bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach
Authors: Zhang Weiwei , Wu Hao , Li Ziyi 
Published: October 2020

Abstract

Motivation
It is a common practice in epigenetics research to profile DNA methylation on tissue samples, which is usually a mixture of different cell types. To properly account for the mixture, estimating cell compositions has been recognized as an important first step. Many methods were developed for quantifying cell compositions from DNA methylation data, but they mostly have limited applications due to lack of reference or prior information.

Results
We develop Tsisal, a novel complete deconvolution method which accurately estimate cell compositions from DNA methylation data without any prior knowledge of cell types or their proportions. Tsisal is a full pipeline to estimate number of cell types, cell compositions and identify cell-type-specific CpG sites. It can also assign cell type labels when (full or part of) reference panel is available. Extensive simulation studies and analyses of seven real datasets demonstrate the favorable performance of our proposed method compared with existing deconvolution methods serving similar purpose.

Availability and implementation
The proposed method Tsisal is implemented as part of the R/Bioconductor package TOAST at https://bioconductor.org/packages/TOAST.

Supplementary information
Supplementary data are available at Bioinformatics online.
SNHG5 inhibits the progression of EMT through the ubiquitin-degradation of MTA2 in oesophageal cancer
Authors: Wei Sisi , Sun Shiping , Zhou Xinliang , Zhang Cong , Li Xiaoya , Dai Suli , Wang Yaojie , Zhao Lianmei , Shan Baoen 
Published: October 2020

Abstract
A substantial fraction of transcripts are known as long noncoding RNAs (lncRNAs), and these transcripts play pivotal roles in the development of cancer. However, little information has been published regarding the functions of lncRNAs in oesophageal squamous cell carcinoma (ESCC) and the underlying mechanisms. In our previous studies, we demonstrated that small nucleolar RNA host gene 5 (SNHG5), a known lncRNA, is dysregulated in gastric cancer (GC). In this study, we explored the expression and function of SNHG5 in development of ESCC. SNHG5 was found to be downregulated in human ESCC tissues and cell lines, and this downregulation was associated with cancer progression, clinical outcomes and survival rates of ESCC patients. Furthermore, we also found that overexpression of SNHG5 significantly inhibited the proliferation, migration and invasion of ESCC cells in vivo and in vitro. Notably, we found that metastasis-associated protein 2 (MTA2) was pulled down by SNHG5 in ESCC cells using RNA pulldown assay. We also found that SNHG5 reversed the epithelial–mesenchymal transition by interacting with MTA2. In addition, overexpression of SNHG5 downregulated the transcription of MTA2 and caused its ubiquitin-mediated degradation. Thus, overexpression of MTA2 partially abrogated the effect of SNHG5 in ESCC cell lines. Furthermore, we found that MTA2 mRNA expression was significantly elevated in ESCC specimens, and a negative correlation between SNHG5 and MTA2 expression was detected. Overall, this study demonstrated, for the first time, that SNHG5-regulated MTA2 functions as an important player in the progression of ESCC and provide a new potential therapeutic strategy for ESCC.
Left brachial artery: one more way to percutaneous insertion of IMPELLA 2.5L circulatory support for high-risk percutaneous coronary intervention – a case report
Authors: Sganzerla Paolo , Cinelli Francesco , Capoferri Andrea , Rondi Mauro 
Published: October 2020

Abstract

Background
Percutaneous circulatory support allows the performance of coronary interventions in ever more complex anatomic and clinical situations. The large-bore systems currently available need a suitable vascular calibre to be inserted restricting percutaneous access mainly to the common femoral artery.

Case summary
We present the case of a 64-year-old man, admitted with an acute coronary syndrome and congestive heart failure, due to triple-vessel coronary artery disease with left main involvement and left ventricular dysfunction. He was successfully treated with percutaneous coronary intervention (PCI) supported through an IMPELLA 2.5L circulatory system. Concomitant severe and diffuse peripheral vascular disease did not allow femoral insertion of the circulatory support which was therefore successfully introduced through a left brachial percutaneous approach.

