Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics.

As sequencing read length has increased, researchers have quickly adopted longer reads for their experiments. Here, we examine 14 pathogen or host-pathogen differential gene expression data sets to assess whether using longer reads is warranted. A variety of data sets was used to assess what genomic attributes might affect the outcome of differential gene expression analysis including: gene density, operons, gene length, number of introns/exons and intron length. No genome attribute was found to influence the data in principal components analysis, hierarchical clustering with bootstrap support, or regression analyses of pairwise comparisons that were undertaken on the same reads, looking at all combinations of paired and unpaired reads trimmed to 36, 54, 72 and 101 bp. Read pairing had the greatest effect when there was little variation in the samples from different conditions or in their replicates (e.g. little differential gene expression). But overall, 54 and 72 bp reads were typically most similar. Given differences in costs and mapping percentages, we recommend 54 bp reads for organisms with no or few introns and 72 bp reads for all others. In a third of the data sets, read pairing had absolutely no effect, despite paired reads having twice as much data. Therefore, single-end reads seem robust for differential-expression analyses, but in eukaryotes paired-end reads are likely desired to analyse splice variants and should be preferred for data sets that are acquired with the intent to be community resources that might be used in secondary data analyses

Validation of the Chronic Pain Acceptance Questionnaire-8 in an Australian pain clinic sample

Background: Recently, an 8-item short-form version of the Chronic Pain Acceptance Questionnaire (CPAQ-8) was developed predominantly in an internet sample. Further investigation of the factor structure in a multidisciplinary pain clinic sample is required. Investigation of the concurrent validity of the CPAQ-8 after accounting for the effects of variables commonly measured in the pain clinic setting is also necessary. Purpose: This study examines the factor structure and concurrent validity of the CPAQ-8 in a sample of treatmentseeking patients who attended a multidisciplinary pain clinic. Methods: Participants were 334 patients who attended an Australian multidisciplinary pain service. Participants completed the CPAQ, a demographic questionnaire, and measures of patient adjustment and functioning. Results: Confirmatory factor analysis identified a two-factor 8-item model consisting of Activity Engagement and Pain Willingness factors (SRMR=0.039, RMSEA=0.063, CFI=0.973, TLI=0.960) was superior to both the CPAQ and CPAQ with an item removed. The CPAQ and CPAQ-8 total scores were highly correlated (r=0.93). After accounting for pain intensity, the CPAQ-8 was a significant predictor of depression, anxiety, stress, and disability. The subscales of the CPAQ-8 were both unique contributors to depression and disability in regression analyses, after accounting for pain intensity and kinesiophobia, and after accounting for pain intensity and catastrophizing. Conclusions: The CPAQ-8 has a sound factor structure and similar psychometric properties to the CPAQ; it may have clinical utility as a measure of pain acceptance in treatmentseeking, chronic pain patients

A Multicenter Examination and Strategic Revisions of the Yale Global Tic Severity Scale

Objective To examine the internal consistency and distribution of the Yale Global Tic Severity Scale (YGTSS) scores to inform modification of the measure. Methods This cross-sectional study included 617 participants with a tic disorder (516 children and 101 adults), who completed an age-appropriate diagnostic interview and the YGTSS to evaluate tic symptom severity. The distributions of scores on YGTSS dimensions were evaluated for normality and skewness. For dimensions that were skewed across motor and phonic tics, a modified Delphi consensus process was used to revise selected anchor points. Results Children and adults had similar clinical characteristics, including tic symptom severity. All participants were examined together. Strong internal consistency was identified for the YGTSS Motor Tic score (α = 0.80), YGTSS Phonic Tic score (α = 0.87), and YGTSS Total Tic score (α = 0.82). The YGTSS Total Tic and Impairment scores exhibited relatively normal distributions. Several subscales and individual item scales departed from a normal distribution. Higher scores were more often used on the Motor Tic Number, Frequency, and Intensity dimensions and the Phonic Tic Frequency dimension. By contrast, lower scores were more often used on Motor Tic Complexity and Interference, and Phonic Tic Number, Intensity, Complexity, and Interference. Conclusions The YGTSS exhibits good internal consistency across children and adults. The parallel findings across Motor and Phonic Frequency, Complexity, and Interference dimensions prompted minor revisions to the anchor point description to promote use of the full range of scores in each dimension. Specific minor revisions to the YGTSS Phonic Tic Symptom Checklist were also proposed

Elevated glutamatergic compounds in pregenual anterior cingulate in pediatric autism spectrum disorder demonstrated by 1H MRS and 1H MRSI.

