bluuebunny/crossref_metadata_2025_split huggingface dataset:
Decoding multilevel relationships with the human tissue-cell-molecule network
Authors: Hou Siyu , Zhang Peng , Yang Kuo , Wang Lan , Ma Changzheng , Li Yanda , Li Shao 
Published: April 2022

AbstractUnderstanding the biological functions of molecules in specific human tissues or cell types is crucial for gaining insights into human physiology and disease. To address this issue, it is essential to systematically uncover associations among multilevel elements consisting of disease phenotypes, tissues, cell types and molecules, which could pose a challenge because of their heterogeneity and incompleteness. To address this challenge, we describe a new methodological framework, called Graph Local InfoMax (GLIM), based on a human multilevel network (HMLN) that we established by introducing multiple tissues and cell types on top of molecular networks. GLIM can systematically mine the potential relationships between multilevel elements by embedding the features of the HMLN through contrastive learning. Our simulation results demonstrated that GLIM consistently outperforms other state-of-the-art algorithms in disease gene prediction. Moreover, GLIM was also successfully used to infer cell markers and rewire intercellular and molecular interactions in the context of specific tissues or diseases. As a typical case, the tissue-cell-molecule network underlying gastritis and gastric cancer was first uncovered by GLIM, providing systematic insights into the mechanism underlying the occurrence and development of gastric cancer. Overall, our constructed methodological framework has the potential to systematically uncover complex disease mechanisms and mine high-quality relationships among phenotypical, tissue, cellular and molecular elements.
Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol
Authors: Chen Qingjian , Wu Qi-Nian , Rong Yu-Ming , Wang Shixiang , Zuo Zhixiang , Bai Long , Zhang Bei , Yuan Shuqiang , Zhao Qi 
Published: April 2022

AbstractMultiple primary tumor (MPT) is a special and rare cancer type, defined as more than two primary tumors presenting at the diagnosis in a single patient. The molecular characteristics and tumorigenesis of MPT remain unclear due to insufficient approaches. Here, we present MPTevol, a practical computational framework for comprehensively exploring the MPT from multiregion sequencing (MRS) experiments. To verify the utility of MPTevol, we performed whole-exome MRS for 33 samples of a rare patient with triple-primary tumors and three metastatic sites and systematically investigated clonal dynamics and metastatic routines. MPTevol assists in comparing genomic profiles across samples, detecting clonal evolutionary history and metastatic routines and quantifying the metastatic history. All triple-primary tumors were independent origins and their genomic characteristics were consistent with corresponding sporadic tumors, strongly supporting their independent tumorigenesis. We further showed two independent early monoclonal seeding events for the metastases in the ovary and uterus. We revealed that two ovarian metastases were disseminated from the same subclone of the primary tumor through undergoing whole-genome doubling processes, suggesting metastases-to-metastases seeding occurred when tumors had similar microenvironments. Surprisingly, according to the metastasis timing model of MPTevol, we found that primary tumors of about 0.058–0.124 cm diameter have been disseminating to distant organs, which is much earlier than conventional clinical views. We developed MPT-specialized analysis framework MPTevol and demonstrated its utility in explicitly resolving clonal evolutionary history and metastatic seeding routines with a rare MPT case. MPTevol is implemented in R and is available at https://github.com/qingjian1991/MPTevol under the GPL v3 license.
VisuStatR: visualizing motility and morphology statistics on images in R
Authors: Harmel Christoph , Sid Ahmed Samy , Koch Robin , Tünnermann Jana , Distler Tania , Imle Andrea , Giorgetti Luca , Bahn Emanuel , Fackler Oliver T , Graw Frederik 
Published: April 2022

Abstract

Motivation
Live-cell microscopy has become an essential tool for analyzing dynamic processes in various biological applications. Thereby, high-throughput and automated tracking analyses allow the simultaneous evaluation of large numbers of objects. However, to critically assess the influence of individual objects on calculated summary statistics, and to detect heterogeneous dynamics or possible artifacts, such as misclassified or -tracked objects, a direct mapping of gained statistical information onto the actual image data would be necessary.

Results
We present VisuStatR as a platform independent software package that allows the direct visualization of time-resolved summary statistics of morphological characteristics or motility dynamics onto raw images. The software contains several display modes to compare user-defined summary statistics and the underlying image data in various levels of detail.

