bluuebunny/crossref_metadata_2025_split huggingface dataset:
The socialization of markets
Authors: Moon Jeremy 
Published: April 2017

Abstract
‘The socialization of markets’ is concerned with how and why corporate social responsibility (CSR) has become more institutionalized. It considers the ways in which CSR features in some markets, thereby shaping a ‘business case’ for CSR. Markets have become ever more socialized as non-economic criteria increasingly feature in market transactions. As companies both respond to and reinforce this trend, they consolidate CSR as part of ‘business as usual’, and new, shared, and legitimized norms of appropriate business behaviour emerge. The socialization of markets results from the interaction of market, social, and governmental factors. Companies retain a critical role in shaping products and services that foster and reward demands for social criteria in market decisions.
Contextualizing History-as-Adaptation: An Interdisciplinary Comparison of Historical Revisionism
Authors: Weiser Frans 
Published: April 2017

AbstractThe return to history in the humanities during the 1980s prompted literary and film scholars to question historiography’s empirical scientific status, as they instead argued that history shared more in common with fiction while their own fields of study provided means of democratizing the historical record. The concept of history-as-adaptation, recently introduced by Laurence Raw and Defne Ersin Tutan, and further developed by Tom Leitch, draws upon several of the same goals as these earlier revisionist critiques. This article contextualizes how external revision of history has been used by disciplines as a means of solidifying their own identities, despite the fact that history departments have not responded to such criticism. Through a cross-disciplinary analysis of the postmodern interrogation of historical claims, I seek to not only contextualize the adaptive turn but also demonstrate how the field’s comparative identity provides a means of transcending oppositional discourse. Drawing on the work of Robert Berkhofer, I establish a supplemental interpretation of history-as-adaptation, demonstrating the advantages of applying adaptive strategies to the documentary framework at the heart of historical methodology.
DMINDA 2.0: integrated and systematic views of regulatory DNA motif identification and analyses
Authors: Yang Jinyu , Chen Xin , McDermaid Adam , Ma Qin 
Published: April 2017

Abstract

Motivation
Motif identification and analyses are important and have been long-standing computational problems in bioinformatics. Substantial efforts have been made in this field during the past several decades. However, the lack of intuitive and integrative web servers impedes the progress of making effective use of emerging algorithms and tools.

Results
Here we present an integrated web server, DMINDA 2.0, which contains: (i) five motif prediction and analyses algorithms, including a phylogenetic footprinting framework; (ii) 2125 species with complete genomes to support the above five functions, covering animals, plants and bacteria and (iii) bacterial regulon prediction and visualization.

Availability and Implementation
DMINDA 2.0 is freely available at http://bmbl.sdstate.edu/DMINDA2.

Supplementary information
Supplementary data are available at Bioinformatics online.
Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference
Authors: Train Clément-Marie , Glover Natasha M , Gonnet Gaston H , Altenhoff Adrian M , Dessimoz Christophe 
Published: April 2017

Abstract

Motivation
Accurate orthology inference is a fundamental step in many phylogenetics and comparative analysis. Many methods have been proposed, including OMA (Orthologous MAtrix). Yet substantial challenges remain, in particular in coping with fragmented genes or genes evolving at different rates after duplication, and in scaling to large datasets. With more and more genomes available, it is necessary to improve the scalability and robustness of orthology inference methods.

Results
We present improvements in the OMA algorithm: (i) refining the pairwise orthology inference step to account for same-species paralogs evolving at different rates, and (ii) minimizing errors in the pairwise orthology verification step by testing the consistency of pairwise distance estimates, which can be problematic in the presence of fragmentary sequences. In addition we introduce a more scalable procedure for hierarchical orthologous group (HOG) clustering, which are several orders of magnitude faster on large datasets. Using the Quest for Orthologs consortium orthology benchmark service, we show that these changes translate into substantial improvement on multiple empirical datasets.

