Culture of urine specimens by use of chromID CPS Elite medium can expedite Escherichia coli identification and reduce hands-on time in the clinical laboratory

Urine is one of the most common specimen types submitted to the clinical microbiology laboratory; the use of chromogenic agar is one method by which the laboratory might expedite culture results and reduce hands-on time and materials required for urine culture analysis. The objective of our study was to compare chromID CPS Elite (bioMérieux), a chromogenic medium, to conventional primary culture medium for evaluation of urine specimens. Remnant urine specimens (n = 200) were inoculated into conventional media and into chromID CPS Elite agar (chromID). The time to identification and consumables used were documented for both methods. Clinically significant pathogen(s) were recovered from 51 cultures using conventional media, with Escherichia coli being the most frequently recovered organism (n = 22). The rate of exact uropathogen agreement between conventional and chromogenic media was 82%, while overall categorical agreement was 83.5% The time interval between plating and final organism identification was decreased with chromID agar versus conventional media for E. coli (mean of 24.4 h versus 27.1 h, P < 0.001). Using chromID, clinically significant cultures required less hands-on time per culture (mean of 1 min and 2 s [1:02 min]) compared to conventional media (mean of 1:31 min). In addition, fewer consumables (2.4 versus 3.3 sticks and swabs) and rapid biochemical tests (1.0 versus 1.9) were necessary using chromID versus conventional media. Notably, antimicrobial susceptibility testing demonstrated good overall agreement (97.4%) between the chromID and conventional media for all antibiotics tested. chromID CPS Elite is accurate for uropathogen identification, reduces consumable usage, and may expedite the identification of E. coli in clinical specimens

Metabolism, Gas Exchange, and Carbon Spiraling in Rivers

Ecosystem metabolism, that is, gross primary productivity (GPP) and ecosystem respiration (ER), controls organic carbon (OC) cycling in stream and river networks and is expected to vary predictably with network position. However, estimates of metabolism in small streams outnumber those from rivers such that there are limited empirical data comparing metabolism across a range of stream and river sizes. We measured metabolism in 14 rivers (discharge range 14–84 m3 s−1) in the Western and Midwestern United States (US). We estimated GPP, ER, and gas exchange rates using a Lagrangian, 2-station oxygen model solved in a Bayesian framework. GPP ranged from 0.6–22 g O2 m−2 d−1 and ER tracked GPP, suggesting that autotrophic production supports much of riverine ER in summer. Net ecosystem production, the balance between GPP and ER was 0 or greater in 4 rivers showing autotrophy on that day. River velocity and slope predicted gas exchange estimates from these 14 rivers in agreement with empirical models. Carbon turnover lengths (that is, the distance traveled before OC is mineralized to CO2) ranged from 38 to 1190 km, with the longest turnover lengths in high-sediment, arid-land rivers. We also compared estimated turnover lengths with the relative length of the river segment between major tributaries or lakes; the mean ratio of carbon turnover length to river length was 1.6, demonstrating that rivers can mineralize much of the OC load along their length at baseflow. Carbon mineralization velocities ranged from 0.05 to 0.81 m d−1, and were not different than measurements from small streams. Given high GPP relative to ER, combined with generally short OC spiraling lengths, rivers can be highly reactive with regard to OC cycling. © 2015, Springer Science+Business Media New York

Oncogenetics of Lung Cancer Induced by Environmental Carcinogens

The molecular landscape of non-tobacco-induced primary lung tumors displays specific oncogenetic features. The etiology of these tumors has been largely associated with exposure to well-established environmental lung carcinogens such as radon, arsenic, and asbestos. Environmental carcinogens can induce specific genetic and epigenetic alterations in lung tissue, leading to aberrant function of lung cancer oncogenes and tumor suppressor genes. These molecular events result in the disruption of key cellular mechanisms, such as protection against oxidative stress and DNA damage-repair, which promotes tumor development and progression. This chapter provides a comprehensive discussion of the specific carcinogenic mechanisms associated with exposure to radon, arsenic, and asbestos. It also summarizes the main protein-coding and non-coding genes affected by exposure to these environmental agents, and the underlying molecular mechanisms promoting their deregulation in lung cancer. Finally, the chapter examines the anticipated challenges in personalized intervention strategies in non-tobacco-induced lung cancer

