bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput identification of viral termini and packaging mechanisms in virome datasets using PhageTermVirome
Authors: Garneau Julian R. , Legrand Véronique , Marbouty Martial , Press Maximilian O. , Vik Dean R. , Fortier Louis-Charles , Sullivan Matthew B. , Bikard David , Monot Marc 
Published: September 2021

AbstractViruses that infect bacteria (phages) are increasingly recognized for their importance in diverse ecosystems but identifying and annotating them in large-scale sequence datasets is still challenging. Although efficient scalable virus identification tools are emerging, defining the exact ends (termini) of phage genomes is still particularly difficult. The proper identification of termini is crucial, as it helps in characterizing the packaging mechanism of bacteriophages and provides information on various aspects of phage biology. Here, we introduce PhageTermVirome (PTV) as a tool for the easy and rapid high-throughput determination of phage termini and packaging mechanisms using modern large-scale metagenomics datasets. We successfully tested the PTV algorithm on a mock virome dataset and then used it on two real virome datasets to achieve the rapid identification of more than 100 phage termini and packaging mechanisms, with just a few hours of computing time. Because PTV allows the identification of free fully formed viral particles (by recognition of termini present only in encapsidated DNA), it can also complement other virus identification softwares to predict the true viral origin of contigs in viral metagenomics datasets. PTV is a novel and unique tool for high-throughput characterization of phage genomes, including phage termini identification and characterization of genome packaging mechanisms. This software should help researchers better visualize, map and study the virosphere. PTV is freely available for downloading and installation at https://gitlab.pasteur.fr/vlegrand/ptv.
Impact of genotypic errors with equal and unequal family contribution on accuracy of genomic prediction in aquaculture using simulation
Authors: Khalilisamani N. , Thomson P. C. , Raadsma H. W. , Khatkar M. S. 
Published: September 2021

AbstractGenotypic errors, conflict between recorded genotype and the true genotype, can lead to false or biased population genetic parameters. Here, the effect of genotypic errors on accuracy of genomic predictions and genomic relationship matrix are investigated using a simulation study based on population and genomic structure comparable to black tiger prawn, Penaeus monodon. Fifty full-sib families across five generations with phenotypic and genotypic information on 53 K SNPs were simulated. Ten replicates of different scenarios with three heritability estimates, equal and unequal family contributions were generated. Within each scenario, four SNP densities and three genotypic error rates in each SNP density were implemented. Results showed that family contribution did not have a substantial impact on accuracy of predictions across different datasets. In the absence of genotypic errors, 3 K SNP density was found to be efficient in estimating the accuracy, whilst increasing the SNP density from 3 to 20 K resulted in a marginal increase in accuracy of genomic predictions using the current population and genomic parameters. In addition, results showed that the presence of even 10% errors in a 10 and 20 K SNP panel might not have a severe impact on accuracy of predictions. However, below 10 K marker density, even a 5% error can result in lower accuracy of predictions.
Gestalts at threshold could reveal Gestalts as predictions
Authors: Costa Thiago Leiros , Wagemans Johan 
Published: September 2021

AbstractWe review and revisit the predictive processing inspired “Gestalts as predictions” hypothesis. The study of Gestalt phenomena at and below threshold can help clarify the role of higher-order object selective areas and feedback connections in mid-level vision. In two psychophysical experiments assessing manipulations of contrast and configurality we showed that: (1) Gestalt phenomena are robust against saliency manipulations across the psychometric function even below threshold (with the accuracy gains and higher saliency associated with Gestalts being present even around chance performance); and (2) peak differences between Gestalt and control conditions happened around the time where responses to Gestalts are starting to saturate (mimicking the differential contrast response profile of striate vs. extra-striate visual neurons). In addition, Gestalts are associated with steeper psychometric functions in all experiments. We propose that these results reflect the differential engagement of object-selective areas in Gestalt phenomena and of information- or percept-based processing, as opposed to energy- or stimulus-based processing, more generally. In addition, the presence of nonlinearities in the psychometric functions suggest differential top-down modulation of the early visual cortex. We treat this as a proof of principle study, illustrating that classic psychophysics can help assess possible involvement of hierarchical predictive processing in Gestalt phenomena.
Scaling theory of rubber sliding friction
Authors: Hentschke Reinhard , Plagge Jan 
Published: September 2021

