bluuebunny/crossref_metadata_2025_split huggingface dataset:
BiRen: predicting enhancers with a deep-learning-based model using the DNA sequence alone
Authors: Yang Bite , Liu Feng , Ren Chao , Ouyang Zhangyi , Xie Ziwei , Bo Xiaochen , Shu Wenjie 
Published: February 2017

Abstract

Motivation
Enhancer elements are noncoding stretches of DNA that play key roles in controlling gene expression programmes. Despite major efforts to develop accurate enhancer prediction methods, identifying enhancer sequences continues to be a challenge in the annotation of mammalian genomes. One of the major issues is the lack of large, sufficiently comprehensive and experimentally validated enhancers for humans or other species. Thus, the development of computational methods based on limited experimentally validated enhancers and deciphering the transcriptional regulatory code encoded in the enhancer sequences is urgent.

Results
We present a deep-learning-based hybrid architecture, BiRen, which predicts enhancers using the DNA sequence alone. Our results demonstrate that BiRen can learn common enhancer patterns directly from the DNA sequence and exhibits superior accuracy, robustness and generalizability in enhancer prediction relative to other state-of-the-art enhancer predictors based on sequence characteristics. Our BiRen will enable researchers to acquire a deeper understanding of the regulatory code of enhancer sequences.

Availability and Implementation
Our BiRen method can be freely accessed at https://github.com/wenjiegroup/BiRen.

Supplementary information
Supplementary data are available at Bioinformatics online.
Speed 2.0: Evaluating Access to Universal Digital Highways
Authors: Ahlfeldt Gabriel , Koutroumpis Pantelis , Valletti Tommaso 
Published: February 2017

AbstractThis paper shows that having access to a fast Internet connection is an important determinant of capitalization effects in property markets. Our empirical strategy combines a boundary discontinuity design with controls for time-invariant effects and arbitrary macroeconomic shocks at a very local level to identify the causal effect of broadband speed on property prices from variation that is plausibly exogenous. Applying this strategy to a micro data set from England between 1995 and 2010 we find a significantly positive effect, but diminishing returns to speed. Our results imply that disconnecting an average property from a high-speed first-generation broadband connection (offering Internet speed up to 8 Mbit/s) would depreciate its value by 2.8%. In contrast, upgrading such a property to a faster connection (offering speeds up to 24 Mbit/s) would increase its value by no more than 1%. We decompose this effect by income and urbanization, finding considerable heterogeneity. These estimates are used to evaluate proposed plans to deliver fast broadband universally. We find that increasing speed and connecting unserved households pass a cost–benefit test in urban and some suburban areas, whereas the case for universal delivery in rural areas is not as strong. (JEL: L1, H4, R2)
The nature of the Lyman α emitter CR7: a persisting puzzle
Authors: Pacucci Fabio , Pallottini Andrea , Ferrara Andrea , Gallerani Simona 
Published: February 2017

Abstract
The peculiar emission properties of the z ∼ 6.6 Lyα emitter COSMOS redshift 7 (CR7) have been initially interpreted with the presence of either a direct collapse black hole (DCBH) or a substantial mass of Pop III stars. Instead, updated photometric observations by Bowler et al. seem to suggest that CR7 is a more standard system. Here, we confirm that the original DCBH hypothesis is consistent also with the new data. Using radiation-hydrodynamic simulations, we reproduce the new infrared photometry with two models involving a Compton-thick DCBH of mass ≈7 × 106 M⊙ accreting (a) metal-free (Z = 0) gas with column density NH = 8 × 1025 cm−2 or (b) low-metallicity gas (Z = 5 × 10−3 Z⊙) with NH = 3 × 1024 cm−2. The best-fitting model reproduces the photometric data to within 1σ. Such metals can be produced by weak star-forming activity occurring after the formation of the DCBH. The main contribution to the Spitzer/IRAC 3.6 μm photometric band in both models is due to He i/He ii λλ4714, 4687 emission lines, while the contribution of [O iii] λλ4959, 5007 emission lines, if present, is sub-dominant. Spectroscopic observations with JWST will be required to ultimately clarify the nature of CR7.
The Cost of Brain Surgery: Awake vs Asleep Craniotomy for Perirolandic Region Tumors
Authors: Eseonu Chikezie I. , Rincon-Torroella Jordina , ReFaey Karim , Quiñones-Hinojosa Alfredo 
Published: February 2017

Abstract

BACKGROUND: Cost effectiveness has become an important factor in the health care system, requiring surgeons to improve efficacy of procedures while reducing costs. An awake craniotomy (AC) with direct cortical stimulation (DCS) presents one method to resect eloquent region tumors; however, some authors assert that this procedure is an expensive alternative to surgery under general anesthesia (GA) with neuromonitoring.