Tumour Suppressor Genes with Oncogenic Roles in Lung Cancer

Lung cancer is one of the most common cancers and the leading cause of cancer-related deaths worldwide. High-throughput sequencing efforts have uncovered the molecular heterogeneity of this disease, unveiling several genetic and epigenetic disruptions driving its development. Unlike oncogenes, tumour suppressor genes negatively regulate cell cycle control and exhibit loss-of-function alterations in cancer. Although tumour suppressor genes are more frequently disrupted, oncogenes are more likely to be drug-targeted. Many genes are described as presenting both tumour suppressive and oncogenic functions in different tumour types or even within the natural history of the disease in a single tumour. In this chapter, we describe current knowledge of tumour suppressor genes in lung tissues, focusing on tumour suppressor/oncogene duality

Reliability and validity of the Wolfram Unified Rating Scale (WURS)

BACKGROUND: Wolfram syndrome (WFS) is a rare, neurodegenerative disease that typically presents with childhood onset insulin dependent diabetes mellitus, followed by optic atrophy, diabetes insipidus, deafness, and neurological and psychiatric dysfunction. There is no cure for the disease, but recent advances in research have improved understanding of the disease course. Measuring disease severity and progression with reliable and validated tools is a prerequisite for clinical trials of any new intervention for neurodegenerative conditions. To this end, we developed the Wolfram Unified Rating Scale (WURS) to measure the severity and individual variability of WFS symptoms. The aim of this study is to develop and test the reliability and validity of the Wolfram Unified Rating Scale (WURS). METHODS: A rating scale of disease severity in WFS was developed by modifying a standardized assessment for another neurodegenerative condition (Batten disease). WFS experts scored the representativeness of WURS items for the disease. The WURS was administered to 13 individuals with WFS (6-25 years of age). Motor, balance, mood and quality of life were also evaluated with standard instruments. Inter-rater reliability, internal consistency reliability, concurrent, predictive and content validity of the WURS were calculated. RESULTS: The WURS had high inter-rater reliability (ICCs>.93), moderate to high internal consistency reliability (Cronbach’s α = 0.78-0.91) and demonstrated good concurrent and predictive validity. There were significant correlations between the WURS Physical Assessment and motor and balance tests (r(s)>.67, p<.03), between the WURS Behavioral Scale and reports of mood and behavior (r(s)>.76, p<.04) and between WURS Total scores and quality of life (r(s)=-.86, p=.001). The WURS demonstrated acceptable content validity (Scale-Content Validity Index=0.83). CONCLUSIONS: These preliminary findings demonstrate that the WURS has acceptable reliability and validity and captures individual differences in disease severity in children and young adults with WFS

Linkages between Cigarette Smoking Outcome Expectancies and Negative Emotional Vulnerability

The present investigation examined whether smoking outcome expectancies, as measured by the Smoking Consequences Questionnaire (SCQ; [Brandon, T.H., & Baker, T.B., (1991). The Smoking Consequences Questionnaire: The subjective expected utility of smoking in college students. Psychological Assessment, 3, 484–491.]), were incrementally related to emotional vulnerability factors among an adult sample of 202 daily cigarette smokers (44.6% women; Mage= 23.78 years, SD = 9.69 years). After controlling for cigarettes smoked/day, past 30-day marijuana use, current alcohol consumption, and coping style, negative reinforcement/negative affect reduction outcome expectancies were significantly associated with greater levels of negative affectivity, emotional dysregulation, and anxiety sensitivity. The observed effects for negative reinforcement/negative affect reduction also were independent of shared variance with other outcome expectancies. Negative personal consequences outcome expectancies were significantly and incrementally related to anxiety sensitivity, but not negative affectivity or emotional dysregulation. Findings are discussed in terms of the role of negative reinforcement/ negative affect reduction smoking outcome expectancies and clinically-relevant negative emotional vulnerability for better understanding cigarette smoking-negative mood problem

Small Noncoding RNA Expression in Cancer

Despite an inability to encode proteins, small noncoding RNAs (sncRNAs) have critical functions in the regulation of gene expression. They have demonstrated roles in cancer development and progression and are frequently dysregulated. Here we review the biogenesis and mechanism of action, expression patterns, and detection methods of two types of sncRNAs frequently described in cancer: miRNAs and piRNAs. Both miRNAs and piRNAs have been observed to play both oncogenic and tumor-suppressive roles, with miRNAs acting to directly regulate the mRNA of key cancer-associated genes, while piRNAs play crucial roles in maintaining the integrity of the epigenetic landscape. Elucidating these important functions of sncRNAs in normal and cancer biology relies on numerous in silico workflows and tools to profile sncRNA expression. Thus, we also discuss the key detection methods for cancer-relevant sncRNAs, including the discovery of genes that have yet to be described