AbstractCurrent theoretical descriptions of rubber or elastomer friction are complex—usually due to extensive mathematical detail describing the topography of the solid surface. In addition, the viscoelastic properties of the elastomer material itself, in particular if the rubber is highly filled, further increase the complexity. On the other hand, experimental coefficients of sliding friction plotted versus sliding speed, temperature or other parameters do not contain much structure, which suggests that a less detailed approach is possible. Here we investigate the coefficient of sliding friction on dry surfaces via scaling and dimensional analysis. We propose that adhesion promotes viscoelastic dissipation by increasing the deformation amplitude at relevant length scales. Finally, a comparatively simple expression for the coefficient of friction is obtained, which allows an intuitive understanding of the underlying physics and fits experimental data for various speeds, temperatures, and pressures.
The radiographic relationship between the cortical overlap view (COV) and the tip of the greater trochanter
Authors: Link Bjorn-Christian , van Veelen Nicole M. , Boernert Katja , Kittithamvongs Piyabuth , Beeres Frank J.P. , de Boer Hans H. , Migliorini Filippo , Nebelung Sven , Knobe Matthias , Ruchholtz Steffen , Babst Reto , Jiamton Chittawee 
Published: September 2021

AbstractFor proximal femoral nailing, choosing the proper entry point with the aid of C-arm imaging is crucial. Therefore, obtaining accurate radiological views that facilitate sound identification of the tip of the greater trochanter (GT) is of utmost importance. The aim of this study was to define a radiological view characterised by reproducible radiographic landmarks which will allow the reliable identification of the tip of the GT in the anteroposterior view. Anatomical and radiographic features of 16 cadaveric femurs were analysed. The cortical overlap view (COV), characterised by the radiological overlap of the density line of the piriform fossa and the intertrochanteric crest, was identified. It marks the rotation of the proximal femur at which the GT can be accurately identified and used to determine the desired entry point for a proximal femoral nail. Trainees and fully qualified orthopedic trauma surgeons were asked to identify the correct COV in radiological imaging series. Mean internal rotation of the femur to achieve a COV was 17.5° (range 12.8°–21.8°). In the COV the tip of the GT is the highest visible point and the mean distance from the cortical overlap line to the tip of the GT is 4.45 mm. Intra- and inter-rater reliability was high with ICC(2,k) = 0.932 and ICC(2,k) = 0.987 respectively. Trainees achieved higher rates of correct COV identification than specialists. There was no significant correlation between the internal rotation of the femur to achieve the COV and femoral antetorsion. In conclusion, the COV is a highly reproducible radiological view that is characterised by radiographic landmarks easy to recognise. It allows for accurate identification of the tip of the GT, which can be used by the surgeon as a reference to determine the desired entry point for an intramedullary nail.
Individuals with bipolar disorder have a higher level of uric acid than major depressive disorder: a case–control study
Authors: Lu Zhe , Wang Yingtan , Xun Guanglei 
Published: September 2021

AbstractAt present, no well-established biomarkers were ever found to distinguish unipolar depression and bipolar disorder (BD). This study aimed to provide a clearer comparison of UA levels between BD and major depressive disorder. Peripheral UA of 119 patients with BD in acute stage (AS) and 77 in remission stage (RS), and 95 patients with UD in AS and 61 in RS were measured, so were 180 healthy controls. UA levels in BD group were higher than UD and HC groups regardless of the AS or RS, while differences in UA levels between UD group and HC group were not significant. Differences in UA levels of BD-M (bipolar mania/hypomania) were higher than BD-D (bipolar depression) subgroups, and UA levels of BD-M and BD-D subgroups were higher than UD and HC groups. The comparison of number of participants with hyperuricemia among groups confirmed the above results. There were no significant differences in UA levels of between drug-use and drug-free/naïve subgroups. UA could distinguish BD and UD significantly both in acute and remission stage. The study suggests patients with BD had a higher level of UA than UD, especially in mania episode. UA may be a potential biomarker to distinguish BD from UD.
Microbial community of soda Lake Van as obtained from direct and enriched water, sediment and fish samples
Authors: Ersoy Omeroglu Esra , Sudagidan Mert , Yurt Mediha Nur Zafer , Tasbasi Behiye Busra , Acar Elif Esma , Ozalp Veli Cengiz 
Published: September 2021

