bluuebunny/crossref_metadata_2025_split huggingface dataset:
TFEB-mediated increase in peripheral lysosomes regulates store-operated calcium entry
Authors: Sbano Luigi , Bonora Massimo , Marchi Saverio , Baldassari Federica , Medina Diego L. , Ballabio Andrea , Giorgi Carlotta , Pinton Paolo 
Published: January 2017

AbstractLysosomes are membrane-bound organelles mainly involved in catabolic processes. In addition, lysosomes can expel their contents outside of the cell via lysosomal exocytosis. Some of the key steps involved in these important cellular processes, such as vesicular fusion and trafficking, require calcium (Ca2+) signaling. Recent data show that lysosomal functions are transcriptionally regulated by transcription factor EB (TFEB) through the induction of genes involved in lysosomal biogenesis and exocytosis. Given these observations, we investigated the roles of TFEB and lysosomes in intracellular Ca2+ homeostasis. We studied the effect of transient modulation of TFEB expression in HeLa cells by measuring the cytosolic Ca2+ response after capacitative Ca2+ entry activation and Ca2+ dynamics in the endoplasmic reticulum (ER) and directly in lysosomes. Our observations show that transient TFEB overexpression significantly reduces cytosolic Ca2+ levels under a capacitative influx model and ER re-uptake of calcium, increasing the lysosomal Ca2+ buffering capacity. Moreover, lysosomal destruction or damage abolishes these TFEB-dependent effects in both the cytosol and ER. These results suggest a possible Ca2+ buffering role for lysosomes and shed new light on lysosomal functions during intracellular Ca2+ homeostasis.
Transcript profile analysis reveals important roles of jasmonic acid signalling pathway in the response of sweet potato to salt stress
Authors: Zhang Huan , Zhang Qian , Zhai Hong , Li Yan , Wang Xiangfeng , Liu Qingchang , He Shaozhen 
Published: January 2017

AbstractSweet potato is an important food and bio-energy crop, and investigating the mechanisms underlying salt tolerance will provide information for salt-tolerant breeding of this crop. Here, the root transcriptomes of the salt-sensitive variety Lizixiang and the salt-tolerant line ND98 were compared to identify the genes and pathways involved in salt stress responses. In total, 8,744 and 10,413 differentially expressed genes (DEGs) in Lizixiang and ND98, respectively, were involved in salt responses. A lower DNA methylation level was detected in ND98 than in Lizixiang. In both genotypes, the DEGs, which function in phytohormone synthesis and signalling and ion homeostasis, may underlie the different degrees of salt tolerance. Significant up-regulations of the genes involved in the jasmonic acid (JA) biosynthesis and signalling pathways and ion transport, more accumulation of JA, a higher degree of stomatal closure and a lower level of Na+ were found in ND98 compared to Lizixiang. This is the first report on transcriptome responses to salt tolerance in sweet potato. These results reveal that the JA signalling pathway plays important roles in the response of sweet potato to salt stress. This study provides insights into the mechanisms and genes involved in the salt tolerance of sweet potato.
Synergy of Lewis and Brønsted acids on catalytic hydrothermal decomposition of carbohydrates and corncob acid hydrolysis residues to 5-hydroxymethylfurfural
Authors: Wang Chao , Zhang Liming , Zhou Tian , Chen Jiachuan , Xu Feng 
Published: January 2017

Abstract5-hydroxymethylfurfural (HMF) is an important platform molecule in the synthesis of various chemicals and materials. Herein, we reported a simple and effective dehydration of glucose-based carbohydrates to HMF in a biphasic system containing cyclopentyl methyl ether as the organic phase and AlCl3 with minute amounts of HCl as co-catalysts. The results showed that the mixed catalysts had a positive synergistic catalytic effect on glucose conversion to HMF compared with single AlCl3 or HCl catalyst. For glucose, the highest HMF yield of 54.5% was achieved at 175 °C for 20 min. More importantly, the optimal catalytic system was so efficient that it achieved one of the highest reported yields of HMF (30.5%) directly from corncob acid hydrolysis residues. Thus, the catalytic system can become a promising route for effective utilization of biomass in future biorefineries.
Quantifying the effectiveness of ITS in improving safety of VRUs
Authors: Silla Anne , Rämä Pirkko , Leden Lars , van Noort Martijn , de Kruijff Janiek , Bell Daniel , Morris Andrew , Hancox Graham , Scholliers Johan 
Published: January 2017

