bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeting bone morphogenetic protein signalling in midbrain dopaminergic neurons as a therapeutic approach in Parkinson's disease
Authors: O'Keeffe Gerard W. , Hegarty Shane V. , Sullivan Aideen M. 
Published: February 2017

Parkinson's disease (PD) is the second most common neurodegenerative disease, characterized by the degeneration of midbrain dopaminergic (mDA) neurons and their axons, and aggregation of α-synuclein, which leads to motor and late-stage cognitive impairments. As the motor symptoms of PD are caused by the degeneration of a specific population of mDA neurons, PD lends itself to neurotrophic factor therapy. The goal of this therapy is to apply a neurotrophic factor that can slow down, halt or even reverse the progressive degeneration of mDA neurons. While the best known neurotrophic factors are members of the glial cell line-derived neurotrophic factor (GDNF) family, their lack of clinical efficacy to date means that it is important to continue to study other neurotrophic factors. Bone morphogenetic proteins (BMPs) are naturally secreted proteins that play critical roles during nervous system development and in the adult brain. In this review, we provide an overview of the BMP ligands, BMP receptors (BMPRs) and their intracellular signalling effectors, the Smad proteins. We review the available evidence that BMP–Smad signalling pathways play an endogenous role in mDA neuronal survival in vivo, before outlining how exogenous application of BMPs exerts potent effects on mDA neuron survival and axon growth in vitro and in vivo. We discuss the molecular mechanisms that mediate these effects, before highlighting the potential of targeting the downstream effectors of BMP–Smad signalling as a novel neuroprotective approach to slow or stop the degeneration of mDA neurons in PD.
Reference‐invariant permittivity and thickness measurement of lossy liquid materials
Authors: Hasar U.C. , Bute M. 
Published: February 2017

A microwave method has been proposed to retrieve the complex permittivity and thickness of lossy dielectric liquids, which result in at least 10 dB attenuation, using reference‐plane‐invariant reflection scattering (S‐) parameters. The CST Microwave Studio simulation program was first used to validate the method. Then, the permittivity and thickness of lossy distilled water sample poured over a polyethylene sample holder were measured from reference‐invariant reflection‐only S‐parameter measurements at the X‐band. The method was compared with other methods in the literature to analyse its accuracy.
Low power‐consumption mid‐infrared distributed feedback quantum cascade laser for gas‐sensing application
Authors: Hashimoto J. , Yoshinaga H. , Mori H. , Tsuji Y. , Murata M. , Kato T. , Ekawa M. , Iguchi Y. , Katsuyama T. 
Published: February 2017

A low power‐consumption distributed feedback quantum cascade laser (DFB‐QCL) is developed for gas‐sensing in 7 μm wavelength region. The threshold power‐consumption was as low as 0.93 W with the sufficient output power of 20 mW at 20°C under continuous‐wave condition. In addition, it maintained a single‐mode operation between −40 and 50°C without a mode‐hopping, leading to a total wavelength shift of 66 nm. This DFB‐QCL would be suitable for gas‐sensing application.
Safety and Efficacy of a Novel “Hybrid Closure” Technique in Large-Bore Arteriotomies
Authors: Amponsah Michael , Tayal Rajiv , Khakwani Zain , Sinclair Michael , Wasty Najam 
Published: February 2017