OBJECTIVE: To evaluate the cost effectiveness and clinical outcomes between AC and GA patients.

METHODS: Retrospective analysis of a cohort of 17 patients with perirolandic gliomas who underwent an AC with DCS were case-control matched with 23 patients with perirolandic gliomas who underwent surgery under GA with neuromonitoring (ie, motor-evoked potentials, somatosensory-evoked potentials, phase reversal). Inpatient costs, quality-adjusted life years (QALY), extent of resection, and neurological outcome were compared between the groups.

RESULTS: Total inpatient expense per patient was $34 804 in the AC group and $46 798 in the GA group (P = .046). QALY score for the AC group was 0.97 and 0.47 for the GA group (P = .041). The incremental cost per QALY for the AC group was $82 720 less than the GA group. Postoperative Karnofsky performance status was 91.8 in the AC group and 81.3 in the GA group (P = .047). Length of hospitalization was 4.12 days in the AC group and 7.61 days in the GA group (P = .049).

CONCLUSION: The total inpatient costs for awake craniotomies were lower than surgery under GA. This study suggests better cost effectiveness and neurological outcome with awake craniotomies for perirolandic gliomas.
Development of an item bank for computerized adaptive testing of self-reported cognitive difficulty in cancer patients
Authors: Dirven Linda , Taphoorn Martin JB , Groenvold Mogens , Habets Esther JJ , Aaronson Neil K , Conroy Thierry , Reijneveld Jaap C , Young Teresa , Petersen Morten Aa ,   on behalf of the EORTC Quality of Life Group
Published: February 2017

Abstract

Background
The European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Group is developing computerized adaptive testing (CAT) versions of each scale of the EORTC Quality of Life Questionnaire (EORTC QLQ-C30). This study aims to develop an item bank for the EORTC QLQ-C30 cognitive functioning scale, which can be used for CAT.

Methods
The complete developmental approach comprised four phases: (I) conceptualization and literature search, (II) operationalization, (III) pretesting, and (IV) field-testing. This paper describes phases I–III.
I) A literature search was performed to identify self-report instruments and items measuring cognitive complaints on concentration and memory. II) A multistep item-selection procedure was applied to select and generate items that were relevant and compatible with the ‘QLQ-C30 item style.’ III) Cancer patients from different countries evaluated the item list for wording (ie, whether items were difficult, confusing, annoying, upsetting or intrusive), and whether relevant issues were missing.

Results
A list of 439 items was generated by the literature search. In the multistep item-selection procedure, these items were evaluated for relevance, redundancy, clarity, and response format, resulting in an list of 45 items. A total of 32 patients evaluated this item list in the pretesting phase, resulting in a preliminary list of 44 items.

Conclusion
Phase I–III resulted in an item list of 44 items measuring self-reported cognitive complaints that was endorsed by international experts and cancer patients in several countries. This list will be evaluated for its psychometric characteristics in phase IV.
Elevated Voriconazole Level Associated With Hallucinations and Suicidal Ideation: A Case Report
Authors: Jansen Jeffrey W. , Sen Sumon K. , Moenster Ryan P. 
Published: February 2017

Abstract
Voriconazole, a broad-spectrum antifungal, has been associated with visual and auditory hallucinations. We report the case of patient being treated with voriconazole for pulmonary aspergillosis who developed visual hallucinations and new suicidal ideation with plan. Voriconazole troughs were supratherapeutic (9.0 mcg/mL) and the patient was positive for the CYP2C19*1/*2 allele.
Radical Dissection of Greater Palatine Artery and Dynamic Reconstruction of Cleft Palate
Authors: Fayyaz Ghulam Qadir , Gill Nauman Ahmad , Chaudry Ayesha , Ishaq Irfan , Aslam Muhammad , Shamim Romaisa , Kafeel Mirza Muhammad , Aazam Muhammad , Sailer Hermann , Ganatra Muhammad Ashraf 
Published: February 2017

Background:
Restoration of proper anatomy and physiology is an integral part of cleft palate repair. The senior author has devised a new technique of radical release of greater palatine vessels, which helps in achieving tension-free closure of palatal cleft. In addition, release and transposition of palatal muscles is performed without the use of operative microscope, resulting in improved palatal function. This technique is applicable to all types of clefts of the palate and can be performed on adult patients as well.

