bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endoscopic full-thickness transoral outlet reduction with semicircumferential endoscopic submucosal dissection
Authors: Hollenbach Marcus , Selig Lars , Lellwitz Sylvia , Beer Sebastian , Feisthammel Jürgen , Rosendahl Jonas , Schaumburg Tiffany , Mössner Joachim , Hoffmeister Albrecht 
Published: April 2019

Abstract
Background Endoscopic full-thickness transoral outlet reduction (efTOR) is a therapeutic option to reduce a dilated gastrojejunal anastomosis (GJA) after Roux-en-Y gastric bypass (RYGB). Mucosal ablation with argon plasma coagulation (APC) is usually performed to achieve tissue adaptation. However, rupture of sutures before scarring can lead to recurrent dilatation of the GJA. Here, we describe efTOR with a semicircumferential endoscopic submucosal dissection (ESD-efTOR) as an alternative to APC-efTOR.
Methods We enrolled 41 patients with comparable baseline characteristics (APC-efTOR 26; ESD-efTOR 15). The main objectives were reduction in the GJA diameter and in ruptured sutures. Technical success, complications, total weight loss (TWL), and percentage of total and excess weight loss (%TWL and %EWL) at 3 and 12 months, were assessed.
Results ESD-efTOR resulted in significantly fewer ruptured sutures (20 % vs. 69 %; P = 0.004) and a greater reduction in the GJA (major 20 % vs. 0 %; minor 54 % vs. 37 %; no reduction 13 % vs. 58 %; P = 0.02) after 3 months. Technical efficacy, examination time, and rate of complications were comparable.
Conclusions ESD-efTOR resulted in a significantly greater reduction in the GJA diameter and a lower risk of ruptured sutures compared with APC-efTOR.
Incidence and Risk Factors for Clostridium Difficile-Associated Diarrhea Following Revision Total Hip Arthroplasty
Authors: Curtis Gannon L. , Yokhana Sanar S. , Samuel Linsen T. , Higuera-Rueda Carlos A. , Little Bryan E. , Darwiche Hussein L. 
Published: April 2019

Abstract
Clostridium difficile-associated diarrhea (CDAD) is a well-known cause of complications and increased hospital cost following surgery. As CDAD rates continue to be adopted as a quality metric by institutions, it is important to detect high-risk patients prior to surgery, including revision total hip arthroplasty (rTHA). This study was performed to identify the incidence and risk factors of CDAD within 30 days of rTHA. The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) was accessed from 2015 to 2016 to identify rTHA procedures. Overall, 4,178 patients were included. Preoperative and perioperative variables were analyzed as potential risk factors for the development of CDAD. To compare categorical variables, Chi-square and Fisher's exact tests were used, while t-tests were used to detect differences in continuous variables. Independent risk factors for CDAD were identified using stepwise logistic regression. The rate of CDAD was found to be 0.5% (20/4,178) within 30 days of rTHA. Preoperative functional dependence (odds ratio [OR] = 3.34; p = 0.035) and dyspnea (OR = 3.80; p = 0.019), were statistically significant risk factors for the development of CDAD after rTHA. Septic revision was not a significant risk factor for CDAD (OR = 2.50; p = 0.082). The incidence of CDAD after rTHA in the United States is approximately 0.5%. Independent risk factors for CDAD include preoperative functional dependence and dyspnea. High-risk patients must be identified prior to surgery and antibiotic selection for other infections should be managed judiciously.
Biggish data: Friedrich Engels, material ecology, and Victorian data
Authors: Parham John 
Published: April 2019

ABSTRACT
Through Friedrich Engels’ The Condition of the Working Class in England (1845), this article examines two prominent themes in environmental humanities – vital ecological materialism and ‘big data’. Engels’ vivid descriptions of factories, houses, and environment shared the central tenets of ‘material ecology’ – ‘thing power’ (Jane Bennett); ‘intra-actions’ of social and material agency (Karen Barad); ‘trans-corporeality’ (Stacy Alaimo) – and met Bennett’s call to align vital and historical materialism. The main body of the paper connects his analysis both to current debates about integrating ‘big data’ into social science and the humanities and to comparable nineteenth-century developments in statistics and data visualisation. Engels articulated the working-class condition by blending four distinct modes of investigation: big data; qualitative survey research; literary thick description; and theory (the nascent critique of capitalist political economy). Such a mix remains rich with possibilities for sociology and humanities not only in communicating but in generating knowledge about complex ecologies.
A Study about Principle Component Analysis and Eigenface for Facial Extraction
Authors: Erwin  , Azriansyah M , Hartuti N , Fachrurrozi Muhammad , Adhi Tama Bayu 
Published: April 2019

