bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autopilot system design on monohull USV- LSS01 using PID- based sliding mode control method
Authors: Alim M F A , Kadir R E A , Gamayanti N , Santoso A , Bilfaqih Y , Sahal M 
Published: February 2021

Abstract
The Autopilot system for Unmanned Surface Vehicle (USV) can be applied by Sliding Mode Control which is a high frequency switching based control method and has discontinuous control action causing chattering on the system. Therefore, the Sliding Mode Control with natural control signal using a PID controller structure is applied to the USV. By using Sliding Mode Control, USV is expected to move accurately from the expected waypoint without any chattering on the system. The stability of the whole loop of system regulation is ensured using the Lyapunov stability function. The simulation results for autopilot system validate that the control parameters fit the time constant controller design specification and have zero steady-state errors. Further, autopilot system with waypoint navigation relatively generates small Mean Square Error (MSE) of waypoint.
Investigation of non-thermal atmospheric plasma for the degradation of avermectin solution
Authors: LV Yue , ZOU Liang , LI Huidong , CEHN Zilei , WANG Xiaolong , SUN Ying , FANG Liping , ZHAO Tong , ZHANG Yuantao 
Published: February 2021

Abstract
Increasing concern with regard to food safety in the presence of pesticide residues (PRs) on the surface of agricultural products has resulted in the rapid development of practical degrading technologies for corresponding PRs. In this paper, an unconventional method of degrading pesticides, non-thermal atmospheric plasma (NTAP), was proposed to degrade the avermectin (AVM) in aqueous solution. Optical emission spectroscopy shows that NTAP, consisting of filamentary streamers, contains a variety of reactive oxygen species (ROS) that may interact with AVM. The high-performance liquid chromatography (HPLC)-MS/MS results indicate that the efficiency of AVM degradation seriously depends on multiple operation parameters of the NTAP, including the applied voltage, treatment time and gas flow rate. The maximum degradation rate of AVM was observed to be 97.47% after 240 s exposure under NTAP with an applied voltage of 18 kV and gas flow rate of 1 l min−1. Molecular dynamics simulation based on a reactive force field for the interaction between O (ground state atomic oxygen) and AVM was performed to analyze the underpinning mechanisms. The simulation result shows the possible pathways of the NTAP-generated O degrading AVM by destroying the glycosyl group or fracturing the ester group.
Lattice parameter of Am, Np bearing MOX fuel: an empirical potential study
Authors: Caglak Emre , Labeau Pierre-Etienne 
Published: February 2021

Abstract
An empirical potential study was performed for the americium (Am), neptunium (Np) containing uranium (U) and Plutonium (Pu) mixed oxides (MOX). The configurational space of a complex U1-y-y′-y″PuyAmy′Npy″O2 system was predicted by the rigid lattice Monte Carlo method. Based on the computing time and efficiency performance, the method was found to rapidly converge towards the optimal configuration. From that configuration, the relaxed lattice parameter of Am, Np bearing MOX fuel was investigated and compared with available literature data. As a result, a linear behaviour of the lattice parameter as a function of Am, Np content was observed.
Recent progress in self-healing conductive materials and flexible sensors with desired functional repairability
Authors: Zhou Cun , Liu Jize , Lv Zhen , Luo Yongyue , Zhang Xinxing 
Published: February 2021

Abstract
Flexible sensors with skin-like self-healing and sensing properties are now drawing great attention for their prospective application in many promising fields, including electronic skins, wearable electronics and soft robots. However, the unavoidable irregularity external stimuli and repetitive motions usually resulting in function loss. So, the self-healing abilities on both mechanical and electrical characters are highly attractive. Till now, numerous studies have been given to realize the self-healing of mechanical properties, while the repair of electrical properties still remains a great concern. Herein, the current main methods to prepare self-healing flexible sensors are summarized and discussed, consisting of self-healing materials with conductive layers, self-healing materials with embedded conductive network and self-healing ionic conducting hydrogels. Finally, a summary and perspective on future research directions and the potential of each strategy are given.
Learning to unknot
Authors: Gukov Sergei , Halverson James , Ruehle Fabian , Sułkowski Piotr 
Published: February 2021

Abstract
We introduce natural language processing into the study of knot theory, as made natural by the braid word representation of knots. We study the UNKNOT problem of determining whether or not a given knot is the unknot. After describing an algorithm to randomly generate N-crossing braids and their knot closures and discussing the induced prior on the distribution of knots, we apply binary classification to the UNKNOT decision problem. We find that the Reformer and shared-QK Transformer network architectures outperform fully-connected networks, though all perform at