Materials and Methods:
This is a retrospective case series of cleft palate repairs performed over a period of 3 years. Single-stage repair with modified Bardach’s technique for complete cleft palate and von Langenbeck’s technique for incomplete cleft palate with radical release of greater palatine vessels and levator complex retropositioning was performed. The outcome measures were closure of palatal defect and speech production. A follow-up of at least 6 months was completed in each patient.

Results:
A total of 1568 patients were included in the study. Their age ranged from 9 months to 54 years. The overall fistula rate was 6.1%. Improvement of speech was observed even in adult patients.

Conclusions:
Radical release of greater palatine artery and levator complex transposition can dramatically improve results of cleft palate repair. This technique helps in dynamic reconstruction of cleft palate and can be effectively applied in all age groups.
Asymptomatic Infection in Decompensated Full-Thickness Corneal Grafts Referred for Repeat Penetrating Keratoplasty
Authors: Nahum Yoav , Leon Pia , Ricci-Filipovic Benedetta Azzurra , Camposampiero Davide , Ponzin Diego , Busin Massimo 
Published: February 2017

Purpose:
We report a case series of asymptomatic infections affecting failed corneal grafts in patients referred for repeat penetrating keratoplasty (PK).

Methods:
In this retrospective, noncomparative, interventional case series, we reviewed the medical records of all repeat PK procedures performed at Villa Serena-Villa Igea private Hospitals (Forlì, Italy) between January 2011 and March 2016. Specifically, preoperative and postoperative slit-lamp examinations, and the results of histological and bacteriological examinations, were noted.

Results:
Fifty-three repeat PKs were performed in the study period. All patients were referred because of long-standing graft decompensation with stromal scars or surface irregularities, thus unsuitable for endothelial keratoplasty. None was referred because of presumed infection. Histological examination of the explanted buttons showed the presence of microorganisms of various types in 7 eyes. Cultures were positive in 4 of these cases and in one additional case Staphylococcus aureus was grown in culture, but was not seen in the histology specimen. None of the patients presented with unusual pain, tearing, or discomfort. Preoperative abnormal clinical findings included epithelial defect (n = 6), focal whitening of corneal stroma (n = 5), crystalline keratopathy (n = 1), and an elevated pigmented lesion (n = 1). After repeat PK, recurrence of the infection was seen in 5 of 7 (71%) cases, 2 of which required a third PK procedure.

Conclusions:
Apparently quiet eyes with failed PK can harbor slow-growing asymptomatic infection. An epithelial defect in a failed PK graft should raise suspicion of infection. Routine cultures and histological examination of the excised corneal buttons are instrumental in the diagnosis of these infections and can guide further treatment.
Ocular Surface Epithelial Atypia Mimicking Squamous Neoplasia in Association With Ulcerative Colitis
Authors: Ong Sally S. , Walter Scott D. , Chen Xi , Vora Gargi K. , Daluvoy Melissa , Proia Alan D. , Mruthyunjaya Prithvi 
Published: February 2017

Purpose:
Inflammatory bowel disease may be associated with extraintestinal manifestations. We report a case of severe reactive epithelial atypia resembling ocular surface squamous neoplasia (OSSN) in a patient with ulcerative colitis (UC).

Methods:
Case report.

Results:
A 32-year-old woman presented with sequential, progressive keratoconjunctival lesions in the left and right eyes, and both lesions were excised. Anterior segment optical coherence tomography demonstrated features similar to OSSN, whereas histological examination revealed severe reactive epithelial atypia mimicking severe dysplasia. Shortly after treatment of the second eye, the patient was diagnosed with UC. Residual disease improved dramatically in response to systemic corticosteroids.