This paper presents the results of a safety impact assessment, providing quantitative estimates of the safety impacts of ten intelligent transport systems (ITS) which were designed to improve safety, mobility and comfort of vulnerable road users (VRUs). The evaluation method originally developed to assess safety impacts of ITS for cars was now adapted for assessing safety impacts of ITS for VRUs. The main results of the assessment showed that nine ITS included in the quantitative safety impact assessment affected traffic safety in a positive way by preventing fatalities and injuries. At full penetration the highest effects were obtained for Pedestrian and Cyclists Detection System + Emergency Braking (PCDS+EBR), VRU Beacon System (VBS) and Intersection Safety (INS). The estimates for PCDS+EBR showed the maximum reduction of 7.5% on all road fatalities at full penetration, which comes down to an medium estimate of around 1,900 fatalities saved per year in the EU‐28 when applying the 2012 accident data and 100% penetration rate. The results regarding future scenarios showed the highest effects in number of reduced fatalities per system in the European Union (EU)‐28 in 2030 for PCDS+EBR (−200 fatalities), Blind Spot Detection (BSD) (−22 fatalities), INS (−20 fatalities) and VBS (−11 fatalities).
The realization of information focus in monolingual and bilingual native Spanish
Authors: Leal Tania , Destruel Emilie , Hoot Bradley 
Published: January 2017

Abstract
The strategies used to signal information focus — the non-presupposed part of a sentence — in Spanish are under debate. The literature suggests that focus must appear rightmost; however, empirical evidence shows that speakers also realize focus in-situ. Moreover, there is limited research investigating the effects of language variety or knowledge of another language on focus marking. We address these questions via a paced elicited production task, testing speakers who learned Spanish naturalistically in infancy, including two groups of monolinguals and two groups of Spanish/English bilinguals: (a) Spanish natives who learned English after childhood, and (b) early bilinguals exposed to English in early childhood (heritage speakers). Confirming previous empirical studies, results show that all participant groups choose a similar range of focus-marking strategies, vastly preferring in-situ marking with rightmost marking used rarely. Results challenge both theoretical accounts of Spanish focus realization and expectations of special vulnerability at the syntax-discourse interface for bilinguals.
Current and future management of the young child with early onset wheezing
Authors: Burbank Allison J. , Szefler Stanley J. 
Published: January 2017

Purpose of review
In this review, we discuss current thinking in relation to available guidelines for the care of preschool-aged children with recurrent wheezing, while highlighting the gaps in our knowledge and discussing changes that could occur over the next 5 years.

Recent findings
The Asthma Predictive Index as well as allergen-specific IgE, peripheral eosinophil count and exhaled nitric oxide are perhaps underutilized sources of information that can assist in predicting progression to asthma and response to therapies. Inhaled corticosteroids and leukotriene receptor antagonists decrease impairment and exacerbation frequency in wheezing children but are not disease modifying. Macrolides may be useful during acute wheezing episodes for preventing progression to more severe symptoms. Monoclonal antibodies targeting IgE and TH2 cytokines have been successful in trials of adults and older children with asthma, but trials in younger children are needed.

Summary
Establishing the phenotype and endotype of young wheezing children can be useful for prognostication of future asthma risk as well as for selection of the most appropriate treatment. Primary asthma prevention strategies are needed during the critical developmental window in early life prior to the onset of irrecoverable loss of lung function.
ASSESSMENT OF THE RETINAL STRUCTURE IN CHILDREN WITH INCONTINENTIA PIGMENTI
Authors: Mangalesh Shwetha , Chen Xi , Tran-Viet Du , Viehland Christian , Freedman Sharon F. , Toth Cynthia A. 
Published: January 2017

Purpose:
This report aims at expanding the current knowledge of retinal microanatomy in children with incontinentia pigmenti using hand-held spectral domain optical coherence tomography (SDOCT).

