bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Speech and Functional Outcomes in Tongue Reconstruction after Hemiglossectomy
Authors: Yi Chang Ryul , Jeong Woo Shik , Oh Tae Suk , Koh Kyung S. , Choi Jong-Woo 
Published: April 2020

Abstract
Background Reconstruction in tongue cancer to restore the shape and function of the tongue without airway obstruction in the narrow oral cavity is challenging for reconstructive surgeons. Herein, the authors retrospectively analyzed flaps to reveal the factors that affect the functional outcome of tongue reconstruction.
Methods Herein, we retrospectively reviewed 30 patients (men, 16; women, 14; mean age, 50.3 years) who underwent the hemi-tongue reconstruction followed by speech therapy between 2009 and 2017. Data about postoperative chemotherapy and radiotherapy were collected. The dimensions (width and length) of the flaps were measured. Speech outcomes were assessed under the conditions of varying distances of the tongue tip from lower incisors when it was protruded, retracted, and elevated. Lateralization was evaluated based on the count of teeth reached by the tip of the tongue from the midline.
Results Preoperative chemotherapy and radiotherapy significantly influenced tongue retraction, tongue articulation, and intelligibility (p = 0.006, 0.002, 0.048, respectively). Postoperative chemotherapy did not statistically significantly influence any outcome measure. Contralateralization of the tongue was significantly decreased in the postoperative radiotherapy group (p = 0.029). The length of the flap showed highly negative correlation with articulation and intelligibility (p = 0.009, p< 0.001, respectively). The width of the flap was not correlated with the outcomes.
Conclusion We proved that unlike chemotherapy, postoperative radiotherapy influences the functional outcome of tongue reconstruction. The dimensions, particularly the length of the flap, were also important for restoring the reconstructed tongue function.
Better Safe than Sorry: Interventional Radiology Should Be Prepared for the Coronavirus Disease 2019 Pandemic
Authors: Babu Arul A.S. , Padmanabhan Aswin , Khera Pushpinder S. , Sonwalkar Hemant 
Published: April 2020

AbstractCoronavirus disease 2019 (COVID-19) is a viral pneumonia that has plagued the world for much of the first quarter of 2020 and was recently declared a global pandemic. The caregivers must be aware of the disease and take steps to curb its transmission within the premises of our care settings (hospitals/clinics). In this article, we suggest a few proactive steps that can be taken at the institutional and departmental levels to break the transmission chain.
Determining the correct stoichiometry of Kv2.1/Kv6.4 heterotetramers, functional in multiple stoichiometrical configurations
Authors: Möller Lena , Regnier Glenn , Labro Alain J. , Blunck Rikard , Snyders Dirk J. 
Published: April 2020

Significance
Voltage-gated potassium (Kv) channels play a key role in cellular electrical excitability. While various Kv subunits assemble to homotetrameric functional channels, the silent subfamilies KvS exclusively form heterotetramers with Kv2 subunits and thus regulate their biophysical properties in a tissue-specific way. Despite the vast functional research, key aspects of the heterotetrameric architecture remain controversial, including the stoichiometry with which KvS and Kv2 can assemble. We used concatemers and single subunit counting in combination to show that Kv2/Kv6 assemble in a 2:2 stoichiometry following the general dimer-of-dimer mechanism for channel formation. We demonstrate how to objectively choose the most likely model for single subunit counting data, which is applicable for any multimeric complex and will help choosing models confidently.
Electron temperature of the solar wind
Authors: Boldyrev Stanislav , Forest Cary , Egedal Jan 
Published: April 2020

Significance
The problem of solar wind heating is one of the long-standing fundamental problems of space plasma physics. We propose that the electron component of the solar wind plasma is heated by electrons streaming from the hot solar corona and slowly losing their energy due to weak Coulomb collisions. Our first-principle kinetic derivation predicts the scaling of the solar wind electron temperature with the heliocentric distance, which is in good agreement with observations. Our theory reveals the role of the non-Maxwellian electron distribution function in the heating mechanism, and it may be valuable for interpreting the results of in situ satellite measurements.
Machine learning for learner English
Authors: Ballier Nicolas , Canu Stéphane , Petitjean Caroline , Gasso Gilles , Balhana Carlos , Alexopoulou Theodora , Gaillat Thomas 
Published: April 2020

