bluuebunny/crossref_metadata_2025_split huggingface dataset:
Various localized epigenetic marks predict expression across 54 samples and reveal underlying chromatin state enrichments
Authors: Devadas Lalita , Yen Angela , Kellis Manolis 
Published: November 2015

AbstractHere, we predict gene expression from epigenetic features based on public data available through the Epigenome Roadmap Project [1]. This rich new dataset includes samples from primary tissues, which to our knowledge have not previously been studied in this context. Specifically, we used computational machine learning algorithms on five histone modifications to predict gene expression in a variety of samples. Our models reveal a high predictive accuracy, especially in cell cultures, with predictive ability dependent on sample type and anatomy. The relative importance of each histone mark feature varied across samples. We localized each histone mark signal to its relevant region, revealing that chromatin state enrichment varies greatly between histone marks. Our results provide several novel insights into epigenetic regulation of transcription in new contexts.
Resources for the comprehensive discovery of functional RNA elements
Authors: Sundararaman Balaji , Zhan Lijun , Blue Steven , Stanton Rebecca , Elkins Keri , Olson Sara , Wei Xintao , Van Nostrand Eric L. , Huelga Stephanie C. , Smalec Brendan M. , Wang Xiaofeng , Hong Eurie L. , Davidson Jean M. , Lecuyer Eric , Graveley Brenton R. , Yeo Gene W. 
Published: November 2015

SummaryTranscriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck to the application of these methods in diverse cell-lines, tissues and developmental stages, is the availability of validated IP-quality antibodies. Using IP followed by immunoblot assays, we have developed a validated repository of 438 commercially available antibodies that interrogate 365 unique RBPs. In parallel, 362 short-hairpin RNA (shRNA) constructs against 276 unique RBPs were also used to confirm specificity of these antibodies. These antibodies can characterize subcellular RBP localization. With the burgeoning interest in the roles of RBPs in cancer, neurobiology and development, these resources are invaluable to the broad scientific community. Detailed information about these resources is publicly available at the ENCODE portal (https://www.encodeproject.org/).HighlightsAntibodies against 365 unique RBPs successfully immunoprecipitate the RBPsShort-hairpin RNAs against 276 unique RBPs confirm the specificity of RBP antibodiesAntibodies characterize subcellular localization of RBPsAntibody and hairpin RNA information are provided athttps://www.encodeproject.org/
4C-ker: A method to reproducibly identify genome-wide interactions captured by 4C-Seq experiments
Authors: Raviram Ramya , Rocha Pedro P. , Müller Christian L. , Miraldi Emily R. , Badri Sana , Fu Yi , Swanzey Emily , Proudhon Charlotte , Snetkova Valentina , Bonneau Richard , Skok Jane 
Published: November 2015

ABSTRACT4C-Seq has proven to be a powerful technique to identify genome-wide interactions with a single locus of interest (or “bait”) that can be important for gene regulation. However, analysis of 4C-Seq data is complicated by the many biases inherent to the technique. An important consideration when dealing with 4C-Seq data is the differences in resolution of signal across the genome that result from differences in 3D distance separation from the bait. This leads to the highest signal in the region immediately surrounding the bait and increasingly lower signals in far-cisandtrans. Another important aspect of 4C-Seq experiments is the resolution, which is greatly influenced by the choice of restriction enzyme and the frequency at which it can cut the genome. Thus, it is important that a 4C-Seq analysis method is flexible enough to analyze data generated using different enzymes and to identify interactions across the entire genome. Current methods for 4C-Seq analysis only identify interactions in regions near the bait or in regions located in far-cisandtrans, but no method comprehensively analyzes 4C signals of different length scales. In addition, some methods also fail in experiments where chromatin fragments are generated using frequent cutter restriction enzymes. Here, we describe 4C-ker, a Hidden-Markov Model based pipeline that identifies regions throughout the genome that interact with the 4C bait locus. In addition we incorporate methods for the identification of differential interactions in multiple 4C-seq datasets collected from different genotypes or experimental conditions. Adaptive window sizes are used to correct for differences in signal coverage in near-bait regions, far-cisandtranschromosomes. Using several datasets, we demonstrate that 4C-ker outperforms all existing 4C-Seq pipelines in its ability to reproducibly identify interaction domains at all genomic ranges with different resolution enzymes.AUTHORS SUMMARYCircularized chromosome conformation capture, or 4C-Seq is a technique developed to identify regions of the genome that are in close spatial proximity to a single locus of interest (‘bait’). This technique is used to detect regulatory interactions between promoters and enhancers and to characterize the nuclear environment of different regions within and across different cell types. So far, existing methods for 4C-Seq data analysis do not comprehensively identify interactions across the entire genome due to biases in the technique that are related to the decrease in 4C signal that results from increased 3D distance from the bait. To compensate for these weaknesses in existing methods we developed 4C-ker, a method that explicitly models these biases to improve the analysis of 4C-Seq to better understand the genome wide interaction profile of an individual locus.
Optimal derotation of shared acceleration time series by determining relative spatial alignment
Authors: Mayrhofer René , Hlavacs Helmut , Findling Rainhard Dieter 
Published: November 2015

