bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospects and challenges of cancer systems medicine: from genes to disease networks
Authors: Karimi Mohammad Reza , Karimi Amir Hossein , Abolmaali Shamsozoha , Sadeghi Mehdi , Schmitz Ulf 
Published: August 2021

AbstractIt is becoming evident that holistic perspectives toward cancer are crucial in deciphering the overwhelming complexity of tumors. Single-layer analysis of genome-wide data has greatly contributed to our understanding of cellular systems and their perturbations. However, fundamental gaps in our knowledge persist and hamper the design of effective interventions. It is becoming more apparent than ever, that cancer should not only be viewed as a disease of the genome but as a disease of the cellular system. Integrative multilayer approaches are emerging as vigorous assets in our endeavors to achieve systemic views on cancer biology. Herein, we provide a comprehensive review of the approaches, methods and technologies that can serve to achieve systemic perspectives of cancer. We start with genome-wide single-layer approaches of omics analyses of cellular systems and move on to multilayer integrative approaches in which in-depth descriptions of proteogenomics and network-based data analysis are provided. Proteogenomics is a remarkable example of how the integration of multiple levels of information can reduce our blind spots and increase the accuracy and reliability of our interpretations and network-based data analysis is a major approach for data interpretation and a robust scaffold for data integration and modeling. Overall, this review aims to increase cross-field awareness of the approaches and challenges regarding the omics-based study of cancer and to facilitate the necessary shift toward holistic approaches.
LipiDisease: associate lipids to diseases using literature mining
Authors: More Piyush , Bindila Laura , Wild Philipp , Andrade-Navarro Miguel , Fontaine Jean-Fred 
Published: August 2021

AbstractSummaryLipids exhibit an essential role in cellular assembly and signaling. Dysregulation of these functions has been linked with many complications including obesity, diabetes, metabolic disorders, cancer and more. Investigating lipid profiles in such conditions can provide insights into cellular functions and possible interventions. Hence the field of lipidomics is expanding in recent years. Even though the role of individual lipids in diseases has been investigated, there is no resource to perform disease enrichment analysis considering the cumulative association of a lipid set. To address this, we have implemented the LipiDisease web server. The tool analyzes millions of records from the PubMed biomedical literature database discussing lipids and diseases, predicts their association and ranks them according to false discovery rates generated by random simulations. The tool takes into account 4270 diseases and 4798 lipids. Since the tool extracts the information from PubMed records, the number of diseases and lipids will be expanded over time as the biomedical literature grows.Availability and implementationThe LipiDisease webserver can be freely accessed at http://cbdm-01.zdv.uni-mainz.de:3838/piyusmor/LipiDisease/.Supplementary informationSupplementary data are available at Bioinformatics online.
Predicting correlated outcomes from molecular data
Authors: Rauschenberger Armin , Glaab Enrico 
Published: August 2021

Abstract

Motivation
Multivariate (multi-target) regression has the potential to outperform univariate (single-target) regression at predicting correlated outcomes, which frequently occur in biomedical and clinical research. Here we implement multivariate lasso and ridge regression using stacked generalization.

Results
Our flexible approach leads to predictive and interpretable models in high-dimensional settings, with a single estimate for each input–output effect. In the simulation, we compare the predictive performance of several state-of-the-art methods for multivariate regression. In the application, we use clinical and genomic data to predict multiple motor and non-motor symptoms in Parkinson’s disease patients. We conclude that stacked multivariate regression, with our adaptations, is a competitive method for predicting correlated outcomes.

Availability and implementation
The R package joinet is available on GitHub (https://github.com/rauschenberger/joinet) and cran (https://cran.r-project.org/package=joinet).

