bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dark matter and H i in ultra-diffuse galaxy UGC 2162
Authors: Sengupta Chandreyee , Scott T C , Chung Aeree , Wong O Ivy 
Published: July 2019

ABSTRACT
Our GMRT (Giant Metrewave Radio Telescope) H i observations of the ultra-diffuse galaxy (UDG) UGC 2162, projected ∼ 300 kpc from the centre of the M 77 group, reveal it to a have an extended H i disc ($R_{\rm H\,{\small I}}/R_{25}$ ∼ 3.3) with a moderate rotational velocity (Vrot ∼ 31 km s−1). This Vrotis in line with that of dwarf galaxies with similar H i mass. We estimate an Mdyn of ∼1.14 × 109 M⊙ within the galaxy’s $R_ \rm {H\,{\small I}}$ ∼ 5.2 kpc. Additionally, our estimates of M200 for the galaxy from NFW models are in the range of 5.0–8.8 × 1010 M⊙. Comparing UGC 2162 to samples of UDGs with H i detections show it to have amongst the smallest Re with its MH i/M* being distinctly higher and g – icolour slightly bluer than typical values in those samples. We also compared H i and dark matter (DM) halo properties of UGC 2162 with dwarf galaxies in the LITTLE THINGS sample and find its DM halo mass and profile are within the range expected for a dwarf galaxy. While we were unable to determine the origin of the galaxy’s present-day optical form from our study, its normal H i rotation velocity in relation to its H i mass, H i morphology, environment, and dwarf mass DM halo ruled out some of the proposed ultra-diffuse galaxy formation scenarios for this galaxy.
SDSS-IV MaNGA: effects of morphology in the global and local star formation main sequences
Authors: Cano-Díaz M , Ávila-Reese V , Sánchez S F , Hernández-Toledo H M , Rodríguez-Puebla A , Boquien M , Ibarra-Medel H 
Published: July 2019

ABSTRACT
We study the global star formation rate (SFR) versus stellar mass (M*) correlation, and the spatially resolved SFR surface density (ΣSFR) versus stellar mass surface density (Σ*) correlation, in a sample of ∼2000 galaxies from the MaNGA MPL-5 survey. We classify galaxies and spatially resolved areas into star forming and retired according to their ionization processes. We confirm the existence of a star-forming main sequence (SFMS) for galaxies and spatially resolved areas, and show that they have the same nature, with the global as a consequence of the local one. The latter presents a bend below a limit Σ* value, ≈3 × 107 M$\odot$ kpc−2, which is not physical. Using only star-forming areas (SFAs) above this limit, a slope and a scatter of ≈1 and ≈0.27 dex are determined. The retired galaxies/areas strongly segregate from their respective SFMSs, by ∼−1.5 dex on average. We explore how the global/local SFMSs depend on galaxy morphology, finding that for star-forming galaxies and SFAs, there is a trend to lower values of star formation activity with earlier morphological types, which is more pronounced for the local SFMS. The morphology not only affects the global SFR due to the diminish of SFAs with earlier types, but also affects the local SF process. Our results suggest that the local SF at all radii is established by some universal mechanism partially modulated by morphology. Morphology seems to be connected to the slow aging and sharp decline of the SF process, and on its own it may depend on other properties as the environment.
Detectability of neutron star merger afterglows
Authors: Gottlieb Ore , Nakar Ehud , Piran Tsvi 
Published: July 2019

