bluuebunny/crossref_metadata_2025_split huggingface dataset:
A highly efficient murine model of experimental myopia
Authors: Jiang Xiaoyan , Kurihara Toshihide , Kunimi Hiromitsu , Miyauchi Maki , Ikeda Shin-ichi , Mori Kiwako , Tsubota Kinya , Torii Hidemasa , Tsubota Kazuo 
Published: January 2018

AbstractDespite the global pandemic of myopia, the precise molecular mechanism of the onset of myopia remains largely unknown. This is partially because of the lack of efficient murine myopic models that allow genetic manipulation at low cost. Here we report a highly practical and reproducible lens-induced myopia model by specially designed frames and lenses for mice. A lens power dependent myopic induction in mice was shown until minus 30 diopter lenses. The phenotype was significantly stronger than form-deprivation myopia. We presented the protocol for precise evaluations of the state of myopia, including refraction, corneal curvature and axial length using up-to-date devices. We also found that myopic mouse eyes showed decreased visual acuity on optokinetic response examination. Finally, we confirmed the anti-myopic effect of 1% atropine using this model, which showed its potential in drug screening. The strong phenotype, stable evaluation and the potential for gene manipulation utilizing the presented method in mice will accelerate the translational research of myopia.
Orbital-anisotropic electronic structure in the nonmagnetic state of BaFe2(As1−xP
x
)2 superconductors
Authors: Sonobe T. , Shimojima T. , Nakamura A. , Nakajima M. , Uchida S. , Kihou K. , Lee C. H. , Iyo A. , Eisaki H. , Ohgushi K. , Ishizaka K. 
Published: January 2018

AbstractHigh-temperature superconductivity in iron-pnictides/chalcogenides arises in balance with several electronic and lattice instabilities. Beside the antiferromagnetic order, the orbital anisotropy between Fe 3d
xz
and 3d
yz
occurs near the orthorhombic structural transition in several parent compounds. However, the extent of the survival of orbital anisotropy against the ion-substitution remains to be established. Here we report the composition (x) and temperature (T) dependences of the orbital anisotropy in the electronic structure of a BaFe2(As1−xP
x
)2 system by using angle-resolved photoemission spectroscopy. In the low-x regime, the orbital anisotropy starts to evolve on cooling from high temperatures above both antiferromagnetic and orthorhombic transitions. By increasing x, it is gradually suppressed and survives in the optimally doped regime. We find that the in-plane orbital anisotropy persists in a large area of the nonmagnetic phase, including the superconducting dome. These results suggest that the rotational symmetry-broken electronic state acts as the stage for superconductivity in BaFe2(As1−xP
x
)2.
Evaluating upper limb impairments in multiple sclerosis by exposure to different mechanical environments
Authors: Pellegrino Laura , Coscia Martina , Muller Margit , Solaro Claudio , Casadio Maura 
Published: January 2018

AbstractMultiple sclerosis is a chronic, autoimmune and neurodegenerative disease affecting multiple functional systems and resulting in motor impairments associated with muscle weakness and lack of movement coordination. We quantified upper limb motor deficits with a robot-based assessment including behavioral and muscle synergy analysis in 11 multiple sclerosis subjects with mild to moderate upper limb impairment (9 female; 50 ± 10 years) compared to 11 age- and gender- matched controls (9 female; 50 ± 9 years). All subjects performed planar reaching tasks by moving their upper limb or applying force while grasping the handle of a robotic manipulandum that generated four different environments: free space, assistive or resistive forces, and rigid constraint. We recorded the activity of 15 upper body muscles. Multiple sclerosis subjects generated irregular trajectories. While activities in isolated arm muscles appeared generally normal, shoulder muscle coordination with arm motions was impaired and there was a marked co-activation of the biceps and triceps in extension movements. Systematic differences in timing and organization of muscle synergies have also been observed. This study supports the definition of new biomarkers and rehabilitative treatments for improving upper limb motor coordination in multiple sclerosis.
‘Cold shock’ increases the frequency of homology directed repair gene editing in induced pluripotent stem cells
Authors: Guo Q. , Mintier G. , Ma-Edmonds M. , Storton D. , Wang X. , Xiao X. , Kienzle B , Zhao D. , Feder John N. 
Published: January 2018