Supplementary information
Supplementary data are available at Bioinformatics online.
Data Proliferation, Reconciliation, and Synthesis in Viral Ecology
Authors: Gibb Rory , Albery Gregory F , Becker Daniel J , Brierley Liam , Connor Ryan , Dallas Tad A , Eskew Evan A , Farrell Maxwell J , Rasmussen Angela L , Ryan Sadie J , Sweeny Amy , Carlson Colin J , Poisot Timothée 
Published: August 2021

Abstract
The fields of viral ecology and evolution are rapidly expanding, motivated in part by concerns around emerging zoonoses. One consequence is the proliferation of host–virus association data, which underpin viral macroecology and zoonotic risk prediction but remain fragmented across numerous data portals. In the present article, we propose that synthesis of host–virus data is a central challenge to characterize the global virome and develop foundational theory in viral ecology. To illustrate this, we build an open database of mammal host–virus associations that reconciles four published data sets. We show that this offers a substantially richer view of the known virome than any individual source data set but also that databases such as these risk becoming out of date as viral discovery accelerates. We argue for a shift in practice toward the development, incremental updating, and use of synthetic data sets in viral ecology, to improve replicability and facilitate work to predict the structure and dynamics of the global virome.
Surgical repair of diastasis recti abdominis provides long-term improvement of abdominal core function and quality of life: a 3-year follow-up
Authors: Olsson Anders , Kiwanuka Olivia , Wilhelmsson Sofia , Sandblom Gabriel , Stackelberg Otto 
Published: August 2021

Abstract

Background
Diastasis recti abdominis (DRA) is a condition affecting many post-partum women. The aim of this study was to evaluate long-term results of surgical repair of DRA in a cohort of post-partum women.

Methods
Sixty post-partum women with DRA and training-resistant core dysfunctions were included. Surgical repair was performed with suture plication of the linea alba. Abdominal core function was evaluated with the abdominal trunk function protocol (ATFP) including a self-report questionnaire and seven functional tests. Urinary incontinence and quality of life were evaluated with the Urogenital Distress Inventory (UDI-6), the Incontinence Impact Questionnaire (IIQ-7) and the SF-36 questionnaire. Follow-up was performed at 1 and 3 years after surgery.

Results
Response rate at the 3-year follow-up was 86.7 per cent for the disability rating index (DRI) questionnaire; and 71.7 per cent for the ATFP, UDI-6, IIQ-7 and SF-36 questionnaires. All DRI parameters were improved (P &lt; 0.001) after 3 years of follow-up compared with preoperative values. The functional tests in the ATFP showed an improvement in core muscle strength and stability (P &lt; 0.001), back muscle strength (P &lt; 0.001) and abdominal muscle strength (P = 0.002) compared to preoperative values as well as an improvement of core muscle strength and stability compared with the 1-year follow-up values (P = 0.003). UDI-6 and IIQ-7 results were improved (P &lt; 0.001 and P = 0.004) compared with preoperative values and showed consistent values compared with the 1-year follow-up (P = 0.09 and P = 1.0). Quality of life measured with SF-36 was improved compared with preoperative values and showed consistent values compared with the 1-year follow-up.

Conclusion
The functional improvement of surgical reconstruction of the DRA persisted for 3 years in this series of post-partum women with DRA.
A Case Study of Social Work Leadership in the Pandemic Intervention in Wuhan
Authors: Yu Zhihong , Luo Hai , Tan Weijia , Niu Liya 
Published: August 2021

Abstract
Social workers in Wuhan, China were among the first to respond to the public health crisis caused by Coronavirus disease (COVID-19) in early 2020. Social workers in Wuhan developed and implemented an effective interventional model integrating online and offline volunteers of multiple professions—the ‘4 + 1’ model—to support affected individuals in the process of battling the pandemic. Transformational social work leadership played a vital role in the widely adopted model in China, characterised by idealised influence—attributed (or charisma); idealised influence—behavioural; inspirational motivation; intellectual stimulation and individual consideration. Contextual performance is also discussed, followed by a discussion on why social work can play a leadership role in inter-disciplinary intervention in the pandemic crisis. The article concludes with the areas social workers can improve on for the betterment of leadership.
Quasi-symmetries in complex networks: a dynamical model approach
Authors: Rosell-Tarragó Gemma , Díaz-Guilera Albert 
Published: August 2021