≳

95% accuracy. Perhaps surprisingly, we find that accuracy increases with the length of the braid word, and that the networks learn a direct correlation between the confidence of their predictions and the degree of the Jones polynomial. Finally, we utilize reinforcement learning (RL) to find sequences of Markov moves and braid relations that simplify knots and can identify unknots by explicitly giving the sequence of unknotting actions. Trust region policy optimization (TRPO) performs consistently well, reducing

≳

80% of the unknots with up to 96 crossings we tested to the empty braid word, and thoroughly outperformed other RL algorithms and random walkers. Studying these actions, we find that braid relations are more useful in simplifying to the unknot than one of the Markov moves.
Is credibility a guide to possibility? A challenge for toy models in science
Authors: Sjölin Wirling Ylwa 
Published: February 2021

AbstractSeveral philosophers of science claim that scientific toy models afford knowledge of possibility, but answers to the question of why toy models can be expected to competently play this role are scarce. The main line of reply is that toy models support possibility claims insofar as they are credible. I raise a challenge for this credibility-thesis, drawing on a familiar problem for imagination-based modal epistemologies, and argue that it remains unanswered in the current literature. The credibility-thesis has a long way to go if it is to account for the epistemic merits of toy models.
BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R
Authors: Rinchai Darawan , Roelands Jessica , Toufiq Mohammed , Hendrickx Wouter , Altman Matthew C , Bedognetti Davide , Chaussabel Damien 
Published: February 2021

Abstract

Motivation
We previously described the construction and characterization of fixed reusable blood transcriptional module repertoires. More recently we released a third iteration (‘BloodGen3’ module repertoire) that comprises 382 functionally annotated modules and encompasses 14 168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires.

Results
We have developed and describe here an R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states.

Availability and implementation
The BloodGen3Module package and documentation are freely available from Github: https://github.com/Drinchai/BloodGen3Module.

Supplementary information
Supplementary data are available at Bioinformatics online.
lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning
Authors: Lin Yang , Pan Xiaoyong , Shen Hong-Bin 
Published: February 2021

Abstract

Motivation
Long non-coding RNAs (lncRNAs) are generally expressed in a tissue-specific way, and subcellular localizations of lncRNAs depend on the tissues or cell lines that they are expressed. Previous computational methods for predicting subcellular localizations of lncRNAs do not take this characteristic into account, they train a unified machine learning model for pooled lncRNAs from all available cell lines. It is of importance to develop a cell-line-specific computational method to predict lncRNA locations in different cell lines.

Results
In this study, we present an updated cell-line-specific predictor lncLocator 2.0, which trains an end-to-end deep model per cell line, for predicting lncRNA subcellular localization from sequences. We first construct benchmark datasets of lncRNA subcellular localizations for 15 cell lines. Then we learn word embeddings using natural language models, and these learned embeddings are fed into convolutional neural network, long short-term memory and multilayer perceptron to classify subcellular localizations. lncLocator 2.0 achieves varying effectiveness for different cell lines and demonstrates the necessity of training cell-line-specific models. Furthermore, we adopt Integrated Gradients to explain the proposed model in lncLocator 2.0, and find some potential patterns that determine the subcellular localizations of lncRNAs, suggesting that the subcellular localization of lncRNAs is linked to some specific nucleotides.

Availabilityand implementation
The lncLocator 2.0 is available at www.csbio.sjtu.edu.cn/bioinf/lncLocator2 and the source code can be found at https://github.com/Yang-J-LIN/lncLocator2.
Privacy-preserving and robust watermarking on sequential genome data using belief propagation and local differential privacy
Authors: Öksüz Abdullah Çağlar , Ayday Erman , Güdükbay Uğur 
Published: February 2021

Abstract

Motivation
Genome data is a subject of study for both biology and computer science since the start of the Human Genome Project in 1990. Since then, genome sequencing for medical and social purposes becomes more and more available and affordable. Genome data can be shared on public websites or with service providers (SPs). However, this sharing compromises the privacy of donors even under partial sharing conditions. We mainly focus on the liability aspect ensued by the unauthorized sharing of these genome data. One of the techniques to address the liability issues in data sharing is the watermarking mechanism.

Results
To detect malicious correspondents and SPs—whose aim is to share genome data without individuals’ consent and undetected—, we propose a novel watermarking method on sequential genome data using belief propagation algorithm. In our method, we have two criteria to satisfy. (i) Embedding robust watermarks so that the malicious adversaries cannot temper the watermark by modification and are identified with high probability. (ii) Achieving ϵ-local differential privacy in all data sharings with SPs. For the preservation of system robustness against single SP and collusion attacks, we consider publicly available genomic information like Minor Allele Frequency, Linkage Disequilibrium, Phenotype Information and Familial Information. Our proposed scheme achieves 100% detection rate against the single SP attacks with only 3% watermark length. For the worst case scenario of collusion attacks (50% of SPs are malicious), 80% detection is achieved with 5% watermark length and 90% detection is achieved with 10% watermark length. For all cases, the impact of ϵ on precision remained negligible and high privacy is ensured.