AbstractThe “preclose” technique employing two Perclose (P) devices is well established for large-bore artery (LBA) hemostasis. Occasionally, only one Perclose deploys successfully during the initial preclose because of arterial calcification necessitating the use of the crossover balloon technique to achieve hemostasis at the LBA. We sought to determine if the combined use of one Perclose and either one Angioseal or one Mynx vascular closure device (VCD) is a safe alternative closure technique large-bore arteriotomy closure.In total, 40 patients underwent high-risk percutaneous coronary intervention (HRPCI) with Impella support, of whom 38 had common femoral artery (CFA) arteriotomies and 2 underwent percutaneous axillary arteriotomy (AA). Prior to Impella insertion, one Perclose device was predeployed. At the end of HRPCI, Impella was removed and a 0.035″ wire was inserted through the Impella sheath. This sheath was then withdrawn over the wire, and partially deployed Perclose was fully deployed. A 6-Fr sheath was advanced over a 0.035″ wire into the CFA or AA, achieving hemostasis and reducing the LBA to a 6-Fr size. The 6-Fr arteriotomy was closed with a 6-Fr Mynx or Angioseal VCD. Patients were followed at day 1 and day 30.Hybrid closure was successful in 38 of 40 cases. In one case of Mynx balloon rupture, hemostasis was achieved with heparin reversal and manual compression. In the case of Perclose failure, crossover balloon tamponade at arteriotomy site and external manual compression achieved hemostasis. Patients were free of complications at day 1 and day 30.Hybrid closure with one Perclose and either one Mynx or one Angioseal VCD is safe and effective for LBA closure.
Complications and Cost Analysis of Intraoperative Arterial Complications in Head and Neck Free Flap Reconstruction
Authors: Chu Michael , Nelson Jonas , Basta Marten , Gerety Patrick , Kanchwala Suhail , Wu Liza , Chang Catherine 
Published: February 2017

Background Microvascular anastomotic patency is fundamental to head and neck free flap reconstructive success. The aims of this study were to identify factors associated with intraoperative arterial anastomotic issues and analyze the impact on subsequent complications and cost in head and neck reconstruction.
Methods A retrospective review was performed on all head and neck free flap reconstructions from 2005 to 2013. Patients with intraoperative, arterial anastomotic difficulties were compared with patients without. Postoperative outcomes and costs were analyzed to determine factors associated with microvascular arterial complications. A regression analysis was performed to control for confounders.
Results Total 438 head and neck free flaps were performed, with 24 (5.5%) having intraoperative arterial complications. Patient groups and flap survival between the two groups were similar. Free flaps with arterial issues had higher rates of unplanned reoperations (p < 0.001), emergent take-backs (p = 0.034), and major surgical (p = 0.002) and respiratory (p = 0.036) complications. The overall cost of reconstruction was nearly double in patients with arterial issues (p = 0.001). Regression analysis revealed that African American race (OR = 5.5, p < 0.009), use of vasopressors (OR = 6.0, p = 0.024), end-to-side venous anastomosis (OR = 4.0, p = 0.009), and use of internal fixation hardware (OR =3.5, p = 0.013) were significantly associated with arterial complications.
Conclusion Intraoperative arterial complications may impact complications and overall cost of free flap head and neck reconstruction. Although some factors are nonmodifiable or unavoidable, microsurgeons should nonetheless be aware of the risk association. We recommend optimizing preoperative comorbidities and avoiding use of vasopressors in head and neck free flap cases to the extent possible.
Shear Stress Induces Change in Extracellular Signal-Regulated Kinase 5 Levels with Sustained Activation under Disturbed and Continuous Laminar Flow
Authors: Shalaby S. , Chitragari G. , Sumpio B. , Sumpio B. 
Published: February 2017

