bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of Reproducibility of Diffusion Tensor Imaging in the Brachial Plexus at 3.0 T
Authors: Ho Michael J. , Manoliu Andrei , Kuhn Felix Pierre , Stieltjes Bram , Klarhöfer Markus , Feiweier Thorsten , Marcon Magda , Andreisek Gustav 
Published: March 2017

Objective
The aim of this study was to evaluate the reproducibility of 3 T magnetic resonance imaging diffusion tensor imaging (DTI) of the brachial plexus in healthy subjects.

Methods
Ten healthy volunteers were included, and morphological and DTI sequences of the nerve roots of the brachial plexus from C5 to T1 of both sides were repeatedly acquired on a 3 T magnetic resonance system (MAGNETOM Skyra; Siemens Healthcare, Erlangen, Germany). A prototype diffusion-weighted single-shot echo-planar imaging sequence-enabling slice-specific shim adjustments was performed with b-values of 0 and 800 s/mm2 in 30 gradient directions, resulting in an acquisition time of about 6 minutes each in axial orientation. Between scans, subjects were moved and repositioned in the scanner, coils were reinserted, and new localizers were acquired. Image analysis was performed using MITK Diffusion software toolkit. Two independent readers performed diffusion data postprocessing, and regions of interest (ROIs) were set on the proximal postganglionic trunk at each spinal level, bilaterally to obtain values for fractional anisotropy (FA) and mean diffusivity (MD). Interreader and intrareader agreement as well as test-retest reproducibility of DTI metrics were assessed.

Results
Intraclass correlation coefficients (ICCs) for interreader and intrareader agreement did not differ significantly between measurements for FA and MD. In particular, ICCs for interreader agreement of FA ranged from 0.741 to 0.961 and that of MD ranged from 0.802 to 0.998, and ICCs for intrareader agreement of FA ranged from 0.759 to 0.949 and that of MD ranged from 0.796 to 0.998. The test-retest reproducibility of DTI metrics showed an overall moderate to strong correlation (r > 0.707), with few minor exceptions, for both FA and MD values.

Conclusions
Diffusion tensor imaging metrics in the brachial plexus are reproducible. Future applications of DTI for a possible clinical use should be further investigated.
Carpal Tunnel Syndrome Grading Using High-Resolution Ultrasonography
Authors: El Habashy Hala R. , El Hadidy Reem A. , Ahmed Sandra M. , El Sayed Basma B. , Ahmed Aya S. 
Published: March 2017

Purpose:
Carpal tunnel syndrome (CTS) is a common entrapment neuropathy of the wrist. The diagnosis of CTS has been a concern for physicians for a long time. The aim of this study is to evaluate the use of the median nerve (MN) cross-sectional area (CSA) in the wrist compared with the CSA in the forearm to grade the severity of CTS in Egyptian patients.

Methods:
The CSAs of the MN in the wrist and forearm were measured in 72 wrists that were diagnosed with CTS via nerve conduction studies and 80 healthy wrists. The CTS group was subdivided into three subgroups (mild, moderate, and severe CTS). The ratio of the CSA of the MN in the wrist to that in the forearm was used to calculate cutoff values for CTS grading.

Results:
There were positive correlations between the CSAs of the MN in the wrist and MN conduction latency. At a wrist–forearm ratio of 1.7, the high-resolution ultrasonography showed 96.1% accuracy in the detection of CTS.

Conclusions:
High-resolution ultrasonography can be used in CTS grading.
Mechanistic movement models to understand epidemic spread
Authors: Fofana Abdou Moutalab , Hurford Amy 
Published: March 2017

