bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single Individual Haplotype Reconstruction Using Fuzzy C-Means Clustering With Minimum Error Correction
Authors: Olyaee Mohammad Hossein , Khanteymoori Alireza 
Published: October 2020

AbstractEvolution of human genetics is one of the most interesting areas for researchers. Determination of Haplotypes not only makes valuable information for this purpose but also performs a major role in investigating the probable relation between diseases and genomes. Determining haplotypes by experimental methods is a time-consuming and expensive task. Recent progress in high throughput sequencing allows researchers to use computational methods for this purpose. Although, several algorithms have been proposed but they are less accurate when the error rate of input fragments increases. In this paper, first, a fuzzy conflict graph is constructed based on the similarities of all input fragments and next, the cluster centers are used as initial centers by fuzzy c-means (FCM) algorithm. The proposed method has been tested on several real datasets and compared with some current methods. The comparison with the existing approaches shows that our method can be a complementary role among the others.
Single-trial dynamics of hippocampal spatial representations are modulated by reward value
Authors: Michon Frédéric , Krul Esther , Sun Jyh-Jang , Kloosterman Fabian 
Published: October 2020

AbstractReward value is known to modulate learning speed in spatial memory tasks, but little is known about its influence on the dynamical changes in hippocampal spatial representations. Here, we monitored the trial-to-trial changes in hippocampal place cell activity during the acquisition of place-reward associations with varying reward size. We show a faster reorganization and stabilization of the hippocampal place map when a goal location is associated with a large reward. The reorganization is driven by both rate changes and the appearance and disappearance of place fields. The occurrence of hippocampal replay activity largely followed the dynamics of changes in spatial representations. Replay patterns became more selectively tuned towards behaviorally relevant experiences over the course of learning. These results suggests that high reward value enhances memory retention via accelerating the formation and stabilization of the hippocampal cognitive map and enhancing its reactivation during learning.
Synergies analysis produces consistent results between motion analysis laboratories
Authors: MacWilliams Bruce A. , McMulkin Mark L. , Rozumalski Adam , Schwartz Michael H. 
Published: October 2020

AbstractAimThe dynamic motor control index during walking (walk-DMC) has been shown to be related to patient outcomes and there has been an increasing interest from motion analysis centers regarding using this metric in their own practice. However, the methods for computing the index reported in the literature are not consistent. Here we propose a standardized method and investigate if this leads to results that are consistent between laboratories.MethodComparisons of typically developing controls are made between three independent motion analysis centers. Comparisons are also made between the proposed and previously published methods. A program script to compute thewalk-DMCwas used for this study and is made freely available with this manuscript.ResultsUsing this script, results are highly consistent between three participating centers. The currently proposed method results in a wider distribution ofwalk-DMCvalues than those previously reported.InterpretationUsing consistent processing methods, synergy measures are equivalent between centers. The major differences between current and published data are attributed to the use of concatenation of several walking trials.
Multifractality distinguishes reactive from proactive cascades in postural control
Authors: Kelty-Stephen Damian G. , Furmanek Mariusz P. , Mangalam Madhur 
Published: October 2020

AbstractIntermittency is a flexible control process entailing context-sensitive engagement with task constraints. The present work aims to situate the intermittency of dexterous behavior explicitly in multifractal modeling for non-Gaussian cascade processes. Multiscale probability density function (PDF) analysis of the center of pressure (CoP) fluctuations during quiet upright standing yields non-Gaussianity parameters lambda exhibiting task-sensitive curvilinear relationships with timescale. The present reanalysis aims for a finer-grained accounting of how non-Gaussian cascade processes might align with known, separable postural processes. It uses parallel decomposition of non-Gaussianity lambda-vs.-timescale and CoP. Orthogonal polynomials decompose lambda curvilinearity, and rambling-trembling analysis decomposes CoP into relatively more intentional rambling (displacement to new equilibrium points) and less intentional trembling sway (deviations around new equilibrium points). Modeling orthogonal polynomials of non-Gaussianity’s lambda-vs.-timescale relationship allows us to differentiate linear from quadratic decay, each of which indicates scale-invariant and scale-dependent cascades, respectively. We tested whether scale-dependent and scale-invariant cascades serve different roles, that is, responding to destabilizing task demands and supporting the proactive movement to a new equilibrium point, respectively. We also tested whether these cascades appear more clearly in rambling rather than trembling sway. More generally, we test whether multifractal nonlinear correlations supports this capacity of postural control to this two-step differentiation: both into rambling vs. trembling, then into scale-dependent vs. scale-invariant cascades within rambling sway. The results supported these hypotheses. Thus, the present work aligns specific aspects of task setting with aspects of cascade dynamics and confirms multifractal foundations of the organism-task relationship.
Cuttlefish: Fast, parallel, and low-memory compaction of de Bruijn graphs from large-scale genome collections
Authors: Khan Jamshed , Patro Rob 
Published: October 2020