Availability and implementation
https://github.com/acoksuz/PPRW\_SGD\_BPLDP

Supplementary information
Supplementary data are available at Bioinformatics online.
Difference in Severe Acute Respiratory Syndrome Coronavirus 2 Attack Rate Between Children and Adults May Reflect Bias
Authors: Hyde Zoë 
Published: February 2021

Abstract
The epidemiology of coronavirus disease 2019 in children has been challenging to establish, owing to the high prevalence of asymptomatic infection in this population. Lower secondary attack rates in children compared with adults have been observed in household contact studies, but there is evidence that this may reflect lower testing in children and reduced exposure, rather than a genuine difference in biological susceptibility. In addition, children may shed infectious virus for a shorter period than adults and their antibody response may be less broad, with implications for both polymerase chain reaction and serological testing. Improvements in study design, data collection, and data interpretation are required to better understand the epidemiology of coronavirus disease 2019 in children.
Higher educational level in patients with eosinophilic esophagitis: a comparative analysis
Authors: Roth René , Safroneeva Ekaterina , Saner Zilian Catherine , Schreiner Philipp , Rossel Jean-Benoit , Bopp Matthias , Greuter Thomas , Scharl Michael , Pittet Valérie , Rogler Gerhard , Schoepfer Alain , Straumann Alex , Biedermann Luc 
Published: February 2021

Summary

Background
Eosinophilic esophagitis is a chronic inflammatory gastrointestinal disease with a high prevalence in younger, atopic males. In our clinical practice, we observed a striking preponderance of patients having a high educational background. The purposes of this study were first to assess the level of education of eosinophilic esophagitis patients and second to compare the findings to patients with inflammatory bowel disease, another chronic immune-mediated condition of the gastrointestinal tract, and with the Swiss general population.

Methods
Using a questionnaire, we assessed the educational level of adult patients who have attended Swiss Eosinophilic Esophagitis Clinics in the past. In addition, the educational level of the parents was assessed as well. We calculated the proportions of patients and parents who have obtained a higher educational level. Data from the Swiss Inflammatory Bowel Disease Cohort Study and from the Swiss general population served as confirmation and as comparison, respectively.

Results
A total of 277 successfully contacted patients (response rate 69.1%; mean age 51.1 years, 73% male) participated. A significantly higher proportion of surveyed eosinophilic esophagitis patients had a high International Standard Classification of Education level (66.8%, P &lt; 0.001) compared with inflammatory bowel disease patients (n = 2534; 34.2%, P &lt; 0.001) and to the Swiss general population (n = 6,066,907; 30.5% P &lt; 0.001).

Conclusion
Our analysis confirms the clinical observation that eosinophilic esophagitis patients have a significantly higher educational level compared with the general population and to patients with other chronic inflammatory diseases of the gastrointestinal tract. As a limitation, this impressive finding remains on a purely descriptive level.
Exploring the concept of centralization of surgery for benign esophageal diseases: a Delphi based consensus from the European Society for Diseases of the Esophagus
Authors: Lugaresi Marialuisa , Nafteux Philippe , Nilsson Magnus , Reynolds John V , Rosati Riccardo , Schoppmann Sebastian F , Targarona Eduardo M , Mattioli Sandro 
Published: February 2021

Summary
Surgery for benign esophageal diseases may be complex, requiring specialist training, but currently, unlike oncologic surgery, it is not centralized. The aim of the study was to explore the opinion of European surgeons on the centralization of surgery for benign esophageal diseases. A web-based questionnaire, developed through a modified Delphi process, was administered to general and thoracic surgeons of 33 European surgical societies. There were 791 complete responses (98.5%), in 59.2% of respondents, the age ranged between 41 and 60 years, 60.3% of respondents worked in tertiary centers. In 2017, the number of major surgical procedures performed for any esophageal disease by respondents was &lt;10 for 56.5% and &gt;100 for 4.5%; in responder’s hospitals procedures number was &lt;10 in 27% and &gt;100 in 15%. Centralization of surgery for benign esophageal diseases was advocated by 83.4%, in centers located according to geographic/population criteria (69.3%), in tertiary hospitals (74.5%), with availability of advanced diagnostic and interventional technologies (88.4%), in at least 10 beds units (70.5%). For national and international centers accreditation/certification, criteria approved included in-hospital mortality and morbidity (95%), quality of life oriented follow-up after surgery (88.9%), quality audits (82.6%), academic research (58.2%), and collaboration with national and international centers (76.6%); indications on surgical procedures volumes were variable. The present study strongly supports the centralization of surgery for benign esophageal diseases, in large part modeled on the principles that have underpinned the centralization of cancer surgery internationally, with emphasis on structure, process, volumes, quality audit, and clinical research.
Thirteen-year trends in cardiovascular risk in men and women with chronic coronary syndrome
Authors: Olesen Kevin Kris Warnakula , Jensen Esben Skov , Gyldenkerne Christine , Würtz Morten , Mortensen Martin Bødtker , Nørgaard Bjarne Linde , Sørensen Henrik Toft , Bøtker Hans Erik , Maeng Michael 
Published: February 2021