AbstractSoda lakes are saline and alkaline ecosystems that are considered to have existed since the first geological records of the world. These lakes support the growth of ecologically and economically important microorganisms due to their unique geochemistry. Microbiota members of lakes are valuable models to study the link between community structure and abiotic parameters such as pH and salinity. Lake Van is the largest endroheic lake and in this study, bacterial diversity of lake water, sediment, and pearl mullet (inci kefali; Alburnus tarichi), an endemic species of fish which are collected from different points of the lake, are studied directly and investigated meticulously using a metabarcoding approach after pre-enrichment. Bacterial community structures were identified using Next Generation Sequencing of the 16S rRNA gene. The analysis revealed that the samples of Lake Van contain high level of bacterial diversity. Direct water samples were dominated by Proteobacteria, Cyanobacteria, and Bacteroidota, on the other hand, pre-enriched water samples were dominated by Proteobacteria and Firmicutes at phylum-level. In direct sediment samples Proteobacteria, whereas in pre-enriched sediment samples Firmicutes and Proteobacteria were determined at highest level. Pre-enriched fish samples were dominated by Proteobacteria and Firmicutes at phylum-level. In this study, microbiota members of Lake Van were identified by taxonomic analysis.
Connectivity alterations in autism reflect functional idiosyncrasy
Authors: Benkarim Oualid , Paquola Casey , Park Bo-yong , Hong Seok-Jun , Royer Jessica , Vos de Wael Reinder , Lariviere Sara , Valk Sofie , Bzdok Danilo , Mottron Laurent , C. Bernhardt Boris 
Published: September 2021

AbstractAutism spectrum disorder (ASD) is commonly understood as an alteration of brain networks, yet case-control analyses against typically-developing controls (TD) have yielded inconsistent results. Here, we devised a novel approach to profile the inter-individual variability in functional network organization and tested whether such idiosyncrasy contributes to connectivity alterations in ASD. Studying a multi-centric dataset with 157 ASD and 172 TD, we obtained robust evidence for increased idiosyncrasy in ASD relative to TD in default mode, somatomotor and attention networks, but also reduced idiosyncrasy in lateral temporal cortices. Idiosyncrasy increased with age and significantly correlated with symptom severity in ASD. Furthermore, while patterns of functional idiosyncrasy were not correlated with ASD-related cortical thickness alterations, they co-localized with the expression patterns of ASD risk genes. Notably, we could demonstrate that patterns of atypical idiosyncrasy in ASD closely overlapped with connectivity alterations that are measurable with conventional case-control designs and may, thus, be a principal driver of inconsistency in the autism connectomics literature. These findings support important interactions between inter-individual heterogeneity in autism and functional signatures. Our findings provide novel biomarkers to study atypical brain development and may consolidate prior research findings on the variable nature of connectome level anomalies in autism.
Modelling human liver fibrosis in the context of non-alcoholic steatohepatitis using a microphysiological system
Authors: Kostrzewski Tomasz , Snow Sophie , Battle Anya Lindström , Peel Samantha , Ahmad Zahida , Basak Jayati , Surakala Manasa , Bornot Aurelie , Lindgren Julia , Ryaboshapkina Maria , Clausen Maryam , Lindén Daniel , Maass Christian , Young Lucy May , Corrigan Adam , Ewart Lorna , Hughes David 
Published: September 2021

