bluuebunny/crossref_metadata_2025_split huggingface dataset:
The time evolution of dusty protoplanetary disc radii: observed and physical radii differ
Authors: Rosotti Giovanni P , Tazzari Marco , Booth Richard A , Testi Leonardo , Lodato Giuseppe , Clarke Cathie 
Published: April 2019

ABSTRACT
Protoplanetary disc surveys conducted with Atacama Large Millimetre Array (ALMA) are measuring disc radii in multiple star-forming regions. The disc radius is a fundamental quantity to diagnose whether discs undergo viscous spreading, discriminating between viscosity or angular momentum removal by winds as drivers of disc evolution. Observationally, however, the sub-mm continuum emission is dominated by the dust, which also drifts inwards, complicating the picture. In this paper we investigate, using theoretical models of dust grain growth and radial drift, how the radii of dusty viscous protoplanetary discs evolve with time. Despite the existence of a sharp outer edge in the dust distribution, we find that the radius enclosing most of the dust mass increases with time, closely following the evolution of the gas radius. This behaviour arises because, although dust initially grows and drifts rapidly on to the star, the residual dust retained on Myr time-scales is relatively well coupled to the gas. Observing the expansion of the dust disc requires using definitions based on high fractions of the disc flux (e.g. 95 per cent) and very long integrations with ALMA, because the dust grains in the outer part of the disc are small and have a low sub-mm opacity. We show that existing surveys lack the sensitivity to detect viscous spreading. The disc radii they measure do not trace the mass radius or the sharp outer edge in the dust distribution, but the outer limit of where the grains have significant sub-mm opacity. We predict that these observed radii should shrink with time.
The relativistic jet of the γ-ray emitting narrow-line Seyfert 1 galaxy PKS J1222+0413
Authors: Kynoch Daniel , Landt Hermine , Ward Martin J , Done Chris , Boisson Catherine , Baloković Mislav , Angelakis Emmanouil , Myserlis Ioannis 
Published: April 2019

ABSTRACT
We present a multifrequency study of PKS J1222+0413 (4C +04.42), currently the highest redshift γ-ray emitting narrow-line Seyfert 1 (γ-NLS1). We assemble a broad spectral energy distribution (SED) including previously unpublished datasets: X-ray data obtained with the NuSTAR and Neil Gehrels Swift observatories; near-infrared, optical, and UV spectroscopy obtained with VLT X-shooter; and multiband radio data from the Effelsberg telescope. These new observations are supplemented by archival data from the literature. We apply physical models to the broad-band SED, parametrizing the accretion flow and jet emission to investigate the disc–jet connection. PKS J1222+0413 has a much greater black hole mass than most other NLS1s, MBH ≈ 2 × 108 M$\odot$, similar to those found in flat spectrum radio quasars (FSRQs). Therefore this source provides insight into how the jets of γ-NLS1s relate to those of FSRQs.
Investigating the diversity of Type Ia supernova spectra with the open-source relational data base kaepora
Authors: Siebert M R , Foley R J , Jones D O , Angulo R , Davis K , Duarte A , Strasburger E , Conlon M , Kazmi N , Nishimoto R , Schubert M , Sun L , Tippens R 
Published: April 2019

