bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Family-Based Education on the Quality of Life of Persons With Type 2 Diabetes: A Randomized Clinical Trial
Authors: Ebrahimi Hossein , Ashrafi Zahra , Rudsari Daryadokht Masroor , Parsayekta Zohreh , Haghani Hamid 
Published: August 2017

ABSTRACT

Background:
Diabetes, a disease with increasing prevalence, requires comprehensive support from family members to ensure that sufferers are able to perform daily activities. The chronic nature of diabetes and its potential side effects impose high financial costs on patients and families, reduce their quality of life (QOL), and change the lifestyle of both patients and their families.

Purpose:
The aim of this study was to investigate the effects of a family-based training program on QOL in persons with Type 2 diabetes.

Methods:
A randomized clinical trial was used to assess the effects of an educational program on QOL both before and after 12 weeks of training for the experimental group (40 patients and families) and of standard care for the control group (40 patients) at an endocrinology clinic in a hospital in Iran. A demographic and social questionnaire and the QOL questionnaire for patients with Type 2 diabetes were used for data collection. The study groups were selected using block randomization sampling, and results were analyzed using descriptive and inferential statistics.

Results:
Both the experimental and control groups were homogeneousin terms of demographic characteristics and QOL before the intervention. The results of the mean score of patient QOL after the 12-week training program showed a significant difference between the scores for the two groups of patients in the physical, mental, social, economic, disease, and treatment dimensions. Moreover, the total score and QOL of the experimental group improved significantly after the patients’ families had attended the training program.

Conclusions/Implications for Practice:
Educating the families of patients was shown in this study to improve the QOL of the patient. The design of educational programs for nursing students must emphasize the role of the family in the care of chronic patients.
Antiviral Therapy in Patients With Chronic Hepatitis C-related Hepatocellular Carcinoma Responding to Palliative Treatment
Authors: Yu Jung-Hwan , Kim Ja Kyung , Lee Kwan Sik , Lee Jung Il 
Published: August 2017

Background/Aim:
Advances in hepatitis C virus (HCV) treatment offer high sustained virologic response rates with minimal side-effects. However, benefits of eradicating HCV in hepatocellular carcinoma (HCC) patients whose life expectancies are hard to be determined after palliative therapy still needs to be assessed. This study sought to evaluate prognostic factors for survival in HCV-related HCC patients that responded to the palliative HCC treatment to speculate whether treating HCV would be beneficial in these patients.

Materials and Methods:
In this retrospective cohort study, the medical records of 97 patients that showed complete or partial response to the initial HCC treatment were included.

Results:
Receiving HCV treatment [hazard ratio (HR), 0.244; 95% confidence interval (CI), 0.075-0.788; P=0.018] increased the survival, whereas partial response to the initial HCC treatment (HR, 1.795; 95% CI, 1.071-3.008; P=0.026) and increased Child-Turcotte-Pugh score (HR, 2.017; 95% CI, 1.196-3.403; P=0.009) reduced the survival. From 97 patients, 16 patients were eventually treated for HCV. The mean time from the last HCC therapy to HCV treatment was 16.9±13.9 months. The median time of follow-up after HCV treatment was 10.0 months (range, 3 to 47 mo). Among the HCV-treated patients 3 patients had HCC recurred. The time to progression in HCV-treated patients were significantly longer than those untreated for HCV (P=0.032).

Conclusions:
Although treating HCV in HCC patient that undergo noncurative HCC treatment is still debatable, this study results carefully suggest that HCV-related HCC patients that responded to the initial HCC palliative treatment might benefit from HCV treatment.
Serial quantification of brain oxygenation in acute stroke using streamlined-qBOLD
Authors: Stone Alan J , Harston George WJ , Carone Davide , Okell Thomas W , Kennedy James , Blockley Nicholas P 
Published: August 2017