Conclusions:
Severe ocular surface epithelial atypia resembling OSSN may be seen in association with UC.
Successful Medical Management of Presumptive Pythium insidiosum Keratitis
Authors: Ramappa Muralidhar , Nagpal Ritu , Sharma Savitri , Chaurasia Sunita 
Published: February 2017

Purpose:
To describe the previously unreported successful treatment of presumptive Pythium keratitis (PK) with medical therapy alone.

Methods:
A 42-year-old female homemaker presented to us with a 15-day history of pain and redness in the right eye after a trivial injury. Her vision was 20/80 at presentation. Slit-lamp biomicroscopy revealed a central, dense and dry-looking, grayish-white infiltrate reaching mid stroma. The infiltrate had feathery margins and was surrounded by multiple tentacle-like lesions and peripherally expanding pinhead-sized subepithelial lesions. The contralateral eye was essentially normal. Diagnostic corneal scraping on smears revealed broad, aseptate, hyaline filaments with ribbon-like folds; very characteristic of Pythium species. Confocal imaging revealed fungal filaments. Based on corroborative evidence, a diagnosis of presumptive PK was made. She was administered a combination therapy consisting of eye drop linezolid 0.2% 1 hourly, azithromycin 1% 2 hourly, atropine sulfate 1% thrice daily, and oral azithromycin 500 mg once daily for 3 days in a week.

Results:
After initial worsening in the form of stromal expansion, regression of pinhead-sized lesions was seen with onset of scarring by as early as day 4 of intense medical therapy. The tentacle-like lesions did not worsen. On day 8, significant resolution was noted with scarring, and by the end of 2 weeks, the entire stromal lesion had scarred and complete resolution of expanding tentacles was observed in 3 weeks.

Conclusions:
Presumptive Pythium keratitis of the patient completely resolved with antibacterial treatment alone. It is pertinent for ophthalmologists to be aware of this new treatment regimen.
Suicide in Guyana: Nurses' Perspectives
Authors: Anthony Maureen , Groh Carla , Gash Jean 
Published: February 2017

ABSTRACT
Guyana, an English-speaking country on the north coast of South America, has the highest suicide rate in the world. Nurses are an integral part of the healthcare team working with patients experiencing psychological distress and are uniquely qualified to add to the discourse on factors contributing to the high suicide rate in Guyana. The purpose of this study was to explore the attitudes and experiences of nurses and nurse assistants in Guyana related to suicide. Nine registered nurses and nurse assistants who worked at a private hospital in Georgetown, Guyana, were recruited to participate in a focus group. The focus group lasted approximately 70 minutes and was recorded. The audio recordings were later transcribed word for word. Four themes emerged from the data: family issues as they relate to the high suicide rate, suicide attempts as a cry for help, lack of support, and coping mechanisms used by nurses when caring for victims of attempted suicide. Nurses are uniquely positioned to intervene with families in crisis, whether it be suicide, suicide attempts, or the underlying factors of family dysfunction, child maltreatment, poverty, or alcoholism. Establishing forensic nursing as a specialty in Guyana would validate this important role through education and certification of nurses.
Genetic control of erythropoiesis
Authors: Tumburu Laxminath , Thein Swee Lay 
Published: February 2017

Purpose of review
The discovery of several genetic variants associated with erythroid traits and subsequent elucidation of their functional mechanisms are exemplars of the power of the new genetic and genomic technology. The present review highlights findings from recent genetic studies related to the control of erythropoiesis and dyserythropoiesis, and fetal hemoglobin, an erythroid-related trait.

Recent findings
Identification of the genetic modulators of erythropoiesis involved two approaches: genome-wide association studies (GWASs) using single nucleotide polymorphism (SNP) arrays that revealed the common genetic variants associated with erythroid phenotypes (hemoglobin, red cell count, MCV, MCH) and fetal hemoglobin; and massive parallel sequencing such as whole genome sequencing (WGS) and whole exome sequencing (WES) that led to the discovery of the rarer variants (GFI1B, SBDS, RPS19, PKLR, EPO, EPOR, KLF1, GATA1). Functional and genomic studies aided by computational approaches and gene editing technology refined the regions encompassing the putative causative SNPs and confirmed their regulatory role at different stages of erythropoiesis.