Purpose
– The purpose of this article is to improve detection of common movement. Detecting if two or multiple devices are moved together is an interesting problem for different applications. However, these devices may be aligned arbitrarily with regards to each other, and the three dimensions sampled by their respective local accelerometers can therefore not be directly compared. The typical approach is to ignore all angular components and only compare overall acceleration magnitudes – with the obvious disadvantage of discarding potentially useful information.

Design/methodology/approach
– This paper contributes a method to analytically determine relative spatial alignment of two devices based on their acceleration time series. The method uses quaternions to compute the optimal rotation with regards to minimizing the mean squared error.

Findings
– Based on real-world experimental data from smartphones and smartwatches shaken together, the paper demonstrates the effectiveness of the method with a magnitude squared coherence metric, for which an improved equal error rate (EER) of 0.16 (when using derotation) over an EER of 0.18 (when not using derotation) is shown.

Practical implications
– After derotation, the reference system of one device can be (locally and independently) aligned with the other, and thus all three dimensions can consequently be compared for more accurate classification.

Originality/value
– Without derotating time series, angular information cannot be used for deciding if devices have been moved together. To the best of the authors
'
knowledge, this is the first analytic approach to find the optimal derotation of the coordinate systems, given only the two 3D time acceleration series of devices (supposedly) moved together. It can be used as the basis for further research on improved classification toward acceleration-based device pairing.
Reducing isocyanate exposure and asthma risk in motor vehicle repair
Authors: Piney Mark , Llewellyn Diane , O'Hara Rachel , Saunders John , Cocker John , Jones Kate , Fishwick David 
Published: November 2015

Purpose
– Exposure to isocyanates was the leading cause of occupational asthma in the UK. Motor vehicle repair (MVR) bodyshop paint sprayers were at greatest risk, despite widespread use of air-fed breathing apparatus and ventilated booths. Most paint sprayers work in small and medium enterprises (SMEs). The purpose of the Health and Safety Executive (HSE) project, described in this paper, is to improve exposure control measures in at least 20 per cent of MVR bodyshops, and reduce the risk of occupational asthma. The paper aims to discuss this issue.

Design/methodology/approach
– A three-stranded plan consisted of: Safety and Health Awareness Days (SHADs); workplace inspections; and third-party stakeholder communications. The impact of various parts of the project were evaluated.

Findings
– Approximately 18 per cent of bodyshops in the UK attended one of 32 SHADs, following which over 90 per cent of delegates expressed an “intention to act” to improve exposure control measures. A local assessment showed that at least 50 per cent of bodyshops improved exposure control measures. An evaluation of 109 inspections found that enforcement action was taken at 40 per cent of visits. Third-party engagement produced a joint HSE-industry designed poster, new agreed guidance on spray booths and dissemination of SHAD material. Knowledge of booth clearance time has become widespread, and 85 per cent of booths now have pressure gauges. Biological monitoring data show that, post-SHAD, exposures were lower.

