bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole transcriptome expression profiling of mouse limb tendon development by using RNA‐seq
Authors: Liu Han , Xu Jingyue , Liu Chia‐Feng , Lan Yu , Wylie Christopher , Jiang Rulang 
Published: February 2015

ABSTRACTTendons are fibrous connective tissues that transmit force between muscle and bone. Whereas the molecular and cellular mechanisms of bone and muscle development have been well studied, that of tendon development is poorly understood. Using the Scx‐GFP transgenic mice, we isolated GFP+ cells from the developing mouse limbs at E11.5, E13.5, and E15.5, respectively, and carried out whole transcriptome RNA‐seq analysis. Comparing the gene expression profiles of GFP+ and GFP− cells in the E13.5 limb isolated over 1,500 genes that exhibited enrichment of mRNA expression by at least 1.5‐fold in the GFP+ cells. Of these, 778 genes showed expression up‐regulated by more than 1.5‐fold from E11.5 to E13.5 and 516 genes showed expression up‐regulated by more than 1.5‐fold from E13.5 to E15.5 in the GFP+ cell population. Interestingly, over 30 genes encoding transcription factors are among the early‐activated genes in the GFP+ cells. Whole mount and section in situ hybridization analyses showed that many of these transcription factor genes have distinct patterns of expression during limb development and identified Foxf2 expression as a specific marker for differentiated dorsal limb tendon cells. Together, these data provide a valuable resource for further investigation of the molecular mechanisms regulating tendon development. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 33:840–848, 2015.
Phenotypic variability of CMT4C in a French‐Canadian kindred
Authors: Varley Talia L. , Bourque Pierre R. , Baker Steven K. 
Published: March 2015

ABSTRACTIntroductionCharcot‐Marie‐Tooth type 4C (CMT4C) is an autosomal recessive dysmyelinating neuropathy characterized by precocious and rapidly progressive scoliosis.MethodsPatients in a French‐Canadian kindred were evaluated with clinical examination, electrophysiologic study, and genomic DNA extraction.ResultsSix of 10 siblings were clinically symptomatic with supportive electrophysiologic features. The proband presented with regional side‐to‐side sensorimotor asymmetry, typical pes cavus without obvious scoliosis, and unremarkable plain films of the spine. Affected siblings all share symptoms of foot deformity but have variable onset of neuropathic symptoms, degree of extremity weakness, progression of symptoms, and, most notably, evidence of scoliosis. DNA sequence analysis revealed a novel combination of 2 known recessive mutations, p.R904X and p.R954X, in the SH3TC2 gene.ConclusionsA broad spectrum of phenotypes should be considered in the possible diagnosis of CMT4C. The absence of scoliosis or late‐onset symptoms should not exclude SH3TC2 from the list of candidate genes under consideration. Age of onset and clinical features were variable and suggest that polygenic factors contribute to the final phenotype. Muscle Nerve 52:444–449, 2015
Impact of the Cd2+ treatment on the electrical properties of Cu2ZnSnSe4 and Cu(In,Ga)Se2 solar cells
Authors: Ben Messaoud Khaled , Buffière Marie , Brammertz Guy , ElAnzeery Hossam , Oueslati Souhaib , Hamon Jonathan , Kniknie Bas J. , Meuris Marc , Amlouk Mosbah , Poortmans Jef 
Published: February 2015

AbstractThe present contribution aims at determining the impact of modifying the properties of the absorber/buffer layer interface on the electrical performance of Cu2ZnSnSe4 (CZTSe) thin‐film solar cells, by using a Cd2+ partial electrolyte (Cd PE) treatment of the absorber before the buffer layer deposition. In this work, CZTSe/CdS solar cells with and without Cd PE treatment were compared with their respective Cu(In,Ga)Se2 (CIGSe)/CdS references. The Cd PE treatment was performed in a chemical bath for 7 min at 70 °C using a basic solution of cadmium acetate. X‐ray photoemission spectroscopy measurements have revealed the presence of Cd at the absorber surface after the treatment. The solar cells were characterized using current density–voltage (J–V), external quantum efficiency, and drive‐level capacitance profiling measurements. For the CZTSe‐based devices, the fill factor increased from 57.7% to 64.0% when using the Cd PE treatment, leading to the improvement of the efficiency (η) from 8.3% to 9.0% for the best solar cells. Similar observations were made on the CIGSe solar cell reference. This effect comes from a considerable reduction of the series resistance (RS) of the dark and light J–V, as determined using the one‐diode model. The crossover effect between dark and light J–V curves is also significantly reduced by Cd PE treatment. Copyright © 2015 John Wiley & Sons, Ltd.
Protective Effects of Human iPS-Derived Retinal Pigmented Epithelial Cells in Comparison with Human Mesenchymal Stromal Cells and Human Neural Stem Cells on the Degenerating Retina inrd1mice
Authors: Sun Jianan , Mandai Michiko , Kamao Hiroyuki , Hashiguchi Tomoyo , Shikamura Masayuki , Kawamata Shin , Sugita Sunao , Takahashi Masayo 
Published: February 2015

