bluuebunny/crossref_metadata_2025_split huggingface dataset:
MolFinder: an evolutionary algorithm for the global optimization of molecular properties and the extensive exploration of chemical space using SMILES
Authors: Kwon Yongbeom , Lee Juyong 
Published: March 2021

AbstractHere, we introduce a new molecule optimization method, MolFinder, based on an efficient global optimization algorithm, the conformational space annealing algorithm, and the SMILES representation. MolFinder finds diverse molecules with desired properties efficiently without any training and a large molecular database. Compared with recently proposed reinforcement-learning-based molecule optimization algorithms, MolFinder consistently outperforms in terms of both the optimization of a given target property and the generation of a set of diverse and novel molecules. The efficiency of MolFinder demonstrates that combinatorial optimization using the SMILES representation is a promising approach for molecule optimization, which has not been well investigated despite its simplicity. We believe that our results shed light on new possibilities for advances in molecule optimization methods.
Genomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes
Authors: Lim Jaewon , Park Hong-Tae , Ko Seyoung , Park Hyun-Eui , Lee Gyumin , Kim Suji , Shin Min-Kyoung , Yoo Han Sang , Kim Donghyuk 
Published: March 2021

AbstractMycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne’s disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.
Liver organoids in domestic animals: an expected promise for metabolic studies
Authors: Baquerre Camille , Montillet Guillaume , Pain Bertrand 
Published: March 2021

AbstractThe liver is one of the most important organs, both in terms of the different metabolic processes (energy, lipid, ferric, uric, etc.) and of its central role in the processes of detoxification of substances of food origin or noxious substances (alcohol, drugs, antibiotics, etc.). The development of a relevant model that reproduces some of the functions of this tissue has become a challenge, in particular for human medicine. Thus, in recent years, most studies aimed at producing hepatocytes in vitro with the goal of developing hepatic 3D structures have been carried out in the human model. However, the tools and protocols developed using this unique model can also be considered to address physiological questions specific to this tissue in other species, such as the pig, chicken, and duck. Different strategies are presently being considered to carry out in vitro studies of the hepatic metabolism of these agronomic species.
Improved two-way double-relay selection technique for cooperative wireless communications
Authors: Alabed Samer , Maaz Issam , Al-Rabayah Mohammad 
Published: March 2021

AbstractIn this article, a novel two-way double-relay selection strategy with its bit error rate (BER) performance analysis is proposed. In this novel strategy, as a first step we choose two relays out of a set of relay-nodes in a way to maximize the system performance in terms of BER and complexity. In the second step, the selected relays apply orthogonal space-time coding scheme using the three-phase protocol to establish a two-way communication between the transceivers, which will lead to a significant improvement in the achievable diversity and coding gain with a very low decoding complexity by using a symbol-wise decoder. Furthermore, the performance of the overall system is further enhanced through the use of a network coding method at the selected relay-nodes. Moreover, this paper proposes the analytical approximation of the BER performance. As well, we show that the analytical results match perfectly the simulated ones. In addition, we prove that our strategy outperforms the current state-of-the-art ones by proposing a better cooperative communication system in terms of BER.
Low-complexity sparse-aware multiuser detection for large-scale MIMO systems
Authors: Ran Rong , Oh Hayoung 
Published: March 2021

AbstractSparse-aware (SA) detectors have attracted a lot attention due to its significant performance and low-complexity, in particular for large-scale multiple-input multiple-output (MIMO) systems. Similar to the conventional multiuser detectors, the nonlinear or compressive sensing based SA detectors provide the better performance but are not appropriate for the overdetermined multiuser MIMO systems in sense of power and time consumption. The linear SA detector provides a more elegant tradeoff between performance and complexity compared to the nonlinear ones. However, the major limitation of the linear SA detector is that, as the zero-forcing or minimum mean square error detector, it was derived by relaxing the finite-alphabet constraints, and therefore its performance is still sub-optimal. In this paper, we propose a novel SA detector, named single-dimensional search-based SA (SDSB-SA) detector, for overdetermined uplink MIMO systems. The proposed SDSB-SA detector adheres to the finite-alphabet constraints so that it outperforms the conventional linear SA detector, in particular, in high SNR regime. Meanwhile, the proposed detector follows a single-dimensional search manner, so it has a very low computational complexity which is feasible for light-ware Internet of Thing devices for ultra-reliable low-latency communication. Numerical results show that the the proposed SDSB-SA detector provides a relatively better tradeoff between the performance and complexity compared with several existing detectors.
Xylitol enhances synthesis of propionate in the colon via cross-feeding of gut microbiota
Authors: Xiang Shasha , Ye Kun , Li Mian , Ying Jian , Wang Huanhuan , Han Jianzhong , Shi Lihua , Xiao Jie , Shen Yubiao , Feng Xiao , Bao Xuan , Zheng Yiqing , Ge Yin , Zhang Yalin , Liu Chang , Chen Jie , Chen Yuewen , Tian Shiyi , Zhu Xuan 
Published: March 2021