AbstractMotivationThe construction of the compacted de Bruijn graph from collections of reference genomes is a task of increasing interest in genomic analyses. These graphs are increasingly used as sequence indices for short and long read alignment. Also, as we sequence and assemble a greater diversity of genomes, the colored compacted de Bruijn graph is being used as the basis for efficient methods to perform comparative genomic analyses on these genomes. Therefore, designing time and memory efficient algorithms for the construction of this graph from reference sequences is an important problem.ResultsWe introduce a new algorithm, implemented in the toolCuttlefish, to construct the (colored) compacted de Bruijn graph from a collection of one or more genome references. Cuttlefish introduces a novel approach of modeling de Bruijn graph vertices as finite-state automata; it constrains these automata’s state-space to enable tracking their transitioning states with very low memory usage. Cuttlefish is fast and highly parallelizable. Experimental results demonstrate that it scales much better than existing approaches, especially as the number and the scale of the input references grow. On our test hardware, Cuttlefish constructed the graph for 100 human genomes in under 9 hours, using ~29 GB of memory while no other tested tool completed this task. On 11 diverse conifer genomes, the compacted graph was constructed by Cuttlefish in under 9 hours, using ~84 GB of memory, while the only other tested tool that completed this construction on our hardware took over 16 hours and ~289 GB of memory.AvailabilityCuttlefish is written inC++14, and is available under an open source license athttps://github.com/COMBINE-lab/cuttlefish.Contactrob@cs.umd.eduSupplementary informationSupplementary text are available atBioinformaticsonline.
The Effect of post Chlamydia Trachomatis Infection treatment on Reactive Oxygen Species and Sperm Parameters of Infertile Men
Authors: Azmakan Reza , Yazdi Reza Salman , Farahi Faramarz , Esmaeili Vahid , Bidoki Seyed Kazem , Jafari Saied 
Published: October 2020

ABSTRACTBackgroundChlamydia trachomatis (CT) infection is often mentioned as a silent disease. Reactive oxygen species (ROS) can also cause Sperm apoptosis and have negative impact on Sperm parameters. The objectives of this study were to elucidate the association between Sperm parameters and ROS caused by CT infections resulting in male Infertility as well as evaluating the role of antibiotic therapy.Materials and methodsA total of 848 infertile males having normal and abnormal Sperm parameters were included. After Semen sampling, the CT IgA were measured by Elisa and confirmed by Nested PCR. ROS was determined by Chemiluminescence. After treatment under the direct supervision of the private urologists. Then, the second Semen samples were taken and subjected to tests on Sperm parameters and ROS levels as assessed again.ResultsThe levels of ROS and morphology were improved following the treatments (P<0.05). Antibiotic therapy due to CT infection, could reduce ROS, improve normal morphology and recover some of Semen parameters.ConclusionsOur findings indicate that CT infection and Sperm parameters were associated with the rate of ROS in infertile men. However, after treatment, ROS value dropped allowing the recovery of certain Sperm parameters. Antibiotic therapy can improve some Semen quality parameters and treat the male Infertility.Reza Azmakan,rezaazmakan@yahoo.com, Department of Andrology, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran,https://orcid.org/0000-0001-6718-3348.
Clinical correlations of SARS-CoV-2 antibody responses in patients with COVID-19 infection
Authors: DeSimone Mia , Simmons Daimon P , Tolan Nicole , Melanson Stacy , Petrides Athena , Tanasijevic Milenko , Schur Peter 
Published: October 2020