AbstractIt has been proposed that metabolic markers of baseline brain oxygenation have a role to play in the early identification of the ischemic penumbra. Streamlined-qBOLD is a magnetic resonance imaging technique that does not require exogenous contrast. It is a refinement of the quantitative BOLD methodology that provides a simplified approach to mapping and quantifying baseline brain oxygenation related parameters (reversible transverse relaxation rate (R2′), deoxygenated blood volume (DBV) and deoxyhaemoglobin concentration ([dHb])) in a clinically relevant manner. Streamlined-qBOLD was applied to an exploratory cohort of acute stroke patients in a serial imaging study. Detailed voxel-level analysis was used to quantify the metabolic profile of ischaemic tissue on presentation and investigate these metrics in relation to tissue outcome. Individual patient examples illustrate the appropriate interpretation of R2′, DBV and [dHb] in acute stroke and demonstrate the ability of this method to deliver regional information related to oxygen metabolism in the ischaemic tissue. Regional analysis confirms that R2′, DBV and [dHb] vary between regions of ischaemia with different tissue outcomes.
Imaging specific cellular glycan structures using glycosyltransferases via click chemistry
Authors: Wu Zhengliang L , Person Anthony , Anderson Matthew , Burroughs Barbara , Tatge Timothy , Zou Yonglong , Wang Liangchun , Geders Todd , Sackstein Robert 
Published: August 2017

AbstractHeparan sulfate (HS) is a polysaccharide fundamentally important for biologically activities. T/Tn antigens are universal carbohydrate cancer markers. Here, we report the specific imaging of these carbohydrates using a mesenchymal stem cell line and human umbilical vein endothelial cells (HUVEC). The staining specificities were demonstrated by comparing imaging of different glycans and validated by either removal of target glycans, which results in loss of signal, or installation of target glycans, which results in gain of signal. As controls, representative key glycans including O-GlcNAc, lactosaminyl glycans and hyaluronan were also imaged. HS staining revealed novel architectural features of the extracellular matrix (ECM) of HUVEC cells. Results from T/Tn antigen staining suggest that O-GalNAcylation is a rate-limiting step for O-glycan synthesis. Overall, these highly specific approaches for HS and T/Tn antigen imaging should greatly facilitate the detection and functional characterization of these biologically important glycans.
Neurons in primate entorhinal cortex represent gaze position in multiple spatial reference frames
Authors: Meister Miriam L. R. , Buffalo Elizabeth A. 
Published: August 2017

AbstractPrimates predominantly rely on vision to gather information from the environment, and neurons representing visual space and gaze position are found in many brain areas. Within the medial temporal lobe, a brain region critical for memory, neurons in the entorhinal cortex of macaque monkeys exhibit spatial selectivity for gaze position. Specifically, the firing rate of single neurons reflects fixation location within a visual image (Killian et al., 2012). In the rodents, entorhinal cells such as grid cells, border cells, and head direction cells show spatial representations aligned to visual environmental features instead of the body (Hafting et al., 2005, Solstad et al. 2008, Sargolini et al., 2006, Diehl et al., 2017). However, it is not known whether similar allocentric representations exist in primate entorhinal cortex. Here, we recorded neural activity in the entorhinal cortex in two male rhesus monkeys during a naturalistic, free-viewing task. Our data reveal that a majority of entorhinal neurons represent gaze position, and that simultaneously recorded neurons exhibit distinct spatial reference frames, with some neurons aligning to the visual image and others aligning to the monkey’s head position. Our results also show that entorhinal neural activity can be used to predict gaze position with a high degree of accuracy. These findings demonstrate that visuospatial representation is a fundamental property of entorhinal neurons in primates, and suggest that entorhinal cortex may support relational memory and motor planning by coding attentional locus in distinct, behaviorally relevant frames of reference.Significance StatementThe entorhinal cortex, a brain area important for memory, shows striking spatial activity in rodents through grid cells, border cells, head direction cells, and nongrid spatial cells. The majority of entorhinal neurons signal the location of a rodent relative to visual environmental cues, representing the location of the animal relative to space in the world instead of the body. Recently, our laboratory found that entorhinal neurons can signal location of gaze while a monkey visually explores images. Here, we report that spatial entorhinal neurons are widespread in the monkey, and these neurons are capable of showing a world-based spatial reference frame locked to the bounds of explored images. These results help connect the extensive findings in rodents to the primate.
Parallel Factor ChIP Provides Essential Internal Control for Quantitative Differential ChIP-Seq
Authors: Guertin Michael J , Cullen Amy E , Markowetz Florian , Holding Andrew N 
Published: August 2017