Abstract
We present a public, open-source relational data base (we name kaepora) containing a sample of 4975 spectra of 777 Type Ia supernovae (SNe Ia). Since we draw from many sources, we significantly improve the spectra by inspecting these data for quality, removing galactic emission lines and cosmic rays, generating variance spectra, and correcting for the reddening caused by both MW and host-galaxy dust. With our data base, we organize this homogenized data set by 56 unique categories of SN-specific and spectrum-specific metadata. With kaepora, we produce composite spectra of subpopulations of SNe Ia and examine how spectral features correlate with various SN properties. These composite spectra reproduce known correlations with phase, light-curve shape, and host-galaxy morphology. With our large data set, we are also able to generate fine-grained composite spectra simultaneously over both phase and light-curve shape. The colour evolution of our composite spectra is consistent with other SN Ia template spectra, and the spectral properties of our composite spectra are in rough agreement with these template spectra with some subtle differences. We investigate the spectral differences of SNe Ia that occur in galaxies with varying morphologies. Controlling for light-curve shape, which is highly correlated with host-galaxy morphology, we find that SNe Ia residing in late-type and early-type galaxies have similar spectral properties at multiple epochs. However for SNe Ia in these different environments, their spectra appear to have Ca ii near-infrared triplet features that have slightly different strengths. Although this is apparent in the composite spectra and there is some difference in the populations as seen by individual spectra, this difference is not large enough to indicate differences in the underlying populations. All individual spectra and metadata are available in our open-source data base kaepora along with the tools developed for this investigation to facilitate future investigations of SN Ia properties.
Human Migration and the Spread of the Nematode Parasite Wuchereria bancrofti
Authors: Small Scott T , Labbé Frédéric , Coulibaly Yaya I , Nutman Thomas B , King Christopher L , Serre David , Zimmerman Peter A 
Published: April 2019

AbstractThe human disease lymphatic filariasis causes the debilitating effects of elephantiasis and hydrocele. Lymphatic filariasis currently affects the lives of 90 million people in 52 countries. There are three nematodes that cause lymphatic filariasis, Brugia malayi, Brugia timori, and Wuchereria bancrofti, but 90% of all cases of lymphatic filariasis are caused solely by W. bancrofti (Wb). Here we use population genomics to reconstruct the probable route and timing of migration of Wb strains that currently infect Africa, Haiti, and Papua New Guinea (PNG). We used selective whole genome amplification to sequence 42 whole genomes of single Wb worms from populations in Haiti, Mali, Kenya, and PNG. Our results are consistent with a hypothesis of an Island Southeast Asia or East Asian origin of Wb. Our demographic models support divergence times that correlate with the migration of human populations. We hypothesize that PNG was infected at two separate times, first by the Melanesians and later by the migrating Austronesians. The migrating Austronesians also likely introduced Wb to Madagascar where later migrations spread it to continental Africa. From Africa, Wb spread to the New World during the transatlantic slave trade. Genome scans identified 17 genes that were highly differentiated among Wb populations. Among these are genes associated with human immune suppression, insecticide sensitivity, and proposed drug targets. Identifying the distribution of genetic diversity in Wb populations and selection forces acting on the genome will build a foundation to test future hypotheses and help predict response to current eradication efforts.
SPADE web service for prediction of allergen IgE epitopes
Authors: Dall’Antonia Fabio , Keller Walter 
Published: April 2019

Abstract
The specific interaction of allergens with IgE antibodies and the allergen mediated cross-linking of receptor-bound IgE are key events of allergic diseases. The elucidation of the IgE binding sites (the epitopes) on the allergen surface is an important goal of allergy research. Only few allergen-specific IgE epitopes have been determined experimentally to date. Epitope prediction methods represent a viable alternative to experimental methods and have worked well with linear epitopes. However, as most IgE epitopes are of conformational and/or discontinuous nature sequence based prediction methods have had limited success in these cases. Here, we present the web server of the program SPADE (https://spade.uni-graz.at), which is the server implementation of a previously published program (1). In this approach we utilize the structural homology of cross-reactive allergens combined with the immunological cross-reactivity data for the discrimination of putative IgE-binding sites from non-cross-reactive surface patches. The method, although predictive, does not rely on machine-learning algorithms and does not require training data. The SPADE server features an easy-to-use interface, an automated pipeline consisting of third-party, as well as own, newly developed routines and a comprehensive output page.
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)
Authors: Raudvere Uku , Kolberg Liis , Kuzmin Ivan , Arak Tambet , Adler Priit , Peterson Hedi , Vilo Jaak 
Published: April 2019

