Construction and performance of a novel capture-mark-release moth trap

Mark-recapture studies can provide important information about moth movement as well as habitat preference across a landscape, but to date, such studies tend to be species-specific or require labor-intensive methodologies. To address this challenge, we designed a capture-mark-release-trap (CMRT) featuring a cooling unit attached to a black light trap. The CMRT captures and incapacitates moths throughout the night until the morning, when they can be marked on-site and released. Moths captured with the CMRT during summer of 2016 had a recapture rate of 1.6%, similar to those of previous studies. Importantly, because moths are immobilized by the CMRT, they can be handled and marked with ease, reducing the opportunities to damage specimens prior to release. The CMRT trap can capture a wide array of moth species and may facilitate an increase in the monitoring of moth movement across landscapes

Failure to meet aerobic fitness standards among urban elementary students

The aim of this study was to explore the relationship of aerobic fitness with the elementary school environment and student characteristics among 4th and 5th grade children attending urban public schools in St. Louis, MO, USA. This cross-sectional study was conducted during 2012–2015 and included 2381 children (mean age 10.5 y) who completed the FITNESSGRAM® 20-m Progressive Aerobic Cardiovascular Endurance Run. Healthy Fitness Zone (HFZ) was defined according to FITNESSGRAM® aerobic capacity criteria. Other student-level variables included age, race, National School Lunch Program eligibility, BMI z-score, weight status, and daily pedometer steps. School environment variables included playground features and playground safety, physical education and recess practices, and school census tract data on vacant houses and median household income. Bivariate analyses with sex stratification were used to identify student-level and school-level predictors of failure to achieve the aerobic HFZ; predictors were then included in a multivariable logistic regression model. Failure to meet the aerobic HFZ was observed among 33% of boys and 57% of girls. School environment was not predictive, but higher age and fewer daily steps were: each additional year of age was associated with 41% higher odds of failing to meet the aerobic HFZ among boys and 100% higher odds among girls. Conversely, each additional 1000 daily steps was associated with 15% (boys) and 13% (girls) lower odds of failure. Obesity posed a 60% higher risk of failure to meet HFZ among girls. These results highlight the importance of childhood physical activity opportunities, especially for girls residing in low-resource areas. Keywords: Aerobic fitness, School, Environment, Student, Child, Urban, Low-resourc

Transcriptome sequencing reveals altered long intergenic non-coding RNAs in lung cancer

BACKGROUND: Long intergenic non-coding RNAs (lncRNAs) represent an emerging and under-studied class of transcripts that play a significant role in human cancers. Due to the tissue- and cancer-specific expression patterns observed for many lncRNAs it is believed that they could serve as ideal diagnostic biomarkers. However, until each tumor type is examined more closely, many of these lncRNAs will remain elusive. RESULTS: Here we characterize the lncRNA landscape in lung cancer using publicly available transcriptome sequencing data from a cohort of 567 adenocarcinoma and squamous cell carcinoma tumors. Through this compendium we identify over 3,000 unannotated intergenic transcripts representing novel lncRNAs. Through comparison of both adenocarcinoma and squamous cell carcinomas with matched controls we discover 111 differentially expressed lncRNAs, which we term lung cancer-associated lncRNAs (LCALs). A pan-cancer analysis of 324 additional tumor and adjacent normal pairs enable us to identify a subset of lncRNAs that display enriched expression specific to lung cancer as well as a subset that appear to be broadly deregulated across human cancers. Integration of exome sequencing data reveals that expression levels of many LCALs have significant associations with the mutational status of key oncogenes in lung cancer. Functional validation, using both knockdown and overexpression, shows that the most differentially expressed lncRNA, LCAL1, plays a role in cellular proliferation. CONCLUSIONS: Our systematic characterization of publicly available transcriptome data provides the foundation for future efforts to understand the role of LCALs, develop novel biomarkers, and improve knowledge of lung tumor biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0429-8) contains supplementary material, which is available to authorized users

Ruminococcal cellulosome systems from rumen to human

This article is protected by copyright. All rights reserved. The authors appreciate the kind assistance of Miriam Lerner (ImmunArray Ltd. Company, Rehovot, Israel) with experiments involving the MicroGrid II arrayer. This research was supported by a grant (No. 1349) to EAB also from the Israel Science Foundation (ISF) and a grant (No. 24/11) issued to RL by The Sidney E. Frank Foundation also through the ISF. Additional support was obtained from the establishment of an Israeli Center of Research Excellence (I-CORE Center No. 152/11) managed by the Israel Science Foundation, from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel, by the Weizmann Institute of Science Alternative Energy Research Initiative (AERI) and the Helmsley Foundation. The authors also appreciate the support of the European Union, Area NMP.2013.1.1-2: Self-assembly of naturally occurring nanosystems: CellulosomePlus Project number: 604530 and an ERA-IB Consortium (EIB.12.022), acronym FiberFuel. HF and SHD acknowledge support from the Scottish Government Food Land and People programme and from BBSRC grant no. BB/L009951/1. In addition, EAB is grateful for a grant from the F. Warren Hellman Grant for Alternative Energy Research in Israel in support of alternative energy research in Israel administered by the Israel Strategic Alternative Energy Foundation (I-SAEF). E.A.B. is the incumbent of The Maynard I. and Elaine Wishner Chair of Bio-organic ChemistryPeer reviewedPostprin