Availability and Implementation
This new OMA 2.0 algorithm is used in the OMA database (http://omabrowser.org) from the March 2017 release onwards, and can be run on custom genomes using OMA standalone version 2.0 and above (http://omabrowser.org/standalone).
Clinical exome sequencing reports: current informatics practice and future opportunities
Authors: Swaminathan Rajeswari , Huang Yungui , Astbury Caroline , Fitzgerald-Butt Sara , Miller Katherine , Cole Justin , Bartlett Christopher , Lin Simon 
Published: April 2017

AbstractThe increased adoption of clinical whole exome sequencing (WES) has improved the diagnostic yield for patients with complex genetic conditions. However, the informatics practice for handling information contained in whole exome reports is still in its infancy, as evidenced by the lack of a common vocabulary within clinical sequencing reports generated across genetic laboratories. Genetic testing results are mostly transmitted using portable document format, which can make secondary analysis and data extraction challenging. This paper reviews a sample of clinical exome reports generated by Clinical Laboratory Improvement Amendments–certified genetic testing laboratories at tertiary-care facilities to assess and identify common data elements. Like structured radiology reports, which enable faster information retrieval and reuse, structuring genetic information within clinical WES reports would help facilitate integration of genetic information into electronic health records and enable retrospective research on the clinical utility of WES. We identify elements listed as mandatory according to practice guidelines but are currently missing from some of the clinical reports, which might help to organize the data when stored within structured databases. We also highlight elements, such as patient consent, that, although they do not appear within any of the current reports, may help in interpreting some of the information within the reports. Integrating genetic and clinical information would assist the adoption of personalized medicine for improved patient care and outcomes.
Laparoscopic Hysterectomy With Morcellation Versus Abdominal Hysterectomy for Presumed Fibroids: An Updated Decision Analysis Following the 2014 FDA Safety Communications
Authors: Siedhoff Matthew T. , Doll Kemi M. , Clarke-Pearson Daniel L. , Rutstein Sarah E. 
Published: April 2017

(Abstracted from Am J Obstet Gynecol 2017;216:259.e1–259.e6)
Increasing concern that use of electric power morcellation during hysterectomy for benign conditions may result in the spread of an occult leiomyosarcoma (LMS) led the US Food and Drug Administration (FDA) to issue safety communications in April 2014 and November 2014, recommending that this procedure should not be used in perimenopausal and postmenopausal women. These communications significantly changed practice patterns of many gynecologic surgeons, increasing rates of abdominal hysterectomy (AH), and possibly resulting in more complications for patients.
Electronic Fetal Monitoring, Cerebral Palsy, and Caesarean Section: Assumptions Versus Evidence
Authors: Nelson Karin B. , Sartwelle Thomas P. , Rouse Dwight J. 
Published: April 2017

(Abstracted from BMJ 2016;355:i6405)
The ever-increasing rate of cesarean delivery may be attributed to a large extent to the extensive use of electronic fetal monitoring (EFM). Initial introduction of EFM was done to enable early identification of fetal asphyxia, thereby preventing mortality or long-term neurological morbidity, particularly cerebral palsy.
Prenatal cfDNA Screening Results Indicative of Maternal Neoplasm: Survey of Current Practice and Management Needs
Authors: Giles Meagan E. , Murphy Lauren , Krstić Nevena , Sullivan Cathy , Hashmi Syed S. , Stevens Blair 
Published: April 2017

(Abstracted from Prenat Diagn 2017;37(2):126–132)
The discovery of cell-free fetal DNA (cfDNA) that is free-floating in the serum has led to the development of screening technologies, both in obstetrics and oncology. Circulating cfDNA in the serum of pregnant women is the basis of noninvasive prenatal testing (NIPT).
Nail Matrix Pathology in Cronkhite–Canada Syndrome: The First Case Report
Authors: Chuamanochan Mati , Tovanabutra Napatra , Mahanupab Pongsak , Kongkarnka Sarawut , Chiewchanvit Siri 
Published: April 2017