Abstract
Biological data analysis often deals with lists of genes arising from various studies. The g:Profiler toolset is widely used for finding biological categories enriched in gene lists, conversions between gene identifiers and mappings to their orthologs. The mission of g:Profiler is to provide a reliable service based on up-to-date high quality data in a convenient manner across many evidence types, identifier spaces and organisms. g:Profiler relies on Ensembl as a primary data source and follows their quarterly release cycle while updating the other data sources simultaneously. The current update provides a better user experience due to a modern responsive web interface, standardised API and libraries. The results are delivered through an interactive and configurable web design. Results can be downloaded as publication ready visualisations or delimited text files. In the current update we have extended the support to 467 species and strains, including vertebrates, plants, fungi, insects and parasites. By supporting user uploaded custom GMT files, g:Profiler is now capable of analysing data from any organism. All past releases are maintained for reproducibility and transparency. The 2019 update introduces an extensive technical rewrite making the services faster and more flexible. g:Profiler is freely available at https://biit.cs.ut.ee/gprofiler.
Rapid functional activation of a horizontally transferred eukaryotic gene in a bacterial genome in the absence of selection
Authors: Li Zhichao , Bock Ralph 
Published: April 2019

Abstract
Horizontal gene transfer has occurred between organisms of all domains of life and contributed substantially to genome evolution in both prokaryotes and eukaryotes. Phylogenetic evidence suggests that eukaryotic genes horizontally transferred to bacteria provided useful new gene functions that improved metabolic plasticity and facilitated adaptation to new environments. How these eukaryotic genes evolved into functional bacterial genes is not known. Here, we have conducted a genetic screen to identify the mechanisms involved in functional activation of a eukaryotic gene after its transfer into a bacterial genome. We integrated a eukaryotic selectable marker gene cassette driven by expression elements from the red alga Porphyridium purpureum into the genome of Escherichia coli. Following growth under non-selective conditions, gene activation events were indentified by antibiotic selection. We show that gene activation in the bacterial recipient occurs at high frequency and involves two major types of spontaneous mutations: deletion and gene amplification. We further show that both mechanisms result in promoter capture and are frequently triggered by microhomology-mediated recombination. Our data suggest that horizontally transferred genes have a high probability of acquiring functionality, resulting in their maintenance if they confer a selective advantage.
“Public Health, Public Goods, and Market Failure”
Authors: Horne L Chad 
Published: April 2019

Abstract
This discussion revises and extends Jonny Anomaly's ‘public goods’ account of public health ethics in light of recent criticism from Richard Dees. Public goods are goods that are both non-rival and non-excludable. What is significant about such goods is that they are not always provided efficiently by the market. Indeed, the state can sometimes realize efficiency gains either by supplying such goods directly or by compelling private purchase. But public goods are not the only goods that the market may fail to provide efficiently. This point to a way of broadening the public goods account of public health to accommodate Dees' counterexamples, without abandoning its distinctive appeal. On the market failures approach to public health ethics, the role of public health is to correct public health-related market failures of all kinds, so far as possible. The underlying moral commitment is to economic efficiency in the sense of Pareto: if we can re-allocate resources in the economy so as to raise the welfare of some without lowering the welfare of any other, we ought to do so.
Give People a Break: Slips and Moral Responsibility
Authors: Rudy-Hiller Fernando 
Published: April 2019

AbstractI examine the question of whether people are sometimes morally blameworthy for what I call ‘slips’: wrongful actions or omissions that a good-willed (or at least no ill-willed) agent inadvertently performs due to a non-negligent failure to be aware of relevant considerations. I focus in particular on the capacitarian answer to this question, according to which possession of the requisite capacities to be aware of relevant considerations and respond appropriately explains blameworthiness for slips. I argue, however, that capacitarianism fails to show that agents have responsibility level control over their slips and, consequently, fails to show that it is reasonable to expect agents to avoid this kind of wrongdoing. I conclude that people are typically not blameworthy for their slips, but only regarding the backward-looking, desert-entailing type of blame that has been at issue in this debate. I suggest that ordinary intuitions about blameworthiness for slips can be accommodated by appealing to other types of responsibility and blame.
Take-Up and Targeting: Experimental Evidence from SNAP
Authors: Finkelstein Amy , Notowidigdo Matthew J 
Published: April 2019

