The Small RNA Teg41 Regulates Expression of the Alpha Phenol-Soluble Modulins and Is Required for Virulence in \u3ci\u3eStaphylococcus aureus\u3c/i\u3e

Small RNAs (sRNAs) remain an understudied class of regulatory molecules in bacteria in general and in Gram-positive bacteria in particular. In the major human pathogen Staphylococcus aureus, hundreds of sRNAs have been identified; however, only a few have been characterized in detail. In this study, we investigate the role of the sRNA Teg41 in S. aureus virulence. We demonstrate that Teg41, an sRNA divergently transcribed from the locus that encodes the cytolytic alpha phenolsoluble modulin (αPSM) peptides, plays a critical role in αPSM production. Overproduction of Teg41 leads to an increase in αPSM levels and a corresponding increase in hemolytic activity from S. aureus cells and cell-free culture supernatants. To identify regions of Teg41 important for its function, we performed an in silico RNA-RNA interaction analysis which predicted an interaction between the 3= end of Teg41 and the αPSM transcript. Deleting a 24-nucleotide region from the S. aureus genome, corresponding to the 3= end of Teg41, led to a 10-fold reduction in αPSM-dependent hemolytic activity and attenuation of virulence in a murine abscess model of infection. Restoration of hemolytic activity in the Teg41Δ3= strain was possible by expressing full-length Teg41 in trans. Restoration of hemolytic activity was also possible by expressing the 3= end of Teg41, suggesting that this region of Teg41 is necessary and sufficient for αPSMdependent hemolysis. Our results show that Teg41 is positively influencing αPSM production, demonstrating for the first time regulation of the αPSM peptides by an sRNA in S. aureus

Cosmological parameters from SDSS and WMAP

We measure cosmological parameters using the three-dimensional power spectrum P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in combination with WMAP and other data. Our results are consistent with a ``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt, tensor modes or massive neutrinos. Adding SDSS information more than halves the WMAP-only error bars on some parameters, tightening 1 sigma constraints on the Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when dropping prior assumptions about curvature, neutrinos, tensor modes and the equation of state. Our results are in substantial agreement with the joint analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive consistency check with independent redshift survey data and analysis techniques. In this paper, we place particular emphasis on clarifying the physical origin of the constraints, i.e., what we do and do not know when using different data sets and prior assumptions. For instance, dropping the assumption that space is perfectly flat, the WMAP-only constraint on the measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running tilt, neutrino mass and equation of state in the list of free parameters, many constraints are still quite weak, but future cosmological measurements from SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt figures available at http://www.hep.upenn.edu/~max/sdsspars.htm

Study protocol: a randomized controlled trial of a computer-based depression and substance abuse intervention for people attending residential substance abuse treatment

Background: A large proportion of people attending residential alcohol and other substance abuse treatment have a co-occurring mental illness. Empirical evidence suggests that it is important to treat both the substance abuse problem and co-occurring mental illness concurrently and in an integrated fashion. However, the majority of residential alcohol and other substance abuse services do not address mental illness in a systematic way. It is likely that computer delivered interventions could improve the ability of substance abuse services to address co-occurring mental illness. This protocol describes a study in which we will assess the effectiveness of adding a computer delivered depression and substance abuse intervention for people who are attending residential alcohol and other substance abuse treatment. Methods/Design. Participants will be recruited from residential rehabilitation programs operated by the Australian Salvation Army. All participants who satisfy the diagnostic criteria for an alcohol or other substance dependence disorder will be asked to participate in the study. After completion of a baseline assessment, participants will be randomly assigned to either a computer delivered substance abuse and depression intervention (treatment condition) or to a computer-delivered typing tutorial (active control condition). All participants will continue to complete The Salvation Army residential program, a predominantly 12-step based treatment facility. Randomisation will be stratified by gender (Male, Female), length of time the participant has been in the program at the commencement of the study (4 weeks or less, 4 weeks or more), and use of anti-depressant medication (currently prescribed medication, not prescribed medication). Participants in both conditions will complete computer sessions twice per week, over a five-week period. Research staff blind to treatment allocation will complete the assessments at baseline, and then 3, 6, 9, and 12 months post intervention. Participants will also complete weekly self-report measures during the treatment period. Discussion. This study will provide comprehensive data on the effect of introducing a computer delivered, cognitive behavioral therapy based co-morbidity treatment program within a residential substance abuse setting. If shown to be effective, this intervention can be disseminated within other residential substance abuse programs. Trial registration. Australia and New Zealand Clinical Trials Register (ANZCTR): ACTRN12611000618954

Disparities in self-reported postpartum depression among Asian, Hawaiian, and Pacific Islander women in Hawai‘i: Pregnancy, Risk, Assessment, and Monitoring System (PRAMS), 2004-2007