ABSTRACT
VLBI and JVLA observations revealed that GW170817 involved a narrow jet (θj ≈ 4°) that dominated the afterglow peak at our viewing angle, θobs ≈ 20°. This implies that at the time of the afterglow peak, the observed signal behaved like an afterglow of a top-hat jet seen at θobs ≫ θj, and it can be modelled by analytic expressions that describe such jets. We use a set of numerical simulations to calibrate these analytic relations and obtain generic equations for the peak time and flux of such an afterglow as seen from various observing angles. Using the calibrated equations and the estimated parameters of GW170817, we estimate the detectability of afterglows from future double neutron star mergers during the Advanced LIGO/Virgo observation run O3. GW170817 took place at a relatively low-density environment. Afterglows of similar events will be detectable only at small viewing angles, θobs ≲ 20°, and only 20 per cent of the GW detections of these events will be accompanied by a detectable afterglow. At higher densities, more typical to sGRB sites, up to $70\,\rm{per\,cent}$ of the GW detections are expected to be followed by a detectable afterglow, typically at θobs ∼ 30°. We also provide the latest time one should expect an afterglow detection. We find that for typical parameters, if the jet emission had not been detected within about a year after the merger, it is unlikely to be ever detected.
A Nationwide Survey of Cytomegalovirus Prevention Strategies in Kidney Transplant Recipients in a Resource-Limited Setting
Authors: Bruminhent Jackrapong , Bushyakanist Asalaysa , Kantachuvesiri Surasak , Kiertiburanakul Sasisopin 
Published: July 2019

AbstractObjectiveStrategies to prevent cytomegalovirus (CMV) infection in resource-limited settings have been under-explored. We investigated CMV prevention strategies utilized among transplant centers in Thailand.MethodA questionnaire on CMV prevention strategies for kidney transplant (KT) recipients was developed using a web-based electronic survey website (www.surveymonkey.com). The survey was delivered to 31 transplant centers in Thailand. One infectious disease physician (ID) and 1 nephrologist (NP) from each center were included.ResultsThere were 43 respondents from 26 of the 31 transplant centers (84%), including 26 (60%) IDs and 17 (40%) NPs. Forty-one 95% (41/43) physicians agreed on the necessity of CMV prevention. Of these, 77% (33/43) physicians implemented prevention strategies for their patients. Interventions included preemptive approaches (48%), prophylaxis (45%), hybrid approaches; surveillance after prophylaxis (3%), and CMV-specific immunity-guided approaches (3%). For CMV-seropositive KT recipients, use of preemptive approaches (84%) exceeded prophylaxis (12%). However, 81% of the former preferred targeted prophylaxis in patients receiving antithymocyte globulin therapy. Sixty-five percent and 93% of physicians started preemptive therapy when plasma CMV DNA loads reached 2000 and 3000 copies/mL (1820 and 2730 IU/mL), respectively. A significantly greater percentage of NPs initiated preemptive therapy at a plasma CMV DNA load of 1820 IU/mL compared with IDs (88% vs 50%; P = .02). The most common barrier to prevention strategy implementation was financial inaccessibility of oral valganciclovir (67%) and quantitative CMV DNA testing (12%).ConclusionsMost physicians agreed on a need for preemptive approaches, although prophylaxis was targeted in those receiving intense immunosuppression. The financial implication is the main barrier for CMV prevention in Thailand.
Current practice in plankton metabarcoding: optimization and error management
Authors: Santoferrara Luciana F 
Published: July 2019

AbstractHigh-throughput sequencing of a targeted genetic marker is being widely used to analyze biodiversity across taxa and environments. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations. Improved study designs and alternative sampling, lab and bioinformatic procedures have progressively enhanced data quality, but some problems persist. This article provides a framework to recognize and bypass the main types of errors that can affect metabarcoding data: false negatives, false positives, artifactual variants, disproportions and incomplete or incorrect taxonomic identifications. It is crucial to discern potential error impacts on different ecological parameters (e.g. taxon distribution, community structure, alpha and beta-diversity), as error management implies compromises and is thus directed by the research question. Synthesis of multiple plankton metabarcoding evaluations (mock sample sequencing or microscope comparisons) shows that high-quality data for qualitative and some semiquantitative goals can be achieved by implementing three checkpoints: first, rigorous protocol optimization; second, error minimization; and third, downstream analysis that considers potentially remaining biases. Conclusions inform us about the reliability of metabarcoding for plankton studies and, because plankton provides unique chances to compare genotypes and phenotypes, the robustness of this method in general.
Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
Authors: Whidden Chris , Claywell Brian C , Fisher Thayer , Magee Andrew F , Fourment Mathieu , Matsen Frederick A 
Published: July 2019