Abstract
This paper discusses machine learning techniques for the prediction of Common European Framework of Reference (CEFR)
levels in a learner corpus. We summarise the CAp 2018 Machine Learning (ML) competition, a
classification task of the six CEFR levels, which map linguistic competence in a foreign language onto six reference levels. The goal of
this competition was to produce a machine learning system to predict learners’ competence levels from written productions comprising between
20 and 300 words and a set of characteristics computed for each text extracted from the French component of the EFCAMDAT data (Geertzen et al., 2013). Together with the description of the competition, we provide an analysis of
the results and methods proposed by the participants and discuss the benefits of this kind of competition for the learner corpus research
(LCR) community. The main findings address the methods used and lexical bias introduced by the task.
Bifurcation of critical sets and relaxation oscillations in singular fast-slow systems
Authors: Nyman Karl H M , Ashwin Peter , Ditlevsen Peter D 
Published: April 2020

Abstract
Fast-slow dynamical systems have subsystems that evolve on vastly different timescales, and bifurcations in such systems can arise due to changes in any or all subsystems. We classify bifurcations of the critical set (the equilibria of the fast subsystem) and associated fast dynamics, parametrized by the slow variables. Using a distinguished parameter approach we are able to classify bifurcations for one fast and one slow variable. Some of these bifurcations are associated with the critical set losing manifold structure. We also conjecture a list of generic bifurcations of the critical set for one fast and two slow variables. We further consider how the bifurcations of the critical set can be associated with generic bifurcations of attracting relaxation oscillations under an appropriate singular notion of equivalence.
Strong pairing in two dimensions: pseudogaps, domes, and other implications
Authors: Wang Xiaoyu , Chen Qijin , Levin K 
Published: April 2020

Abstract
This paper addresses the transition from the normal to the superfluid state in strongly correlated two dimensional fermionic superconductors and Fermi gases. We arrive at the Berezinskii–Kosterlitz–Thouless (BKT) temperature T
BKT as a function of attractive pairing strength by associating it with the onset of ‘quasi-condensation’ in the normal phase. Our approach builds on a criterion for determining the BKT transition temperature for atomic gases which is based on a well established quantum Monte Carlo analysis of the phase space density. This latter quantity, when derived from BCS–BEC crossover theory for fermions, leads to non-monotonic behavior for T
BKT as a function of the attractive interaction or inverse scattering length. In Fermi gases, this implies a robust superconducting dome followed by a long tail from the flat BEC asymptote, rather similar to what is observed experimentally. For lattice systems we find that T
BKT has an absolute maximum of the order of 0.1E
F. We discuss how our results compare with those derived from the Nelson–Kosterlitz criterion based on the mean field superfluid density and the approach to the transition from below. While there is agreement in the strict mean-field BCS regime at weak coupling, we find that at moderate pairing strength bosonic excitations cause a substantial increase in T
BKT followed by an often dramatic decrease before the system enters the BEC regime.
Correlation between protein concentration and bacterial cell size can reveal mechanisms of gene expression
Authors: Nieto-Acuña César , Arias-Castro Juan Carlos , Vargas-García César , Sánchez Carlos , Pedraza Juan Manuel 
Published: April 2020

Abstract
Classically, gene expression is modeled as a chemical process with reaction rates dependent on the concentration of the reactants (typically, DNA loci, plasmids, RNA, enzymes, etc). Other variables like cell size are in general ignored. Size dynamics can become an important variable due to the low number of many of these reactants, imperfectly symmetric cell partitioning and molecule segregation. In this work we measure the correlation between size and protein concentration by observing the gene expression of the RpOD gene from a low-copy plasmid in Escherichia coli during balanced growth in different media. A positive correlation was found, and we used it to examine possible models of cell size dynamics and plasmid replication. We implemented a previously developed model describing the full gene expression process including transcription, translation, loci replication, cell division and molecule segregation. By comparing with the observed correlation, we determine that the transcription rate must be proportional to the size times the number of plasmids. We discuss how fluctuations in plasmid segregation, due to the low copy number, can impose limits in this correlation.
Neural decoding of electrocorticographic signals using dynamic mode decomposition
Authors: Shiraishi Yoshiyuki , Kawahara Yoshinobu , Yamashita Okito , Fukuma Ryohei , Yamamoto Shota , Saitoh Youichi , Kishima Haruhiko , Yanagisawa Takufumi 
Published: April 2020

