bluuebunny/crossref_metadata_2025_split huggingface dataset:
The ocean-atmospheric condition around Pieh Islands – Western Sumatra, Indonesia and its role on coral reef resilience
Authors: Corvianawatie C , Abrar M , Wouthuyzen S , Darmawan  , Kusumo S , Samsuardi  , Yennafri  , Salatalohi A , Hanif A , Permana S , Arrafat M Y , Tanto T A 
Published: November 2018

Abstract
Pieh Islands located at the Western Sumatra is one of the most affected areas by massive coral bleaching during 2015-2016. The persistence warming or cooling of sea surface temperature due to regional climate phenomena such as El Niño Southern Oscillation (ENSO) and Indian Ocean Dipole (IOD) put the coral reef into stress condition leading into coral bleaching. However, corals have an ability to recover from such bleaching condition into normal state by reducing its stressors. A suitable oceanographic condition such as normal range of temperature and salinity, low nutrient concentration, and low sedimentation rate could support corals recovery process. This study aims to understand the variability of the ocean and atmospheric data and its role in coral reef recovery. Data gained from in situ measurements of water quality at Pieh Marine Conservation Area (PMCA) on June 2018. Several historical ocean-atmospheric data were collected to analyze their temporal variability. It is confirmed that the bleaching event was caused by positive IOD and El Niño condition in 2015-2016. However, there is the sign of coral reef recovery during 2017-2018 which is suggested due to the relatively normal condition of the ocean and atmospheric parameters in Pieh Islands.
A Case Report of a Breast Implant–Associated Plasmacytoma and Literature Review of Non-ALCL Breast Implant–Associated Neoplasms
Authors: Beydoun Ahmed Sam , Ovalle Fernando , Brannock Kristina , Gobble Ryan M 
Published: November 2018

Abstract

Lymphomas associated with breast implants are rare, with the most common being anaplastic large cell lymphoma (ALCL). Non-ALCL breast implant–associated lymphomas are even more rare, with only a small handful of such neoplasms reported to date. Given the need to better understand these pathologies as well as the increasing clinical and media attention being paid to these diseases, we review the available literature of hematolymphoid neoplasms other than ALCL associated with breast implants and describe the first case of a patient diagnosed with a primary breast implant–associated plasmacytoma.

Level of Evidence: 5
An equivariant Bayesian convolutional network predicts recombination hotspots and accurately resolves binding motifs
Authors: Brown Richard C , Lunter Gerton 
Published: November 2018

Abstract

Motivation
Convolutional neural networks (CNNs) have been tremendously successful in many contexts, particularly where training data are abundant and signal-to-noise ratios are large. However, when predicting noisily observed phenotypes from DNA sequence, each training instance is only weakly informative, and the amount of training data is often fundamentally limited, emphasizing the need for methods that make optimal use of training data and any structure inherent in the process.

Results
Here we show how to combine equivariant networks, a general mathematical framework for handling exact symmetries in CNNs, with Bayesian dropout, a version of Monte Carlo dropout suggested by a reinterpretation of dropout as a variational Bayesian approximation, to develop a model that exhibits exact reverse-complement symmetry and is more resistant to overtraining. We find that this model combines improved prediction consistency with better predictive accuracy compared to standard CNN implementations and state-of-art motif finders. We use our network to predict recombination hotspots from sequence, and identify binding motifs for the recombination–initiation protein PRDM9 previously unobserved in this data, which were recently validated by high-resolution assays. The network achieves a predictive accuracy comparable to that attainable by a direct assay of the H3K4me3 histone mark, a proxy for PRDM9 binding.

Availability and implementation
https://github.com/luntergroup/EquivariantNetworks

Supplementary information
Supplementary data are available at Bioinformatics online.
EpistasisRank and EpistasisKatz: interaction network centrality methods that integrate prior knowledge networks
Authors: Parvandeh Saeid , McKinney Brett A 
Published: November 2018

Abstract

Motivation
An important challenge in gene expression analysis is to improve hub gene selection to enrich for biological relevance or improve classification accuracy for a given phenotype. In order to incorporate phenotypic context into co-expression, we recently developed an epistasis-expression network centrality method that blends the importance of gene–gene interactions (epistasis) and main effects of genes. Further blending of prior knowledge from functional interactions has the potential to enrich for relevant genes and stabilize classification.

