methods
Recommended best practice for COS domain development was followed: (i) identification of potential outcome domains: a long list was generated through an up-to-date LS literature search, including information collected during the LS priority-setting partnership; (ii) provisional agreement of outcome domains: a three-stage multi-stakeholder international electronic-Delphi (e-Delphi) consensus study; (iii) final agreement of outcome domains: online consensus meeting with international stakeholders including anonymized voting.

Results
In total, 123 participants (77 patients, 44 health professionals, 2 researchers) from 20 countries completed three rounds of the e-Delphi study. Eleven outcome domains were rated as ‘critical’ and were discussed at the online consensus meetings. The first set of consensus meetings involved 42 participants from 12 countries. Consensus was met for ‘symptoms’ (100% agreed) and ‘QoL – LS-specific’ (92% agreed). After the second set of meetings, involving 29 participants from 12 countries, ‘clinical (visible) signs’ also met consensus (97% agreed).

Conclusions
The international community has agreed on three key outcome domains to measure in all future LS clinical trials. We recommend that trialists and systematic reviewers incorporate these domains into study protocols with immediate effect. CORALS will now work with stakeholders to select an outcome measurement instrument per prioritized core domain.
Pyoderma gangrenosum and myeloproliferative neoplasms
Authors: Langabeer Stephen E 
Published: January 2023

Teaser text (No Figure)Pyoderma gangrenosum can be associated with haematological malignancies but rarely a myeloproliferative neoplasm. A review of requests for molecular detection of myeloproliferative neoplasm driver mutations in patients with pyoderma gangrenosum was performed and revealed that testing for these mutations is unwarranted in cases where there are no clinical, haematological or morphological features of a myeloproliferative neoplasm present.
High-fidelity transmission of auditory symbolic material is associated with reduced right–left neuroanatomical asymmetry between primary auditory regions
Authors: Lumaca Massimo , Bonetti Leonardo , Brattico Elvira , Baggio Giosuè , Ravignani Andrea , Vuust Peter 
Published: January 2023

Abstract
The intergenerational stability of auditory symbolic systems, such as music, is thought to rely on brain processes that allow the faithful transmission of complex sounds. Little is known about the functional and structural aspects of the human brain which support this ability, with a few studies pointing to the bilateral organization of auditory networks as a putative neural substrate. Here, we further tested this hypothesis by examining the role of left–right neuroanatomical asymmetries between auditory cortices. We collected neuroanatomical images from a large sample of participants (nonmusicians) and analyzed them with Freesurfer’s surface-based morphometry method. Weeks after scanning, the same individuals participated in a laboratory experiment that simulated music transmission: the signaling games. We found that high accuracy in the intergenerational transmission of an artificial tone system was associated with reduced rightward asymmetry of cortical thickness in Heschl’s sulcus. Our study suggests that the high-fidelity copying of melodic material may rely on the extent to which computational neuronal resources are distributed across hemispheres. Our data further support the role of interhemispheric brain organization in the cultural transmission and evolution of auditory symbolic systems.
Ramsey and Keynes revisited
Authors: Gerrard Bill 
Published: January 2023

Abstract
This paper re-assesses Ramsey’s influence on Keynes. It is argued that the Standard View has restricted attention to the implications for probability theory of Ramsey’s criticisms of Keynes’s concepts of logical probability-relations and non-numerical probabilities. Building on the work of both Coates (1996) and Misak (2016), an Alternative View is proposed in which Ramsey’s influence on Keynes is seen as principally philosophical. Specifically, the Alternative View recognises Ramsey’s adoption of the logical pragmatist philosophy of C. S. Peirce from 1924 onwards with a dispositional theory of belief in which beliefs are treated not only as useful mental habits that can successfully guide future actions but also as able to provide true explanations of observed empirical facts. The textual evidence is examined, particularly Keynes’s biographical essay on Ramsey, which, it is argued, supports the contention that Keynes fully appreciated and was sympathetic to Ramsey’s pragmatism especially the importance of vague knowledge and the need for the development of human logic as the study of reasonable human behaviour.
A small circulating miRNAs signature predicts mortality and adverse cardiovascular outcomes in chronic hemodialysis patients
Authors: Bolignano Davide , Greco Marta , Presta Pierangela , Duni Anila , Vita Caterina , Pappas Ethymios , Mirabelli Maria , Lakkas Lampros , Naka Katerina K , Brunetti Antonio , Foti Daniela Patrizia , Andreucci Michele , Coppolino Giuseppe , Dounousi Evangelia 
Published: January 2023

ABSTRACT

Background
Chronic hemodialysis (HD) patients exhibit severe morpho-functional cardiac alterations, putting them at a high risk of death and adverse cardiovascular (CV) outcomes. Despite the fact that an unbalanced expression of various microRNAs (miRNAs) has been related to pathological cardiac remodeling and worse CV outcomes, scarce evidence exists on their role in this setting.