AbstractRetinitis pigmentosa (RP) is a group of visual impairments characterized by progressive rod photoreceptor cell loss due to a genetic background. Pigment epithelium-derived factor (PEDF) predominantly secreted by the retinal pigmented epithelium (RPE) has been reported to protect photoreceptors in retinal degeneration models, including rd1. In addition, clinical trials are currently underway outside Japan using human mesenchymal stromal cells and human neural stem cells to protect photoreceptors in RP and dry age-related macular degeneration, respectively. Thus, this study aimed to investigate the rescue effects of induced pluripotent stem (iPS)-RPE cells in comparison with those types of cells used in clinical trials on photoreceptor degeneration in rd1 mice. Cells were injected into the subretinal space of immune-suppressed 2-week-old rd1 mice. The results demonstrated that human iPS-RPE cells significantly attenuated photoreceptor degeneration on postoperative days (PODs) 14 and 21 and survived longer up to at least 12 weeks after operation than the other two types of graft cells with less immune responses and apoptosis. The mean PEDF concentration in the intraocular fluid in RPE-transplanted eyes was more than 1 µg/ml at PODs 14 and 21, and this may have contributed to the protective effect of RPE transplantation. Our findings suggest that iPS-RPE cells serve as a competent source to delay photoreceptor degeneration through stable survival in degenerating ocular environment and by releasing neuroprotective factors such as PEDF. Stem Cells 2015;33:1543–1553
Recruitment of striatonigral disinhibitory and nigrotectal inhibitory GABAergic pathways during the organization of defensive behavior by mice in a dangerous environment with the venomous snake Bothrops alternatus (Reptilia, Viperidae)
Authors: Almada Rafael Carvalho , Coimbra Norberto Cysne 
Published: February 2015

ABSTRACTThe neuropsychopharmacological basis of fear‐ or panic‐related behavior has been the focus of several studies. Some mesencephalic tectum (MT) structures, such as the superior colliculus (SC) and dorsal periaqueductal gray matter (dPAG), are considered to be responsible for the control of defensive responses evoked during threatening situations. Furthermore, the pars reticulata of the substantia nigra (SNpr) sends inputs to the SC that can work as a sensory channel to MT neurons fundamental for the elaboration of defensive responses. The purpose of the present study was to investigate the role of striato‐nigral GABAergic inputs in the activity of nigro‐tectal outputs during the elaboration of defensive behavior using a GABAA receptor selective blockade in the MT of mice confronted pre‐treated with Bothrops alternatus. Mice with injections of physiological saline into the SNpr and treated with a GABAA receptor selective antagonist in the MT displayed an increase in panic‐related behavior, expressed by an increase in the duration of freezing, frequency of nonoriented escape and frequency of total escape responses during the confrontation with the snake. However, intra‐SNpr injections of cobalt chloride followed by MT injections of bicuculline caused a significant decrease in the duration of freezing and total escape responses. In addition, intra‐SNpr injections of lidocaine followed by MT injections of bicuculline caused an increase in panic‐related behavior. The results highlight the involvement of SNpr and MT structures in the organization of defensive behaviors and suggest an inhibitory control of striatonigral‐nigrotectal pathways during the elaboration of fear‐ and panic‐related behavior. Synapse 69:299–313, 2015. © 2015 Wiley Periodicals, Inc.
Overview of emerging memristor families from resistive memristor to spintronic memristor
Authors: Wang Lei , Yang CiHui , Wen Jing , Gai Shan , Peng YuanXiu 
Published: February 2015

