bluuebunny/crossref_metadata_2025_split huggingface dataset:
WGE: a CRISPR database for genome engineering
Authors: Hodgkins Alex , Farne Anna , Perera Sajith , Grego Tiago , Parry-Smith David J. , Skarnes William C. , Iyer Vivek 
Published: May 2015

Abstract
Summary: The rapid development of CRISPR-Cas9 mediated genome editing techniques has given rise to a number of online and stand-alone tools to find and score CRISPR sites for whole genomes. Here we describe the Wellcome Trust Sanger Institute Genome Editing database (WGE), which uses novel methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks. WGE is open, extensible and can be set up to compute and present CRISPR sites for any genome.
Availability and implementation: The WGE database is freely available at www.sanger.ac.uk/htgt/wge
Contact: vvi@sanger.ac.uk or skarnes@sanger.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Vert
Versus
Verre
: Vegetal Violence in Huysmans's
En Rade
Authors: Scott Hannah 
Published: May 2015

Abstract

In Joris-Karl Huysmans's 1887 novel
En rade
, Jacques Marles and his wife Louise, beset by financial troubles, flee Paris to find safe harbour in a dilapidated rural chateau. At first glance, this country setting seems to display all the stereotypical features of pastoral fantasy; however, Huysmans uses implicit urban rhetoric and imagery to create a wry subversion of the natural idyll. The comforts of nature are denied to the male subject as the countryside is stripped of its promise of escapism. This article examines, firstly, Huysmans's use of signifiers of urban unrest to turn nature's exuberance into a corollary for human, revolutionary violence. Secondly, it focuses specifically on glass and glass-breaking at the hands of an aggressive Mother Nature, evoking memories of urban destruction and Parisian civil strife. The association of nature with violence culminates in the invasion of the chateau and its looking glasses by green, the colour of nature, forcing this distressing natural world between man and his own narcissistic reflection. Huysmans reveals that the natural world is no more an ally than the unruly urban masses, and confronts the reader with the inexorable violence of vegetation.
A spatially resolved pressure-based approach to evaluate combined effects of human activities and management in marine ecosystems
Authors: Goodsir Freya , Bloomfield Helen J. , Judd Adrian D. , Kral Filip , Robinson Leonie A. , Knights Antony M. 
Published: May 2015

AbstractOur oceans are heavily utilized by a wide variety of human activities that exert pressures which negatively impact marine ecosystems, occasionally leading to unsustainable rates of exploitation. A linkage framework approach can be used to make independent associations between sectors, activities, and the pressures they introduce. However, in reality, many different sectors and their associated activities overlap in time and space, potentially changing the severity of their impact as pressures combine, and undermine the efforts of environmental managers to mitigate the harmful effects of those activities. Here, we present a spatially resolved approach to assess the potential for combined effects using a linkage framework assessment. Using illustrative examples from the Northeast Atlantic, we show the likelihood of changes in pressure severity as a result of multiple overlapping activities. Management options to limit pressure introduction are explored and their benefit—measured as a reduction in the area of seabed impacted—assessed. In its simplest form, the approach can be used to develop potential precautionary management options in areas where data availability is poor and more comprehensive management measures where data are more widely available.
Mackerel predation on herring larvae during summer feeding in the Norwegian Sea
Authors: Skaret Georg , Bachiller Eneko , Langøy Herdis , Stenevik Erling K. 
Published: May 2015