AbstractExtracellular signal-regulated kinase 5 (ERK5) has been reported to regulate endothelial integrity and protect from vascular dysfunction under laminar flow. Previously reported research indicates that under laminar flow ERK5 is activated with production of atheroprotective molecules. However, the characterization of ERK5 activation and levels under different flow patterns has not been investigated.Confluent HUVECs were serum-starved then seeded on glass slides. HUVECs incubated in 1% FBS were exposed to continuous laminar flow (CLF), to-and-fro flow (TFF), or pulsatile forward flow (PFF) in a parallel plate flow chamber. At the end of experimentation, cell lysates were immunoblotted with antibodies to phospho-ERK5 and total ERK5. ERK5 activation was assessed by the levels of phosphorylated ERK5. The densitometric mean ± SEM is calculated and analyzed by ANOVA. p < 0.05 is considered significant.Levels of ERK5 decreased with all flow conditions with the largest decrease in TFF flow condition. TFF and CLF exhibited sustained ERK5 phosphorylation in HUVECs stimulated for up to 4 hours. PFF had transient phosphorylation of ERK5 at 2 hours, which then became undetectable at 4 hours of exposure to flow. Also, TFF and CLF both showed decreased levels at 4 hours, suggesting a decrease in activation for these flow conditions.Exposure of HUVEC to different types of shear stress results in varying patterns of activation of ERK5. Activation of ERK5 with TFF suggests a role in the pathogenesis of atherosclerosis and vascular remodeling under disturbed flow conditions.
Emergence of communities and diversity in social networks
Authors: Han Xiao , Cao Shinan , Shen Zhesi , Zhang Boyu , Wang Wen-Xu , Cressman Ross , Stanley H. Eugene 
Published: February 2017

Significance
Understanding how communities emerge is a fundamental problem in social and economic systems. Here, we experimentally explore the emergence of communities in social networks, using the ultimatum game as a paradigm for capturing individual interactions. We find the emergence of diverse communities in static networks is the result of the local interaction between responders with inherent heterogeneity and rational proposers in which the former act as community leaders. In contrast, communities do not arise in populations with random interactions, suggesting that a static structure stabilizes local communities and social diversity. Our experimental findings deepen our understanding of self-organized communities and of the establishment of social norms associated with game dynamics in social networks.
Localization of the gate and selectivity filter of the full-length P2X7 receptor
Authors: Pippel Anja , Stolz Michaela , Woltersdorf Ronja , Kless Achim , Schmalzing Günther , Markwardt Fritz 
Published: February 2017

Significance
The P2X7 receptor (P2X7R) was the first ion channel that was suggested to transform from cation selective into nonselective by undergoing a dilatation in the diameter of its transmembrane pathway following sustained activation. This change requires that the selectivity filter behave as a dynamic structure. Here, we used a single-channel analysis of cysteine substitution mutants to find that the gate and selectivity filter of P2X7R are colocalized and primarily determined by one single residue, S342. We found the agonist-opened selectivity filter to be completely stable over time, indicating that use-dependent dilatation of the channel diameter does not occur. Instead, P2X7R exhibits striking susceptibility to remain in the open state for longer when the channel pore contains slowly or nonpermeating cations.
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius
Authors: Liu Kai , Xu Dongpo , Li Jia , Bian Chao , Duan Jinrong , Zhou Yanfeng , Zhang Minying , You Xinxin , You Yang , Chen Jieming , Yu Hui , Xu Gangchun , Fang Di-an , Qiang Jun , Jiang Shulun , He Jie , Xu Junmin , Shi Qiong , Zhang Zhiyong , Xu Pao 
Published: February 2017

Abstract

Background
Chinese clearhead icefish, Protosalanx hyalocranius, is a representative icefish species with economic importance and special appearance. Due to its great economic value in China, the fish was introduced into Lake Dianchi and several other lakes from the Lake Taihu half a century ago. Similar to theSinocyclocheilus cavefish, the clearhead icefish has certain cavefish-like traits, such as transparent body and nearly scaleless skin. Here, we provide the whole genome sequence of this surface-dwelling fish and generated a draft genome assembly, aiming at exploring molecular mechanisms for the biological interests.

Findings
A total of 252.1 Gb of raw reads were sequenced. Subsequently, a novel draft genome assembly was generated, with the scaffold N50 reaching 1.163 Mb. The genome completeness was estimated to be 98.39 % by using the CEGMA evaluation. Finally, we annotated 19 884 protein-coding genes and observed that repeat sequences account for 24.43 % of the genome assembly.