Discussion
To the best of our knowledge, this is the first report of a brachial, percutaneous placement of the IMPELLA 2.5L system to support a high-risk PCI procedure. In appropriately selected patients, this approach could be an option when common vascular accesses are not available.
Case report of severe PCR-confirmed COVID-19 myocarditis in a European patient manifesting in mid January 2020
Authors: Hudowenz Ole , Klemm Philipp , Lange Uwe , Rolf Andreas , Schultheiss Heinz-Peter , Hamm Christian , Müller-Ladner Ulf , Wegner Franz 
Published: October 2020

Abstract

Background
Viral genesis is the most common cause of myocarditis. COVID-19-associated myocarditis seems to be a notable extrapulmonary manifestation, which may result in the need for a different treatment. There has been no positive polymerase chain reaction (PCR) testing of SARS-CoV-2 in heart specimens, thus far.

Case summary
A 48-year-old male patient presented with fever, dyspnoea, and haemoptysis. Laboratory findings showed highly elevated inflammatory and cardiac damage markers. Thoracic computed tomography (CT) revealed bilateral, patchy peripheral ground-glass opacities with a crazy-paving pattern, focal consolidations, and mild pleural effusions. Cardiac imaging with echocardiography and magnetic resonance imaging (MRI) detected a reduced biventricular function. MRI additionally showed myocardial oedema and late gadolinium enhancement. Lung and heart biopsies were performed, revealing alveolitis with necrosis and acute lymphocytic myocarditis. Testing for usual cardiotropic viruses was negative, and no aspects of vasculitis or granuloma could be found. Due to fulfilling the criteria, the patient was diagnosed with rheumatic vasculitis. Treatment with cyclophosphamide and steroids was initiated. Later, the patient reported a history of travel to Tyrol in mid January. Consequently, PCR testing for SARS-CoV-2 was performed, which was positive in the heart specimen. Immunosuppressive treatment was discontinued. During a follow-up visit at the end of April, the patient’s recovery was stable.

Discussion
In COVID-19 infections, myocardial inflammation can be present as an extrapulmonary manifestation. Positive PCR testing confirms myocardial invasion of the virus. Imaging and laboratory studies correlate with the histopathological findings, and thus should be performed in COVID-19 patients who are suspicious for myocarditis. Supportive treatment with steroids may be useful in these patients.
A simple technique of artificial chordae implantation in robotic cardiac surgery using a novel tube device supporting expanded polytetrafluoroethylene chordae ligation
Authors: Tedoriya Takeo , Okano Ryoi , Fukuzumi Masaomi , Miyauchi Tadamasa 
Published: October 2020

Abstract
Artificial chordae implantation is an important technique for treating leaflet lesions in mitral valve repair. Considering that the expanded polytetrafluoroethylene (ePTFE) suture is slippery on the surface, adequate ligation without laxity should be critically considered, especially in robotic surgery. To resolve this issue, we applied a novel device that controls the length of an ePTFE suture (Chordarizer) for artificial chordae implantation in robotic mitral valve repair. After assessing the mitral valve via the right side of the left atrium, we stitched a CV-4 ePTFE suture to the target papillary muscle. Using a calliper, we measured the length of the artificial chordae and passed the CV-4 through the appropriate Chordarizer. Then, we stitched the CV-4 to the tip of the leaflet from the left ventricle side and tied it using da Vinci arms. Finally, the Chordarizer was peeled away. Chordarizer ensured safe and reliable artificial chordae implantation procedures with robotic mitral surgery, by maintaining the desired CV4 length.
In-hospital mortality and organ failure after open and endovascular thoraco-abdominal aortic surgery can be predicted by increased levels of circulating dipeptidyl peptidase 3
Authors: Gombert Alexander , Barbati Mohammad , Kotelis Drosos , Simon Tim-Philipp , Breuer Thomas , Hartmann Oliver , Santos Karine , Bergmann Deborah , Schulte Janin , Marx Gernot , Jacobs Michael , Stoppe Christian 
Published: October 2020

Abstract

OBJECTIVES
Endovascular and open thoraco-abdominal aortic aneurysm (TAAA) repair is associated with specific complications. Circulating dipeptidyl peptidase 3 (cDPP3) is a novel biomarker that shows a strong association with organ failure which has not been assessed in surgical settings. Therefore, the objective of this study was to assess the prognostic capabilities of cDPP3 for predicting patient survival and organ failure following open and endovascular TAAA repair.