Abstract
Background
Xylitol, a white or transparent polyol or sugar alcohol, is digestible by colonic microorganisms and promotes the proliferation of beneficial bacteria and the production of short-chain fatty acids (SCFAs), but the mechanism underlying these effects remains unknown. We studied mice fed with 0%, 2% (2.17 g/kg/day), or 5% (5.42 g/kg/day) (weight/weight) xylitol in their chow for 3 months. In addition to the in vivo digestion experiments in mice, 3% (weight/volume) (0.27 g/kg/day for a human being) xylitol was added to a colon simulation system (CDMN) for 7 days. We performed 16S rRNA sequencing, beneficial metabolism biomarker quantification, metabolome, and metatranscriptome analyses to investigate the prebiotic mechanism of xylitol. The representative bacteria related to xylitol digestion were selected for single cultivation and co-culture of two and three bacteria to explore the microbial digestion and utilization of xylitol in media with glucose, xylitol, mixed carbon sources, or no-carbon sources. Besides, the mechanisms underlying the shift in the microbial composition and SCFAs were explored in molecular contexts.

Results
In both in vivo and in vitro experiments, we found that xylitol did not significantly influence the structure of the gut microbiome. However, it increased all SCFAs, especially propionate in the lumen and butyrate in the mucosa, with a shift in its corresponding bacteria in vitro. Cross-feeding, a relationship in which one organism consumes metabolites excreted by the other, was observed among Lactobacillus reuteri, Bacteroides fragilis, and Escherichia coli in the utilization of xylitol. At the molecular level, we revealed that xylitol dehydrogenase (EC 1.1.1.14), xylulokinase (EC 2.7.1.17), and xylulose phosphate isomerase (EC 5.1.3.1) were key enzymes in xylitol metabolism and were present in Bacteroides and Lachnospiraceae. Therefore, they are considered keystone bacteria in xylitol digestion. Also, xylitol affected the metabolic pathway of propionate, significantly promoting the transcription of phosphate acetyltransferase (EC 2.3.1.8) in Bifidobacterium and increasing the production of propionate.

Conclusions
Our results revealed that those key enzymes for xylitol digestion from different bacteria can together support the growth of micro-ecology, but they also enhanced the concentration of propionate, which lowered pH to restrict relative amounts of Escherichia and Staphylococcus. Based on the cross-feeding and competition among those bacteria, xylitol can dynamically balance proportions of the gut microbiome to promote enzymes related to xylitol metabolism and SCFAs.
Can we change binge eating behaviour by interventions addressing food-related impulsivity? A systematic review
Authors: İnce Başak , Schlatter Johanna , Max Sebastian , Plewnia Christian , Zipfel Stephan , Giel Katrin Elisabeth , Schag Kathrin 
Published: March 2021

Abstract
Background
An extensive amount of research has underlined the potential role of impulsivity in the development and maintenance of binge eating behaviour. Food-related impulsivity has particularly received attention given its close relationship with overeating and binge eating episodes. Besides the available evidence, our understanding regarding the effectiveness of treatment modalities for binge eating targeting impulsivity and related constructs (e.g., food craving, inhibitory control, and reward sensitivity) is limited. Thus, this systematic review aimed to investigate whether binge eating behaviour is changeable by interventions that are impulsivity-focused and food-related and whether one of these interventions is superior to the others.

Method
A search on PubMed and PsycINFO was performed for relevant articles published up to September 2020. Studies delivering food-related impulsivity treatment to individuals suffering from binge eating episodes and including a control condition without this treatment were investigated. Following the search, 15 studies meeting the eligibility criteria were analysed.

Results
Analyses revealed that available impulsivity-focused approaches can be categorised as psychotherapy, pharmacotherapy, computer-assisted cognitive training, and direct neuromodulation interventions. Regarding their effectiveness, it appeared that all of these approaches might be promising to change food-related impulsivity in individuals with binge eating episodes, particularly to decrease binge eating symptoms. However, a superior intervention approach in this early state of evidence could not be determined, although food-related cue exposure, transcranial direct current stimulation, and the combination of several interventions seem fruitful.