AbstractCoronavirus disease 19 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Understanding the clinical correlations of antibodies produced by infected individuals will be critical for incorporating antibody results into clinical management. This study was an observational cohort study to evaluate antibody responses in individuals with PCR-confirmed COVID-19, including 48 hospitalized patients diagnosed with COVID-19 by real-time polymerase chain reaction (RT-PCR) at a large tertiary care medical center. Serum samples were obtained from patients at various time points during the disease course and tested for IgM and IgG antibodies against SARS-CoV-2. Medical records were reviewed, and antibody levels were compared with clinical and laboratory findings. Patients did not have high levels of antibodies within one week of symptoms, but most had detectable IgM and IgG antibodies between 8 and 29 days after onset of symptoms. Some individuals did not develop measurable levels of IgM or IgG antibodies. IgM antibodies were associated with elevated ALT, but there were no other significant associations. We did not observe significant associations of SARS-CoV-2 antibodies with clinical outcomes, including intubation and death. SARS-CoV-2 IgM and IgG antibodies were unlikely to be detected in the first week of infection or in severely immunocompromised individuals. Although we did not observe associations with clinical outcomes, IgM antibodies were associated with higher ALT levels. Antibody production reflects the virus-specific immune response, which is important for immunity but also drives pathology, and antibody levels may be important for guiding treatment of individuals with COVID-19.
COVID-19 among patients with hepatitis B or hepatitis C: A systematic review
Authors: Mirzaie Hossein , Vahidi Mohammad , Shokoohi Mostafa , Darvishian Maryam , Sharifi Hamid , Sharafi Heidar , Karamouzian Mohammad 
Published: October 2020

ABSTRACTBackground & aimsHepatic manifestations of coronavirus disease 2019 (COVID-19) are common among people infected with hepatitis B virus (HBV) and hepatitis C virus (HCV). This systematic review aimed to summarize the evidence on COVID-19 patients with HBV or HCV co-infections.MethodsWe searched multiple electronic databases and preprint servers from December 1, 2019 to August 9, 2020. Studies were included if they reported quantitative empirical data on COVID-19 patients with HBV or HCV co-infections. Descriptive analyses were reported and data were narratively synthesized. Quality assessments was completed using the Joanna Briggs Institute critical appraisal tools.ResultsOut of the 941 identified records, 28 studies were included. Of the eligible studies, 235 patients with COVID-19 were infected with HBV and 22 patients with HCV. Most patients were male and mean age was 49.8 and 62.8 in patients with HBV and HCV, respectively. Death proportion was 6% among COVID-19-HBV and 13% among COVID-19-HCV co-infected patients. Among COVID-19 patients, 34.1% and 76.2% reported at least one comorbidity besides HBV and HCV infections, mainly hypertension and diabetes mellites type 2. The most common COVID-19-related symptoms in both HBV and HCV groups were fever, cough and dyspnea. ICU admission was reported in 14.1% and 21.4% of individuals with HBV and HCV, respectively.ConclusionsOur findings suggest a considerable risk of morbidity and mortality among COVID-19 patients with HBV and HCV. Careful assessment of hepatic manifestations upon admission of patients could help improve health outcomes among COVID-19 patients with HBV or HCV co-infections.Key PointsHepatic manifestations of COVID-19 are common among people infected with HBV and HCV.Among COVID-19 patients, 34.1% and 76.2% reported at least one comorbidity besides HBV and HCV infections.The most common COVID-19-related symptoms in both HBV and HCV groups were fever, cough and dyspnea.There is a considerable risk of mortality among COVID-19 patients with HBV and HCV.
Object-Attribute Biclustering for Elimination of Missing Genotypes in Ischemic Stroke Genome-Wide Data
Authors: Ignatov Dmitry I. , Khvorykh Gennady V. , Khrunin Andrey V. , Nikolić Stefan , Shaban Makhmud , Petrova Elizaveta A. , Koltsova Evgeniya A. , Takelait Fouzi , Egurnov Dmitrii 
Published: October 2020

