bluuebunny/crossref_metadata_2025 huggingface dataset:
Imprints of mass accretion history on the shape of the intracluster medium and the TX–M relation
Authors: Chen Huanqing , Avestruz Camille , Kravtsov Andrey V , Lau Erwin T , Nagai Daisuke
Published: October 2019

We use a statistical sample of galaxy clusters from a large cosmological N-body + hydrodynamics simulation to examine the relation between morphology, or shape, of the X-ray emitting intracluster medium (ICM) and the mass accretion history of the galaxy clusters. We find that the mass accretion rate (MAR) of a cluster is correlated with the ellipticity of the ICM. The correlation is largely driven by material accreted in the last ∼4.5 Gyr, indicating a characteristic time-scale for relaxation of cluster gas. Furthermore, we find that the ellipticity of the outer regions (R ∼ R500c) of the ICM is correlated with the overall MAR of clusters, while ellipticity of the inner regions (≲0.5 R500c) is sensitive to recent major mergers with mass ratios of ≥1:3. Finally, we examine the impact of variations in cluster mass accretion history on the X-ray observable–mass scaling relations. We show that there is a continuous anticorrelation between the residuals in the TX–M relation and cluster MARs, within which merging and relaxed clusters occupy extremes of the distribution rather than form two peaks in a bimodal distribution, as was often assumed previously. Our results indicate that the systematic uncertainties in the X-ray observable–mass relations can be mitigated by using the information encoded in the apparent ICM ellipticity.
The SAMI Galaxy Survey: rules of behaviour for spin-ellipticity radial tracks in galaxies
Authors: Rawlings Alexander , Foster Caroline , van de Sande Jesse , Taranu Dan S , Croom Scott M , Bland-Hawthorn Joss , Brough Sarah , Bryant Julia J , Colless Matthew , Lagos Claudia del P , Konstantopoulos Iraklis S , Lawrence Jon S , López-Sánchez Ángel R , Lorente Nuria P F , Medling Anne M , Oh Sree , Owers Matt S , Richards Samuel N , Scott Nicholas , Sweet Sarah M , Yi Sukyoung K
Published: October 2019

We study the behaviour of the spin-ellipticity radial tracks for 507 galaxies from the Sydney AAO Multiobject Integral Field (SAMI) Galaxy Survey with stellar kinematics out to ≥1.5Re. We advocate for a morpho-dynamical classification of galaxies, relying on spatially resolved photometric and kinematic data. We find the use of spin-ellipticity radial tracks is valuable in identifying substructures within a galaxy, including embedded and counter-rotating discs, that are easily missed in unilateral studies of the photometry alone. Conversely, bars are rarely apparent in the stellar kinematics but are readily identified on images. Consequently, we distinguish the spin-ellipticity radial tracks of seven morpho-dynamical types: elliptical, lenticular, early spiral, late spiral, barred spiral, embedded disc, and 2σ galaxies. The importance of probing beyond the inner radii of galaxies is highlighted by the characteristics of galactic features in the spin-ellipticity radial tracks present at larger radii. The density of information presented through spin-ellipticity radial tracks emphasizes a clear advantage to representing galaxies as a track, rather than a single point, in spin-ellipticity parameter space.
The multiphase gas structure and kinematics in the circumnuclear region of NGC 5728
Authors: Shimizu T Taro , Davies R I , Lutz D , Burtscher L , Lin M , Baron D , Davies R L , Genzel R , Hicks E K S , Koss M , Maciejewski W , Müller-Sánchez F , Orban de Xivry G , Price S H , Ricci C , Riffel R , Riffel R A , Rosario D , Schartmann M , Schnorr-Müller A , Sternberg A , Sturm E , Storchi-Bergmann T , Tacconi L , Veilleux S
Published: October 2019

We report on our combined analysis of HST, VLT/MUSE, VLT/SINFONI, and ALMA observations of the local Seyfert 2 galaxy, NGC 5728 to investigate in detail the feeding and feedback of the active galactic nucleus (AGN). The data sets simultaneously probe the morphology, excitation, and kinematics of the stars, ionized gas, and molecular gas over a large range of spatial scales (10 pc to 10 kpc). NGC 5728 contains a large stellar bar that is driving gas along prominent dust lanes to the inner 1 kpc where the gas settles into a circumnuclear ring. The ring is strongly star forming and contains a substantial population of young stars as indicated by the lowered stellar velocity dispersion and gas excitation consistent with H ii regions. We model the kinematics of the ring using the velocity field of the CO (2–1) emission and stars and find it is consistent with a rotating disc. The outer regions of the disc, where the dust lanes meet the ring, show signatures of inflow at a rate of 1 M$\odot$ yr−1. Inside the ring, we observe three molecular gas components corresponding to the circular rotation of the outer ring, a warped disc, and the nuclear stellar bar. The AGN is driving an ionized gas outflow that reaches a radius of 250 pc with a mass outflow rate of 0.08 M$\odot$ yr−1 consistent with its luminosity and scaling relations from previous studies. While we observe distinct holes in CO emission which could be signs of molecular gas removal, we find that largely the AGN is not disrupting the structure of the circumnuclear region.
Analysis of spiral structure in the accretion disc of the nova-like cataclysmic variable EC21178–5417
Authors: Ruiz-Carmona R , Khangale Z N , Woudt P A , Groot P J
Published: October 2019

