bluuebunny/crossref_metadata_2025_split huggingface dataset:
GenoSurf: metadata driven semantic search system for integrated genomic datasets
Authors: Canakoglu Arif , Bernasconi Anna , Colombo Andrea , Masseroli Marco , Ceri Stefano 
Published: October 2019

Abstract
Many valuable resources developed by world-wide research institutions and consortia describe genomic datasets that are both open and available for secondary research, but their metadata search interfaces are heterogeneous, not interoperable and sometimes with very limited capabilities. We implemented GenoSurf, a multi-ontology semantic search system providing access to a consolidated collection of metadata attributes found in the most relevant genomic datasets; values of 10 attributes are semantically enriched by making use of the most suited available ontologies. The user of GenoSurf provides as input the search terms, sets the desired level of ontological enrichment and obtains as output the identity of matching data files at the various sources. Search is facilitated by drop-down lists of matching values; aggregate counts describing resulting files are updated in real time while the search terms are progressively added. In addition to the consolidated attributes, users can perform keyword-based searches on the original (raw) metadata, which are also imported; GenoSurf supports the interplay of attribute-based and keyword-based search through well-defined interfaces. Currently, GenoSurf integrates about 40 million metadata of several major valuable data sources, including three providers of clinical and experimental data (TCGA, ENCODE and Roadmap Epigenomics) and two sources of annotation data (GENCODE and RefSeq); it can be used as a standalone resource for targeting the genomic datasets at their original sources (identified with their accession IDs and URLs), or as part of an integrated query answering system for performing complex queries over genomic regions and metadata.
Morphometric analysis of the palatal shape and arch dimension in subjects with buccally displaced canine
Authors: Mucedero Manuela , Rozzi Matteo , Di Fusco Giulia , Danesi Carlotta , Cozza Paola 
Published: October 2019

SummaryObjectivesTo analyse morphological variations of the palate shape and maxillary arch dimension between a group of subjects with unilaterally or bilaterally buccally impacted maxillary canines and a control group (CG) by means of 3D geometric morphometric (GMM).MaterialsPre-treatment records of 50 subjects (16 males and 34 females; mean age 13.9 years ± 1.8) with one or both canines buccally displaced were collected retrospectively. A CG of 50 subjects was selected from a list of orthodontic patients at the same dental hospital. The experimental group, buccally displaced canine (BDC) was divided in two groups: unilateral buccally displaced canine (UBDC) and bilateral buccally displaced canine (BBDC). To analyse the palate’s shape and maxillary arch dimension, study casts were scanned. To study the entirety of the palatal shape, 3D GMM analysis was used. To analyse the maxillary arch dimension, the virtual three-dimensional models were measured with a specific software (VAM, Vectra, Canfield Scientific, Fairfield, New Jersey, USA).ResultsWhen comparing the groups with the GMM analysis, patients with BDC showed a statistically significant narrower and higher palatal vault. About the analysis of linear measurements, the intercanine width, the anterior and posterior segment length were significantly smaller in BDC, UBDC, and BBDC subjects when compared with the controls and there were no differences between UBDC versus BBDC groups.ConclusionsPatients with buccally displaced permanent canine tended to have maxillary transverse constriction and variation in palatal vault morphology. The morphometric variation of the palatine vault and arch dimensions can be considered a clinical factor associated with the presence of BDC.
Host specificity in diatom–bacteria interactions alleviates antagonistic effects
Authors: Stock Willem , Blommaert Lander , De Troch Marleen , Mangelinckx Sven , Willems Anne , Vyverman Wim , Sabbe Koen 
Published: October 2019

