bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting moderate or complex congenital heart defects in adults from an electronic health records system
Authors: Diallo Alpha Oumar , Krishnaswamy Asha , Shapira Stuart K , Oster Matthew E , George Mary G , Adams Jenna C , Walker Elizabeth R , Weiss Paul , Ali Mohammed K , Book Wendy 
Published: September 2018

Abstract

Background
The prevalence of moderate or complex (moderate-complex) congenital heart defects (CHDs) among adults is increasing due to improved survival, but many patients experience lapses in specialty care or their CHDs are undocumented in the medical system. There is, to date, no efficient approach to identify this population.

Objective
To develop and assess the performance of a risk score to identify adults aged 20-60 years with undocumented specific moderate-complex CHDs from electronic health records (EHR).

Methods
We used a case-control study (596 adults with specific moderate-complex CHDs and 2384 controls). We extracted age, race/ethnicity, electrocardiogram (EKG), and blood tests from routine outpatient visits (1/2009 through 12/2012). We used multivariable logistic regression models and a split-sample (4: 1 ratio) approach to develop and internally validate the risk score, respectively. We generated receiver operating characteristic (ROC) c-statistics and Brier scores to assess the ability of models to predict the presence of specific moderate-complex CHDs.

Results
Out of six models, the non-blood biomarker model that included age, sex, and EKG parameters offered a high ROC c-statistic of 0.96 [95% confidence interval: 0.95, 0.97] and low Brier score (0.05) relative to the other models. The adult moderate-complex congenital heart defect risk score demonstrated good accuracy with 96.4% sensitivity and 80.0% specificity at a threshold score of 10.

Conclusions
A simple risk score based on age, sex, and EKG parameters offers early proof of concept and may help accurately identify adults with specific moderate-complex CHDs from routine EHR systems who may benefit from specialty care.
Free-form modelling of galaxy clusters: a Bayesian and data-driven approach
Authors: Olamaie Malak , Hobson Michael P , Feroz Farhan , Grainge Keith J B , Lasenby Anthony , Perrott Yvette C , Rumsey Clare , Saunders Richard D E 
Published: September 2018

ABSTRACTA new method is presented for modelling the physical properties of galaxy clusters. Our technique moves away from the traditional approach of assuming specific parameterized functional forms for the variation of physical quantities within the cluster, and instead allows for a ‘free-form’ reconstruction, but one for which the level of complexity is determined automatically by the observational data and may depend on position within the cluster. This is achieved by representing each independent cluster property as some interpolating or approximating function that is specified by a set of control points, or ‘nodes’, for which the number of nodes, together with their positions and amplitudes, are allowed to vary and are inferred in a Bayesian manner from the data. We illustrate our nodal approach in the case of a spherical cluster by modelling the electron pressure profile Pe(r) in analyses both of simulated Sunyaev–Zel’dovich (SZ) data from the Arcminute MicroKelvin Imager (AMI) and of real AMI observations of the cluster MACS J0744+3927 in the CLASH sample. We demonstrate that one may indeed determine the complexity supported by the data in the reconstructed Pe(r), and that one may constrain two very important quantities in such an analysis: the cluster total volume integrated Comptonization parameter (Ytot) and the extent of the gas distribution in the cluster (rmax). The approach is also well-suited to detecting clusters in blind SZ surveys, in the case where the population of radio sources is known in advance.
SURVEY OF KEY RADIATION SAFETY PRACTICES IN INTERVENTIONAL RADIOLOGY: AN IRISH AND ENGLISH STUDY
Authors: O’Hora L , Ryan M L , Rainford L 
Published: September 2018

