Phylogenetic organization of bacterial activity.

Phylogeny is an ecologically meaningful way to classify plants and animals, as closely related taxa frequently have similar ecological characteristics, functional traits and effects on ecosystem processes. For bacteria, however, phylogeny has been argued to be an unreliable indicator of an organism\u27s ecology owing to evolutionary processes more common to microbes such as gene loss and lateral gene transfer, as well as convergent evolution. Here we use advanced stable isotope probing with (13)C and (18)O to show that evolutionary history has ecological significance for in situ bacterial activity. Phylogenetic organization in the activity of bacteria sets the stage for characterizing the functional attributes of bacterial taxonomic groups. Connecting identity with function in this way will allow scientists to begin building a mechanistic understanding of how bacterial community composition regulates critical ecosystem functions.The ISME Journal advance online publication, 4 March 2016; doi:10.1038/ismej.2016.28

Ovarian cancer survival population differences: a "high resolution study" comparing Philippine residents, and Filipino-Americans and Caucasians living in the US

<p>Abstract</p> <p>Background</p> <p>In contrast to most other forms of cancer, data from some developing and developed countries show surprisingly similar survival rates for ovarian cancer. We aimed to compare ovarian cancer survival in Philippine residents, Filipino-Americans and Caucasians living in the US, using a high resolution approach, taking potential differences in prognostic factors into account.</p> <p>Methods</p> <p>Using databases from the SEER 13 and from the Manila and Rizal Cancer Registries, age-adjusted five-year absolute and relative survival estimates were computed using the period analysis method and compared between Filipino-American ovarian cancer patients with cancer patients from the Philippines and Caucasians in the US. Cox proportional hazards modelling was used to determine factors affecting survival differences.</p> <p>Results</p> <p>Despite more favorable distribution of age and cancer morphology and similar stage distribution, 5-year absolute and relative survival were lower in Philippine residents (Absolute survival, AS, 44%, Standard Error, SE, 2.9 and Relative survival, RS, 49.7%, SE, 3.7) than in Filipino-Americans (AS, 51.3%, SE, 3.1 and RS, 54.1%, SE, 3.4). After adjustment for these and additional covariates, strong excess risk of death for Philippine residents was found (Relative Risk, RR, 2.45, 95% confidence interval, 95% CI, 1.99-3.01). In contrast, no significant differences were found between Filipino-Americans and Caucasians living in the US.</p> <p>Conclusion</p> <p>Multivariate analyses disclosed strong survival disadvantages of Philippine residents compared to Filipino-American patients, for which differences in access to health care might have played an important role. Survival is no worse among Filipino-Americans than among Caucasians living in the US.</p