ABSTRACTWhile different microalgae tend to be associated with different bacteria, it remains unclear whether such specific associations are beneficial for the microalgae. We assessed the impact of bacterial isolates, derived from various marine benthic diatoms, on the growth of several strains belonging to the Cylindrotheca closterium diatom species complex. We first tested the effect of 35 different bacterial isolates on the growth of a single C. closterium strain, and then evaluated the impact of 8 of these isolates on the growth of 6 C. closterium strains and 1 Cylindrotheca fusiformis strain. Surprisingly, most interactions were neutral to antagonistic. The interactions were highly specific, with diatom growth in the presence of specific bacteria differing between Cylindrotheca strains and species, and closely related bacteria eliciting contrasting diatom growth responses. These differences could be related to the origin of the bacterial isolates, as only isolates from foreign diatom hosts significantly reduced diatom growth, implying coadaptation between different Cylindrotheca strains and their associated bacteria. Interestingly, the antagonistic effect of a Marinobacter strain was alleviated by the presence of a microbial inoculum that was native to the diatom host, suggesting that coadapted bacteria might also benefit their host indirectly by preventing the establishment of harmful bacteria.
Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP)
Authors: Carpenter Eric J , Matasci Naim , Ayyampalayam Saravanaraj , Wu Shuangxiu , Sun Jing , Yu Jun , Jimenez Vieira Fabio Rocha , Bowler Chris , Dorrell Richard G , Gitzendanner Matthew A , Li Ling , Du Wensi , K. Ullrich Kristian , Wickett Norman J , Barkmann Todd J , Barker Michael S , Leebens-Mack James H , Wong Gane Ka-Shu 
Published: October 2019

Abstract

Background
The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae).

Findings
This data release accompanies the initiative's final/capstone publication on a set of 3 analyses inferring species trees, whole genome duplications, and gene family expansions. These and previous analyses are based on de novo transcriptome assemblies and related gene predictions. Here, we assess their data and assembly qualities and explain how we detected potential contaminations.

Conclusions
These data will be useful to plant and/or evolutionary scientists with interests in particular gene families, either across the green plant tree of life or in more focused lineages.
A ranking system based on inverse data envelopment analysis
Authors: Soleimani-Chamkhorami Khosro , Hosseinzadeh Lotfi Farhad , Jahanshahloo Gholamreza , Rostamy-Malkhalifeh Mohsen 
Published: October 2019

Abstract
Inverse (DEA) is an approach to estimate the expected input/output variation levels when the efficiency score reminds unchanged. Essentially, finding most efficient decision-making units (DMUs) or ranking units is an important problem in DEA. A new ranking system for ordering extreme efficient units based on inverse DEA is introduced in this article. In the adopted method, here the amount of required increment of inputs by increasing the outputs of the unit under evaluation is obtained through the proposed models. By obtaining these variations, this proposed methodology enables the researcher to rank the efficient DMUs in an appropriate manner. Through the analytical theorem, it is proved that suggested models here are feasible. These newly introduced models are validated through a data set of commercial banks and a numerical example.
Reproduction of white-tailed deer in a seasonally dry tropical forest of Costa Rica: a test of aseasonality
Authors: Fuller Todd K , Silva Alexander M , Montalvo Victor H , Sáenz-Bolaños Carolina , Carrillo J Eduardo 
Published: October 2019

Abstract
The reproductive season of white-tailed deer (Odocoileus virginianus) has been hypothesized to be aseasonal south of about 14°–18°N latitude, where annual variation in day length is low. We tested this idea by using camera-trap data (1,336 photographed individuals identified by age and sex) collected during 2011–2017 in the dry tropical forest of Santa Rosa National Park, northwest Costa Rica, where wet and dry seasons are well-defined. We identified variation in monthly occurrence of spotted deer fawns, as well as the status of antler growth of male deer, specifically related to the very seasonal environment of the region. Year-round reproduction likely occurs, but the rainfall pattern in the area greatly influences the relative frequency of reproductive indicators, with most births occurring during the dry season, and a second peak occurring toward the latter part of the wet season. We speculate that food resources are the major influence on reproductive patterns, and that variation in types and timing of food resource availability likely account for the variation in reproductive patterns.
The effect of urban development on visitor numbers to nearby protected nature conservation sites
Authors: Weitowitz Damiano C , Panter Chris , Hoskin Rachel , Liley Durwyn 
Published: October 2019

