bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Efficacy of Istradefylline for Treating Mild Wearing-Off in Parkinson Disease
Authors: Yabe Ichiro , Kitagawa Mayumi , Takahashi Ikuko , Matsushima Masaaki , Sasaki Hidenao 
Published: October 2017

Objectives
The adenosine A2A antagonist istradefylline has been used to treat Parkinson disease (PD) with symptoms of wearing-off since 2013 in Japan. Previous randomized controlled trials of istradefylline compared with placebo included PD patients experiencing an average daily OFF time of more than 2 hours. The purpose of this study is to assess the efficacy of 20 mg/d istradefylline in PD subjects experiencing an average daily OFF time of 3 hours or less.

Methods
Fifteen patients were enrolled into this retrospective study. They received 20 mg/d istradefylline for 12 weeks. Changes in the Unified Parkinson's Disease Rating Scale part III scores in the ON state (ON-UPDRS-III) scores and daily OFF time were assessed at baseline and after 4, 8, and 12 weeks of administration of istradefylline.

Results
At baseline, all subjects had shorter daily OFF times, lower doses of L-DOPA and higher ON-UPDRS-III scores than those in previous randomized controlled trials. Twelve weeks of istradefylline significantly reduced ON-UPDRS-III scores (P < 0.001, Wilcoxon signed rank test). Eleven patients (73%) showed more than 50% reductions in ON-UPDRS-III scores. Improvement of ON-UPDRS-III was significantly correlated with baseline ON-UPDRS-III, and the mean ON-UPDRS-III score at end point was 12.1.

Conclusions
Our result suggests that 20 mg/d istradefylline significantly improved motor functions in PD patients with mild wearing-off.
Electrophysiology of Olfactory and Optic Nerve in Outpatient and Intraoperative Settings
Authors: Hariharan Praveen , Balzer Jeffery R. , Anetakis Katherine , Crammond Donald J. , Thirumala Parthasarathy D. 
Published: October 2017

Summary:
Evoked potentials are time-locked electrophysiologic potentials recorded in response to standardized stimuli using scalp electrodes. These responses provide good temporal resolution and have been used in various clinical and intraoperative settings. Olfactory evoked potentials (OEPs) may be used as an adjunct tool in identifying patients of Parkinson disease and Alzheimer dementia. In clinical practice, visual evoked potentials (VEPs) are particularly useful in identifying subclinical cases of optic neuritis and in treatment surveillance. In recent times, pattern electroretinograms and photopic negative response have been gaining attention in identifying glaucoma suspects. During surgical manipulation, there is a risk of damage to optic or olfactory nerve. Intraoperative neurophysiologic monitoring can provide information regarding the integrity of olfactory or visual pathway. OEPs and VEPs, however, show high degree of variability and are not reliable tools because the responses are extremely susceptible to volatile anesthetic agents. Newer techniques that could possibly circumvent these drawbacks have been developed but are not used extensively. In this article, we briefly review the available techniques to obtain OEPs and VEPs, diagnostic applications, the utility of intraoperative monitoring, the limitations of the current techniques, and the future directions for research.
Quantum-like dynamics applied to cognition: a consideration of available options
Authors: Broekaert Jan , Basieva Irina , Blasiak Pawel , Pothos Emmanuel M. 
Published: October 2017

Quantum probability theory (QPT) has provided a novel, rich mathematical framework for cognitive modelling, especially for situations which appear paradoxical from classical perspectives. This work concerns the dynamical aspects of QPT, as relevant to cognitive modelling. We aspire to shed light on how the mind's driving potentials (encoded in Hamiltonian and Lindbladian operators) impact the evolution of a mental state. Some existing QPT cognitive models do employ dynamical aspects when considering how a mental state changes with time, but it is often the case that several simplifying assumptions are introduced. What kind of modelling flexibility does QPT dynamics offer without any simplifying assumptions and is it likely that such flexibility will be relevant in cognitive modelling? We consider a series of nested QPT dynamical models, constructed with a view to accommodate results from a simple, hypothetical experimental paradigm on decision-making. We consider Hamiltonians more complex than the ones which have traditionally been employed with a view to explore the putative explanatory value of this additional complexity. We then proceed to compare simple models with extensions regarding both the initial state (e.g. a mixed state with a specific orthogonal decomposition; a general mixed state) and the dynamics (by introducing Hamiltonians which destroy the separability of the initial structure and by considering an open-system extension). We illustrate the relations between these models mathematically and numerically.
This article is part of the themed issue ‘Second quantum revolution: foundational questions’.
Contextuality in canonical systems of random variables
Authors: Dzhafarov Ehtibar N. , Cervantes Víctor H. , Kujala Janne V. 
Published: October 2017