A framework for human microbiome research

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies

Structure, function and diversity of the healthy human microbiome

Author Posting. © The Authors, 2012. This article is posted here by permission of Nature Publishing Group. The definitive version was published in Nature 486 (2012): 207-214, doi:10.1038/nature11234.Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat’s signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81–99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.This research was supported in part by National Institutes of Health grants U54HG004969 to B.W.B.; U54HG003273 to R.A.G.; U54HG004973 to R.A.G., S.K.H. and J.F.P.; U54HG003067 to E.S.Lander; U54AI084844 to K.E.N.; N01AI30071 to R.L.Strausberg; U54HG004968 to G.M.W.; U01HG004866 to O.R.W.; U54HG003079 to R.K.W.; R01HG005969 to C.H.; R01HG004872 to R.K.; R01HG004885 to M.P.; R01HG005975 to P.D.S.; R01HG004908 to Y.Y.; R01HG004900 to M.K.Cho and P. Sankar; R01HG005171 to D.E.H.; R01HG004853 to A.L.M.; R01HG004856 to R.R.; R01HG004877 to R.R.S. and R.F.; R01HG005172 to P. Spicer.; R01HG004857 to M.P.; R01HG004906 to T.M.S.; R21HG005811 to E.A.V.; M.J.B. was supported by UH2AR057506; G.A.B. was supported by UH2AI083263 and UH3AI083263 (G.A.B., C. N. Cornelissen, L. K. Eaves and J. F. Strauss); S.M.H. was supported by UH3DK083993 (V. B. Young, E. B. Chang, F. Meyer, T. M. S., M. L. Sogin, J. M. Tiedje); K.P.R. was supported by UH2DK083990 (J. V.); J.A.S. and H.H.K. were supported by UH2AR057504 and UH3AR057504 (J.A.S.); DP2OD001500 to K.M.A.; N01HG62088 to the Coriell Institute for Medical Research; U01DE016937 to F.E.D.; S.K.H. was supported by RC1DE0202098 and R01DE021574 (S.K.H. and H. Li); J.I. was supported by R21CA139193 (J.I. and D. S. Michaud); K.P.L. was supported by P30DE020751 (D. J. Smith); Army Research Office grant W911NF-11-1-0473 to C.H.; National Science Foundation grants NSF DBI-1053486 to C.H. and NSF IIS-0812111 to M.P.; The Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231 for P.S. C.; LANL Laboratory-Directed Research and Development grant 20100034DR and the US Defense Threat Reduction Agency grants B104153I and B084531I to P.S.C.; Research Foundation - Flanders (FWO) grant to K.F. and J.Raes; R.K. is an HHMI Early Career Scientist; Gordon&BettyMoore Foundation funding and institutional funding fromthe J. David Gladstone Institutes to K.S.P.; A.M.S. was supported by fellowships provided by the Rackham Graduate School and the NIH Molecular Mechanisms in Microbial Pathogenesis Training Grant T32AI007528; a Crohn’s and Colitis Foundation of Canada Grant in Aid of Research to E.A.V.; 2010 IBM Faculty Award to K.C.W.; analysis of the HMPdata was performed using National Energy Research Scientific Computing resources, the BluBioU Computational Resource at Rice University

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Does mate choice take place in free-living prairie voles Microtus ochrogaster? Evidence from field data

We used live-trapping data collected during a long-term study of the social organization of prairie vole Microtus ochrogaster, to investigate pair formation and break-up in this species. Most male-female pairs that formed in spring consisted of survivors of communal groups. Whether pairs formed from males and females from the same or different communal groups, the individuals were not family members. When new pairs formed during summer-autumn they typically consisted of unrelated individuals that had been wandering throughout the study site. Thus, our field data indicate that prairie voles avoided pairing with family members. We found no evidence that free-living females based their choice of mate on body mass, or that females preferred sexually experienced to sexually inexperienced males in the field or under semi-natural laboratory conditions. In our study population, pairs that separated were characterized by lower reproductive success, prior to separation, than were pairs that remained together. At any given time, the number of potential mates for males and females was limited. Thus, it seems likely that few individuals had the opportunity to compare simultaneously the characteristics of two or more potential mates. We suggest that pair formation in our study population most likely was opportunistic, with individuals pairing with the first available mate.published or submitted for publicationis peer reviewe

A Preliminary Investigation of a New Pictorial Method of Measuring Aggression-Supportive Cognition Among Young Aggressive Males

A new pictorial assessment was developed to measure aggression-supportive cognitions among young aggressive male students. The assessment was comprised of 17 watercolor ambiguous sketches that could be interpreted in either an aggressive or a benign manner (e.g., two young people facing each other with their arms folded). The results showed that high trait aggressive male students were more likely to make hostile attributions of the pictures, providing significantly more themes of entitlement and power in the stories they generated about the pictures. Aggressive male students also endorsed significantly more aggression-supportive cognitions on a self-report measure and provided some supporting qualitative accounts of physically aggressive encounters. The results of this study are discussed and evaluated with reference to future work with young violent adolescents

Emergency department utilization following pediatric gastrostomy tube placement is driven by a small cohort of patients