Abstract
The existence of symmetries in complex networks has a significant effect on network dynamic behaviour. Nevertheless, beyond topological symmetry, one should consider the fact that real-world networks are exposed to fluctuations or errors, as well as mistaken insertions or removals. Therefore, the resulting approximate symmetries remain hidden to standard symmetry analysis—fully accomplished by discrete algebra software. There have been a number of attempts to deal with approximate symmetries. In the present work we provide an alternative notion of these weaker symmetries, which we call ‘quasi-symmetries’. Differently from other definitions, quasi-symmetries remain free to impose any invariance of a particular network property and they are obtained from the phase differences at the steady-state configuration of an oscillatory dynamical model: the Kuramoto–Sakaguchi model. The analysis of quasi-symmetries unveils otherwise hidden real-world networks attributes. On the one hand, we provide a benchmark to determine whether a network has a more complex pattern than that of a random network with regard to quasi-symmetries, namely, if it is structured into separate quasi-symmetric groups of nodes. On the other hand, we define the ‘dual-network’, a weighted network (and its corresponding binnarized counterpart) that effectively encodes all the information of quasi-symmetries in the original network. The latter is a powerful instrument for obtaining worthwhile insights about node centrality (obtaining the nodes that are unique from that act as imitators with respect to the others) and community detection (quasi-symmetric groups of nodes).
Potential of unenhanced computed tomography as a screening tool for acute aortic syndromes
Authors: Otani Takayuki , Ichiba Toshihisa , Kashiwa Kenichiro , Naito Hiroshi 
Published: August 2021

Abstract

Aims
Contrast-enhanced computed tomography (CE-CT) is the gold standard for diagnosing acute aortic syndromes (AAS). Unenhanced computed tomography (unenhanced-CT) also provides specific findings for AAS; however, its diagnostic ability is not well discussed. This study aims to evaluate the potential of unenhanced-CT as an AAS screening tool.

Methods and results
We retrospectively examined AAS patients who visited our hospital between 2011 and 2021 to validate the diagnostic value of unenhanced-CT alone and along with the aortic dissection detection risk score (ADD-RS) plus D-dimer. Acute aortic syndrome was assessed as detectable using unenhanced-CT with any of the following findings: pericardial haemorrhage, high-attenuation haematoma, and displacement of intimal calcification or a flap. Of the 316 AAS cases, 292 (92%) were detectable with unenhanced-CT. Twenty-four (8%) cases undetectable with unenhanced-CT involved younger patients [median (interquartile range), 45 (42–51) years vs. 72 (63–80) years, P &lt; 0.001] and patients more frequently complicated with a patent false lumen (79% vs. 42%, P &lt; 0.001). Acute aortic syndrome-detection rate with unenhanced-CT increased with age, reaching 98% (276/282) in those ≥50 years of age and 100% (121/121) in those ≥75 years of age. With the ADD-RS plus D-dimer, there was only one AAS case undetectable with unenhanced-CT among patients ≥50 years of age, except for cases with the ADD-RS ≥1 plus D-dimer levels of ≥0.5 μg/mL.

Conclusion
Acute aortic syndromes in younger patients and patients with a patent false lumen could be misdiagnosed with unenhanced-CT alone. The combination of the ADD-RS plus D-dimer and unenhanced-CT could minimize AAS misdiagnosis while avoiding over-testing with CE-CT.
The digital heart–lung unit: applications of exponential technology
Authors: Sadeghi Amir H , Ooms Joris F W , Van Mieghem Nicolas M , Mahtab Edris A F , Bogers Ad J J C 
Published: August 2021

Abstract
Exponential technologies such as virtual reality (VR), computational modelling, and additive manufacturing have emerged in the field of cardiology and cardiothoracic surgery. An increasing number of publications that evaluate the clinical role of these technologies are becoming available. Moreover, there is an increase in the number of hospitals and departments that have implemented digital and exponential solutions in clinical workflow. In our centre, we have adopted various exponential technologies in order to improve clinical pre-procedural workflow, patient care, and training and education. In order to provide our view and approach on the implementation of these technologies, in this article, we provide an overview of the currently applied modalities including immersive VR, three-dimensional (3D) computational modelling, VR-based simulations, and additive manufacturing (3D printing). Moreover, we present the potential of these applications in cardiovascular and cardiothoracic medicine, and additionally, we will provide key facilitators, challenges, and recommendations to adopting these technologies in clinical practice.
Significantly favourable outcome for patients with non-small-cell lung cancer stage IIIA/IIIB and single-station persistent N2 (skip or additionally N1) disease after multimodality treatment
Authors: Stamatis Georgios , Müller Stefanie , Weinreich Gerhard , Schwarz Birte , Eberhardt Wilfried , Pöttgen Christoph , Aigner Clemens 
Published: August 2021