Abstract
In the course of the past two decades, Atlantic mackerel, Scomber scombrus, have expanded their summer feeding distribution in the Norwegian Sea substantially, and now potentially overlap with pelagic larvae of Norwegian spring-spawning herring, Clupea harengus, as these drift northwards. Mackerel are known to be opportunistic predators, and the aim of this study was to evaluate mackerel predation in an area of overlap between mackerel and herring larvae, with particular focus on predation on herring larvae. In early June 2013, we followed a predefined transect in the expected core larvae distribution area on the Norwegian coastal shelf between about 66°N and 69°N. The transect was repeated twice, and samples of mackerel for stomach analyses and subsequent herring larvae samples were obtained at pre-defined stations. Mackerel were caught in all but one of the trawl hauls, but were hardly ever observed acoustically, suggesting that they were dispersed close to the surface throughout the study area. Herring larvae were caught in all samples. Calanoid copepods were the dominant prey of the mackerel, but 45% of the mackerel guts contained herring larvae, with a maximum of 225 larvae counted in a single gut. Both the frequency of guts containing herring larvae and the average amount of herring larvae increased in line with increasing abundance of larvae. On the other hand, no spatial correlation between mackerel abundance and herring larvae abundance was found at the station level. The results suggest that mackerel fed opportunistically on herring larvae, and that predation pressure therefore largely depends on the degree of overlap in time and space. Rough areal projections suggest that the mackerel would be capable of consuming the herring larvae present in the investigation area in 6–7 d, and that such predation therefore could have regulatory effects on stocks of Norwegian spring-spawning herring.
Dark halos of M 31 and the Milky Way
Authors: Sofue Yoshiaki 
Published: May 2015

Abstract
Grand rotation curves (GRC) within ∼ 400 kpc of M 31 and the Milky Way were constructed by combining disk rotation velocities and radial velocities of satellite galaxies and globular clusters. The GRC for the Milky Way was revised using the most recent solar rotation velocity. The derived GRCs were deconvolved into a de Vaucouleurs bulge, exponential disk, and a dark halo with a Navarro–Frenk–White (NFW) density profile by least-χ2 fitting. Comparison of the best-fitting parameters revealed similarities between the disks and bulges of the two galaxies, whereas the dark-halo mass of M 31 was found to be twice that of the Galaxy. We show that the NFW model may be a realistic approximation of the observed dark halos in these two giant spirals.
Unicameral Bone Cysts in the Humerus: Treatment Outcomes
Authors: Kadhim Muayad , Sethi Samir , Thacker Mihir M. 
Published: May 2015

Background:
Several treatment modalities have been described for the treatment of unicameral bone cysts (UBC). The aim of this study was to examine the outcome of various treatment modalities of UBC in a specific anatomic location, the humerus.

Methods:
This study is a retrospective case-only study of patients with humeral UBC with minimum follow-up of 1 year. Medical records and radiographs were assessed and UBC healing status was determined based on most recent follow-up radiographs and divided into 3 groups (healed, partially healed, and not healed). Descriptive statistics were utilized to summarize study outcome.

Results:
Sixty-eight patients (54 boys and 14 girls) with humeral UBC comprised the study population. Sixty-four cases (94.1%) presented with a pathologic fracture. Fifty-one cases were in the proximal metaphysis and 17 were in the diaphysis. Mean age at diagnosis was 9.2±3.7 years, and mean follow-up was 4.0±2.6 years. Twenty-five patients were treated with observation, 38 by injection (27 with steroids and 11 with bone marrow), and 5 by open surgery. Patients who underwent open surgery had relatively larger cyst length, width, and cyst index, and all healed or partially healed at last follow-up. UBC persistence was observed in 29% of diaphyseal and 27.5% of metaphyseal cysts. Of the 19 patients with persistence, 8 were treated with observation, 9 with steroid injection, and 2 with bone marrow injection. Inner wall disruption before injection was performed in 17 patients (24% did not heal), whereas 21 patients did not have inner wall disruption (33% did not heal). Twenty patients received >1 injection. Eleven patients complained of pain at the last visit (8 had a persistent cyst, 2 were partially healed, and 1 had a healed UBC).

Conclusions:
Complete healing of humeral UBC is challenging to achieve irrespective of treatment modality. UBCs treated with open surgery tended to heal better. Unhealed cysts were more likely to be associated with pain.

Level of Evidence:
Level III—a retrospective comparative study.
A Longitudinal Review of Gait Following Treatment for Idiopathic Clubfoot: Gait Analysis at 2 and 5 Years of Age
Authors: Jeans Kelly A. , Erdman Ashley L. , Jo Chan-Hee , Karol Lori A. 
Published: May 2015

Background:
Initial correction following nonoperative (NonOp) treatment for idiopathic clubfoot has been reported in 95% of feet by age 2; however, by age 4, approximately one third of feet undergo surgery due to relapse. The purpose of this study was to assess the longitudinal effect of growth and surgical (Sx) intervention on gait following NonOp and Sx treatment for clubfoot.