The Neutral Gas Dynamics of the Nearby Magellanic Irregular Galaxy UGCA 105

We present new low-resolution HI spectral line imaging, obtained with the Karl G. Jansky Very Large Array (JVLA), of the star-forming Magellanic irregular galaxy UGCA 105. This nearby (D = 3.39+/-0.25 Mpc), low mass [M_HI=(4.3+/-0.5)x10^8 Solar masses] system harbors a large neutral gas disk (HI radius ~7.2 kpc at the N_HI=10^20 cm^-2 level) that is roughly twice as large as the stellar disk at the B-band R_25 isophote. We explore the neutral gas dynamics of this system, fitting tilted ring models in order to extract a well-sampled rotation curve. The rotation velocity rises in the inner disk, flattens at 72+/-3 km/s, and remains flat to the last measured point of the disk (~7.5 kpc). The dynamical mass of UGCA 105 at this outermost point, (9+/-2)x10^9 Solar masses, is ~10 times as large as the luminous baryonic components (neutral atomic gas and stars). The proximity and favorable inclination (55 degrees) of UGCA 105 make it a promising target for high-resolution studies of both star formation and rotational dynamics in a nearby low-mass galaxy.Comment: The Astronomical Journal, in pres

Improved antibacterial activity of 1,3,4-oxadiazole-based compounds that restrict Staphylococcus aureus growth independent of LtaS function

The lipoteichoic acid (LTA) biosynthesis pathway has emerged as a promising antimicrobial therapeutic target. Previous studies identified the 1,3,4 oxadiazole compound 1771 as an LTA inhibitor with activity against Gram-positive pathogens. We have succeeded in making six 1771 derivatives and, through subsequent hit validation, identified the incorporation of a pentafluorosulfanyl substituent as central in enhancing activity. Our newly described derivative, compound 13, showed a 16- to 32-fold increase in activity compared to 1771 when tested against a cohort of multidrug-resistant Staphylococcus aureus strains while simultaneously exhibiting an improved toxicity profile against mammalian cells. Molecular techniques were employed in which the assumed target, lipoteichoic acid synthase (LtaS), was both deleted and overexpressed. Neither deletion nor overexpression of LtaS altered 1771 or compound 13 susceptibility; however, overexpression of LtaS increased the MIC of Congo red, a previously identified LtaS inhibitor. These data were further supported by comparing the docking poses of 1771 and derivatives in the LtaS active site, which indicated the possibility of an additional target(s). Finally, we show that both 1771 and compound 13 have activity that is independent of LtaS, extending to cover Gram-negative species if the outer membrane is first permeabilized, challenging the classification that these compounds are strict LtaS inhibitors

GREAT3 results I: systematic errors in shear estimation and the impact of real galaxy morphology

We present first results from the third GRavitational lEnsing Accuracy Testing (GREAT3) challenge, the third in a sequence of challenges for testing methods of inferring weak gravitational lensing shear distortions from simulated galaxy images. GREAT3 was divided into experiments to test three specific questions, and included simulated space- and ground-based data with constant or cosmologically-varying shear fields. The simplest (control) experiment included parametric galaxies with a realistic distribution of signal-to-noise, size, and ellipticity, and a complex point spread function (PSF). The other experiments tested the additional impact of realistic galaxy morphology, multiple exposure imaging, and the uncertainty about a spatially-varying PSF; the last two questions will be explored in Paper II. The 24 participating teams competed to estimate lensing shears to within systematic error tolerances for upcoming Stage-IV dark energy surveys, making 1525 submissions overall. GREAT3 saw considerable variety and innovation in the types of methods applied. Several teams now meet or exceed the targets in many of the tests conducted (to within the statistical errors). We conclude that the presence of realistic galaxy morphology in simulations changes shear calibration biases by $\sim 1$ per cent for a wide range of methods. Other effects such as truncation biases due to finite galaxy postage stamps, and the impact of galaxy type as measured by the S\'{e}rsic index, are quantified for the first time. Our results generalize previous studies regarding sensitivities to galaxy size and signal-to-noise, and to PSF properties such as seeing and defocus. Almost all methods' results support the simple model in which additive shear biases depend linearly on PSF ellipticity.Comment: 32 pages + 15 pages of technical appendices; 28 figures; submitted to MNRAS; latest version has minor updates in presentation of 4 figures, no changes in content or conclusion