bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary Analysis of Bile Acid-Conjugating Enzymes Reveals a Complex Duplication and Reciprocal Loss History
Authors: Kirilenko Bogdan M , Hagey Lee R , Barnes Stephen , Falany Charles N , Hiller Michael 
Published: October 2019

AbstractTo fulfill their physiological functions, bile acids are conjugated with amino acids. In humans, conjugation is catalyzed by bile acid coenzyme A: amino acid N-acyltransferase (BAAT), an enzyme with a highly conserved catalytic triad in its active site. Interestingly, the conjugated amino acids are highly variable among mammals, with some species conjugating bile acids with both glycine and taurine, whereas others conjugate only taurine. The genetic origin of these bile acid conjugation differences is unknown. Here, we tested whether mutations in BAAT’s catalytic triad could explain bile acid conjugation differences. Our comparative analysis of 118 mammals first revealed that the ancestor of placental mammals and marsupials possessed two genes, BAAT and BAATP1, that arose by a tandem duplication. This duplication was followed by numerous gene losses, including BAATP1 in humans. Losses of either BAAT or BAATP1 largely happened in a reciprocal fashion, suggesting that a single conjugating enzyme is generally sufficient for mammals. In intact BAAT and BAATP1 genes, we observed multiple changes in the catalytic triad between Cys and Ser residues. Surprisingly, although mutagenesis experiments with the human enzyme have shown that replacing Cys for Ser greatly diminishes the glycine-conjugating ability, across mammals we found that this residue provides little power in predicting the experimentally measured amino acids that are conjugated with bile acids. This suggests that the mechanism of BAAT’s enzymatic function is incompletely understood, despite relying on a classic catalytic triad. More generally, our evolutionary analysis indicates that results of mutagenesis experiments may not easily be extrapolatable to other species.
δ-Related Biomarkers Attenuate Multiple Alzheimer’s Disease Conversion Risks and Offer Targets for Intervention
Authors: Royall Donald R , Palmer Raymond F 
Published: October 2019

AbstractBackgroundWe tested certain serum proteins’ ability to mediate the effects of demographic variables on prospective 5-year conversion to clinical “Alzheimer’s disease” from non-demented states (i.e. normal control and mild cognitive impairment). The proteins were rationally selected from previously published mediators of those same variables’ (plural posessive) association with the latent variable “δ,” a novel omnibus dementia severity metric.MethodsEach protein’s attenuation of its risk factor’s independent association with conversion was performed using logistic regression, adjusted for education, ethnicity, self-reported diabetes mellitus, and hypertension, among initially non-demented Mexican American and non-Hispanic white (N = 772) participants in the Texas Alzheimer’s Research and Care Consortium.ResultsA total of 70 (9.1%) non-demented participants at baseline converted to “Alzheimer’s disease”, with a mean follow-up of 5.4 years. Age &gt;80 years (odds ratio = 3.1), 30-item Geriatric Depression Scale &gt;10/30 (odds ratio = 2.3), female gender (odds ratio = 2.2), and the presence of an apolipoprotein E ε4 allele (odds ratio = 2.4) were independently associated with prospective conversion. These effects were fully attenuated by five serum proteins: age: insulin-like growth factor-binding protein 2 and epidermal growth factor receptor 1; depression: resistin; gender: thrombopoietin; and apolipoprotein E: C-reactive protein.ConclusionClinical dementia arises from the sum of independent δ-related processes. This analysis provides proof of concept for the rational selection of antidementia targets and offers a foundation for precision antidementia therapy.
Group velocity maps using subspace and Trans-dimensional inversions: ambient noise tomography in the Western part of Java, Indonesia
Authors: Rosalia Shindy , Cummins Phil , Widiyantoro Sri , Yudistira Tedi , Nugraha Andri Dian , Hawkins Rhys 
Published: October 2019