We present an extensive Doppler tomography study of the eclipsing nova-like EC21178–5417, which exhibits the classic accretion disc signature in the form of double-peak emission lines in its spectrum. Doppler tomograms confirm the presence of a strong, two-armed spiral pattern visible in the majority of the spectral lines studied. This makes EC21178–5417 one of the very few nova-likes that show spiral structure in their discs. We also report night-to-night changes in the position and relative strength of the spiral arms, revealing fluctuations on the conditions in the accretion disc.
Learning the relationship between galaxies spectra and their star formation histories using convolutional neural networks and cosmological simulations
Authors: Lovell Christopher C , Acquaviva Viviana , Thomas Peter A , Iyer Kartheik G , Gawiser Eric , Wilkins Stephen M
Published: October 2019

We present a new method for inferring galaxy star formation histories (SFH) using machine learning methods coupled with two cosmological hydrodynamic simulations. We train convolutional neural networks to learn the relationship between synthetic galaxy spectra and high-resolution SFHs from the eagle and Illustris models. To evaluate our SFH reconstruction we use Symmetric Mean Absolute Percentage Error (SMAPE), which acts as a true percentage error in the low error regime. On dust-attenuated spectra we achieve high test accuracy (median SMAPE = 10.5 per cent). Including the effects of simulated observational noise increases the error (12.5 per cent), however this is alleviated by including multiple realizations of the noise, which increases the training set size and reduces overfitting (10.9 per cent). We also make estimates for the observational and modelling errors. To further evaluate the generalization properties we apply models trained on one simulation to spectra from the other, which leads to only a small increase in the error (median SMAPE $\sim 15{\,{\rm {per\, cent}}}$). We apply each trained model to SDSS DR7 spectra, and find smoother histories than in the $\textsf{vespa}$ catalogue. This new approach complements the results of existing spectral energy distribution fitting techniques, providing SFHs directly motivated by the results of the latest cosmological simulations.
Using HARPS-N to characterize the long-period planets in the PH-2 and Kepler-103 systems
Authors: Dubber Sophie C , Mortier Annelies , Rice Ken , Nava Chantanelle , Malavolta Luca , Giles Helen , Coffinet Adrien , Charbonneau David , Vanderburg Andrew , Bonomo Aldo S , Boschin Walter , Buchhave Lars A , Cameron Andrew Collier , Cosentino Rosario , Dumusque Xavier , Ghedina Adriano , Harutyunyan Avet , Haywood Raphaëlle D , Latham David , López-Morales Mercedes , Micela Giusi , Molinari Emilio , Pepe Francesco A , Phillips David , Piotto Giampaolo , Poretti Ennio , Sasselov Dimitar , Sozzetti Alessandro , Udry Stéphane
Published: October 2019

We present confirmation of the planetary nature of PH-2b, as well as the first mass estimates for the two planets in the Kepler-103 system. PH-2b and Kepler-103c are both long-period and transiting, a sparsely populated category of exoplanets. We use Kepler light-curve data to estimate a radius, and then use HARPS-N radial velocities to determine the semi-amplitude of the stellar reflex motion and, hence, the planet mass. For PH-2b we recover a 3.5σ mass estimate of $M_\mathrm{ p} = 109^{+30}_{-32}$ M⊕ and a radius of Rp = 9.49 ± 0.16 R⊕. This means that PH-2b has a Saturn-like bulk density and is the only planet of this type with an orbital period P > 200 d that orbits a single star. We find that Kepler-103b has a mass of $M_{\text{p,b}} = 11.7^{+4.31}_{-4.72}$ M⊕ and Kepler-103c has a mass of $M_{\text{p,c}} = 58.5^{+11.2}_{-11.4}$ M⊕. These are 2.5σ and 5σ results, respectively. With radii of $R_{\text{p,b}} = 3.49^{+0.06}_{-0.05}$ R⊕ and $R_{\text{p,c}} = 5.45^{+0.18}_{-0.17}$ R⊕, these results suggest that Kepler-103b has a Neptune-like density, while Kepler-103c is one of the highest density planets with a period P > 100 d. By providing high-precision estimates for the masses of the long-period, intermediate-mass planets PH-2b and Kepler-103c, we increase the sample of long-period planets with known masses and radii, which will improve our understanding of the mass–radius relation across the full range of exoplanet masses and radii.
The International Pulsar Timing Array: second data release
Authors: Perera B B P , DeCesar M E , Demorest P B , Kerr M , Lentati L , Nice D J , Osłowski S , Ransom S M , Keith M J , Arzoumanian Z , Bailes M , Baker P T , Bassa C G , Bhat N D R , Brazier A , Burgay M , Burke-Spolaor S , Caballero R N , Champion D J , Chatterjee S , Chen S , Cognard I , Cordes J M , Crowter K , Dai S , Desvignes G , Dolch T , Ferdman R D , Ferrara E C , Fonseca E , Goldstein J M , Graikou E , Guillemot L , Hazboun J S , Hobbs G , Hu H , Islo K , Janssen G H , Karuppusamy R , Kramer M , Lam M T , Lee K J , Liu K , Luo J , Lyne A G , Manchester R N , McKee J W , McLaughlin M A , Mingarelli C M F , Parthasarathy A P , Pennucci T T , Perrodin D , Possenti A , Reardon D J , Russell C J , Sanidas S A , Sesana A , Shaifullah G , Shannon R M , Siemens X , Simon J , Spiewak R , Stairs I H , Stappers B W , Swiggum J K , Taylor S R , Theureau G , Tiburzi C , Vallisneri M , Vecchio A , Wang J B , Zhang S B , Zhang L , Zhu W W , Zhu X J
Published: October 2019