Recent research in autism spectrum disorder (ASD) has aroused interest in anterior cingulate cortex and in the neurometabolite glutamate. We report two studies of pregenual anterior cingulate cortex (pACC) in pediatric ASD. First, we acquired in vivo single-voxel proton magnetic resonance spectroscopy ((1)H MRS) in 8 children with ASD and 10 typically developing controls who were well matched for age, but with fewer males and higher IQ. In the ASD group in midline pACC, we found mean 17.7% elevation of glutamate + glutamine (Glx) (p<0.05) and 21.2% (p<0.001) decrement in creatine + phosphocreatine (Cr). We then performed a larger (26 subjects with ASD, 16 controls) follow-up study in samples now matched for age, gender, and IQ using proton magnetic resonance spectroscopic imaging ((1)H MRSI). Higher spatial resolution enabled bilateral pACC acquisition. Significant effects were restricted to right pACC where Glx (9.5%, p<0.05), Cr (6.7%, p<0.05), and N-acetyl-aspartate + N-acetyl-aspartyl-glutamate (10.2%, p<0.01) in the ASD sample were elevated above control. These two independent studies suggest hyperglutamatergia and other neurometabolic abnormalities in pACC in ASD, with possible right-lateralization. The hyperglutamatergic state may reflect an imbalance of excitation over inhibition in the brain as proposed in recent neurodevelopmental models of ASD

Star Formation at 4<z<64 < z < 6 From the Spitzer Large Area Survey with Hyper-Suprime-Cam (SPLASH)

Using the first 50% of data collected for the Spitzer Large Area Survey with Hyper-Suprime-Cam (SPLASH) observations on the 1.8 deg$^2$ Cosmological Evolution Survey (COSMOS) we estimate the masses and star formation rates of 3398 $M_*>10^{10}M_\odot$ star-forming galaxies at $4 < z < 6$ with a substantial population up to $M_* \gtrsim 10^{11.5} M_\odot$. We find that the strong correlation between stellar mass and star formation rate seen at lower redshift (the "main sequence" of star-forming galaxies) extends to $z\sim6$. The observed relation and scatter is consistent with a continued increase in star formation rate at fixed mass in line with extrapolations from lower-redshift observations. It is difficult to explain this continued correlation, especially for the most massive systems, unless the most massive galaxies are forming stars near their Eddington-limited rate from their first collapse. Furthermore, we find no evidence for moderate quenching at higher masses, indicating quenching either has not occurred prior to $z \sim 6$ or else occurs rapidly, so that few galaxies are visible in transition between star-forming and quenched.Comment: ApJL, accepte

Nurses\u27 Alumnae Association Bulletin, June 1969

Alumnae President\u27s Message Officers and Chairmen Financial Report Progressive Changes at Jefferson School of Nursing Report Student Activities School of Practical Nursing Report Jefferson Expansion Report Clerk-Typist Report Committee Reports Resume of Alumnae Meetings Class News 1969 CLINIC Correspondence Notice

The Next Generation Virgo Cluster Survey - Infrared (NGVS-IR): I. A new Near-UV/Optical/Near-IR Globular Cluster selection tool

The NGVS-IR project (Next Generation Virgo Survey - Infrared) is a contiguous near-infrared imaging survey of the Virgo cluster of galaxies. It complements the optical wide-field survey of Virgo (NGVS). The current state of NGVS-IR consists of Ks-band imaging of 4 deg^2 centered on M87, and J and Ks-band imaging of 16 deg^2 covering the region between M49 and M87. In this paper, we present the observations of the central 4 deg^2 centered on Virgo's core region. The data were acquired with WIRCam on the Canada-France-Hawaii Telescope and the total integration time was 41 hours distributed in 34 contiguous tiles. A survey-specific strategy was designed to account for extended galaxies while still measuring accurate sky brightness within the survey area. The average 5\sigma limiting magnitude is Ks=24.4 AB mag and the 50% completeness limit is Ks=23.75 AB mag for point source detections, when using only images with better than 0.7" seeing (median seeing 0.54"). Star clusters are marginally resolved in these image stacks, and Virgo galaxies with \mu_Ks=24.4 AB mag arcsec^-2 are detected. Combining the Ks data with optical and ultraviolet data, we build the uiK color-color diagram which allows a very clean color-based selection of globular clusters in Virgo. This diagnostic plot will provide reliable globular cluster candidates for spectroscopic follow-up campaigns needed to continue the exploration of Virgo's photometric and kinematic sub-structures, and will help the design of future searches for globular clusters in extragalactic systems. Equipped with this powerful new tool, future NGVS-IR investigations based on the uiK diagram will address the mapping and analysis of extended structures and compact stellar systems in and around Virgo galaxies.Comment: 23 pages, 18 figures. Accepted for publication in ApJ