AbstractMissing genotypes can affect the efficacy of machine learning approaches to identify the risk genetic variants of common diseases and traits. The problem occurs when genotypic data are collected from different experiments with different DNA microarrays, each being characterised by its pattern of uncalled (missing) genotypes. This can prevent the machine learning classifier from assigning the classes correctly. To tackle this issue, we used well-developed notions of object-attribute biclusters and formal concepts that correspond to dense subrelations in the binary relationpatients×SNPs. The paper contains experimental results on applying a biclustering algorithm to a large real-world dataset collected for studying the genetic bases of ischemic stroke. The algorithm could identify large dense biclusters in the genotypic matrix for further processing, which in return significantly improved the quality of machine learning classifiers. The proposed algorithm was also able to generate biclusters for the whole dataset without size constraints in comparison to the In-Close4 algorithm for generation of formal concepts.
Fragile X Premutation rCGG Repeats Impairs Synaptic Growth and Synaptic Transmission atDrosophilalarval Neuromuscular Junction
Authors: Bhat Sajad Ahmad , Yousuf Adil , Mushtaq Zeeshan , Kumar Vimlesh , Qurashi Abrar 
Published: October 2020

AbstractFragile X-associated tremor/ataxia syndrome (FXTAS) is a progressive neurodegenerative disease manifesting in the premutation (PM) carriers of theFMR1gene with alleles bearing 55-200 CGG repeats. The discovery of a broad spectrum of clinical and cell developmental abnormalities among PM carriers with or without FXTAS, and in model systems suggests that neurodegeneration seen in FXTAS could be the inevitable end-result of pathophysiological processes set during early development. Hence, it is imperative to trace early pathological abnormalities. Our previous studies have shown that transgenicDrosophilacarrying human-derived fragile X premutation-length CGG repeats are sufficient to cause neurodegeneration. Here, we used the same transgenicDrosophilamodel to understand the effects of fragile X premutation-length CGG repeats on the structure and function of the developing nervous system. We show that presynaptic expression of the premutation length CGG repeats restricts synaptic growth, reduces the number of synaptic boutons, leads to aberrant presynaptic varicosities, and impairs synaptic transmission at the larval neuromuscular junctions (NMJs). The postsynaptic analysis shows both glutamate receptor and subsynaptic reticulum proteins are normal. However, a high percentage of boutons show the reduced density of Bruchpilot protein, a key component of presynaptic active zones required for vesicle release. The electrophysiological analysis shows a significant reduction in the quantal content, a measure of total synaptic vesicles released per excitation potential. Together these findings endorse that synapse perturbation caused by rCGG repeats mediate presynaptically during larval NMJ development.
Benchmarking small variant detection with ONT reveals high performance in challenging regions
Authors: Møller Peter L. , Holley Guillaume , Beyter Doruk , Nyegaard Mette , Halldórsson Bjarni V. 
Published: October 2020

AbstractBackgroundThe development of long read sequencing (LRS) has led to greater access to the human genome. LRS produces long read lengths at the cost of high error rates and has shown to be more useful in calling structural variants than short read sequencing (SRS) data. In this paper we evaluate how to use LRS data from Oxford Nanopore Technologies (ONT) to call small variants in regions in- and outside the reach of SRS.ResultsCalling single nucleotide polymorphisms (SNPs) with ONT data has comparable accuracy to Illumina when evaluating against the Genome in a Bottle truth set v4.2. In the major histocompatibility complex (MHC) and regions where mapping short reads is difficult, the F-measure of ONT calls exceeds those of short reads by 2-4% when sequence coverage is 20X or greater.We develop recommendations for how to perform small variant calling with LRS data and improve current approaches to the difficult regions by re-genotyping variants to increase the F-measure from 97.24% to 98.78%. Furthermore, we show how LRS can call variants in genomic regions inaccessible to SRS, including medically relevant genes such asSTRCandCFC1B.ConclusionsAlthough small variant calling in LRS data is still immature, current methods are clearly useful in difficult and inaccessible regions of the genome, enabling variant calling in medically relevant genes not accessible to SRS.
Tolerogenic Dendritic Cells Shape a Transmissible Gut Microbiota that Protects from Metabolic Diseases
Authors: Lécuyer Emelyne , Roy Tiphaine Le , Gestin Aurélie , Lacombe Amélie , Philippe Catherine , Ponnaiah Maharajah , Huré Jean-Baptiste , Fradet Magali , Ichou Farid , Boudebbouze Samira , Huby Thierry , Gautier Emmanuel , Rhimi Moez , Maguin Emmanuelle , Kapel Nathalie , Gérard Philippe , Venteclef Nicolas , Garlatti Michèle , Chassaing Benoit , Lesnik Philippe 
Published: October 2020