Abstract
Interventional radiology is a rapidly evolving speciality with potential to deliver high patient radiation doses, as a result high standards of radiation safety practice are imperative. IR radiation safety practice must be considered before during and after procedures through appropriate patient consent, dose monitoring and patient follow-up. This questionnaire-based study surveyed fixed IR departments across Ireland and England to establish clinical practice in relation to radiation safety. Pre-procedure IR patient consent includes all radiation effects in 11% of cases. The patient skin dose surrogate parameter of Kerma to air at a reference point (Kar) is under-reported. Only 39% of respondents use a substantial radiation dose level and inform patients after these have been reached. Poor compliance with unambiguous, readily available best practice guidance was observed throughout highlighting patient communication, patient dose quantification and subsequent patient dose management concerns.
PERFORMANCE OF THE INSTADOSETM DOSEMETER FOR INTERVENTIONAL RADIOLOGY AND CARDIOLOGY APPLICATION
Authors: Garzón W J , Khoury H , Ovalle S A M , Medeiros R B 
Published: September 2018

Abstract
The aim of this article was to verify the performance of the Mirion InstadoseTM dosemeter under clinical conditions and to compare its response in typical X-ray fields used during interventional and cardiology procedures with the TLD-100, usually used for radiation dosimetry. It was also objective of this study to verify the feasibility of using the InstadoseTM dosemeter response at the chest level for estimation of occupational eye lens dose in cardiology and interventional radiology. Initially the response of the dosemeter was tested using continuous X-ray beams and the results showed that the Instadose dosemeter present a satisfactory behavior of the most important dosimetric properties based on the tests as described in the IEC 62387 standard. The measurements performed in clinical conditions showed that the InstadoseTM dosemeter response was comparable to that of TL dosemeters used in interventional radiology and cardiology procedures and there is a correlation between the eye lens doses and the chest doses measured with the InstadoseTM. Based on the results obtained, we recommend the use of the InstadoseTM dosemeter for purposes of occupational whole-body monitoring of medical staff in interventional radiology and cardiology procedures.
Context triggers the retrieval of long-term memories into working memory to guide attention
Authors: Itthipuripat Sirawaj , Woodman Geoffrey F 
Published: September 2018

SummaryHow do we know what we are looking for in familiar scenes and surroundings? Here we tested a novel hypothesis derived from theories of human memory that working memory (WM) buffers mnemonic contents retrieved from long-term memory (LTM) to control attention. To test this hypothesis, we measured the electrical fields recorded noninvasively from human subjects’ as they searched for specific sets of objects in learned contexts. We found that the subjects’ WM-indexing brain activity tracked the number of real-world objects people learned to search for in each context. Moreover, the level of this WM activity predicted the inter-subject variability in behavioral performance. Together, our results demonstrate that familiar contexts can trigger the transfer of information from LTM to WM to provide top-down attentional control.
Interpretation of ‘Omics dynamics in a single subject using local estimates of dispersion between two transcriptomes
Authors: Li Qike , Zaim Samir Rachid , Aberasturi Dillon , Berghout Joanne , Li Haiquan , Vitali Francesca , Kenost Colleen , Zhang Helen Hao , Lussier Yves A. 
Published: September 2018

AbstractCalculating Differentially Expressed Genes (DEGs) from RNA-sequencing requires replicates to estimate gene-wise variability, infeasible in clinics. By imposing restrictive transcriptome-wide assumptions limiting inferential opportunities of conventional methods (edgeR, NOISeq-sim, DESeq, DEGseq), comparing two conditions without replicates (TCWR) has been proposed, but not evaluated. Under TCWR conditions (e.g., unaffected tissue vs. tumor), differences of transformed expression of the proposed individualized DEG (iDEG) method follow a distribution calculated across a local partition of related transcripts at baseline expression; thereafter the probability of each DEG is estimated by empirical Bayes with local false discovery rate control using a two-group mixture model. In extensive simulation studies of TCWR methods, iDEG and NOISeq are more accurate at 5%<DEGs<20% (precision>90%, recall>75%, false_positive_rate<1%) and 30%<DEGs<40% (precision=recall∼90%), respectively.The proposed iDEG method borrows localized distribution information from the same individual, a strategy that improves accuracy to compare transcriptomes in absence of replicates at low DEGs conditions. http://www.lussiergroup.org/publications/iDEG
Truncated power-law distribution of group sizes in antelope
Authors: Minasandra Pranav , Isvaran Kavita 
Published: September 2018