Results
We develop two new expression-epistasis centrality methods that incorporate interaction prior knowledge. The first extends our SNPrank (EpistasisRank) method by incorporating a gene-wise prior knowledge vector. This prior knowledge vector informs the centrality algorithm of the inclination of a gene to be involved in interactions by incorporating functional interaction information from the Integrative Multi-species Prediction database. The second method extends Katz centrality to expression-epistasis networks (EpistasisKatz), extends the Katz bias to be a gene-wise vector of main effects and extends the Katz attenuation constant prefactor to be a prior-knowledge vector for interactions. Using independent microarray studies of major depressive disorder, we find that including prior knowledge in network centrality feature selection stabilizes the training classification and reduces over-fitting.

Availability and implementation
Methods and examples provided at https://github.com/insilico/Rinbix and https://github.com/insilico/PriorKnowledgeEpistasisRank.

Supplementary information
Supplementary data are available at Bioinformatics online.
“Build Rapport, Otherwise No Screening Tools in the World Are Going to Help”: Frontline Service Providers’ Views on Current Screening Tools for Elder Abuse
Authors: Brijnath Bianca , Gahan Luke , Gaffy Ellen , Dow Briony 
Published: November 2018

Abstract

Background and Objectives
Without an effective screening tool, accompanied by clear guidelines of what to do when elder abuse is suspected, health workers may face challenges when asking questions about elder abuse. This study aimed to find the most effective and acceptable existing elder abuse screening tool and to create guidelines for using the tool.

Research Design and Methods
A rapid review of the literature identified existing validated elder abuse screening tools. Then, 5 tools (Vulnerability to Abuse Screening Scale [VASS], Elder Abuse Suspicion Index [EASI], Elder Assessment Instrument [EAI], Caregiver Abuse Screen [CASE], and Brief Abuse Screen for the Elderly [BASE]), selected based on their internal rigor, were presented to health professionals to assess the tools’ relevance to their practice. Three focus groups were held with 23 health professionals in Victoria, Australia, in 2017. Data were thematically analyzed.

Results
None of the tools were deemed suitable by participants for use in their practice. Criticisms of the tools included: using outdated terminology, asking binary questions, asking multiple questions at once, failure to consider the older person’s cognitive status, failure to consider how culture mediates elder abuse, and failure to outline a referral pathway to those administering the tool. Participants emphasized that the screening tool must promote trust and rapport between the assessor and the older person to solicit a story on this sensitive subject.

Discussion and Implications
A successful elder abuse screening tool must be concise, easy to use, account for the older person’s health and social vulnerabilities, and outline a referral pathway if elder abuse is suspected.
Protecting the Rights of Children with Intersex Conditions from Nonconsensual Gender-Conforming Medical Interventions: The View from Europe
Authors: Garland Jameson , Slokenberga Santa 
Published: November 2018

Abstract
Nonconsensual gender-conforming interventions on children with intersex conditions have recently come under sharp criticism from human rights authorities within the United Nations, the Council of Europe, and the European Union, which have identified these interventions as violating children’s rights to bodily integrity, privacy, and protection from violence, torture, and degrading treatment. Responding largely to requests for intervention from nongovernmental organizations, these authorities have called upon nations to reform their legal frameworks, both to prevent these rights violations and to redress them. To date, however, few nations have endeavored to prohibit nonconsensual gender-conforming procedures on children with intersex conditions, and none have enacted significant reforms of their frameworks to redress rights violations. This particular ‘compliance gap’ between human rights recommendations and law reform stems from a failure of national legal orders to formally recognize the scope of rights that are threatened by nonconsensual gender-conforming interventions—rights that are well-established as part of states’ positive obligations to prevent physical and psychological harm to children. This article, therefore, analyzes the nature of the rights at stake and the importance of reporting human rights violations to generate direct calls for reform wherever violations occur. The article further analyzes how developments in Europe may have special significance for legal framework reforms—particularly if they facilitate judicial actions against national authorities through the European Convention of Human Rights, which may serve as a model for litigation elsewhere.
Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions
Authors: Kobren Shilpa Nadimpalli , Singh Mona 
Published: November 2018