AbstractUsing CRISPR/Cas9 delivered as a RNA modality in conjunction with a lipid specifically formulated for large RNA molecules, we demonstrate that homology directed repair (HDR) rates between 20–40% can be achieved in induced pluripotent stem cells (iPSC). Furthermore, low HDR rates (between 1–20%) can be enhanced two- to ten-fold in both iPSCs and HEK293 cells by ‘cold shocking’ cells at 32 °C for 24–48 hours following transfection. This method can also increases the proportion of loci that have undergone complete sequence conversion across the donor sequence, or ‘perfect HDR’, as opposed to partial sequence conversion where nucleotides more distal to the CRISPR cut site are less efficiently incorporated (‘partial HDR’). We demonstrate that the structure of the single-stranded DNA oligo donor can influence the fidelity of HDR, with oligos symmetric with respect to the CRISPR cleavage site and complementary to the target strand being more efficient at directing ‘perfect HDR’ compared to asymmetric non-target strand complementary oligos. Our protocol represents an efficient method for making CRISPR-mediated, specific DNA sequence changes within the genome that will facilitate the rapid generation of genetic models of human disease in iPSCs as well as other genome engineered cell lines.
MtNRLK1, a CLAVATA1-like leucine-rich repeat receptor-like kinase upregulated during nodulation in Medicago truncatula
Authors: Laffont Carole , De Cuyper Carolien , Fromentin Justine , Mortier Virginie , De Keyser Annick , Verplancke Christa , Holsters Marcelle , Goormachtig Sofie , Frugier Florian 
Published: January 2018

AbstractPeptides are signaling molecules regulating various aspects of plant development, including the balance between cell division and differentiation in different meristems. Among those, CLAVATA3/Embryo Surrounding Region-related (CLE-ESR) peptide activity depends on leucine-rich-repeat receptor-like-kinases (LRR-RLK) belonging to the subclass XI. In legume plants, such as the Medicago truncatula model, specific CLE peptides were shown to regulate root symbiotic nodulation depending on the LRR-RLK SUNN (Super Numeric Nodules). Amongst the ten M. truncatula LRR-RLK most closely related to SUNN, only one showed a nodule-induced expression, and was so-called MtNRLK1 (Nodule-induced Receptor-Like Kinase 1). MtNRLK1 expression is associated to root and nodule vasculature as well as to the proximal meristem and rhizobial infection zone in the nodule apex. Except for the root vasculature, the MtNRLK1 symbiotic expression pattern is different than the one of MtSUNN. Functional analyses either based on RNA interference, insertional mutagenesis, and overexpression of MtNRLK1 however failed to identify a significant nodulation phenotype, either regarding the number, size, organization or nitrogen fixation capacity of the symbiotic organs formed.
Spatial and temporal evolution of natural and anthropogenic dust events over northern China
Authors: Wang Xin , Liu Jun , Che Huizheng , Ji Fei , Liu Jingjing 
Published: January 2018

AbstractMineral dust interacts with radiation and cloud microphysics in East Asia can affect local and regional climate. In this study, we found that the occurrences of dust storms, blowing dust, and floating dust over northern China has decreased 76.7%, 68.5%, and 64.5% considerably since the beginning of this century. Based on a multi-dimensional ensemble empirical mode decomposition (MEEMD) method, a steady decrease in zonal maximum wind speed (up to −0.95 m/s) in the Northern Hemisphere was largely responsible for this recent decline in dust event occurrences. Then, a new detection technique that combines multi-satellite datasets with surface observations of dust events is developed to estimate the contribution of anthropogenic dust column burden from disturbed soils to the observed total dust. It is found that the percentage of the anthropogenic dust column burdens to total mineral dust is up to 76.8% by human activities during 2007–2014 in eastern China, but only less than 9.2% near desert source regions in northwestern China. However, we note that the anthropogenic effects on the dust loading for both regions are non-negligible.
Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes
Authors: Kogawa Masato , Hosokawa Masahito , Nishikawa Yohei , Mori Kazuki , Takeyama Haruko 
Published: January 2018