Methods:
We reviewed OCT scans from 7 children (4 weeks–13 years) obtained either in the clinic or during an examination under anesthesia. The scans were analyzed for anatomical changes in the outer and inner retina, by certified graders. Medical records were assessed for systemic findings.

Results:
We observed abnormal retinal findings unilaterally in three children. We found inner and outer retinal thinning temporally in two participants. This thinning was present prior to and persisted after treatment. One child showed a distorted foveal contour and significant retinal thickening secondary to dense epiretinal membrane and vitreomacular traction. All other children had normal retinae.

Conclusion:
Hand-held SDOCT imaging of the retina has brought to light additional retinal structural defects that were not previously reported or visualized via routine clinical ophthalmic examination including retinal photography. Despite a normal foveal structure and visual acuity, we identified inner and outer retinal thinning on SDOCT which may benefit from future functional assessment such as visual field testing.
Perioperative β-Blockers in Patients Undergoing Noncardiac Surgery-Scientific Misconduct and Clinical Guidelines
Authors: Karam Dhauna , Arora Rohit 
Published: January 2017

Background:
β-blocker use in perioperative period of noncardiac surgeries has been a topic of debate since many years. Earlier studies conducted in the 90s showed decreased cardiac adverse events and improved postoperative outcomes with β-blocker use. Based on this, the ACCF and ESC published guidelines strongly supporting β-blocker use. But contemporaneous studies conducted revealed conflicting evidence and have also proven some of the earlier studies to be fraudulent. Although ACCF guidelines have been updated to partially reflect the changes, ESC guidelines continue to support β-blocker use.

Areas of Uncertainty:
In light of the ACCF and ESC guidelines supporting β-blocker use in perioperative period of noncardiac surgeries, our aim was to review the available literature and consolidate evidence in this regard.

Data Sources:
PubMed search was conducted to include relevant studies between 1950 and 2015.

Results:
We reviewed 24 eligible studies and few debates conducted in this regard. Based on our review, our findings were as follows: β-blockers should be continued throughout perioperative period in patients who were on β-blockers before surgery for other indications such as angina, hypertension, and symptomatic arrhythmias. Preoperative β-blockers are indicated in patients undergoing high risk vascular surgery or those having high preoperative Cardiac Risk Index Score. In patients with intermediate-to-low cardiac risk, the proven benefit is not sufficient enough to suggest universal use.

Conclusions:
Based on our review, we conclude that the use of β-blockers in perioperative period of noncardiac surgeries should be determined on an individual basis based on risk–benefit analysis. Guideline organizations should update their recommendations based on new evidence.
Point-of-Care Sexually Transmitted Infection Diagnostics: Proceedings of the STAR Sexually Transmitted Infection—Clinical Trial Group Programmatic Meeting
Authors: Cristillo Anthony D. , Bristow Claire C. , Peeling Rosanna , Van Der Pol Barbara , de Cortina Sasha Herbst , Dimov Ivan K. , Pai Nitika Pant , Jin Shin Dong , Chiu Ricky Y.T. , Klapperich Catherine , Madhivanan Purnima , Morris Sheldon R. , Klausner Jeffrey D. 
Published: January 2017