AbstractNon-alcoholic steatohepatitis (NASH) is a common form of chronic liver disease characterised by lipid accumulation, infiltration of immune cells, hepatocellular ballooning, collagen deposition and liver fibrosis. There is a high unmet need to develop treatments for NASH. We have investigated how liver fibrosis and features of advanced clinical disease can be modelled using an in vitro microphysiological system (MPS). The NASH MPS model comprises a co-culture of primary human liver cells, which were cultured in a variety of conditions including+/− excess sugar, fat, exogenous TGFβ or LPS. The transcriptomic, inflammatory and fibrotic phenotype of the model was characterised and compared using a system biology approach to identify conditions that mimic more advanced clinical disease. The transcriptomic profile of the model was shown to closely correlate with the profile of patient samples and the model displayed a quantifiable fibrotic phenotype. The effects of Obeticholic acid and Elafibranor, were evaluated in the model, as wells as the effects of dietary intervention, with all able to significantly reduce inflammatory and fibrosis markers. Overall, we demonstrate how the MPS NASH model can be used to model different aspects of clinical NASH but importantly demonstrate its ability to model advanced disease with a quantifiable fibrosis phenotype.
Individual Differences in Phonetic Plasticity Across Native and Nonnative Contexts
Authors: Heffner Christopher C. , Myers Emily B. 
Published: September 2021

Purpose
Individuals vary in their ability to learn the sound categories of nonnative languages (nonnative phonetic learning) and to adapt to systematic differences, such as accent or talker differences, in the sounds of their native language (native phonetic learning). Difficulties with both native and nonnative learning are well attested in people with speech and language disorders relative to healthy controls, but substantial variability in these skills is also present in the typical population. This study examines whether this individual variability can be organized around a common ability that we label “phonetic plasticity.”

Method

A group of healthy young adult participants (
N
= 80), who attested they had no history of speech, language, neurological, or hearing deficits, completed two tasks of nonnative phonetic category learning, two tasks of learning to cope with variation in their native language, and seven tasks of other cognitive functions, distributed across two sessions. Performance on these 11 tasks was compared, and exploratory factor analysis was used to assess the extent to which performance on each task was related to the others.

Results
Performance on both tasks of native learning and an explicit task of nonnative learning patterned together, suggesting that native and nonnative phonetic learning tasks rely on a shared underlying capacity, which is termed “phonetic plasticity.” Phonetic plasticity was also associated with vocabulary, comprehension of words in background noise, and, more weakly, working memory.

Conclusions
Nonnative sound learning and native language speech perception may rely on shared phonetic plasticity. The results suggest that good learners of native language phonetic variation are also good learners of nonnative phonetic contrasts.

Supplemental Material

https://doi.org/10.23641/asha.16606778
Suggestions for Improving the Investigation of Gesture in Aphasia
Authors: Stark Brielle C. , Clough Sharice , Duff Melissa 
Published: September 2021

Purpose
When we speak, we gesture, and indeed, persons with aphasia gesture more frequently. The reason(s) for this is still being investigated, spurring an increase in the number of studies of gesture in persons with aphasia. As the number of studies increases, so too does the need for a shared set of best practices for gesture research in aphasia. After briefly reviewing the importance and use of gesture in persons with aphasia, this viewpoint puts forth methodological and design considerations when evaluating gesture in persons with aphasia.

Method & Results
We explore several different design and methodological considerations for gesture research specific to persons with aphasia, such as video angle specifications, data collection techniques, and analysis considerations. The goal of these suggestions is to develop transparent and reproducible methods for evaluating gesture in aphasia to build a solid foundation for continued work in this area.

Conclusions
We have proposed that it is critical to evaluate multimodal communication in a methodologically robust way to facilitate increased knowledge about the relationship of gesture to spoken language, cognition, and to other aspects of living with aphasia and recovery from aphasia. We conclude by postulating future directions for gesture research in aphasia.
V838 Monocerotis as seen by ALMA: A remnant of a binary merger in a triple system
Authors: Kamiński Tomek , Tylenda Romuald , Kiljan Aleksandra , Schmidt Mirek , Lisiecki Krzysztof , Melis Carl , Frankowski Adam , Joshi Vishal , Menten Karl M. 
Published: September 2021