Abstract
Domains are fundamental subunits of proteins, and while they play major roles in facilitating protein–DNA, protein–RNA and other protein–ligand interactions, a systematic assessment of their various interaction modes is still lacking. A comprehensive resource identifying positions within domains that tend to interact with nucleic acids, small molecules and other ligands would expand our knowledge of domain functionality as well as aid in detecting ligand-binding sites within structurally uncharacterized proteins. Here, we introduce an approach to identify per-domain-position interaction ‘frequencies’ by aggregating protein co-complex structures by domain and ascertaining how often residues mapping to each domain position interact with ligands. We perform this domain-based analysis on ∼91000 co-complex structures, and infer positions involved in binding DNA, RNA, peptides, ions or small molecules across 4128 domains, which we refer to collectively as the InteracDome. Cross-validation testing reveals that ligand-binding positions for 2152 domains are highly consistent and can be used to identify residues facilitating interactions in ∼63–69% of human genes. Our resource of domain-inferred ligand-binding sites should be a great aid in understanding disease etiology: whereas these sites are enriched in Mendelian-associated and cancer somatic mutations, they are depleted in polymorphisms observed across healthy populations. The InteracDome is available at http://interacdome.princeton.edu.
125. eGISP: Enhanced Surveillance of Neisseria gonorrhoeae Antimicrobial Susceptibility in the United States
Authors: Quilter Laura , Cyr Sancta St , Abitria Vincent , Ancharski Andrew , Bautista Ilene , Bazan Jose , Carifo Karen , Ervin Melissa , Harrison Rebecca , Hoogenboom Aaron , Peterson Amy , Pham Cau , Snyder Brandon , Turner Abigail Norris , Torrone Elizabeth 
Published: November 2018

Abstract

Background
The Gonococcal Isolate Surveillance Project (GISP), which monitors trends in N. gonorrhoeae susceptibility among men with gonococcal urethritis in sexually transmitted disease (STD) clinics, has informed treatment recommendations for 3 decades. However, it has been speculated that susceptibility patterns may differ in women, as well as in the pharynx and rectum. We describe preliminary findings from the enhanced GISP (eGISP), which expands surveillance to pharyngeal, rectal, and endocervical isolates.

Methods
In August 2017, select jurisdictions were funded to collect urogenital and extragenital specimens from men and women seen in participating STD clinics. Positive gonorrhea cultures were sent to regional laboratories for antimicrobial susceptibility testing (AST) by agar dilution. Isolates with elevated minimum inhibitory concentration (MIC) to azithromycin (AZI) (MIC ≥2.0 μg/mL), cefixime (CFX) (MIC ≥0.25 μg/mL), and/or ceftriaxone (CRO) (MIC ≥0.125 μg/mL) were designated as Alert isolates. Clinical and epidemiological data were linked to AST results.

Results
From August 2017 to February 2018, 4 clinics in 4 jurisdictions submitted 468 positive gonococcal specimens for AST; 36.1% were from men who have sex with men (MSM), 51.9% from men who have sex with women (MSW), and 12.0% from women. Overall, 71.8% were urethral, 7.9% endocervical, 7.1% rectal, and 13.2% pharyngeal. Seventy-two isolates (15.4%) were Alerts: 97.2% (N = 70) had elevated MICs to AZI, 2.8% (N = 2) had elevated MICs to CFX, and none had elevated MICs to CRO. No isolate had elevated MICs to both AZI and CFX. Among MSM, 15.9% of urogenital isolates and 16.1% of extragenital isolates had an elevated AZI MIC. Among MSW, 11.8% of urogenital isolates and 14.3% of pharyngeal isolates had an elevated AZI MIC. Among women, 24.3% of endocervical isolates and 26.3% of extragenital isolates had an elevated AZI MIC.

Conclusion
Preliminary eGISP data suggest that enhanced surveillance of pharyngeal, rectal, and endocervical isolates is feasible and that elevated MICs to azithromycin are common among males and females. Including isolates from extragenital anatomic sites and women may help strengthen N. gonorrhoeae surveillance capacity.