In this paper, we describe the International Pulsar Timing Array second data release, which includes recent pulsar timing data obtained by three regional consortia: the European Pulsar Timing Array, the North American Nanohertz Observatory for Gravitational Waves, and the Parkes Pulsar Timing Array. We analyse and where possible combine high-precision timing data for 65 millisecond pulsars which are regularly observed by these groups. A basic noise analysis, including the processes which are both correlated and uncorrelated in time, provides noise models and timing ephemerides for the pulsars. We find that the timing precisions of pulsars are generally improved compared to the previous data release, mainly due to the addition of new data in the combination. The main purpose of this work is to create the most up-to-date IPTA data release. These data are publicly available for searches for low-frequency gravitational waves and other pulsar science.
A nearby luminous AGN sample optically selected from Hubble Space Telescope
Authors: Li Shuang-Liang
Published: October 2019

In this work, a nearby luminous active galactic nucleus (AGN) sample is selected from Hubble Space Telescope(HST), where only sources with both X-ray emission observed by Chandra/XMM–Newton and radio flux detected by Very Large Array (VLA)/Very Long Baseline Array (VLBA)/very long baseline interferometry (VLBI)/Multi-Element Radio Linked Interferometer Network (MERLIN) are adopted to keep high precision. Finally, we get a sample of 30 luminous AGNs, which consists of 11 radio-loud AGNs (RLAGN) and 19 radio-quiet AGNs (RQAGN). It is found that the relationship between RUV and αox, which was first reported by Li & Xie in low-luminosity AGNs (LLAGN), and other relationships are all absent in RLAGN, probably due to the complex physical process therein. Our results indicate that the X-ray emission from jet should play an important role in RLAGN and further support the transition of accretion mode between LLAGN and RLAGN. On the other hand, the traditional relationships in RQAGN, such as αox and λ, Γ and λ, are found to be well consistent with previous works.
A PSF-based Approach to TESS High quality data Of Stellar clusters (PATHOS) – I. Search for exoplanets and variable stars in the field of 47 Tuc
Authors: Nardiello D , Borsato L , Piotto G , Colombo L S , Manthopoulou E E , Bedin L R , Granata V , Lacedelli G , Libralato M , Malavolta L , Montalto M , Nascimbeni V
Published: October 2019

The TESS mission will survey ∼85  per cent of the sky, giving us the opportunity of extracting high-precision light curves of millions of stars, including stellar cluster members. In this work, we present our project ‘A PSF-based Approach to TESS High quality data Of Stellar clusters’ (PATHOS), aimed at searching and characterize candidate exoplanets and variable stars in stellar clusters using our innovative method for the extraction of high-precision light curves of stars located in crowded environments. Our technique of light-curve extraction involves the use of empirical point spread functions (PSFs), an input catalogue and neighbour-subtraction. The PSF-based approach allows us to minimize the dilution effects in crowded environments and to extract high-precision photometry for stars in the faint regime (G > 13). For this pilot project, we extracted, corrected, and analysed the light curves of 16 641 stars located in a dense region centred on the globular cluster 47 Tuc. We were able to reach the TESS magnitude T ∼ 16.5 with a photometric precision of ${\sim} 1{{\ \rm per\ cent}}$ on the 6.5-h time-scale; in the bright regime we were able to detect transits with depth of ∼34 parts per million. We searched for variables and candidate transiting exoplanets. Our pipeline detected one planetary candidate orbiting a main-sequence star in the Galactic field. We analysed the period–luminosity distribution for red-giant stars of 47 Tuc and the eclipsing binaries in the field. Light curves are uploaded on the Mikulski Archive for Space Telescopes under the project PATHOS.
The life cycle of the Central Molecular Zone – I. Inflow, star formation, and winds
Authors: Armillotta Lucia , Krumholz Mark R , Di Teodoro Enrico M , McClure-Griffiths N M
Published: October 2019

We present a study of the gas cycle and star formation history in the central 500 pc of the Milky Way, known as Central Molecular Zone (CMZ). Through hydrodynamical simulations of the inner 4.5 kpc of our Galaxy, we follow the gas cycle in a completely self-consistent way, starting from gas radial inflow due to the Galactic bar, the channelling of this gas into a dense, star-forming ring/stream at ≈200–300 pc from the Galactic centre, and the launching of galactic outflows powered by stellar feedback. We find that star formation activity in the CMZ goes through oscillatory burst/quench cycles, with a period of tens to hundreds of Myr, characterized by roughly constant gas mass but order-of-magnitude level variations in the star formation rate. Comparison with the observed present-day star formation rate of the CMZ suggests that we are currently near a minimum of this cycle. Stellar feedback drives a mainly two-phase wind off the Galactic disc. The warm phase dominates the mass flux, and carries $100\!-\!200{{\ \rm per\ cent}}$ of the gas mass converted into stars. However, most of this gas goes into a fountain and falls back on to the disc rather than escaping the Galaxy. The hot phase carries most of the energy, with a time-averaged energy outflow rate of $10\!-\!20{{\ \rm per\ cent}}$ of the supernova energy budget.
SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble
Authors: Huh Ruth , Yang Yuchen , Jiang Yuchao , Shen Yin , Li Yun
Published: October 2019