Abstract:
Cronkhite–Canada Syndrome (CCS) presents with gastrointestinal polyposis and the triad of cutaneous abnormalities including nail dystrophy, alopecia, and hyperpigmentation of the skin. The etiology is not well understood. The histology of skin lesion in CCS has not been routinely described. Especially, the nail matrix pathology has not been reported. In this study, the authors report the nail matrix pathology in a patient with CCS. Interestingly, the histologic evaluation revealed matrix hypergranulosis. Because matrix hypergranulosis is commonly found in several inflammatory nail diseases, this discovery points out that an inflammatory process is probably one of the important pathogeneses in CCS.
The Effect of Tranilast 8% Liposomal Gel Versus Placebo on Post-Cesarean Surgical Scars: A Prospective Double-Blind Split-Scar Study
Authors: Kohavi Libi , Sprecher Eli , Zur Eyal , Artzi Ofir 
Published: April 2017

BACKGROUND
Tranilast (N-[3, 4-dimethoxycinnamoyl] anthranilic acid), an antiallergic drug, has been shown to attenuate scar formation possibly through inhibition of transforming growth factor beta 1 activity and consequent suppression of collagen synthesis in fibroblasts.

OBJECTIVE
The authors aimed at evaluating the efficacy and safety of tranilast 8% gel in improving the appearance and symptoms of new post-cesarean section surgical wounds.

METHODS
In this prospective double-blind split-scar study, the authors treated each half scar of 26 women with either tranilast 8% liposomal gel or tranilast-free liposomal gel (placebo). Treatment was applied twice daily for 3 months. Twenty women completed the trial. Scar halves were evaluated by 2 investigators and by the patients 9 months after the last application using the Patient and Observer Scar Assessment Scale (POSAS). The participants also rated overall satisfaction and recorded side effects of the treatment.

RESULTS
The mean POSAS scores at 9 months post-treatment were significantly lower for tranilast-treated half scars compared with placebo-treated half scars (p < .001). The women were significantly more satisfied with the tranilast-treated half-scar appearance (p = .002). Three participants reported itching and erythema on the tranilast-treated side.

CONCLUSION
Topical tranilast 8% gel provided significantly better postcaesarian section scar cosmesis and user satisfaction compared with placebo.
CHANGES IN CENTRAL CHOROIDAL THICKNESS AFTER TREATMENT OF DIABETIC MACULAR EDEMA WITH INTRAVITREAL BEVACIZUMAB CORRELATION WITH CENTRAL MACULAR THICKNESS AND BEST-CORRECTED VISUAL ACUITY
Authors: Nourinia Ramin , Ahmadieh Hamid , Nekoei Elnaz , Malekifar Parviz , Tofighi Zahra 
Published: April 2017

Purpose:
To assess the effect of intravitreal injection of bevacizumab on central choroidal thickness (CCT) and its relationship with central macular thickness (CMT) and best-corrected visual acuity (BCVA) changes in eyes with center-involving diabetic macular edema.

Methods:
This prospective interventional case series included 20 eyes of 20 patients with center-involving diabetic macular edema naive to treatment. The BCVA assessment, complete eye examination, enhanced depth optical coherence tomography, and fluorescein angiography were performed at baseline followed by 3 monthly intravitreal injection of bevacizumab. The treated eyes underwent BCVA evaluation and enhanced depth optical coherence tomography at Months 1, 2, 3, and 6 after the first injection. Change of the CCT was the primary outcome measure. Secondary outcome measures included BCVA and CMT changes and their relationship with CCT changes.

Results:
Mean age of patients was 63.1 ± 8.0 (range, 52–75) years. Mean baseline CCT was 265 ± 79 μm, which reduced to 251 ± 81 μm and 232 ± 82 μm at Months 3 and 6, respectively (P < 0.001). Corresponding values for CMT were 470 ± 107 μm, 392 ± 104 μm, and 324 ± 122 μm, respectively (P < 0.001). The BCVA improved from 20/60 at baseline to 20/50 at Month 3 and 20/40 at Month 6 (P = 0.007). Each 1 μm decrease in CCT was associated with 2.74 μm reduction in CMT and 0.1 Early Treatment Diabetic Retinopathy Study letter score improvement in BCVA (P < 0.001 and P = 0.001, respectively).