Abstract
We develop a framework for welfare analysis of interventions designed to increase take-up of social safety net programs in the presence of potential behavioral biases. We calibrate the key parameters using a randomized field experiment in which 30,000 elderly individuals not enrolled in—but likely eligible for—the Supplemental Nutrition Assistance Program (SNAP) are either provided with information that they are likely eligible, provided with this information and offered assistance in applying, or are in a “status quo” control group. Only 6% of the control group enrolls in SNAP over the next nine months, compared to 11% of the Information Only group and 18% of the Information Plus Assistance group. The individuals who apply or enroll in response to either intervention have higher net income and are less sick than the average enrollee in the control group. We present evidence consistent with the existence of optimization frictions that are greater for needier individuals, which suggests that the poor targeting properties of the interventions reduce their welfare benefits.
Association of Intracranial Hypertension With Calvarial and Skull Base Thinning
Authors: Rabbani Cyrus C. , Patel Janaki M. , Nag Amit , Schueth Elizabeth , Saltagi Mohamad Z. , Kao Richard , Nelson Rick F. 
Published: April 2019

Objective:
Determine if patients with increased opening pressure (OP) on lumbar puncture (LP) have thinner calvaria and skull bases.

Study Design:
Retrospective cohort study.

Setting:
Tertiary referral center.

Patients:
Patients (≥18 yr of age) who had a recorded OP on LP and high-resolution computed tomography imaging of the head. Patient age, sex, body mass index were calculated. Intracranial hypertension (IH) was defined with an OP≥25 cm-H2O and low intracranial pressure with an OP<15 cm-H2O.

Intervention:
Measurement of calvarial, zygoma, and skull base thickness when blinded to OP with three-dimensional slicer and radiologic calipers.

Main Outcome Measures:
Association of calvarial, skull base, and zygoma thickness with OP and age.

Results:
Fifty-eight patients were included with a mean (SD) age of 53.1 (16.2) years and average (SD) body mass index of 30.1 (9.1) kg/m2. Patients with IH had thinner mean (SD) calvaria (3.01 [0.81] versus 2.70 [0.58] mm; p = 0.036) and skull bases (5.17 [1.22] versus 4.60 [1.42] mm; p = 0.043) when compared with patients without IH. The mean (SD) extracranial zygoma thickness was similar between the two groups (5.09 [0.76] versus 5.00 [0.73] mm; p = 0.56). General linear model regression demonstrated advancing age was associated with increasing calvarial thickness in patients without IH and calvarial thinning in patients with IH (p = 0.038).

Conclusion:
IH is independently associated with intracranial bone (calvaria and skull base) thinning and not extracranial (zygoma) thinning. Skull thinning occurs with IH and advancing age. These findings support a possible role of increased ICP in the pathophysiologic development of spontaneous cerebrospinal fluid leaks.
Mastoid Cavity Myiasis: A Case Report and Review of the Literature
Authors: Kahane Jacob , Longworth Caleena , Dickson Crystal , Ng Matthew 
Published: April 2019

Objective:
We report a case study of mastoid cavity aural myiasis in an urban developed setting and review the relevant literature.

Data Source:
Retrospective case report and review of the English literature via PubMed.

Data Selection:
English-language articles concerning aural myiasis and mastoid cavity myiasis were included.

Data Extraction:
Two previous case reports of mastoid cavity myiasis were identified and analyzed.

Conclusion:
Neglected mastoid cavity care, low socioeconomic status, poor personal hygiene, homelessness, and chronic suppurative otitis media are likely contributing factors to this uncommon presentation occurring in an urban setting.
Code Team Structure and Training in the Pediatric Resuscitation Quality International Collaborative
Authors: Pfeiffer Stephen , Lauridsen Kasper Glerup , Wenger Jesse , Hunt Elizabeth A. , Haskell Sarah , Atkins Dianne L. , Duval-Arnould Jordan M. , Knight Lynda J. , Cheng Adam , Gilfoyle Elaine , Su Felice , Balikai Shilpa , Skellett Sophie , Hui Mok Yee , Niles Dana E. , Roberts Joan S. , Nadkarni Vinay M. , Tegtmeyer Ken , Dewan Maya ,   for the Pediatric Resuscitation Quality Collaborative Investigators
Published: April 2019

Objectives
Code team structure and training for pediatric in-hospital cardiac arrest are variable. There are no data on the optimal structure of a resuscitation team. The objective of this study is to characterize the structure and training of pediatric code teams in sites participating in the Pediatric Resuscitation Quality Collaborative.