Clustering is an essential step in the analysis of single cell RNA-seq (scRNA-seq) data to shed light on tissue complexity including the number of cell types and transcriptomic signatures of each cell type. Due to its importance, novel methods have been developed recently for this purpose. However, different approaches generate varying estimates regarding the number of clusters and the single-cell level cluster assignments. This type of unsupervised clustering is challenging and it is often times hard to gauge which method to use because none of the existing methods outperform others across all scenarios. We present SAME-clustering, a mixture model-based approach that takes clustering solutions from multiple methods and selects a maximally diverse subset to produce an improved ensemble solution. We tested SAME-clustering across 15 scRNA-seq datasets generated by different platforms, with number of clusters varying from 3 to 15, and number of single cells from 49 to 32 695. Results show that our SAME-clustering ensemble method yields enhanced clustering, in terms of both cluster assignments and number of clusters. The mixture model ensemble clustering is not limited to clustering scRNA-seq data and may be useful to a wide range of clustering applications.
The economics of water scarcity and variability
Authors: Damania Richard
Published: October 2019

Does the availability or variability of water matter for the economy? Does it meaningfully impact the growth and development trajectory of a country? It may seem surprising that answers to these most basic of questions remain elusive. The aim of this paper is to summarize recent work on the economic impacts of water scarcity and variability. The paper finds that there is strong evidence that variations in rainfall and water availability have significant impacts on particular sectors, such as agriculture, human capital, and even conflict. But paradoxically evidence of impacts on economic growth and other measures of aggregate economic activity remains ambiguous. The paper explains reasons for this anomaly and explores the pathways through which water impacts the economy. The paper provides a synthesis of key developments in the literature, identifies methodological gaps, and suggests policy solutions.
The myositis clinical phenotype associated with anti-Zo autoantibodies: a case series of nine UK patients
Authors: Tansley Sarah L , Betteridge Zoe , Lu Hui , Davies Emma , Rothwell Simon , New Paul P , Chinoy Hector , Gordon Patrick , Gunawardena Harsha , Lloyd Mark , Stratton Richard , Cooper Robert , McHugh Neil J
Published: October 2019

Objectives

It has been over 10 years since the first report of autoantibodies directed against phenylalanyl tRNA synthetase (anti-Zo) in a patient with features of the anti-synthetase syndrome. In that time no further cases have been published. Here we aim to characterize more fully the clinical phenotype of anti-Zo–associated myositis by describing the clinical features of nine patients.

Methods

Anti-Zo was identified by protein-immunoprecipitation in patients referred for extended spectrum myositis autoantibody testing at our laboratory. Results were confirmed by immunodepletion using a reference serum. Medical records were retrospectively reviewed to provide detailed information of the associated clinical phenotype for all identified patients. Where possible, HLA genotype was imputed using Illumina protocols.

Results

Nine patients with anti-Zo were identified. The median age at disease onset was 51 years, and six patients were female. Seven patients had evidence of inflammatory muscle disease, seven of interstitial lung disease and six of arthritis. The reported pattern of interstitial lung disease varied with usual interstitial pneumonia, non-specific interstitial pneumonia and organizing pneumonia all described. Other features of the anti-synthetase syndrome such as RP and mechanics hands were common. HLA data was available for three patients, all of whom had at least one copy of the HLA 8.1 ancestral haplotype.

Conclusion

Patients with anti-Zo presenting with features of the anti-synthetase syndrome and interstitial lung disease is a common finding. Like other myositis autoantibodies, there is likely to be a genetic association with the HLA 8.1 ancestral haplotype.
Reframing, Reconciling, and Individualizing: How LGBTQ Activist Groups Shape Approaches to Religion and Sexuality
Authors: Coley Jonathan S
Published: October 2019

Past research reveals the multiple ways that people grapple with the connections between religious and sexual identities. Some people perceive religious identities to be in conflict with lesbian, gay, bisexual, or queer (LGBQ) identities, but others believe such identities to be compatible. Some people look to religious authorities for guidance in understanding the connections between religious and LGBQ identities, whereas others rely on strategies of religious individualism. What factors affect people’s approaches to understanding the connections between religious and sexual identities? Drawing on 77 interviews with participants in lesbian, gay, bisexual, transgender, and queer (LGBTQ) activist groups at four Christian colleges and universities, and employing Goffmanian insights, this article shows how LGBTQ activist groups’ different audiences inspire distinct approaches to understanding religion and sexuality. The study demonstrates that activist groups can powerfully shape understandings of seemingly disparate social identities and suggests a theoretical framework for future research.
Stress Reduction Strategies Used by Midlife Black Women to Target Cardiovascular Risk
Authors: Jones Holly J. , Norwood Carolette R. , Bankston Karen , Bakas Tamilyn
Published: October 2019

Background

Midlife black women are at a high risk for cardiovascular disease and experience higher morbidity and mortality rates. Chronic life stress contributes to the existent cardiovascular-related disparities for midlife black women.

