bluuebunny/crossref_metadata_2025_split huggingface dataset:
MusiteDeep: a deep-learning framework for general and kinase-specific phosphorylation site prediction
Authors: Wang Duolin , Zeng Shuai , Xu Chunhui , Qiu Wangren , Liang Yanchun , Joshi Trupti , Xu Dong 
Published: August 2017

Abstract

Motivation
Computational methods for phosphorylation site prediction play important roles in protein function studies and experimental design. Most existing methods are based on feature extraction, which may result in incomplete or biased features. Deep learning as the cutting-edge machine learning method has the ability to automatically discover complex representations of phosphorylation patterns from the raw sequences, and hence it provides a powerful tool for improvement of phosphorylation site prediction.

Results
We present MusiteDeep, the first deep-learning framework for predicting general and kinase-specific phosphorylation sites. MusiteDeep takes raw sequence data as input and uses convolutional neural networks with a novel two-dimensional attention mechanism. It achieves over a 50% relative improvement in the area under the precision-recall curve in general phosphorylation site prediction and obtains competitive results in kinase-specific prediction compared to other well-known tools on the benchmark data.

Availability and implementation
MusiteDeep is provided as an open-source tool available at https://github.com/duolinwang/MusiteDeep.

Supplementary information
Supplementary data are available at Bioinformatics online.
Estimating network edge probabilities by neighbourhood smoothing
Authors: Zhang Yuan , Levina Elizaveta , Zhu Ji 
Published: August 2017

SummaryThe estimation of probabilities of network edges from the observed adjacency matrix has important applications to the prediction of missing links and to network denoising. It is usually addressed by estimating the graphon, a function that determines the matrix of edge probabilities, but this is ill-defined without strong assumptions on the network structure. Here we propose a novel computationally efficient method, based on neighbourhood smoothing, to estimate the expectation of the adjacency matrix directly, without making the structural assumptions that graphon estimation requires. The neighbourhood smoothing method requires little tuning, has a competitive mean squared error rate and outperforms many benchmark methods for link prediction in simulated and real networks.
Forensic Implications in Disruptive Behavior Disorders
Authors: Hans Steiner , Whitney Daniels , Michael Kelly , Christina Stadler 
Published: August 2017

Abstract
This chapter tackles the complex task of putting the knowledge base of disruptive behavior disorders (DBDs) into a forensic context. The chapter first discusses the landmark legal cases that created a novel space for conceptualizing the psychopathology of crime. The implications of DBDs for culpability, rehabilitation, and institutional treatments. Real cases are used to prepare the clinician for the special challenges the psychiatric consultant to justice settings and the expert witness inevitably will face when involving themselves with DBD cases, the courts, justice settings, and follow-up care after incarceration. Special emphasis is put on the almost ubiquitous complexity of clinical syndromes in forensic cases that calls for considerable sophistication and breadth of clinical experience to do justice to this most difficult population.
Summary and Epilogue
Authors: Hans Steiner , Whitney Daniels , Michael Kelly , Christina Stadler 
Published: August 2017

Abstract
This final chapter provides an overview and summary of the major findings in each of the previous chapters (introduction, taxonomy and diagnosis; epidemiology; etiology; treatment; forensic implications). It concludes by highlighting the necessary future studies to guarantee continued progress in the field of disruptive behavior disorders. It is our hope that this book will serve a helpful guide for clinicians who are on the front lines caring for the most at risk youth in our communities. It is also our wish that this text help inspire a new generation of learners to pursue careers in this most rewarding field of study and public service.
Systematic Identification of LAEs for Visible Exploration and Reionization Research Using Subaru HSC (SILVERRUSH). I. Program strategy and clustering properties of ∼2000 Lyα emitters at z = 6–7 over the 0.3–0.5 Gpc2 survey area
Authors: Ouchi Masami , Harikane Yuichi , Shibuya Takatoshi , Shimasaku Kazuhiro , Taniguchi Yoshiaki , Konno Akira , Kobayashi Masakazu , Kajisawa Masaru , Nagao Tohru , Ono Yoshiaki , Inoue Akio K , Umemura Masayuki , Mori Masao , Hasegawa Kenji , Higuchi Ryo , Komiyama Yutaka , Matsuda Yuichi , Nakajima Kimihiko , Saito Tomoki , Wang Shiang-Yu 
Published: August 2017

