Taphonomic and Diagenetic Pathways to Protein Preservation, Part II: The Case of Brachylophosaurus canadensis Specimen MOR 2598

Recent recoveries of peptide sequences from two Cretaceous dinosaur bones require paleontologists to rethink traditional notions about how fossilization occurs. As part of this shifting paradigm, several research groups have recently begun attempting to characterize biomolecular decay and stabilization pathways in diverse paleoenvironmental and diagenetic settings. To advance these efforts, we assessed the taphonomic and geochemical history of Brachylophosaurus canadensis specimen MOR 2598, the left femur of which was previously found to retain endogenous cells, tissues, and structural proteins. Combined stratigraphic and trace element data show that after brief fluvial transport, this articulated hind limb was buried in a sandy, likely-brackish, estuarine channel. During early diagenesis, percolating groundwaters stagnated within the bones, forming reducing internal microenvironments. Recent exposure and weathering also caused the surficial leaching of trace elements from the specimen. Despite these shifting redox regimes, proteins within the bones were able to survive through diagenesis, attesting to their remarkable resiliency over geologic time. Synthesizing our findings with other recent studies reveals that oxidizing conditions in the initial ~48 h postmortem likely promote molecular stabilization reactions and that the retention of early-diagenetic trace element signatures may be a useful proxy for molecular recovery potential

On the possible role of elemental carbon in the formation of reduced chondrules

Recent experiments have been designed to produce chondrule textures via flash melting while simultaneously studying the nature of chondrule precursors. However, these experiments have only been concerned with silicate starting material. This is a preliminary report concerning what effects elemental carbon, when added to the silicate starting material, has on the origin of chondrules produced by flash melting

Information-theoretic interpretation of quantum error-correcting codes

Quantum error-correcting codes are analyzed from an information-theoretic perspective centered on quantum conditional and mutual entropies. This approach parallels the description of classical error correction in Shannon theory, while clarifying the differences between classical and quantum codes. More specifically, it is shown how quantum information theory accounts for the fact that "redundant" information can be distributed over quantum bits even though this does not violate the quantum "no-cloning" theorem. Such a remarkable feature, which has no counterpart for classical codes, is related to the property that the ternary mutual entropy vanishes for a tripartite system in a pure state. This information-theoretic description of quantum coding is used to derive the quantum analogue of the Singleton bound on the number of logical bits that can be preserved by a code of fixed length which can recover a given number of errors.Comment: 14 pages RevTeX, 8 Postscript figures. Added appendix. To appear in Phys. Rev.

Peginterferon Alfa-2a and Ribavirin for 16 or 24 Weeks in HCV Genotype 2 or 3

Background Patients infected with hepatitis C virus (HCV) genotype 2 or 3 have sustained virologic response rates of approximately 80% after receiving treatment with peginterferon and ribavirin for 24 weeks. We conducted a large, randomized, multinational, noninferiority trial to determine whether similar efficacy could be achieved with only 16 weeks of treatment with peginterferon alfa-2a and ribavirin. Methods We randomly assigned 1469 patients with HCV genotype 2 or 3 to receive 180 μg of peginterferon alfa-2a weekly, plus 800 mg of ribavirin daily, for either 16 or 24 weeks. A sustained virologic response was defined as an undetectable serum HCV RNA level (milliliter) 24 weeks after the end of treatment. Results The study failed to demonstrate that the 16-week regimen was noninferior to the 24-week regimen. The sustained virologic response rate was significantly lower in patients treated for 16 weeks than in patients treated for 24 weeks (62% vs. 70%; odds ratio for 16 weeks vs. 24 weeks, 0.67; 95% confidence interval, 0.54 to 0.84; P Conclusions Treatment with peginterferon and ribavirin for 16 weeks in patients infected with HCV genotype 2 or 3 results in a lower overall sustained virologic response rate than treatment with the standard 24-week regimen. (ClinicalTrials.gov number, NCT00077636.

Identification of genes expressed by immune cells of the colon that are regulated by colorectal cancer-associated variants.

A locus on human chromosome 11q23 tagged by marker rs3802842 was associated with colorectal cancer (CRC) in a genome-wide association study; this finding has been replicated in case-control studies worldwide. In order to identify biologic factors at this locus that are related to the etiopathology of CRC, we used microarray-based target selection methods, coupled to next-generation sequencing, to study 103 kb at the 11q23 locus. We genotyped 369 putative variants from 1,030 patients with CRC (cases) and 1,061 individuals without CRC (controls) from the Ontario Familial Colorectal Cancer Registry. Two previously uncharacterized genes, COLCA1 and COLCA2, were found to be co-regulated genes that are transcribed from opposite strands. Expression levels of COLCA1 and COLCA2 transcripts correlate with rs3802842 genotypes. In colon tissues, COLCA1 co-localizes with crystalloid granules of eosinophils and granular organelles of mast cells, neutrophils, macrophages, dendritic cells and differentiated myeloid-derived cell lines. COLCA2 is present in the cytoplasm of normal epithelial, immune and other cell lineages, as well as tumor cells. Tissue microarray analysis demonstrates the association of rs3802842 with lymphocyte density in the lamina propria (p = 0.014) and levels of COLCA1 in the lamina propria (p = 0.00016) and COLCA2 (tumor cells, p = 0.0041 and lamina propria, p = 6 × 10(-5)). In conclusion, genetic, expression and immunohistochemical data implicate COLCA1 and COLCA2 in the pathogenesis of colon cancer. Histologic analyses indicate the involvement of immune pathways