Abstract

Objective. Brain-computer interfaces (BCIs) using electrocorticographic (ECoG) signals have been developed to restore the communication function of severely paralyzed patients. However, the limited amount of information derived from ECoG signals hinders their clinical applications. We aimed to develop a method to decode ECoG signals using spatiotemporal patterns characterizing movement types to increase the amount of information gained from these signals. Approach. Previous studies have demonstrated that motor information could be decoded using powers of specific frequency bands of the ECoG signals estimated by fast Fourier transform (FFT) or wavelet analysis. However, because FFT is evaluated for each channel, the temporal and spatial patterns among channels are difficult to evaluate. Here, we used dynamic mode decomposition (DMD) to evaluate the spatiotemporal pattern of ECoG signals and evaluated the accuracy of motor decoding with the DMD modes. We used ECoG signals during three types of hand movements, which were recorded from 11 patients implanted with subdural electrodes. From the signals at the time of the movements, the modes and powers were evaluated by DMD and FFT and were decoded using support vector machine. We used the Grassmann kernel to evaluate the distance between modes estimated by DMD (DMD mode). In addition, we decoded the DMD modes, in which the phase components were shuffled, to compare the classification accuracy. Main results. The decoding accuracy using DMD modes was significantly better than that using FFT powers. The accuracy significantly decreased when the phases of the DMD mode were shuffled. Among the frequency bands, the DMD mode at approximately 100 Hz demonstrated the highest classification accuracy. Significance. DMD successfully captured the spatiotemporal patterns characterizing the movement types and contributed to improving the decoding accuracy. This method can be applied to improve BCIs to help severely paralyzed patients communicate.
Elliptic solutions for higher order KdV equations
Authors: Hayashi Masahito , Shigemoto Kazuyasu , Tsukioka Takuya 
Published: April 2020

Abstract
We study higher order KdV equations from the GL(2,

R

) ≅ SO(2,1) Lie group point of view. We find elliptic solutions of higher order KdV equations up to the ninth order. We argue that the main structure of the trigonometric/hyperbolic/elliptic N-soliton solutions for higher order KdV equations is the same as that of the original KdV equation. Pointing out that the difference is only the time dependence, we find N-soliton solutions of higher order KdV equations can be constructed from those of the original KdV equation by properly replacing the time-dependence. We discuss that there always exist elliptic solutions for all higher order KdV equations.
A new insight on structural and some functional aspects of peri-endodermal thickenings, a specific layer in Noccaea caerulescens roots
Authors: Kováč Ján , Lux Alexander , Soukup Milan , Weidinger Marieluise , Gruber Daniela , Lichtscheidl Irene , Vaculík Marek 
Published: April 2020

AbstractBackground and AimsCell walls of the peri-endodermis, a layer adjacent to the endodermis in alpine pennycress (Noccaea caerulescens) roots, form C-shaped peri-endodermal thickenings (PETs). Despite its specific position close to the endodermis, the assumed similarity of PETs to phi thickenings in many other species, and the fact that N. caerulescens is a well-studied heavy-metal-hyperaccumulating plant, the PET as a root trait is still not understood.MethodsHere, we characterized PET cell walls by histochemical techniques, Raman spectroscopy, immunolabelling and electron microscopy. Moreover, a role of PETs in solute transport was tested and compared with Arabidopsis thaliana plants, which do not form PETs in roots.Key ResultsCell walls with PETs have a structured relief mainly composed of cellulose and lignin. Suberin, typical of endodermal cells, is missing but pectins are present on the inner surface of the PET. Penetrating dyes are not able to cross PETs either by the apoplasmic or the symplasmic pathway, and a significantly higher content of metals is found in root tissues outside of PETs than in innermost tissues.ConclusionsBased on their development and chemical composition, PETs are different from the endodermis and closely resemble phi thickenings. Contrarily, the different structure and dye impermeability of PETs, not known in the case of phi thickenings, point to an additional barrier function which makes the peri-endodermis with PETs a unique and rare layer.
Monotocy and the evolution of plural breeding in mammals
Authors: Lukas Dieter , Clutton-Brock Tim 
Published: April 2020