An overlooked aspect of disease ecology is considering how and why animals come into contact with one and other resulting in disease transmission. Mathematical models of disease spread frequently assume mass-action transmission, justified by stating that susceptible and infectious hosts mix readily, and foregoing any detailed description of host movement. Numerous recent studies have recorded, analysed and modelled animal movement. These movement models describe how animals move with respect to resources, conspecifics and previous movement directions and have been used to understand the conditions for the occurrence and the spread of infectious diseases when hosts perform a type of movement. Here, we summarize the effect of the different types of movement on the threshold conditions for disease spread. We identify gaps in the literature and suggest several promising directions for future research. The mechanistic inclusion of movement in epidemic models may be beneficial for the following two reasons. Firstly, the estimation of the transmission coefficient in an epidemic model is possible because animal movement data can be used to estimate the rate of contacts between conspecifics. Secondly, unsuccessful transmission events, where a susceptible host contacts an infectious host but does not become infected can be quantified. Following an outbreak, this enables disease ecologists to identify ‘near misses’ and to explore possible alternative epidemic outcomes given shifts in ecological or immunological parameters.
This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Global change, parasite transmission and disease control: lessons from ecology
Authors: Cable Joanne , Barber Iain , Boag Brian , Ellison Amy R. , Morgan Eric R. , Murray Kris , Pascoe Emily L. , Sait Steven M. , Wilson Anthony J. , Booth Mark 
Published: March 2017

Parasitic infections are ubiquitous in wildlife, livestock and human populations, and healthy ecosystems are often parasite rich. Yet, their negative impacts can be extreme. Understanding how both anticipated and cryptic changes in a system might affect parasite transmission at an individual, local and global level is critical for sustainable control in humans and livestock. Here we highlight and synthesize evidence regarding potential effects of ‘system changes’ (both climatic and anthropogenic) on parasite transmission from wild host–parasite systems. Such information could inform more efficient and sustainable parasite control programmes in domestic animals or humans. Many examples from diverse terrestrial and aquatic natural systems show how abiotic and biotic factors affected by system changes can interact additively, multiplicatively or antagonistically to influence parasite transmission, including through altered habitat structure, biodiversity, host demographics and evolution. Despite this, few studies of managed systems explicitly consider these higher-order interactions, or the subsequent effects of parasite evolution, which can conceal or exaggerate measured impacts of control actions. We call for a more integrated approach to investigating transmission dynamics, which recognizes these complexities and makes use of new technologies for data capture and monitoring, and to support robust predictions of altered parasite dynamics in a rapidly changing world.
This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Who acquires infection from whom and how? Disentangling multi-host and multi-mode transmission dynamics in the ‘elimination’ era
Authors: Webster Joanne P. , Borlase Anna , Rudge James W. 
Published: March 2017

Multi-host infectious agents challenge our abilities to understand, predict and manage disease dynamics. Within this, many infectious agents are also able to use, simultaneously or sequentially, multiple modes of transmission. Furthermore, the relative importance of different host species and modes can itself be dynamic, with potential for switches and shifts in host range and/or transmission mode in response to changing selective pressures, such as those imposed by disease control interventions. The epidemiology of such multi-host, multi-mode infectious agents thereby can involve a multi-faceted community of definitive and intermediate/secondary hosts or vectors, often together with infectious stages in the environment, all of which may represent potential targets, as well as specific challenges, particularly where disease elimination is proposed. Here, we explore, focusing on examples from both human and animal pathogen systems, why and how we should aim to disentangle and quantify the relative importance of multi-host multi-mode infectious agent transmission dynamics under contrasting conditions, and ultimately, how this can be used to help achieve efficient and effective disease control.This article is part of the themed issue ‘Opening the black box: re-examining the ecology and evolution of parasite transmission’.
Distinct blood DNA methylation profiles in subtypes of orofacial cleft
Authors: Sharp Gemma C , Ho Karen , Davies Amy , Stergiakouli Evie , Humphries Kerry , McArdie Wendy , Sandy Jonathan , Davey Smith George , Lewis Sarah , Relton Caroline L 
Published: March 2017