PURPOSE: Pediatric gastrostomy tubes (G-tubes) are associated with frequent postoperative problems and consumption of healthcare resources. We hypothesized that a small cohort of patients disproportionately drives healthcare resource utilization after G-tube insertion. This study aimed to characterize this population in order to implement evidence-based pathways to reduce healthcare utilization after G-tube insertion. METHODS: All surgically placed pediatric G-tubes at a quaternary care center between March 2011 and June 2018 were retrospectively reviewed. Healthcare utilization including radiographic studies, emergency department (ED) visits, hospital admissions, procedures, and diagnoses was abstracted. Encounter specific charges based on CPT codes were collected. Statistical analyses were performed with Mann Whitney U, Fisher\u27s Exact Test, and multivariate nominal logistic regression. Institutional review board approval was obtained. RESULTS: During the study period, 189 patients underwent G-tube insertion; 24% of patients presented to the ED two or more times and accounted for 82% of ED visits. This cohort of high ED utilizers was more likely to present with G-tube dislodgement [both within the first three months (early) and after three months (late)], required more radiographic studies, and accrued significantly more charges compared to low ED utilizers. Multivariate analyses demonstrated high ED utilization was significantly associated with non-Caucasian race and the surgeon performing the procedure. CONCLUSIONS: At our institution, a significant proportion of healthcare utilization following G-tube placement is consumed by a relatively small cohort of children. Future efforts will target patients with two or more G-tube related ED visits or an early G-tube dislodgement for additional education and integration with outpatient resources. TYPE OF STUDY: Retrospective study. LEVEL OF EVIDENCE: Level II

Racial/Ethnic Disparities in Survival after Breast Cancer Diagnosis by Estrogen and Progesterone Receptor Status: A Pooled Analysis

BackgroundLimited studies have investigated racial/ethnic survival disparities for breast cancer defined by estrogen receptor (ER) and progesterone receptor (PR) status in a multiethnic population.MethodsUsing multivariable Cox proportional hazards models, we assessed associations of race/ethnicity with ER/PR-specific breast cancer mortality in 10,366 California women diagnosed with breast cancer from 1993 to 2009. We evaluated joint associations of race/ethnicity, health care, sociodemographic, and lifestyle factors with mortality.ResultsAmong women with ER/PR+ breast cancer, breast cancer-specific mortality was similar among Hispanic and Asian American women, but higher among African American women [HR, 1.31; 95% confidence interval (CI), 1.05-1.63] compared with non-Hispanic White (NHW) women. Breast cancer-specific mortality was modified by surgery type, hospital type, education, neighborhood socioeconomic status (SES), smoking history, and alcohol consumption. Among African American women, breast cancer-specific mortality was higher among those treated at nonaccredited hospitals (HR, 1.57; 95% CI, 1.21-2.04) and those from lower SES neighborhoods (HR, 1.48; 95% CI, 1.16-1.88) compared with NHW women without these characteristics. Breast cancer-specific mortality was higher among African American women with at least some college education (HR, 1.42; 95% CI, 1.11-1.82) compared with NHW women with similar education. For ER-/PR- disease, breast cancer-specific mortality did not differ by race/ethnicity and associations of race/ethnicity with breast cancer-specific mortality varied only by neighborhood SES among African American women.ConclusionsRacial/ethnic survival disparities are more striking for ER/PR+ than ER-/PR- breast cancer. Social determinants and lifestyle factors may explain some of the survival disparities for ER/PR+ breast cancer.ImpactAddressing these factors may help reduce the higher mortality of African American women with ER/PR+ breast cancer

Analysis of global DNA methylation spectrum in acute pain syndrome

IPRO 339 is focused on providing an affordable housing option for the working poor in Juarez, Mexico. This semester we will research the technologies involved in reusing shipping containers for this housing. We will design a prototype housing unit which will relate to other units in an overall community, with services such as commerce, open spaces for activity, and community centers to support them. We wish to design a housing community that embodies the ideals of humanity, affordability, functionality, opportunity, sustainability, durability, safety, culture, and neighborhood. In order to do this, our team for the Spring Semester has set forth the following objectives: • Research and understand the users of our product by looking at the social, economic, and physical factors in Juarez, Mexico and in the Maquiladoras where they work. • Research the most cost efficient and sustainable ways of incorporating plumbing, HVAC, and electricity into the homes. • Research the structural aspects of building this community. • Develop a potential site plan and floor plans and sections for the housing units. • Using our research and designs, develop a proposal for our sponsor, considering the client at hand.Deliverable