Objectives

The purpose of this qualitative study was to describe stress reduction strategies relevant to midlife black women, identify barriers, and generate ideas for the development of a stress reduction wellness intervention for midlife black women.

Methods

A community advisory board consisting of 11 midlife black women from the Midwest was established and charged with exploring life stress and stress-related issues for women like themselves. The community advisory board was led through a series of focus group discussions using open-ended questions focused on stress reduction strategies used by midlife black women, what kept them from incorporating stress reduction strategies into their daily routines, and what would be helpful in a stress reduction routine. Discussions were audiotaped, transcribed, coded, and analyzed using content analysis.

Results

Stress reduction strategies identified included exercise, faith and prayer, self-care, sisterhood, volunteerism, and mindfulness. Barriers to adopting stress reduction behaviors included time, finances, physical limitations, health status, health insurance, and guilt. Suggested modes of delivery for an intervention included informative lectures and coaching, demonstration, team sessions, social media, and continued access.

Conclusions

Findings from this study were consistent with those from a preliminary study focused on midlife black women from the West Coast. Recommendations will inform development of a stress reduction wellness intervention for midlife black women.
Creating a Culture of Caring
Authors: Letcher Deborah C. , Massey Ann M. , Nelson Mary J. , Elverson Cynthia Anderson
Published: October 2019

Background

Preparation of nursing students has traditionally occurred in academic settings where faculty develop programs of study. Practice settings often find themselves investing in significant education and support as the new-graduate nurse transitions into the RN role.

Problem

A gap in preparation exists between academic and practice expectations for the generalist RN role.

Approach

Collaboration among academic and practice partners in the development of a core clinical curriculum, along with supporting content and learning activities, provides enriched clinical experiences that enhance readiness for the practicing role.

Outcomes

The Culture of Caring (COC) Model guides academic and practice partners as a teaching-learning framework for the preparation of nursing students.

Conclusions

The COC clinical curriculum bundles together supporting resources that include a handbook, workbook, faculty pocket guide, calendar, and nursing student cards used to foster the clinical experience.
Discrepancies between Registered and Published Primary and Secondary Outcomes in Randomized Controlled Trials within the Plastic Surgery Literature: A Systematic Review
Authors: Hudson Alexandra S. , Morzycki Alexander D. , Samargandi Osama A. , Williams Jason G.
Published: October 2019

Background:

Recent studies have identified a high incidence of discrepancy between registered and published outcomes in registered medical and surgical randomized controlled trials. This has not yet been studied in the plastic surgery literature.

Methods:

The authors systematically assessed plastic surgery randomized controlled trials published between 2012 and 2016 in seven high-impact plastic surgery journals. Data were collected from the registration website and published articles using a standardized data extraction form.

Results:

A total of 145 randomized controlled trials were identified, with a 39 percent trial registration rate (n = 57). Forty-nine trials were included in the final analysis. Forty-three (88 percent) had a discrepancy between registered and published outcomes: 26 (53 percent) for primary outcome(s), and 39 (80 percent) for secondary outcome(s). The number of discrepancies in an individual trial ranged from one to seven for primary outcomes and one to 12 for secondary outcomes. Aesthetic surgery had the largest number of trials with outcome discrepancies (n = 15). The prevalence of unreported registered outcomes was 13 percent for primary outcomes and 38 percent for secondary outcomes. Registered nonsignificant primary outcomes were published as nonsignificant secondary outcomes in 30 percent of trials. Publishing new nonregistered secondary outcomes (65 percent) and changing the assessment timing of published primary outcomes (61 percent) were the most common types of discrepancies. Discrepancies favored a statistically significant positive outcome in 19 (44 percent) of the 43 trials with an outcome discrepancy. Discrepancies that resulted in published outcomes with improved patient relevance were found in eight trials (16 percent) for primary outcome discrepancies and 14 trials (29 percent) for secondary outcome discrepancies.

Conclusions:

The plastic surgery literature has high rates of discrepancies between registered and published trial outcomes. Outcome reporting discrepancy is even more problematic for secondary outcomes, an area of analysis that has previously been poorly studied. The high rate of discrepancy change favoring a statistically significant outcome and more patient-relevant outcomes may indicate the pressure to demonstrate significant results to be accepted for publication in high-impact journals.
Local socioeconomic status and paramedic students’ academic performance
Authors: Hamel Lydia , Procum Ashley , Hunter Justin , Gridley Donna , O’Connor Kathleen , Fentress Thomas , Goenner Christopher , Khalsa Sahaj , Batt Alan M.
Published: October 2019

Research indicates students of lower socioeconomic status (SES) are educationally disadvantaged. We sought to examine differences in paramedic student academic performance from counties with varying SES in the United States. Student performance data and SES data were combined for counties within the states of California, Mississippi, Louisiana, Texas and Virginia. Linear multiple regression modelling was performed to determine the relationship between income, high school graduation rate, poverty and food insecurity with first-attempt scores on the Fisdap Paramedic Readiness Exam (PRE) versions 3 and 4. Linear regression models indicated that there was a significant relationship between county-level income, poverty, graduation rate, food insecurity, and paramedic student academic performance. It remains unclear what type of relationship exists between individual SES and individual academic performance of paramedic students. These findings support the future collection of individual student level SES data in order to identify issues and mitigate impact on academic performance.
A link between mitochondrial gene expression and life stage morphologies inTrypanosoma cruzi
Authors: Ramirez-Barrios Roger , Susa Emily K. , Faacks Sean P. , Liggett Charles K. , Zimmer Sara L.
Published: October 2019