AbstractBackgroundThere is evidence that different subtypes of orofacial cleft have distinct aetiologies, although the precise molecular mechanisms underlying these are unknown. Given the key role of epigenetic processes such as DNA methylation in embryonic development, it is likely that aberrant DNA methylation may also play a part in the development of orofacial clefts.MethodsIn this study, we explored whether blood samples from children with different cleft subtypes showed distinct DNA methylation profiles.In whole blood samples from 150 children from the Cleft Collective cohort study, we measured DNA methylation at over 450,000 sites on the genome. We then carried out epigenome-wide association studies (EWAS) to test the association between methylation at each site and cleft subtype (cleft lip only CLO n=50; cleft palate only CPO n=50; cleft lip and palate CLP n=50).ResultsWe found four genomic regions differentially methylated in CLO compared to CLP, 17 in CPO compared to CLP and 294 in CPO compared to CLO. These regions included several mapping to genes that have previously been implicated in the development of orofacial clefts (for example,TBX1, COL11A2, HOXA2, PDGFRA) and over 250 novel associations.ConclusionOur finding of distinct methylation profiles in different cleft subtypes might reflect differences in their aetiologies, with DNA methylation either playing a causal role in development of OFC subtypes or reflecting causal genetic or environmental factors.
3D Mapping Reveals Network-specific Amyloid Progression and Subcortical Susceptibility
Authors: Canter RG , Choi H , Wang J , Watson LA , Yao CG , Abdurrob F , Bousleiman SM , Delalle I , Chung K , Tsai L-H 
Published: March 2017

AbstractAlzheimer’s disease is a progressive, neurodegenerative condition for which there is no cure. Prominent hypotheses posit that accumulation of beta-amyloid (Aβ) peptides drives the neurodegeneration that underlies memory loss, however the spatial origins of the lesions remain elusive. Using SWITCH, we created a spatiotemporal map of Aβ deposition in a mouse model of amyloidosis. We report that structures connected by the fornix show primary susceptibility to Aβ accumulation and demonstrate that aggregates develop in increasingly complex networks with age. Notably, the densest early Aβ aggregates occur in the mammillary body coincident with electrophysiological alterations. In later stages, the fornix itself also develops overt Aβ burden. Finally, we confirm Aβ in the mammillary body of postmortem patient specimens. Together, our data suggest that subcortical memory structures are particularly vulnerable to Aβ deposition and that functional alterations within and physical propagation from these regions may underlie the affliction of increasingly complex networks.Author ContributionsRGC, KC, L-HT, ID conceived of the work and planned the experiments.RGC, HC, JW, LAW, CGY, FA, SMB performed experiments and analyzed data.HC built the custom microscope.RGC, L-HT, KC, ID wrote the manuscript.
Compositionally distinct nuclear pore complexes of functionally distinct dimorphic nuclei in ciliateTetrahymena
Authors: Iwamoto Masaaki , Osakada Hiroko , Mori Chie , Fukuda Yasuhiro , Nagao Koji , Obuse Chikashi , Hiraoka Yasushi , Haraguchi Tokuko 
Published: March 2017

SUMMARY STATEMENTOur study demonstrates compositional and structural differences of the nuclear pore complex between the functionally differentiated macronucleus and micronucleus within a single cytoplasm of ciliated protozoa.ABSTRACTThe nuclear pore complex (NPC), a gateway for nucleocytoplasmic trafficking, is composed of about 30 different proteins called nucleoporins. It remains unknown whether the NPCs within a species are homogeneous or vary depending on the cell type, or physiological condition. Here, we present evidence for compositionally distinct NPCs that form within a single cell in a binucleated ciliate. InTetrahymena thermophila,each cell contains both a transcriptionally-active macronucleus (MAC) and a germline micronucleus (MIC). By combiningin silicoanalysis, mass spectrometry analysis for immuno-isolated proteins, and subcellular localization analysis of GFP fused proteins, we identified numerous novel components of MAC and MIC NPCs. Core members of the Nup107-160 scaffold complex were enriched in MIC NPCs. Strikingly, two paralogs of Nup214 and of Nup153 localized exclusively to either MAC or MIC NPCs. Furthermore, the transmembrane components Pom121 and Pom82 localize exclusively to MAC and MIC NPCs, respectively. Our results argue that functional nuclear dimorphism in ciliates is likely to depend on compositional and structural specificity of NPCs.
Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations
Authors: Kim-Hellmuth Sarah , Bechheim Matthias , Pütz Benno , Mohammadi Pejman , Nédélec Yohann , Giangreco Nicholas , Becker Jessica , Kaiser Vera , Fricker Nadine , Beier Esther , Boor Peter , Castel Stephane , Nöthen Markus M. , Barreiro Luis B. , Pickrell Joseph K. , Müller-Myhsok Bertram , Lappalainen Tuuli , Schumacher Johannes , Hornung Veit 
Published: March 2017