Random variables representing measurements, broadly understood to include any responses to any inputs, form a system in which each of them is uniquely identified by its content (that which it measures) and its context (the conditions under which it is recorded). Two random variables are jointly distributed if and only if they share a context. In a canonical representation of a system, all random variables are binary, and every content-sharing pair of random variables has a unique maximal coupling (the joint distribution imposed on them so that they coincide with maximal possible probability). The system is contextual if these maximal couplings are incompatible with the joint distributions of the context-sharing random variables. We propose to represent any system of measurements in a canonical form and to consider the system contextual if and only if its canonical representation is contextual. As an illustration, we establish a criterion for contextuality of the canonical system consisting of all dichotomizations of a single pair of content-sharing categorical random variables.This article is part of the themed issue ‘Second quantum revolution: foundational questions’.
Path-sum solution of the Weyl quantum walk in 3 + 1 dimensions
Authors: D'Ariano G. M. , Mosco N. , Perinotti P. , Tosini A. 
Published: October 2017

We consider the Weyl quantum walk in 3+1 dimensions, that is a discrete-time walk describing a particle with two internal degrees of freedom moving on a Cayley graph of the group

, which in an appropriate regime evolves according to Weyl's equation. The Weyl quantum walk was recently derived as the unique unitary evolution on a Cayley graph of

that is homogeneous and isotropic. The general solution of the quantum walk evolution is provided here in the position representation, by the analytical expression of the propagator, i.e. transition amplitude from a node of the graph to another node in a finite number of steps. The quantum nature of the walk manifests itself in the interference of the paths on the graph joining the given nodes. The solution is based on the binary encoding of the admissible paths on the graph and on the semigroup structure of the walk transition matrices.

This article is part of the themed issue ‘Second quantum revolution: foundational questions’.
Dual RNAseq shows the human mucosal immunity protein, MUC13, is a hallmark ofPlasmodiumexoerythrocytic infection
Authors: LaMonte Gregory M. , Orjuela-Sanchez Pamela , Wang Lawrence , Li Shangzhong , Swann Justine , Cowell Annie N. , Zou Bing Yu , Abdel-Haleem Mohamed Alyaa M. , Villa-Galarce Zaira , Moreno Marta , Tong-Rios Carlos , Vinetz Joseph M. , Lewis Nathan , Winzeler Elizabeth A. 
Published: October 2017

SummaryThe exoerythrocytic stage ofPlasmodiummalaria infection is a critical window for prophylactic intervention. Using a genome-wide dual RNA sequencing of flow-sorted infected and uninfected hepatoma cells we identify the human mucosal immunity gene,Mucin13 (MUC13), as strongly upregulated duringPlasmodiumexoerythrocytic hepatic-stage infection. We confirm thatMUC13expression is upregulated in hepatoma cell lines and primary hepatocytes. In immunofluorescence assays, host MUC13 protein expression distinguishes infected cells from adjacent uninfected cells and shows similar colocalization with parasite biomarkers such as UIS4 and HSP70. We further show that localization patterns are species independent, distinguishing bothP. bergheiandP. vivaxinfected cells, and that MUC13 can be used to identify compounds that inhibit parasite replication in hepatocytes across all Human-infectingPlasmodiumspecies. This data presents a novel interface of host-parasite interactions inPlasmodium, in that a component of host mucosal immunity is reprogrammed to assist the progression of infection.
OnACID: Online Analysis of Calcium Imaging Data in Real Time*
Authors: Giovannucci Andrea , Friedrich Johannes , Kaufman Matt , Churchland Anne , Chklovskii Dmitri , Paninski Liam , Pnevmatikakis Eftychios A. 
Published: October 2017