Context.V838 Mon erupted in 2002, quickly becoming the prototype of a new type of stellar eruption known today as the (luminous) red nova. Red nova outbursts are thought to be caused by stellar mergers. The merger in V838 Mon took place in a triple or higher system involving two B-type stars.Aims.We wish to characterize the merger remnant ~17 yr after the eruption to learn more about the remaining system, the progenitor, and the merger physics.Methods.We mapped the merger site with ALMA at a resolution of ~25 mas, or 148 au for a distance of 5.9 kpc, in continuum dust emission and in rotational lines of simple molecules, including CO, SiO, SO, SO2, AlOH, and H2S. We use radiative transfer calculations to reproduce the architecture of the remnant at the epoch of the ALMA observations. We also make use of optical spectroscopy data obtained mainly with VLT/X-shooter and SALT/HRS.Results.For the first time, we identify the position of the B-type companion relative to the outbursting component of V838 Mon. The stellar remnant is surrounded by a clumpy wind with characteristics similar to those of the winds of red supergiants. The merger product is also associated with an elongated structure of 17.6 × 7.6 mas (104 × 45 au) seen in continuum emission, and which we interpret as a disk seen at a moderate inclination. Maps of continuum and molecular emission also show a complex region of interaction between the B-type star (its gravity, radiation, and wind) and the flow of matter ejected in 2002. The remnant’s molecular mass is about 0.1M⊙and the dust mass is 8.3 × 10−3M⊙. The mass of the atomic component remains unconstrained.Conclusions.The most interesting region for understanding the merger of V838 Mon lies in its direct vicinity and appears elongated, but details of its substructure remain unknown. To study it further and in more detail will require even higher angular resolutions. ALMA maps show us an extreme form of interaction between the merger ejecta and the distant (~250 au) companion. This interaction is similar to that known from the Anteres AB system but at a much higher mass loss rate. The B-type star not only deflects the merger ejecta but also changes its molecular composition with an involvement of circumstellar shocks. The ALMA view of V838 Mon offers the best images of a merger site so far.
Rate-dependent input curve shaping of the piezoelectric actuator based optical resonator cavity displacement characteristics for an external cavity diode laser
Authors: Tian Kai , Liu Zhigang , Jing Tao , Zhu Yu 
Published: September 2021

In an external cavity diode laser, the rate-dependent nonlinearity of the piezoelectric actuator based optical resonator cavity (ORC) restricts its application in high-precision measurements. This paper proposes a rate-dependent nonlinear active suppression method for an ORC system based on the Hammerstein model. Using a back propagation neural network and system identification algorithm, a high-precision rate-dependent Hammerstein model of the ORC system is established. The B-spline curve is used to simplify the input voltage curve, and the optimized voltage curve that can obtain the linear displacement output is solved by the particle swarm optimization algorithm. The experimental results show that in the frequency range of 2–50 Hz, the regression coefficients (R2) of the ascent and descent stages at each experimental frequency of the ORC system increased to over 0.9998 and optimized the curve at the inflection point to suppress the vibration at the inflection point.
Ultrathin space charge layer in hematite photoelectrodes: A theoretical investigation
Authors: Delcompare-Rodriguez P. A. , Seriani N. 
Published: September 2021

The space charge layer in hematite photoelectrodes has been analyzed by means of Poisson–Boltzmann equations, the Stern model, and density functional theory, in view of its application for photoelectrochemical water oxidation. The width of the space charge layer can be smaller than ∼10 Å under experimental conditions. In this regime, a substantial part of the potential drop takes place in the Helmholtz layer, leading to important corrections to the Mott–Schottky behavior of the space charge layer capacitance. These results shed light on an unexpected regime of high photoelectrocatalytic efficiency, different from the classical picture of the electrochemical interface of a semiconducting photocatalyst, which is also amenable to direct study by quantum-mechanical atomistic simulations. Density functional theory has been used to calculate the band bending (BB) in the space charge layer in atomistic models of pristine stoichiometric and hydroxylated surfaces. These surface terminations display BBs of 0.14 and 0.49 eV, respectively, with an increasing width of the space charge layer, however still in the sub-nanometer regime. This work shows that, at high doping, the width of the space charge layer of a hematite photoelectrode can become comparable with interatomic distances.