Summary
In this paper, we compare two different methods for group velocity inversion: iterative, least-squares subspace optimization, and probabilistic sampling based on the Trans-dimensional Bayesian method with tree-based wavelet parameterization. The wavelet parameterization used a hierarchical prior for wavelet coefficients which could adapt to the data. We applied these inversion methods for ambient noise tomography of the western part of Java, Indonesia. This area is an area prone to multiple geological hazards due to its proximity to the subduction of the Australia Plate beneath Eurasia. It is therefore important to have a better understanding of upper crustal structure to support seismic hazard and disaster mitigation efforts in this area. We utilized a new waveform dataset collected from 85 temporary seismometers deployed during 2016–2018. Cross-correlation of the waveform data was applied to retrieve empirical Rayleigh wave Green's functions between station pairs, and the spatial distribution of group velocity was obtained by inverting dispersion curves. Our results show that, although computationally expensive, the Trans-dimensional Bayesian approach offered important advantages over optimization, including more effective explorative of the model space and more robust characterization of the spatial pattern of Rayleigh wave group velocity. Meanwhile, the iterative, least-square subspace optimization suffered from the subjectivity of choice for reference velocity model and regularization parameter values. Our Rayleigh wave group velocity results show that for short (1–10 s) periods group velocity correlates well with surface geology, and for longer periods (13–25 s) it correlates with centers of volcanic activity.
From peer-based to peer-led: redefining the role of peers across the hepatitis C care pathway: HepCare Europe
Authors: Surey Julian , Menezes Dee , Francis Marie , Gibbons John , Sultan Binta , Miah Ala , Abubakar Ibrahim , Story Alistair 
Published: October 2019

Abstract

Background
HCV infection disproportionately affects underserved populations such as homeless individuals, people who inject drugs and prison populations. Peer advocacy can enable active engagement with healthcare services and increase the likelihood of favourable treatment outcomes.

Objectives
This observational study aims to assess the burden of disease in these underserved populations and describe the role of peer support in linking these individuals to specialist treatment services.

Methods
Services were identified if they had a high proportion of individuals with risk factors for HCV, such as injecting drug use or homelessness. Individuals were screened for HCV using point-of-care tests and a portable FibroScan. All positive cases received peer support for linkage to specialist care. Information was gathered on risk factors, demographics and follow-up information regarding linkage to care and treatment outcomes.

Results
A total of 461 individuals were screened, of which 197 (42.7%) were chronically infected with HCV. Referral was made to secondary care for 176 (89.3%) and all received peer support, with 104 (52.8%) individuals engaged with treatment centres. Of these, 89 (85.6%) started treatment and 76 (85.4%) had a favourable outcome. Factors associated with not being approved for treatment were recent homelessness, younger age and current crack cocaine injecting.

Conclusions
Highly trained peer support workers working as part of a specialist outreach clinical team help to identify a high proportion of individuals exposed to HCV, achieve high rates of engagement with treatment services and maintain high rates of treatment success amongst a population with complex needs.
Identification of Metagenomics Structure and Function Associated With Temporal Changes in Rat (Rattus norvegicus) Skin Microbiome During Health and Cutaneous Burn
Authors: Sanjar Fatemeh , Weaver Alan J , Peacock Trent J , Nguyen Jesse Q , Brandenburg Kenneth S , Leung Kai P 
Published: October 2019

Abstract
The cutaneous skin microbiome is host to a vast ensemble of resident microbes that provide essential capabilities including protection of skin barrier integrity and modulation of the host immune response. Cutaneous burn-injury promotes alteration of cutaneous and systemic immune response that can affect both commensal and pathogenic microbes. A cross-sectional study of a limited number of burn patients revealed a difference in the bacteriome of burned versus control participants. Temporal changes of the skin microbiome during health and cutaneous burn-injury remains largely unknown. Furthermore, how this microbial shift relates to community function in the collective metagenome remain elusive. Due to cost considerations and reduced healing time, rodents are frequently used in burn research, despite inherent physiological differences between rodents and human skin. Using a rat burn model, a longitudinal study was conducted to characterize the rat skin bacterial residents and associated community functions in states of health (n = 30) (sham-burned) and when compromised by burn-injury (n = 24). To address the knowledge gap, traumatic thermal injury and disruption of cutaneous surface is associated with genus-level changes in the microbiota, reduced bacterial richness, and altered representation of bacterial genes and associated predicted functions across different skin microbial communities. These findings demonstrate that, upon burn-injury, there is a shift in diversity of the skin’s organismal assemblages, yielding a core microbiome that is distinct at the genome and functional level. Moreover, deviations from the core community correlate with temporal changes post-injury and community transition from the state of cutaneous health to disease (burn-injury).
Mapping User-Centric Internet Geographies: How Similar are Countries in Their Web Use Patterns?
Authors: Ng Yee Man Margaret , Taneja Harsh 
Published: October 2019