METHODS
Thirty-three patients undergoing TAAA repair were assessed in this prospective observational single-centre study. cDPP3 levels were serially measured perioperatively until 72 h after admission to the intensive care unit (ICU). In-hospital mortality and any organ failure were the clinical end points.

RESULTS
Postoperative organ failure was detected in 17 patients (51.5%), and 6 patients died after surgery (18.2%). At 12 h after admission to the ICU, cDPP3 levels were significantly increased in patients who died or developed organ failure (P &lt; 0.001). cDPP3 levels after surgery demonstrated a remarkable predictive accuracy for in-hospital mortality [12 h area under the receiver operating characteristic curve (AUC): 0.907 (P &lt; 0.001), 24 h AUC: 0.815 (P = 0.016), 48 h AUC: 0.914 (P = 0.003)] and the development of organ failure [12 h AUC: 0.882 (P &lt; 0.001), 24 h AUC: 0.850 (P &lt; 0.001), 48 h AUC: 0.846 (P &lt; 0.001)]. Additionally, a significant correlation between cDPP3, the sequential organ failure assessment score and procalcitonin, C-reactive protein and interleukin-6 levels (P &lt; 0.001, P &lt; 0.001, P = 0.011, P = 0.007, respectively) based on all available measurements and time points was observed.

CONCLUSIONS
The present findings highlight the role of cDPP3 as an early, highly specific postoperative biomarker for prediction of in-hospital mortality and organ failure after TAAA repair.
Cephalometry without complex dedicated postprocessing in an oriented magnetic resonance imaging dataset: a pilot study
Authors: März Karoline , Chepura Taras , Plewig Blanka , Haddad Daniel , Weber Daniel , Schmid Matthias , Hirschfelder Ursula , Gölz Lina 
Published: October 2020

Summary

Objectives
Magnetic resonance imaging (MRI) enables a 3D-volume-imaging without ionizing radiation. Therefore, it was the aim of this study to present a post-processing-free method for cephalometric analysis of a MRI-dataset and to examine whether there is a significant difference between cephalometric analysis of conventional 2D cephalograms and MRI scans.

Methods
One MRI scan each was performed on three cadaver heads using a 3T-MR-scanner. Cephalometric analysis was conducted directly on the 3D dataset. All reference points were projected onto a virtual sagittal plane that was perpendicular to the Frankfort horizontal plane. Double-sided points were averaged. Cephalometric angles were measured from the projected points. Results were compared with cephalometric measurements on conventional lateral cephalometric radiographs (LCRs). The cephalometric analysis was performed by five raters.

Results
390-angle measurements were obtained. The inter-rater reliability was high [intraclass correlation coefficients (ICCs) ≥ 0.74 for all angles]. Differences between the measurements on the cephalograms and MRI scans ranged between –0.91° (–1.88°, 0.07°) and 0.97° (–0.63°, 2.57°) on average and were equivalent with respect to a margin of [–2°, 2°] in all angles except L1—Me-Tgo (Bonferroni-Holm-corrected P &lt; 0.05 in all angles except L1—Me-Tgo). The best match was found for the SNA angle.

Conclusion
The clinical comparability of the MRI- and LCR-based cephalometry could be stated. Using MRI in orthodontics would reduce radiation exposure and the risk of stochastic radiation damage, which is of importance especially in younger patients.
Reducing Ageism With Brief Videos About Aging Education, Ageism, and Intergenerational Contact
Authors: Lytle Ashley , Macdonald Jamie , Apriceno MaryBeth , Levy Sheri R 
Published: October 2020

Abstract

Background and Objectives
With an increasing older population, ageism continues to be a significant social issue. Interventions to reduce ageism and improve intergenerational contact are needed.

Research Design and Methods
Building on the Positive Education about Aging and Contact Experiences (PEACE) model, undergraduates in an online experiment were randomly assigned to watch videos that provided education about aging, ageism, and positive intergenerational contact (experimental condition) or education about wallpaper (control condition).

Results
In Part 1, 845 undergraduates in the experimental condition (vs. control condition) reported lower levels of ageism, less negative age stereotypes, more positive age stereotypes, and more aging knowledge in an immediate post-test. In Part 2 (1–6 weeks later), undergraduates in the experimental condition (vs. control condition) reported more positive age stereotypes in a delayed post-test.