AbstractThe immune system plays a major role in human health and disease, and understanding genetic causes of interindividual variability of immune responses is vital. We isolated monocytes from 134 genotyped individuals, stimulated the cells with three defined microbe-associated molecular patterns (LPS, MDP, and ppp-dsRNA), and profiled the transcriptome at three time points. After mapping expression quantitative trait loci (eQTL), we identified 417 response eQTLs (reQTLs) with differing effect between the conditions. We characterized the dynamics of genetic regulation on early and late immune response, and observed an enrichment of reQTLs in distalcis-regulatory elements. Response eQTLs are also enriched for recent positive selection with an evolutionary trend towards enhanced immune response. Finally, we uncover novel reQTL effects in multiple GWAS loci, and show a stronger enrichment of response than constant eQTLs in GWAS signals of several autoimmune diseases. This demonstrates the importance of infectious stimuli modifying genetic predisposition to disease.
Calcium oscillations in wounded fibroblast monolayers are spatially regulated through substrate mechanics
Authors: Lembong Josephine , Sabass Benedikt , Stone Howard A. 
Published: March 2017

ABSTRACTThe maintenance of tissue integrity is essential for the life of multicellular organisms. Healing of a skin wound is a paradigm for how various cell types localize and repair tissue perturbations in an orchestrated fashion. To investigate biophysical mechanisms associated with wound localization, we focus on a model system consisting of a fibroblast monolayer on an elastic substrate. We find that the creation of an edge in the monolayer causes cytosolic calcium oscillations throughout the monolayer. The oscillation frequency increases with cell density, which shows that wound-induced calcium oscillations occur collectively. Inhibition of myosin II reduces the number of oscillating cells, demonstrating a coupling between actomyosin activity and calcium response. The spatial distribution of oscillating cells depends on the stiffness of the substrate. For soft substrates with a Young’s modulusE~ 360 Pa, oscillations occur on average within 0.2 mm distance from the wound edge. Increasing substrate stiffness leads to an average localization of oscillations away from the edge (up to ~0.6 mm). In addition, we use traction force microscopy to determine stresses between cells and substrate. We find that an increase of substrate rigidity leads to a higher traction magnitude. ForE< ~2 kPa, the traction magnitude is strongly concentrated at the monolayer edge, while forE> ~8 kPa, traction magnitude is on average almost uniform beneath the monolayer. Thus, the spatial occurrence of calcium oscillations correlates with the cell-substrate traction. Overall, the experiments with fibroblasts demonstrate a collective, chemomechanical localization mechanism at the edge of a wound with a potential physiological role.
Scalable Multi-Sample Single-Cell Data Analysis by Partition-Assisted Clustering and Multiple Alignments of Networks
Authors: Li Ye Henry , Li Dangna , Samusik Nikolay , Wang Xiaowei , Guan Leying , Nolan Garry P. , Wong Wing Hung 
Published: March 2017

AbstractMass cytometry (CyTOF) has greatly expanded the capability of cytometry. It is now easy to generate multiple CyTOF samples in a single study, with each sample containing single-cell measurement on 50 markers for more than hundreds of thousands of cells. Current methods do not adequately address the issues concerning combining multiple samples for subpopulation discovery, and these issues can be quickly and dramatically amplified with increasing number of samples. To overcome this limitation, we developed Partition-Assisted Clustering and Multiple Alignments of Networks (PAC-MAN) for the fast automatic identification of cell populations in CyTOF data closely matching that of expert manual-discovery, and for alignments between subpopulations across samples to define dataset-level cellular states. PAC-MAN is computationally efficient, allowing the management of very large CyTOF datasets, which are increasingly common in clinical studies and cancer studies that monitor various tissue samples for each subject.Author SummaryRecently, the cytometry field has experienced rapid advancement in the development of mass cytometry (CyTOF). CyTOF enables a significant increase in the ability to monitor 50 or more cellular markers for millions of cells at the single-cell level. Initial studies with CyTOF focused on few samples, in which expert manual discovery of cell types were acceptable. As the technology matures, it is now feasible to collect more samples, which enables systematic studies of cell types across multiple samples. However, the statistical and computational issues surrounding multi-sample analysis have not been previously examined in detail. Furthermore, it was not clear how the data analysis could be scaled for hundreds of samples, such as those in clinical studies. In this work, we present a scalable analysis pipeline that is grounded in strong statistical foundation. Partition-Assisted Clustering (PAC) offers fast and accurate clustering and Multiple Alignments of Networks (MAN) utilizes network structures learned from each homogeneous cluster to organize the data into data-set level clusters. PAC-MAN thus enables the analysis of a large CyTOF dataset that was previously too large to be analyzed systematically; this pipeline can be extended to the analysis of similarly large or larger datasets.
Comparative transcriptome profiling conferring of resistance toFusarium oxysporuminfection between resistant and susceptible tomato
Authors: Zhao Min , Ji Hui-Min , Gao Yin , Cao Xin-Xin , Mao Hui-Yin , Liu Peng , Ouyang Shou-Qiang 
Published: March 2017