Abstract
With half the world now online, a handful of websites dominate globally. Yet little is known about the homogeneity or geographical distinctness of global web use patterns. Focusing beyond popular sites, we inquired into how and why countries are similar in their web use patterns, developing a framework drawing on the literatures on media globalization, as well as Internet geographies. To compute similarities in web use between countries, we utilized an algorithm that considered both ranking positions and overlap counts on ranked lists of the 100 most popular websites for 174 countries, totaling 6,252 unique websites. Findings from a network analysis and from regressions suggest that countries with similar languages and shared borders, as well as those vastly different in their Internet market sizes, tend to have similar web use patterns. Neither are countries particularly similar to the US in web use nor does the prevalence of English speakers have an influence.
Clinical Validity of the PROMIS Pediatric Sleep Measures across Populations of Children with Chronic Illnesses and Neurodevelopment Disorders
Authors: Meltzer Lisa J , Forrest Christopher B , de la Motte Anna , Bevans Katherine B 
Published: October 2019

Abstract

Objective
To examine the clinical validity of the Patient Reported Outcome Measurement Information System (PROMIS) Pediatric Sleep Disturbance (SD) and Sleep-Related Impairment (SRI) short forms.

Methods
Youth (8–17 years) from clinical populations with known SDs (sleep clinic n = 126, autism n = 276, asthma n = 82, asthma + eczema n = 68) and the general population (n = 902) completed the PROMIS Pediatric SD and SRI 8-item short forms, along with established measures of sleep (Children’s Report of Sleep Patterns, Sleep Habits Survey), PROMIS Pediatric Fatigue, and parent-reported clinical indicators (does child have sleep problem, use melatonin, use prescription sleep medication).

Results
Confirmatory factor analyses demonstrated factorial invariance for all clinical groups. Significant differences between the general population and clinical groups were found for SD and SRI (medium to large effect sizes). Convergent validity was demonstrated through separate hierarchical regression models that showed significant associations between parent-reported clinical indicators and SD and SRI, above and beyond clinical group, as well as moderate to strong correlations between the PROMIS sleep measures and both established measures of sleep and fatigue.

Conclusions
The PROMIS Pediatric SD and SRI short forms provide clinicians and researchers a brief, accurate, and valid way to measure patient-reported sleep outcomes in pediatric populations.
Combining Multiple Imputation and Hidden Markov Modeling to Obtain Consistent Estimates of Employment Status
Authors: Boeschoten Laura , Filipponi Danila , Varriale Roberta 
Published: October 2019

Abstract
Recently, a method was proposed that combines multiple imputation and latent class analysis (MILC) to correct for misclassification in combined data sets. A multiply imputed data set is generated which can be used to estimate different statistics of interest in a straightforward manner and can ensure that uncertainty due to misclassification is incorporated in the estimate of the total variance. In this article, MILC is extended by using hidden Markov modeling so that it can handle longitudinal data and correspondingly create multiple imputations for multiple time points. Recently, many researchers have investigated the use of hidden Markov modeling to estimate employment status rates using a combined data set consisting of data originating from the Labor Force Survey (LFS) and register data; this combined data set is used for the setup of the simulation study performed in this article. Furthermore, the proposed method is applied to an Italian combined LFS-register data set. We demonstrate how the MILC method can be extended to create imputations of scores for multiple time points and thereby show how the method can be adapted to practical situations.
Populus euphratica WRKY1 binds the promoter of H+-ATPase gene to enhance gene expression and salt tolerance
Authors: Yao Jun , Shen Zedan , Zhang Yanli , Wu Xia , Wang Jianhui , Sa Gang , Zhang Yuhong , Zhang Huilong , Deng Chen , Liu Jian , Hou Siyuan , Zhang Ying , Zhang Yinan , Zhao Nan , Deng Shurong , Lin Shanzhi , Zhao Rui , Chen Shaoliang 
Published: October 2019