Discussion and Implications
These findings highlight the promise of providing information about aging and positive intergenerational contact to reduce ageism. Brief online educational videos based on the PEACE model hold promise as an effective tool to reach a wide audience and reduce ageism.
Pyntacle: a parallel computing-enabled framework for large-scale network biology analysis
Authors: Parca Luca , Truglio Mauro , Biagini Tommaso , Castellana Stefano , Petrizzelli Francesco , Capocefalo Daniele , Jordán Ferenc , Carella Massimo , Mazza Tommaso 
Published: October 2020

Abstract

Background
Some natural systems are big in size, complex, and often characterized by convoluted mechanisms of interaction, such as epistasis, pleiotropy, and trophism, which cannot be immediately ascribed to individual natural events or biological entities but that are often derived from group effects. However, the determination of important groups of entities, such as genes or proteins, in complex systems is considered a computationally hard task.

Results
We present Pyntacle, a high-performance framework designed to exploit parallel computing and graph theory to efficiently identify critical groups in big networks and in scenarios that cannot be tackled with traditional network analysis approaches.

Conclusions
We showcase potential applications of Pyntacle with transcriptomics and structural biology data, thereby highlighting the outstanding improvement in terms of computational resources over existing tools.
Earthquake source properties from analysis of dynamic ruptures and far-field seismic waves in a damage-breakage model
Authors: Kurzon Ittai , Lyakhovsky Vladimir , Ben-Zion Yehuda 
Published: October 2020

SUMMARYWe present results on earthquake source properties using simulations of dynamic rupture and radiated seismic waves in a continuum damage-breakage rheological model. The source properties are derived by (1) calculation of source parameters directly from the simulated ruptures and (2) observational processing of the far-field radiated waves. The seismic potency, moment, damage-related source term, rupture velocity and effective rigidity are estimated directly from the simulated sources, while the radiation pattern, dominant frequency, directivity, rupture velocity and seismic potency are calculated through analysis of the radiated waves. The potencies calculated directly from the sources are used to validate those estimated by wave analysis. The effective rigidity at the rupture zone during failure is about four times smaller than that of the intact surrounding rocks. Rupture velocity can be estimated by far-field measurements for sources with unidirectional ruptures with prominent rupture directivity. The dominant frequencies for P and S waves $f_d^S/f_d^P$ reflect clearly the rupture duration and have a ratio in the range 0.87–1.12. Seismic potencies obtained through processing the P or S waves have an overall ±15 per cent difference from the source reference values. The calculated values of the coefficient ${\rm{\kappa }}$, relating rupture length to corner or dominant frequency, have strong dependency on the source geometry. Using a strain-rate dependent ${\rm{\kappa }}$, we obtain much weaker dependencies of strain-drop on the dominant frequencies, $\Delta {\rm{\varepsilon }} \propto {( {{f_d}} )^{3/4}}$, than the classical cube-dependency between stress drop and corner frequency, and corresponding weak dependency of average slip on dominant frequency, ${\rm{\bar{D}}} \propto {( {{f_d}} )^{1/2}}$. The obtained analysis procedure and relations can be used to reduce the uncertainty of source properties derived from far-field seismic waves.
Mitral valve surgery after a failed MitraClip procedure
Authors: Melillo Francesco , Baldetti Luca , Beneduce Alessandro , Agricola Eustachio , Margonato Alberto , Godino Cosmo 
Published: October 2020

Abstract

OBJECTIVES
Among patients undergoing transcatheter mitral valve repair with the MitraClip device, a relevant proportion (2–6%) requires open mitral valve surgery within 1 year after unsuccessful clip implantation. The goal of this review is to pool data from different reports to provide a comprehensive overview of mitral valve surgery outcomes after the MitraClip procedure and estimate in-hospital and follow-up mortality.

METHODS
All published clinical studies reporting on surgical intervention for a failed MitraClip procedure were evaluated for inclusion in this meta-analysis. The primary study outcome was in-hospital mortality. Secondary outcomes were in-hospital adverse events and follow-up mortality. Pooled estimate rates and 95% confidence intervals (CIs) of study outcomes were calculated using a DerSimionian–Laird binary random-effects model. To assess heterogeneity across studies, we used the Cochrane Q statistic to compute I2 values.

