bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long Exercise Test in the Interattack Period of Periodic Paralysis: A Useful and Sensitive Diagnostic Tool
Authors: Jin Jiaoting , Hu Fangfang , Li Min , Shang Suhang , Qin Xing , Cao Hongmei , Dang Jingxia 
Published: July 2017

Purpose:
The reference values of long exercise test are inconsistent in previous studies. Our research aims to determine the reference values and improve diagnostic efficiency of long exercise test in periodic paralysis.

Methods:
In this study, 100 healthy controls, 35 non–periodic paralysis patients, and 47 patients with periodic paralysis were recruited. The procedures of long exercise test were conducted following McMannis(1986) method.

Results:
The decrease rate in compound muscle action potential amplitudes was correlated with gender, and it was not influenced by age, height, weight, and exercise. After analyzing receiver operating characteristic curves, the compound muscle action potential amplitude decrease rate was stratified by sex. The mean area under the curve, sensitivity, and specificity were higher in male and female than all pooled subjects. The reference values of compound muscle action potential amplitude decrease rate were 46.8% in male and 26.9% in female, respectively.

Conclusions:
The long exercise test is a useful and sensitive diagnostic tool for primary periodic paralysis and thyrotoxic periodic paralysis. However, the reference values should be set by sex, which has better diagnostic performance, sensitivity, and specificity.
The York Gospels: a one thousand year biological palimpsest
Authors: Teasdale Matthew D. , Fiddyment Sarah , Vnouček Jiří , Mattiangeli Valeria , Speller Camilla , Binois Annelise , Carver Martin , Dand Catherine , Newfield Timothy P. , Webb Christopher C. , Bradley Daniel G. , Collins Matthew J. 
Published: July 2017

AbstractMedieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA we report a cost effective and simple-to-use biomolecular sampling technique. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1,000 year lifespan of this cherished object that remains an active participant in the life of York Minster. This biological data provides insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.
Genome-wide transcription factor binding in leaves from C3and C4grasses
Authors: Burgess Steven J. , Reyna-Llorens Ivan , Stevenson Sean R. , Singh Pallavi , Jaeger Katja , Hibberd Julian M. 
Published: July 2017

AbstractThe majority of plants use C3photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4pathway. In most C4species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4grassesZea mays,Sorghum bicolorandSetaria italicaas well as C3Brachypodium distachyon. In C4species, while bundle sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that impact gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.One sentence summaryGenome-wide patterns of transcription factor bindingin vivodefined by DNaseI for leaves of C3and C4grasses
The effects of an 8-week mindful eating intervention on anticipatory reward responses in striatum and midbrain
Authors: Janssen Lieneke K , Duif Iris , Speckens Anne EM , van Loon Ilke , Wegman Joost , de Vries Jeanne HM , Cools Roshan , Aarts Esther 
Published: July 2017

AbstractObesity is a highly prevalent disease, usually resulting from chronic overeating. Accumulating evidence suggests that increased neural responses during the anticipation of high-calorie food play an important role in overeating. A promising method for counteracting enhanced food anticipation in overeating might be mindfulness-based interventions (MBIs). However, the neural mechanisms by which MBIs can affect food reward anticipation are unclear. In this randomized, actively controlled study, the primary objective was to investigate the effect of an 8-week mindful eating intervention on reward anticipation. On the neural level, we hypothesized that mindful eating would decrease striatal reward anticipation responses. Additionally, responses in the midbrain – from which the reward pathways originate – were explored. Using functional magnetic resonance imaging (fMRI), we tested 58 healthy participants with a wide body mass index range (BMI: 19-35 kg/m2), motivated to change their eating behavior. During scanning they performed an incentive delay task, measuring neural reward anticipation responses to caloric and monetary cues before and after 8 weeks of mindful eating or educational cooking (active control). Compared with the educational cooking intervention, mindful eating affected neural reward anticipation responses, with relatively reduced caloric versus monetary reward responses. This effect was, however, not seen in the striatum, but only in the midbrain. The secondary objective was to assess temporary and long-lasting (one year follow-up) intervention effects on self-reported eating behavior and anthropometric measures (BMI, waist circumference, waist-to-hip-ratio (WHR)). We did not observe effects of the mindful eating intervention on eating behavior. Instead, the control intervention showed temporary beneficial effects on BMI, waist circumference, and diet quality, but not on WHR or self-reported eating behavior, as well as long-lasting increases in knowledge about healthy eating. These results suggest that an 8-week mindful eating intervention may have decreased the relative salience of food cues by affecting midbrain but not striatal reward responses. However, these exploratory results should be verified in confirmatory research.The primary and secondary objectives of the study were registered in the Dutch Trial Register (NTR): NL4923 (NTR5025).
Naked mole-rat acid-sensing ion channel 3 forms nonfunctional homomers, but functional heteromers
Authors: Schuhmacher Laura-Nadine , Callejo Gerard , Srivats Shyam , Smith Ewan St. John 
Published: July 2017