Abstract
We present the SILVERRUSH program strategy and clustering properties investigated with ∼2000 Lyα emitters (LAEs) at z = 5.7 and 6.6 found in the early data of the Hyper Suprime-Cam (HSC) Subaru Strategic Program survey exploiting the carefully designed narrow-band filters. We derive angular correlation functions with the unprecedentedly large samples of LAEs at z = 6–7 over the large total area of 14–21 deg2 corresponding to 0.3–0.5 comoving Gpc2. We obtain the average large-scale bias values of bavg = 4.1 ± 0.2 (4.5 ± 0.6) at z = 5.7 (z = 6.6) for ≳ L* LAEs, indicating a weak evolution of LAE clustering from z = 5.7 to 6.6. We compare the LAE clustering results with two independent theoretical models that suggest an increase of an LAE clustering signal by the patchy ionized bubbles at the epoch of reionization (EoR), and estimate the neutral hydrogen fraction to be $x_{\rm H\,{\small I}}=0.15^{+0.15}_{-0.15}$ at z = 6.6. Based on the halo occupation distribution models, we find that the ≳ L* LAEs are hosted by dark-matter halos with an average mass of $\log (\left\langle M_{\rm h} \right\rangle /M_\odot ) =11.1^{+0.2}_{-0.4}$ ($10.8^{+0.3}_{-0.5}$) at z = 5.7 (6.6) with a Lyα duty cycle of 1% or less, where the results of z = 6.6 LAEs may be slightly biased, due to the increase of the clustering signal at the EoR. Our clustering analysis reveals the low-mass nature of ≳ L* LAEs at z = 6–7, and that these LAEs probably evolve into massive super-L* galaxies in the present-day universe.
Factors Associated with Opioid Initiation in OEF/OIF/OND Veterans with Traumatic Brain Injury
Authors: Hudson Teresa J , Painter Jacob T , Gressler Laura E , Lu Liya , Williams J Silas , Booth Brenda M , Martin Bradley C , Sullivan Mark D , Edlund Mark J 
Published: August 2017

AbstractObjectiveThese analyses examined opioid initiation and chronic use among Iraq (OIF) and Afghanistan (OEF/OND) veterans with a new diagnosis of traumatic brain injury (TBI) in the Veterans Health Administration (VHA).MethodsData were obtained from national VHA data repositories. Analyses included OEF/OIF/OND veterans with a new TBI diagnosis in 2010–2012 who used the VHA at least twice, had not received a VHA opioid prescription in the 365 days before diagnosis, and had at least 365 days of data available after TBI diagnosis.ResultsAnalyses included 35,621 veterans. Twenty-one percent initiated opioids; among new initiators, 23% used chronically. The mean dose was 24.0 mg morphine equivalent dose (MED) daily (SD = 24.26); mean days supplied was 60.52 (SD = 74.69). Initiation was significantly associated with age 36–45 years (odds ratio [OR] = 1.09, 95% CI = 1.01–1.17, P = 0.04), female gender (OR = 1.22, P < 0.001), having back pain (OR = 1.38, P < 0.0001), arthritis/joint pain (OR = 1.24, P < 0.0001), or neuropathic pain (OR = 1.415, P < 0.02). In veterans age 36–45 years, those living in small rural areas had higher odds of chronic opioid use (OR = 1.31, P < 0.0001, and OR = 1.33, P = 0.006, respectively) and back pain (OR = 1.36, P = 0.003). Headache/migraine pain was associated with decreased odds of chronic opioid use (OR = 0.639, P = 0.003).ConclusionsPrevalence of opioid use is relatively low among OEF/OIF/OND veterans with newly diagnosed TBI who are using VHA. Among those who initiated opioids, about 25% use them chronically. Prescribing was mostly limited to moderate doses, with most veterans using opioids for approximately two months of the 12-month study period.
Long-term Outcome of Argon Laser Peripheral Iridoplasty in the Management of Plateau Iris Syndrome Eyes
Authors: Peterson Jeffrey R. , Anderson John W. , Blieden Lauren S. , Chuang Alice Z. , Feldman Robert M. , Bell Nicholas P. 
Published: August 2017

Purpose:
To report long-term (>5 y) outcomes of plateau iris syndrome patients treated with argon laser peripheral iridoplasty (ALPI).