RESULTS
Overall, 20 reports were included, comprising 172 patients. Mean age was 70.5 years (95% CI 67.2–73.7 years). The underlying mitral valve disease was functional mitral regurgitation in 50% and degenerative mitral regurgitation in 49% of cases. The indication for surgery was persistent or recurrent mitral regurgitation (grade &gt;2) in 93% of patients, whereas 6% of patients presented with mitral stenosis. At the time of the operation, 80% of patients presented in New York Heart Association functional class III–IV. Despite favourable intraoperative results, in-hospital mortality was 15%. The rate of periprocedural cerebrovascular accidents was 6%. At a mean follow-up of 12 months, all-cause death was 26.5%. Mitral valve replacement was most commonly required because the possibility of valve repair was jeopardized, likely due to severe valve injury after clip implantation.

CONCLUSIONS
Surgical intervention after failed transcatheter mitral valve intervention is burdened by high in-hospital and 1-year mortality, which reflects reflecting the high-risk baseline profile of the patients. Mitral valve replacement is usually required due to leaflet injury.
Solid Ergodicity and Orbit Equivalence Rigidity for Coinduced Actions
Authors: Drimbe Daniel 
Published: October 2020

AbstractWe prove that the solid ergodicity property is stable with respect to taking coinduction for a fairly large class of coinduced action. More precisely, assume that $\Sigma &lt;\Gamma $ are countable groups such that $g\Sigma g^{-1}\cap \Sigma $ is finite for any $g\in \Gamma \setminus \Sigma $. Then any measure preserving action $\Sigma \curvearrowright X_0$ gives rise to a solidly ergodic equivalence relation if and only if the equivalence relation of the associated coinduced action $\Gamma \curvearrowright X$ is solidly ergodic. We also obtain orbit equivalence rigidity for such actions by showing that the orbit equivalence relation of a rigid or compact measure preserving action $\Sigma \curvearrowright X_0$ of a property (T) group is “remembered” by the orbit equivalence relation of $\Gamma \curvearrowright X$.
Influence of Strongyloides stercoralis Coinfection on the Presentation, Pathogenesis, and Outcome of Tuberculous Meningitis
Authors: Donovan Joseph , Tram Trinh Thi Bich , Phu Nguyen Hoan , Hiep Nguyen Thi Thu , Van Vu Thi Thu , Mui Dang Thi Hong , Ny Nguyen Thi Han , Nghia Ho Dang Trung , Hanh Nguyen Ho Hong , Tan Le Van , Thuong Nguyen Thuy Thuong , Thwaites Guy E 
Published: October 2020

Abstract

Background
Helminth infections may modulate the inflammatory response to Mycobacterium tuberculosis and influence disease presentation and outcome. Strongyloides stercoralis is common among populations with high tuberculosis prevalence. Our aim was to determine whether S. stercoralis coinfection influenced clinical presentation, cerebrospinal fluid (CSF) inflammation, and outcome from tuberculous meningitis (TBM).

Methods
From June 2017 to December 2019, 668 Vietnamese adults with TBM, enrolled in the ACT HIV or LAST ACT trials (NCT03092817 and NCT03100786), underwent pretreatment S. stercoralis testing by serology, stool microscopy, and/or stool polymerase chain reaction. Comparisons of pretreatment TBM severity, CSF inflammation (including cytokines), and 3-month clinical end points were performed in groups with or without active S. stercoralis infection.

Results
Overall, 9.4% participants (63 of 668) tested positive for S. stercoralis. Active S. stercoralis infection was significantly associated with reduced pretreatment CSF neutrophil counts (median [interquartile range], 3/μL [0–25/μL] vs 14 /μL [1–83/μL]; P = .04), and with reduced CSF interferon ɣ, interleukin 2, and tumor necrosis factor α concentrations (11.4 vs 56.0 pg/mL [P = .01], 33.1 vs 54.5 pg/mL [P = .03], and 4.5 vs 11.9 pg/mL [P = .02], respectively), compared with uninfected participants. Neurological complications by 3 months were significantly reduced in participants with active S. stercoralis infection compared with uninfected participants (3.8% [1 of 26] vs 30.0% [33 of 110], respectively; P = .01).

Conclusions
S. stercoralis coinfection may modulate the intracerebral inflammatory response to M. tuberculosis and improve TBM clinical outcomes.