Mineralogy, early marine diagenesis, and the chemistry of shallow-water carbonate sediments

Shallow-water carbonate sediments constitute the bulk of sedimentary carbonates in the geologic record and are widely used archives of Earth’s chemical and climatic history. One of the main limitations in interpreting the geochemistry of ancient carbonate sediments is the potential for post-depositional diagenetic alteration. In this study, we use paired measurements of calcium (44Ca/40Ca or δ44Ca) and magnesium (26Mg/24Mg or δ26Mg) isotope ratios in sedimentary carbonates and associated pore-fluids as a tool to understand the mineralogical and diagenetic history of Neogene shallow-water carbonate sediments from the Bahamas and southwest Australia. We find that the Ca and Mg isotopic composition of bulk carbonate sediments at these sites exhibits systematic stratigraphic variability that is related to both mineralogy and early marine diagenesis. The observed variability in bulk sediment Ca isotopes is best explained by changes in the extent and style of early marine diagenesis from one where the composition of the diagenetic carbonate mineral is determined by the chemistry of the fluid (fluid-buffered) to one where the composition of the diagenetic carbonate mineral is determined by the chemistry of the precursor sediment (sediment-buffered). Our results indicate that this process, together with variations in carbonate mineralogy (aragonite, calcite, and dolomite), plays a fundamental and underappreciated role in determining the regional and global stratigraphic expressions of geochemical tracers (δ13C, δ18O, major, minor, and trace elements) in shallow-water carbonate sediments in the geologic record. Our results also provide evidence that a large shallow-water carbonate sink that is enriched in 44Ca can explain the mismatch between the δ44/40Ca value of rivers and deep-sea carbonate sediments and call into question the hypothesis that the δ44/40Ca value of seawater depends on the mineralogy of primary carbonate precipitations (e.g. ‘aragonite seas’ and ‘calcite seas’). Finally, our results for sedimentary dolomites suggest that paired measurements of Ca and Mg isotopes may provide a unique geochemical fingerprint of mass transfer during dolomitization to better understand the paleo-environmental information preserved in these enigmatic but widespread carbonate minerals

Comparison of generalized estimating equations and quadratic inference functions using data from the National Longitudinal Survey of Children and Youth (NLSCY) database

<p>Abstract</p> <p>Background</p> <p>The generalized estimating equations (GEE) technique is often used in longitudinal data modeling, where investigators are interested in population-averaged effects of covariates on responses of interest. GEE involves specifying a model relating covariates to outcomes and a plausible correlation structure between responses at different time periods. While GEE parameter estimates are consistent irrespective of the true underlying correlation structure, the method has some limitations that include challenges with model selection due to lack of absolute goodness-of-fit tests to aid comparisons among several plausible models. The quadratic inference functions (QIF) method extends the capabilities of GEE, while also addressing some GEE limitations.</p> <p>Methods</p> <p>We conducted a comparative study between GEE and QIF via an illustrative example, using data from the "National Longitudinal Survey of Children and Youth (NLSCY)" database. The NLSCY dataset consists of long-term, population based survey data collected since 1994, and is designed to evaluate the determinants of developmental outcomes in Canadian children. We modeled the relationship between hyperactivity-inattention and gender, age, family functioning, maternal depression symptoms, household income adequacy, maternal immigration status and maternal educational level using GEE and QIF. Basis for comparison include: (1) ease of model selection; (2) sensitivity of results to different working correlation matrices; and (3) efficiency of parameter estimates.</p> <p>Results</p> <p>The sample included 795, 858 respondents (50.3% male; 12% immigrant; 6% from dysfunctional families). QIF analysis reveals that gender (male) (odds ratio [OR] = 1.73; 95% confidence interval [CI] = 1.10 to 2.71), family dysfunctional (OR = 2.84, 95% CI of 1.58 to 5.11), and maternal depression (OR = 2.49, 95% CI of 1.60 to 2.60) are significantly associated with higher odds of hyperactivity-inattention. The results remained robust under GEE modeling. Model selection was facilitated in QIF using a goodness-of-fit statistic. Overall, estimates from QIF were more efficient than those from GEE using AR (1) and Exchangeable working correlation matrices (Relative efficiency = 1.1117; 1.3082 respectively).</p> <p>Conclusion</p> <p>QIF is useful for model selection and provides more efficient parameter estimates than GEE. QIF can help investigators obtain more reliable results when used in conjunction with GEE.</p

Utilisation of an operative difficulty grading scale for laparoscopic cholecystectomy