ABSTRACTAcid-sensing ion channels (ASICs) form both homotrimeric and heterotrimeric ion channels that are activated by extracellular protons and are involved in a wide range of physiological and pathophysiological processes, including pain and anxiety. ASIC proteins can form both homotrimeric and heterotrimeric ion channels. The ASIC3 subunit has been shown to be of particular importance in the peripheral nervous system with pharmacological and genetic manipulations demonstrating a role in pain. Naked mole-rats, despite having functional ASICs, are insensitive to acid as a noxious stimulus and show diminished avoidance of acidic fumes, ammonia and carbon dioxide. Here we cloned naked mole-rat ASIC3 (nmrASIC3) and used a cell surface biotinylation assay to demonstrate that it traffics to the plasma membrane, but using whole-cell patch-clamp electrophysiology we observed that nmrASIC3 is insensitive to both protons and the non-proton ASIC3 agonist 2-Guanidine-4-methylquinazoline (GMQ). However, in line with previous reports of ASIC3 mRNA expression in dorsal root ganglia (DRG) neurons, we found that the ASIC3 antagonist APETx2 reversibly inhibits ASIC-like currents in naked mole-rat DRG neurons. We further show that like the proton-insensitive ASIC2b and ASIC4, nmrASIC3 forms functional, proton sensitive heteromers with other ASIC subunits. An amino acid alignment of ASIC3s between 9 relevant rodent species and human identified unique sequence differences that might underlie the proton insensitivity of nmrASIC3. However, introducing nmrASIC3 differences into rat ASIC3 (rASIC3) produced only minor differences in channel function, and replacing nmrASIC3 sequence with that of rASIC3 did not produce a proton-sensitive ion channel. Our observation that nmrASIC3 forms nonfunctional homomers may reflect a further adaptation of the naked mole-rat to living in an environment with high-carbon dioxide levels.
Machine Learning for Large-Scale Quality Control of 3D Shape Models in Neuroimaging
Authors: Petrov Dmitry , Gutman Boris A. , (Julie) Yu Shih-Hua , van Erp Theo G.M. , Turner Jessica A. , Schmaal Lianne , Veltman Dick , Wang Lei , Alpert Kathryn , Isaev Dmitry , Zavaliangos-Petropulu Artemis , Ching Christopher R.K. , Calhoun Vince , Glahn David , Satterthwaite Ted , Andreasen Ole Andreas , Borgwardt Stefan , Howells Fleur , Groenewold Nynke , Voineskos Aristotle , Radua Joaquim , Potkin Steven G. , Crespo-Facorro Benedicto , Tordesillas-Gutiérrez Diana , Shen Li , Lebedeva Irina , Spalletta Gianfranco , Donohoe Gary , Kochunov Peter , Rosa Pedro G.P. , James Anthony , Dannlowski Udo , Baune Bernhard T. , Aleman André , Gotlib Ian H. , Walter Henrik , Walter Martin , Soares Jair C. , Gur Ruben C. , Doan N. Trung , Agartz Ingrid , Westlye Lars T. , Harrisberger Fabienne , Riecher-Rössler Anita , Uhlmann Anne , Stein Dan J. , Dickie Erin W. , Pomarol-Clotet Edith , Fuentes-Claramonte Paola , Canales-Rodríguez Erick Jorge , Salvador Raymond , Huang Alexander J. , Roiz-Santiañez Roberto , Cong Shan , Tomyshev Alexander , Piras Fabrizio , Vecchio Daniela , Banaj Nerisa , Ciullo Valentina , Hong Elliot , Busatto Geraldo , Zanetti Marcus V. , Serpa Mauricio H. , Cervenka Simon , Kelly Sinead , Grotegerd Dominik , Sacchet Matthew D. , Veer Ilya M. , Li Meng , Wu Mon-Ju , Irungu Benson , Thompson Paul M. ,   for the ENIGMA consortium
Published: July 2017