Originality/value
– A sustained national project using clear, relevant, tested messages delivered via different routes, had a sector-wide impact in bodyshops. It is probable that the project has improved isocyanate exposure control in at least 20 per cent of bodyshops. The generic lessons could be applied to other widespread SME businesses.
Mystery shoppers: an evaluation of their use in monitoring performance
Authors: Douglas Jacqueline 
Published: November 2015

Purpose
– The purpose of this paper is to examine what mystery shopping is, why it is used and how mystery customers are trained and how the information collected is fed back to the client organisation.

Design/methodology/approach
– The approach was to use an online survey of mystery shoppers compares the reality of the situation with the best practice identified from the extant literature.

Findings
– The main outcome was that results identify good and bad practices in all areas of the process and guidelines for the recruitment, training and monitoring of mystery shoppers are proposed including in-depth training in all aspects of the job.

Research limitations/implications
– A sample of 85 mystery shoppers was used and only in the UK. It would be interesting to widen this out internationally.

Practical implications
– Mystery shoppers are used worldwide by services to evaluate the performance of their front-line people and processes but are their evaluations valid and reliable? This research identifies good and bad practice which should help managers to design their training for mystery shoppers.

Originality/value
– The paper addresses a gap in the literature on the perceptions of mystery shoppers.
Achieving quality in printing: some determining factors in the printing industry in Ghana
Authors: Graham Nicholas Kingsley , Owusu Isaac 
Published: November 2015

Purpose– Implementing quality programmes faces challenges and are not able to yield the needed results. The purpose of this paper is to examine the extent to which three key variables referred to as employee development, empowerment and participation (EDEP) determine the success of a quality programme of printing firms in Ghana.Design/methodology/approach– The study is purely quantitative and data were collected from a cross-sectional survey of workers from printing firms in Ghana. The questionnaire instrument assesses the practices of the firms on development, empowerment and participation of employees. Descriptive, correlation and multiple regression analyses were performed to ascertain the contribution and relationship of the variables to quality achievement.Findings– EDEP is directly and significantly related to print quality achievement. Among the three variables, participation has the greatest effect and contributes significantly to quality achievement. This is followed by empowerment, which has moderate effect on successful quality programme.Research limitations/implications– The study was unable to evaluate entire Total Quality Management dimensions. More extended research, preferably longitudinal study, is needed to establish how EDEP affect quality achievement in organisations.Practical implications– Achieving quality printing depends on the level of attention to EDEP. The study suggests that when employees participate fully in quality drive and self-manage their actions and duties, high-quality printing can be assured.Social implications– The study provides useful information on factors that have been overlooked or given less attention, yet affect quality programmes of the firms.Originality/value– The study empirically measure critical success factors of a quality in the printing firms.
Travel agencies’ perception of ISO 9001 certification
Authors: Mak Lui Ming 
Published: November 2015

Purpose
– The purpose of this paper is to increase awareness regarding the implementation of a quality management system in the travel agency sector by identifying similarities and differences in the perception of the ISO 9001 certification by travel agencies in China and Hong Kong as well as to provide potential recommendations to Kenya and to other countries developing tourism industries.

Design/methodology/approach
– The comparative study approach is used to compare perceptions of the ISO 9001 certification by travel agencies in China and Hong Kong.

Findings
– Travel agencies in Kenya, China, and Hong Kong promote the benefits but address the shortcomings and challenges of implementing the ISO 9001 certification simultaneously. This certification certainly benefited travel agencies in terms of marketing, but sustaining these effects remains a challenge.

Research limitations/implications
– The comparative approach, while important, cannot be considered a “scientific” approach at present. The current research compared the findings of two studies; however, these works are limited in that they use different data collection methodologies. Consequently, the results may vary.