Abstract
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In this article, we present an efficient parallelized method to map out the high likelihood set of phylogenetic tree topologies via systematic search, which we show to be a good approximation of the high posterior set of tree topologies on the data sets analyzed. Here, “likelihood” of a topology refers to the tree likelihood for the corresponding tree with optimized branch lengths. We call this method “phylogenetic topographer” (PT). The PT strategy is very simple: starting in a number of local topology maxima (obtained by hill-climbing from random starting points), explore out using local topology rearrangements, only continuing through topologies that are better than some likelihood threshold below the best observed topology. We show that the normalized topology likelihoods are a useful proxy for the Bayesian posterior probability of those topologies. By using a nonblocking hash table keyed on unique representations of tree topologies, we avoid visiting topologies more than once across all concurrent threads exploring tree space. We demonstrate that PT can be used directly to approximate a Bayesian consensus tree topology. When combined with an accurate means of evaluating per-topology marginal likelihoods, PT gives an alternative procedure for obtaining Bayesian posterior distributions on phylogenetic tree topologies.
A Comparison of Costs: How California Teaching Hospitals Achieved Slower Growth Than Nonteaching Hospitals in Operating Room Costs From 2005 to 2014
Authors: Childers Christopher P. , Maggard-Gibbons Melinda , Nuckols Teryl 
Published: July 2019

Purpose
Historically, teaching hospitals have had higher costs than nonteaching hospitals, introducing potential financial risk in value-based payment models. This study compared risk-adjusted operating room (OR) costs between California teaching and nonteaching hospitals.

Method
Using 2,992 financial statements from fiscal years (FYs) 2005–2014, the authors extracted data for OR total costs, components of direct costs, and indirect costs. Cross-sectional and longitudinal models estimated OR costs per minute of surgery by teaching status, ownership, case mix index, and geographic area.

Results
Risk-adjusted cost was $9.44 per minute less in teaching than nonteaching hospitals in FY 2014 (95% CI, 3.03–15.85, P = .004). Between FY 2005 and FY 2014, OR costs grew more slowly at teaching hospitals because of slower wage growth and indirect costs per minute (−$0.13 and −$0.77 per minute per year, respectively, P = .005 and P < .001). Hourly pay rose more at teaching hospitals ($0.26 per hour per year, P = .008) but was offset by slower full-time equivalents growth (−0.002 per 10,000 OR minutes per year, P = .001). Between FY 2005 and FY 2014, operative volume increased at teaching hospitals and decreased at nonteaching hospitals.

Conclusions
By 2014, California teaching hospitals had lower OR costs per minute than nonteaching hospitals because of relative labor productivity gains and slower indirect cost growth. The latter likely resulted from a volume shift from nonteaching to teaching facilities. These trends will help teaching hospitals compete under value-based models. Implications for patients and nonteaching hospitals warrant evaluation.
“Getting Out of That Siloed Mentality Early”: Interprofessional Learning in a Longitudinal Placement for Early Medical Students
Authors: Rivera Josette , O’Brien Bridget , Wamsley Maria 
Published: July 2019

Purpose
Although descriptions of interprofessional education often focus on interactions among students from multiple professions, embedding students from 1 profession in clinical settings may also provide rich opportunities for interprofessional learning (IPL). This study examines affordances and barriers to medical students’ interactions with and opportunities to learn from health care professionals while learning health systems science in clinical workplaces.

Method
In May 2017, 14 first-year medical students at the University of California, San Francisco participated in a semistructured interview about IPL experiences during a 17-month, weekly half-day clinical microsystem placement focused on systems improvement (SI) projects and clinical skills. Communities of practice and workplace learning frameworks informed the interview guide. The authors analyzed interview transcripts using conventional qualitative content analysis.

Results
The authors found much variation among the 14 students’ interprofessional interactions and experiences in 12 placement sites (7 outpatient, 4 inpatient, 1 emergency department). Factors influencing the depth of interprofessional interactions included the nature of the SI project, clinical workflow, student and staff schedules, workplace culture, and faculty coach facilitation of interprofessional interactions. Although all students endorsed the value of learning about and from diverse health care professionals, they were reluctant to engage with, or “burden,” them.