Postpartum depression affects 10–20% of women and causes significant morbidity and mortality among mothers, children, families, and society, but little is known about postpartum depression among the individual Asian and Pacific Islander racial/ethnic groups. This study sought to identify the prevalence of postpartum depression among common Asian and Pacific Islander racial/ethnic groups. Data from the Hawaii Pregnancy Risk Assessment and Monitoring System (PRAMS), a population-based surveillance system on maternal behaviors and experiences before, during, and after the birth of a live infant, were analyzed from 2004 through 2007 and included 7,154 women. Questions on mood and interest in activities since giving birth were combined to create a measure of Self-reported Postpartum Depressive Symptoms (SRPDS). A series of generalized logit models with maternal race or ethnicity adjusted for other sociodemographic characteristics evaluated associations between SRPDS and an intermediate level of symptoms as possible indicators of possible SRPDS. Of all women in Hawaii with a recent live birth, 14.5% had SRPDS, and 30.1% had possible SRPDS. The following Asian and Pacific Islander racial or ethnic groups were studied and found to have higher odds of SRPDS compared with white women: Korean (adjusted odds ratio [AOR] = 2.8;95% confidence interval [CI]: 2.0–4.0), Filipino (AOR = 2.2;95% CI: 1.7–2.8), Chinese (AOR = 2.0;95% CI: 1.5–2.7), Samoan (AOR = 1.9;95% CI: 1.2–3.2), Japanese (AOR = 1.6;95% CI: 1.2–2.2), Hawaiian (AOR = 1.7;95% CI: 1.3–2.1), other Asian (AOR = 3.3;95% CI: 1.9–5.9), other Pacific Islander (AOR = 2.2;95% CI: 1.5–3.4), and Hispanic (AOR = 1.9;95% CI: 1.1–3.4). Women who had unintended pregnancies (AOR = 1.4;95% CI: 1.2–1.6), experienced intimate partner violence (AOR = 3.7;95% CI: 2.6–5.5), smoked (AOR = 1.5;95% CI: 1.2–2.0), used illicit drugs (AOR = 1.9;95% CI: 1.3–3.9), or received Women, Infant, and Children (WIC) benefits during pregnancy (AOR = 1.4;95% CI: 1.2–2.6) were more likely to have SRPDS. Several groups also were at increased risk for possible SRPDS, although this risk was not as prominent as seen with the risk for SRPDS. One in seven women reported SRPDS, and close to a third reported possible SRPDS. Messages about postpartum depression should be incorporated into current programs to improve screening, treatment, and prevention of SRPDS for women at risk

Accident Research Manual

DOT-FH-11-9424Included in this manual is a compilation of sound research techniques that can be used by the engineer/analyst to carry out research related to highway accidents. Because highway engineering administrators must daily decide how best to spend limited numbers of safety dollars, they need to have results from properly conducted and clearly presented accident research for inputs in this decision-making process. This manual was prepared to meet the continuing need for upgraded research, both in the area of analysis of relationships between accidents and other variables and in the area of countermeasure evaluation. The manual is designed for use by the engineer/analyst who has some background in statistical analysis. The manual contains material related to 1) the rationale and the need for improving the level of existing research, 2) the underlying issues that researchers must be familiar with, 3) the components and methodologies used in the two basic types of accident research--research aimed at evaluating countermeasures and research aimed at identifying and examining underlying relationships between accidents and other highway factors, 4) the preparation and distribution of research results, and 5) summary guidelines for the engineer/analyst to use in his research. The manual has been developed for use in classroom training, as a reference text, and/or in a self-study program. Review questions, self-study pre- and post-tests, and references to related texts and articles are included

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

The performance of Protected Areas for biodiversity under climate change

Global environmental changes have been driving large-scale shifts in the distributions of species and in the composition of biological communities. This has thrown the continuing value of Protected Areas (PAs) into question, given that PAs remain static, whereas species move, and they are predicted to continue to move under future climate scenarios. We consider empirical evidence on the observed performance of PAs during the last 40 years of anthropogenic climate change. Despite some losses of populations and species, PAs have continued to accommodate many species, which have shifted to higher elevations, to polewards-facing aspects, and into cooler microhabitats within PAs as the climate has warmed. Even when species have declined in some PAs, they often remain more abundant inside than outside PAs. Furthermore, losses from some PAs are offset by increases in others. As species expand their ranges polewards across fragmented landscapes in response to climate warming, the majority are disproportionately colonizing PAs as they go. Hence, PA networks are acting as stepping-stones of suitable breeding conditions and facilitating range shifts, with many species remaining protected across PA networks as a whole. Finally, there is some evidence that appropriate management of PAs may be able to slow climate-related declines and accelerate expansions. The 40-year track record of species responding to environmental change in PAs suggests that networks of PAs have been essential to biodiversity conservation and are likely to continue to fulfil this role in the future. The challenge for managers will be to consider the balance between retaining current species and encouraging colonization by new species