Childhood and Adolescent Pesticide Exposure and Breast Cancer Risk

To date, epidemiological studies have not strongly supported an association between pesticide exposure and breast cancer. However, few previous studies had the ability to assess specific time periods of exposure. Studies that relied on adult serum levels of metabolites of organochlorine pesticides may not accurately reflect exposure during developmental periods. Further, exposure assessment often occurred after diagnosis and key tumor characteristics, such as hormone receptor status, have rarely been available to evaluate tumor-subtype specific associations. We examine the association between pesticide exposure during childhood and adolescence and breast cancer risk in the prospective Sister Study cohort (N=50,844 women) to assess this relation by tumor subtype

NRG Oncology-Radiation Therapy Oncology Group Study 1014: 1-Year Toxicity Report From a Phase 2 Study of Repeat Breast-Preserving Surgery and 3-Dimensional Conformal Partial-Breast Reirradiation for In-Breast Recurrence.

PURPOSE: To determine the associated toxicity, tolerance, and safety of partial-breast reirradiation. METHODS AND MATERIALS: Eligibility criteria included in-breast recurrence occurring \u3e1 year after whole-breast irradiation, \u3c3 \u3ecm, unifocal, and resected with negative margins. Partial-breast reirradiation was targeted to the surgical cavity plus 1.5 cm; a prescription dose of 45 Gy in 1.5 Gy twice daily for 30 treatments was used. The primary objective was to evaluate the rate of grade ≥3 treatment-related skin, fibrosis, and/or breast pain adverse events (AEs), occurring ≤1 year from re-treatment completion. A rate of ≥13% for these AEs in a cohort of 55 patients was determined to be unacceptable (86% power, 1-sided α = 0.07). RESULTS: Between 2010 and 2013, 65 patients were accrued, and the first 55 eligible and with 1 year follow-up were analyzed. Median age was 68 years. Twenty-two patients had ductal carcinoma in situ, and 33 had invasive disease: 19 ≤1 cm, 13 \u3e1 to ≤2 cm, and 1 \u3e2 cm. All patients were clinically node negative. Systemic therapy was delivered in 51%. All treatment plans underwent quality review for contouring accuracy and dosimetric compliance. All treatment plans scored acceptable for tumor volume contouring and tumor volume dose-volume analysis. Only 4 (7%) scored unacceptable for organs at risk contouring and organs at risk dose-volume analysis. Treatment-related skin, fibrosis, and/or breast pain AEs were recorded as grade 1 in 64% and grade 2 in 7%, with only 1 ( CONCLUSION: Partial-breast reirradiation with 3-dimensional conformal radiation therapy after second lumpectomy for patients experiencing in-breast failures after whole-breast irradiation is safe and feasible, with acceptable treatment quality achieved. Skin, fibrosis, and breast pain toxicity was acceptable, and grade 3 toxicity was rare

Long non-coding RNA LCAL62 / LINC00261 is associated with lung adenocarcinoma prognosis

Background: More than half of non-small cell lung cancer (NSCLC) patients present with metastatic disease at initial diagnosis with an estimated five-year survival rate of ~5%. Despite advances in understanding primary lung cancer oncogenesis metastatic disease remains poorly characterized. Recent studies demonstrate important roles of long non-coding RNAs (lncRNAs) in tumor physiology and as prognostic markers. Therefore, we present the first transcriptome analysis to identify lncRNAs altered in metastatic lung adenocarcinoma leading to the discovery and characterization of the lncRNA Patients and methods: RNA-Seq, microarray, nanoString expression, and clinical data from 1,116 LUAD patients across six independent cohorts and 83 LUAD cell lines were used to discover and evaluate the survival association of metastasis associated lncRNAs. Coexpression and gene set enrichment analyses were used to establish gene regulatory networks and implicate metastasis associated lncRNAs in specific biological processes. Results: Our integrative analysis discovered Conclusion: We discovered tha

Utility of Two iPhone Device Apps in Assessing Heart Rate at Rest and During Activity