Abstract

OBJECTIVES
Persistent lymph nodes infiltration after neoadjuvant treatment remains a controversial topic in the treatment of stage III non-small-cell lung cancer (NSCLC). The aim of this study is to identify subgroups with persistent N2 disease, who could experience survival benefit from the addition of surgery.

METHODS
A retrospective mono-institutional study was conducted to analyse all patients with a final histopathology of NSCLC and persistent mediastinal disease after induction chemotherapy or chemoradiotherapy and surgery from January 1998 to June 2015.

RESULTS
A total of 145 patients (93 men, 52 women) fulfilled the inclusion criteria. The median age was 60 years (range 38–78). A total of 82 (56.5%) patients received a lobectomy, 48 (33.1%) a pneumonectomy, 11 (7.6%) a bilobectomy and 4 (2.6%) an anatomical segmentectomy; 128 (88.3%) were completely resected (R0). Operative mortality was 2.6% (4 patients), and morbidity was 35.2% (51 patients). Overall survival at 5 years was 47.3% (n = 19) for single N2 (skip), 30.2% (n = 16) for single N2 and N1 lymph nodes and under 5% (n = 1) for multiple mediastinal stations disease. Overall survival at 5 years after lobectomy/bilobectomy was not statistically different than after pneumonectomy (33.5% vs 20.5%, P = 0.082). Disease-free survival at 5 years was 30.6% (n = 6) for ypN2a1, 23.4% (n = 7) for ypN2a2 and under 5% (n = 1) for ypN2b status.

CONCLUSIONS
Lobectomy or bilobectomy has to be taken into account as a potentially curative option with promising long-term results for patients after induction treatment and persistent single-station N2 involvement (skip or additionally N1 status).

Trial registry number
14-6138-BO.
Invasive and non-invasive assessment of ischaemia in chronic coronary syndromes: translating pathophysiology to clinical practice
Authors: Demir Ozan M , Rahman Haseeb , van de Hoef Tim P , Escaned Javier , Piek Jan J , Plein Sven , Perera Divaka 
Published: August 2021

Abstract
Intracoronary physiology testing has emerged as a valuable diagnostic approach in the management of patients with chronic coronary syndrome, circumventing limitations like inferring coronary function from anatomical assessment and low spatial resolution associated with angiography or non-invasive tests. The value of hyperaemic translesional pressure ratios to estimate the functional relevance of coronary stenoses is supported by a wealth of prognostic data. The continuing drive to further simplify this approach led to the development of non-hyperaemic pressure-based indices. Recent attention has focussed on estimating physiology without even measuring coronary pressure. However, the reduction in procedural time and ease of accessibility afforded by these simplifications needs to be counterbalanced against the increasing burden of physiological assumptions, which may impact on the ability to reliably identify an ischaemic substrate, the ultimate goal during catheter laboratory assessment. In that regard, measurement of both coronary pressure and flow enables comprehensive physiological evaluation of both epicardial and microcirculatory components of the vasculature, although widespread adoption has been hampered by perceived technical complexity and, in general, an underappreciation of the role of the microvasculature. In parallel, entirely non-invasive tools have matured, with the utilization of various techniques including computational fluid dynamic and quantitative perfusion analysis. This review article appraises the strengths and limitations for each test in investigating myocardial ischaemia and discusses a comprehensive algorithm that could be used to obtain a diagnosis in all patients with angina scheduled for coronary angiography, including those who are not found to have obstructive epicardial coronary disease.
Prognostic value of comprehensive intracoronary physiology assessment early after heart transplantation
Authors: Ahn Jung-Min , Zimmermann Frederik M , Arora Satish , Solberg Ole-Geir , Angerås Oskar , Rolid Katrine , Rafique Muzammil , Aaberge Lars , Karason Kristjan , Okada Kozo , Luikart Helen , Khush Kiran K , Honda Yasuhiro , Pijls Nico H J , Lee Sang Eun , Kim Jae-Joong , Park Seung-Jung , Gullestad Lars , Fearon William F 
Published: August 2021

Abstract

Aims
We evaluated the long-term prognostic value of invasively assessing coronary physiology after heart transplantation in a large multicentre registry.