The protozoanTrypanosoma cruzihas a complicated dual-host life cycle, and starvation can trigger transition from the replicating insect stage to the mammalian-infectious nonreplicating insect stage (epimastigote to trypomastigote differentiation). Abundance of some mature RNAs derived from its mitochondrial genome increase during culture starvation ofT.cruzifor unknown reasons. Here we examineT. cruzimitochondrial gene expression in the mammalian intracellular replicating life stage (amastigote), and uncover implications of starvation-induced changes in gene expression in insect-stage cells. Mitochondrial RNA levels in general were found to be lowest in actively replicating amastigotes. We discovered that mitochondrial respiration decreases during starvation, despite the previously-observed increases in mitochondrial mRNAs encoding electron transport chain components. Surprisingly,T. cruziepimastigotes in replete medium grow at normal rates when we genetically compromised their ability to perform insertion/deletion editing and thereby generate mature forms of some mitochondrial mRNAs. However, these cells, when starved, were impeded in the epimastigote to trypomastigote transition. Further, they experience a short-flagella phenotype that may also be linked to differentiation. We hypothesize a scenario where levels of mature RNA species or editing in the singleT. cruzimitochondrion are linked to differentiation by a yet-unknown signaling mechanism.
KinasepKipred: A Predictive Model for Estimating Ligand-Kinase Inhibitor Constant (pKi)
Authors: Govinda KC , Hassan Md Mahmudulla , Sirimulla Suman
Published: October 2019

Kinases are one of the most important classes of drug targets for therapeutic use. Algorithms that can accurately predict the drug-kinase inhibitor constant (pKi) of kinases can considerably accelerate the drug discovery process. In this study, we have developed computational models, leveraging machine learning techniques, to predict ligand-kinase (pKi) values. Kinase-ligand inhibitor constant (Ki) data was retrieved from Drug Target Commons (DTC) and Metz databases. Machine learning models were developed based on structural and physicochemical features of the protein and, topological pharmacophore atomic triplets fingerprints of the ligands. Three machine learning models [random forest (RFR), extreme gradient boosting (XGBoost) and artificial neural network (ANN)] were tested for model development. The performance of our models were evaluated using several metrics with 95% confidence interval. RFR model was finally selected based on the evaluation metrics on test datasets and used for web implementation. The best and selected model achieved a Pearson correlation coefficient (R) of 0.887 (0.881, 0.893), root-mean-square error (RMSE) of 0.475 (0.465, 0.486), Concordance index (Con. Index) of 0.854 (0.851, 0.858), and an area under the curve of receiver operating characteristic curve (AUC-ROC) of 0.957 (0.954, 0.960) during the internal 5-fold cross validation.

Availability

GitHub: https://github.com/sirimullalab/KinasepKipred, Docker: sirimullalab/kinasepkipred

Implementation

https://drugdiscovery.utep.edu/pki/

Graphical TOC Entry
Transcranial Electrical Stimulation Motor Threshold Combined with Reverse-Calculated Electric Field Modeling Can Determine Individualized tDCS Dosage
Authors: Caulfield Kevin A. , Badran Bashar W. , DeVries William H. , Summers Philipp M. , Kofmehl Emma , Li Xingbao , Borckardt Jeffrey J. , Bikson Marom , George Mark S.
Published: October 2019

Background

Unique amongst brain stimulation tools, transcranial direct current stimulation (tDCS) currently lacks an easy method for individualizing dosage.

Objective

Can one individually dose tDCS? We developed a novel method of reverse-calculating electric-field (E-field) models based on Magnetic Resonance Imaging (MRI) scans that can determine individualized tDCS dose. We also sought to develop an MRI-free method of individualizing tDCS dose by measuring transcranial magnetic stimulation (TMS) motor threshold (MT) and single pulse, suprathreshold transcranial electrical stimulation (TES) MT and regressing it against E-field modeling.

Methods

In 29 healthy adults, we acquired TMS MT, TES MT, and structural MRI scans with a fiducial marking the motor hotspot. We then computed a “reverse-calculated tDCS dose” of tDCS applied at the scalp needed to cause a 1.00V/m E-field at the cortex. Finally, we examined whether the predicted E-field values correlated with each participant’s measured TMS MT or TES MT.

Results

We were able to determine a reverse-calculated tDCS dose for each participant. The Transcranial Electrical Stimulation MT, but not the Transcranial Magnetic Stimulation MT, significantly correlated with the calculated tDCS dose determined by E-field modeling (R2 = 0.509, p < 0.001).