Originality/value
– More similarities than differences were determined in the terms of costs among travel agencies in China and Hong Kong. Various differences were identified with respect to the perceived benefits from the ISO 9001 certification. This finding can be regarded as both a challenge and an opportunity.
Characterization of the ecological role of genes mediating acid resistance in Lactobacillus reuteri during colonization of the gastrointestinal tract
Authors: Krumbeck Janina A. , Marsteller Nathan L. , Frese Steven A. , Peterson Daniel A. , Ramer‐Tait Amanda E. , Hutkins Robert W. , Walter Jens 
Published: November 2015

SummaryRodent‐derived strains of Lactobacillus reuteri densely colonize the forestomach of mice and possess several genes whose predicted functions constitute adaptations towards an acidic environment. The objective of this study was to systematically determine which genes of L. reuteri 100‐23 contribute to tolerance towards host gastric acid secretion. Genes predicted to be involved in acid resistance were inactivated, and their contribution to survival under acidic conditions was confirmed in model gastric juice. Fitness of five mutants that showed impaired in vitro acid resistance were then compared through competition experiments in ex‐germ‐free mice that were either treated with omeprazole, a proton‐pump inhibitor that suppresses acid secretion in the stomach, or left untreated. This analysis revealed that the urease cluster was the predominant factor in mediating resistance to gastric acid production. Population levels of the mutant, which were substantially decreased in untreated mice, were almost completely restored through omeprazole, demonstrating that urease production in L. reuteri is mainly devoted to overcome gastric acid. The findings provide novel information on the mechanisms by which L. reuteri colonizes its gastric niche and demonstrate that in silico gene predictions and in vitro tests have limitations for predicting the ecological functions of colonization factors in bacterial symbionts.
Effect of silymarin alcoholic extract on surgery‐induced intraperitoneal adhesion in rats
Authors: Karimi Mehrdad , Parsaei Pouya , Shafiei‐Alavijeh Soheil , Rafieian‐Kopaei Mahmoud , Asadi S. Yazdan 
Published: November 2015

AimAdhesion formation is the greatest complication in abdominal surgery. Silybum marianum (S. marianum) extract contains phenolic compounds whit antioxidant activities, thus could reduce adhesion formation. The aim of the present study was to examine its effect on intraabdominal adhesion.Patients and MethodsThirty male Wistar rats were randomly divided into three groups. Groups A and B received 1 per cent and 5 per cent concentrations of the S. marianum extract, and group C (control group) received distilled water. After anaesthesia was administered, the abdominal wall was opened and three shallow, longitudinal and transverse incisions (2 cm in length) were made on the right wall of the abdomen. A 2 × 2 cm piece was removed from the peritoneal surface on the left side of the abdominal wall; 3 mL of S. marianum extract or distilled water was then administered into the abdominal cavity. Adhesion degrees were determined according to the Canbaz scale. Histopathological examination was also determined according to the severity of fibrosis and inflammation. Data analysis was performed using SPSS version16.ResultsThere was significant difference in the adhesion formation between the groups (P = 0.023). The adhesion degree in groups A and B were significantly lower than that of the control (P < 0.05). In the histopathological examination, significant differences were observed between the control and extract‐treated groups in term of fibrosis and inflammation (P < 0.05).ConclusionS. marianum extract has preventive effects on post‐laparotomy intraabdominal adhesion. Therefore, through further clinical studies, S. marianum extract and its derived compounds might be used in humans for the treatment of these complications.
Outcomes of duodenojejunostomy (the Grégoire procedure) for obstruction or perforation of the third and fourth portions of the duodenum
Authors: Sabbagh Charles , Dhahri Abdennaceur , Mariage Maxime , Ntouba Alexandre , Yzet Thierry , Regimbeau Jean‐Marc 
Published: November 2015