Conclusions
There are significant IPL opportunities for early medical students in longitudinal placements focused on SI and clinical skills. Formal curricular activities, SI projects conducive to interprofessional interactions, and faculty development can enhance the quality of workplace-based IPL.
Interleukin-10 Does Not Augment Osseous Regeneration in the Scarred Calvarial Defect Achieved with Low-Dose Biopatterned BMP2
Authors: Brooker Jack E. , Bykowski Michael R. , Camison Liliana , Yerneni Saigopalakrishna , Campbell Phil G. , Weiss Lee , Mooney Mark P. , Cray James J. , Cooper Gregory M. , Losee Joseph E. 
Published: July 2019

Background:
Large calvarial defects represent a major reconstructive challenge, as they do not heal spontaneously. Infection causes inflammation and scarring, further reducing the healing capacity of the calvaria. Bone morphogenetic protein-2 (BMP2) has been shown to stimulate osteogenesis but has significant side effects in high doses. BMP2 has not been tested in combination with antiinflammatory cytokines such as interleukin-10.

Methods:
Sixteen New Zealand White rabbits underwent 15 × 15-mm flap calvarectomies. The flap was incubated in Staphylococcus aureus and replaced, and infection and scarring were allowed to develop. The flap was subsequently removed and the wound débrided. A 15 × 15-mm square of acellular dermal matrix biopatterned with low-dose BMP2, interleukin-10, or a combination was implanted. Computed tomographic scans were taken over 42 days. Rabbits were then killed and histology was performed.

Results:
Defects treated with BMP2 showed significantly (p < 0.05) greater osseous regeneration than untreated controls. Interleukin-10 did not significantly augment the healing achieved with BMP2, and interleukin-10 alone did not significantly increase healing compared with controls. Histology showed evidence of bone formation in defects treated with BMP2. Untreated controls and defects treated with interleukin-10 alone showed only fibrous tissue in the defect site.

Conclusions:
Low-dose BMP2 delivered directly to the scarred calvarial defect augments bony healing. Interleukin-10 at the dose applied did not significantly augment healing alone or in combination with BMP2. Healing had not finished at 42 days and analysis at later time points or the use of higher doses of BMP2 may yield greater healing.
Three-Dimensional Outcome Assessments of Cleft Lip and Palate Patients Undergoing Maxillary Advancement
Authors: Wu Te-Ju , Lee Yi-Hao , Chang Yu-Jen , Lin Shiu-Shiung , Lin Feng-Chang , Kim Yong-Il , Ko Ching-Chang , Lai Jui-Pin 
Published: July 2019

Background:
The aim of this retrospective case series study was to compare three-dimensional postsurgical outcomes of patients with cleft lip and palate following maxillary advancement.

Methods:
Fifty consecutive cleft lip and palate patients who underwent whole-pieced Le Fort I advancements were assigned to the major (advancement ≥ 5 mm) or minor (advancement < 5 mm) groups. Three-dimensional surgical simulation was used for presurgical evaluation and planning. Virtual triangles of the presurgical, simulated, and 6-month postoperative stages were used for comparison. Translational and angular changes of each endpoint (A-point, MxR, and MxL) on the virtual triangles and reference planes were recorded and analyzed. Relationships between possible related variables and outcome discrepancies from simulations among all subgroups were also investigated.

Results:
Analysis of covariance and the least significant difference test revealed that the outcome discrepancy measurements were affected by different combinations of independent variables. The reliability test showed high consistency of the authors’ method for three-dimensional measurements.

Conclusions:
The actual surgical outcomes of cleft lip and palate patients differed from the virtual simulations. The outcome discrepancies are impacted by multiple factors. The outcome discrepancies of all rotational surgical corrections (roll, yaw, and pitch) were positively correlated to the degree of planned surgical movement. Meanwhile, bilateral cleft lip and palate patients are more likely to incur outcome discrepancies in yaw correction with major maxillary advancement. However, a maxillary advancement cutoff value of 5 mm would not necessarily lead to significant translational outcome discrepancies among cleft lip and palate patients.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data
Authors: Danesh Gonché , Virlogeux Victor , Ramière Christophe , Charre Caroline , Cotte Laurent , Alizon Samuel 
Published: July 2019