AbstractMemristor is a fundamental circuit element in addition to resistor, capacitor, and inductor. As it can remember its resistance state even encountering a power off, memristor has recently received widespread applications from non-volatile memory to neural networks. The current memristor family mainly comprises resistive memristor, polymeric memristor, ferroelectric memristor, manganite memristor, resonant-tunneling diode memristor, and spintronic memristor in terms of the materials the device is made of. In order to help researcher better understand the physical principles of the memristor, and thus to provide a promising prospect for memristor devices, this paper presents an overview of memristor materials properties, switching mechanisms, and potential applications. The performance comparison among different memristor members is also given.
Monitoring frequency influences the analysis of resting behaviour in a forest carnivore
Authors: Carvalho Filipe , Carvalho Rafael , Galantinho Ana , Mira António , Beja Pedro 
Published: February 2015

AbstractResting sites are key structures for many mammalian species, which can affect reproduction, survival, population density, and even species persistence in human‐modified landscapes. As a consequence, an increasing number of studies has estimated patterns of resting site use by mammals, as well as the processes underlying these patterns, though the impact of sampling design on such estimates remain poorly understood. Here we address this issue empirically, based on data from 21 common genets radiotracked during 28 months in Mediterranean forest landscapes. Daily radiotracking data was thinned to simulate every other day and weekly monitoring frequencies, and then used to evaluate the impact of sampling regime on estimates of resting site use. Results showed that lower monitoring frequencies were associated with major underestimates of the average number of resting sites per animal, and of site reuse rates and sharing frequency, though no effect was detected on the percentage use of resting site types. Monitoring frequency also had a major impact on estimates of environmental effects on resting site selection, with decreasing monitoring frequencies resulting in higher model uncertainty and reduced power to identify significant explanatory variables. Our results suggest that variation in monitoring frequency may have had a strong impact on intra‐ and interspecific differences in resting site use patterns detected in previous studies. Given the errors and uncertainties associated with low monitoring frequencies, we recommend that daily or at least every other day monitoring should be used whenever possible in studies estimating resting site use patterns by mammals.
EPA guidance on how to improve the image of psychiatry and of the psychiatrist
Authors: Bhugra D. , Sartorius N. , Fiorillo A. , Evans-Lacko S. , Ventriglio A. , Hermans M.H.M. , Vallon P. , Dales J. , Racetovic G. , Samochowiec J. , Roca Bennemar M. , Becker T. , Kurimay T. , Gaebel W. 
Published: February 2015

AbstractStigma against mental illness and the mentally ill is well known. However, stigma against psychiatrists and mental health professionals is known but not discussed widely. Public attitudes and also those of other professionals affect recruitment into psychiatry and mental health services. The reasons for this discriminatory attitude are many and often not dissimilar to those held against mentally ill individuals. In this Guidance paper we present some of the factors affecting the image of psychiatry and psychiatrists which is perceived by the public at large. We look at the portrayal of psychiatry, psychiatrists in the media and literature which may affect attitudes. We also explore potential causes and explanations and propose some strategies in dealing with negative attitudes. Reduction in negative attitudes will improve recruitment and retention in psychiatry. We recommend that national psychiatric societies and other stakeholders, including patients, their families and carers, have a major and significant role to play in dealing with stigma, discrimination and prejudice against psychiatry and psychiatrists.
Manual segmentation qualification platform for the EADC‐ADNI harmonized protocol for hippocampal segmentation project
Authors: Duchesne Simon , Valdivia Fernando , Robitaille Nicolas , Mouiha Abderazzak , Valdivia F. Abiel , Bocchetta Martina , Apostolova Liana G. , Ganzola Rossana , Preboske Greg , Wolf Dominik , Boccardi Marina , Jack Clifford R. , Frisoni Giovanni B. ,   EADC‐ADNI Working Group on The Harmonized Protocol for Manual Hippocampal Segmentation and for the Alzheimer's Disease Neuroimaging Initiative
Published: February 2015