Abstract

Aims
To examine combined and sex-specific temporal changes in risks of adverse cardiovascular events and coronary revascularization in patients with chronic coronary syndrome undergoing coronary angiography.

Methods and results
We included all patients with stable angina pectoris and coronary artery disease examined by coronary angiography in Western Denmark from 2004 to 2016. Patients were stratified by examination year interval: 2004–2006, 2007–2009, 2010–2012, and 2013–2016. Outcomes were 2-year risk of myocardial infarction, ischaemic stroke, cardiac death, and all-cause death estimated by adjusted incidence rate ratios using patients examined in 2004–2006 as reference. A total of 29 471 patients were included, of whom 70% were men. The 2-year risk of myocardial infarction [2.8% vs. 1.9%, adjusted incidence rate ratio 0.65, 95% confidence interval (CI) 0.53–0.81], ischaemic stroke (1.8% vs. 1.1%, adjusted incidence rate ratio 0.48, 95% CI 0.37–0.64), cardiac death (2.1% vs. 0.9%, adjusted incidence rate ratio 0.38, 95% CI 0.29–0.51), and all-cause death (5.0% vs. 3.6%, adjusted incidence rate ratio 0.65, 95% CI 0.55–0.76) decreased from the first examination interval (2004–2006) to the last examination interval (2013–2016). Coronary revascularizations also decreased (percutaneous coronary intervention: 51.6% vs. 42.5%; coronary artery bypass grafting: 24.6% vs. 17.5%). Risk reductions were observed in both men and women, however, women had a lower absolute risk.

Conclusion
The risk for adverse cardiovascular events decreased substantially in both men and women with chronic coronary syndrome from 2004 to 2016. These results most likely reflect the cumulative effect of improvements in the management of chronic coronary artery disease.
A randomized study of yoga therapy for the prevention of recurrent reflex vasovagal syncope
Authors: Shenthar Jayaprakash , Gangwar Ritesh Singh , Banavalikar Bharatraj , Benditt David G , Lakkireddy Dhanunjaya , Padmanabhan Deepak 
Published: February 2021

Abstract

Aims
Vasovagal syncope (VVS) is a common cardiovascular dysautonomic disorder that significantly impacts health and quality of life (QoL). Yoga has been shown to have a positive influence on cardiovascular autonomics. This study assessed the effectiveness of yoga therapy on the recurrence of VVS and QoL.

Methods and results
We randomized subjects with recurrent reflex VVS (&gt;3 episodes in the past 1 year) and positive head-up tilt test to guideline-directed therapy (Group 1) or yoga therapy (Group 2). Patients in Group 1 were advised guideline-directed treatment and Group 2 was taught yoga by a certified instructor. The primary endpoint was VVS recurrences and QoL. Between June 2015 and February 2017, 97 highly symptomatic VVS patients were randomized (Group 1: 47 and Group 2: 50). The mean age was 33.1 ± 16.6 years, male:female of 40:57, symptom duration of 17.1 ± 20.7 months, with a mean of 6.4 ± 6.1 syncope episodes. Over a follow-up of 14.3 ± 2.1 months Group 2 had significantly lower syncope burden compared with Group 1 at 3 (0.8 ± 0.9 vs. 1.8 ± 1.4, P &lt; 0.001), 6 (1.0 ± 1.2 vs. 3.4 ± 3.0, P &lt; 0.001), and at 12 months (1.1 ± 0.8 vs. 3.8 ± 3.2, P &lt; 0.001). The Syncope functional score questionnaire was significantly lower in Group 2 compared with Group 1 at 3 (31.4 ± 7.2 vs. 64.1 ± 11.5, P &lt; 0.001), 6 (26.4 ± 6.3 vs. 61.4 ± 10.7, P &lt; 0.001), and 12 months (22.2 ± 4.7 vs. 68.3 ± 11.4, P &lt; 0.001).

Conclusion
For patients with recurrent VVS, guided yoga therapy is superior to conventional therapy in reducing symptom burden and improving QoL.