Evaluating the Roles of Rainout and Post-Condensation Processes in a Landfalling Atmospheric River with Stable Isotopes in Precipitation and Water Vapor

Atmospheric rivers (ARs), and frontal systems more broadly, tend to exhibit prominent “V” shapes in time series of stable isotopes in precipitation. Despite the magnitude and widespread nature of these “V” shapes, debate persists as to whether these shifts are driven by changes in the degree of rainout, which we determine using the Rayleigh distillation of stable isotopes, or by post-condensation processes such as below-cloud evaporation and equilibrium isotope exchange between hydrometeors and surrounding vapor. Here, we present paired precipitation and water vapor isotope time series records from the 5–7 March 2016, AR in Bodega Bay, CA. The stable isotope composition of surface vapor along with independent meteorological constraints such as temperature and relative humidity reveal that rainout and post-condensation processes dominate during different portions of the event. We find that Rayleigh distillation controls during peak AR conditions (with peak rainout of 55%) while post-condensation processes have their greatest effect during periods of decreased precipitation on the margins of the event. These results and analyses inform critical questions regarding the temporal evolution of AR events and the physical processes that control them at local scales

Optimising the analysis of transcript data using high density oligonucleotide arrays and genomic DNA-based probe selection

Background: Affymetrix GeneChip arrays are widely used for transcriptomic studies in a diverse range of species. Each gene is represented on a GeneChip array by a probe-set, consisting of up to 16 probe-pairs. Signal intensities across probe-pairs within a probe-set vary in part due to different physical hybridisation characteristics of individual probes with their target labelled transcripts. We have previously developed a technique to study the transcriptomes of heterologous species based on hybridising genomic DNA (gDNA) to a GeneChip array designed for a different species, and subsequently using only those probes with good homology. Results: Here we have investigated the effects of hybridising homologous species gDNA to study the transcriptomes of species for which the arrays have been designed. Genomic DNA from Arabidopsis thaliana and rice (Oryza sativa) were hybridised to the Affymetrix Arabidopsis ATH1 and Rice Genome GeneChip arrays respectively. Probe selection based on gDNA hybridisation intensity increased the number of genes identified as significantly differentially expressed in two published studies of Arabidopsis development, and optimised the analysis of technical replicates obtained from pooled samples of RNA from rice. Conclusion: This mixed physical and bioinformatics approach can be used to optimise estimates of gene expression when using GeneChip arrays

Contrasting local and long-range-transported warm ice-nucleating particles during an atmospheric river in coastal California, USA

Ice-nucleating particles (INPs) have been found to influence the amount, phase and efficiency of precipitation from winter storms, including atmospheric rivers.Warm INPs, those that initiate freezing at temperatures warmer than -10°C, are thought to be particularly impactful because they can create primary ice in mixed-phase clouds, enhancing precipitation efficiency. The dominant sources of warm INPs during atmospheric rivers, the role of meteorology in modulating transport and injection of warm INPs into atmospheric river clouds, and the impact of warm INPs on mixed-phase cloud properties are not well-understood. In this case study, time-resolved precipitation samples were collected during an atmospheric river in northern California, USA, during winter 2016. Precipitation samples were collected at two sites, one coastal and one inland, which are separated by about 35 km. The sites are sufficiently close that air mass sources during this storm were almost identical, but the inland site was exposed to terrestrial sources of warm INPs while the coastal site was not. Warm INPs were more numerous in precipitation at the inland site by an order of magnitude. Using FLEXPART (FLEXible PARTicle dispersion model) dispersion modeling and radar-derived cloud vertical structure, we detected influence from terrestrial INP sources at the inland site but did not find clear evidence of marine warm INPs at either site.We episodically detected warm INPs from long-range-transported sources at both sites. By extending the FLEXPART modeling using a meteorological reanalysis, we demonstrate that long-range-transported warm INPs were observed only when the upper tropospheric jet provided transport to cloud tops. Using radar-derived hydrometeor classifications, we demonstrate that hydrometeors over the terrestrially influenced inland site were more likely to be in the ice phase for cloud temperatures between 0 and -10°C. We thus conclude that terrestrial and long-rangetransported aerosol were important sources of warm INPs during this atmospheric river. Meteorological details such as transport mechanism and cloud structure were important in determining (i) warm INP source and injection temperature and (ii) ultimately the impact of warm INPs on mixed-phase cloud properties

Using genomic DNA-based probe-selection to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species

