bluuebunny/crossref_metadata_2025_split huggingface dataset:
Galaxies lacking dark matter in the Illustris simulation
Authors: Haslbauer M. , Dabringhausen J. , Kroupa P. , Javanmardi B. , Banik I. 
Published: May 2019

Context. Any viable cosmological model in which galaxies interact predicts the existence of primordial and tidal dwarf galaxies (TDGs). In particular, in the standard model of cosmology (ΛCDM), according to the dual dwarf galaxy theorem, there must exist both primordial dark matter-dominated and dark matter-free TDGs with different radii.
Aims. We study the frequency, evolution, and properties of TDGs in a ΛCDM cosmology.
Methods. We use the hydrodynamical cosmological Illustris-1 simulation to identify TDG candidates (TDGCs) and study their present-day physical properties. The positions of galaxies in the radius–mass plane, depending on their nonbaryonic content, are compared with observational data and other simulations. We also present movies on the formation of a few galaxies lacking dark matter, confirming their tidal dwarf nature. Tidal dwarf galaxy candidates can however also be formed via other mechanisms, such as from ram-pressure-stripped material or, speculatively, from cold-accreted gas.
Results. We find 97 TDGCs with Mstellar > 5 × 107M⊙ at redshift z = 0, corresponding to a co-moving number density of 2.3 × 10−4 h3 cMpc−3. The most massive TDGC has Mtotal = 3.1 × 109 M⊙, comparable to that of the Large Magellanic Cloud. Tidal dwarf galaxy candidates are phase-space-correlated, reach high metallicities, and are typically younger than dark matter-rich dwarf galaxies.
Conclusions. We report for the first time the verification of the dual dwarf theorem in a self-consistent ΛCDM cosmological simulation. Simulated TDGCs and dark matter-dominated galaxies populate different regions in the radius–mass diagram in disagreement with observations of early-type galaxies. The dark matter-poor galaxies formed in Illustris-1 have comparable radii to observed dwarf galaxies and to TDGs formed in other galaxy-encounter simulations. In Illustris-1, only 0.17 percent of all selected galaxies with Mstellar = 5 × 107−109 M⊙ are TDGCs or dark matter-poor dwarf galaxies. The occurrence of NGC 1052-DF2-type objects is discussed.
Sparkling nights and very hot days on WASP-18b: the formation of clouds and the emergence of an ionosphere
Authors: Helling Ch. , Gourbin P. , Woitke P. , Parmentier V. 
Published: May 2019

Context. WASP-18b is an ultra-hot Jupiter with a temperature difference of up to 2500 K between day and night. Such giant planets begin to emerge as a planetary laboratory for understanding cloud formation and gas chemistry in well-tested parameter regimes in order to better understand planetary mass loss and for linking observed element ratios to planet formation and evolution.
Aims. We aim to understand where clouds form, their interaction with the gas-phase chemistry through depletion and enrichment, the ionisation of the atmospheric gas, and the possible emergence of an ionosphere on ultra-hot Jupiters.
Methods. We used 1D profiles from a 3D atmosphere simulation for WASP-18b as input for kinetic cloud formation and gas-phase chemical equilibrium calculations. We solved our kinetic cloud formation model for these 1D profiles, which sample the atmosphere of WASP-18b at 16 different locations along the equator and in the mid-latitudes. We derived the gas-phase composition consistently.
Results. The dayside of WASP-18b emerges as completely cloud-free as a result of the very high atmospheric temperatures. In contrast, the nightside is covered in geometrically extended and chemically heterogeneous clouds with dispersed particle size distributions. The atmospheric C/O ratio increases to >0.7 and the enrichment of the atmospheric gas with cloud particles is ρd/ρgas > 10−3. The clouds that form at the limbs appear located farther inside the atmosphere, and they are the least extended. Not all day- to nightside terminator regions form clouds. The gas phase is dominated by H2, CO, SiO, H2O, H2S, CH4, and SiS. In addition, the dayside has a substantial degree of ionisation that is due to ions such as Na+, K+, Ca+, and Fe+. Al+ and Ti+ are the most abundant of their element classes. We find that WASP-18b, as one example for ultra-hot Jupiters, develops an ionosphere on the dayside.
G-quadruplex–forming GGA repeat region functions as a negative regulator of the Ccnb1ip1 enhancer
Authors: Islam Izzul , Baba Yuji , Witarto Arief Budi , Yoshida Wataru 
Published: May 2019