Abstract
Facial recognition is one of the most successful applications of image analysis and understanding. This paper presents a Principal Component Analysis (PCA) and eigenface method for facial feature extraction. Several performance metrics, i.e. accuracy, precision, and recall are taken into account as a baseline of experiment. Furthermore, two public data sets, namely SOF (Speech on faces) and MIT CBCL Facerec are incorporated in the experiment. Based on our experimental result, it can be revealed that PCA has performed well in terms of accuracy, precision, and recall metrics by 0.598, 0.63, and 0.598, respectively.
The Critical Study of Mutual Coherence Properties on Compressive Sensing Framework for Sparse Reconstruction Performance: Compression vs Measurement System
Authors: Andryani Nur Afny C. , Dwi Pradnyana Kadek , Gunawan Dadang 
Published: April 2019

Abstract
Compressive Sensing (CS) framework becomes well known since its ability to recover signal only by using less sampling required by Shanon-Nyquist theorem. The lack of required sampling is no longer constraint for having good reconstruction performance. The load is shifted to the reconstruction procedure instead of the sampling acquisition process. As long as the signal can be guaranteed sparse, the CS based method is able to provide high reconstruction accuracy. One of the CS principle is incoherence property, which can be represented by mutual coherence value. It represents the coherence between the sensing matrix and the sparse base dictionary. The theory said the less coherence between those two parameters, the more precise the reconstruction is. In fact, it is not consistently applied. The research presented on this paper find that, the theory is consistent for reconstruction on compression system, while it is not applied on the reconstruction of measurement system. Other properties are found to be more representative on assigning necessary condition for reconstruction performance on measurement system.
Design and preliminary performance tests of the IFMIF-LIPAc Cryoplant
Authors: Renard B. , Machefel A. , Maebara S. , Phillips G. , Pruneri G. , Brédy Ph. , Riquelme A. , Vincent B. , Legrand J. , Gire C. , Ebisawa T. , Wanner M. 
Published: April 2019

Abstract
Special features of this Cryoplant are first given with operating purpose, main constraints, design choices for this cryoplant which will cool down a superconductive module (SRF Linac) of an accelerator currently under installation in Japan. The relationship between compliance with Japanese regulations and the successful hydraulic, electric and instrumentation tests are discussed. Measurements of refrigeration power and liquefaction rate were achieved inside the Dewar, and margin power was measured. Further functional and performance tests were conducted in order to demonstrate the correct operation of the cryogenic lines and distribution systems. These tests were performed successfully without the cryomodule, in anticipation to its installation and operation.
Nonmuscle myosin IIA and IIB differentially modulate migration and alter gene expression in primary mouse tumorigenic cells
Authors: Halder Debdatta , Saha Shekhar , Singh Raman K. , Ghosh Indranil , Mallick Ditipriya , Dey Sumit K. , Ghosh Arijit , Das Benu Brata , Ghosh Somiranjan , Jana Siddhartha S. 
Published: April 2019

Though many cancers are known to show up-regulation of nonmuscle myosin (NM) IIA and IIB, the mechanism by which NMIIs aid in cancer development remains unexplored. Here we demonstrate that tumor-generating, fibroblast-like cells isolated from 3-methylcholanthrene (3MC)-induced murine tumor exhibit distinct phospho-dependent localization of NMIIA and NMIIB at the perinuclear area and tip of the filopodia and affect cell migration differentially. While NMIIA-KD affects protrusion dynamics and increases cell directionality, NMIIB-KD lowers migration speed and increases filopodial branching. Strategically located NMIIs at the perinuclear area colocalize with the linker of nucleoskeleton and cytoskeleton (LINC) protein Nesprin2 and maintain the integrity of the nuclear-actin cap. Interestingly, knockdown of NMIIs results in altered expression of genes involved in epithelial-to-mesenchymal transition, angiogenesis, and cellular senescence. NMIIB-KD cells display down-regulation of Gsc and Serpinb2, which is strikingly similar to Nesprin2-KD cells as assessed by quantitative PCR analysis. Further gene network analysis predicts that NMIIA and NMIIB may act on similar pathways but through different regulators. Concomitantly, knockdown of NMIIA or NMIIB lowers the growth rate and tumor volume of 3MC-induced tumor in vivo. Altogether, these results open a new window to further investigate the effect of LINC-associated perinuclear actomyosin complex on mechanoresponsive gene expression in the growing tumor.
Hypertension Contributes to Neuropathy in Patients With Type 1 Diabetes
Authors: Ponirakis Georgios , Petropoulos Ioannis N , Alam Uazman , Ferdousi Maryam , Asghar Omar , Marshall Andrew , Azmi Shazli , Jeziorska Maria , Mahfoud Ziyad R , Boulton Andrew J M , Efron Nathan , Nukada Hitoshi , Malik Rayaz A 
Published: April 2019