Heart rate (HR) is a critical physiological variable used for prescribing exercise, assessing fitness level and tracking fitness improvements. Electrocardiography (ECG) stands as the criterion measure of HR. While recent development of HR-detecting mobile device applications (apps) has made evaluating HR more convenient; their degree of accuracy is unknown. Therefore, the purpose of this current study was to examine the accuracy and reliability of two-iPhone applications to detect HR at rest and during low-intensity exercise conditions. Eighteen female and 22 male subjects (26 + 9.5 yrs) were prepped for simultaneous detection of HR via three methods: ECG and two HR-detecting apps. App 1, a camera-based app called Azumio Instant Heart Rate (CAM), was used by placement of a finger over the camera lens of the mobile device. App 2, a microphone-based app called Heart Monitor by Bluespark, was employed via placement of an external microphone over the radial pulse. The participants underwent a series of 5-minute stages: seated rest followed by cycle then treadmill walking at low intensities. HR was recorded concurrently, at several time intervals from the three methods once a steady-state HR was reached. The means of the three devices were compared via ANOVA with the significance level set, a priori, at 0.05. Correlation analysis was employed to investigate relationships between the apps and ECG. No statistical difference was found between the CAM and ECG HR (p \u3e 0.05) during the resting and cycle stages. However, during the treadmill phase, there was a significant difference (p = 0.018) between CAM and ECG. Nevertheless, there was a significant (p \u3c 0.05), positive correlation between CAM and ECG under the resting, cycle and treadmill conditions (r = .966, r = .984, r = .877, respectively). Significant differences (p \u3c 0.05) were found for each condition when comparing ECG and MIC HR. Data also revealed poor correlations (p \u3e 0.05; r between -.004 and -.136) between MIC and ECG. The utility of CAM and MIC-based apps to detect HR remains in question as evidence appears to indicate exercise mode and app specificity. Caution should be shown when using these devices. The CAM-based app may accurately detect HR during resting and seated cycling but not during treadmill activity. The MIC-based app is not recommended for use in any condition. Of note, statistical significance may not mitigate usefulness when considering the accuracy of palpation. Additional research is necessary

Aerococcus urinae isolated from women with lower urinary tract symptoms: In vitro aggregation and genome analysis

Aerococcus urinae is increasingly recognized as a potentially significant urinary tract bacterium. A. urinae has been isolated from urine collected from both males and females with a wide range of clinical conditions, including urinary tract infection (UTI), urgency urinary incontinence (UUI), and overactive bladder (OAB). A. urinae is of particular clinical concern because it is highly resistant to many antibiotics and, when undiagnosed, can cause invasive and life-threatening bacteremia, sepsis, or soft tissue infections. Previous genomic characterization studies have examined A. urinae strains isolated from patients experiencing UTI episodes. Here, we analyzed the genomes of A. urinae strains isolated as part of the urinary microbiome from patients with UUI or OAB. Furthermore, we report that certain A. urinae strains exhibit aggregative in vitro phenotypes, including flocking, which can be modified by various growth medium conditions. Finally, we performed in-depth genomic comparisons to identify pathways that distinguish flocking and nonflocking strains. IMPORTANCE Aerococcus urinae is a urinary bacterium of emerging clinical interest. Here, we explored the ability of 24 strains of A. urinae isolated from women with lower urinary tract symptoms to display aggregation phenotypes in vitro. We sequenced and analyzed the genomes of these A. urinae strains. We performed functional genomic analyses to determine whether the in vitro hyperflocking aggregation phenotype displayed by certain A. urinae strains was related to the presence or absence of certain pathways. Our findings demonstrate that A. urinae strains have different propensities to display aggregative properties in vitro and suggest a potential association between phylogeny and flocking

INTEGRATE: Gene fusion discovery using whole genome and transcriptome data

While next-generation sequencing (NGS) has become the primary technology for discovering gene fusions, we are still faced with the challenge of ensuring that causative mutations are not missed while minimizing false positives. Currently, there are many computational tools that predict structural variations (SV) and gene fusions using whole genome (WGS) and transcriptome sequencing (RNA-seq) data separately. However, as both WGS and RNA-seq have their limitations when used independently, we hypothesize that the orthogonal validation from integrating both data could generate a sensitive and specific approach for detecting high-confidence gene fusion predictions. Fortunately, decreasing NGS costs have resulted in a growing quantity of patients with both data available. Therefore, we developed a gene fusion discovery tool, INTEGRATE, that leverages both RNA-seq and WGS data to reconstruct gene fusion junctions and genomic breakpoints by split-read mapping. To evaluate INTEGRATE, we compared it with eight additional gene fusion discovery tools using the well-characterized breast cell line HCC1395 and peripheral blood lymphocytes derived from the same patient (HCC1395BL). The predictions subsequently underwent a targeted validation leading to the discovery of 131 novel fusions in addition to the seven previously reported fusions. Overall, INTEGRATE only missed six out of the 138 validated fusions and had the highest accuracy of the nine tools evaluated. Additionally, we applied INTEGRATE to 62 breast cancer patients from The Cancer Genome Atlas (TCGA) and found multiple recurrent gene fusions including a subset involving estrogen receptor. Taken together, INTEGRATE is a highly sensitive and accurate tool that is freely available for academic use