Abstract
New housing development can result in impacts on nearby protected nature conservation sites, even if development is outside the site boundary. High levels of housing may be associated with adverse impacts on ecological features in protected sites from increased recreation pressure. However, few studies have investigated the spatial link between housing and visitor numbers. An understanding of the impact of housing on visitor use, especially the distances at which housing relates to recreation levels and the importance of other factors (e.g. parking provision) is essential to inform the assessment of new housing and is relevant to strategic planning of development within the UK. We use a long-term visitor dataset (2003–8) to disentangle the housing–visitor association at foot-only and parking locations on important nature conservation sites. We conclude with negative binomial regressions that model the effect of housing on visitor numbers, while controlling for habitat, parking provision and season.
Our results demonstrate that more housing consistently means more visitors to protected sites, across most habitats. This is particularly the case for on-foot visitors that originate from housing within 1.5 km, highlighting that additional housing development in proximity to protected sites is likely to significantly increase recreation pressure. For visitor numbers at parking locations, levels of housing within 15 km of protected sites were also a significant predictor, but depended on habitat type. These results demonstrate that housing allocations closer to protected sites are likely to have a greater impact in terms of visitor numbers and may help underpin future assessments of strategic plans.
Educate, Try, and Share: A Feasibility Study to Assess the Acceptance and Use of Reiki as an Adjunct Therapy for Chronic Pain in Military Health Care Facilities
Authors: Gantt MeLisa , Orina Judy Ann T 
Published: October 2019

Abstract

Introduction
Reiki, a biofield energy therapy, continues to struggle in finding its permanent place among the portfolio of complementary and alternative medicine modalities in many military health care facilities. Although it has been shown to help in the management of pain, lack of knowledge and limited first-hand experience impact its foothold. The purpose of this feasibility study was to (1) educate participants about the concept of Reiki, (2) give participants the opportunity to experience six Reiki therapy sessions and subsequently assess outcomes on chronic pain, and (3) assess participants’ impression of and willingness to continue using and recommending Reiki therapy as adjunct for the treatment of chronic pain.

Methods
Using a prospective repeated measures pre- and postintervention design, a convenience sample of 30 military health care beneficiaries with chronic pain were educated about Reiki and received six 30-minute Reiki sessions over 2 to 3 weeks. Pain was assessed using a battery of pain assessment tools as well as assessment of impression of and willingness to share the concept of Reiki. This study was approved by the U.S. Army Medical Research and Materiel Command Institutional Review Board (No. M10617).

Results
Repeated measures ANOVA analyses showed that there was significant decrease (P &lt; 0.001) in present, average, and worst pain over the course of the six sessions with the most significant effect occurring up to the fourth session. When a variety of descriptor of pain was assessed, Reiki had a significant effect on 12 out of the 22 assessed, with the most significant effect on pain that was described as tingling/pins and needles (P = 0.001), sharp (P = 0.001), and aching (P = 0.001). Pain’s interference with general activity, walking, relationships, sleep, enjoyment of life, and stress significantly decreased (P &lt; 0.001 to P = 0.002). Impression of improvement scores increased 27% by session 6, and one’s knowledge about Reiki improved 43%. Eighty-one percent of the participants stated that they would consider scheduling Reiki sessions if they were offered with 70% desiring at least four sessions per month.

Conclusion
A 30-minute Reiki session, performed by a trained Reiki practitioner, is feasible in an outpatient setting with possible positive outcomes for participants who are willing to try at least four consecutive sessions. Reiki has the ability to impact a variety of types of pain as well as positively impacting those activities of life that pain often interferes with. However, education and the opportunity to experience this energy healing modality are key for its acceptance in military health care facilities as well as more robust clinical studies within the military health care system to further assess its validity and efficacy.
Lack of association between modifiable exposures and glioma risk: A Mendelian randomisation analysis
Authors: Saunders Charlie N , Cornish Alex J , Kinnersley Ben , Law Philip J , Claus Elizabeth B , Il’yasova Dora , Schildkraut Joellen , Barnholtz-Sloan Jill S , Olson Sara H , Bernstein Jonine L , Lai Rose K , Chanock Stephen , Rajaraman Preetha , Johansen Christoffer , Jenkins Robert B , Melin Beatrice S , Wrensch Margaret R , Sanson Marc , Bondy Melissa L , Houlston Richard S 
Published: October 2019

Abstract

Background
The etiological basis of glioma is poorly understood. We have used genetic markers in a Mendelian Randomisation (MR) framework to examine if lifestyle, cardiometabolic and inflammatory factors influence the risk of glioma. This methodology reduces bias from confounding and is not affected by reverse causation.