Abstract

BACKGROUND
Diabetic peripheral neuropathy (DPN) can lead to foot ulceration and amputation. There are currently no disease-modifying therapies for DPN. The aim of this study was to determine if hypertension contributes to DPN in patients with type 1 diabetes mellitus (T1DM).

METHODS
Subjects with T1DM (n = 70) and controls (n = 78) underwent a comprehensive assessment of DPN.

RESULTS
Hypertension was present in 40 of 70 T1DM subjects and 20 of 78 controls. Hypertension was associated with abnormal nerve conduction parameters (P = 0.03 to <0.001), increased vibration perception threshold (P = 0.01) and reduced corneal nerve fiber density and length (P = 0.02) in subjects with T1DM. However, after adjusting for confounding factors only tibial compound motor action potential and nerve conduction velocity were associated with hypertension (P = 0.03) and systolic blood pressure (P < 0.01 to <0.0001). Hypertension had no effect on neuropathy in subjects without diabetes.

CONCLUSIONS
This study shows that hypertension is associated with impaired nerve conduction in T1DM. It supports previous small trials showing that angiotensin-converting enzyme inhibitors improve nerve conduction and advocates the need for larger clinical trials with blood pressure lowering agents in DPN.
Agreement Between Ambulatory and Home Blood Pressure Monitoring in Detecting Nighttime Hypertension and Nondipping Patterns in the General Population
Authors: Lindroos Annika S , Kantola Ilkka , Salomaa Veikko , Juhanoja Eeva P , Sivén Sam S , Jousilahti Pekka , Jula Antti M , Niiranen Teemu J 
Published: April 2019

Abstract

BACKGROUND
Nighttime blood pressure (BP) and nondipping pattern are strongly associated with hypertensive end-organ damage. However, no previous studies have compared the diagnostic agreement between ambulatory and home monitoring in detecting these BP patterns in the general population.

METHODS
We studied a population-based sample of 180 persons aged 32–80 years. The study protocol included 24-hour ambulatory BP monitoring, home daytime measurements over 7 days, home nighttime measurements (6 measurements over 2 consecutive nights using a timer-equipped home device), and ultrasound measurements for left ventricular mass index (LVMI) and carotid intima-media thickness (IMT). We defined nondipping as a &lt;10% reduction in nighttime BP compared with daytime BP, and nighttime hypertension as BP ≥ 120/70 mm Hg.

RESULTS
The agreement between ambulatory and home monitoring for detecting nighttime hypertension was good (80%, κ = 0.56, P &lt; 0.001). However, their agreement in detecting nondipping status was poor (54%, κ = 0.12, P = 0.09). The magnitude of ambulatory systolic BP dipping percent was 1.7% higher than on home monitoring (P = 0.004), whereas no difference was observed for diastolic BP dipping (difference: 0.7%, P = 0.33). LVMI and IMT were significantly greater among individuals with nighttime hypertension than in normotensive individuals, irrespective of the measurement method. However, only ambulatory nondippers, but not home nondippers, had more advanced end-organ damage than dippers.

CONCLUSION
We observed a good agreement between ambulatory and home BP monitoring in detecting nighttime hypertension in the general population. Two-night home monitoring could offer an inexpensive and feasible method for the diagnosis of nighttime hypertension.
Variant Score Ranker—a web application for intuitive missense variant prioritization
Authors: Du Juanjiangmeng , Sudarsanam Monica , Pérez-Palma Eduardo , Ganna Andrea , Francioli Laurent , Iqbal Sumaiya , Niestroj Lisa-Marie , Leu Costin , Weisburd Ben , Poterba Tim , Nürnberg Peter , Daly Mark J , Palotie Aarno , May Patrick , Lal Dennis 
Published: April 2019

Abstract

Motivation
The correct classification of missense variants as benign or pathogenic remains challenging. Pathogenic variants are expected to have higher deleterious prediction scores than benign variants in the same gene. However, most of the existing variant annotation tools do not reference the score range of benign population variants on gene level.