Methods:
Children with idiopathic clubfoot were seen for gait analysis at 2 and 5 years of age. Kinematic data were collected at both visits, and kinetic data were collected at age 5 years. Group comparisons were made between feet treated with the Ponseti casting technique (Ponseti) and the French physical therapy method (PT) and between feet treated nonoperatively and surgically. Comparisons were made between feet treated with a limited release or tendon transfer (fair) and those treated with a full posteromedial release (poor). The α was set to 0.05 for all statistical analyses.

Results:
Gait data from 181 children with 276 idiopathic clubfeet were collected at both age 2 and 5 years. Each foot was initially treated with either the Ponseti (n=132) or PT (n=144) method but by the 5-year visit, 30 Ponseti and 61 PT feet required surgery. Gait outcomes showed limitations primarily in the Sx clubfeet. Normal ankle motion was only present in 17% of Ponseti and 21% of PT feet by age 5 following Sx management. Sx PT feet showed persistent intoeing at age 2 and 5. Within the Sx group, feet initially treated with PT had a clinically significant reduction in ankle power compared with those treated initially by the Ponseti method. Feet treated with posteromedial releases had significantly less ankle power than those treated with limited surgery or that remained NonOp at 5 years.

Conclusions:
This longitudinal study shows subtle changes between 2 and 5 years, and continues to support a NonOp approach in the treatment of clubfoot.

Level of Evidence:
Level II—therapeutic.
Surgical Hip Dislocation for the Treatment of Intra-Articular Injuries and Hip Instability Following Traumatic Posterior Dislocation in Children and Adolescents
Authors: Novais Eduardo N. , Heare Travis C. , Hill Mary K. , Mayer Stephanie W. 
Published: May 2015

Background:
Traumatic posterior hip dislocation in children is a rare injury that typically is treated with closed reduction. Surgical treatment is typically recommended for nonconcentric reduction with joint space asymmetry with entrapped labrum or an osteochondral fragment. The surgical hip dislocation (SHD) approach allows for full assessment of the acetabulum and femoral head and has been our preferred surgical strategy. The purpose of this study was to (1) describe the intra-articular pathologic findings seen at the time of SHD; and (2) to investigate hip pain, function, and activity level of a cohort of children and adolescents after open treatment of a posterior hip dislocation using the SHD approach.

Methods:
Following IRB approval, 23 patients who sustained a traumatic posterior hip dislocation between January 2009 and December 2013 were identified. In 8/23 (34.8%) patients there was evidence of nonconcentric reduction after closed treatment and surgical treatment was performed using the SHD approach. Seven male and 1 female (mean age, 11.2 y; range, 6 to 14.6 y) were followed for an average of 28 months (range, 13 to 67 mo). The modified Harris Hip Score (mHHS) and the University of California Los Angeles activity score assessed clinical hip outcome and activity level at minimum of 1 year after surgery.

Results:
Six patients were treated after an acute trauma, whereas 2 were treated after recurrent dislocations. Five patients were involved in motor vehicle accidents and 3 in sports-related injuries. Intraoperative findings include posterior labral avulsion in all patients, fracture of the cartilaginous posterior wall (n=3), and femoral head chondral injuries (n=5) and fracture (n=1). The labral root was repaired using suture anchor technique in 7/8 patients and resected in 1. In 2 patients, labral repair was complemented by screw fixation of the posterior wall. All but one patient (mHHS=94) reported maximum mHHS. The University of California Los Angeles activity score was 10 for 5/8 patients and 7 in 3 patients. No case of femoral head osteonecrosis was noted. One patient developed an asymptomatic heterotopic ossification.