AbstractSingle-cell genomics is a straightforward approach to obtain genomes from uncultured microbes. However, sequence reads from a single-cell amplified genome (SAG) contain significant bias and chimeric sequences. Here, we describe Cleaning and Co-assembly of a Single-Cell Amplified Genome (ccSAG), a novel analytical workflow to obtain composite single-cell genomes with elimination of sequence errors. By the integration of ccSAG with a massively parallel single-cell genome amplification platform based on droplet microfluidics, we can generate multiple SAGs and effectively integrate them into the composite genomes quality equivalent to the data obtained from bulk DNA. We obtained two novel draft genomes from single gut microbial cells with high completeness (>96.6%) and extremely low contamination (<1.25%). Moreover, we revealed the presence of single nucleotide polymorphisms in the specific gene by sequence comparison at the single-cell level. Thus, the workflow yields near-complete genomes from uncultured microbes, and enables analyses of genetic heterogeneity within identical strains.
First in situ evidence of wakes in the far field behind offshore wind farms
Authors: Platis Andreas , Siedersleben Simon K. , Bange Jens , Lampert Astrid , Bärfuss Konrad , Hankers Rudolf , Cañadillas Beatriz , Foreman Richard , Schulz-Stellenfleth Johannes , Djath Bughsin , Neumann Thomas , Emeis Stefan 
Published: January 2018

AbstractMore than 12 GW of offshore wind turbines are currently in operation in European waters. To optimise the use of the marine areas, wind farms are typically clustered in units of several hundred turbines. Understanding wakes of wind farms, which is the region of momentum and energy deficit downwind, is important for optimising the wind farm layouts and operation to minimize costs. While in most weather situations (unstable atmospheric stratification), the wakes of wind turbines are only a local effect within the wind farm, satellite imagery reveals wind-farm wakes to be several tens of kilometres in length under certain conditions (stable atmospheric stratification), which is also predicted by numerical models. The first direct in situ measurements of the existence and shape of large wind farm wakes by a specially equipped research aircraft in 2016 and 2017 confirm wake lengths of more than tens of kilometres under stable atmospheric conditions, with maximum wind speed deficits of 40%, and enhanced turbulence. These measurements were the first step in a large research project to describe and understand the physics of large offshore wakes using direct measurements, together with the assessment of satellite imagery and models.
Deep brain stimulation induces sparse distributions of locally modulated neuronal activity
Authors: Xiao YiZi , Agnesi Filippo , Bello Edward M. , Zhang Simeng , Vitek Jerrold L. , Johnson Matthew D. 
Published: January 2018

AbstractDeep brain stimulation (DBS) therapy is a potent tool for treating a range of brain disorders. High frequency stimulation (HFS) patterns used in DBS therapy are known to modulate neuronal spike rates and patterns in the stimulated nucleus; however, the spatial distribution of these modulated responses are not well understood. Computational models suggest that HFS modulates a volume of tissue spatially concentrated around the active electrode. Here, we tested this theory by investigating modulation of spike rates and patterns in non-human primate motor thalamus while stimulating the cerebellar-receiving area of motor thalamus, the primary DBS target for treating Essential Tremor. HFS inhibited spike activity in the majority of recorded cells, but increasing stimulation amplitude also shifted the response to a greater degree of spike pattern modulation. Modulated responses in both categories exhibited a sparse and long-range spatial distribution within motor thalamus, suggesting that stimulation preferentially affects afferent and efferent axonal processes traversing near the active electrode and that the resulting modulated volume strongly depends on the local connectome of these axonal processes. Such findings have important implications for current clinical efforts building predictive computational models of DBS therapy, developing directional DBS lead technology, and formulating closed-loop DBS strategies.
Accuracy of fetal fibronectin for the prediction of preterm birth in symptomatic twin pregnancies: a pilot study
Authors: Fuchs Florent , Lefevre Clémentine , Senat Marie-Victoire , Fernandez Hervé 
Published: January 2018