Disclosures
All authors: No reported disclosures.
150. Relative Effectiveness of High-Dose and Standard-Dose Influenza Vaccine Against Influenza-Related Hospitalization Among Older Adults—United States, 2015–2017
Authors: Doyle Joshua , Beacham Lauren , Alyanak Elif , Gaglani Manjusha , Martin Emily T , Middleton Don , Silveira Fernanda P , Talbot H Keipp , Zimmerman Richard , Flannery Brendan , Ferdinands Jill M 
Published: November 2018

Abstract

Background
Seasonal influenza causes substantial morbidity and mortality, and older adults are disproportionately affected. Newer vaccines have been developed for use in people 65 years and older, including a trivalent inactivated vaccine with a 4-fold higher dose of antigen (IIV-HD). In recent years, the use of IIV-HD has increased sufficiently to evaluate its effectiveness compared with standard-dose inactivated influenza vaccines (IIV-SD).

Methods
Hospitalized patients with acute respiratory illness were enrolled in an observational vaccine effectiveness study at 8 hospitals in 4 states participating in the United States Hospitalized Adult Influenza Vaccine Effectiveness Network during the 2015–2016 and 2016–2017 influenza seasons. Predominant influenza A virus subtypes were H1N1 and H3N2, respectively, during these seasons. All enrolled patients were tested for influenza virus with polymerase chain reaction. Receipt and type of influenza vaccine was determined from electronic records and chart review. Odds of laboratory-confirmed influenza were compared among vaccinated and unvaccinated patients. Relative odds of laboratory-confirmed influenza were determined for patients who received IIV-HD or IIV-SD, and adjusted for potential confounding variables via logistic regression.

Results
Among 1,744 enrolled patients aged ≥ 65 years, 1,105 (63%) were vaccinated; among those vaccinated, 621 (56%) received IIV-HD and 484 (44%) received IIV-SD. Overall, 315 (18%) tested positive for influenza, including 97 (6%) who received IIV-HD, 86 (5%) who received IIV-SD, and 132 (8%) who were unvaccinated. Controlling for age, race, sex, enrollment site, date of illness, index of comorbidity, and influenza season, the adjusted odds of influenza among patients vaccinated with IIV-HD vs. IIV-SD were 0.72 (P = 0.06, 95% CI: 0.52 to 1.01).

Conclusion
Comparison of high-dose vs. standard-dose vaccine effectiveness during 2 recent influenza seasons (1 H1N1 and 1 H3N2-predominant) suggested relative benefit (nonsignificant) of high-dose influenza vaccine in protecting against influenza-associated hospitalization among persons aged 65 years and older; additional years of data are needed to confirm this finding.

Disclosures
H. K. Talbot, sanofi pasteur: Investigator, Research grant. Gilead: Investigator, Research grant. MedImmune: Investigator, Research grant. Vaxinnate: Safety Board, none. Seqirus: Safety Board, none.
166. TGF-β Restricts T-cell IFNg Production in Pulmonary Tuberculous Granulomas
Authors: Gern Benjamin , Adams Kristin , Plumlee Courtney , Gerner Michael , Urdahl Kevin 
Published: November 2018

Abstract

Background
IFNg production by CD4 T cells has been thought to be critical for immunity against Mycobacterium tuberculosis (Mtb); however, recent studies show that IFNg-producing CD4 T cells are more effective at preventing dissemination than controlling Mtb in the lung. Because optimal control of Mtb infection requires direct interactions between CD4 T cells and Mtb-infected cells presenting cognate antigen on MHCII, we sought to determine the location of CD4 T-cell antigen recognition and IFNg production in the Mtb-infected lung.

Methods
We infected mice with an ultra-low dose (ULD) of Mtb (1–3 CFU), a model developed in our laboratory which results in well-circumscribed granulomas that recapitulate many features of human Mtb granulomas. Using immunohistochemistry and quantitative imaging, we examined their lungs 35 days later for phenotypic and spatial analysis of T-cell receptor (TCR) signaling (using IRF4) and IFNγ production. We tested the antigen specificity of these responses with an adoptive transfer of both Mtb-specific and OVA-specific control CD4 T cells into ULD Mtb-infected mice. To assess the role of TGFβ signaling on T-cell localization and function, we performed the same analysis in mice lacking the TGFβ receptor (TGFβR) on T cells.