High-density oligonucleotide (oligo) arrays are a powerful tool for transcript profiling. Arrays based on GeneChip® technology are amongst the most widely used, although GeneChip® arrays are currently available for only a small number of plant and animal species. Thus, we have developed a method to improve the sensitivity of high-density oligonucleotide arrays when applied to heterologous species and tested the method by analysing the transcriptome of Brassica oleracea L., a species for which no GeneChip® array is available, using a GeneChip® array designed for Arabidopsis thaliana (L.) Heynh. Genomic DNA from B. oleracea was labelled and hybridised to the ATH1-121501 GeneChip® array. Arabidopsis thaliana probe-pairs that hybridised to the B. oleracea genomic DNA on the basis of the perfect-match (PM) probe signal were then selected for subsequent B. oleracea transcriptome analysis using a .cel file parser script to generate probe mask files. The transcriptional response of B. oleracea to a mineral nutrient (phosphorus; P) stress was quantified using probe mask files generated for a wide range of gDNA hybridisation intensity thresholds. An example probe mask file generated with a gDNA hybridisation intensity threshold of 400 removed > 68 % of the available PM probes from the analysis but retained >96 % of available A. thaliana probe-sets. Ninety-nine of these genes were then identified as significantly regulated under P stress in B. oleracea, including the homologues of P stress responsive genes in A. thaliana. Increasing the gDNA hybridisation intensity thresholds up to 500 for probe-selection increased the sensitivity of the GeneChip® array to detect regulation of gene expression in B. oleracea under P stress by up to 13-fold. Our open-source software to create probe mask files is freely available http://affymetrix.arabidopsis.info/xspecies/ webcite and may be used to facilitate transcriptomic analyses of a wide range of plant and animal species in the absence of custom arrays

Immunological consequences of using three different clinical/laboratory techniques of emulsifying peptide-based vaccines in incomplete Freund's adjuvant

Incomplete Freund's adjuvant (IFA) serves as a carrier for water-in-oil emulsion (W/O) vaccines. The stability of such emulsions greatly affects vaccine safety and efficacy since continued presence of antigen depots at lymphoid organs releasing low-level antigens is known to stimulate a potent immune response and high-level systemic release of antigens can lead to tolerance. W/O emulsions for the purpose of clinical and laboratory peptide-based vaccinations have been prepared using the techniques of syringe extrusion, vortex or high-speed homogenization. There is no consensus in the field over which technique would be best to use and no immunological data are available that compare the three techniques. In this study, we compared the immune responses induced by a peptide-based vaccine prepared using vortex, syringe-extrusion and homogenization. The vaccination led to tumor rejection by mice vaccinated with the peptide-based vaccine prepared using all three techniques. The immunological data from the in vivo cytotoxicity assay showed a trend for lower responses and a higher variability and greater range in the immune responses induced by a vaccine that was emulsified by the vortex or homogenizer techniques as compared to the syringe-extrusion technique. There were statistically significant lower numbers of IFNγ-secreting cells induced when the mice were vaccinated with a peptide-based vaccine emulsion prepared using the vortex compared to the syringe-extrusion technique. At a suboptimal vaccine dose, the mice vaccinated with a peptide-based vaccine emulsion prepared using the vortex technique had the largest tumors compared to the syringe-extrusion or the homogenizer technique. In the setting of a busy pharmacy that prepares peptide-based vaccine emulsions for clinical studies, the vortex technique can still be used but we urge investigators to take special care in their choice of mixing vessels for the vortex technique as that can influence the stability of the emulsion. However, in instances where the optimal dose is unknown, we caution investigators against using the vortex technique to prepare the peptide-based vaccine emulsions. Overall, we report that all three techniques can be used to prepare peptide-based vaccine emulsions under optimal dose conditions and we discuss important details regarding the proper preparation of the emulsions

A diagnostic dilemma in breast pathology – benign fibroadenoma with multinucleated stromal giant cells

Fibroadenomas are common benign breast tumours that display a characteristic pathological morphology, although several epithelial and stromal variations exist. A very rare histological finding is the presence of multinucleated giant cells throughout the stroma of a benign fibroadenoma. Cells of this type, which are more commonly found incidentally within the interlobular stroma of breast tissue, are benign and should not be mistaken for malignant cells on microscopic examination. Unfortunately a lack of awareness of this pathological entity can lead to diagnostic confusion amongst pathologists resulting in the multinucleate giant cells being mistaken for highly mitotic cells and consequently the fibroadenoma being mistaken for a malignant lesion. This may have serious implications for the subsequent management of the patient. The presence of this unusual cell type in the stroma does not alter the prognosis of otherwise benign lesion. We encountered two such cases at our institution in a six month period recently. We present their histories along with relevant radiological, microscopic and immunohistochemical features, followed by a discussion of this unusual pathological entity

Chronic disease prevalence and associations in a cohort of Australian men: The Florey Adelaide Male Ageing Study (FAMAS)

Background An increasing proportion of Australia's chronic disease burden is carried by the ageing male. The aim of this study was to determine the prevalence of asthma, cancer, diabetes, angina and musculoskeletal conditions and their relationship to behavioural and socio-demographic factors in a cohort of Australian men. Methods Self-reports of disease status were obtained from baseline clinic visits (August 2002 – July 2003 & July 2004 – May 2005) from 1195 randomly selected men, aged 35–80 years and living in the north-west regions of Adelaide. Initially, relative risks were assessed by regression against selected variables for each outcome. Where age-independent associations were observed with the relevant chronic disease, independent variables were fitted to customized multiadjusted models. Results The prevalence of all conditions was moderately higher in comparison to national data for age-matched men. In particular, there was an unusually high rate of men with cancer. Multiadjusted analyses revealed age as a predictor of chronic conditions (type 2 diabetes mellitus, angina, cancer & osteoarthritis). A number of socio-demographic factors, independent of age, were associated with chronic disease, including: low income status (diabetes), separation/divorce (asthma), unemployment (cancer), high waist circumference (diabetes), elevated cholesterol (angina) and a family history of obesity (angina). Conclusion Socio-demographic factors interact to determine disease status in this broadly representative group of Australian men. In addition to obesity and a positive personal and family history of disease, men who are socially disadvantaged (low income, unemployed, separated) should be specifically targeted by public health initiatives.Sean A Martin, Matthew T Haren, Anne W Taylor, Sue M Middleton and Gary A Wittert for Members of the Florey Adelaide Male Ageing Study (FAMAS