Availability and implementation
VisuStatR is a free and open-source R-package, containing a user-friendly graphical-user interface and is available via GitHub at https://github.com/grrchrr/VisuStatR/ under the MIT+ license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Continuous chromatin state feature annotation of the human epigenome
Authors: Daneshpajouh Habib , Chen Bowen , Shokraneh Neda , Masoumi Shohre , Wiese Kay C , Libbrecht Maxwell W 
Published: April 2022

Abstract

Motivation
Segmentation and genome annotation (SAGA) algorithms are widely used to understand genome activity and gene regulation. These methods take as input a set of sequencing-based assays of epigenomic activity, such as ChIP-seq measurements of histone modification and transcription factor binding. They output an annotation of the genome that assigns a chromatin state label to each genomic position. Existing SAGA methods have several limitations caused by the discrete annotation framework: such annotations cannot easily represent varying strengths of genomic elements, and they cannot easily represent combinatorial elements that simultaneously exhibit multiple types of activity. To remedy these limitations, we propose an annotation strategy that instead outputs a vector of chromatin state features at each position rather than a single discrete label. Continuous modeling is common in other fields, such as in topic modeling of text documents. We propose a method, epigenome-ssm-nonneg, that uses a non-negative state space model to efficiently annotate the genome with chromatin state features. We also propose several measures of the quality of a chromatin state feature annotation and we compare the performance of several alternative methods according to these quality measures.

Results
We show that chromatin state features from epigenome-ssm-nonneg are more useful for several downstream applications than both continuous and discrete alternatives, including their ability to identify expressed genes and enhancers. Therefore, we expect that these continuous chromatin state features will be valuable reference annotations to be used in visualization and downstream analysis.

Availability and implementation
Source code for epigenome-ssm is available at https://github.com/habibdanesh/epigenome-ssm and Zenodo (DOI: 10.5281/zenodo.6507585).

Supplementary information
Supplementary data are available at Bioinformatics online.
Reshoring by small firms: dual sourcing strategies and local subcontracting in value chains
Authors: Canello Jacopo , Buciuni Giulio , Gereffi Gary 
Published: April 2022

Abstract
This article assesses how the reshoring of manufacturing activities by micro and small enterprises (MSEs) affects the performances of co-located subcontracting networks and the reconfiguration of global value chains (GVCs). We utilize quantitative microdata of Italian MSEs operating in the clothing and footwear industries during the 2008–2015 period. Empirically MSE reshoring does not have a significant impact on domestic subcontractors’ birth rates and survival chances, whereas it is positively associated with their productivity growth. Most MSEs in our sample adopt a dual sourcing strategy, expanding their global production networks while preserving their local supply base. Local and global production networks are not two alternative paradigms of industrial organization; they can be complementary and mutually reinforce each other.
Can ketogenic dietary interventions slow disease progression in ADPKD: what we know and what we don't
Authors: Ong Albert C M , Torra Roser 
Published: April 2022

ABSTRACTAutosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease leading to kidney failure. To date, there is no cure for the disease although there is one approved disease-modifying therapy: tolvaptan. In this context, a common question that ADPKD patients ask in clinical practice is whether there is anything they can do to slow their disease by modifying their diet or lifestyle. Recent evidence from experimental PKD models has shown the potential benefits of caloric restriction, high water intake and especially ketogenic diets in preserving kidney function. Whether these benefits are translatable to humans remains unknown. In this issue of CKJ, Strubl et al. report results of a self-enrolled survey of autosomal dominant polycystic kidney disease (ADPKD) patients who have self-administered a ketogenic diet [1]. These results provide interesting insights into the tolerability, potential benefits and harms of such an intervention that could inform a future clinical trial.
Reperfusion therapy for ST-elevation myocardial infarction complicated by cardiogenic shock: the European Society of Cardiology EurObservational programme acute cardiovascular care-European association of PCI ST-elevation myocardial infarction registry
Authors: Zeymer Uwe , Ludman Peter , Danchin Nicolas , Kala Petr , Laroche Cécile , Gale Chris P , Maggioni Aldo P , Siabani Soraya , Sadeghi Masoumeh , Wafa Ahmed , Bartus Stanislaw , Weidinger Franz 
Published: April 2022

Abstract

Aims
To determine the current state of the use of reperfusion and adjunctive therapies and in-hospital outcomes in European Society of Cardiology (ESC) member and affiliated countries for patients with ST-segment elevation myocardial infarction (STEMI) complicated by cardiogenic shock (CS).