AbstractOptical imaging methods using calcium indicators are critical for monitoring the activity of large neuronal populations in vivo. Imaging experiments typically generate a large amount of data that needs to be processed to extract the activity of the imaged neuronal sources. While deriving such processing algorithms is an active area of research, most existing methods require the processing of large amounts of data at a time, rendering them vulnerable to the volume of the recorded data, and preventing realtime experimental interrogation. Here we introduce OnACID, an Online framework for the Analysis of streaming Calcium Imaging Data, including i) motion artifact correction, ii) neuronal source extraction, and iii) activity denoising and deconvolution. Our approach combines and extends previous work on online dictionary learning and calcium imaging data analysis, to deliver an automated pipeline that can discover and track the activity of hundreds of cells in real time, thereby enabling new types of closed-loop experiments. We apply our algorithm on two large scale experimental datasets, benchmark its performance on manually annotated data, and show that it outperforms a popular offline approach.
Glioma Through the Looking GLASS: the Glioma Longitudinal Analysis consortium, molecular evolution of diffuse gliomas
Authors:   The GLASS consortium, Aldape Kenneth , Amin Samirkumar B , Ashley David M , Barnholtz-Sloan Jill S , Bates Amanda J , Beroukhim Rameen , Bock Christoph , Brat Daniel J , Claus Elizabeth B , Costello Joseph F , de Groot John F , Finocchiaro Gaetano , French Pim J , Gan Hui K , Griffith Brent , Herold-Mende Christel C , Horbinski Craig , Iavarone Antonio , Kalkanis Steven N , Karabatsou Konstantina , Kim Hoon , Kouwenhoven Mathilde CM , McDonald Kerrie L , Miletic Hrvoje , Nam Do-Hyun , Ng Ho Keung , Niclou Simone P , Noushmehr Houtan , Ormond D Ryan , Poisson Laila M , Reifenberger Guido , Roncaroli Federico , Sa Jason K , Sillevis Smitt Peter AE , Smits Marion , Souza Camila F , Tabatabai Ghazaleh , Van Meir Erwin G , Verhaak Roel GW , Watts Colin , Wesseling Pieter , Woehrer Adelheid , Yung WK Alfred , Jungk Christine , Hau Ann-Christin , Dyck Eric van , Westerman Bart A , Yin Julia , Abiola Olajide , Khasraw Mustafa , Sulman Erik P , Muscat Andrea M 
Published: October 2017

AbstractAdult diffuse glioma are a diverse group of intracranial neoplasms associated with a disproportional large number of productive life years lost, thus imposing a highly emotional and significant financial burden on society. Patient death is the result of an aggressive course of disease following diagnosis. The Cancer Genome Atlas and similar projects have provided a comprehensive understanding of the somatic alterations and molecular subtypes of glioma at diagnosis. However, gliomas undergo significant molecular evolution during the malignant transformation. We review current knowledge on genomic, epigenomic and transcriptomic abnormalities before and after disease recurrence. We outline an effort to systemically catalogue the longitudinal changes in gliomas, the Glioma Longitudinal Analysis Consortium. The GLASS initiative will provide essential insights into the evolution of glioma towards a lethal phenotype with the potential to reveal targetable vulnerabilities, and ultimately, improved outcomes for a patient population in need.
Magnetic resonance imaging does not reveal structural alterations in the brain of synesthetes
Authors: Dojat M. , Pizzagalli F. , Hupé JM 
Published: October 2017

AbstractSeveral publications have reported structural changes in the brain of synesthetes compared to controls, either local differences or differences in connectivity. In the present study, we pursued this quest for structural brain differences that might support the subjective experience of synaesthesia. In particular, for the first time in this field, we investigated brain folding in comparing 45 sulcal shapes in each hemisphere of control and grapheme-color synesthete populations. To overcome flaws relative to data interpretation based only on p-values, common in the synesthesia literature, we report confidence intervals of effect sizes. Moreover, our statistical maps are displayed without introducing the classical, but misleading, p-value level threshold. We adopt such a methodological procedure to facilitate appropriate data interpretation and promote the New Statistics approach. Based on structural or diffusion magnetic resonance imaging data, we did not find any strong cerebral anomaly, in sulci, tissue volume, tissue density or fiber organization that could support synesthetic color experience. Finally, by sharing our complete datasets, we strongly support the multi-center construction of a sufficient large dataset repository for detecting, if any, subtle brain differences that may help understanding how a subjective experience, such as synesthesia, is mentally constructed.
Biased gene retention in the face of massive nuclear introgression obscures species relationships
Authors: Forsythe Evan S. , Nelson Andrew D. L. , Beilstein Mark A. 
Published: October 2017

AbstractPhylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We exploit a suite of genomic resources to show that introgressive hybridization occurred between close relatives of Arabidopsis, impacting our understanding of species relationships in the group. The composition of introgressed and retained genes indicates that selection against incompatible cytonuclear and nuclear-nuclear interactions likely acted during introgression, while neutral processes also contributed to genome composition through the retention of ancient haplotype blocks. We also developed a divergence-based test to distinguish donor from recipient lineages without the requirement of additional taxon-sampling. Finally, to our great surprise, we find that cytonuclear discordance appears to have arisen via extensive nuclear, rather than cytoplasmic, introgression, meaning that most of the genome was displaced during introgression, while only a small proportion of native alleles were retained.
Timing of gene expression in a cell-fate decision system
Authors: Aymoz Delphine , Solé Carme , Pierre Jean-Jerrold , Schmitt Marta , de Nadal Eulàlia , Posas Francesc , Pelet Serge 
Published: October 2017

AbstractDuring development, morphogens provide extracellular cues allowing cells to select a specific fate by inducing complex transcriptional programs. The mating pathway in budding yeast offers simplified settings to understand this process. Pheromone secreted by the mating partner triggers the activity of a MAPK pathway, which results in the expression of hundreds of genes. Using a dynamic expression reporter, we quantified the kinetics of gene expression in single cells upon exogenous pheromone stimulation and in the physiological context of mating. In both conditions, we observed striking differences in the timing of induction of mating-responsive promoters. Biochemical analyses and generation of synthetic promoter variants demonstrated how the interplay between transcription factor binding and nucleosomes contribute to determine the kinetics of transcription in a simplified cell-fate decision system.One Sentence SummaryQuantitative and dynamic single cell measurements in the yeast mating pathway uncover a complex temporal orchestration of gene expression events.
Neuropathic mutations in MORC2 perturb GHKL ATPase dimerization dynamics and epigenetic silencing by multiple structural mechanisms
Authors: Douse Christopher H. , Bloor Stuart , Liu Yangci , Shamin Maria , Tchasovnikarova Iva A. , Timms Richard T. , Lehner Paul J. , Modis Yorgo 
Published: October 2017

AbstractMissense mutations inMORC2cause neuropathies including spinal muscular atrophy and Charcot-Marie-Tooth disease. We recently identified MORC2 as an effector of epigenetic silencing by the HUSH complex. Here we report the biochemical and cellular activities of MORC2 variants, alongside crystal structures of wild-type and neuropathic forms of a human MORC2 fragment comprising the GHKL-type ATPase module and CW-type zinc finger. This fragment dimerizes upon binding ATP and contains a hinged, functionally critical coiled coil insertion absent in other GHKL ATPases. We find that dimerization and DNA binding of the MORC2 ATPase module transduce HUSH-dependent silencing. Disease mutations change the dynamics of dimerization by distinct structural mechanisms: destabilizing the ATPase-CW module, trapping the ATP lid or perturbing the dimer interface. These defects lead to modulation of HUSH function, thus providing a molecular basis for understanding MORC2-associated neuropathies.
Initiation, elongation and realignment during influenza virus mRNA synthesis
Authors: te Velthuis Aartjan J.W. , Oymans Judith 
Published: October 2017