Cross-validation of a Prediction Equation for Energy Expenditure of an Acute Resistance Exercise Bout

Previously, our laboratory introduced a regression equation for predicting net kcal consumption of a resistance exercise (RE) bout: Total net kcal = 0.874(height, cm) - 0.596(age, years) - 1.016(fat mass, kg) + 1.638(lean mass, kg) + 2.461(total volume x 10-3) - 110.742 (R2 = 0.773, SEE=28.5 kcal). PURPOSE: The purpose of this study was to validate this regression equation using the same variables as predictors. METHODS: Forty-seven healthy, active subjects (23 men, 24 women, 20-58 yrs, 173.5 ± 10.5 cm, 85.5 ± 19.0 kg, VO2max 36.0 ± 8.4 ml/kg/min) were randomly divided into validation and cross-validation groups (nv = 24, ncv = 23). The validation group’s data was used to develop an equation to predict net kcal consumption, which was applied to the cross-validation group’s data to estimate net kcal consumption. Similarly, a prediction equation was derived from the cross-validation group’s raw data and applied to that of the validation group. The strength of the relationship between each group’s measured and estimated net kcal consumption was assessed via correlational analysis. RESULTS: Multiple linear regression yielded the following estimates of net kcal consumption: validation net kcal = 1.125(height, cm) – 0.662(age, years) – 0.800(fat mass, kg) + 1.344(lean mass, kg) + 2.278(total volume x 10-3) – 144.846 (R2 = 0.751, p \u3c 0.0001, SEE=29.7 kcal); cross-validation net kcal = 0.515(height, cm) - 0.520(age, years) - 1.220(fat mass, kg) + 1.995(lean mass, kg) + 2.620(total volume x 10-3) – 59.988 (R2 = 0.823, p \u3c 0.0001, SEE=29.2 kcal). These equations had a cross-validation coefficient of 0.902 and a double cross-validation coefficient of 0.863. CONCLUSION: The strong relationship between the measured and estimated net kcal consumption of both the cross-validation and validation group lead us to conclude that the regression equation derived by this laboratory is valid for estimating net energy expenditure for a total RE bout

Subtypes of adolescent sedative/anxiolytic misusers: A latent profile analysis

Few empirically-based taxonomies of nonmedical prescription drug misusers have been published. This study used latent profile analysis (LPA) to identify classes of adolescent sedative/anxiolytic misusers

Significant Predictors of Nonalcoholic Fatty Liver Disease in Texas Firefighters

Risk factors for Nonalcoholic Fatty Liver Disease (NAFLD) include obesity, hypertension, dyslipidemia, and diabetes mellitus. Not only are these prevalent in the general US population, but they are also present at high rates in a specific subset responsible for public safety – firefighters. PURPOSE: The aim of the present study is to use logistic regression to predict the likelihood of occurrence of NAFLD in firefighters using a subset of health-related factors associated with common cardiometabolic risk factors. METHODS: Data were collected on 136 firefighters (128 males, 8 females; 36.3 ± 9.0 yrs; 95.7 ± 17.0 kg; 178.9 ± 7.4 cm; 29.8 ± 4.2 kg/m2) participating in FITLIFE, a university-based fitness program at Texas A&M University. Nominal logistic regression with stepwise removal was used to estimate the best model to predict fatty liver disease. Stepwise removal identified resting systolic blood pressure (RSBP, mm HG), Body Mass Index (BMI, kg/m2), visceral adipose tissue (VAT, cm2), whether or not has hypertension or is on medication (HTNMED; 0=No,1=Yes), and plasma triglyceride concentrations (TG, mg/dL) as independent predictors (p\u3c0.05). Odds ratios (OR) were calculated to determine the change in the odds of NAFLD per unit increase in each predictor. RESULTS: Logistic regression yielded the following equation to predict the probability of developing NAFLD: Logit = -22.5176 + 0.0918(RSBP) + 0.2154(BMI) + 0.0065(TG) + 0.0161(VAT) + 1.830(HTNMED) (R2 = 0.4655, p \u3c 0.001). Of the predictors, the ORs from largest to smallest were 6.235, 1.240, 1.096, 1.016, and 1.002 for HTNMED, BMI, RSBP, VAT, and TG, respectively. CONCLUSION: Using RSBP, BMI, VAT, TG, and HTNMED as predictors, this study demonstrates that the probability of developing NAFLD in Texas firefighters can be reasonably predicted. This regression model and individual predictors may be used by health practitioners as a cost-effective screening tool to identify those at higher risk for NAFLD