ABSTRACT
An enhancer located upstream of the transcriptional start site of Ccnb1ip1 containing two GGA-rich regions and a 14-GGA repeat (GGA)14 region has been previously identified. Three copies of four GGA repeats in the c-myb promoter that form a tetrad:heptad:heptad:tetrad (T:H:H:T) dimerized G-quadruplex (G4) structure reportedly functions as both a transcriptional repressor and activator. Here, the secondary structures of the two GGA-rich and (GGA)14 regions were analyzed using circular dichroism spectral analysis, which indicated that the two GGA-rich DNAs formed parallel-type G4 structures, whereas (GGA)14 DNA formed the T:H:H:T dimerized G4 structure. Reporter assays demonstrated that individual regions did not show enhancer activity; however, the deletion of the (GGA)14 region resulted in 1.5-fold higher enhancer activity than that of the whole enhancer. These results indicate that the (GGA)14 region that forms the T:H:H:T dimerized G4 structure functions as a negative regulator of the Ccnb1ip1 enhancer.
Modeling cellular metabolomic effects of oxidative stress impacts from hydrogen peroxide and cigarette smoke on human lung epithelial cells
Authors: Yamaguchi Mei S , McCartney Mitchell M , Falcon Alexandria K , Linderholm Angela L , Ebeler Susan E , Kenyon Nicholas J , Harper Richart H , Schivo Michael , Davis Cristina E 
Published: May 2019

Abstract
The respiratory system is continuously exposed to variety of biological and chemical irritants that contain reactive oxygen species, and these are well known to cause oxidative stress responses in lung epithelial cells. There is a clinical need to identify biomarkers of oxidative stress which could potentially support early indicators of disease and health management. To identify volatile biomarkers of oxidative stress, we analyzed the headspace above human bronchial epithelial cell cultures (HBE1) before and after hydrogen peroxide (H2O2) and cigarette smoke extract (CSE) exposure. Using stir bar and headspace sorptive extraction-gas chromatography-mass spectrometry, we searched for volatile organic compounds (VOC) of these oxidative measures. In the H2O2 cell peroxidation experiments, four different H2O2 concentrations (0.1, 0.5, 10, 50 mM) were applied to the HBE1 cells, and VOCs were collected every 12 h over the time course of 48 h. In the CSE cell peroxidation experiments, four different smoke extract concentrations (0%, 10%, 30%, 60%) were applied to the cells, and VOCs were collected every 12 h over the time course of 48 h. We used partial-least squares (PLS) analysis to identify putative compounds from the mass spectrometry results that highly correlated with the known applied oxidative stress. We observed chemical emissions from the cells that related to both the intensity of the oxidative stress and followed distinct time courses. Additionally, some of these chemicals are aldehydes, which are thought to be non-invasive indicators of oxidative stress in exhaled human breath. Together, these results illustrate a powerful in situ cell culture model of oxidative stress that can be used to explore the putative biological genesis of exhaled breath biomarkers that are often observed in human clinical studies.
Associations Between Loss of ARID1A Expression and Clinicopathologic and Genetic Variables in T1 Early Colorectal Cancer
Authors: Kishida Yoshihiro , Oishi Takuma , Sugino Takashi , Shiomi Akio , Urakami Kenichi , Kusuhara Masatoshi , Yamaguchi Ken , Kitagawa Yuko , Ono Hiroyuki 
Published: May 2019

Abstract

Objectives
To evaluate the relationships between adenine-thymine-rich interactive domain 1A (ARID1A) expression and the clinicopathologic features in T1 colorectal cancer (CRC) and to investigate whether the presence of ARID1A protein is related to genetic changes.