ABSTRACTA key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes in occupancy. Analysis-based normalisation methods were developed for transcriptomic data and these are dependent on the underlying assumption that total transcription does not change between conditions. For genome-wide changes in transcription factor binding, these assumptions do not hold true. The challenges in normalisation are confounded by experimental variability during sample preparation, processing, and recovery.We present a novel normalisation strategy utilising an internal standard of unchanged peaks for reference. Our method can be readily applied to monitor genome-wide changes by ChIP-seq that are otherwise lost or misrepresented through analytical normalisation. We compare our approach to normalisation by total read depth and two alternative methods that utilise external experimental controls to study transcription factor binding. We successfully resolve the key challenges in quantitative ChIP-seq analysis and demonstrate its application by monitoring the loss of Estrogen Receptor-alpha (ER) binding upon fulvestrant treatment, ER binding in response to estrodiol, ER mediated change in H4K12 acetylation and profiling ER binding in Patient-Derived Xenographs. This is supported by an adaptable pipeline to normalise and quantify differential transcription factor binding genome-wide and generate metrics for differential binding at individual sites.Abstract FigureGRAPHICAL ABSTRACT
Generation, selection and transcriptomic profiling of human neuromesodermal and spinal cord progenitors in vitro
Authors: Verrier Laure , Davidson Lindsay , Gierliński Marek , Storey Kate G. 
Published: August 2017

AbstractRobust protocols for directed differentiation of human pluripotent cells are needed to establish the extent to which mechanisms operating in model organisms are relevant to our own development. Recent work in vertebrate embryos has identified neuromesodermal progenitors as a bipotent cell population that contributes to paraxial mesoderm and spinal cord. However, precise protocols forin vitrodifferentiation of human neuromesodermal progenitors are lacking. Informed by signalling activities during spinal cord generation in amniote embryos, we show here that transient dual-SMAD inhibition, together with retinoic acid (dSMADi-RA), provides rapid and reproducible induction of human spinal cord progenitors from neuromesodermal progenitors. We use CRISPR-Cas9 to engineer a GFP-reporter for a neuromesodermal progenitor-associated transcription factorNkx1.2in human embryonic stem cells, to facilitate selection of this cell population. RNA-sequencing (RNA-Seq) was then used to identify human and conserved neuromesodermal progenitor transcriptional signatures, validate this differentiation protocol and implicate new pathways and processes in human neural differentiation. This optimised protocol, novel reporter line and transcriptomic data are useful resources with which to dissect cellular and molecular mechanisms regulating the generation of human spinal cord, allow scale-up of distinct cell populations for global analyses, including proteomic, biochemical and chromatin interrogation and open up translational opportunities.
HPeV-3 predominated amongParechovirus Apositive infants in the summer of 2013-2014 in Queensland, Australia
Authors: McNeale Donna , Wang Claire Y.T. , Arden Katherine E. , Mackay Ian M. 
Published: August 2017

AbstractParechoviruses (HPeV) are not new viruses and are found in the respiratory tract and central nervous system of children and adults in conjunction with a range of acute illnesses. During an Australian outbreak of HPeV in the summer of 2013, we performed PCR-based screening and genotyping to determine whether ill Queensland infants were infected by HPeV. HPeVs were detected among 25/62 samples, identified as HPeV-3 from 23 that could be genotyped. These variants closely matched those occurring during and after the 2013 HPeV season. The inclusion of HPeV screening should be considered among acutely ill young infants during summer.HighlightsHPeV-3 was the most commonParechovirus Agenotype in Queensland summer of 2013/14HPeV testing should be routine among testing of infants with acute CNS - related symptomsHPeV is a seasonal virusSubgenomic phylogenetic analysis of HPeVs can be confounded by the presence of recombination
Resolution of Reprogramming Transition States by Single Cell RNA-Sequencing
Authors: Guo Lin , Wang Xiaoshan , Gao Mingwei , Lin Lihui , Kuang Junqi , Mai Yuanbang , Wu Fang , Liu He , Yang Jiaqi , Chu Shilong , Song Hong , Liu Yujian , Liu Jiadong , Wang Jinyong , Pan Guangjin , Hutchins Andrew P. , Liu Jing , Chen Jiekai , Pei Duanqing 
Published: August 2017