SummaryGroup size distributions are instrumental in understanding group behaviour in animal populations. We analysed group size data of the blackbuck,Antilope cervicapra,from six different field sites to estimate the group size distribution of this antelope. We show that an exponentially truncated power law (called the polylog distribution in this paper) is the best fitting distribution, against the simple power law and lognormal distributions as other contenders, and the exponential distribution as a control. To show this, we use two likelihood based methods (AICs and likelihood ratios). Finally, we show that polylog distribution parameters can be used to better understand group dynamics, by using them to explore how habitat openness affects group behaviour.
Genetic and neuroanatomical support for functional brain network dynamics in epilepsy
Authors: Reddy Pranav G. , Betzel Richard F. , Khambhati Ankit N. , Shah Preya , Kini Lohith , Litt Brian , Lucas Timothy H. , Davis Kathryn A. , Bassett Danielle S. 
Published: September 2018

AbstractFocal epilepsy is a devastating neurological disorder that affects an overwhelming number of patients world-wide, many of whom prove resistant to medication. The efficacy of current innovative technologies for the treatment of these patients has been stalled by the lack of accurate and effective methods to fuse multimodal neuroimaging data to map anatomical targets driving seizure dynamics. Here we propose a parsimonious model that explains how large-scale anatomical networks and shared genetic constraints shape inter-regional communication in focal epilepsy. In extensive ECoG recordings acquired from a group of patients with medically refractory focal-onset epilepsy, we find that ictal and preictal functional brain network dynamics can be accurately predicted from features of brain anatomy and geometry, patterns of white matter connectivity, and constraints complicit in patterns of gene coexpression, all of which are conserved across healthy adult populations. Moreover, we uncover evidence that markers of non-conserved architecture, potentially driven by idiosyncratic pathology of single subjects, are most prevalent in high frequency ictal dynamics and low frequency preictal dynamics. Finally, we find that ictal dynamics are better predicted by white matter features and more poorly predicted by geometry and genetic constraints than preictal dynamics, suggesting that the functional brain network dynamics manifest in seizures rely on – and may directly propagate along – underlying white matter structure that is largely conserved across humans. Broadly, our work offers insights into the generic architectural principles of the human brain that impact seizure dynamics, and could be extended to further our understanding, models, and predictions of subject-level pathology and response to intervention.
Mechanical Coupling Coordinates the Co-elongation of Axial and Paraxial Tissues in Avian Embryos
Authors: Xiong Fengzhu , Ma Wenzhe , Bénazéraf Bertrand , Mahadevan L. , Pourquié Olivier 
Published: September 2018

SUMMARYTissues undergoing morphogenesis impose mechanical effects on one another. How developmental programs adapt to or take advantage of these effects remains poorly explored. Here, using a combination of live imaging, modeling, and microsurgical perturbations, we show that the axial and paraxial tissues in the forming avian embryonic body coordinate their rates of elongation through mechanical interactions. First, a cell motility gradient drives paraxial presomitic mesoderm (PSM) expansion, resulting in compression of the axial neural tube and notochord; second, elongation of axial tissues driven by PSM compression and polarized cell intercalation pushes the caudal progenitor domain posteriorly; finally, the axial push drives progenitors to emigrate into the PSM to maintain tissue growth and cell motility. These interactions form an engine-like positive feedback loop, which ensures the tissue-coupling and self-sustaining characteristics of body elongation. Our results suggest a general role of inter-tissue forces in the coordination of complex morphogenesis involving distinct tissues.
Manipulation of microbiota reveals altered myelination and white matter plasticity in a model of Huntington disease
Authors: Radulescu Carola I. , Garcia-Miralles Marta , Sidik Harwin , Bardile Costanza Ferrari , Mohammad Yusof Nur Amirah Binte , Lee Hae Ung , Pei Ho Eliza Xin , Chu Collins Wenhan , Layton Emma , Low Donovan , De Sessions Paola Florez , Pettersson Sven , Ginhoux Florent , Pouladi Mahmoud A. 
Published: September 2018