Summary
Five meta-analysis of GWASs identified 17 genetic loci associated with erythroid phenotypes, which are potential regulators of erythropoiesis. Some of these loci showed pleiotropy associated with multiple erythroid traits, suggesting undiscovered molecular mechanisms and challenges underlying erythroid biology. Other sequencing strategies (WGS and WES) further elucidated the role of rare variants in dyserythropoiesis. Integration of common and rare variant studies with functional assays involving latest genome-editing technologies will significantly improve our understanding of the genetics underlying erythropoiesis and erythroid disorders.
Endothelial cell disease: emerging knowledge from cerebral cavernous malformations
Authors: Lampugnani Maria Grazia , Malinverno Matteo , Dejana Elisabetta , Rudini Noemi 
Published: February 2017

Purpose of review
Endothelial cells dysfunctions are crucial determinants of several human diseases. We review here the most recent reports on endothelial cell defects in cerebral cavernous malformations (CCMs), particularly focusing on adherens junctions. CCM is a vascular disease that affects specifically the venous microvessels of the central nervous system and which is caused by loss-of-function mutation in any one of the three CCM genes (CCM1, 2 or 3) in endothelial cells. The phenotypic result of these mutations are focal vascular malformations that are permeable and fragile causing neurological symptoms and occasionally haemorrhagic stroke.

Recent findings
CCM is still an incurable disease, as no pharmacological treatment is available, besides surgery. The definition of the molecular alterations ensuing loss of function mutation of CCM genes is contributing to orientate the testing of targeted pharmacological tools.
Several signalling pathways are altered in the three genotypes in a similar way and concur in the acquisition of mesenchymal markers in endothelial cells. However, also genotype-specific defects are reported, in particular for the CCM1 and CCM3 mutation.

Summary
Besides the specific CCM disease, the characterization of endothelial alterations in CCM has the potentiality to shed light on basic molecular regulations as the acquisition and maintenance of organ and vascular site specificity of endothelial cells.
Predictors of Acquisition of Competitive Employment for People Enrolled in Supported Employment Programs
Authors: Corbière Marc , Lecomte Tania , Reinharz Daniel , Kirsh Bonnie , Goering Paula , Menear Matthew , Berbiche Djamal , Genest Karine , Goldner Elliot M. 
Published: February 2017

Abstract
This study aims at assessing the relative contribution of employment specialist competencies working in supported employment (SE) programs and client variables in determining the likelihood of obtaining competitive employment. A total of 489 persons with a severe mental illness and 97 employment specialists working in 24 SE programs across three Canadian provinces were included in the study. Overall, 43% of the sample obtained competitive work. Both client variables and employment specialist competencies, while controlling for the quality of SE programs implementation, predicted job acquisition. Multilevel analyses further indicated that younger client age, shorter duration of unemployment, and client use of job search strategies, as well as the working alliance perceived by the employment specialist, were the strongest predictors of competitive employment for people with severe mental illness, with 51% of variance explained. For people with severe mental illness seeking employment, active job search behaviors, relational abilities, and employment specialist competencies are central contributors to acquisition of competitive employment.
Body Dysmorphic, Obsessive-Compulsive, and Social Anxiety Disorder Beliefs as Predictors of In Vivo Stressor Responding
Authors: Parsons E. Marie , Straub Kelsey T. , Smith April R. , Clerkin Elise M. 
Published: February 2017

Abstract
This study tested the potential transdiagnostic nature of body dysmorphic disorder (BDD), obsessive-compulsive disorder (OCD), and social anxiety disorder (SAD) beliefs, in addition to testing the specificity of those beliefs, in predicting how individuals responded to symptom-specific stressors. Participants included 127 adults (75% women) with a broad range of symptom severity. Path analysis was used to evaluate whether specific maladaptive beliefs predicted distress in response to symptom-relevant stressors over and above other beliefs and baseline distress. SAD beliefs emerged as a significant predictor of distress in response to a mirror gazing (BDD-relevant), a thought (OCD-relevant), and a public speaking (SAD-relevant) task, controlling for other disorder beliefs and baseline distress. BDD beliefs were also a robust predictor of BDD stressor responding. Results suggest that social anxiety-relevant beliefs may function as a transdiagnostic risk factor that predicts in vivo symptoms across a range of problem areas.