Conclusion:
After treatment of diabetic macular edema with intravitreal injection of bevacizumab, CCT decreased and this reduction significantly correlated with CMT reduction and vision improvement.
OUTER NUCLEAR LAYER THINNING IN PACHYCHOROID PIGMENT EPITHELIOPATHY
Authors: Ersoz M. Giray , Karacorlu Murat , Arf Serra , Hocaoglu Mumin , Sayman Muslubas Isil 
Published: April 2017

Purpose:
To compare the average thicknesses of central inner retinal layers in eyes with pachychoroid pigment epitheliopathy (PPE), with uncomplicated pachychoroid (UCP), and of healthy subjects.

Methods:
Medical records of patients with PPE and UCP were retrospectively reviewed. Twenty-nine eyes with foveal PPE, 30 eyes with UCP, and 29 eyes of healthy subjects were included. Spectral-domain optical coherence tomography with enhanced depth imaging was used for all optical coherence tomography scans. Mean central inner retinal layer thicknesses were measured in 1-mm-diameter circle with Spectralis automated segmentation software and compared between groups.

Results:
The outer nuclear layer (ONL) and the sum of the outer plexiform layer and ONL were significantly thinner in the PPE group than the UCP and control groups (ONL: P < 0.001, P < 0.001; outer plexiform layer + ONL: P = 0.002, P = 0.002, respectively). There was no significant difference between groups regarding thickness of the outer plexiform layer and other inner retinal layers. Eyes with UCP and normal eyes did not differ.

Conclusion:
The ONL is thinner in eyes with PPE. The degenerative process of pachychoroid spectrum diseases may begin with retinal pigment epithelium alterations before subretinal fluid accumulation. The PPE lesions, commonly seen above pachyvessels, may be an indicator of photoreceptor apoptosis.
Five Phases of Recovery and Rehabilitation After Allogeneic Stem Cell Transplantation
Authors: van der Lans Mariska C.M. , Witkamp Frederika E. , Oldenmenger Wendy H. , Broers Annoek E.C. 
Published: April 2017

Background:
For patients with a hematological malignancy, allogeneic stem cell transplantation (alloSCT) is a treatment modality that may cause a wide range of problems. Little is known about the process of recovery and rehabilitation and the problems that alloSCT patients are confronted with during the first-year posttransplant.

Objective:
This study explored the problems of patients during the first year after alloSCT, to better understand the process of recovery and rehabilitation.

Methods:
In a qualitative study, hemato-oncology patients were interviewed 1-year posttransplant. The semistructured interviews were transcribed verbatim, coded, and analyzed using constant comparative analysis.

Results:
Ten participants were included until saturation of data was reached. The patients had experienced various problems and had gone through an individual process of recovery and rehabilitation. Nevertheless, 5 phases could be distinguished: (1) survive, (2) on the receiving end, (3) bring under control, (4) start recuperation, and (5) retrospection. The duration of each phase varied between patients.

Conclusion:
Although patients experienced individual problems after alloSCT, they all followed a common pathway. Posttransplant care might be improved by adjusting the care to the distinct phases that the patients pass through.

Implications for Practice:
Nurses can play an important role in achieving improvements in posttransplant care by adjusting care to the individual needs of patients within the distinct phases.
Future nursing research should confirm and refine this process of recovery and rehabilitation and assess the effects of improvement measures in alloSCT patients and in other populations.
Exploring the Best Practices of Nursing Research Councils in Magnet® Organizations
Authors: Day Jennifer , Lindauer Cathleen , Parks Joyce , Scala Elizabeth 
Published: April 2017

OBJECTIVE
The objective of this descriptive qualitative study was to identify best practices of nursing research councils (NRCs) at Magnet®-designated hospitals.

BACKGROUND
Nursing research (NR) is essential, adding to the body of nursing knowledge. Applying NR to the bedside improves care, enhances patient safety, and is an imperative for nursing leaders.

METHODS
We interviewed NR designees at 26 Magnet-recognized hospitals about the structure and function of their NRCs and used structural coding to identify best practices.