AbstractThe RNA-dependent RNA polymerase (RdRp) of the influenza A virus replicates and transcribes the viral genome segments in the nucleus of the host cell. To transcribe these viral genome segments, the RdRp ‘snatches’ capped RNA oligonucleotides from nascent host cell mRNAs and aligns these primers to the ultimate or penultimate nucleotide of the segments for the initiation of viral mRNA synthesis. It has been proposed that this initiation process is not processive and that the RdRp uses a prime-realign mechanism during transcription. Here we providein vitroevidence for the existence of this transcriptional prime-realign mechanism, but show that it only functions efficiently for primers that are short or can not stably base pair with the template. In addition, we demonstrate that transcriptional elongation is dependent on the priming loop of the PB1 subunit of the RdRp. We propose that the prime-realign mechanism may be used to rescue abortive transcription initiation events or cope with sequence variation among primers. Overall, these observations advance our mechanistic understanding of how the influenza A virus initiates transcription correctly and efficiently.ImportanceThe influenza A virus causes severe disease in humans and is considered a major global health threat. The virus replicates and transcribes its genome using an enzyme called the RNA polymerase. To ensure that the genome is amplified faithfully and abundant viral mRNAs are made for viral protein synthesis, the viral RNA polymerase must transcribe the viral genome efficiently. In this report, we characterise a structure inside the polymerase that contributes to the efficiency of viral mRNA synthesis.
C3D: A tool to predict 3D genomic interactions between cis-regulatory elements
Authors: Mehdi Tahmid , Bailey Swneke D. , Guilhamon Paul , Lupien Mathieu 
Published: October 2017

ABSTRACTMotivationThe 3D genome architecture influences the regulation of genes by facilitating chromatin interactions between distal cis-regulatory elements and gene promoters. We implement Cross Cell-type Correlation based on DNA accessibility (C3D), a highly customizable computational tool that predicts chromatin interactions using an unsupervised algorithm that utilizes correlations in chromatin measurements, such as DNaseI hypersensitivity signals.ResultsC3D accurately predicts 32.7%, 18.3% and 24.1% of interactions, validated by ChIA-PET assays, between promoters and distal regions that overlie DNaseI hypersensitive sites in K562, MCF-7 and GM12878 cells, respectively.AvailabilitySource code is open-source and freely available on GitHub (https://github.com/LupienLabOrganization/C3D) under the GNU GPLv3 license. C3D is implemented in Bash and R; it runs on any platform with Bash (≥4.0), R (≥3.1.1) and BEDTools (≥2.19.0). It requires the following R packages: GenomicRanges, Sushi, data.table, preprocessCore and dynamicTreeCut.
Genetic Analysis of Deep Phenotyping Projects in Common Disorders
Authors: Gershon Elliot S. , Pearlson Godfrey , Keshavan Matcheri S. , Tamminga Carol , Clementz Brett , Buckley Peter F. , Alliey-Rodriguez Ney , Liu Chunyu , Sweeney John A. , Keedy Sarah , Meda Shashwath , Tandon Neeraj , Shafee Rebecca , Bishop Jeffrey R. , Ivleva Elena I. 
Published: October 2017

AbstractSeveral studies of complex psychotic disorders with large numbers of neurobiological phenotypes are currently under way, in living patients and controls, and on assemblies of brain specimens. Genetic analyses of such data typically present challenges, because of the choice of underlying hypotheses on genetic architecture of the studied disorders and phenotypes, large numbers of phenotypes, the appropriate multiple testing corrections, limited numbers of subjects, imputations required on missing phenotypes and genotypes, and the cross-disciplinary nature of the phenotype measures. Advances in genotype and phenotype imputation, and in genome-wide association (GWAS) methods, are useful in dealing with these challenges. As compared with the more traditional single-trait analyses, deep phenotyping with simultaneous genome-wide analyses serves as a discovery tool for previously unsuspected relationships of phenotypic traits with each other, and with specific molecular involvements.
Genetic reagents for making split-GAL4 lines in Drosophila
Authors: Dionne Heather , Hibbard Karen L. , Cavallaro Amanda , Kao Jui-Chun , Rubin Gerald M. 
Published: October 2017

AbstractThe ability to reproducibly target expression of transgenes to small, defined subsets of cells is a key experimental tool for understanding many biological processes. The Drosophila nervous system contains thousands of distinct cell types and it has generally not been possible to limit expression to one or a few cell types when using a single segment of genomic DNA as an enhancer to drive expression. Intersectional methods, in which expression of the transgene only occurs where two different enhancers overlap in their expression patterns, can be used to achieve the desired specificity. This report describes a set of over 2,800 transgenic lines for use with the split-GAL4 intersectional method.