AimAlthough obstruction and perforation of the third and fourth portions of the duodenum are rare, they are usually encountered in an emergency setting. The objective of the present study was to characterize the outcomes of duodenojejunostomy for the obstruction or perforation of the third and fourth portions of the duodenum.Patients and MethodsThis was a retrospective, single‐centre study (evidence level V). From January 2004 to March 2013, all patients having undergone a duodenojejunostomy for damage to the third or fourth portions of the duodenum were included in the study.ResultsThe study population consisted of three women (33.3 per cent) and six men (66.7 men). The mean age was 52 years (range: 22–81). Three patients (33.3 per cent) had an obstruction, and the remaining six (66.7 per cent) had a perforation. The aetiology for all cases of obstruction was jejunal metastasis of lung cancer (n = 3). The mean operating time was 190.7 min (range: 100–275). All anastomoses were lateroterminal and were hand‐sewn between the genu inferius and the first jejunal loop. The mean time to refeeding was 6 days (range: 5–9), and the mean duration of postoperative gastroparesis was 8 days (range: 4–21). The mean length of hospital stay was 23 days (range: 15–50). The median Clavien score was 2 (0–5). The mortality rate was 11.2 per cent (n = 1).ConclusionDuodenojejunostomy protects patients from obstruction and enables rapid refeeding. It has an acceptable morbidity rate and can be easily performed in an emergency setting.
Creative ways of talking: a narrative literature review concerning emotional support for adults with mild or moderate learning difficulties
Authors: MacDonald Dee 
Published: November 2015

Accessible summary

A group of adults with mild‐to‐moderate learning difficulties said they found it hard at times to find someone to talk to who understands them.

They said this was important because everybody should have someone to talk to and share their feelings with.

They wanted to know what had been written about this, and what research had been done.

A literature review was undertaken and found that the emotional lives of adults with learning difficulties have not been researched very much.

Often supporters do not realise that people with learning difficulties would like more opportunities to talk and share their feelings.

Adults with learning difficulties are good at supporting each other and more could be done to help this to happen.

AbstractBackground: Adults with mild or moderate learning difficulties identified a need for more opportunities to access appropriate emotional support.Materials and Methods: A narrative literature review was undertaken. Factors associated with dealing with emotional unrest, such as self‐esteem/self‐awareness, a person's attitude to having learning difficulties, emotional competency and friendship issues are discussed.Results: The review provides evidence that emotional unrest exists but receives little attention from supporters due to an emphasis on practical issues associated with an inclusion agenda. The review highlights a lack of research on emotional support for adults and explores reasons for this.Conclusion: The value that people with learning difficulties place on support from others with learning difficulties, that is peer support, emerges as a theme and an argument is presented for further inclusive research in this area.
Detection of anal dysplasia is enhanced by narrow band imaging and acetic acid
Authors: Inkster M. D. , Wiland H. O. , Wu J. S. 
Published: November 2015

AbstractAimAnal intraepithelial neoplasia precedes the development of anal squamous cell carcinoma. Detection of the lesion is essential to management. This paper describes a prospective study to detect and ablate anal squamous intraepithelial lesions (SILs) using white light narrow band imaging (NBI) and NBI with acetic acid (NBIA).MethodSixty patients with abnormal anal cytology and risk factors for anal dysplasia underwent examination of the anoderm with a high definition gastroscope and NBIA. Targeted biopsies were taken and the lesions were ablated and characterized histopathologically. Visualization of the anal transitional zone was facilitated by retroflexion and examination through a disposable anoscope.ResultsTargeted biopsies were taken from lesions in 58 patients. No lesion was seen in two patients. Histopathology showed SIL in 48 (80.0%) of 60 biopsies. One biopsy showed lymphoid aggregates. Biopsies in nine (15%) of the 60 patients showed normal mucosa. Lesions were seen in white light in 27 (45%) of the 60 cases, NBI in 39 (65%) and NBIA in 57 (95%). There was no major morbidity. Sensitivity analysis showed that all methods were significantly different from each other.ConclusionAnal SIL in the anal transitional zone and anal canal can be identified by NBIA. Patient selection influences findings. Limitations include small sample size and non‐randomization.