Conclusion
We report the first draft genome of the Chinese clearhead icefish. The genome assembly will provide a solid foundation for further molecular breeding and germplasm resource protection in Chinese clearhead icefish, as well as other icefishes. It is also a valuable genetic resource for revealing the molecular mechanisms for the cavefish-like characters.
GUIdock-VNC: using a graphical desktop sharing system to provide a browser-based interface for containerized software
Authors: Mittal Varun , Hung Ling-Hong , Keswani Jayant , Kristiyanto Daniel , Lee Sung Bong , Yeung Ka Yee 
Published: February 2017

Abstract

Background
Software container technology such as Docker can be used to package and distribute bioinformatics workflows consisting of multiple software implementations and dependencies. However, Docker is a command line–based tool, and many bioinformatics pipelines consist of components that require a graphical user interface.

Results
We present a container tool called GUIdock-VNC that uses a graphical desktop sharing system to provide a browser-based interface for containerized software. GUIdock-VNC uses the Virtual Network Computing protocol to render the graphics within most commonly used browsers. We also present a minimal image builder that can add our proposed graphical desktop sharing system to any Docker packages, with the end result that any Docker packages can be run using a graphical desktop within a browser. In addition, GUIdock-VNC uses the Oauth2 authentication protocols when deployed on the cloud.

Conclusions
As a proof-of-concept, we demonstrated the utility of GUIdock-noVNC in gene network inference. We benchmarked our container implementation on various operating systems and showed that our solution creates minimal overhead.
Phenobook: an open source software for phenotypic data collection
Authors: Crescente Juan M. , Guidobaldi Fabio , Demichelis Melina , Formica Maria B. , Helguera Marcelo , Vanzetti Leonardo S. 
Published: February 2017

Abstract

Background
Research projects often involve observation, registration, and data processing starting from information obtained in field experiments. In many cases, these tasks are carried out by several persons in different places, times, and ways, adding different levels of complexity and error in data collecting. Furthermore, data processing can be time consuming, and input errors may produce unwanted results.

Results
We have developed a novel, open source software called Phenobook, an easy, flexible, and intuitive tool to organize, collect, and save experimental data for further analyses. Phenobook was conceived to collect phenotypic observations in a user-friendly, cost-effective way. It consists of a web-based software for experiment design, data input and visualization, and exportation, combined with a mobile application for remote data collecting. We provide in this article a detailed description of the developed tool.

Conclusion
Phenobook is a software tool that can be easily implemented in collaborative research and development projects involving data collecting and forward analyses. Adopting Phenobook is expected to improve the involved processes by minimizing input errors, resulting in higher quality and reliability of the research outcomes.
The use of Oxford Nanopore native barcoding for complete genome assembly
Authors: Bayliss Sion C , Hunt Vicky L , Yokoyama Maho , Thorpe Harry A , Feil Edward J 
Published: February 2017

Abstract

Background
The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short read data. The strain we used, MHO_001, represents the important community-acquired methicillin-resistant Staphylococcus aureus lineage USA300.

Findings
Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long read data represented only ~5% to 10% of an average MinION(TM) run (~7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss, and gain of mobile genetic elements.

Conclusion
Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short read data to fully complete a bacterial genome. The ability to complete multiple genomes, for which short read data is already available, from a single MinION(TM) run is set to impact our understanding of accessory genome content, plasmid diversity, and genome rearrangements.
Developmental coordination disorder in children – experimental work and data annotation
Authors: Vařeka Lukáš , Brůha Petr , Mouček Roman , Mautner Pavel , Čepička Ladislav , Holečková Irena 
Published: February 2017

Abstract

Background
Developmental coordination disorder (DCD) is described as a motor skill disorder characterized by a marked impairment in the development of motor coordination abilities that significantly interferes with performance of daily activities and/or academic achievement. Since some electrophysiological studies suggest differences between children with/without motor development problems, we prepared an experimental protocol and performed electrophysiological experiments with the aim of making a step toward a possible diagnosis of this disorder using the event-related potentials (ERP) technique. The second aim is to properly annotate the obtained raw data with relevant metadata and promote their long-term sustainability.