AbstractIn many mammals, breeding females are intolerant of each other and seldom associate closely but, in some, they aggregate in groups that vary in size, stability, and kinship structure. Aggregation frequently increases competition for food, and interspecific differences in female sociality among mammals are commonly attributed to contrasts in ecological parameters, including variation in activity timing, the distribution of resources, as well as the risk of predation. However, there is increasing indication that differences in female sociality are also associated with phylogenetic relationships and with contrasts in life-history parameters. We show here that evolutionary transitions from systems where breeding females usually occupy separate ranges (“singular breeding”) to systems where breeding females usually aggregate (“plural breeding”) have occurred more frequently in monotocous lineages where females produce single young than in polytocous ones where they produce litters. A likely explanation of this association is that competition between breeding females for resources is reduced where they produce single young and is more intense where they produce litters. Our findings reinforce evidence that variation in life-history parameters plays an important role in shaping the evolution of social behavior.
ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs
Authors: Coombe Lauren , Nikolić Vladimir , Chu Justin , Birol Inanc , Warren René L 
Published: April 2020

Abstract

Summary
The ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of different applications, including improving a draft assembly with a reference-grade genome, a short-read assembly with a draft long-read assembly and a draft assembly with an assembly from a closely related species. When scaffolding a human short-read assembly using the reference human genome or a long-read assembly, ntJoin improves the NGA50 length 23- and 13-fold, respectively, in under 13 m, using &lt;11 GB of RAM. Compared to existing reference-guided scaffolders, ntJoin generates highly contiguous assemblies faster and using less memory.

Availability and implementation
ntJoin is written in C++ and Python and is freely available at https://github.com/bcgsc/ntjoin.

Supplementary information
Supplementary data are available at Bioinformatics online.
A novel normalization and differential abundance test framework for microbiome data
Authors: Ma Yuanjing , Luo Yuan , Jiang Hongmei 
Published: April 2020

AbstractMotivationMicrobial communities have been proved to have close relationship with many diseases. The identification of differentially abundant microbial species is clinically meaningful for finding disease-related pathogenic or probiotic bacteria. However, certain characteristics of microbiome data have hurdled the accuracy and effectiveness of differential abundance analysis. The abundances or counts of microbiome species are usually on different scales and exhibit zero-inflation and over-dispersion. Normalization is a crucial step before the differential abundance test. However, existing normalization methods typically try to adjust counts on different scales to a common scale by constructing size factors with the assumption that count distributions across samples are equivalent up to a certain percentile. These methods often yield undesirable results when differentially abundant species are of low to medium abundance level. For differential abundance analysis, existing methods often use a single distribution to model the dispersion of species which lacks flexibility to catch a single species’ distinctiveness. These methods tend to detect a lot of false positives and often lack of power when the effect size is small.ResultsWe develop a novel framework for differential abundance analysis on sparse high-dimensional marker gene microbiome data. Our methodology relies on a novel network-based normalization technique and a two-stage zero-inflated mixture count regression model (RioNorm2). Our normalization method aims to find a group of relatively invariant microbiome species across samples and conditions in order to construct the size factor. Another contribution of the paper is that our testing approach can take under-sampling and over-dispersion into consideration by separating microbiome species into two groups and model them separately. Through comprehensive simulation studies, the performance of our method is consistently powerful and robust across different settings with different sample size, library size and effect size. We also demonstrate the effectiveness of our novel framework using a published dataset of metastatic melanoma and find biological insights from the results.Availability and implementationThe R package ‘RioNorm2’ can be installed from Github athttps://github.com/yuanjing-ma/RioNorm2.Supplementary informationSupplementary data are available at Bioinformatics online.
Metabolism of JQ1, an inhibitor of bromodomain and extra terminal bromodomain proteins, in human and mouse liver microsomes†
Authors: Li Feng , MacKenzie Kevin R , Jain Prashi , Santini Conrad , Young Damian W , Matzuk Martin M 
Published: April 2020