AbstractAs very large studies of complex neuroimaging phenotypes become more common, human quality assessment of MRI-derived data remains one of the last major bottlenecks. Few attempts have so far been made to address this issue with machine learning. In this work, we optimize predictive models of quality for meshes representing deep brain structure shapes. We use standard vertex-wise and global shape features computed homologously across 19 cohorts and over 7500 human-rated subjects, training kernelized Support Vector Machine and Gradient Boosted Decision Trees classifiers to detect meshes of failing quality. Our models generalize across datasets and diseases, reducing human workload by 30-70%, or equivalently hundreds of human rater hours for datasets of comparable size, with recall rates approaching inter-rater reliability.
Temporal transitions of spontaneous brain activity
Authors: Ma Zhiwei , Zhang Nanyin 
Published: July 2017

AbstractSpontaneous brain activity, typically investigated using resting-state fMRI (rsfMRI), provides a measure of inter-areal resting-state functional connectivity (RSFC). Previous rsfMRI studies mainly focused on spatial characteristics of RSFC, but the temporal relationship between RSFC patterns is still elusive. Particularly, it remains unknown whether separate RSFC patterns temporally fluctuate in a random manner, or transit in specific orders. Here we investigated temporal transitions between characteristic RSFC patterns in awake rats and humans. We found that transitions between RSFC patterns were reproducible and significantly above chance, suggesting that RSFC pattern transitions were nonrandom. The organization of RSFC pattern transitions in rats was analyzed using graph theory. Pivotal RSFC patterns in transitions were identified including hippocampal, thalamic and striatal networks. This study has revealed nonrandom temporal relationship between characteristic RSFC patterns in both rats and humans. It offers new insights into understanding the spatiotemporal dynamics of spontaneous activity in the mammalian brain.
Linguistically deprived children: meta-analysis of published research underlines the importance of early syntactic language use for normal brain development
Authors: Vyshedskiy Andrey , Shreyas Mahapatra , Dunn Rita 
Published: July 2017

AbstractWe analyzed all published reports of individuals not exposed to syntactic language until puberty: two feral children, who grew up without hearing any language, and eight deaf linguistic isolates, who grew up communicating to their families using homesign or kitchensign, a system of gestures which allows them to communicate simple commands but lacks much in the way of syntax. A common observation in these individuals is the lifelong difficulty understanding syntax and spatial prepositions, even after many years of rehabilitation. This debilitating condition stands in stark contrast to linguistic isolates’ performance on memory as well as semantic tests: they could easily remember hundreds of newly learned words and identify previously seen objects by name. The lack of syntactic language comprehension in linguistic isolates may stem from inability to understand words and/or grammar or inability to mentally synthesize known objects into novel configurations. We have previously shown that purposeful construction of novel mental images is the function of the lateral prefrontal cortex (LPFC) ability to dynamically control posterior cortex neurons1. Here we have ranked all tests performed on linguistic isolates by their reliance on the LPFC control of the posterior cortex: a) the amount of posterior cortex territory that needs to be recruited by the LPFC and b) the number of disparate objects that have to be combined together by the LPFC in order to answer the test question. According to our analysis, linguistic isolates performed well in all tests that did not involve the LPFC control of the posterior cortex, showed decreasing scores in tests that involved greater recruitment of the posterior cortex by the LPFC, and failed in tests that involved greatest recruitment of posterior cortex necessary for mental synthesis of multiple objects. This pattern is consistent with inadequate frontoposterior connections in linguistic isolates. We discuss implications of these findings for the importance of early syntactic language exposure in formation of frontoposterior connections.
Enhancing the Representational Similarity Between Execution and Imagination of Movement Using Network-Based Brain Computer Interfacing
Authors: Kordjazi Neda , Koravand Amineh , Sveistrup Heidi 
Published: July 2017