AbstractBackgroundThe use of hippocampal volumetry as a biomarker for Alzheimer’s disease (AD) requires that tracers from different laboratories comply with the same segmentation method. Here we present a platform for training and qualifying new tracers to perform the manual segmentation of the hippocampus on magnetic resonance images (MRI) following the European Alzheimer's Disease Consortium and Alzheimer's Disease Neuroimaging Initiative (EADC‐ADNI) Harmonized Protocol (HarP). Our objective was to demonstrate that the training process embedded in the platform leads to increased compliance and qualification with the HarP.MethodThirteen new tracers' segmentations were compared with benchmark images with respect to: (a) absolute segmentation volume; (b) spatial overlap of contour with the reference using the Jaccard similarity index; and (c) spatial distance of contour with the reference. Point by point visual feedback was provided through three training phases on 10 MRI. Tracers were then tested on 10 different MRIs in the qualification phase.ResultsStatistical testing of training over three phases showed a significant increase of Jaccard (i.e. mean Jaccard overlap P < .001) between phases on average for all raters, demonstrating that training positively increased compliance with the HarP. Based on these results we defined qualification thresholds which all tracers were able to meet.ConclusionsThis platform is an adequate infrastructure allowing standardized training and evaluation of tracers' compliance with the HarP. This is a necessary step allowing the use of hippocampal volumetry as a biomarker for AD in clinical and research centers.
The angulation of the septal structures impacts ventricular imbalance in atrioventricular septal defects with a common atrioventricular junction
Authors: Ahmad Zaheer , Lim Zek , Roman Kevin , Haw Marcus , Anderson Robert H. , Vettukattil Joseph 
Published: March 2015

AbstractObjectiveMultiplanar re-formatting of full-volume three-dimensional echocardiography data sets offers new insights into the morphology of atrioventricular septal defects. We hypothesised that distortion of the alignment between the atrial and ventricular septums results in imbalanced venous return to the ventricles, with consequent proportional ventricular hypoplasia.MethodsA single observer evaluated 31 patients, with a mean age of 52.09 months, standard deviation of 55, and with a range from 2 to 264 months, with atrioventricular septal defects, of whom 17 were boys. Ventricular imbalance, observed in nine patients, was determined by two-dimensional assessment, and confirmed at surgical inspection in selected cases when a univentricular strategy was undertaken. Offline analysis using multiplanar re-formatting was performed. A line was drawn though the length of the ventricular septum and a second line along the plane of the atrial septum, taking the angle between these two lines as the atrioventricular septal angle. We compared the angle between 22 patients with adequately sized ventricles, and those with ventricular imbalance undergoing univentricular repair.ResultsIn the 22 patients undergoing biventricular repair, the septal angle was 0 in 14 patients; the other eight patients having angles ranging from 1 to 36, with a mean angle of 7.4°, and standard deviation of 11.1°.The mean angle in the nine patients with ventricle imbalance was 28.6°, with a standard deviation of 3.04°, and with a range from 26 to 35°. Of those undergoing univentricular repair, two patients died, with angles of 26 and 30°, respectively.ConclusionsThe atrioventricular septal angle derived via multiplanar formatting gives important information regarding the degree of ventricular hypoplasia and imbalance. When this angle is above 25°, patients are likely to have ventricular imbalance requiring univentricular repair.
A sublimation heat engine
Authors: Wells Gary G. , Ledesma-Aguilar Rodrigo , McHale Glen , Sefiane Khellil 
Published: March 2015

AbstractHeat engines are based on the physical realization of a thermodynamic cycle, most famously the liquid–vapour Rankine cycle used for steam engines. Here we present a sublimation heat engine, which can convert temperature differences into mechanical work via the Leidenfrost effect. Through controlled experiments, quantified by a hydrodynamic model, we show that levitating dry-ice blocks rotate on hot turbine-like surfaces at a rate controlled by the turbine geometry, temperature difference and solid material properties. The rotational motion of the dry-ice loads is converted into electric power by coupling to a magnetic coil system. We extend our concept to liquid loads, generalizing the realization of the new engine to both sublimation and the instantaneous vapourization of liquids. Our results support the feasibility of low-friction in situ energy harvesting from both liquids and ices. Our concept is potentially relevant in challenging situations such as deep drilling, outer space exploration or micro-mechanical manipulation.
RETRACTED ARTICLE: Pre-activation of mesenchymal stem cells with TNF-α, IL-1β and nitric oxide enhances its paracrine effects on radiation-induced intestinal injury
Authors: Chen Hao , Min Xiao-Hui , Wang Qi-Yi , Leung Felix W. , Shi Liu , Zhou Yu , Yu Tao , Wang Chuan-Ming , An Geng , Sha Wei-Hong , Chen Qi-Kui 
Published: March 2015