ABASTRCATTomato Fusarium wilt caused byFusarium oxysporumf. sp.lycopersici(FOL) is a destructive disease of tomato worldwide which causes severe yield loss of the crops. As exploring gene expression and function approaches constitute an initial point for investigating pathogen-host interaction, we performed a transcriptional analysis to unravel regulated genes in tomato infected by FOL. Differentially expressed genes (DEG) upon inoculation with FOL were presented at twenty-four hours post-inoculation including four treatments: Moneymaker_H2O, Moneymaker_FOL, Motelle_H2O and Motelle_FOL. A total of more than 182.6 million high quality clean reads from the four libraries were obtained. A large overlap was found in DEGs between susceptible tomato cultivar Moneymaker and resistant tomato cultivar Motelle. All Gene Ontology terms were mainly classified into catalytic activity, metabolic process and binding. However, Gene Ontology enrichment analysis evidenced specific categories in infected Motelle. Statistics of pathway enrichment of DEGs resulted that the taurine and hypotaurine metabolism, the stibenoid, diarylheptanoid and gingerol biosynthesis, the starch and sucrose metabolism were the top three pathway affected in both groups. Interestingly, plant-pathogen pathway was greatly regulated in Motelle treated with FOL. Combining with qRT-PCR facilitated the identification of regulated pathogenicity associated genes upon infected resistant or susceptible tomato. Our data showed that a coordinated machinery played a critical role in prompting the response, which could help in generating models of mediated resistance responses with assessment of genomic gene expression patterns.
Neuron density fundamentally relates to architecture and connectivity of the primate cerebral cortex
Authors: Beul Sarah F. , Hilgetag Claus C. 
Published: March 2017

AbstractStudies of structural brain connectivity have revealed many intriguing features of complex cortical networks. To advance integrative theories of cortical organization, an understanding is required of how connectivity interrelates with other aspects of brain structure. Recent studies have suggested that interareal connectivity may be related to a variety of macroscopic as well as microscopic architectonic features of cortical areas. However, it is unclear how these features are inter-dependent and which of them most strongly and fundamentally relate to structural corticocortical connectivity. Here, we systematically investigated the relation of a range of microscopic and macroscopic architectonic features of cortical organization, namely layer III pyramidal cell soma size, dendritic synapse count, dendritic synapse density and dendritic tree size as well as area neuron density, to multiple properties of cortical connectivity, using a comprehensive, up-to-date structural connectome of the primate brain. Importantly, relationships were investigated by multi-variate analyses to account for the interrelations of features. Of all considered factors, the classical architectonic parameter of neuron density most strongly and consistently related to essential features of cortical connectivity (existence and laminar patterns of projections, area degree), and in conjoint analyses largely abolished effects of cellular morphological features. These results reveal neuron density as a central architectonic indicator of the primate cerebral cortex that is closely related to essential aspects of brain connectivity and is also highly indicative of further features of the architectonic organization of cortical areas such as the considered cellular morphological measures. Our findings integrate several aspects of cortical micro-and macroscopic organization, with implications for cortical development and function.