Conclusions:
When open reduction is recommended for the treatment of intra-articular pathologies and hip instability following traumatic dislocation of the hip in children and adolescents, the SHD is an excellent approach that allows surgical correction of the damaged bony and soft-tissue structures including repair of the capsule-labral complex, and reduction and internal fixation of the cartilaginous posterior wall and femoral head fractures.

Level of Evidence:
Level IV.
Experience With Anti-TNF-α Biologic Agents in Succession in Patients With Crohn’s Disease
Authors: Ferges William , Rampertab Saroja Devi , Shafqet Muhammad , Salimi Qasim , You Geoffrey , Yousefzadeh Eleazer , Cheng Jerry Q. , Das Kiron M. 
Published: May 2015

Goals:
Our aim was to identify and compare the effectiveness of antitumor necrosis factor biologics when used as initial agents and when used in succession for the treatment of moderate to severe Crohn’s disease (CD).

Background:
Studies directly comparing the efficacy of biologics are lacking. When one biologic loses efficacy, patients are often treated with an alternate biologic. The effectiveness of this strategy has not been thoroughly investigated.

Study:
This is a retrospective cohort study from a database of 153 patients with CD treated with infliximab, adalimumab, or certolizumab pegol. Response rates determined by physician global assessment were compared between biologics when given as initial agents and after failure of 1 or 2 prior biologics.

Results:
There were no significant differences in response between infliximab (64.5%), adalimumab (60.0%), and certolizumab pegol (66.7%) when given as initial biologics. As second-line or third-line agents after prior biologic failure, there was a trend toward increased response with infliximab (83.3%) versus adalimumab (52.7%) and certolizumab pegol (59.4%); however, this did not meet statistical significance. After failure or loss of response of 2 previous biologics, use of a third biologic was still effective with a response rate of 54.2%.

Conclusions:
All 3 biologics have similar efficacy in the treatment of CD when given as initial agents. Infliximab has a trend toward increased response after prior biologic failure; however, this did not meet statistical significance. Even after loss of response or failure of 2 previous biologics, trial of a third alternate biologic is an effective strategy.
ReproPhylo: An Environment for Reproducible Phylogenomics
Authors: Szitenberg Amir , John Max , Blaxter Mark L. , Lunt David H. 
Published: May 2015

AbstractThe reproducibility of experiments is key to the scientific process, and particularly necessary for accurate reporting of analyses in data-rich fields such as phylogenomics. We present ReproPhylo, a phylogenomic analysis environment developed to ensure experimental reproducibility, to facilitate the handling of large-scale data, and to assist methodological experimentation. Reproducibility, and instantaneous repeatability, is built in to the ReproPhylo system, and does not require user intervention or configuration because it stores the experimental workflow as a single, serialized Python object containing explicit provenance and environment information. This ‘single file’ approach ensures the persistence of provenance across iterations of the analysis, with changes automatically managed by the version control program Git. ReproPhylo produces an extensive human-readable report, and generates a comprehensive experimental archive file, both of which are suitable for submission with publications. The system facilitates thorough experimental exploration of both parameters and data. ReproPhylo is a platform independent CC0 python module, and is easily installed as a Docker image, with an Jupyter GUI, or as a slimmer version in a Galaxy distribution.
Strigolactone Regulates Leaf Senescence in Concert with Ethylene in Arabidopsis
Authors: Ueda Hiroaki , Kusaba Makoto 
Published: May 2015