Recommended practices for computerized clinical decision support and knowledge management in community settings: a qualitative study

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to identify recommended practices for computerized clinical decision support (CDS) development and implementation and for knowledge management (KM) processes in ambulatory clinics and community hospitals using commercial or locally developed systems in the U.S.</p> <p>Methods</p> <p>Guided by the Multiple Perspectives Framework, the authors conducted ethnographic field studies at two community hospitals and five ambulatory clinic organizations across the U.S. Using a Rapid Assessment Process, a multidisciplinary research team: gathered preliminary assessment data; conducted on-site interviews, observations, and field surveys; analyzed data using both template and grounded methods; and developed universal themes. A panel of experts produced recommended practices.</p> <p>Results</p> <p>The team identified ten themes related to CDS and KM. These include: 1) workflow; 2) knowledge management; 3) data as a foundation for CDS; 4) user computer interaction; 5) measurement and metrics; 6) governance; 7) translation for collaboration; 8) the meaning of CDS; 9) roles of special, essential people; and 10) communication, training, and support. Experts developed recommendations about each theme. The original Multiple Perspectives framework was modified to make explicit a new theoretical construct, that of Translational Interaction.</p> <p>Conclusions</p> <p>These ten themes represent areas that need attention if a clinic or community hospital plans to implement and successfully utilize CDS. In addition, they have implications for workforce education, research, and national-level policy development. The Translational Interaction construct could guide future applied informatics research endeavors.</p

Isotopic ordering in atmospheric O2 as a tracer of ozone photochemistry and the tropical atmosphere

The distribution of isotopes within O2 molecules can be rapidly altered when they react with atomic oxygen. This mechanism is globally important: while other contributions to the global budget of O2 impart isotopic signatures, the O(3P) + O2 reaction resets all such signatures in the atmosphere on subdecadal timescales. Consequently, the isotopic distribution within O2 is determined by O3 photochemistry and the circulation patterns that control where that photochemistry occurs. The variability of isotopic ordering in O2 has not been established, however. We present new measurements of 18O18O in air (reported as Δ36 values) from the surface to 33 km altitude. They confirm the basic features of the clumped-isotope budget of O2: Stratospheric air has higher Δ36 values than tropospheric air (i.e., more 18O18O), reflecting colder temperatures and fast photochemical cycling of O3. Lower Δ36 values in the troposphere arise from photochemistry at warmer temperatures balanced by the influx of high-Δ36 air from the stratosphere. These observations agree with predictions derived from the GEOS-Chem chemical transport model, which provides additional insight. We find a link between tropical circulation patterns and regions where Δ36 values are reset in the troposphere. The dynamics of these regions influences lapse rates, vertical and horizontal patterns of O2 reordering, and thus the isotopic distribution toward which O2 is driven in the troposphere. Temporal variations in Δ36 values at the surface should therefore reflect changes in tropospheric temperatures, photochemistry, and circulation. Our results suggest that the tropospheric O3 burden has remained within a ±10% range since 1978

In-hospital Depression Predicts Early Hospital Readmission after an Acute Coronary Syndrome: Preliminary Data from TRACE-CORE

Background: Hospital systems, patients and providers seek to avert rehospitalizations within 30 days for patients admitted with an acute coronary syndrome (ACS). Rehospitalizations within 30 days of discharge are often considered preventable and to reflect poor in-hospital management or discharge practices. However, independent associations of psychosocial factors with early rehospitalization in patients admitted with an ACS have not been examined. Methods: A multi-racial cohort of 1,540 patients admitted with an ACS reported psychosocial factors via standardized questionnaires in an in-hospital interview. One month following discharge, patients were interviewed via phone and reported hospital readmissions. We used logistic regression models to estimate odds ratios (ORs) and 95% confidence intervals (CIs) of the association between in-hospital psychosocial characteristics (depression, anxiety, and perceived stress), health literacy and numeracy, and cognitive status, with self-reported readmission within 30 days. Results: Participants were 34% female and 17% non-white, with a mean age of 62 years and a mean length of stay of 4.1 days. Rehospitalization was reported for 14% (n=208) of participants, 77% of which were due to CVD. In univariate analyses, in-hospital severe depression, anxiety, and high stress were associated with higher odds of early readmission, whereas low health numeracy was associated with lower odds of early readmission. Severe depression remained associated with higher odds and low health numeracy remained associated with lower odds of early readmission in a multivariable model including covariates associated on univariate testing with rehospitalization. Conclusions: Early readmission after hospitalization for an ACS was common and associated with in-hospital depression and health numeracy. Notably, depression and health numeracy were the only predictors independently associated with readmission in multivariable analyses. We speculate that the lower likelihood of readmission for those with low numeracy may be related to less engagement with the healthcare system. In-hospital screening for depression and characterization of health numeracy may help stratify risk for early rehospitalization after an ACS