Synoptic tool for reporting of hematological and lymphoid neoplasms based on World Health Organization classification and College of American Pathologists checklist

<p>Abstract</p> <p>Background</p> <p>Synoptic reporting, either as part of the pathology report or replacing some free text component incorporates standardized data elements in the form of checklists for pathology reporting. This ensures the pathologists make note of these findings in their reports, thereby improving the quality and uniformity of information in the pathology reports.</p> <p>Methods</p> <p>The purpose of this project is to develop the entire set of elements in the synoptic templates or "worksheets" for hematologic and lymphoid neoplasms using the World Health Organization (WHO) Classification and the College of American Pathologists (CAP) Cancer Checklists. The CAP checklists' content was supplemented with the most updated classification scheme (WHO classification), specimen details, staging as well as information on various ancillary techniques such as cytochemical studies, immunophenotyping, cytogenetics including Fluorescent In-situ Hybridization (FISH) studies and genotyping. We have used a digital synoptic reporting system as part of an existing laboratory information system (LIS), CoPathPlus, from Cerner DHT, Inc. The synoptic elements are presented as discrete data points, so that a data element such as tumor type is assigned from the synoptic value dictionary under the value of tumor type, allowing the user to search for just those cases that have that value point populated.</p> <p>Results</p> <p>These synoptic worksheets are implemented for use in our LIS. The data is stored as discrete data elements appear as an accession summary within the final pathology report. In addition, the synoptic data can be exported to research databases for linking pathological details on banked tissues.</p> <p>Conclusion</p> <p>Synoptic reporting provides a structured method for entering the diagnostic as well as prognostic information for a particular pathology specimen or sample, thereby reducing transcription services and reducing specimen turnaround time. Furthermore, it provides accurate and consistent diagnostic information dictated by pathologists as a basis for appropriate therapeutic modalities. Using synoptic reports, consistent data elements with minimized typographical and transcription errors can be generated and placed in the LIS relational database, enabling quicker access to desired information and improved communication for appropriate cancer management. The templates will also eventually serve as a conduit for capturing and storing data in the virtual biorepository for translational research. Such uniformity of data lends itself to subsequent ease of data viewing and extraction, as demonstrated by rapid production of standardized, high-quality data from the hemopoietic and lymphoid neoplasm specimens.</p

Disparities in the frequency of fruit and vegetable consumption by socio-demographic and lifestyle characteristics in Canada

<p>Abstract</p> <p>Background</p> <p>The health benefits of adequate fruit and vegetable (F&V) consumption are significant and widely documented. However, many individuals self-report low F&V consumption frequency per day. This paper examines the disparities in the frequency of F&V consumption by socio-demographic and lifestyle characteristics.</p> <p>Method</p> <p>This study uses a representative sample of 93,719 individuals from the Canadian Community Health Survey (2007). A quantile regression model is estimated in order to capture the differential effects of F&V determinants across the conditional distribution of F&V consumption.</p> <p>Results</p> <p>The conditional and unconditional analyses reveal the existence of a socioeconomic gradient in F&V consumption frequency, in which the low income-education groups consume F&V less frequently than the high income-education groups. We also find significant disparities in F&V consumption frequency by demographic and lifestyle characteristics. The frequency of F&V consumption is relatively lower among: males, those in middle age, singles, smokers, individuals with weak social interaction and households with no children. The quantile regression results show that the association between F&V consumption frequency, and socio-demographic and lifestyle factors varies significantly along the conditional F&V consumption distribution. In particular, individual educational attainment is positively and significantly associated with F&V consumption frequency across different parts of the F&V distribution, while the income level matters only over the lower half of the distribution. F&V consumption follows a U-shaped pattern across the age categories. Those aged 30-39, 40-49 and 50-59 years consume F&V less frequently than those aged 18-29 years. The smallest F&V consumption is among the middle aged adults (40-49).</p> <p>Conclusions</p> <p>Understanding the socio-demographic and lifestyle characteristics of individuals with low F&V consumption frequency could increase the effectiveness of policies aimed at promoting F&V consumption. The differential effects of individual characteristics along the F&V consumption distribution suggest the need for a multifaceted approach to address the variation in F&V consumption frequency.</p

EnvMine: A text-mining system for the automatic extraction of contextual information