Methods
We evaluated circulating levels of a selected miRNAs panel (30a-5p, 23a-3p, 451a and let7d-5p) in 74 chronic HD patients together with a thorough clinical and echocardiography assessment. Individuals were then prospectively followed (median 22 months). The primary endpoint was a composite of all-cause and CV mortality and non-fatal CV events.

Results
Circulating levels of all miRNAs were lower in HD patients as compared with healthy controls and independently correlated to the severity of cardiac dysfunction. miRNA 30a-5p, 23a-3p and 451a expression was even lower in 30 subjects (40.5%) reaching the composite endpoint (P &lt; .001), while no differences were reported for let7d-5p. The predictive value of these miRNAs was supported by univariate followed by multivariate Cox regression analyses [hazard ratio (HR) ranging from 0.943 to 0.995; P = .05 to .02] while Kaplan–Meier analyses confirmed a faster progression to the endpoint in individuals displaying miRNA levels below an optimal receiver operating characteristic–derived cut-off value (P ranging from .001 to &lt;.0001; crude HRs 7.95 to 8.61).

Conclusions
Lower circulating levels of miRNA 30-5p, 23a-3p and 451a in HD patients may reflect cardiac abnormalities and predict a higher risk of worse clinical outcomes in the short mid-term. Future studies on larger HD populations are needed to generalize these findings.
Sex Hormone-Binding Globulin and Risk of Coronary Heart Disease in Men and Women
Authors: Li Jie , Zheng Lingling , Chan Kei Hang Katie , Zou Xia , Zhang Jihui , Liu Jundong , Zhong Qingwei , Madsen Tracy E , Wu Wen-Chih , Manson JoAnn E , Yu Xueqing , Liu Simin 
Published: January 2023

AbstractBackgroundThe role of sex hormone-binding globulin (SHBG) levels in clinical risk stratification and intervention for coronary heart disease (CHD) remains uncertain. We aimed to examine whether circulating levels of SHBG are predictive of CHD risk in men and women.MethodsWe investigated the association between SHBG and the risk of incident CHD in 128 322 men and 135 103 women free of CHD at baseline in the prospective United Kingdom Biobank (UKB) cohort. The unconfounded associations were estimated using Mendelian randomization (MR) analysis. We further conducted a meta-analysis to integrate currently available prospective evidence. CHD events included nonfatal and fatal myocardial infarction and coronary revascularization.ResultsIn the UKB, during a median of 11.7 follow-up years, 10 405 men and 4512 women developed CHD. Serum levels of SHBG were monotonically associated with a decreased risk of CHD in both men (adjusted hazard ratio [HR] per log nmol/L increase in SHBG: 0.88 [0.83–0.94]) and women (HR: 0.89 [0.83–0.96]). MR-based analyses suggested causality and a dose-response relationship of SHBG with CHD risk. A cumulative meta-analysis including 216 417 men and 138 282 women from 11 studies showed that higher levels of SHBG were prospectively associated with decreased CHD risk in men comparing the highest with the lowest quartile: pooled relative risk (RR) 0.81 (0.74–0.89) and women (pooled RR: 0.86 [0.78–0.94]).ConclusionsHigher circulating SHBG levels were directly and independently predictive of lower CHD risk in both men and women. The utility of SHBG for CHD risk stratification and prediction warrants further study.
Choosing exogeneity assumptions in potential outcome models
Authors: Masten Matthew A , Poirier Alexandre 
Published: January 2023

SummaryThere are many kinds of exogeneity assumptions. How should researchers choose among them? When exogeneity is imposed on an unobservable like a potential outcome, we argue that the form of exogeneity should be chosen based on the kind of selection on unobservables it allows. Consequently, researchers can assess the plausibility of any exogeneity assumption by studying the distributions of treatment given the unobservables that are consistent with that assumption. We use this approach to study two common exogeneity assumptions: quantile and mean independence. We show that both assumptions require a kind of nonmonotonic relationship between treatment and the potential outcomes. We discuss how to assess the plausibility of this kind of treatment selection. We also show how to define a new and weaker version of quantile independence that allows for monotonic selection on unobservables. We then show the implications of the choice of exogeneity assumption for identification. We apply these results in an empirical illustration of the effect of child soldiering on wages.
Representativeness in randomised clinical trials supporting acute coronary syndrome guidelines
Authors: Mas-Llado Caterina , Gonzalez-Del-Hoyo Maribel , Siquier-Padilla Joan , Blaya-Peña Laura , Coughlan J J , García de la Villa Bernardo , Peral Vicente , Rossello Xavier 
Published: January 2023

Abstract

Aims
Clinical practice guidelines (CPGs) are published to guide the management of acute coronary syndrome (ACS). We aimed to critically appraise the representativeness and standard of care of randomised clinical trials (RCTs) supporting CPGs for ACS.

