Characterization of shifts of koala (Phascolarctos cinereus) intestinal microbial communities associated with antibiotic treatment.

Koalas (Phascolarctos cinereus) are arboreal marsupials native to Australia that eat a specialized diet of almost exclusively eucalyptus leaves. Microbes in koala intestines are known to break down otherwise toxic compounds, such as tannins, in eucalyptus leaves. Infections by Chlamydia, obligate intracellular bacterial pathogens, are highly prevalent in koala populations. If animals with Chlamydia infections are received by wildlife hospitals, a range of antibiotics can be used to treat them. However, previous studies suggested that koalas can suffer adverse side effects during antibiotic treatment. This study aimed to use 16S rRNA gene sequences derived from koala feces to characterize the intestinal microbiome of koalas throughout antibiotic treatment and identify specific taxa associated with koala health after treatment. Although differences in the alpha diversity were observed in the intestinal flora between treated and untreated koalas and between koalas treated with different antibiotics, these differences were not statistically significant. The alpha diversity of microbial communities from koalas that lived through antibiotic treatment versus those who did not was significantly greater, however. Beta diversity analysis largely confirmed the latter observation, revealing that the overall communities were different between koalas on antibiotics that died versus those that survived or never received antibiotics. Using both machine learning and OTU (operational taxonomic unit) co-occurrence network analyses, we found that OTUs that are very closely related to Lonepinella koalarum, a known tannin degrader found by culture-based methods to be present in koala intestines, was correlated with a koala's health status. This is the first study to characterize the time course of effects of antibiotics on koala intestinal microbiomes. Our results suggest it may be useful to pursue alternative treatments for Chlamydia infections without the use of antibiotics or the development of Chlamydia-specific antimicrobial compounds that do not broadly affect microbial communities

High Redshift Massive Quiescent Galaxies are as Flat as Star Forming Galaxies: The Flattening of Galaxies and the Correlation with Structural Properties in CANDELS/3D-HST

We investigate the median flattening of galaxies at $0.2<z<4.0$ in all five CANDELS/3D-HST fields via the apparent axis ratio $q$. We separate the sample into bins of redshift, stellar-mass, s\'ersic index, size, and UVJ determined star-forming state to discover the most important drivers of the median $q$ ($q_{med}$). Quiescent galaxies at $z10^{11}M_{\odot}$ are rounder than those at lower masses, consistent with the hypothesis that they have grown significantly through dry merging. The massive quiescent galaxies at higher redshift become flatter, and are as flat as star forming massive galaxies at $2.5<z<3.5$, consistent with formation through direct transformations or wet mergers. We find that in quiescent galaxies, correlations with $q_{med}$ and $M_{*}$, $z$ and $r_{e}$ are driven by the evolution in the s\'ersic index ($n$), consistent with the growing accumulation of minor mergers at lower redshift. Interestingly, $n$ does not drive these trends fully in star-forming galaxies. Instead, the strongest predictor of $q$ in star-forming galaxies is the effective radius, where larger galaxies are flatter. Our findings suggest that $q_{med}$ is tracing bulge-to-total ($B/T$) galaxy ratio which would explain why smaller/more massive star-forming galaxies are rounder than their extended/less massive analogues, although it is unclear why s\'ersic index correlates more weakly with flattening for star forming galaxies than for quiescent galaxies.Comment: 13 pages, 11 figures, accepted to Ap

CcNav: Understanding Compiler Optimizations in Binary Code

Program developers spend significant time on optimizing and tuning programs. During this iterative process, they apply optimizations, analyze the resulting code, and modify the compilation until they are satisfied. Understanding what the compiler did with the code is crucial to this process but is very time-consuming and labor-intensive. Users need to navigate through thousands of lines of binary code and correlate it to source code concepts to understand the results of the compilation and to identify optimizations. We present a design study in collaboration with program developers and performance analysts. Our collaborators work with various artifacts related to the program such as binary code, source code, control flow graphs, and call graphs. Through interviews, feedback, and pair-analytics sessions, we analyzed their tasks and workflow. Based on this task analysis and through a human-centric design process, we designed a visual analytics system Compilation Navigator (CcNav) to aid exploration of the effects of compiler optimizations on the program. CcNav provides a streamlined workflow and a unified context that integrates disparate artifacts. CcNav supports consistent interactions across all the artifacts making it easy to correlate binary code with source code concepts. CcNav enables users to navigate and filter large binary code to identify and summarize optimizations such as inlining, vectorization, loop unrolling, and code hoisting. We evaluate CcNav through guided sessions and semi-structured interviews. We reflect on our design process, particularly the immersive elements, and on the transferability of design studies through our experience with a previous design study on program analysis.Comment: IEEE VIS VAST 202