Abstract
Conditioned medium from mesenchymal stem cells (MSC-CM) may represent a promising alternative to MSCs transplantation, however, the low concentrations of growth factors in non-activated MSC-CM hamper its clinical application. Recent data indicated that the paracrine potential of MSCs could be enhanced by inflammatory factors. Herein, we pre-activated bone-marrow-derived MSCs under radiation-induced inflammatory condition (MSCIEC-6(IR)) and investigated the evidence and mechanism for the differential effects of MSC-CMIEC-6(IR) and non-activated MSC-CM on radiation-induced intestinal injury (RIII). Systemic infusion of MSC-CMIEC-6(IR), but not non-activated MSC-CM, dramatically improved intestinal damage and survival of irradiated rats. Such benefits may involve the modulation of epithelial regeneration and inflammation, as indicated by the regeneration of intestinal epithelial/stem cells, the regulation of the pro-/anti-inflammatory cytokine balance. The mechanism for the superior paracrine efficacy of MSCIEC-6(IR) is related to a higher secretion of regenerative, immunomodulatory and trafficking molecules, including the pivotal factor IGF-1, induced by TNF-α, IL-1β and nitric oxide partially via a heme oxygenase-1 dependent mechanism. Together, our findings suggest that pre-activation of MSCs with TNF-α, IL-1β and nitric oxide enhances its paracine effects on RIII via a heme oxygenase-1 dependent mechanism, which may help us to maximize the paracrine potential of MSCs.
GlycoProfileAssigner: automated structural assignment with error estimation for glycan LC data
Authors: Duffy Fergal J. , Rudd Pauline M. 
Published: February 2015

Abstract
Motivation: Sequencing glycan structures is a difficult problem that requires the use of multiple experimental approaches. One powerful approach to glycan sequencing is the combination of liquid chromatography with sequential exoglycosidase digestions; however, interpreting this can be difficult and time-consuming. To aid this process, we introduce GlycoProfileAssigner, software for automated structural assignment of glycan profile data from liquid chromatography experiments.
Results: GlycoProfileAssigner has been tested on human IgG data, and can retrieve the correct structure in 14 out of 16 peaks tested.
Availability and Implementation: The programme and its source code is available at https://bitbucket.org/fergaljd/glycoprofileassigner
Contact: pauline.rudd@nibrt.ie
Supplementary information: Supplementary data are available at Bioinformatics online.
An experimental demonstration of the critical depth principle
Authors: Diehl Sebastian , Berger Stella A. , Soissons Quentin , Giling Darren P. , Stibor Herwig 
Published: March 2015

AbstractSverdrup's critical depth hypothesis, which has had an almost canonical status in biological oceanography, has recently been challenged as a universal explanation for the formation of oceanic spring blooms, and several alternative hypotheses have been proposed. Arguments pro and contra alternative explanations have so far relied on theoretical considerations and purely observational data. In this paper, we propose that mesocosm experiments with natural plankton communities could make important contributions to the resolution of the issue. We first briefly review the foundations of the critical depth concept and derive an approximate relationship that relates optically scaled critical depth (=“critical optical depth”, i.e. the product of the light attenuation coefficient and the critical depth) to light-dependent phytoplankton production in the mixed surface layer. We describe how this relationship can be used to scale experimental mesocosms such that they reproduce ambient light conditions of natural water columns from the surface down to the critical depth and beyond. We illustrate the power of the approach with a mesocosm study in which we experimentally controlled the onset of the spring bloom of a lake plankton community through the manipulation of optically scaled mixed-layer depth. This experiment may be the first experimental demonstration of the critical depth principle acting on a natural plankton community. Compensation light intensity (=minimum average mixed-layer light intensity required to trigger a bloom of the ambient plankton community) could be constrained to be somewhat above 3.2 moles PAR m−2 d−1, corresponding to a critical optical depth of 10.5. We compare these numbers to estimates from marine systems and end with a discussion of how experiments could be designed to (i) more accurately determine the critical depth in a given system and (ii) resolve among competing hypotheses for vernal bloom onset.