The distribution of progesterone in body fluids and tissues of the dairy cow

A careful study was carried out of the method of Short (1956a) and Rowlands and Short (1959) for the estimation of progesterone in plasma and in corpora lutea respectively. For bovine plasma it was found necessary to acetylate the first chromatogram eluate with an acetic anhydride/pyridine mixture and subject the residue to a further chromatography step. These additional steps in-creased the specificity of the method for progesterone and at the same time yielded a comparatively pure final product. In addition the incorporation of a radioactive marker to calculate individual recoveries was found to be an advantage in both plasma and luteal samples. Using the above method plasma- progesterone con-centration was measured throughout the oestrous cycle in six normal dairy cows. The general pattern consisted of a gradual rise in progesterone concentration from near zero levels on the day of oestrus (day 1) until day 5 when a more rapid rise occurred up to a level of about 1.0 ug/100 ml plasma on day 9. The level remained at about this value until day 16 when a decline occurred until near zero levels 213 were reached on the subsequent day of oestrus. There appeared to be a considerable variation in the maximum levels attained during mid-cycle in individual cows. The range of values at this time in the six animals used was 0.63 to 1.44 ug/100 ml plasma. The removal of the corpus luteum or ovaries during mid-cycle in the cow resulted in an initial rapid drop in plasma progesterone concentration followed by a more gradual decline, The fact that this occurred after the removal of either the corpus luteum or the ovaries indicated that the residual progesterone level did not originate from ovarian tissue other than the corpus luteum. It was tentatively suggested that the residual level could be duo to a contribution from either the adrenal gland or the body fat depots. The subsequent determination of comparatively high levels of progesterone in the body fat of cows at mid. cycle emphasised the latter as the more likely of the two sources, with the reservation that an adrenal contribution due to surgical stress could not be ruled out completely. The rapid disappearance of injected progesterone from the circulating blood of the cow was in keeping with the observations made in other species. There was evidence to show that this was partly due to catabolism of the progesterone molecule and partly due to uptake by the body tissues, probably the body fat. Furthermore it was shown that renal excretion of progesterone per se did not occur to any appreciable extent. The half life of progesterone in the blood of the cow appeared to be in the order of 6 minutes. Progesterone in the body fat of cows at mid-cycle sac found to be 5 to 10 times that in the plasma and the identification of the progesterone from this source wan confirmed by infra-red analysis and gas/liquid chromatography. In fat from coup early in the cycle, from ovari-atomised cows and from bullocks, progesterone was not present in any measurable quantity. Progesterone was also found in cows milk where it appeared to reflect the levels found in plasma. However, in spite of milk being more available than plasma, owing to its high fat content, it was not considered to be a better source of material for the study of progesterone metabolism in the cow. Plasma and luteal levels of progesterone were studied in a series of 40 cows at 16 and 26 days after 215 insemination. The levels of progesterone in the pregnant and non pregnant animals when slaughtered at 16 days were of the same order, while at 26 days the marked difference between the levels in pregnant and non-pregnant cows could be accounted for by evidence of a recent ovulation in all cows in the latter group. In this series of 40 cows there appeared to be a relationship between the plasma levels and both the luteal weight and progesterone content. The higher blood levels appeared to be associated with the heaviest glands which in general contained more progesterone. Conversely, low blood levels were observed with small glands which generally contained less progesterone. The absolute and relative amounts of 2093 hydroxyprogesterone did not vary significantly among the groups. Progesterone levels were investigated in certain clinical oases made available through the Veterinary Hospital, namely cases of hydrops allantois and oases of retained foetal membranes. However, progesterone levels in these animals did not appear to differ significantly from those found in normal cows

Estimation of the national disease burden of influenza-associated severe acute respiratory illness in Kenya and Guatemala : a novel methodology

Background: Knowing the national disease burden of severe influenza in low-income countries can inform policy decisions around influenza treatment and prevention. We present a novel methodology using locally generated data for estimating this burden. Methods and Findings: This method begins with calculating the hospitalized severe acute respiratory illness (SARI) incidence for children <5 years old and persons ≥5 years old from population-based surveillance in one province. This base rate of SARI is then adjusted for each province based on the prevalence of risk factors and healthcare-seeking behavior. The percentage of SARI with influenza virus detected is determined from provincial-level sentinel surveillance and applied to the adjusted provincial rates of hospitalized SARI. Healthcare-seeking data from healthcare utilization surveys is used to estimate non-hospitalized influenza-associated SARI. Rates of hospitalized and non-hospitalized influenza-associated SARI are applied to census data to calculate the national number of cases. The method was field-tested in Kenya, and validated in Guatemala, using data from August 2009–July 2011. In Kenya (2009 population 38.6 million persons), the annual number of hospitalized influenza-associated SARI cases ranged from 17,129–27,659 for children <5 years old (2.9–4.7 per 1,000 persons) and 6,882–7,836 for persons ≥5 years old (0.21–0.24 per 1,000 persons), depending on year and base rate used. In Guatemala (2011 population 14.7 million persons), the annual number of hospitalized cases of influenza-associated pneumonia ranged from 1,065–2,259 (0.5–1.0 per 1,000 persons) among children <5 years old and 779–2,252 cases (0.1–0.2 per 1,000 persons) for persons ≥5 years old, depending on year and base rate used. In both countries, the number of non-hospitalized influenza-associated cases was several-fold higher than the hospitalized cases. Conclusions: Influenza virus was associated with a substantial amount of severe disease in Kenya and Guatemala. This method can be performed in most low and lower-middle income countries