Patients and Methods:
A retrospective chart review was performed on all patients with plateau iris syndrome treated with ALPI from 1996 to 2007. The study included 22 eyes from 22 patients with plateau iris after peripheral iridotomy that were followed for at least 1 year after ALPI. The primary outcome was incidence of needing any intraocular pressure (IOP)-lowering medications or surgery (either a filtering procedure or phacoemulsification). Demographic and baseline clinical data were summarized by mean (±SD) or frequency (percentage). Snellen best-corrected visual acuity was converted to logMAR. The paired t test was used to compare IOP changes, number of IOP-lowering medications, and best-corrected visual acuity from baseline to annual follow-up.

Results:
Mean follow-up was 76 months. Only 2 (9%) eyes maintained an IOP<21 mm Hg without requiring medication or surgery. Seventeen (77%) eyes underwent surgery at an average of 49.1±7.9 months after ALPI. Eight (36%) eyes underwent filtering surgery, and 9 (41%) eyes underwent phacoemulsification. Three months after cataract extraction, no eyes required IOP-lowering medication.

Conclusions:
The beneficial effects of ALPI last for <4 years, with the majority of patients (77%) requiring surgery. Phacoemulsification alone was a successful treatment for plateau iris in our patient population.
The South Carolina Environmental Public Health Tracking Program's Role in Monitoring and Reducing Occupational Exposure to Lead: Public Health Actions in Collaboration with the South Carolina Occupational Safety and Health Administration
Authors: Davis Harley T. , Lynes Chelsea , Corley H. Reed 
Published: August 2017

Per South Carolina (SC) Law §44-29-10, all blood lead test records are reportable. The SC Environmental Public Health Tracking (SC EPHT) program is directly involved in blood lead surveillance in SC, as it maintains the blood lead record database. Although Adult Blood Lead Epidemiology and Surveillance funding from the Centers for Disease Control and Prevention was discontinued in 2013, SC EPHT has continued to monitor and record adult blood lead test records.
In 2012, SC EPHT signed a memorandum of understanding with the SC Occupational Safety and Health Administration (SC OSHA). Per this agreement, quarterly reports of elevated adult blood lead concentrations (≥25 μg/dL) are supplied to SC OSHA, along with North American Industry Classification System codes of employers. This information is used for industrial inspections, mitigation, and abatement related to lead. The SC EPHT program's collaboration with SC OSHA has resulted in a number of public health actions that have improved the health and well-being of workers in SC. Of the 3 nationally accepted SC public health actions related to occupational lead exposure, 2 detail investigations and citations by SC OSHA. The other describes internal analyses conducted by the SC EPHT program regarding elevated blood lead levels in adults and associations with specific North American Industry Classification System codes.
In this review, we outlined the role of SC EPHT related to adult blood lead surveillance in SC, including implementation of the memorandum of understanding with SC OSHA. We also examined demographics of adult blood lead records in SC for 2010-2015 and summarized public health actions related to occupational lead exposure in SC. Since federal funding for the SC EPHT program was initiated in 2009, the program has played an important part in lead surveillance in SC. The resulting health benefits to those with the potential for occupational exposure to lead are extremely important.
E-Media Use and Preferences for Physical Activity and Public Health Information: Results of a Web-Based Survey
Authors: Jake-Schoffman Danielle E. , Wilcox Sara , Kaczynski Andrew T. , Turner-McGrievy Gabrielle , Friedman Daniela B. , West Delia S. 
Published: August 2017

Context:
As social media (eg, Twitter) continues to gain widespread popularity, health research and practice organizations may consider combining it with other electronic media (e-media) channels (eg, Web sites, e-newsletters) within their communication plans. However, little is known about added benefits of using social media when trying to reach public health audiences about physical activity.

Objective:
Learn about current use and preference for e-media communication channels among physical activity researchers and practitioners.