The Evolution of the Fractions of Quiescent and Star-forming Galaxies as a Function of Stellar Mass Since z=3: Increasing Importance of Massive, Dusty Star-forming Galaxies in the Early Universe

Using the UltraVISTA DR1 and 3D-HST catalogs, we construct a stellar-mass-complete sample, unique for its combination of surveyed volume and depth, to study the evolution of the fractions of quiescent galaxies, moderately unobscured star-forming galaxies, and dusty star-forming galaxies as a function of stellar mass over the redshift interval $0.2 \le z \le 3.0$. We show that the role of dusty star-forming galaxies within the overall galaxy population becomes more important with increasing stellar mass, and grows rapidly with increasing redshift. Specifically, dusty star-forming galaxies dominate the galaxy population with $\log{(M_{\rm star}/M_{\odot})} \gtrsim 10.3$ at $z\gtrsim2$. The ratio of dusty and non-dusty star-forming galaxies as a function of stellar mass changes little with redshift. Dusty star-forming galaxies dominate the star-forming population at $\log{(M_{\rm star}/M_{\odot})} \gtrsim 10.0-10.5$, being a factor of $\sim$3-5 more common, while unobscured star-forming galaxies dominate at $\log{(M_{\rm star}/M_{\odot})} \lesssim 10$. At $\log{(M_{\rm star}/M_{\odot})} > 10.5$, red galaxies dominate the galaxy population at all redshift $z<3$, either because they are quiescent (at late times) or dusty star-forming (in the early universe).Comment: 7 pages, 4 figures, 1 table. Accepted by Astrophysical Journal Letters after minor revisio

Field emission from single-, double-, and multi-walled carbon nanotubes chemically attached to silicon

The chemical attachment and field emission (FE) properties of single-walled carbon nanotubes (SWCNTs), double-walled carbon nanotubes (DWCNTs), and multi-walled carbon nanotubes (MWCNTs) chemically attached to a silicon substrate have been investigated. A high density of CNTs was revealed by atomic force microscopy imaging with orientation varying with CNT type. Raman spectroscopy was used to confirm the CNT type and diameter on the surfaces. The field emission properties of the surfaces were studied and both current-voltage and Fowler-Nordheim plots were obtained. The SWCNTs exhibited superior FE characteristics with a turn-on voltage (Eto) of 1.28 V μm−1 and electric field enhancement factor (β) of 5587. The DWCNT surface showed an Eto of 1.91 V μm−1 and a β of 4748, whereas the MWCNT surface exhibited an Eto of 2.79 V μm−1 and a β of 3069. The emission stability of each CNT type was investigated and it was found that SWCNTs produced the most stable emission. The differences between the FE characteristics and stability are explained in terms of the CNT diameter, vertical alignment, and crystallinity. The findings suggest that strength of substrate adhesion and CNT crystallinity play a major role in FE stability. Comparisons to other FE studies are made and the potential for device application is discussed

The mass, colour, and structural evolution of today's massive galaxies since z~5

In this paper, we use stacking analysis to trace the mass-growth, colour evolution, and structural evolution of present-day massive galaxies ($\log(M_{*}/M_{\odot})=11.5$) out to $z=5$. We utilize the exceptional depth and area of the latest UltraVISTA data release, combined with the depth and unparalleled seeing of CANDELS to gather a large, mass-selected sample of galaxies in the NIR (rest-frame optical to UV). Progenitors of present-day massive galaxies are identified via an evolving cumulative number density selection, which accounts for the effects of merging to correct for the systematic biases introduced using a fixed cumulative number density selection, and find progenitors grow in stellar mass by $\approx1.5~\mathrm{dex}$ since $z=5$. Using stacking, we analyze the structural parameters of the progenitors and find that most of the stellar mass content in the central regions was in place by $z\sim2$, and while galaxies continue to assemble mass at all radii, the outskirts experience the largest fractional increase in stellar mass. However, we find evidence of significant stellar mass build up at $r4$ probing an era of significant mass assembly in the interiors of present day massive galaxies. We also compare mass assembly from progenitors in this study to the EAGLE simulation and find qualitatively similar assembly with $z$ at $r<3~\mathrm{kpc}$. We identify $z\sim1.5$ as a distinct epoch in the evolution of massive galaxies where progenitors transitioned from growing in mass and size primarily through in-situ star formation in disks to a period of efficient growth in $r_{e}$ consistent with the minor merger scenario.Comment: 19 pages, 14 figures, accepted for publicatio