AbstractOpioid substitution and syringes exchange programs have drastically reduced hepatitis C virus (HCV) spread in France but HCV sexual transmission in men having sex with men (MSM) has recently arisen as a significant public health concern. The fact that the virus is transmitting in a heterogeneous population, with ‘new’ and ‘classical’ hosts, makes prevalence and incidence rates poorly informative. However, additional insights can be gained by analyzing virus phylogenies inferred from dated genetic sequence data. By combining a phylodynamics approach based on Approximate Bayesian Computation (ABC) and an original transmission model, we estimate key epidemiological parameters of an ongoing HCV epidemic among MSMs in Lyon (France). We show that this new epidemic is largely independent of the ‘classical’ HCV epidemics and that its doubling time is ten times lower (0.44 yearsversus4.37 years). These results have practical implications for HCV control and illustrate the additional information provided by virus genomics in public health.
CD44 regulates epigenetic plasticity by mediating iron endocytosis
Authors: Müller Sebastian , Sindikubwabo Fabien , Cañeque Tatiana , Lafon Anne , Versini Antoine , Lombard Bérangère , Loew Damarys , Durand Adeline , Vallot Céline , Baulande Sylvain , Servant Nicolas , Rodriguez Raphaël 
Published: July 2019

SUMMARYCD44 is a transmembrane glycoprotein that is linked to various biological processes reliant on the epigenetic plasticity of cells, including development, inflammation, immune responses, wound healing and cancer progression. While thoroughly studied, functional regulatory roles of this so-called ‘cell surface marker’ remain elusive. Here, we report the discovery that CD44 mediates endocytosis of iron interacting with hyaluronates in tumorigenic cell lines and primary cancer cells. We found that this glycan-mediated iron endocytosis mechanism is enhanced during epithelial-mesenchymal transition, unlike the canonical transferrin-dependent pathway. This transition is further characterized by molecular changes required for iron-catalyzed oxidative demethylation of the repressive histone mark H3K9me2 that governs the expression of mesenchymal genes.CD44itself is transcriptionally regulated by nuclear iron, demonstrating a positive feedback loop, which is in contrast to the negative regulation of transferrin receptor by excess iron. Finally, we show that epigenetic plasticity can be altered by interfering with iron homeostasis using small molecules. This comprehensive study reveals an alternative iron uptake mechanism that prevails in the mesenchymal state of mammalian cells, illuminating a central role of iron as a rate-limiting regulator of epigenetic plasticity.
Assessing auditory processing endophenotypes associated with Schizophrenia in individuals with 22q11.2 Deletion Syndrome
Authors: Francisco Ana A. , Foxe John J. , Horsthuis Douwe J. , DeMaio Danielle , Molholm Sophie 
Published: July 2019

AbstractBackground22q11.2 Deletion Syndrome (22q11.2DS) is the strongest known molecular risk factor for schizophrenia. Brain responses to auditory stimuli have been studied extensively in schizophrenia and described as potential biomarkers of vulnerability to psychosis. We sought to understand whether these responses might aid in differentiating individuals with 22q11.2DS as a function of psychotic symptoms, and ultimately serve as signals of risk for schizophrenia.MethodsA duration oddball paradigm and high-density electrophysiology were used to test auditory processing in 26 individuals with 22q11.2DS (13-35 years old, 17 females) with varying degrees of psychotic symptomatology and in 26 age- and sex-matched neurotypical controls (NT). Presentation rate varied across three levels, to examine the effect of increasing demands on memory and the integrity of sensory adaptation. We tested whether N1 and mismatch negativity (MMN), typically reduced in schizophrenia, related to clinical/cognitive measures, and how they were affected by presentation rate.ResultsN1 adaptation effects interacted with psychotic symptomatology: Compared to an NT group, individuals with 22q11.2DS but no psychotic symptomatology presented larger adaptation effects, whereas those with psychotic symptomatology presented smaller effects. In contrast, individuals with 22q11.2DS showed increased effects of presentation rate on MMN amplitude, regardless of the presence of symptoms. While IQ and working memory were lower in the 22q11.2DS group, these measures did not correlate with the electrophysiological data.ConclusionsThese findings suggest the presence of two distinct mechanisms: One intrinsic to 22q11.2DS resulting in increased N1 and MMN responses; another related to psychosis leading to a decreased N1 response.