Design:
A Web-based survey was used, open for responses from August 20, 2015, through January 5, 2016. Survey participation was voluntary and anonymous. The survey was advertised through multiple channels targeting physical activity researchers and practitioners, including announcements on professional listservs and in e-newsletters, Twitter, and posts on Facebook pages of public health organizations.

Setting and Participants:
A total of 284 survey respondents had complete data.

Main Outcome Measures:
Typical use of e-media to receive, seek out, and share information about physical activity and health and what appeals to researchers and practitioners for professional use.

Results:
Most respondents preferred non–social media channels to social media and these preferences did not differ widely when examining subgroups such as researchers versus practitioners or social media users versus nonusers. There were few differences by respondent demographics, though younger respondents reported using social media more than older respondents. However, limiting analyses to respondents who identified as social media users, only about 1% of respondents ranked social media sources as their preferred channels for information; thus, most people would continue to be reached if communication remained largely via non–social media e-media channels.

Conclusions:
The present study supports growing evidence that careful surveying of a target audience should be undertaken when considering new communication channels, as preference and use may not support the effort required to create and maintain resource-intensive strategies like social media.
The Usefulness of Individual-Level HIV Surveillance Data to Initiate Statewide HIV Partner Services: Experiences From Hawaii and New Mexico
Authors: Beltrami John , Gans Andrew , Wozniak Michelle , Murphy John , Puesta Benjamin , Kennebrew Daphne , Angie Allen Mary , O'Connor Kevin 
Published: August 2017

Context:
Partner services are a broad array of services that should be offered to persons with human immunodeficiency virus (HIV) and that are based on a process through which HIV-infected persons are interviewed to elicit information about their sex and needle-sharing partners. Human immunodeficiency virus testing of partners can result in a high yield of newly diagnosed HIV positivity, but despite this yield and the benefits of partners knowing their exposures and HIV status, partner services are often not conducted.

Objective:
We sought to determine the newly diagnosed HIV positivity and benefits to 2 health departments that conducted demonstration projects that focused on statewide HIV partner services.

Design:
The main sources of information used for this case study analysis included the health department funding applications, progress reports and final reports submitted to the Centers for Disease Control and Prevention, and records of communications between Centers for Disease Control and Prevention and the health departments. Required quantitative reporting included the number of partners tested and the number of partners with newly diagnosed confirmed HIV infection. Required qualitative reporting included how health departments benefited from their demonstration project activities.

Setting:
Hawaii and New Mexico.

Participants:
Sex and needle-sharing partners of persons who were newly diagnosed with HIV infection.

Intervention:
The use of HIV surveillance data to initiate statewide HIV partner services.

Main Outcome Measure:
Newly diagnosed HIV positivity.

Results:
During 2012-2015, the newly diagnosed HIV positivity among partners was 18% (78/427): 16% (17/108) in Hawaii and 19% (61/319) in New Mexico. The health departments benefited from improved collaborations among HIV prevention program and surveillance staff and among the health departments, providers, and AIDS service organizations.

Conclusions:
Hawaii and New Mexico each achieved a high newly diagnosed HIV positivity and benefited from improved local collaborations. As a result of the success of these projects, both health departments have continued the activities since the end of category C funding by securing alternative funding sources.
Heterochronic Developmental Shifts Underlie Floral Diversity withinJaltomata(Solanaceae)
Authors: Kostyun Jamie L. , Preston Jill C. , Moyle Leonie C. 
Published: July 2017

AbstractBackgroundHeterochronic shifts during mid to late stages of organismal development have been proposed as key mechanisms generating phenotypic diversity. To determine whether late heterochronic shifts underlie derived floral morphologies withinJaltomata(Solanaceae) – a genus whose species have extensive and recently evolved floral diversity – we compared floral development of four diverse species (including an ambiguously ancestral or secondarily derived rotate, two putatively independently evolved campanulate, and a tubular morph) to the ancestral rotate floral form, as well as to an outgroup that shares this ancestral floral morphology.ResultsWe determined that early floral development (<1 mm bud diameter, corresponding to completion of organ whorl initiation) is very similar among all species, but that different mature floral forms are distinguishable by mid-development (>1 mm diameters) due to differential growth acceleration of corolla traits. Floral ontogeny among similar mature rotate forms remains comparable until late stages, while somewhat different patterns of organ growth are found between species with similar campanulate forms.ConclusionsOur data suggest shared floral patterning during early-stage development, but that different heterochronic shifts during mid- and late-stage development contributes to divergent floral traits. Heterochrony thus appears to have been important in the rapid and repeated diversification ofJaltomataflowers.
The contribution of genetic variation ofStreptococcus pneumoniaeto the clinical manifestation of invasive pneumococcal disease
Authors: Cremers Amelieke JH , Mobegi Fredrick M , van der Gaast –de Jongh Christa , van Weert Michelle , van Opzeeland Fred J , Vehkala Minna , Knol Mirjam J , Bootsma Hester J , Välimäki Niko , Meis Jacques F , Bentley Stephen , van Hijum Sacha AFT , Corander Jukka , Zomer Aldert L , Ferwerda Gerben , de Jonge Marien I 
Published: July 2017