Methods and results
American and European CPGs for ST- and non-ST-elevation ACS were screened to extract all references (n = 2128) and recommendations (n = 600). Among the 407 primary publications of RCTs (19.1%), there were 52.6 and 73.2% recruiting patients in North America and Europe, respectively, whereas other regions were largely under-represented (e.g. 25.3% RCTs recruited in Asia). There was 68.6% RCTs enrolling patient with ACS, whereas the remaining 31.4% did not enrol any patient with ACS. There was under-representation of some important subgroups, including elderly, female (29.9%), and non-white patients (&lt;20%). The incidence and type of reperfusion reported in these RCTs were not reflective of current clinical practice (the percentage of patients who underwent percutaneous coronary intervention (PCI) among all RCTs was 42.7%; whereas for ST-Elevation Myocardial Infarction patients, the number of participants who underwent fibrinolysis was 3.3-fold higher than those who underwent primary PCI). All-cause mortality in these RCTs was 11.9% in RCTs with a follow-up ≤ 1 year.

Conclusion
Randomised clinical trials supporting CPGs for ACS are not fully representative of the diversity of the ACS population and their current standard of care. While some of these issues with representativeness may be explained by how evidence has been accrued over time, efforts should be made by trialists to ensure that the evidence supporting CPGs is representative of the wider ACS population.
Location, Location, Location: Manufacturing and House Price Growth
Authors: Feng Xiangyu , Jaimovich Nir , Rao Krishna , Terry Stephen J , Vincent Nicolas 
Published: January 2023

Abstract
Exploiting data on tens of millions of housing transactions, we show that (1) house prices grew by less in manufacturing-heavy US regions, (2) this pattern is especially present for the lowest-value homes and that (3) price declines coincided with worse labour market outcomes, consistent with an income channel. Counterfactual accounting exercises reveal that regional differences in the growth of these lowest-value homes are an important driver of the changes in overall house price inequality. Hence, the economic decline in manufacturing-heavy areas extends far beyond income and employment flows to house prices.
Extension and management pathways for enhanced farm sustainability: evidence from Irish dairy farms
Authors: Balaine Lorraine , Läpple Doris , Dillon Emma J , Buckley Cathal 
Published: January 2023

Abstract
This article examines pathways among farmers’ extension participation, the uptake of recommended farm management practices and economic and environmental sustainability. We explore the ‘win-win’, efficiency-based focus of the Irish hybrid extension programme using an unbalanced panel dataset of dairy farms from 2010 to 2019. We apply two-way fixed effects regression models and sensitivity analyses to ensure the robustness of our results to effect heterogeneity and omitted variable bias. Our findings reveal that extension participation has a limited association with the adoption of recommended practices. These practices might be associated with economic benefits, while their environmental effects are not evident. Additionally, extension participation is not found to have a direct association with sustainability outcomes. These findings have important implications for extension programmes that focus on economic and environmental outcomes.
Improving representativeness in trials: a call to action from the Global Cardiovascular Clinical Trialists Forum
Authors: Filbey Lynaea , Zhu Jie Wei , D’Angelo Francesca , Thabane Lehana , Khan Muhammad Shahzeb , Lewis Eldrin , Patel Manesh R , Powell-Wiley Tiffany , Miranda J Jaime , Zuhlke Liesl , Butler Javed , Zannad Faiez , Van Spall Harriette G C 
Published: January 2023

Abstract
Participants enrolled in cardiovascular disease (CVD) randomized controlled trials are not often representative of the population living with the disease. Older adults, children, women, Black, Indigenous and People of Color, and people living in low- and middle-income countries are typically under-enrolled in trials relative to disease distribution. Treatment effect estimates of CVD therapies have been largely derived from trial evidence generated in White men without complex comorbidities, limiting the generalizability of evidence. This review highlights barriers and facilitators of trial enrollment, temporal trends, and the rationale for representativeness. It proposes strategies to increase representativeness in CVD trials, including trial designs that minimize the research burden on participants, inclusive recruitment practices and eligibility criteria, diversification of clinical trial leadership, and research capacity-building in under-represented regions. Implementation of such strategies could generate better and more generalizable evidence to reduce knowledge gaps and position the cardiovascular trial enterprise as a vehicle to counter existing healthcare inequalities.