Methods
We retrospectively studied 219 surgically resected T1 CRCs. ARID1A expression was assessed by immunohistochemical methods, and the correlation between ARID1A expression and clinicopathologic features was evaluated. The relationship between ARID1A expression and 409 cancer-related gene mutations was also evaluated using next-generation sequencing (NGS).

Results
Immunohistochemical staining indicated negative ARID1A expression in 4.6%. Loss of ARID1A expression was significantly associated with younger age, lymphatic invasion, and lymph node metastasis (LNM). NGS showed that PKHD1, RNF213, and MSH6 mutations were more frequent in ARID1A-negative tumors, whereas KRAS mutations were more common in ARID1A-positive tumors.

Conclusions
In T1 CRC, negative ARID1A expression was correlated with early onset, lymphatic invasion, and LNM. Mutations in some cancer-related genes were possibly related with ARID1A expression.
Incorporating spatial–anatomical similarity into the VGWAS framework for AD biomarker detection
Authors: Huang Meiyan , Yu Yuwei , Yang Wei , Feng Qianjin ,   Alzheimer’s Disease Neuroimaging Initiative
Published: May 2019

Abstract

Motivation
The detection of potential biomarkers of Alzheimer’s disease (AD) is crucial for its early prediction, diagnosis and treatment. Voxel-wise genome-wide association study (VGWAS) is a commonly used method in imaging genomics and usually applied to detect AD biomarkers in imaging and genetic data. However, existing VGWAS methods entail large computational cost and disregard spatial correlations within imaging data. A novel method is proposed to solve these issues.

Results
We introduce a novel method to incorporate spatial correlations into a VGWAS framework for the detection of potential AD biomarkers. To consider the characteristics of AD, we first present a modification of a simple linear iterative clustering method for spatial grouping in an anatomically meaningful manner. Second, we propose a spatial–anatomical similarity matrix to incorporate correlations among voxels. Finally, we detect the potential AD biomarkers from imaging and genetic data by using a fast VGWAS method and test our method on 708 subjects obtained from an Alzheimer’s Disease Neuroimaging Initiative dataset. Results show that our method can successfully detect some new risk genes and clusters of AD. The detected imaging and genetic biomarkers are used as predictors to classify AD/normal control subjects, and a high accuracy of AD/normal control classification is achieved. To the best of our knowledge, the association between imaging and genetic data has yet to be systematically investigated while building statistical models for classifying AD subjects to create a link between imaging genetics and AD. Therefore, our method may provide a new way to gain insights into the underlying pathological mechanism of AD.

Availability and implementation
https://github.com/Meiyan88/SASM-VGWAS.
Nearly random designs with greatly improved balance
Authors: Krieger A M , Azriel D , Kapelner A 
Published: May 2019

SummaryWe present a procedure that divides a set of experimental units into two groups that are similar on a prespecified set of covariates and are almost as random as with a complete randomization. Under complete randomization, the difference in the standardized average between treatment and control is $O_{\rm p}(n^{-1/2})$, which may be material in small samples. We present an algorithm that reduces imbalance to $O_{\rm p}(n^{-3})$ for one covariate and $O_{\rm p}\{n^{-(1 + 2/p)}\}$ for $p$ covariates, but whose assignments are, strictly speaking, nonrandom. In addition to the metric of maximum eigenvalue of allocation variance, we introduce two metrics that capture departures from randomization and show that our assignments are nearly as random as complete randomization in terms of all measures. Simulations illustrate the results, and inference is discussed. An R package to generate designs according to our algorithm and other popular designs is available.
Using SimulATe to model the effects of antibiotic selective pressure on the dynamics of pathogenic bacterial populations
Authors: David Pedro H C , Sá-Pinto Xana , Nogueira Teresa 
Published: May 2019