Abstract
The goal of the point-of-care (POC) sexually transmitted infection (STI) Diagnostics meeting was to review the state-of-the-art research and develop recommendations for the use of POC STI diagnostics. Experts from academia, government, nonprofit, and industry discussed POC diagnostics for STIs such as Chlamydia trachomatis, human papillomavirus, Neisseria gonorrhoeae, Trichomonas vaginalis, and Treponema pallidum. Key objectives included a review of current and emerging technologies, clinical and public health benefits, POC STI diagnostics in developing countries, regulatory considerations, and future areas of development. Key points of the meeting are as follows: (i) although some rapid point-of-care tests are affordable, sensitive, specific, easy to perform, and deliverable to those who need them for select sexually transmitted infections, implementation barriers exist at the device, patient, provider, and health system levels; (ii) further investment in research and development of point-of-care tests for sexually transmitted infections is needed, and new technologies can be used to improve diagnostic testing, test uptake, and treatment; (iii) efficient deployment of self-testing in supervised (ie, pharmacies, clinics, and so on) and/or unsupervised (ie, home, offices, and so on) settings could facilitate more screening and diagnosis that will reduce the burden of sexually transmitted infections; (iv) development of novel diagnostic technologies has outpaced the generation of guidance tools and documents issued by regulatory agencies; and (v) questions regarding quality management are emerging including the mechanism by which poor-performing diagnostics are removed from the market and quality assurance of self-testing is ensured.
Polycomb-Mediated Chromatin Loops Revealed by a Sub-Kilobase Resolution Chromatin Interaction Map
Authors: Eagen Kyle P. , Lieberman Aiden Erez , Kornberg Roger D. 
Published: January 2017

ABSTRACTThe locations of chromatin loops inDrosophilawere determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or “anchors” are associated with CTCF protein in mammals, loop anchors inDrosophilawere found most often in association with the polycomb group (PcG) protein Polycomb (Pc), a subunit of Polycomb Repressive Complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors. Although DNA looping has most commonly been associated with enhancer-promoter communication, our results indicate that loops are also associated with gene repression.
Identification of Mechanisms of Functional Signaling Between Human Hippocampus Regions
Authors: Sanchez-Romero Ruben , Ramsey Joseph D. , Liang Jackson C. , Glymour Clark 
Published: January 2017

AbstractBackgroundStandard BOLD connectivity analyses depend on aggregating the signals of individual voxels within regions of interest (ROIs). In certain cases, this spatial aggregation implies a loss of valuable functional and anatomical information about subsets of voxels that drive the ROI level connectivity.New MethodWe use the FGES algorithm, a data-driven score-based graphical search method, to identify subsets of voxels that are chiefly responsible for exchanging signals between ROIs. We apply the method to high-resolution resting state functional magnetic resonance imaging (rs-fMRI) data from medial temporal lobe regions of interest of a single healthy individual measured repeated times over a year and a half.ResultsThe FGES algorithm recovered subsets of voxels within larger medial temporal lobe ROIs of entorhinal cortex and hippocampus subfields that show spatially consistency across different scanning sessions, and are statistically significant under tests that validate the role of these subsets as main drivers of effective connectivity between hippocampal regions of interest.Comparison with Existing MethodsIn contrast to standard functional connectivity methods, the FGES algorithm is robust against false positive connections produced by transitive closures of adjacencies (correlation methods) and common effect conditioning (Markov random field methods).ConclusionsThe FGES algorithm allows for identification of communication subsets of voxels driving the connectivity between regions of interest, recovering valuable anatomical and functional information that is lost when ROIs are aggregated. The FGES algorithm is specially suited for voxelwise connectivity research, given its short running time and scalability to big data problems.
Predicting Transcriptional Regulatory Activities with Deep Convolutional Networks
Authors: Paggi Joe , Lamb Andrew , Tian Kevin , Hsu Irving , Cedoz Pierre-Louis , Kawthekar Prasad 
Published: January 2017

AbstractMassively parallel reporter assays (MPRAs) are a method to probe the effects of short sequences on transcriptional regulation activity. In a MPRA, short sequences are extracted from suspected regulatory regions, inserted into reporter plasmids, transfected into cell-types of interest, and the transcriptional activity of each reporter is assayed. Recently, Ernst et al. presented MPRA data covering 15750 putative regulatory regions. We trained a multitask convolutional neural network architecture using these sequence expression readouts which predicts as output the expression level outputs across four combinations of cell types and promoters. The model allows for the assigning of importance scores to each base throughin silicomutagenesis, and the resulting importance scores correlated well with regions enriched for conservation and transcription factor binding.
CRISPR-RT: A web service for designing CRISPR-C2c2 crRNA with improved target specificity
Authors: Zhu Houxiang , Richmond Emily , Liang Chun 
Published: January 2017