Conclusions

Reverse-calculation E-field modeling, alone or in combination with TES MT, shows promise as a method to individualize tDCS dose. The large range of the reverse-calculated tDCS doses between subjects underscores the likely need to individualize tDCS dose. If these results are confirmed in future studies, TES MT may evolve into an inexpensive and quick method to individualize tDCS dose.
Microbiota-directed fibre activates both targeted and secondary metabolic shifts in the distal gut
Authors: Michalak Leszek , Gaby John Christian , Lagos Leidy , La Rosa Sabina Leanti , Hvidsten Torgeir R. , Tétard-Jones Catherine , Willats William G.T. , Terrapon Nicolas , Lombard Vincent , Henrissat Bernard , Dröge Johannes , Arntzen Magnus Ø. , Hagen Live Heldal , Øverland Margareth , Pope Phillip B. , Westereng Bjørge
Published: October 2019

Beneficial modulation of the gut microbiome has high-impact implications not only in humans, but also in livestock that sustain our current societal needs. In this context, we have tailored an acetylated galactoglucomannan (AcGGM) fibre to match unique enzymatic capabilities of Roseburia and Faecalibacterium species, both renowned butyrate-producing gut commensals. The accuracy of AcGGM was tested within the complex endogenous gut microbiome of pigs, wherein we resolved 355 metagenome-assembled genomes together with quantitative metaproteomes. In AcGGM-fed pigs, both target populations differentially expressed AcGGM-specific polysaccharide utilization loci, including novel, mannan-specific esterases that are critical to its deconstruction. However, AcGGM-inclusion also manifested a “butterfly effect”, whereby numerous metabolic changes and interdependent cross-feeding pathways were detected in neighboring non-mannolytic populations that produce short-chain fatty acids. Our findings show that intricate structural features and acetylation patterns of dietary fibre can be customized to specific bacterial populations, with potential to create greater modulatory effects at large.
Single-nucleus RNA-seq identifies Huntington disease astrocyte states
Authors: Al-Dalahmah Osama , Sosunov Alexander A , Shaik A , Ofori Kenneth , Liu Yang , Vonsattel Jean Paul , Adorjan Istvan , Menon Vilas , Goldman James E
Published: October 2019

Huntington Disease (HD) is an inherited movement disorder caused by expanded CAG repeats in the Huntingtin gene. We have used single nucleus RNASeq (snRNASeq) to uncover cellular phenotypes that change in the disease, investigating single cell gene expression in cingulate cortex of patients with HD and comparing the gene expression to that of patients with no neurological disease. In this study, we focused on astrocytes, although we found significant gene expression differences in neurons, oligodendrocytes, and microglia as well. In particular, the gene expression profiles of astrocytes in HD showed multiple signatures, varying in phenotype from cells that had markedly upregulated metallothionein and heat shock genes, but had not completely lost the expression of genes associated with normal protoplasmic astrocytes, to astrocytes that had substantially upregulated GFAP and had lost expression of many normal protoplasmic astrocyte genes as well as metallothionein genes. When compared to astrocytes in control samples, astrocyte signatures in HD also showed downregulated expression of a number of genes, including several associated with protoplasmic astrocyte function and lipid synthesis. Thus, HD astrocytes appeared in variable transcriptional phenotypes, and could be divided into several different “states”, defined by patterns of gene expression. Ultimately, this study begins to fill the knowledge gap of single cell gene expression in HD and provide a more detailed understanding of the variation in changes in gene expression during astrocyte “reactions” to the disease.
Listener’s vmPFC simulates speaker choices when reading between the lines
Authors: Mi Qingtian , Wang Cong , Camerer Colin F. , Zhu Lusha
Published: October 2019

Humans possess a remarkable ability to understand what is and is not being said by conservational partners. An important class of models hypothesize that listeners decode the intended meaning of an utterance by assuming speakers speak cooperatively, simulating the speaker’s rational choice process and inverting this process for recovering the speaker’s most probable meaning. We investigated whether and how rational simulations of speakers are represented in the listener’s brain, when subjects participated in a referential communication game inside fMRI. In three experiments, we show that listener’s ventromedial prefrontal cortex encodes the probabilistic inference of what a cooperative speaker should say given a communicative goal and context. The listener’s striatum responds to the amount of update on the intended meaning, consistent with inverting a simulated mental model. These findings suggest a neural generative mechanism subserved by the frontal-striatal circuits that underlies our ability to understand communicative and, more generally, social actions.
Reinforcement Learning for Bio-Retrosynthesis
Authors: Koch Mathilde , Duigou Thomas , Faulon Jean-Loup
Published: October 2019

Metabolic engineering aims to produce chemicals of interest from living organisms, to advance towards greener chemistry. Despite efforts, the research and development process is still long and costly and efficient computational design tools are required to explore the chemical biosynthetic space. Here, we propose to explore the bio-retrosynthesis space using an Artificial Intelligence based approach relying on the Monte Carlo Tree Search reinforcement learning method, guided by chemical similarity. We implement this method in RetroPath RL, an open-source and modular command line tool. We validate it on a golden dataset of 20 manually curated experimental pathways as well as on a larger dataset of 152 successful metabolic engineering projects. Moreover, we provide a novel feature, that suggests potential media supplements to complement the enzymatic synthesis plan.
Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments
Authors: Baharav Tavor Z. , Kamath Govinda M. , Tse David N. , Shomorony Ilan
Published: October 2019

A key step in many genomic analysis pipelines is the identification of regions of similarity between pairs of DNA sequencing reads. This task, known as pairwise sequence alignment, is a heavy computational burden, particularly in the context of third-generation long-read sequencing technologies, which produce noisy reads. This issue is commonly addressed via a two-step approach: first, we filter pairs of reads which are likely to have a large alignment, and then we perform computationally intensive alignment algorithms only on the selected pairs. The Jaccard similarity between the set of k-mers of each read can be shown to be a proxy for the alignment size, and is usually used as the filter. This strategy has the added benefit that the Jaccard similarities don’t need to be computed exactly, and can instead be efficiently estimated through the use of min-hashes. This is done by hashing all k-mers of a read and computing the minimum hash value (the min-hash) for each read. For a randomly chosen hash function, the probability that the min-hashes are the same for two distinct reads is precisely their k-mer Jaccard similarity. Hence, one can estimate the Jaccard similarity by computing the fraction of min-hash collisions out of the set of hash functions considered.