AbstractBackgroundDifferent clinical manifestations of invasive pneumococcal disease (IPD) have thus far mainly been explained by patient characteristics. Here we studied the contribution of pneumococcal genetic variation to IPD phenotype.MethodsThe index cohort consisted of 349 patients admitted to two Dutch hospitals between 2000-2011 with pneumococcal bacteraemia. We performed genome-wide association studies to identify pneumococcal lineages, genes and allelic variants associated with 23 clinical IPD phenotypes. The identified associations were validated in a nationwide (n=482) and a post-pneumococcal vaccination cohort (n=121). The contribution of confirmed pneumococcal genotypes to the clinical IPD phenotype, relative to known clinical predictors, was tested by regression analysis.FindingsThe presence of pneumococcal geneslaAwas a nationwide confirmed independent predictor of meningitis (OR=10.5, p=0.001), as was sequence cluster 9 (OR=3.68, p=0.057). A set of 4 pneumococcal genes co-located on a prophage was a confirmed independent predictor of 30-day mortality (OR=3.4, p=0.003). We could detect the pneumococcal variants of concern in these patients’ blood samples by molecular amplification. In the post-vaccination cohort where the distribution of both patient characteristics and pneumococcal serotypes had changed, the relative importance of the prophage was no longer supported.InterpretationKnowledge of pneumococcal genotypic variants improved our clinical risk assessment for detrimental manifestations of IPD. This provides us with novel opportunities to target, anticipate or avert the pathogenic effects that are related to particular pneumococcal variants. Therefore, future diagnostics should facilitate prompt appreciation of pathogen diversity in clinical sepsis management. Ongoing surveillance is warranted to monitor the clinical value of information on pathogen variants in dynamic microbial and susceptible host populations.FundingNone.
Dainik Bhaskar: live no negative
Authors: Parsad Chandan , Prashar Sanjeev , Sahay Vinita 
Published: August 2017

Subject area
Strategic Marketing Management. This case is also relevant for discussion in other courses like brand management.

Study level/applicability
Postgraduate Management students.

Case overview
Just before the official launch of “no-negative” news edition by Dainik Bhaskar Corp. Ltd, there was widespread speculation that the group was risking too much by going against the set convention of the newspaper industry. The common belief in the industry was “If it bleeds, it leads” and “good news is no news”. While endeavoring to do away with this perception, the management needed answers to questions like “Would it really be an attractive proposition for the readers?”, “Was the group compromising the role and responsibilities of press in presenting the truth to the world?” and “How would it add value to the brand?” The entire debate was pivoted around the sustainability of positive marketing strategy and “Is it a good idea to go forward with No Negative?” For decades, Dainik Bhaskar was known for its strategy of capturing untapped markets or denting into monopolistic markets and become a leader. This case is an odyssey of moving away from the “me-too” to category (positive newspaper) positioning. The main objective of this case is to build the concept and rudiments of positive marketing in practical perspectives using the backdrop of the Hindi newspaper industry and its largest player breaking the myth “only negative news sell”. Besides this, the case also evolves the process of institutionalizing positive marketing in organizations.

Expected learning outcomes
The primary objective of teaching through this case is to make students aware and understand the emerging strategy of positive marketing and its ability to break through the present clutter in the market. It also elaborates on how companies can use this tool for differentiating themselves from others.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.

Subject code
CSS 8: Marketing.