Methods and results
ESC EurObservational Research Programme prospective international cohort study of admissions with STEMI within 24 h of symptom onset (196 centres; 26 ESC member and 3 affiliated countries). Of 11 462 patients enrolled, 448 (3.9%) had CS. Patients with compared to patients without CS, less frequently received primary percutaneous coronary intervention (PCI) (65.5% vs. 72.2%) and fibrinolysis (15.9% vs. 19.0), and more often had no reperfusion therapy (19.0% vs. 8.5%). Mechanical support devices (intraaortic ballon pump 11.2%, extracoporeal membrane oxygenation 0.7%, other 1.1%) were used infrequently in CS. Bleeding definition academic research consortium 2–5 bleeding complications (10.1% vs. 3.0%, P &lt; 0.01) and stroke (4.2% vs. 0.9%, P &lt; 0.01) occurred more frequently in patients with CS. In-hospital mortality was 10-fold higher (35.5% vs. 3.1%) in patients with CS. Mortality in patients with CS in the groups with PCI, fibrinolysis, and no reperfusion therapy were 27.4%, 36.6%, and 62.4%, respectively.

Conclusion
In this multi-national registry, patients with STEMI complicated by CS less frequently receive reperfusion therapy than patients with STEMI without CS. Early mortality in patients with CS not treated with primary PCI is very high. Therefore, strategies to improve clinical outcome in STEMI with CS are needed.
The Woolfes of Wine Street: Middling Culture and Community in Bristol, 1600–1620
Authors: Davies Callan 
Published: April 2022

Abstract
This article provides an in-depth cultural study of England’s urban middling sort—those in-between wage labourers and the gentry—at the beginning of the seventeenth century, concentrating on one community in a major street in Bristol. This demographic has long been of interest to historians seeking to understand the major social changes of the early modern period, but little is known about the total urban experience of such individuals prior to the Restoration. Wine Street was home to goldsmiths’ standings and shops, instrument-makers, inn-holding widows, aldermen, mayors, and one of the longest-running playhouses in early modern England outside of London—a venue run by Nicholas and Margaret Woolfe. This study seeks to understand more about the everyday lives of this crucial demographic through a holistic micro-history of one particular community—grounding them in a specific place and time and providing an earlier case-study than is generally available in existing literature. Doing so demonstrates how middling status was complicated and defined by neighbourhood, marriage, widowhood, and inheritance. More widely, this group of Wine Street tradespeople, artisans and proprietors lived in a location that was in large part distinguished by forms of ‘play’, the elastic early modern term used here to refer to various forms of commercial recreation, from drama to inn-going to luxury shopping. I establish how, in such urban environments, middling status can be distinctly recognised in the imbrication of play with cultural and commercial identity.
Apical root resorptions in girls with Turner syndrome: a controlled longitudinal study
Authors: Kjellberg Heidrun , Lundgren Ted , Barrenäs Marie Louise , Rizell Sara 
Published: April 2022

Summary

Objectives
To study, longitudinally, the development of apical root resorptions (ARRs) in Turner syndrome (TS) and to correlate these to the karyotype and orthodontic treatment.

Materials and methods
Thirty girls with TS participated in the study, mean age 10.8 years (6.6–23.4) at the first registration (T1), and 14.3 years (9.2–25.2) at the second registration (T2). Forty girls without TS, orthodontically untreated, served as controls. ARR was diagnosed in panoramic radiographs, and root/crown ratios of the lower permanent first molar were measured at T1 and T2 with a mean follow-up period of 42 (11–89) months.

Results
During the follow-up period, ARR was seen in 40% of all TS patients and in 2.5% in the control group. The majority displayed ARR on the distal root of the mandibular first permanent molars (30%). ARR at T2 was seen in 56% of 45,X and isochromosome karyotype and 21% of every other TS karyotype patients. AAR was seen in 5 out of 12 TS patients with orthodontic treatment. No statistically significant differences in root/crown ratios between T1 and T2 were found.