Methods
From May to July 2017, an anonymous voluntary survey was distributed to 18 sites in the international Pediatric Resuscitation Quality Collaborative. The survey content was developed by the study investigators and iteratively adapted by consensus. Descriptive statistics were calculated.

Results
All sites have a designated code team and hospital-wide code team activation system. Code team composition varies greatly across sites, with teams consisting of 3 to 17 members. Preassigned roles for code team members before the event occur at 78% of sites. A step stool and backboard are used during resuscitations in 89% of surveyed sites. Cardiopulmonary resuscitation (CPR) feedback is used by 72% of the sites. Of those sites that use CPR feedback, all use an audiovisual feedback device incorporated into the defibrillator and 54% use a CPR coach. Multidisciplinary and simulation-based code team training is conducted by 67% of institutions.

Conclusions
Code team structure, equipment, and training vary widely in a survey of international children's hospitals. The variations in team composition, role assignments, equipment, and training described in this article will be used to facilitate future studies regarding the impact of structure and training of code teams on team performance and patient outcomes.
Immunological and Neurometabolite Changes Associated With Switch From Efavirenz to an Integrase Inhibitor
Authors: Asundi Archana , Robles Yvonne , Starr Tyler , Landay Alan , Kinslow Jennifer , Ladner Joshua , White Laura , Plank Rebeca M. , Melbourne Kathleen , Weisholtz Daniel , Bennett Monica , Pan Hong , Stern Emily , Lin Alexander , Kuritzkes Daniel R. , Lin Nina H. 
Published: April 2019

Background:
The biological mechanisms by which efavirenz (EFV) causes central nervous system (CNS) effects are unclear. The objective of this pilot study was to elucidate the mechanisms underlying these CNS effects by correlating well-described neuropsychological (NP) changes with neurometabolites and immunologic markers following switch off EFV.

Setting:
Two single-arm parallel switch studies among HIV-infected adults in Boston, USA, from 2015 to 2017.

Methods:
Twenty asymptomatic HIV-infected adults on EFV-containing regimens were switched to an integrase strand transfer inhibitor-based regimen for 8 weeks. NP assessments were conducted before and after switch and correlated with neurometabolite changes measured using magnetic resonance spectroscopy and immunological markers. All pre-EFV and post-EFV measures were evaluated using matched-paired analyses.

Results:
NP testing demonstrated improvement in the domains of mood, cognition, and sleep off EFV. Magnetic resonance spectroscopy revealed decreases in the neurometabolite glutathione level (P = 0.03), a marker of oxidative stress after switch. Inhibitory neuronal activity as reflected by gamma-amino butyric acid levels increased (P = 0.03), whereas excitatory neurotransmitters glutamine + glutamate (Glx) and aspartate decreased (P = 0.04, 0.001). Switching off EFV was also associated with changes in inflammatory markers; plasma markers sCD14 (P = 0.008) decreased, whereas I-FABP and TNFRI levels increased (P = 0.05, 0.03). Cellular markers CD4+ and CD8+ HLA−DR−/CD38+ subsets both increased (P = 0.05, 0.02).

Conclusions:
Even asymptomatic participants showed improvements in NP parameters when switched off EFV. These improvements were associated with decreased CNS oxidative stress and excitatory neuronal activity. Changes in immune activation biomarkers suggested overall decreased inflammation. EFV may exert CNS effects through oxidative and inflammatory pathways, providing insight into possible mechanisms of EFV neurotoxicity.