Results
The data from 32 school children (16 with possible DCD and 16 in the control group) were collected. Each dataset contains raw electroencephalography (EEG) data in the BrainVision format and provides sufficient metadata (such as age, gender, results of the motor test, and hearing thresholds) to allow other researchers to perform analysis. For each experiment, the percentage of ERP trials damaged by blinking artifacts was estimated. Furthermore, ERP trials were averaged across different participants and conditions, and the resulting plots are included in the manuscript. This should help researchers to estimate the usability of individual datasets for analysis.

Conclusions
The aim of the whole project is to find out if it is possible to make any conclusions about DCD from EEG data obtained. For the purpose of further analysis, the data were collected and annotated respecting the current outcomes of the International Neuroinformatics Coordinating Facility Program on Standards for Data Sharing, the Task Force on Electrophysiology, and the group developing the Ontology for Experimental Neurophysiology. The data with metadata are stored in the EEG/ERP Portal.
NanoSim: nanopore sequence read simulator based on statistical characterization
Authors: Yang Chen , Chu Justin , Warren René L , Birol Inanç 
Published: February 2017

Abstract

Background
The MinION sequencing instrument from Oxford Nanopore Technologies (ONT) produces long read lengths from single-molecule sequencing – valuable features for detailed genome characterization. To realize the potential of this platform, a number of groups are developing bioinformatics tools tuned for the unique characteristics of its data. We note that these development efforts would benefit from a simulator software, the output of which could be used to benchmark analysis tools.

Results
Here, we introduce NanoSim, a fast and scalable read simulator that captures the technology-specific features of ONT data and allows for adjustments upon improvement of nanopore sequencing technology. The first step of NanoSim is read characterization, which provides a comprehensive alignment-based analysis and generates a set of read profiles serving as the input to the next step, the simulation stage. The simulation stage uses the model built in the previous step to produce in silico reads for a given reference genome. NanoSim is written in Python and R. The source files and manual are available at the Genome Sciences Centre website: http://www.bcgsc.ca/platform/bioinfo/software/nanosim.

Conclusion
In this work, we model the base-calling errors of ONT reads to inform the simulation of sequences with similar characteristics. We showcase the performance of NanoSim on publicly available datasets generated using the R7 and R7.3 chemistries and different sequencing kits and compare the resulting synthetic reads to those of other long-sequence simulators and experimental ONT reads. We expect NanoSim to have an enabling role in the field and benefit the development of scalable next-generation sequencing technologies for the long nanopore reads, including genome assembly, mutation detection, and even metagenomic analysis software.
Paths to Respectability: Consumption and Stigma Management in the Contemporary Black Middle Class
Authors: Crockett David 
Published: February 2017

AbstractWhen confronted with racial stigma, how do people manage it? What specific arrangements of objects and tactics do they mobilize to make everyday life more tolerable (if not more equal)? The politics of respectability (respectability) is one such arrangement. Respectability makes life more tolerable by offering a counternarrative that disavows stigma through status-oriented displays. This strategy of action emerged alongside mass consumer culture in the late 19th century, but what relevance does it have to those who are stigmatized in contemporary consumer culture? Based on ethnographic interviews and observations with middle-class African Americans, respectability remains an important strategy that has undergone profound changes since its origins while still operating in similar ways. In the late 20th century it fractured into two related but distinct counternarratives: (1) “discern and avoid,” which seeks distance from whatever is stigmatized, and (2) “destigmatize,” using black culture as a source of high status. Perceptions of how well either counternarrative manages stigma depend on how ideology, strategy, and consumption are connected via specific sociohistorical features of place and individual power resources. I illustrate those connections through four cases that show perceived success and perceived failure for each counternarrative.