AbstractPlasma membrane proton pumps play a crucial role in maintaining ionic homeostasis in salt-resistant Populus euphratica under saline conditions. High levels of NaCl (200 mM) induced PeHA1 expression in P. euphratica roots and leaves. We isolated a 2022 bp promoter fragment upstream of the translational start of PeHA1 from P. euphratica. The promoter–reporter construct PeHA1-pro::GUS was transferred to tobacco plants, demonstrating that β-glucuronidase activities increased in root, leaf, and stem tissues under salt stress. DNA affinity purification sequencing revealed that PeWRKY1 protein targeted the PeHA1 gene. We assessed the salt-induced transcriptional response of PeWRKY1 and its interaction with PeHA1 in P. euphratica. PeWRKY1 binding to the PeHA1 W-box in the promoter region was verified by a yeast one-hybrid assay, EMSA, luciferase reporter assay, and virus-induced gene silencing. Transgenic tobacco plants overexpressing PeWRKY1 had improved expression of NtHA4, which has a cis-acting W-box in the regulatory region, and improved H+ pumping activity in both in vivo and in vitro assays. We conclude that salt stress up-regulated PeHA1 transcription due to the binding of PeWRKY1 to the W-box in the promoter region of PeHA1. Thus, we conclude that enhanced H+ pumping activity enabled salt-stressed plants to retain Na+ homeostasis.
The MOSDEF survey: direct-method metallicities and ISM conditions at z ∼ 1.5–3.5
Authors: Sanders Ryan L , Shapley Alice E , Reddy Naveen A , Kriek Mariska , Siana Brian , Coil Alison L , Mobasher Bahram , Shivaei Irene , Freeman William R , Azadi Mojegan , Price Sedona H , Leung Gene , Fetherolf Tara , de Groot Laura , Zick Tom , Fornasini Francesca M , Barro Guillermo 
Published: October 2019

ABSTRACT
We present detections of [O iii] λ4363 and direct-method metallicities for star-forming galaxies at z = 1.7–3.6. We combine new measurements from the MOSFIRE Deep Evolution Field (MOSDEF) survey with literature sources to construct a sample of 18 galaxies with direct-method metallicities at z &gt; 1, spanning 7.5 &lt; 12+log(O/H) &lt; 8.2 and log(M*/M⊙) = 7–10. We find that strong-line calibrations based on local analogues of high-redshift galaxies reliably reproduce the metallicity of the z &gt; 1 sample on average. We construct the first mass–metallicity relation at z &gt; 1 based purely on direct-method O/H, finding a slope that is consistent with strong-line results. Direct-method O/H evolves by ≲0.1 dex at fixed M* and star formation rate from z ∼ 0 to 2.2. We employ photoionization models to constrain the ionization parameter and ionizing spectrum in the high-redshift sample. Stellar models with supersolar O/Fe and binary evolution of massive stars are required to reproduce the observed strong-line ratios. We find that the z &gt; 1 sample falls on the z ∼ 0 relation between ionization parameter and O/H, suggesting no evolution of this relation from z ∼ 0 to z ∼ 2. These results suggest that the offset of the strong-line ratios of this sample from local excitation sequences is driven primarily by a harder ionizing spectrum at fixed nebular metallicity compared to what is typical at z ∼ 0, naturally explained by supersolar O/Fe at high redshift caused by rapid formation time-scales. Given the extreme nature of our z &gt; 1 sample, the implications for representative z ∼ 2 galaxy samples at ∼1010 M⊙ are unclear, but similarities to z &gt; 6 galaxies suggest that these conclusions can be extended to galaxies in the epoch of reionization.
The stellar population of metal-poor galaxies at z ≈ 0.8 and the evolution of the mass–metallicity relation
Authors: Weldon Andrew , Ly Chun , Cooper Michael 
Published: October 2019

ABSTRACT
We present results from deep Spitzer/Infrared Array Camera (IRAC) observations of 28 metal-poor, strongly star-forming galaxies selected from the DEEP2 Galaxy Survey. By modelling infrared and optical photometry, we derive stellar masses and other stellar properties. We determine that these metal-poor galaxies have low stellar masses, M⋆ ≈ 108.1–109.5 M⊙. Combined with the Balmer-derived star formation rates (SFRs), these galaxies have average inverse SFR/M⋆ of ≈100 Myr. The evolution of stellar mass–gas metallicity relation to z ≈ 0.8 is measured by combining the modelled masses with previously obtained spectroscopic measurements of metallicity from [O iii] λ4363 detections. Here, we include measurements for 79 galaxies from the Metal Abundances across Cosmic Time Survey. Our mass–metallicity relation is lower at a given stellar mass than at z = 0.1 by 0.27 dex. This demonstrates a strong evolution in the mass–metallicity relation, $(1+z)^{-1.45^{+0.61}_{-0.76}}$. We find that the shape of the z ≈ 0.8 mass-metallicity relation, a steep rise in metallicity at low stellar masses, transitioning to a plateau at higher masses, is consistent with z ∼ 0.1 studies. We also compare the evolution in metallicity between z ≈ 0.8 and z ∼ 0.1 against recent strong-line diagnostic studies at intermediate redshifts and find good agreement. Specifically, we find that lower mass galaxies (4 × 108 M⊙) built up their metal content 1.6 times more rapidly than higher mass galaxies (1010 M⊙). Finally, we examine whether the mass–metallicity relation has a secondary dependence on SFR, and statistically concluded that there is no strong secondary dependence for z ≈ 0.8 low-mass galaxies.
Susceptibility of planetary atmospheres to mass loss and growth by planetesimal impacts: the impact shoreline
Authors: Wyatt M C , Kral Q , Sinclair C A 
Published: October 2019