AbstractLeaf senescence is not a passive degenerative process; it represents a process of nutrient relocation, in which materials are salvaged for growth at a later stage or to produce the next generation. Leaf senescence is regulated by various factors, such as darkness, stress, aging, and phytohormones. Strigolactone is a recently identified phytohormone, and it has multiple functions in plant development, including repression of branching. Although strigolactone is implicated in the regulation of leaf senescence, little is known about its molecular mechanism of action. In this study, strigolactone biosynthesis mutant strains of Arabidopsis (Arabidopsis thaliana) showed a delayed senescence phenotype during dark incubation. The strigolactone biosynthesis genes MORE AXIALLY GROWTH3 (MAX3) and MAX4 were drastically induced during dark incubation and treatment with the senescence-promoting phytohormone ethylene, suggesting that strigolactone is synthesized in the leaf during leaf senescence. This hypothesis was confirmed by a grafting experiment using max4 as the stock and Columbia-0 as the scion, in which the leaves from the Columbia-0 scion senesced earlier than max4 stock leaves. Dark incubation induced the synthesis of ethylene independent of strigolactone. Strigolactone biosynthesis mutants showed a delayed senescence phenotype during ethylene treatment in the light. Furthermore, leaf senescence was strongly accelerated by the application of strigolactone in the presence of ethylene and not by strigolactone alone. These observations suggest that strigolactone promotes leaf senescence by enhancing the action of ethylene. Thus, dark-induced senescence is regulated by a two-step mechanism: induction of ethylene synthesis and consequent induction of strigolactone synthesis in the leaf.
Monitoring or tunneling by large shareholders: evidence from China private listed companies
Authors: Song Xiaobao 
Published: May 2015

Purpose– The purpose of this paper is to analyze the relationship between ownership concentration and company performance in China private listed companies.Design/methodology/approach– By taking into account of the difference of managerial positions of large shareholders in listed companies (whether they assume the posts as presidents or general managers), and based on the two agency theories, the paper analyzes the state dependency of the relationship between ownership concentration and the company performance of listed companies with the samples of China private listed companies from 2003 to 2011.Findings– The paper finds that if the large shareholders assume no posts in the listed companies, there is an invertedUshape relation between shareholding ratio of the largest shareholders and the company performance. This result indicates the inadequate or excessive monitoring to the companies by the large shareholders according to different shareholding ratios. If large shareholders assume posts in the listed companies, there is aUshape relation between shareholding ratio of the largest shareholders and the company performance. This result indicates the tunneling and propping to the small shareholders by the large shareholders according to different shareholding ratios.Research limitations/implications– This paper has not taken the influence of earnings management of the listed companies.Practical implications– For strengthening the protection of investors, proper distinction shall be made among shareholders of different conditions, and difference of roles large shareholders play in the company under different conditions shall be understood correctly, so as to formulate and perfect market rules for corporate governance, rather than just restraining the power (rights) of large shareholders. The study in this paper is for helping understand the different roles large shareholders play under different corporate governance conditions.Originality/value– First, different from the research paradigm of relationship between ownership concentration and company performance in existing literature, the paper discriminates the study background with the post-assuming conditions of large shareholders in listed companies and believes that relationship between ownership concentration and company performance shall be presented differently under different post-assuming conditions. Second, by using monitoring theory and tunneling and propping theory to explain the behaviors of large shareholders under different post-assuming conditions respectively, a new theory explanation view is provided for explaining the relation between ownership concentration and company performance.
Mobile coupons: what to offer, to whom, and where?
Authors: Khajehzadeh Saman , Oppewal Harmen , Tojib Dewi 
Published: May 2015

Purpose
– This paper aims to investigate the redemption of promotional offers in a mobile service context. It specifically studies how mobile coupon redemption depends on the type of product offered, the convenience of accessing a retailer and the consumer’s shopping motivation. Retailers increasingly use mobile coupon services as a complementary channel to send promotional offers to consumers.

Design/methodology/approach
– Two studies examine how the three factors interact in determining coupon redemption. Both involve a scenario-based experiment. Participants are over 750 members of an online panel in the USA.

Findings
– The results show that when the retailer offers a hedonic product, consumers’ shopping motivation matters more, whereas when the retailer offers a utilitarian product, consumers’ location dominates their redemption intentions.

Research limitations/implications
– One limitation of this research is the use of hypothetical scenarios. Although this limitation was addressed by conducting a quasi-experiment, future research could be carried out using a field experiment.

Practical implications
– Results suggest that in a mobile channel, personalization of promotions is more important for utilitarian shoppers than for hedonic shoppers.

Originality/value
– Drawing on the theories of regulatory focus and preference for the status quo, this paper posits that mobile coupon redemption is determined by whether the offer requires consumers to divert from their focal shopping motivation (i.e. their status quo). The authors explain this difference by showing the mediating role of regulatory fit.