RESULTS
Most organizations link NR and evidence-based practice. Council membership includes leadership and clinical nurses. Councils conduct scientific reviews for nursing studies, supporting nurse principal investigators. Tracking and reporting of NR vary widely and are challenging. Councils provide education, sponsor research days, and collaborate interprofessionally, including with academic partners.

CONCLUSIONS
Findings from this study demonstrate the need to create formal processes to track and report NR and to develop outcome-focused NR education.
Actinomyces in Pregnancy: A Review of the Literature
Authors: Estrada Sarah M. , Magann Everett F. , Napolitano Peter G. 
Published: April 2017

Importance

Actinomyces is commonly found in many areas of the body where it derives a benefit without harming the host. When it does infect the host during pregnancy, is that infection a threat to the obstetric patient and does that infection cause adverse pregnancy outcomes?

Objective
The aim of this study was to review what is known about Actinomyces infections and the impact of an Actinomyces infection on pregnancy outcomes.

Evidence Acquisition
A PubMed search was undertaken with the search years unlimited to April 1, 2016, and restricted to articles in English. The search terms included “actinomyces,” “pregnancy,” “prenatal,” “maternal,” “actinomyces infection,” “pregnancy,” “chorioamnionitis,” “preterm labor,” “premature birth,” or “postpartum actinomyces.”

Results
Eighteen of the 154 identified articles are the basis of this review. Actinomyces is a rod-like positive bacterium. The diagnosis of an Actinomyces infection can be by culture or Gram stain. Actinomyces is commensal and typically only infects after a mucosal break or lesion. Seventeen cases were identified in pregnancy. Ten cases were complicated by chorioamnionitis and a preterm delivery. A nidus leading to infection was identified in 12 of the cases including women with a cervical cerclage, dental abscesses, appendicitis, renal actinomycosis, and ovarian abscesses. Adverse pregnancy outcomes have been linked with periodontal disease, but treatment did not prevent preterm delivery in a randomized, blinded, controlled trial.

Conclusions

Actinomyces infections in pregnancy are rare but, if they occur, have been linked primarily with preterm deliveries.

Target Audience
Obstetricians and gynecologists, family physicians

Learning Objectives
After completing this activity, the learner should be better able to identify the areas of the body where Actinomyces infections occur and how the infections typically occur, identify the pathophysiologic changes that occur during pregnancy that might lead to an Actinomyces infection and how that infection may affect pregnancy outcomes, and describe the treatment for mild and severe Actinomyces infections.
Evolution and multiple roles of the Pancrustacea specific transcription factorzeldain insects
Authors: Ribeiro Lupis , Tobias-Santos Vitória , Santos Danielle , Antunes Felipe , Feltran Geórgia , de Souza Menezes Jackson , Aravind L. , Venancio Thiago Motta , Fonseca Rodrigo Nunes da 
Published: April 2017

SummaryGene regulatory networks (GRN) evolve as a result of the coevolutionary process acting on transcription factors and the cis-regulatory modules (CRMs) they bind. The zinc-finger transcription factor (TF)zelda(zld) is essential for maternal zygotic transition (MZT) inDrosophila melanogaster, where it directly binds over thousand CRMs to regulate chromatin accessibility.D. melanogasterdisplays a long germ type of embryonic development, where all segments are simultaneously generated along the whole egg. However, it remains unclear ifzldis also involved in MZT of short-germ insects (including those from basal lineages) or in other biological processes. Here we show thatzldis an innovation of the Pancrustacea lineage, being absent in more distant arthropods (e.g. chelicerates) and other organisms. To better understandzld’sancestral function, we thoroughly investigated its roles in a short-germ beetle,Tribolium castaneum, using molecular biology and computational approaches. Our results demonstrate roles forzldnot only during the MZT, but also in posterior segmentation and patterning of imaginal disc derived structures. Further, we also demonstrate thatzldis critical for posterior segmentation in the hemipteranRhodnius prolixus, indicating this function predates the origin of holometabolous insects and was subsequently lost in long-germ insects. Our results unveil new roles ofzldin maintaining pluripotent state of progenitor cells at the posterior region and suggest that changes in expression ofzld(and probably other pioneer TFs) are critical in the evolution of insect GRNs.