AbstractOur goal was to evaluate the performance of fetal fibronectin (fFN) test alone or combined with cervical length (CL), to predict spontaneous preterm birth (PTB) in symptomatic twin pregnancies. We carry out a short pilot study including all uncomplicated diamniotic twin pregnancies with symptoms of preterm labor (PTL) and intact membranes at 24–33 weeks + 6 days of gestation. Studied outcome were spontaneous delivery within 7 and 14 days of testing and spontaneous PTB at <34 and <37 weeks of gestation. Among 40 women, fFN test was positive in 3 of them (7.5%). Regardless of the outcome studied CL did not significantly predict PTB. Performance of fFN was sensitivity (66.7%), specificity (97.2%), positive predictive value (66.7%), negative predictive value (97.2%), positive likelihood ratio (LR) (24.0), and negative LR (0.3) to predict spontaneous PTB within 7 days (p = 0.01). Thus, 66.1% of patients with a positive fFN test would deliver within 7 days versus 2.4% if negative testing; starting with a pre-test probability of 7.5%. Combining CL and fFN did not enable to increase enough positive LR or decrease significantly negative LR. In conclusion, fFN test alone might have a better ability to detect spontaneous delivery within 7 days among symptomatic twin pregnancies.
Arrhythmogenicity of fibro-fatty infiltrations
Authors: De Coster Tim , Claus Piet , Kazbanov Ivan V. , Haemers Peter , Willems Rik , Sipido Karin R. , Panfilov Alexander V. 
Published: January 2018

AbstractThe onset of cardiac arrhythmias depends on electrophysiological and structural properties of cardiac tissue. One of the most important changes leading to arrhythmias is characterised by the presence of a large number of non-excitable cells in the heart, of which the most well-known example is fibrosis. Recently, adipose tissue was put forward as another similar factor contributing to cardiac arrhythmias. Adipocytes infiltrate into cardiac tissue and produce in-excitable obstacles that interfere with myocardial conduction. However, adipose infiltrates have a different spatial texture than fibrosis. Over the course of time, adipose tissue also remodels into fibrotic tissue. In this paper we investigate the arrhythmogenic mechanisms resulting from the presence of adipose tissue in the heart using computer modelling. We use the TP06 model for human ventricular cells and study how the size and percentage of adipose infiltrates affects basic properties of wave propagation and the onset of arrhythmias under high frequency pacing in a 2D model for cardiac tissue. We show that although presence of adipose infiltrates can result in the onset of cardiac arrhythmias, its impact is less than that of fibrosis. We quantify this process and discuss how the remodelling of adipose infiltrates affects arrhythmia onset.
Understanding non-linear effects from Hill-type dynamics with application to decoding of p53 signaling
Authors: Shi Xiaomin , Reimers Jeffrey R. 
Published: January 2018

AbstractAnalytical equations are derived depicting four possible scenarios resulting from pulsed signaling of a system subject to Hill-type dynamics. Pulsed Hill-type dynamics involves the binding of multiple signal molecules to a receptor and occurs e.g., when transcription factor p53 orchestrates cancer prevention, during calcium signaling, and during circadian rhythms. The scenarios involve: (i) enhancement of high-affinity binders compared to low-affinity ones, (ii) slowing reactions involving high-affinity binders, (iii) transfer of the clocking of low-affinity binders from the signal molecule to the products, and (iv) a unique clocking process that produces incremental increases in the activity of high-affinity binders with each signal pulse. In principle, these mostly non-linear effects could control cellular outcomes. An applications to p53 signaling is developed, with binding to most gene promoters identified as category (iii) responses. However, currently unexplained enhancement of high-affinity promoters such as CDKN1a (p21) by pulsed signaling could be an example of (i). In general, provision for all possible scenarios is required in the design of mathematical models incorporating pulsed Hill-type signaling as some aspect.
Reducing acquisition time for MRI-based forensic age estimation
Authors: Neumayer Bernhard , Schloegl Matthias , Payer Christian , Widek Thomas , Tschauner Sebastian , Ehammer Thomas , Stollberger Rudolf , Urschler Martin 
Published: January 2018