Conclusion
Efforts to treat binge eating behaviour with interventions focusing on food-related impulsivity appear to be promising, particularly concerning binge eating frequency, and also for food craving and inhibitory control. Given limited research and varying methods, it was not possible to conclude whether one impulsivity-focused intervention can be considered superior to others.
A false-pouch closure technique with an intact superior peroneal retinaculum for recurrent dislocation of the peroneal tendon
Authors: Matsui Tomohiro , Kumai Tsukasa , Shinohara Yasushi , Kanzaki Noriyuki , Noguchi Koji , Tanaka Hirofumi , Sugimoto Takeshi , Yabiku Hiroki , Higashiyama Ichiro 
Published: March 2021

Abstract
Purpose
To evaluate the usefulness of the false-pouch closure technique with an intact superior peroneal retinaculum (SPR).

Methods
From 2016 to 2020, 30 patients with recurrent dislocation of the peroneal tendon were treated with the current procedure. Clinical outcomes, including the time to resume running, the rate and time to return to sports, and the American Orthopaedic Foot and Ankle Society (AOFAS) Ankle-Hind Foot score, were evaluated preoperatively and at the last follow-up.

Results
The rate of return to the pre-injury level of sports activity was 93.3%, and the mean duration to return to running and sports was 8.0 ± 2.8 weeks (range: 3–12 weeks) and 14.4 ± 3.2 weeks (range: 10–24 weeks), respectively. The mean preoperative AOFAS score was 79.7 ± 9.6 points (range: 41–90), which improved significantly to 98.9 ± 3.2 (87–100) postoperatively (p < 0.01).

Conclusion
The false-pouch closure technique with suture tape and anchors had a reliable clinical outcome and can enable the early return of patients to their sports activities.

Level of evidence
IV, Case series
Nutritional perspectives on sickle cell disease in Africa: a systematic review
Authors: Nartey Eunice Berko , Spector Jonathan , Adu-Afarwuah Seth , Jones Catherine L. , Jackson Alan , Ohemeng Agartha , Shah Rajiv , Koryo-Dabrah Alice , Kuma Amma Benneh-Akwasi , Hyacinth Hyacinth I. , Steiner-Asiedu Matilda 
Published: March 2021

Abstract
Background
Sickle cell disease (SCD) is an inherited blood disorder that predominantly affects individuals in sub-Saharan Africa. However, research that elucidates links between SCD pathophysiology and nutritional status in African patients is lacking. This systematic review aimed to assess the landscape of studies in sub-Saharan Africa that focused on nutritional aspects of SCD, and highlights gaps in knowledge that could inform priority-setting for future research.

Methods
The study was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Inclusion criteria comprised original, peer-reviewed research published between January 1995 and November 2020 involving individuals in Africa with any phenotypic variant of SCD and at least one nutritional status outcome. Nutritional status outcomes were defined as those that assessed dietary intakes, growth/anthropometry, or nutritional biomarkers. Databases used were Ovid Embase, Medline, Biosis and Web of Science.

Results
The search returned 526 articles, of which 76 were included in the final analyses. Most investigations (67%) were conducted in Nigeria. Studies were categorized into one of three main categories: descriptive studies of anthropometric characteristics (49%), descriptive studies of macro- or micronutrient status (41%), and interventional studies (11%). Findings consistently included growth impairment, especially among children and adolescents from sub-Saharan Africa. Studies assessing macro- and micronutrients generally had small sample sizes and were exploratory in nature. Only four randomized trials were identified, which measured the impact of lime juice, long-chain fatty acids supplementation, ready-to-use supplementary food (RUSF), and oral arginine on health outcomes.

Conclusions
The findings reveal a moderate number of descriptive studies, most with small sample sizes, that focused on various aspects of nutrition and SCD in African patients. There was a stark dearth of interventional studies that could be used to inform evidence-based changes in clinical practice. Findings from the investigations were generally consistent with data from other regional settings, describing a significant risk of growth faltering and malnutrition among individuals with SCD. There is an unmet need for clinical research to better understand the potential benefits of nutrition-related interventions for patients with SCD in sub-Saharan Africa to promote optimal growth and improve health outcomes.
Automatic question generation and answer assessment: a survey
Authors: Das Bidyut , Majumder Mukta , Phadikar Santanu , Sekh Arif Ahmed 
Published: March 2021

AbstractLearning through the internet becomes popular that facilitates learners to learn anything, anytime, anywhere from the web resources. Assessment is most important in any learning system. An assessment system can find the self-learning gaps of learners and improve the progress of learning. The manual question generation takes much time and labor. Therefore, automatic question generation from learning resources is the primary task of an automated assessment system. This paper presents a survey of automatic question generation and assessment strategies from textual and pictorial learning resources. The purpose of this survey is to summarize the state-of-the-art techniques for generating questions and evaluating their answers automatically.
Prognostic biomarkers in predicting mortality in respiratory patients with ventilator-associated pneumonia
Authors: Abdelaleem Nermeen A. , Makhlouf Hoda A. , Nagiub Eman M. , Bayoumi Hassan A. 
Published: March 2021

Abstract
Background
Ventilator-associated pneumonia (VAP) is the most common nosocomial infection. Red cell distribution width (RDW) and neutrophil-lymphocyte ratio (NLR) are prognostic factors to mortality in different diseases. The aim of this study is to evaluate prognostic efficiency RDW, NLR, and the Sequential Organ Failure Assessment (SOFA) score for mortality prediction in respiratory patients with VAP.