Results
We present a web-application, Variant Score Ranker, which enables users to rapidly annotate variants and perform gene-specific variant score ranking on the population level. We also provide an intuitive example of how gene- and population-calibrated variant ranking scores can improve epilepsy variant prioritization.

Availability and implementation
http://vsranker.broadinstitute.org

Supplementary information
Supplementary data are available at Bioinformatics online.
Cell-level somatic mutation detection from single-cell RNA sequencing
Authors: Vu Trung Nghia , Nguyen Ha-Nam , Calza Stefano , Kalari Krishna R , Wang Liewei , Pawitan Yudi 
Published: April 2019

Abstract

Motivation
Both single-cell RNA sequencing (scRNA-seq) and DNA sequencing (scDNA-seq) have been applied for cell-level genomic profiling. For mutation profiling, the latter seems more natural. However, the task is highly challenging due to the limited input materials from only two copies of DNA molecules, while whole-genome amplification generates biases and other technical noises. ScRNA-seq starts with a higher input amount, so generally has better data quality. There exists various methods for mutation detection from DNA sequencing, it is not clear whether these methods work for scRNA-seq data.

Results
Mutation detection methods developed for either bulk-cell sequencing data or scDNA-seq data do not work well for the scRNA-seq data, as they produce substantial numbers of false positives. We develop a novel and robust statistical method—called SCmut—to identify specific cells that harbor mutations discovered in bulk-cell data. Statistically SCmut controls the false positives using the 2D local false discovery rate method. We apply SCmut to several scRNA-seq datasets. In scRNA-seq breast cancer datasets SCmut identifies a number of highly confident cell-level mutations that are recurrent in many cells and consistent in different samples. In a scRNA-seq glioblastoma dataset, we discover a recurrent cell-level mutation in the PDGFRA gene that is highly correlated with a well-known in-frame deletion in the gene. To conclude, this study contributes a novel method to discover cell-level mutation information from scRNA-seq that can facilitate investigation of cell-to-cell heterogeneity.

Availability and implementation
The source codes and bioinformatics pipeline of SCmut are available at https://github.com/nghiavtr/SCmut.

Supplementary information
Supplementary data are available at Bioinformatics online.
Valine increases milk fat synthesis in mammary gland of gilts through stimulating AKT/MTOR/SREBP1 pathway†
Authors: Che Long , Xu Mengmeng , Gao Kaiguo , Zhu Cui , Wang Li , Yang Xuefen , Wen Xiaolu , Xiao Hao , Jiang Zongyong , Wu De 
Published: April 2019

Abstract
Lactating mammary glands are among the most active lipogenic organs and provide a large percentage of bioactive lipids and calories for infant growth. The branched-chain amino acid (BCAA) valine is known to modulate fatty acids synthesis in adipose tissue; however, its effects on fat metabolism and the underlying mechanisms in mammary glands remain to be determined. Valine supplementation during late pregnancy significantly increased the contents of total milk fat, triglyceride, sphingomyelin, and polyunsaturated fatty acids in the colostrum of gilts. Further study in porcine mammary epithelial cells (PMECs) confirmed that valine upregulated the phosphorylation levels of AKT-activated MTOR and subsequently induced the nuclear accumulation of sterol regulatory element binding protein 1 (SREBP1), thus increasing the expression of proteins related to fatty acids synthesis and intracellular triacylglycerol content. Inhibition of AKT/MTOR signaling or silencing of SREBP1 in PMECs downregulates the expression of proteins related to fatty acids synthesis and intracellular triacylglycerol content. Our findings indicated that valine enhanced milk fat synthesis of colostrum in porcine mammary glands via the AKT/MTOR/SREBP1 signaling pathway.
Nonparametric independence testing via mutual information
Authors: Berrett T B , Samworth R J 
Published: April 2019