Limitations
The number of patients studied is limited, thus possible differences might be disguised for this reason. Spatial projection errors in panoramic radiograph recordings might have influenced measurement, resulting in an underestimation of ARR.

Conclusions
There is a higher risk for ARR in girls with TS and probably the risk is therefore probably also higher during orthodontic treatment. Thus, if treated, frequent radiographic follow-ups should be taken during the treatment.

Protocol
The protocol was not published before trial commencement.
Careers in arm’s-length contracting: evidence from the Chilean wine-grape market
Authors: Jano Pilar , Hueth Brent 
Published: April 2022

AbstractThis paper investigates the presence of career and promotion-based incentives in the context of arm’s-length contracting between wineries and independent wine-grape farmers. We hypothesise that long-term contracts represent a stage in a farmer’s career after a series of short-term contracts. We develop a conceptual framework to frame the interaction between explicit performance incentives and implicit career incentives arising from the possibility of promotion to a long-term contract, conditional on wineries learning a farmer’s potential for superior-quality production. Based on data from Chilean wine-grape farmers, we find evidence suggesting that implicit market-based incentives, usually studied in the context of employment contracts, are also important in arm’s-length contracts used in procurement of farm output.
OR25. D-dimer characteristics in moderate to severe COVID-19 confirmed patients with fragmented QRS in Hermina Daan Mogot Hospital period August 2020-February 2021
Authors: Angelina A , Chandranegara A F 
Published: April 2022

Abstract

Aims
Fragmented QRS (fQRS) finding in ECG is one of the independent factors responsible for high mortality due to COVID-19. Other factor such as D-dimer is also worth noting as mortality risk increases in patients with higher values. In this study, we described D-dimer characteristics in COVID-19 patients with fQRS in Hermina Daan Mogot Hospital (HDMH).

Methods and Results
Cross-sectional descriptive study was performed in HDMH from May 1st to June 3rd 2021 in moderate to severe COVID-19 confirmed patients with fQRS finding.
Twenty six patients (100%) were included in this study, with 17 (65.4%) subjects are male and 9 (34.6%) being female. Average age of the subjects was 53.65 ± 9.69 years old. fQRS in inferior lead was found in 17 (65.4%) subjects and 1 (3.8%) subject with LBBB. Other leads include 7 (26.9%) in anterior, 1 (3.8%) in lateral, and 1 (3.8%) in infero-lateral lead.
Nineteen (73.1%) subjects were diagnosed with severe COVID-19, and 7 (26.9%) were moderate. Total of intubated patients were 17 (65.4%). Sixteen (61.5%) patients died.
D-dimer value was grouped into &lt;230 ng/mL, 230-500 ng/mL, 501-2000 ng/mL and &gt;2000 ng/mL. Each groups had 3 (11.5%), 3 (11.5%), 15 (57.7%) and 5 (19.2%) subjects. The number of deceased patients in each group was 0 (0%), 1 (33.3%), 10 (66.7%) and 5 (100%), respectively.

Conclusion
According to data collected, there is a connection between mortality of moderate to severe COVID-19 patients with fQRS finding which is increases as D-dimer value rises.
OR34. Evaluation of P wave abnormalities in newly diagnosed COVID-19
Authors: Mulawarman Rido , Ramadhan Muhammad Syahrul , Trifitriana Monica , Mulawarman Hisham , Nurmansyah Muhammad Ikhsan , Halim Rolando Agustian , Maulana Chandra Chandra Agung , Tondas Alexander Edo 
Published: April 2022

Abstract

Aims
The aim of the current study was to evaluate P wave abnormalities, including prolonged P wave duration, prolonged P wave dispersion (PWD) and abnormal P wave axis (PWA) in newly diagnosed COVID-19 patients.

Methods and Results
This is a cross-sectional, single center study with a total of 53 newly diagnosed COVID-19 patients (confirmed with polymerase chain reaction (PCR) test) and 63 age and sex-matched control subjects were included in the study. P wave dispersion, maximum P wave duration, and PWA were calculated manually from 12-lead ECG. Patients with COVID-19 more often had prolonged PWD, defined as PWD ≥ 36 ms compared to control group (37,7% vs 15,9%), (OR = 3,212; 95%CI 1,34 – 7,70; p = 0,007). There were no significant association between COVID-19 and prolonged P wave (defined as maximum P wave duration &gt; 106 ms) (OR = 1,446; 95%CI 0,454 – 4,6; p = 0,531) and abnormal PWA (defined as any value of PWA outside 0 to 75°) (OR = 5,061; 95%CI 0,548 – 46,74; p = 0,115).