ABSTRACTStructural and molecular myelination deficits represent early pathological features of Huntington disease (HD). Recent evidence from germ-free (GF) animals suggests a role for microbiota-gut-brain bidirectional communication in the regulation of myelination. In this study, we aimed to investigate the impact of microbiota on myelin plasticity and oligodendroglial population dynamics in the mixed-sex BACHD mouse model of HD. Ultrastructural analysis of myelin in the corpus callosum revealed alterations of myelin thickness in BACHD GF compared to specific-pathogen free (SPF) mice, whereas no differences were observed between wild-type (WT) groups. In contrast, myelin compaction was altered in all groups when compared to WT SPF animals. Levels of myelin-related proteins were generally reduced, and the number of mature oligodendrocytes was decreased in the prefrontal cortex under GF compared to SPF conditions, regardless of genotype. Minor differences in commensal bacteria at the family and genera levels were found in the gut microbiota of BACHD and WT animals housed in standard living conditions. Our findings indicate complex effects of a germ-free status on myelin-related characteristics, and highlight the adaptive properties of myelination as a result of environmental manipulation.
Modularity, criticality, and evolvability of a developmental gene regulatory network
Authors: Verd Berta , Monk Nicholas AM , Jaeger Johannes 
Published: September 2018

AbstractThe existence of discrete phenotypic traits suggests that the complex regulatory processes which produce them are functionally modular. These processes are usually represented by networks. Only modular networks can be partitioned into intelligible subcircuits able to evolve relatively independently. Traditionally, functional modularity is approximated by detection of modularity in network structure. However, the correlation between structure and function is loose. Many regulatory networks exhibit modular behaviour without structural modularity. Here we partition an experimentally tractable regulatory network—the gap gene system of dipteran insects—using an alternative approach. We show that this system, although not structurally modular, is composed of dynamical modules driving different aspects of whole-network behaviour. All these subcircuits share the same regulatory structure, but differ in components and sensitivity to regulatory interactions. Some subcircuits are in a state of criticality while others are not, which explains the observed differential evolvability of the various expression features in the system.
Visual deprivation independent shift of ocular dominance induced by cross-modal plasticity
Authors: Teichert Manuel , Isstas Marcel , Liebmann Lutz , Hübner Christian A. , Wieske Franziska , Winter Christine , Bolz Jürgen 
Published: September 2018

AbstractThere is convincing evidence that the deprivation of one sense can lead to adaptive neuronal changes in the spared primary sensory cortices. However, the repercussions of late-onset sensory deprivations on functionality of the remaining sensory cortices are poorly understood. Using repeated intrinsic signal imaging we investigated the effects of whisker or auditory deprivation (WD or AD, respectively) on responsiveness of the binocular primary visual cortex (V1) in fully adult mice. The binocular zone of mice is innervated by both eyes, with the contralateral eye always dominating V1 input over ipsilateral eye input, the normal ocular dominance (OD) ratio. Strikingly, we found that 3 days after WD or AD there was a transient shift of OD, which was mediated by a potentiation of V1 input through the ipsilateral eye. This cross-modal effect was accompanied by strengthening of V1 layer 4 synapses, required visual experience through the ipsilateral eye and was mediated by an increase of the excitation/inhibition ratio in V1. Finally, we demonstrate that both WD and AD induced a long-lasting improvement of visual performance. Our data provide evidence that the deprivation of a non-visual sensory modality cross-modally induces experience dependent V1 plasticity and improves visual behavior, even in adult mice.
Cytoskeleton mechanics determine resting size and activation dynamics of platelets
Authors: Mathur Aastha , Correia Sandra Raquel , Dmitrieff Serge , Gibeaux Romain , Kalinina Iana , Quidwai Tooba , Ries Jonas , Nedelec Francois 
Published: September 2018