AbstractThe Yamanaka factors convert mouse embryonic fibroblasts (MEFs) into induced pluripotent stem cells (iPSCs) through a highly heterogeneous process. Here we profile single cells undergoing an optimized 7-day reprogramming process and show that cells start reprogramming relatively in sync, but diverge into two branches around day 2. The first branch of cells expressingCd34/Fxyd5/Pscabecome nonpluripotent. The second one contains cells that are firstOct4+, thenDppa5a+ and pluripotent. We show that IFN-γ blocks this late transition. Our results reveal the heterogeneous nature of somatic cell reprogramming, identifyDppa5aas a marker for pluripotent and innate immunity as a potential barrier for reprogramming.One Sentence SummarySingle cell RNA sequencing reveals a continuum of cell fates from somatic to pluripotent andDppa5aas a marker for chimera-competent iPSCs.
Synergy of Quorum Quenching Enzyme and Quorum Sensing Inhibitor in InhibitingP.aeruginosaQuorum Sensing
Authors: Fong July , Zhang Chaodong , Yang Renliang , Boo Zhao Zhi , Tan Soon Keat , Nielsen Thomas E. , Givskov Michael , Wu Bin , Su Haibin , Yang Liang 
Published: August 2017

ABSTRACTThe threat of antibiotic resistant bacteria has called for alternative antimicrobial strategies that would mitigate the increase of classical resistance mechanism. Many bacteria employ quorum sensing (QS) to govern the production of virulence genes and formation of drug-resistance biofilms. Blocking QS mechanisms have proven to be a functional alternative to conventional antibiotic control of infections. The concepts of quorum sensing inhibitors (QSI) and quorum quenching enzymes (QQ) have been investigated separately. In this study however, we simulated the synergistic effect of QQ and QSI in blocking bacterial QS. This effect was validated by experiments using AiiA and G1 as QQ and QSI respectively onPseudomonas aeruginosaLasR/I and RhlR/I QS circuits. The combination of a QQ and a QSI almost completely blocked theP. aeruginosaQSlasandrhlsystem. Our findings provided a potential application strategy for bacterial QS disruption.
Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome
Authors: Piližota Ivana , Redestig Henning , Dessimoz Christophe 
Published: August 2017

AbstractAs the time and cost of sequencing decrease, the number of available genomes and transcriptomes rapidly increases. Yet the quality of the assemblies and the gene annotations varies considerably and often remains poor, affecting downstream analyses. This is particularly true when fragments of the same gene are annotated as distinct genes and consequently wrongly appear as paralogs. In this study, we introduce two novel phylogenetic tests to infer non-overlapping or partially overlapping genes that are in fact parts of the same gene. One approach collapses branches with low bootstrap support and the other computes a likelihood ratio test. We extensively validated these methods by 1) introducing and recovering fragmentation on the bread wheat,Triticum aestivumcv. Chinese Spring, chromosome 3B; 2) by applying the methods to the low-quality 3B assembly and validating predictions against the high-quality 3B assembly; and 3) by comparing the performance of the proposed methods to the performance of existing methods, namely Ensembl Compara and ESPRIT. Application of this combination to a draft shotgun assembly of the entire bread wheat genome revealed 1221 pairs of genes which are highly likely to be fragments of the same gene. Our approach demonstrates the power of fine-grained evolutionary inferences across multiple species to improving genome assemblies and annotations. An open source software tool is available athttps://github.com/DessimozLab/esprit2.
Drosophilaneural stem cells are polarized by their daughter cells
Authors: Loyer Nicolas , Januschke Jens 
Published: August 2017