However, when the k-mer distribution of the reads being considered is significantly non-uniform, Jaccard similarity is no longer a good proxy for the alignment size. In particular, genome-wide GC biases and the presence of common k-mers increase the probability of a min-hash collision, thus biasing the estimate of alignment size provided by the Jaccard similarity. In this work, we introduce a min-hash-based approach for estimating alignment sizes called Spectral Jaccard Similarity which naturally accounts for an uneven k-mer distribution in the reads being compared. The Spectral Jaccard Similarity is computed by considering a min-hash collision matrix (where rows correspond to pairs of reads and columns correspond to different hash functions), removing an offset, and performing a singular value decomposition. The leading left singular vector provides the Spectral Jaccard Similarity for each pair of reads. In addition, we develop an approximation to the Spectral Jaccard Similarity that can be computed with a single matrix-vector product, instead of a full singular value decomposition.

We demonstrate improvements in AUC of the Spectral Jaccard Similarity based filters over Jaccard Similarity based filters on 40 datasets of PacBio reads from the NCTC collection. The code is available at https://github.com/TavorB/spectral_jaccard_similarity.
Characterization of novel regulators for heat stress tolerance in tomato from Indian sub-continent
Authors: Balyan Sonia , Rao Sombir , Jha Sarita , Bansal Chandni , Das Jaishri Rubina , Mathur Saloni
Published: October 2019

The footprint of tomato cultivation, a cool region crop that exhibits heat stress (HS) sensitivity, is increasing in the tropics/sub-tropics. Knowledge of novel regulatory hot-spots from varieties growing in the Indian sub-continent climatic zones could be vital for developing HS-resilient crops. Comparative transcriptome-wide signatures of a tolerant (CLN1621L) and sensitive (CA4) cultivar-pair short-listed from a pool of varieties exhibiting variable thermo-sensitivity using physiological, survival and yield-related traits revealed redundant to cultivar-specific HS-regulation with more up-regulated genes for CLN1621L than CA4. The anatgonisiticly-expressing genes include enzymes; have roles in plant defense and response to different abiotic stresses. Functional characterization of three antagonistic genes by overexpression and TRV-VIGS silencing established Solyc09g014280 (Acylsugar acyltransferase) and Solyc07g056570 (Notabilis), that are up-regulated in tolerant cultivar, as positive regulators of HS-tolerance and Solyc03g020030 (Pin-II proteinase inhibitor), that is down-regulated in CLN1621L, as negative regulator of thermotolerance. Transcriptional assessment of promoters of these genes by SNPs in stress-responsivecis-elements and promoter swapping experiments in opposite cultivar background showed inherent cultivar-specific orchestration of transcription factors in regulating transcription. Moreover, overexpression of three ethylene response transcription factors (ERF.C1/F4/F5) also improved HS-tolerance in tomato. This study identifies several novel HS-tolerance genes and provides proof of their utility in tomato-thermotolerance.

Highlight

Novel heat stress regulatory pathways uncovered by comparative transcriptome profiling between contrasting tomato cultivars from Indian sub-continent for improving thermotolerance. (20/30)
Freezing displayed by others is a learned cue of danger resulting from co-experiencing own-freezing and shock
Authors: Cruz Andreia , Heinemans Mirjam , Marquez Cristina , Moita Marta A.
Published: October 2019

Social cues of threat are widely reported [1–3], whether actively produced to trigger responses in others, such as the emission of alarm calls, or by-products of an encounter with a predator, like the defensive behaviors themselves, such as an escape flight [4–14]. Although the recognition of social alarm cues is often innate [15–17], in some instances it requires experience to trigger defensive responses [4,7]. One mechanism proposed for how learning from self-experience contributes to social behavior is that of auto-conditioning, whereby subjects learn to associate their own behaviors with the relevant trigger events. Through this process the same behaviors, now displayed by others, gain meaning. [18,19 but see: 20]. Although it has been shown that only animals with prior experience with shock display observational freezing [21–25] suggesting that auto-conditioning could mediate this process, evidence for this hypothesis was lacking. Previously we found that when a rat freezes, the silence that results from immobility triggers observational freezing in its cage-mate, provided the cage-mate had experienced shocks before [24]. Hence, in our study auto-conditioning would correspond to rats learning to associate shock with their own response to it – freezing. Using a combination of behavioral and optogenetic manipulations, here we show that freezing becomes an alarm cue by a direct association with shock. Our work shows that auto-conditioning can indeed modulate social interactions, expanding the repertoire of cues that mediate social information exchange, providing a framework to study how the neural circuits involved in the self-experience of defensive behaviors overlap with the ones involved in socially triggered defensive behaviors.