SummaryPlatelets are cell fragments of various size that help maintain hemostasis. The way platelets respond during a clotting process is known to depend on their size, with important physiological consequences. We characterized the cytoskeleton of platelets as a function of their size. In resting Human and Mice platelets, we find a quadradic law between the size of a platelet and the amount of microtubule polymer it contains. We further estimate the length and number of microtubules in the marginal band using Electron and Super-resolution microscopy. In platelets activated with ADP, the marginal band coils as a consequence of cortical contraction driven by actin. We observe that this elastic coiling response is accompanied by a reversible shortening of the marginal band. Moreover, larger platelets have a higher propensity to coil. These results establish the dynamic equilibrium that is responsible for platelet size and differential response on a more quantitative level.HighlightsPlatelet size scales consistently with amount of polymerized tubulin in both mouse and human.Polymerized actin is required for ADP-induced marginal band coiling.Upon activation, the marginal band exhibits a reversible visco-elastic response involving shortening.Larger marginal bands have a higher propensity to coil than shorter ones.In briefThe cytoskeleton is adapted to platelet size and its mechanical properties determine propensity of a platelet to undergo morphological changes in response to agonists.
Parental Allele-Specific Protein Expression in Single CellsIn Vivo
Authors: Lo Chiu-An , Chen Brian E. 
Published: September 2018

AbstractAllelic expression from each parent-of-origin is important as a backup and to ensure that enough protein products of a gene are produced. Thus far, it is not known how each cell throughout a tissue differs in parental allele expression at the level of protein synthesis. Here, we measure the expression of the Ribosomal protein L13a (Rpl13a) from both parental alleles simultaneously in single cells in the living animal. We use genome-editedDrosophilathat have a quantitative reporter of protein synthesis inserted into the endogenousRpl13alocus. We find that individual cells can have large (>10-fold) differences in protein expression between the two parental alleles. Cells can produce protein from only one allele oftentimes, and time-lapse imaging of protein production from each parental allele in each cell showed that the imbalance in expression from one parental allele over the other can invert over time.One sentence summaryParental allele-specific protein expression varies widely across cells and over time.HighlightsWe used genome editing to insert a quantifiable protein translation reporter into the endogenousRibosomal protein L13agene and thus track the protein expression of both parental alleles simultaneously in every single cell in the awake animal.Cells can have a large difference in protein expression for one parental allele over the other, and this can invert over time, and can occur in clusters of cells within a tissue.We demonstrate the highly variable nature of heterozygous and homozygous definitions across single cells, and over time.Our study demonstrates a new paradigm that can be used to examine inherited epigenetic control of expression from a specific parent-of-origin allele across single clonal cells from a common progenitorin vivo.
Fascetto Interacting Protein (FIP) Regulates Fascetto (PRC1) to Ensure Proper Cytokinesis and Ploidy
Authors: Swider Zachary T. , Ng Rachel K. , Varadarajan Ramya , Fagerstrom Carey J. , Rusan Nasser M 
Published: September 2018

AbstractCell division is critical for development, organ growth, and tissue repair. The later stages of cell division include the formation of the microtubule (MT)-rich central spindle in anaphase, which is required to properly define the cell equator, guide the assembly of the acto-myosin contractile ring, and ultimately ensure complete separation and isolation of the two daughter cells via abscission. Much is known about the molecular machinery that forms the central spindle, including proteins needed to generate the antiparallel overlapping interzonal MTs. One critical protein that has garnered great attention is Protein Regulator of Cytokinesis 1 (PRC1), or Fascetto (Feo) inDrosophila, which forms a homodimer to crosslink interzonal MTs, ensuring proper central spindle formation and cytokinesis. Here, we report on a new direct protein interactor and regulator of Feo we named Fascetto Interacting Protein (FIP). Loss of FIP results in a significant reduction in Feo localization, rapid disassembly of interzonal MTs, and several cytokinesis defects. Simultaneous reduction in Feo and FIP results in tumor-like, DNA-filled masses in the brain. In aggregate our data show that FIP functions upstream of, and acts directly on, Feo to ensure fully accurate cell division.