AbstractControlling the orientation of cell division is important in the context of cell fate choices and tissue morphogenesis. However, the mechanisms providing the required positional information remain incompletely understood. Here we use stem cells of theDrosophilalarval brain that stably maintain their axis of polarity and division between cell cycles to identify cues that orient cell division. Using live cell imaging of cultured brains, laser ablation and genetics we reveal that these cells use the position of their last-born daughter cell as a polarizing cue. Remarkably, this daughter cell derived signal received at one pole of the stem cell has an effect on the opposite pole influencing where apical will be in the next mitosis, thereby directing the orientation of division. Therefore, in addition to known intrinsic cues, stem cells in the developing fly brain are polarized by an extrinsic signal that acts upstream of apico-basal polarity establishment.
A novel VPS33A interaction motif is a master-switch controlling the inhibition and promotion of mammalian Stx17 interactions with SNAP29 and VAMP7 during autophagy
Authors: Saleeb Rebecca S. , Kavanagh Deirdre M. , Dun Alison R. , Dalgarno Paul A , Duncan Rory R 
Published: August 2017

AbstractAutophagosome clearance is accomplished by SNARE-mediated fusion of the vesicle membrane with the endolysosome. This must be carefully regulated to maintain the organisation of the membrane system and prevent mistargeted degradation. Here, we dissect the autophagosomal SNARE complex pathway and its regulation using FLIM-FRET as a readout of protein interactionin situ. We show that within the spatio-temporal framework of the cell, autophagosomal Stx17 preferentially heterodimerises with SNAP29, subsequently associating with VAMP7, not VAMP8 as currently believed. Additionally, we identify for the first time multi-modal regulation of SNARE assembly by the SM protein VPS33A, finding parallels and differences with other syntaxin-SM interactions and suggesting a unifying model of SM regulation. Contrary to current theory, the Stx17 N-peptide interacts in a positionally conserved, but mechanistically divergent manner with VPS33A, providing a late ‘go, no-go’ step for autophagic fusionviaa phosphoserine master-switch.
Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival
Authors: Hornshøj Henrik , Nielsen Morten Muhlig , Sinnott-Armstrong Nicholas A. , Świtnicki Michał P. , Juul Malene , Madsen Tobias , Sallari Richard , Kellis Manolis , Ørntoft Torben , Hobolth Asger , Pedersen Jakob Skou 
Published: August 2017

AbstractCancer develops by accumulation of somatic driver mutations, which impact cellular function. Non-coding mutations in non-coding regulatory regions can now be studied genome-wide and further characterized by correlation with gene expression and clinical outcome to identify driver candidates. Using a new two-stage procedure, called ncDriver, we first screened 507 ICGC whole-genomes from ten cancer types for non-coding elements, in which mutations are both recurrent and have elevated conservation or cancer specificity. This identified 160 significant non-coding elements, including theTERTpromoter, a well-known non-coding driver element, as well as elements associated with known cancer genes and regulatory genes (e.g.,PAX5,TOX3,PCF11,MAPRE3). However, in some significant elements, mutations appear to stem from localized mutational processes rather than recurrent positive selection in some cases. To further characterize the driver potential of the identified elements and shortlist candidates, we identified elements where presence of mutations correlated significantly with expression levels (e.g.TERTandCDH10) and survival (e.g.CDH9andCDH10) in an independent set of 505 TCGA whole-genome samples. In a larger pan-cancer set of 4,128 TCGA exomes with expression profiling, we identified mutational correlation with expression for additional elements (e.g., nearGATA3,CDC6,ZNF217andCTCFtranscription factor binding sites). Survival analysis further pointed toMIR122, a known marker of poor prognosis in liver cancer. This screen for significant mutation patterns followed by correlative mutational analysis identified new individual driver candidates and suggest that some non-coding mutations recurrently affect expression and play a role in cancer development.