<p>Abstract</p> <p>Background</p> <p>For ecological studies, it is crucial to count on adequate descriptions of the environments and samples being studied. Such a description must be done in terms of their physicochemical characteristics, allowing a direct comparison between different environments that would be difficult to do otherwise. Also the characterization must include the precise geographical location, to make possible the study of geographical distributions and biogeographical patterns. Currently, there is no schema for annotating these environmental features, and these data have to be extracted from textual sources (published articles). So far, this had to be performed by manual inspection of the corresponding documents. To facilitate this task, we have developed EnvMine, a set of text-mining tools devoted to retrieve contextual information (physicochemical variables and geographical locations) from textual sources of any kind.</p> <p>Results</p> <p>EnvMine is capable of retrieving the physicochemical variables cited in the text, by means of the accurate identification of their associated units of measurement. In this task, the system achieves a recall (percentage of items retrieved) of 92% with less than 1% error. Also a Bayesian classifier was tested for distinguishing parts of the text describing environmental characteristics from others dealing with, for instance, experimental settings.</p> <p>Regarding the identification of geographical locations, the system takes advantage of existing databases such as GeoNames to achieve 86% recall with 92% precision. The identification of a location includes also the determination of its exact coordinates (latitude and longitude), thus allowing the calculation of distance between the individual locations.</p> <p>Conclusion</p> <p>EnvMine is a very efficient method for extracting contextual information from different text sources, like published articles or web pages. This tool can help in determining the precise location and physicochemical variables of sampling sites, thus facilitating the performance of ecological analyses. EnvMine can also help in the development of standards for the annotation of environmental features.</p

Effect of nitrous oxide on cisatracurium infusion demands: a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Recent studies have questioned our previous understanding on the effect of nitrous oxide on muscle relaxants, since nitrous oxide has been shown to potentiate the action of bolus doses of mivacurium, rocuronium and vecuronium. This study was aimed to investigate the possible effect of nitrous oxide on the infusion requirements of cisatracurium.</p> <p>Methods</p> <p>70 ASA physical status I-III patients aged 18-75 years were enrolled in this randomized trial. The patients were undergoing elective surgery requiring general anesthesia with a duration of at least 90 minutes. Patients were randomized to receive propofol and remifentanil by target controlled infusion in combination with either a mixture of oxygen and nitrous oxide (Nitrous oxide/TIVA group) or oxygen in air (Air/TIVA group). A 0.1 mg/kg initial bolus of cisatracurium was administered before tracheal intubation, followed by a closed-loop computer controlled infusion of cisatracurium to produce and maintain a 90% neuromuscular block. Cumulative dose requirements of cisatracurium during the 90-min study period after bolus administration were measured and the asymptotic steady state rate of infusion to produce a constant 90% block was determined by applying nonlinear curve fitting to the data on the cumulative dose requirement during the study period.</p> <p>Results</p> <p>Controller performance, i.e. the ability of the controller to maintain neuromuscular block constant at the setpoint and patient characteristics were similar in both groups. The administration of nitrous oxide did not affect cisatracurium infusion requirements. The mean steady-state rates of infusion were 0.072 +/- 0.018 and 0.066 +/- 0.017 mg * kg-1 * h-1 in Air/TIVA and Nitrous oxide/TIVA groups, respectively.</p> <p>Conclusions</p> <p>Nitrous oxide does not affect the infusion requirements of cisatracurium.</p> <p>Trial registration</p> <p>ClinicalTrials.gov NCT01152905; European Clinical Trials Database at <url>http://eudract.emea.eu.int/2006-006037-41</url>.</p

Selective Enhancement of Donor Hematopoietic Cell Engraftment by the CXCR4 Antagonist AMD3100 in a Mouse Transplantation Model

The interaction between stromal cell-derived factor-1 (SDF-1) with CXCR4 chemokine receptors plays an important role in hematopoiesis following hematopoietic stem cell transplantation. We examined the efficacy of post transplant administration of a specific CXCR4 antagonist (AMD3100) in improving animal survival and in enhancing donor hematopoietic cell engraftment using a congeneic mouse transplantation model. AMD3100 was administered subcutaneously at 5 mg/kg body weight 3 times a week beginning at day +2 post-transplant. Post-transplant administration of AMD3100 significantly improves animal survival. AMD3100 reduces pro-inflammatory cytokine/chemokine production. Furthermore, post transplant administration of AMD3100 selectively enhances donor cell engraftment and promotes recovery of all donor cell lineages (myeloid cells, T and B lymphocytes, erythrocytes and platelets). This enhancement results from a combined effect of increased marrow niche availability and greater cell division induced by AMD3100. Our studies shed new lights into the biological roles of SDF-1/CXCR4 interaction in hematopoietic stem cell engraftment following transplantation and in transplant-related mortality. Our results indicate that AMD3100 provides a novel approach for enhancing hematological recovery following transplantation, and will likely benefit patients undergoing transplantation