Abstract
This paper considers how planetesimal impacts affect planetary atmospheres. Atmosphere evolution depends on the ratio of gain from volatiles to loss from atmosphere stripping fv; for constant bombardment, atmospheres with fv < 1 are destroyed in finite time, but grow linearly with time for fv > 1. An impact outcome prescription is used to characterise how fv depends on planetesimal impact velocities, size distribution and composition. Planets that are low mass and/or close to the star have atmospheres that deplete in impacts, while high mass and/or distant planets grow secondary atmospheres. Dividing these outcomes is an fv = 1 impact shoreline analogous to Zahnle & Catling’s cosmic shoreline. The impact shoreline’s location depends on assumed impacting planetesimal properties, so conclusions for the atmospheric evolution of a planet like Earth with fv ≈ 1 are only as strong as those assumptions. Application to the exoplanet population shows the gap in the planet radius distribution at ∼1.5R⊕ is coincident with the impact shoreline, which has a similar dependence on orbital period and stellar mass to the observed gap. Given sufficient bombardment, planets below the gap would be expected to lose their atmospheres, while those above could have atmospheres enhanced in volatiles. The level of atmosphere alteration depends on the total bombardment a planet experiences, and so on the system’s (usually unknown) other planets and planetesimals, though massive distant planets would have low accretion efficiency. Habitable zone planets around lower luminosity stars are more susceptible to atmosphere stripping, disfavouring M stars as hosts of life-bearing planets if Earth-like bombardment is conducive to the development of life.
MUSE Analysis of Gas around Galaxies (MAGG) – I: Survey design and the environment of a near pristine gas cloud at z ≈ 3.5
Authors: Lofthouse Emma K , Fumagalli Michele , Fossati Matteo , O’Meara John M , Murphy Michael T , Christensen Lise , Prochaska J Xavier , Cantalupo Sebastiano , Bielby Richard M , Cooke Ryan J , Lusso Elisabeta , Morris Simon L 
Published: October 2019

ABSTRACT
We present the design, methods, and first results of the MUSE Analysis of Gas around Galaxies (MAGG) survey, a large programme on the Multi-Unit Spectroscopic Explorer (MUSE) instrument at the Very Large Telescope (VLT), which targets 28 z &gt; 3.2 quasars to investigate the connection between optically thick gas and galaxies at z ∼ 3–4. MAGG maps the environment of 52 strong absorption line systems at z ≳ 3, providing the first statistical sample of galaxies associated with gas-rich structures in the early Universe. In this paper, we study the galaxy population around a very metal poor gas cloud at z ≈ 3.53 towards the quasar J124957.23−015928.8. We detect three Lyα emitters within $\lesssim 200~\rm km~s^{-1}$ of the cloud redshift, at projected separations $\lesssim 185~\rm ~kpc$ (physical). The presence of star-forming galaxies near a very metal-poor cloud indicates that metal enrichment is still spatially inhomogeneous at this redshift. Based on its very low metallicity and the presence of nearby galaxies, we propose that the most likely scenario for this Lyman Limit System (LLS) is that it lies within a filament which may be accreting on to a nearby galaxy. Taken together with the small number of other LLSs studied with MUSE, the observations to date show a range of different environments near strong absorption systems. The full MAGG survey will significantly expand this sample and enable a statistical analysis of the link between gas and galaxies to pin down the origin of these diverse environments at z ≈ 3–4.