Conclusion
Our study showed that COVID-19 patients are more likely to have prolonged PWD compared to control patients. However, COVID-19 was not significantly associated with prolonged P wave and abnormal PWA. We believe that initial non-invasive evaluation of PWD may serve as a predictor of atrial arrhytmias often found in COVID-19 patients.
OR47. Index of Cardiac Electrophysiological Balance (iCEB) in Patients with COVID-19
Authors: Mulawarman Rido , Ramadhan Muhammad Syahrul , Trifitriana Monica , Mulawarman Hisham , Nurmansyah Muhammad Ikhsan , Maulana Chandra Agung , Tondas Alexander Edo 
Published: April 2022

Abstract

Aims
We aimed to examine whether there is abnormal value of index of cardiac electrophysiological balance (iCEB=QT/QRS) in patients with confirmed coronavirus disease 2019 (COVID-19), which can predict ventricular arrhythmias (VAs), including non-Torsades de Pointes-like ventricular tachycardia/ventricular fibrillation (non-TdPs-like VT/VF) in low iCEB and Torsades de Pointes (TdPs) in high iCEB. We also investigated low voltage ECG among COVID-19 group.

Methods and Results
This is a cross-sectional, single center study with a total of 53 newly diagnosed COVID-19 patients (confirmed with polymerase chain reaction (PCR) test) and 63 age and sex-matched control subjects were included in the study. Electrocardiographic marker of iCEB were calculated manually from 12-lead ECG. Low voltage ECG defined as peak-to-peak QRS voltage less than 5 mm in all limb leads and less than 10 mm in all precordial leads. Patients with COVID-19 more often had low iCEB, defined as iCEB below 3.24 compared to control group (56.6% vs 11.1%), (OR = 10.435; 95%CI 4.015 – 27.123; p = 0.000). There were no significant association between COVID-19 and high iCEB, defined as iCEB above 5.24 (OR = 1.041; 95%CI 0.485 – 2.235; p = 0.917). There were no significant difference of the number of low voltage ECG between COVID-19 and control groups (15.1% vs 6.3%), (OR = 2.622; 95%CI 0.743 - 9.257, p = 0.123).

Conclusion
In this study showed that patients with COVID-19 are more likely to have low iCEB, suggesting that patients with COVID-19 may be proarrhytmic (towards non-TdPs-like VT/VF event), due to the alleged myocardial involvement in SARS-CoV-2 infection.
OR57. Role of Copeptin as a Predictor of Major Adverse Cardiovascular Events (MACE) During Hospitalization on Acute Myocardial Infarction Patient
Authors: Wiratama I P R S , Wasyanto T 
Published: April 2022

Abstract

Aims
Copeptin has been considered as a potential biomarker for AMI which also give information regarding the prognostic of the Acute myocardial infarction (AMI). The aim of this study is to understand the role of copeptin as a predictor of major adverse cardiovascular events (MACE) during hospitalization in AMI patients.

Methods and Results
This was a cohort analytical study on AMI patient at Dr. Moewardi Hospital, whether with STEMI or NSTEMI. We observe the MACE during hospitalization and analyze the cut-off point value for optimal copeptin levels to predict the occurrence of MACE using the ROC curve. Linear multiple regression was conducted to predict determinants of MACE in hospitalization patients. 52 patients recruited in this research (44 males, 8 females). During hospitalization, MACE occurred in 52% of these subjects, with the respective proportions for acute heart failure, cardiogenic shock, arrhythmias, cardiopulmonary resuscitation, and mortality of 28%, 10%, 8%, 4%, and 2%. The ROC curve showed that the cut-off point of copeptin was 2,141.50 pg/mL and area under curve (AUC) value of 0.710 with sensitivity of 75.0%, specificity of 68.80% and accuracy of 71.15%. Hence, the AUC values and accuracy present fair results for predicting MACE during hospitalization in AMI patients.

Conclusion
Copeptin has a role as a predictor of MACE during hospitalization in AMI patients.