SummaryWe propose a test of independence of two multivariate random vectors, given a sample from the underlying population. Our approach is based on the estimation of mutual information, whose decomposition into joint and marginal entropies facilitates the use of recently developed efficient entropy estimators derived from nearest neighbour distances. The proposed critical values may be obtained by simulation in the case where an approximation to one marginal is available or by permuting the data otherwise. This facilitates size guarantees, and we provide local power analyses, uniformly over classes of densities whose mutual information satisfies a lower bound. Our ideas may be extended to provide new goodness-of-fit tests for normal linear models based on assessing the independence of our vector of covariates and an appropriately defined notion of an error vector. The theory is supported by numerical studies on both simulated and real data.
Platelet reactivity and clinical outcomes in acute coronary syndrome patients treated with prasugrel and clopidogrel: a pre-specified exploratory analysis from the TROPICAL-ACS trial
Authors: Aradi Dániel , Gross Lisa , Trenk Dietmar , Geisler Tobias , Merkely Béla , Kiss Róbert Gábor , Komócsi András , Dézsi Csaba András , Ruzsa Zoltán , Ungi Imre , Rizas Konstantinos D , May Andreas E , Mügge Andreas , Zeiher Andreas M , Holdt Lesca , Huber Kurt , Neumann Franz-Josef , Koltowski Lukasz , Huczek Zenon , Hadamitzky Martin , Massberg Steffen , Sibbing Dirk 
Published: April 2019

Abstract

Aims
The value of platelet function testing (PFT) in predicting clinical outcomes and guiding P2Y12-inhibitor treatment is uncertain. In a pre-specified sub-study of the TROPICAL-ACS trial, we assessed ischaemic and bleeding risks according to high platelet reactivity (HPR) and low platelet reactivity (LPR) to ADP in patients receiving uniform prasugrel vs. PFT-guided clopidogrel or prasugrel.

Methods and results
Acute coronary syndrome patients with PFT done 14 days after hospital discharge were included with prior randomization to uniform prasugrel for 12 months (control group, no treatment modification) vs. early de-escalation from prasugrel to clopidogrel and PFT-guided maintenance treatment (HPR: switch-back to prasugrel, non-HPR: clopidogrel). The composite ischaemic endpoint included cardiovascular death, myocardial infarction, or stroke, while key safety outcome was Bleeding Academic Research Consortium (BARC) 2–5 bleeding, from PFT until 12 months. We identified 2527 patients with PFT results available: 1266 were randomized to the guided and 1261 to the control group. Before treatment adjustment, HPR was more prevalent in the guided group (40% vs. 15%), while LPR was more common in control patients (27% vs. 11%). Compared to control patients without HPR on prasugrel (n = 1073), similar outcomes were observed in guided patients kept on clopidogrel [n = 755, hazard ratio (HR): 1.06 (0.57–1.95), P = 0.86] and also in patients with HPR on clopidogrel switched to prasugrel [n = 511, HR: 0.96 (0.47–1.96), P = 0.91]. In contrast, HPR on prasugrel was associated with a higher risk for ischaemic events in control patients [n = 188, HR: 2.16 (1.01–4.65), P = 0.049]. Low platelet reactivity was an independent predictor of bleeding [HR: 1.74 (1.18–2.56), P = 0.005], without interaction (P int = 0.76) between study groups.

Conclusion
Based on this substudy of a randomized trial, selecting prasugrel or clopidogrel based on PFT resulted in similar ischaemic outcomes as uniform prasugrel therapy without HPR. Although infrequent, HPR on prasugrel was associated with increased risk of ischaemic events. Low platelet reactivity was a strong and independent predictor of bleeding both on prasugrel and clopidogrel.
A stochastic model for cancer metastasis: branching stochastic process with settlement
Authors: Frei Christoph , Hillen Thomas , Rhodes Adam 
Published: April 2019

AbstractWe introduce a new stochastic model for metastatic growth, which takes the form of a branching stochastic process with settlement. The moving particles are interpreted as clusters of cancer cells, while stationary particles correspond to micro-tumours and metastases. The analysis of expected particle location, their locational variance, the furthest particle distribution and the extinction probability leads to a common type of differential equation, namely, a non-local integro-differential equation with distributed delay. We prove global existence and uniqueness results for this type of equation. The solutions’ asymptotic behaviour for long time is characterized by an explicit index, a metastatic reproduction number $R_0$: metastases spread for $R_{0}&gt;1$ and become extinct for $R_{0}&lt;1$. Using metastatic data from mouse experiments, we show the suitability of our framework to model metastatic cancer.