Background A reliable system for grading operative difficulty of laparoscopic cholecystectomy would standardise description of findings and reporting of outcomes. The aim of this study was to validate a difficulty grading system (Nassar scale), testing its applicability and consistency in two large prospective datasets. Methods Patient and disease-related variables and 30-day outcomes were identified in two prospective cholecystectomy databases: the multi-centre prospective cohort of 8820 patients from the recent CholeS Study and the single-surgeon series containing 4089 patients. Operative data and patient outcomes were correlated with Nassar operative difficultly scale, using Kendall’s tau for dichotomous variables, or Jonckheere–Terpstra tests for continuous variables. A ROC curve analysis was performed, to quantify the predictive accuracy of the scale for each outcome, with continuous outcomes dichotomised, prior to analysis. Results A higher operative difficulty grade was consistently associated with worse outcomes for the patients in both the reference and CholeS cohorts. The median length of stay increased from 0 to 4 days, and the 30-day complication rate from 7.6 to 24.4% as the difficulty grade increased from 1 to 4/5 (both p < 0.001). In the CholeS cohort, a higher difficulty grade was found to be most strongly associated with conversion to open and 30-day mortality (AUROC = 0.903, 0.822, respectively). On multivariable analysis, the Nassar operative difficultly scale was found to be a significant independent predictor of operative duration, conversion to open surgery, 30-day complications and 30-day reintervention (all p < 0.001). Conclusion We have shown that an operative difficulty scale can standardise the description of operative findings by multiple grades of surgeons to facilitate audit, training assessment and research. It provides a tool for reporting operative findings, disease severity and technical difficulty and can be utilised in future research to reliably compare outcomes according to case mix and intra-operative difficulty

Pantomime (Not Silent Gesture) in Multimodal Communication: Evidence From Children’s Narratives

Pantomime has long been considered distinct from co-speech gesture. It has therefore been argued that pantomime cannot be part of gesture-speech integration. We examine pantomime as distinct from silent gesture, focusing on non-co-speech gestures that occur in the midst of children’s spoken narratives. We propose that gestures with features of pantomime are an infrequent but meaningful component of a multimodal communicative strategy. We examined spontaneous non-co-speech representational gesture production in the narratives of 30 monolingual English-speaking children between the ages of 8- and 11-years. We compared the use of co-speech and non-co-speech gestures in both autobiographical and fictional narratives and examined viewpoint and the use of non-manual articulators, as well as the length of responses and narrative quality. The use of non-co-speech gestures was associated with longer narratives of equal or higher quality than those using only co-speech gestures. Non-co-speech gestures were most likely to adopt character-viewpoint and use non-manual articulators. The present study supports a deeper understanding of the term pantomime and its multimodal use by children in the integration of speech and gesture

Health Aspects of the Pre-Departure Phase of Migration

In the second article in a six-part PLoS Medicine series on Migration & Health, Brian Gushulak and Douglas MacPherson discuss the pre-departure phase of migration and the specific health risks and policy needs associated with this phase

Computational Comparative Study of Tuberculosis Proteomes Using a Model Learned from Signal Peptide Structures

Secretome analysis is important in pathogen studies. A fundamental and convenient way to identify secreted proteins is to first predict signal peptides, which are essential for protein secretion. However, signal peptides are highly complex functional sequences that are easily confused with transmembrane domains. Such confusion would obviously affect the discovery of secreted proteins. Transmembrane proteins are important drug targets, but very few transmembrane protein structures have been determined experimentally; hence, prediction of the structures is essential. In the field of structure prediction, researchers do not make assumptions about organisms, so there is a need for a general signal peptide predictor

Genetic Basis of Virulence Attenuation Revealed by Comparative Genomic Analysis of Mycobacterium tuberculosis Strain H37Ra versus H37Rv

Tuberculosis, caused by Mycobacterium tuberculosis, remains a leading infectious disease despite the availability of chemotherapy and BCG vaccine. The commonly used avirulent M. tuberculosis strain H37Ra was derived from virulent strain H37 in 1935 but the basis of virulence attenuation has remained obscure despite numerous studies. We determined the complete genomic sequence of H37Ra ATCC25177 and compared that with its virulent counterpart H37Rv and a clinical isolate CDC1551. The H37Ra genome is highly similar to that of H37Rv with respect to gene content and order but is 8,445 bp larger as a result of 53 insertions and 21 deletions in H37Ra relative to H37Rv. Variations in repetitive sequences such as IS6110 and PE/PPE/PE-PGRS family genes are responsible for most of the gross genetic changes. A total of 198 single nucleotide variations (SNVs) that are different between H37Ra and H37Rv were identified, yet 119 of them are identical between H37Ra and CDC1551 and 3 are due to H37Rv strain variation, leaving only 76 H37Ra-specific SNVs that affect only 32 genes. The biological impact of missense mutations in protein coding sequences was analyzed in silico while nucleotide variations in potential promoter regions of several important genes were verified by quantitative RT-PCR. Mutations affecting transcription factors and/or global metabolic regulations related to in vitro survival under aging stress, and mutations affecting cell envelope, primary metabolism, in vivo growth as well as variations in the PE/PPE/PE-PGRS family genes, may underlie the basis of virulence attenuation. These findings have implications not only for improved understanding of pathogenesis of M. tuberculosis but also for development of new vaccines and new therapeutic agents