Abstract
Antibiotics are notable weapons in fighting bacteria. Nowadays, however, the effectiveness of antibiotics is severely hindered by the increasing levels of antibiotic resistances in pathogenic bacterial populations, which can persist due to the selective pressure caused by antibiotic exposure. Arguably, the main cause of antibiotic resistances endurance in nature is antibiotic misuse, such as via overusing, inappropriate prescribing as well as the uncontrolled use in agriculture and livestock. There is also a lack of knowledge on appropriate antibiotic usage by the general public. Public scientific literacy and more research on therapeutic practices are fundamental to tackle this problem. Here, we present SimulATe a software which allows the simulation of the effects of antibiotic therapies on bacterial populations during human infections. This software can be used to develop students’ scientific literacy, using infections and antibiotic treatments as context to engage students in scientific practices, and discussions on antibiotic treatment onset and duration or on its use in immunosuppressed or critically ill individuals. SimulATe’s features also allow it to be used for research purposes allowing the simulation of real scenarios and exploration of their outcomes across the parameters’ landscape.
Mapping physiology: biophysical mechanisms define scales of climate change impacts
Authors: Choi Francis , Gouhier Tarik , Lima Fernando , Rilov Gil , Seabra Rui , Helmuth Brian 
Published: May 2019

AbstractThe rocky intertidal zone is a highly dynamic and thermally variable ecosystem, where the combined influences of solar radiation, air temperature and topography can lead to differences greater than 15°C over the scale of centimetres during aerial exposure at low tide. For most intertidal organisms this small-scale heterogeneity in microclimates can have enormous influences on survival and physiological performance. However, the potential ecological importance of environmental heterogeneity in determining ecological responses to climate change remains poorly understood. We present a novel framework for generating spatially explicit models of microclimate heterogeneity and patterns of thermal physiology among interacting organisms. We used drone photogrammetry to create a topographic map (digital elevation model) at a resolution of 2 × 2 cm from an intertidal site in Massachusetts, which was then fed into to a model of incident solar radiation based on sky view factor and solar position. These data were in turn used to drive a heat budget model that estimated hourly surface temperatures over the course of a year (2017). Body temperature layers were then converted to thermal performance layers for organisms, using thermal performance curves, creating ‘physiological landscapes’ that display spatially and temporally explicit patterns of ‘microrefugia’. Our framework shows how non-linear interactions between these layers lead to predictions about organismal performance and survivorship that are distinct from those made using any individual layer (e.g. topography, temperature) alone. We propose a new metric for quantifying the ‘thermal roughness’ of a site (RqT, the root mean square of spatial deviations in temperature), which can be used to quantify spatial and temporal variability in temperature and performance at the site level. These methods facilitate an exploration of the role of micro-topographic variability in driving organismal vulnerability to environmental change using both spatially explicit and frequency-based approaches.
Adult Paederus fuscipes (Coleoptera: Staphylinidae) Beetles Overcome Water Loss With Increased Total Body Water Content, Energy Metabolite Storage, and Reduced Cuticular Permeability: Age, Sex-Specific, and Mating Status Effects on Desiccation
Authors: Wang Chia-Yu , Bong Lee-Jin , Neoh Kok-Boon 
Published: May 2019