AbstractJQ1 is a small-molecule inhibitor of the bromodomain and extra terminal (BET) protein family that potently inhibits the bromodomain testis-specific protein (BRDT), which is essential for spermatogenesis. JQ1 treatment produces a reversible contraceptive effect by targeting the activity of BRDT in mouse male germ cells, validating BRDT as a male contraceptive target. Although JQ1 possesses favourable physical properties, it exhibits a short half-life. Because the details of xenobiotic metabolism play important roles in the optimization of drug candidates and in determining the role of metabolism in drug efficacy, we investigated the metabolism of JQ1 in human and mouse liver microsomes. We present the first comprehensive view of JQ1 metabolism in liver microsomes, distinguishing nine JQ1 metabolites, including three monohydroxylated, one de-tert-butylated, two dihydroxylated, one monohydroxylated/dehydrogenated, one monohydroxylated-de-tert-butylated and one dihydroxylated/dehydrogenated variant of JQ1. The dominant metabolite (M1) in both human and mouse liver microsomes is monohydroxylated on the fused three-ring core. Using recombinant cytochrome P450 (CYP) enzymes, chemical inhibitors and the liver S9 fraction of Cyp3a-null mice, we identify enzymes that contribute to the formation of these metabolites. Cytochrome P450 family 3 subfamily A member 4 (CYP3A4) is the main contributor to the production of JQ1 metabolites in vitro, and the CYP3A4/5 inhibitor ketoconazole strongly inhibits JQ1 metabolism in both human and mouse liver microsomes. Our findings suggest that JQ1 half-life and efficacy might be improved in vivo by co-administration of a selective CYP inhibitor, thereby impacting the use of JQ1 as a probe for BRDT activity in spermatogenesis and as a probe or therapeutic in other systems.
Contribution of senescence in human endometrial stromal cells during proliferative phase to embryo receptivity†
Authors: Tomari Hiroyuki , Kawamura Teruhiko , Asanoma Kazuo , Egashira Katsuko , Kawamura Keiko , Honjo Ko , Nagata Yumi , Kato Kiyoko 
Published: April 2020

Abstract
Successful assisted reproductive technology pregnancy depends on the viability of embryos and endometrial receptivity. However, the literature has neglected effects of the endometrial environment during the proliferative phase on implantation success or failure. Human endometrial stromal cells (hESCs) were isolated from endometrial tissues sampled at oocyte retrieval during the proliferative phase from women undergoing infertility treatment. Primary hESC cultures were used to investigate the relationship between stemness and senescence induction in this population and embryo receptivity. Patients were classified as receptive or non-receptive based on their pregnancy diagnosis after embryo transfer. Biomarkers of cellular senescence and somatic stem cells were compared between each sample. hESCs from non-receptive patients exhibited significantly higher (P &lt; 0.01) proportions of senescent cells, mRNA expressions of CDKN2A and CDKN1A transcripts (P &lt; 0.01), and expressions of genes encoding the senescence-associated secretory phenotype (P &lt; 0.05). hESCs from receptive patients had significantly higher (P &lt; 0.01) mRNA expressions of ABCG2 and ALDH1A1 transcripts. Our findings suggest that stemness is inversely associated with senescence induction in hESCs and, by extension, that implantation failure in infertility treatment may be attributable to a combination of senescence promotion and disruption of this maintenance function in this population during the proliferative phase of the menstrual cycle. This is a promising step towards potentially improving the embryo receptivity of endometrium. The specific mechanism by which implantation failure is prefigured by a loss of stemness among endometrial stem cells, and cellular senescence induction among hESCs, should be elucidated in detail in the future.