AbstractCRISPR-Cas systems have been successfully applied in genome editing. Recently, the CRISPR-C2c2 system has been reported as a tool for RNA editing. Here we describe CRISPR-RT (CRISPRRNA-Targeting), the first web service to help biologists design the crRNA with improved target specificity for the CRISPR-C2c2 system. CRISPR-RT allows users to set up a wide range of parameters, making it highly flexible for current and future research in CRISPR-based RNA editing. CRISPR-RT covers major model organisms and can be easily extended to cover other species. CRISPR-RT will empower researchers in RNA editing. It is available athttp://bioinfolab.miamioh.edu/CRISPR-RT.
riboviz: analysis and visualization of ribosome profiling datasets
Authors: Carja Oana , Xing Tongji , Plotkin Joshua B. , Shah Premal 
Published: January 2017

AbstractUsing high-throughput sequencing to monitor translation in vivo, ribosome profiling can provide critical insights into the dynamics and regulation of protein synthesis in a cell. Since its introduction in 2009, this technique has played a key role in driving biological discovery, and yet it requires a rigorous computational toolkit for widespread adoption. We developed a processing pipeline and browser-based visualization,riboviz, that allows convenient exploration and analysis of riboseq datasets. In implementation,ribovizconsists of a comprehensive and flexible backend analysis pipeline that allows the user to analyze their private unpublished dataset, along with a web application for comparison with previously published public datasets.Availability and implementationJavaScript and R source code and extra documentation are freely available fromhttps://github.com/shahpr/RiboViz, while the web-application is live atwww.riboviz.org.
ICTs and the informal economy: mobile and broadband roles
Authors: Garcia-Murillo Martha , Velez-Ospina Jorge Andres 
Published: January 2017

PurposeThe purpose of this paper is to explore whether information and communication technologies (ICTs) can move people from the informal to the formal sector. ICTs being multipurpose technologies can provide people with information about education, employment opportunities and government services that may potentially allow them to migrate to the formal sector.Design/methodology/approachThe model includes variables that researchers have found to contribute to the growth of informality, such as the state of the economy, the impact of excessive taxes, the impact of regulation, the level of poverty and, of course, ICT metrics, specifically access to both cell phones and broadband as the main two mechanisms through which individuals in the informal sector can obtain information. The analysis relies on a multiple indicators and multiple causes statistical model, to evaluate the hard-to-measure informal economy. A panel data set of 170 countries covering a period of five years was used.FindingsIt was found that ICTs empower people, but such empowerment is not always positive for society. So, while mobile phones reduce transaction costs of informal business, this leads to their growth, as they are only a coordination technology. The empowerment that comes from broadband, meaning greater and deeper access to information and resources, can help reduce this sector of the economy and potentially improve these individuals’ lives as well.Research limitations/implicationsMeasurement of the informal sector is a challenge to researchers precisely because it is hidden. This, like other work in this area, relies on estimates from indirect measures of the informal sector. The results are to be interpreted with caution. In addition, given that this research relies on country-level data, any specific policy decision will have to take particular circumstances into consideration to adapt these results to a specific context.Practical implicationsThis study is important because of the more nuanced effect found between narrow and broadband technologies with respect to the informal economy and because of its policy implications. Given the results, governments should consider broadband as an additional tool to help individuals make the transition from the informal to the formal sector.Social implicationsOnce an individual who works in the informal sector begins to realize the advantages of moving to the formal sector, it with the help of ICTs. This awareness could potentially lead to a slow but steady migration away from the informal economy that can improve the economic conditions of the population in these countries.Originality/valueScholars up to this point have been quite enthusiastic about the benefits of ICTs. In this paper, it was found that the effects are not always positive; a mobile does not help people move away from poverty and, in fact, supports the informal sector. It was found that only broadband can help these entrepreneurs move into the formal sector.