ABSTRACTExcess of chronic contact between microbial motifs and intestinal immune cells are known to trigger a low-grade inflammation involved in many pathologies such as obesity and diabetes.The important skewing of intestinal adaptive immunity in the context of diet-induced obesity (DIO) is well described but how dendritic cells (DCs) participate to these changes is still poorly documented. To address this question, transgenic mice with enhanced DCs lifespan and immunogenicity (DChBcl-2mice), are challenged with a high fat diet.Those mice display resistance to DIO and metabolic alterations. The DIO resistant phenotype is associated with healthier parameters of intestinal barrier function and lower intestinal inflammation. DChBcl-2DIO-resistant mice demonstrate a particular increase in tolerogenic DC numbers and function which is associated with strong intestinal IgA, Th17 and T regulatory immune responses.Microbiota composition and function analyses reveal that the DChBcl-2mice microbiota is characterized by a lower immunogenicity and an enhanced butyrate production. Cohousing experiments and fecal microbial transplantations are sufficient to transfer the DIO resistance status to WT mice demonstrating that maintenance of DCs tolerogenic ability sustains a microbiota able to drive DIO resistance. DCs tolerogenic function is revealed as a new potent target in metabolic diseases management.
Dynamics of central remyelination and treatment evolution in a model of Multiple Sclerosis with Optic Coherence Tomography
Authors: Benítez-Fernández Rocío , Melero-Jerez Carolina , Gil Carmen , de la Rosa Enrique , Martínez Ana , de Castro Fernando 
Published: October 2020

AbstractThe need for remyelinating drugs is essential for healing important diseases such as multiple sclerosis (MS). One of the reasons for the lack of this class of therapies is the impossibility to follow remyelinationin vivo, which is of utmost importance to perform good clinical trials. Here, we show how the optical coherence tomography (OCT), a cheap and non-invasive technique commonly used in ophthalmology, may be used to follow remyelinationin vivoin MS patients. Our pioneer study validates the study of myelin/remyelination in the optic nerve using OCT and reflects what is occurring in non accessible CNS structures, like the spinal cord. For this study we used the oral bioavailable small molecule VP3.15, confirming its therapeutical potential as neuroprotective, antinflammatory and remyelinating drug for MS. Altogether, our present results confirm the usefulness of OCT to monitor the effectivity of remyelinating therapiesin vivoand underscore the relevance of VP3.15 as potential disease modifying drug for MS therapy.
Biogenesis of NDUFS3-less complex I indicates TMEM126A/OPA7 as an assembly factor of the ND4-module
Authors: D’Angelo Luigi , Astro Elisa , De Luise Monica , Kurelac Ivana , Umesh-Ganesh Nikkitha , Ding Shujing , Fearnley Ian M. , Zeviani Massimo , Gasparre Giuseppe , Porcelli Anna Maria , Fernandez-Vizarra Erika , Iommarini Luisa 
Published: October 2020

ABSTRACTComplex I (CI) is the largest enzyme of the mitochondrial respiratory chain and its defects are the main cause of mitochondrial disease. To understand the mechanisms regulating the extremely intricate biogenesis of this fundamental bioenergetic machine, we analyzed the structural and functional consequences of the ablation of NDUFS3, a non-catalytic core subunit. We prove that in diverse mammalian cell types a small amount of functional CI can still be detected in the complete absence of NDUFS3. In addition, we have determined the dynamics of CI disassembly when the amount of NDUFS3 is gradually decreased. The process of degradation of the complex occurs in a hierarchical and modular fashion where the ND4-module remains stable and bound to TMEM126A. We have thus, uncovered the function of TMEM126A, the product of a disease gene causing recessive optic atrophy, as a factor necessary for the correct assembly and function of CI.