AbstractMotor imagery-based brain computer interfacing (MI-BCI) as a neuro-rehabilitation tool aims at facilitating motor improvement using mental practice. However, the effectiveness of MI-BCI in producing clinically meaningful functional outcome is debated. Aside from computational shortcomings, a main limiting obstacle seems to be the substantial representational dissimilarity between movement imagination (MI) and movement execution (ME) on the level of engaged neural networks. This dissimilarity renders inducing functionally effective and long lasting changes in motor behavior through MI challenging. Moreover, the quality and intensity of imagination is highly prone to change on a trial-to-trial basis, based on the subject's state of mind and mental fatigue. This leads to an inconsistent profile of neural activity throughout training, limiting learning in a Hebbian sense. To address these issues, we propose a neuroconnectivity-based paradigm, as a systematic priming technique to be utilized pre-BCI training. In the proposed paradigm, ME-idle representational dissimilarity network (RDN) features are used to detect MI in real-time. This means that to drive the virtual environment, an ME-like activation pattern has to be learned and generated in the brain through MI. This contrasts with conventional BCIs which consider a successful MI, one that results in higher than a threshold change in the power of sensorimotor rhythms. Our results show that four out of five participants achieved a consistent session-to-session enhancement in their net MI-ME network-level similarity (mean change rate of 6.16% ± 4.64 per session). We suggest that the proposed paradigm, if utilized as a priming technique pre-BCI training, can potentially enhance the neural and functional effectiveness. This can be achieved through 1- shifting MI towards engaging ME-related networks to a higher extent, and 2- inducing consistency in MI quality by using the ME-related networks as the ground-truth and thus enhancing the robustness of the activity pattern in the brain. This would in turn lend to the clinical acceptability of BCI as a neurorehabilitation tool.
When the ostrich-algorithm fails: Blanking method affects spike train statistics
Authors: Mottaghi Soheil , Joseph Kevin , Christ Olaf , Feuerstein Thomas J. , Hofmann Ulrich G. 
Published: July 2017

1.AbstractElectrophysiological recordings of neuronal tissue face particular challenges when attempted during electrical stimulation, both in vivo and in vitro. Electrical stimulation may produce undesired electronic artifacts and thus render the recorded signal only partially useful. A commonly used remedy for these artifacts is to temporarily ground the input during the stimulation pulses. In the following study, we quantify the effects of this method on the spike train count, which is called "blanking". Starting a from theoretical standpoint, we deduce a loss of countable action potentials, depending on: width of the blanking window, Frequency of stimulation and neuronal activity. Calculations are corroborated by actual high SNR single cell recordings. We have to state, for therapeutically relevant frequencies of 130 Hz and realistic blanking windows of 2 ms, up to 27% of actual existing spikes are lost. We strongly advice careful and controlled use of blanking circuits when spike rate quantification is attempted.
PaSD-qc: Quality control for single cell whole-genome sequencing data using power spectral density estimation
Authors: Sherman Maxwell A. , Barton Alison R. , Lodato Michael , Vitzthum Carl , Coulter Michael E. , Walsh Christopher A. , Park Peter J. 
Published: July 2017