Climate change, the Great Barrier Reef and the response of Australians

© 2016, Palgrave Macmillan Ltd. All rights reserved. Inspiration, aspirations, attitudes, and perception of threats play a pivotal role in the way that individuals associate themselves with natural environments. These sentiments affect how people connect to natural places, including their behaviours, perceived responsibility, and the management interventions they support. World Heritage Areas hold an important place in the lives of people who visit, aspire to visit, or derive a sense of security and well-being from their existence. Yet, the connection between people and special places is rarely quantified and policymakers find it difficult to incorporate these human dimensions into decision-making processes. Here we describe the personal concern and connection that Australians have with the Great Barrier Reef and discuss how the results may help with its management. We utilize a statistically representative sample of Australian residents (n = 2,002) and show empirically that climate change is perceived to be the biggest threat to the Great Barrier Reef, and that the Great Barrier Reef inspires Australians, promotes pride, and instills a sense of individual identity and collective responsibility to protect it. An increased understanding of the high levels of personal connection to iconic natural resources may help managers to enhance public support for protecting climate-sensitive systems within Australia and around the world

Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

Background Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems. Methodology/Principal Findings The synthesis of 9.6 million bacterial V6-rRNA amplicons for 509 samples that span the global ocean's surface to the deep-sea floor shows that pelagic and benthic communities greatly differ, at all taxonomic levels, and share <10% bacterial types defined at 3% sequence similarity level. Surface and deep water, coastal and open ocean, and anoxic and oxic ecosystems host distinct communities that reflect productivity, land influences and other environmental constraints such as oxygen availability. The high variability of bacterial community composition specific to vent and coastal ecosystems reflects the heterogeneity and dynamic nature of these habitats. Both pelagic and benthic bacterial community distributions correlate with surface water productivity, reflecting the coupling between both realms by particle export. Also, differences in physical mixing may play a fundamental role in the distribution patterns of marine bacteria, as benthic communities showed a higher dissimilarity with increasing distance than pelagic communities. Conclusions/Significance This first synthesis of global bacterial distribution across different ecosystems of the World's oceans shows remarkable horizontal and vertical large-scale patterns in bacterial communities. This opens interesting perspectives for the definition of biogeographical biomes for bacteria of ocean waters and the seabed

Impact of measurement error on testing genetic association with quantitative traits

10.1371/journal.pone.0087044PLoS ONE91-POLN

Taxa-area relationship of aquatic fungi on deciduous leaves

One of the fundamental patterns in macroecology is the increase in the number of observed taxa with size of sampled area. For microbes, the shape of this relationship remains less clear. The current study assessed the diversity of aquatic fungi, by the traditional approach based on conidial morphology (captures reproducing aquatic hyphomycetes) and next generation sequencing (NGS; captures other fungi as well), on graded sizes of alder leaves (0.6 to 13.6 cm2). Leaves were submerged in two streams in geographically distant locations: the Oliveira Stream in Portugal and the Boss Brook in Canada. Decay rates of alder leaves and fungal sporulation rates did not differ between streams. Fungal biomass was higher in Boss Brook than in Oliveira Stream, and in both streams almost 100% of the reads belonged to active fungal taxa. In general, larger leaf areas tended to harbour more fungi, but these findings were not consistent between techniques. Morphospecies-based diversity increased with leaf area in Boss Brook, but not in Oliveira Stream; metabarcoding data showed an opposite trend. The higher resolution of metabarcoding resulted in steeper taxa-accumulation curves than morphospecies-based assessments (fungal conidia morphology). Fungal communities assessed by metabarcoding were spatially structured by leaf area in both streams. Metabarcoding promises greater resolution to assess biodiversity patterns in aquatic fungi and may be more accurate for assessing taxa-area relationships and local to global diversity ratios.This work was supported by the strategic programme UID/BIA/04050/2013 (POCI-01-0145-FEDER-007569), funded by national funds through the Portuguese Foundation for Science and Technology (FCT) I.P. (http://www.fct.pt/) and by the ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalizacao (POCI) and by the project PTDC/AAC-AMB/117068/2010, funded by national funds through FCT I.P. and the European Regional Development Funds through the Operational Competitiveness Program (FEDER-COMPETE). Support from FCT to SD (SFRH/BPD/47574/2008 and SFRH/BPD/109842/2015) and from NSERC Discovery grant program (http://www.nserc-crsng.gc.ca/index_eng.asp) to FB is also acknowledged. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.info:eu-repo/semantics/publishedVersio