Methods and results
Comprehensive intracoronary physiology assessment measuring fractional flow reserve (FFR), the index of microcirculatory resistance (IMR), and coronary flow reserve (CFR) was performed in 254 patients at baseline (a median of 7.2 weeks) and in 240 patients at 1 year after transplantation (199 patients had both baseline and 1-year measurement). Patients were classified into those with normal physiology, reduced FFR (FFR ≤ 0.80), and microvascular dysfunction (either IMR ≥ 25 or CFR ≤ 2.0 with FFR &gt; 0.80). The primary outcome was the composite of death or re-transplantation at 10 years. At baseline, 5.5% had reduced FFR; 36.6% had microvascular dysfunction. Baseline reduced FFR [adjusted hazard ratio (aHR) 2.33, 95% confidence interval (CI) 0.88–6.15; P = 0.088] and microvascular dysfunction (aHR 0.88, 95% CI 0.44–1.79; P = 0.73) were not predictors of death and re-transplantation at 10 years. At 1 year, 5.0% had reduced FFR; 23.8% had microvascular dysfunction. One-year reduced FFR (aHR 2.98, 95% CI 1.13–7.87; P = 0.028) and microvascular dysfunction (aHR 2.33, 95% CI 1.19–4.59; P = 0.015) were associated with significantly increased risk of death or re-transplantation at 10 years. Invasive measures of coronary physiology improved the prognostic performance of clinical variables (χ 2 improvement: 7.41, P = 0.006). However, intravascular ultrasound-derived changes in maximal intimal thickness were not predictive of outcomes.

Conclusion
Abnormal coronary physiology 1 year after heart transplantation was common and was a significant predictor of death or re-transplantation at 10 years.
Nucleus Type-Specific DNA Methylomics Reveals Epigenetic “Memory” of Prior Adaptation in Skeletal Muscle
Authors: Wen Yuan , Dungan Cory M , Mobley C Brooks , Valentino Taylor , von Walden Ferdinand , Murach Kevin A 
Published: August 2021

AbstractUsing a mouse model of conditional and inducible in vivo fluorescent myonuclear labeling (HSA-GFP), sorting purification of nuclei, low-input reduced representation bisulfite sequencing (RRBS), and a translatable and reversible model of exercise (progressive weighted wheel running, PoWeR), we provide the first nucleus type-specific epigenetic information on skeletal muscle adaptation and detraining. Adult (&gt;4 mo) HSA-GFP mice performed PoWeR for 8 wk then detrained for 12 wk; age-matched untrained mice were used to control for the long duration of the study. Myonuclei and interstitial nuclei from plantaris muscles were isolated for RRBS. Relative to untrained, PoWeR caused similar myonuclear CpG hypo- and hyper-methylation of promoter regions and substantial hypomethylation in interstitial nuclear promoters. Over-representation analysis of promoters revealed a larger number of hyper- versus hypo-methylated pathways in both nuclear populations after training and evidence for reciprocal regulation of methylation between nucleus types, with hypomethylation of promoter regions in Wnt signaling-related genes in myonuclei and hypermethylation in interstitial nuclei. After 12 wk of detraining, promoter CpGs in documented muscle remodeling-associated genes and pathways that were differentially methylated immediately after PoWeR were persistently differentially methylated in myonuclei, along with long-term promoter hypomethylation in interstitial nuclei. No enduring gene expression changes in muscle tissue were observed using RNA-sequencing. Upon 4 wk of retraining, mice that trained previously grew more at the whole muscle and fiber type-specific cellular level than training naïve mice, with no difference in myonuclear number. Muscle nuclei have a methylation epi-memory of prior training that may augment muscle adaptability to retraining.