AbstractSingle cell whole-genome sequencing (scWGS) is providing novel insights into the nature of genetic heterogeneity in normal and diseased cells. However, scWGS introduces DNA amplification-related biases that can confound downstream analysis. Here we present a statistical method, with an accompanying package PaSD-qc (PowerSpectralDensity-qc), that evaluates the quality of single cell libraries. It uses a modified power spectral density to assess amplification uniformity, amplicon size distribution, autocovariance, and inter-sample consistency as well as identifies aberrantly amplified chromosomes. We demonstrate the usefulness of this tool in evaluating scWGS protocols and in selecting high-quality libraries from low-coverage data for deep sequencing.
Spatiotemporal DNA Methylome Dynamics of the Developing Mammalian Fetus
Authors: He Yupeng , Hariharan Manoj , Gorkin David U. , Dickel Diane E. , Luo Chongyuan , Castanon Rosa G. , Nery Joseph R. , Lee Ah Young , Williams Brian A. , Trout Diane , Amrhein Henry , Fang Rongxin , Chen Huaming , Li Bin , Visel Axel , Pennacchio Len A. , Ren Bing , Ecker Joseph R. 
Published: July 2017

SummaryGenetic studies have revealed an essential role for cytosine DNA methylation in mammalian development. However, its spatiotemporal distribution in the developing embryo remains obscure. Here, we profiled the methylome landscapes of 12 mouse tissues/organs at 8 developmental stages spanning from early embryogenesis to birth. Indepth analysis of these spatiotemporal epigenome maps systematically delineated ~2 million methylation variant regions and uncovered widespread methylation dynamics at nearly one-half million tissue-specific enhancers, whose human counterparts were enriched for variants involved in genetic diseases. Strikingly, these predicted regulatory elements predominantly lose CG methylation during fetal development, whereas the trend is reversed after birth. Accumulation of non-CG methylation within gene bodies of key developmental transcription factors coincided with their transcriptional repression during later stages of fetal development. These spatiotemporal epigenomic maps provide a valuable resource for studying gene regulation during mammalian tissue/organ progression and for pinpointing regulatory elements involved in human developmental diseases.
Computational Foundations of Natural Intelligence
Authors: van Gerven Marcel 
Published: July 2017

AbstractNew developments in AI and neuroscience are revitalizing the quest to understanding natural intelligence, offering insight about how to equip machines with human-like capabilities. This paper reviews some of the computational principles relevant for understanding natural intelligence and, ultimately, achieving strong AI. After reviewing basic principles, a variety of computational modeling approaches is discussed. Subsequently, I concentrate on the use of artificial neural networks as a framework for modeling cognitive processes. This paper ends by outlining some of the challenges that remain to fulfill the promise of machines that show human-like intelligence.
Limited genetic variation for male mating success reveals low evolutionary potential for thermal plasticity inDrosophila melanogaster
Authors: Waller John T. , Kell Anna , Ballesta Mireia , Giraud Aude , Abbott Jessica K. , Svensson Erik I. 
Published: July 2017

AbstractPopulations respond to novel environmental challenges either through genetic changes, through adaptive phenotypic plasticity for the traits in question, or by a combination of these factors. Here, we investigated the evolutionary potential of phenotypic plasticity for male mating success, locomotory ability, and heating rate (a physiological performance trait) in the fruitflyDrosophila melanogaster, using isogenic male lines from the Drosophila Reference Genome Panel (DGRP) and hemi-clonal males. We quantified thermal reaction norms of how male mating success changed in relation to a temperate gradient, ranging from cold (18 °C) via optimal (24 °C) to hot and stressful environments (either 30 °C or 36 °C). We found significant differences in male mating success and locomotory performance between different lines, as well as significant main effects of temperature, but no significant genotype-by-environment interactions (GEI:s). A statistical power analysis revealed that the variance explained by GEI:s for thermal plasticity using this sample size is likely to be modest or very small, and represent only 4% of the total variation in male mating success. The lack of strong GEI:s for these two behavioral traits contrast with the presence of significant GEI:s for male heating rate, as measured by thermal imaging (infrared camera technology). These results suggest that sexual selection through male mating success is not likely to be efficient in mediating evolutionary rescue through changed plasticity in response to changing temperatures.