AbstractRadiology-based estimation of a living person’s unknown age has recently attracted increasing attention due to large numbers of undocumented immigrants entering Europe. To avoid the application of X-ray-based imaging techniques, magnetic resonance imaging (MRI) has been suggested as an alternative imaging modality. Unfortunately, MRI requires prolonged acquisition times, which potentially represents an additional stressor for young refugees. To eliminate this shortcoming, we investigated the degree of reduction in acquisition time that still led to reliable age estimates. Two radiologists randomly assessed original images and two sets of retrospectively undersampled data of 15 volunteers (N = 45 data sets) applying an established radiological age estimation method to images of the hand and wrist. Additionally, a neural network-based age estimation method analyzed four sets of further undersampled images from the 15 volunteers (N = 105 data sets). Furthermore, we compared retrospectively undersampled and acquired undersampled data for three volunteers. To assess reliability with increasing degree of undersampling, intra-rater and inter-rater agreement were analyzed computing signed differences and intra-class correlation. While our findings have to be confirmed by a larger prospective study, the results from both radiological and automatic age estimation showed that reliable age estimation was still possible for acquisition times of 15 seconds.
Optimising the glaucoma signal/noise ratio by mapping changes in spatial summation with area-modulated perimetric stimuli
Authors: Rountree Lindsay , Mulholland Pádraig J. , Anderson Roger S. , Garway-Heath David F. , Morgan James E. , Redmond Tony 
Published: January 2018

AbstractIdentification of glaucomatous damage and progression by perimetry are limited by measurement and response variability. This study tested the hypothesis that the glaucoma damage signal/noise ratio is greater with stimuli varying in area, either solely, or simultaneously with contrast, than with conventional stimuli varying in contrast only (Goldmann III, GIII). Thirty glaucoma patients and 20 age-similar healthy controls were tested with the Method of Constant Stimuli (MOCS). One stimulus modulated in area (A), one modulated in contrast within Ricco’s area (CR), one modulated in both area and contrast simultaneously (AC), and the reference stimulus was a GIII, modulating in contrast. Stimuli were presented on a common platform with a common scale (energy). A three-stage protocol minimised artefactual MOCS slope bias that can occur due to differences in psychometric function sampling between conditions. Threshold difference from age-matched normal (total deviation), response variability, and signal/noise ratio were compared between stimuli. Total deviation was greater with, and response variability less dependent on defect depth with A, AC, and CR stimuli, compared with GIII. Both A and AC stimuli showed a significantly greater signal/noise ratio than the GIII, indicating that area-modulated stimuli offer benefits over the GIII for identifying early glaucoma and measuring progression.
Potential benefits of mesenchymal stem cells and electroacupuncture on the trophic factors associated with neurogenesis in mice with ischemic stroke
Authors: Kim Yu Ri , Ahn Sung Min , Pak Malk Eun , Lee Hong Ju , Jung Da Hee , Shin Yong-Il , Shin Hwa Kyoung , Choi Byung Tae 
Published: January 2018

AbstractThe beneficial effects of mesenchymal stem cells (MSCs) and electroacupuncture (EA) on neurogenesis and related trophic factors remain unclear. Bone marrow MSCs (mBMSC) were transplanted into the striatum of mice with middle cerebral artery occlusion (MCAO), and EA stimulation was applied at two acupoints, Baihui and Dazhui. EA treatment significantly improved motor function, and a synergistic effect of combined mBMSC and EA treatment was observed. Combined mBMSC and EA treatment reduced prominent atrophic changes in the striatum and led to proliferation of neural progenitor cells in the subventricular zone (SVZ) and the surrounding areas of the striatum (SVZ + striatum) of MCAO mice. The mBMSC and EA treatment markedly enhanced mature brain-derived neurotrophic factor (mBDNF) expression in the SVZ + striatum and hippocampus of mice with MCAO, and combined treatment enhanced neurotrophin-4 (NT4) expression. The number of mBDNF- and NT4-positive neurons in the SVZ + striatum and hippocampus increased following EA treatment. Combined treatment led to an increase in the expression levels of phosphorylated cAMP response element binding protein in the neuroblasts of the striatum. Our results indicate that combined MSC and EA treatment may lead to a better therapeutic effect via co-regulation of neurotrophic factors in the brain, by regulating neurogenesis more than single therapy.