Within and between classroom transmission patterns of seasonal influenza among primary school students in Matsumoto city, Japan

Schools play a central role in the transmission of many respiratory infections. Heterogeneous social contact patterns associated with the social structures of schools (i.e., classes/grades) are likely to influence the within-school transmission dynamics, but data-driven evidence on fine-scale transmission patterns between students has been limited. Using a mathematical model, we analyzed a large-scale dataset of seasonal influenza outbreaks in Matsumoto city, Japan, to infer social interactions within and between classes/grades from observed transmission patterns. While the relative contribution of within-class and within-grade transmissions to the reproduction number varied with the number of classes per grade, the overall within-school reproduction number, which determines the initial growth of cases and the risk of sustained transmission, was only minimally associated with class sizes and the number of classes per grade. This finding suggests that interventions that change the size and number of classes, e.g., splitting classes and staggered attendance, may have a limited effect on the control of school outbreaks. We also found that vaccination and mask-wearing of students were associated with reduced susceptibility (vaccination and mask-wearing) and infectiousness (mask-wearing), and hand washing was associated with increased susceptibility. Our results show how analysis of fine-grained transmission patterns between students can improve understanding of within-school disease dynamics and provide insights into the relative impact of different approaches to outbreak control

Is surgical antibiotic prophylaxis necessary for pediatric orchiopexy?

Introduction Surgeons frequently use surgical antibiotic prophylaxis (SAP), despite limited evidence to support its efficacy. Potential adverse events associated with antibiotic use include allergic reaction (including anaphylaxis), Clostridium difficile infection, and selecting for resistant bacteria. Surgical site infections (SSI) are very rare in patients undergoing clean pediatric urologic procedures. Current guidelines are unclear about the efficacy of surgical antibiotic prophylaxis for prevention of SSI in the pediatric population. Objective It was hypothesized that children who received SAP prior to orchiopexy would have no reduction in surgical site infection (SSI) risk but an increased risk of antibiotic-associated adverse events. Methods A retrospective cohort study was conducted of all males aged between 30 days and 18 years who underwent an orchiopexy (ICD-9 CM 62.5) in an ambulatory or observation setting from 2004 to 2015 using the Pediatric Health Information System database. Inpatients and those with concomitant procedures were excluded. Chi-squared or Fisher's exact tests were used to determine the association between SAP and allergic reaction (defined as a charge for epinephrine or ICD-9 diagnosis code for allergic reaction on the date of surgery) and any of the following within 30 days: SSI, hospital readmission or any repeat hospital encounter. Mixed effects logistic regression was performed, controlling for age, race, and insurance, and clustering of similar practice patterns by hospital. Results A total of 71,767 patients were included: median age was 4.6 years, 61.4% were white, and 49.3% had public insurance; 33.5% received SAP. Of these participants, 996/71,767 (1.4%) had a perioperative allergic reaction and <0.1% were diagnosed with an SSI. On mixed effects logistic regression, those who received SAP had 1.2 times the odds of a perioperative allergic reaction compared with those who did not receive SAP ( P = 0.005). Surgical antibiotic prophylaxis was not associated with decreased rates of SSI, lower hospital readmission, nor a lower chance of a repeat encounter within 30 days. Conclusions In patients undergoing orchiopexy, it was found that SAP did not reduce the risk of postoperative SSI, readmissions, or hospital visits. Patients who received SAP had significantly increased odds of perioperative allergic reaction. This demonstrated that the risks of SAP outweigh the benefits in children undergoing orchiopexy