Methods
We identified genetic instruments for 37 potentially modifiable risk factors and evaluated their association with glioma risk using data from a genome-wide association study of 12,488 glioma patients and 18,169 controls. We used the estimated odds ratio of glioma associated with each of the genetically defined traits to infer evidence for a causal relationship with the following exposures: lifestyle and dietary factors (height, plasma IGF-1, blood carnitine, blood methionine, blood selenium, blood zinc, circulating adiponectin, circulating carotenoids, iron status, serum calcium, vitamin [A1, B12, B6, E and 25-hydroxyvitamin D], fatty acids levels [mono-unsaturated, omega-3 and omega-6] and circulating fetuin-A); cardiometabolic factors (birth weight, HDL cholesterol, LDL cholesterol, total cholesterol, total triglycerides, basal metabolic rate, body fat percentage, body mass index, fasting glucose, fasting proinsulin, HbA1C levels, diastolic and systolic blood pressure, waist circumference, waist-to-hip ratio) were included; inflammatory factors (C-reactive protein (CRP), plasma IL-6 sRa and serum IgE).

Results
After correction for the testing of multiple potential risk factors and excluding associations driven by one single nucleotide polymorphism (SNP) no significant association with glioma risk was observed (i.e. PCorrected > 0.05).

Conclusions
This study did not provide evidence supporting any of the 37 factors examined as having a significant influence on glioma risk.
844. Engagement in HIV Care as an Avenue to Primary Care in Rural South Africa: Results from the Vukuzazi Population Health Platform
Authors: M`yambo Magodoro Itai , Oliver Stephen , Gareta Dickman , Modise Tshwaraganang H , Koole Olivier , Herbst Kobus , Pillay Deenan , Wong Emily , Siedner Mark J 
Published: October 2019

Abstract

Background
The healthcare infrastructure developed in response to the HIV epidemic in sub-Saharan Africa has been proposed as a model to respond to the emerging noncommunicable disease (NCD) burden in the region. However, the evidence for the effectiveness of such a strategy is equivocal.

Methods
We conducted a population-wide health screening among adults ≥15 years within a demographic and health surveillance site (DHSS) in rural South Africa. We collected blood pressure (BP), glycated hemoglobin (HbA1c), HIV disease indicators, and healthcare utilization data. We defined hypertension (HTN) as BP ≥140/90mmHg or use of antihypertensive medication in the past 2 weeks, and diabetes (DM) as HbA1c ≥6.5% or use of hypoglycemic medication in the past two weeks. Cascade of care indicators included: (1) awareness of NCD diagnosis, (2) seeing a provider within the past 6 months; (3) reported use of medication; and (4) disease control, defined as BP <140/90 mmHg or HbA1c <6.5%. We fit regression models to NCD care indicators between people with HIV on ART (PWHA) and HIV negatives. To make population-level estimates, we used inverse probability sampling weights derived from sex- and age-adjusted regression models drawn from the entire DHSS population.

Results
Of 7,992 individuals, 5,911 (74.2%) were HIV-negative and 2,080 (25.8%) were PWHA (Table 1). PWHA had lower prevalence of both DM (6.8% vs. 10.4%) and HTN (18.0% vs. 24.8%). In multivariable models, linkage to HIV care was associated with improved HTN care cascade indicators, but not DM indicators (Figure 1). PWHA had lower systolic BP and HbA1c than HIV negatives (Figures 2 and 3).

Conclusion
Linkage to ART programs may be associated with better HTN but not DM care in rural South Africa. Future work should explore how to translate success in ART programs to other NCDs, and for HIV-negative individuals.

Disclosures
All Authors: No reported Disclosures.
849. Reduced CIED Infections with an Antibacterial Envelope: Microbiologic Analysis of the WRAP-IT Study
Authors: Sohail Muhammad R , Corey G Ralph , Wilkoff Bruce L , Poole Jeanne , Mittal Suneet , Kennergren Charles , Greenspon Arnold J , Cheng Alan , Lande Jeff , Lexcen Daniel R , Tarakji Khaldoun 
Published: October 2019

Abstract

Background
Cardiovascular implantable electronic device (CIED) infections are associated with significant morbidity, mortality, and cost. There is limited evidence on antibiotic prophylactic strategies to prevent CIED infection. Recently, the TYRX Envelope, which elutes a combination of rifampin and minocycline for a minimum of 7 days, was shown to significantly reduce major CIED infections in the WRAP-IT trial. We sought to characterize the pathogens among patients who experienced an infection in the current era.