AbstractThe ability of Paederus beetles to resist desiccation stress is vital to their adaptability in various ecological niches. How water relations and their response to desiccation vary among adult beetles of different age, sex, and mating status is unclear. We examined the water relations of adult Paederus fuscipes Curtis and the mechanisms used to reduce desiccation stress. One-day-old beetles had an exceptionally high percent total body water (%TBW) content and tolerated a high level of %TBW loss. Newly emerged beetles contained a high level of trehalose and 40 to 60% lipid content of their total dry mass, which allowed them to endure desiccation. Beetles that were 10 wk old and older exhibited reduced cuticular permeability. Glucose, glycogen, and lipid contents were crucial throughout most of the adult life span, as they helped compensate for water loss via increased water vapor absorption and metabolic water. In particular, the accumulation of lipid after mating was significant and may further confer tolerance to water loss. The effect of melanization on the desiccation tolerance of beetles was not significant. Females had better tolerance in response to desiccation stress compared with males. We suggest that the observed differences between sexes likely were a function of water relations and an effect of energy metabolite reserves. However, the mortality of females at 24-h postdesiccating stage was marginally significant compared with males. These results demonstrate that P. fuscipes adults prevent dehydration using multiple mechanisms that collectively reduce desiccation stress and increase dehydration tolerance.
Cumulative childhood adversity, adolescent psychiatric disorder and violent offending in young adulthood
Authors: Björkenstam Emma , Burström Bo , Hjern Anders , Vinnerljung Bo , Kosidou Kyriaki , Berg Lisa 
Published: May 2019

Abstract

Background
Childhood adversity (CA) is a risk indicator for psychiatric morbidity. Although CA has been linked to violent offending, limited research has considered adolescent psychiatric disorder as a mediating factor. The current study examined whether adolescent psychiatric disorder mediates the association between CA and violent offending.

Methods
We used a cohort of 476 103 individuals born in 1984–1988 in Sweden. Register-based CAs included parental death, substance abuse and psychiatric disorder, parental criminal offending, parental separation, public assistance, child welfare intervention and residential instability. Adolescent psychiatric disorder was defined as being treated with a psychiatric diagnosis prior to age 20. Estimates of risk of violent offending after age 20 were calculated as incidence rate ratios (IRRs) with 95% confidence intervals (CIs). Mediation was tested with the bootstrap method.

Results
Exposure to CA was positively associated with violent offending, especially when accumulated. Individuals exposed to 4+ CAs who were also treated for psychiatric disorder had a 12-fold elevated risk for violent offending (adjusted IRR 12.2, 95% CI 10.6–14.0). Corresponding IRR among 4+ CA youth with no psychiatric disorder was 5.1 (95% CI 4.5–5.6). Psychiatric disorder mediated the association between CA and violent offending.

Conclusion
CA is associated with elevated risk for violent offending in early adulthood, and the association is partly mediated by adolescent psychiatric disorder. Individuals exposed to cumulative CA who also develop adolescent psychopathology should be regarded as a high-risk group for violent offending, by professionals in social and health services that come into contact with this group.
Health and Psychosocial Needs of Older Adults Who Are Experiencing Homelessness Following Hospital Discharge
Authors: Canham Sarah L , Custodio Karen , Mauboules Celine , Good Chloe , Bosma Harvey 
Published: May 2019

Abstract

Introduction
Though hospitals are a common location where older adults experiencing homelessness receive health care, an understanding of the types of supports needed upon hospital discharge is limited. We examined the unique characteristics of older homeless adults and the health and psychosocial supports required upon hospital discharge.

Design and Methods
Guided by principles of community-based participatory research (CBPR), we conducted 20 in-depth, semi-structured interviews with shelter/housing and health care providers in Metro Vancouver.

Results
Thematic analyses revealed 6 themes: (a) older people experiencing homelessness have unique vulnerabilities upon hospital discharge; (b) following hospital discharge, general population shelters are inappropriate for older adults; (c) shelter/housing options for older adults who have complex health and social needs are limited; (d) shelter/housing for older adults who require medical stabilization and convalescence after hospital discharge is needed; (e) a range of senior-specific shelter/housing options are needed; and (f) unique community supports are needed for older adults upon hospital discharge.

Discussion and Implications
As the population of older adults increases across North America, there is a parallel trend in the increased numbers of older adults who are experiencing homelessness. Not only is there often a need for ongoing medical care and respite, but there is a need for both shelter and housing options that can appropriately support individual needs.