Results
One hundred thirty-six patients mechanically ventilated and developed VAP were included. Clinical characteristics and SOFA score on the day of admission and at diagnosis of VAP, RDW, and NLR were assessed and correlated to mortality. The average age of patients was 58.80 ± 10.53. These variables had a good diagnostic performance for mortality prediction AUC 0.811 for SOFA at diagnosis of VAP, 0.777 for RDW, 0.728 for NLR, and 0.840 for combined of NLR and RDW. The combination of the three parameters demonstrated excellent diagnostic performance (AUC 0.889). A positive correlation was found between SOFA at diagnosis of VAP and RDW (r = 0.446, P < 0.000) and with NLR (r = 0.220, P < 0.010).

Conclusions
NLR and RDW are non-specific inflammatory markers that could be calculated quickly and easily via routine hemogram examination. These markers have comparable prognostic accuracy to severity scores. Consequently, RDW and NLR are simple, yet promising markers for ICU physicians in monitoring the clinical course, assessment of organ dysfunction, and predicting mortality in mechanically ventilated patients. Therefore, this study recommends the use of blood biomarkers with the one of the simplest ICU score (SOFA score) in the rapid diagnosis of critical patients as a daily works in ICU.
De novo formation of early endosomes during Rab5-to-Rab7a transition
Authors: Skjeldal Frode Miltzow , Haugen Linda Hofstad , Mateus Duarte , Frei Dominik M. , Rødseth Anna Vik , Hu Xian , Bakke Oddmund 
Published: March 2021

ABSTRACT
Rab5 and Rab7a are the main determinants of early and late endosomes and are important regulators of endosomal progression. The transport from early endosomes to late endosome seems to be regulated through an endosomal maturation switch, where Rab5 is gradually exchanged by Rab7a on the same endosome. Here, we provide new insight into the mechanism of endosomal maturation, for which we have discovered a stepwise Rab5 detachment, sequentially regulated by Rab7a. The initial detachment of Rab5 is Rab7a independent and demonstrates a diffusion-like first-phase exchange between the cytosol and the endosomal membrane, and a second phase, in which Rab5 converges into specific domains that detach as a Rab5 indigenous endosome. Consequently, we show that early endosomal maturation regulated through the Rab5-to-Rab7a switch induces the formation of new fully functional Rab5-positive early endosomes. Progression through stepwise early endosomal maturation regulates the direction of transport and, concomitantly, the homeostasis of early endosomes.
Maintaining Power Output with Accumulating Levels of Work Done Is a Key Determinant for Success in Professional Cycling
Authors: VAN ERP TEUN , SANDERS DAJO , LAMBERTS ROBERT P. 
Published: March 2021

ABSTRACT

Introduction
This study aimed to investigate if performance measures are related to success in professional cycling and to highlight the influence of prior work done on these performance measures and success.

Methods
Power output data from 26 professional cyclists, in a total of 85 seasons, collected between 2012 and 2019, were analyzed. The cyclists were classified as “climber” or “sprinter” and into category 1 (CAT.1; ≥400 PCSpoints (successful)) and CAT.2 (<400 PCSpoints (less successful)), based on the number of procyclingstats-points (PCSpoints) collected for that particular season. Maximal mean power outputs (MMP) for 20 min, 5 min, 1 min, and 10 s relative to body weight for every season were determined. To investigate the influence of prior work done on these MMP values, six different levels of completed work done were determined, which are based on the amount of completed kilojoules per kilogram (0, 10, 20, 30, 40, and 50 kJ·kg−1). Subsequently, the decline in MMP for each duration (if any) after each level of completed work done was evaluated.

Results
Mixed model revealed that prior work done affects the performance of climbers and sprinters negatively. However, CAT.1 climbers have a smaller decline in 20- and 5-min MMP after high amounts of work done compared with CAT.2 climbers. Similarly, CAT.1 sprinters have a smaller decline in 10-s and 1-min MMP after high amounts of work done compared with CAT.2 sprinters.

Conclusions
It seems that the ability to maintain high MMP (corresponding with the specialization of a cyclist) after high amounts of work done (i.e., fatigue) is an important parameter for success in professional cyclists. These findings suggest that assessing changes in MMP after different workloads might be highly relevant in professional cycling.