Results
Within Mtb-infected lungs, many T cells localize near Mtb cells and undergo TCR signaling. Despite this, we found very few cells producing IFNγ within the granuloma (Figure 1). In our adoptive transfer experiment, both cell types infiltrated the granuloma. The Mtb-specific, but not OVA-specific, T cells had active TCR engagement though only a small fraction of these cells produced IFNγ, and this IFNγ was diminished near Mtb (Figure 2). Conversely, in the TGFβR conditional knockout, we found increased IFNγ production that was highest within the granuloma (Figure 3).

Conclusion
Despite ongoing TCR stimulation in T cells, IFNγ production is restricted in areas where cognate interactions are most likely to occur. TGFβ plays a critical role in mediating this effect, as T cells lacking the receptor can produce more IFNγ near infected cells. These findings help explain why IFNγ-producing T cells have limited capacity to control pulmonary Mtb infection and could guide new strategies for vaccine and immunotherapeutic development.

Disclosures
All authors: No reported disclosures.
860. Immediate Access to Post-Exposure Prophylaxis (PEP) Through a 24/7 New York City PEP Hotline
Authors: Glaser Allison , Kaplan-Lewis Emma , Ventuneac Ana , Gates Wyley , Cruz Michael , Aracena Joaquin , Tider Diane , Duah Bianca , Aberg Judith , Urbina Antonio 
Published: November 2018

Abstract

Background
Oral post-exposure prophylaxis (PEP) is effective in preventing HIV transmission. To minimize barriers to PEP for New York City (NYC) residents, the Institute for Advanced Medicine (IAM), Mount Sinai Health System, and the NYC Department of Health and Mental Health established a 24-hour 7-days PEP hotline to provide eligible callers with immediate access to PEP and follow-up clinical care.

Methods
Data from hotline callers (January to December 2017) was analyzed utilizing multivariable logistic regression to determine whether a call resulted in PEP access within 72 hours of exposure by sociodemographic variables and exposure characteristics. We describe transitions from PEP to PrEP (pre-exposure prophylaxis).

Results
The PEP hotline cohort (n = 1278) was 83% male, 11% female, 1% transgender; 66% LGBTQ and 20% heterosexual; 35% White, 15% Black, 9% Asian; 41% other/unknown; 25% Hispanic; mean age of 30 years (range 14–72). The majority of callers learned about the hotline by Internet search (59%). Mean exposure time prior to call was 31 hours with 57% within 24 hours. Exposures were 98% sexual; 73% anal sex (43% receptive; 30% insertive), 21% vaginal, and 6% other. 63% reported condomless sex and 29% condom failure. 15% of callers reported a partner with HIV. 35% of callers reported alcohol or recreational substances at the time of the exposure. Prior PEP and PrEP use was 20% and 9%, respectively. 91% of callers were eligible for PEP; 69% called afterhours and received a telephone PEP prescription, and 27% called during business hours and were directed to a clinic. Access to PEP within 72 hours of exposure occurred in 1,081 (93%) of eligible callers and within 36 hours in 68%. 90% of callers had confirmed follow-up clinic appointments. Of the 472 callers linked to care at the IAM, 89 (19%) transitioned to PrEP.

Conclusion
This unique program demonstrates a timely initiative to facilitate PEP access to a diverse cohort with the purpose of mitigating risk from potential exposure to HIV. Further investigation is needed to explore adherence to PEP, follow-up testing results, transitions to PrEP for prevention planning, and coordination of health care and substance use services.

Disclosures
E. Kaplan-Lewis, Viiv: Consultant, Consulting fee. J. Aberg, Gilead: Research Contractor, Research support. GSK: Research Contractor, Research support. ViiV: Research Contractor, Research support. A. Urbina, Theratechnologies: Scientific Advisor, Consulting fee. ViiV: Scientific Advisor, Consulting fee. Merck: Scientific Advisor, Consulting fee. Gilead: Scientific Advisor, Consulting fee.