Methods
All patients undergoing CIED replacement, upgrade, revision, or de novo cardiac resynchronization therapy (CRT-D) received standard of care antibiotic prophylaxis and were randomized 1:1 to receive TYRX or not. The primary endpoint was major CIED infection within 12 months of the procedure. Major infection was defined as an infection resulting in (1) system extraction or revision, (2) long-term suppressive antibiotic therapy, or (3) death. Data were analyzed using the Cox proportional hazards regression model.

Results
A total of 6,983 patients were randomized worldwide with 3,495 randomized to receive an envelope and 3,488 randomized to the control. At 12 months, 25 major infections (0.7%) were observed in the envelope group and 42 major infections (1.2%) in the control group, resulting in a 40% reduction of major infections (HR: 0.60, 95% CI: 0.36–0.98, P = 0.04). Of 63 infections assayed, causative pathogens were identified in 36 infections whereas cultures were negative in 27 cases. Staphylococcus species (n = 22) were the predominate pathogens and a 53% reduction was observed with the use of TYRX (Figure 1). Moreover, there was only 1 CIED pocket infection with Staphylococcus species in the envelope group compared with 14 pocket infections in the control group. A comparison of timing of infection in the envelope group showed the presence of 11 endocarditis/bacteremia infections at 103 ± 84 days compared with 14 pocket infections presenting at 70 ± 78 days from the procedure.

Conclusion
In this large randomized trial, the use of the TYRX Envelope containing rifampin and minocycline resulted in a significant reduction of major CIED infections and was effective against staphylococcal species, which are the predominant cause of pocket infections.

Disclosures
All Authors: No reported Disclosures.
890. Bridging the Gap to Help Address the Opioid Crisis: A Novel Model of Care to Integrate Substance Use, Mental Health, and Infectious Disease Services
Authors: Corace Kimberly , Schubert Nicholas , Willows Melanie , Herbert Guy , Garber Gary 
Published: October 2019

Abstract

Background
There is a converging public health crisis as the opioid epidemic and increased injection drug use is driving rates of infectious diseases. Multidisciplinary care, integrating infectious diseases, substance use, and mental health services, is crucial to address this crisis. This study evaluated a novel rapid access care model to improve treatment access for opioid use, mental health, and related infectious diseases.

Methods
The Rapid Access Addiction Medicine (RAAM) clinic is a multidisciplinary, walk-in care model located in a mental health center in Ottawa, Canada. RAAM provides collaborative, inter-agency care, with rapid access to care facilitated through seamless care pathways (i.e., from the emergency department). RAAM offers substance use and mental health treatment, screening and care for infectious diseases, harm reduction, and connection to community services. RAAM patients (N = 411) presenting between April 2018 and January 2019 completed substance use and mental health measures upon intake and 30-day follow-ups. Clinical information was collected via chart review.

Results
Of the total sample, 20% (n = 83; 66% men) had problematic opioid use. Most patients reported high opioid dependence severity (97%), injection drug use (67%), and polysubstance use (97%), including cocaine (62%), alcohol (40%), and amphetamines (35%). Most patients reported anxiety (86%) and depression (75%). The number of patients tested for HIV, HCV, HBV, and other STIs was 29%, 27%, 28%, and 24%, respectively. Most patients tested (61%) were young adults (aged 16–29). Of those tested, 15% tested positive for HCV and treatment initiation was facilitated for 66% of patients (33% resolved spontaneously). At 30-day follow-up, patients showed significantly reduced substance use and improved depression and anxiety (Ps < 0.05).

Conclusion
Patients with problematic opioid use have multiple comorbidities, including undiagnosed infectious diseases; thus, highlighting the need for integrated care models like RAAM. Substance use treatment is an opportune setting to identify and treat infectious diseases in order to improve outcomes and reduce disease transmission. Leadership from infectious disease specialists is key to this successful integration.

Disclosures
All Authors: No reported Disclosures.