Model based Paleozoic atmospheric oxygen estimates: a revisit to GEOCARBSULF

Geological redox proxies increasingly point towards low atmospheric oxygen concentrations during the early Paleozoic Era, with a subsequent protracted rise towards present-day levels. However, these proxies currently only provide qualitative estimates of atmospheric O₂ levels. Global biogeochemical models, in contrast, are commonly employed to generate quantitative estimates for atmospheric O₂ levels through Earth’s history. Estimates for Paleozoic pO₂ generated by GEOCARBSULF, one of the most widely implemented carbon and sulfur cycle models, have historically suggested high atmospheric O₂ levels throughout the Paleozoic, in direct contradiction to competing models. In this study, we evaluate whether GEOCARBSULF can predict relatively low Paleozoic O₂ levels. We first update GEOCARBSULF by adopting the recent compilation of the δ¹³C value of marine buried carbonate and replacing the old formulation of the sulfur isotope fractionation factor with empirical sulfur isotope records. Following this we construct various O₂ evolution scenarios (with low O₂ levels in the early Paleozoic) and examine whether GEOCARBSULF can reproduce these scenarios by varying the weathering/degassing fluxes of carbon and sulfur, or carbonate δ¹³C. We show that GEOCARBSULF can, in fact, maintain low-O₂ (even 1–5% atm) levels through the early Paleozoic by only varying the carbonate δ¹³C within 2 standard deviation (SD) bounds permitted by the geological record. In addition, it can generate a middle–late Paleozoic rise in O₂ concentration, coincident with the diversification of land plants. However, we also argue that tracking atmospheric O₂ levels with GEOCARBSULF is highly dependent on carbonate carbon isotope evolution, and more accurate predictions will come from an improved C isotope record

PubChem3D: Diversity of shape

<p>Abstract</p> <p>Background</p> <p>The shape diversity of 16.4 million biologically relevant molecules from the PubChem Compound database and their 1.46 billion diverse conformers was explored as a function of molecular volume.</p> <p>Results</p> <p>The diversity of shape space was investigated by determining the shape similarity threshold to achieve a maximum on the count of reference shapes per unit of conformer volume. The rate of growth in shape space, as represented by a decreasing shape similarity threshold, was found to be remarkably smooth as a function of volume. There was no apparent correlation between the count of conformers per unit volume and their diversity, meaning that a single reference shape can describe the shape space of many chemical structures. The ability of a volume to describe the shape space of lesser volumes was also examined. It was shown that a given volume was able to describe 40-70% of the shape diversity of lesser volumes, for the majority of the volume range considered in this study.</p> <p>Conclusion</p> <p>The relative growth of shape diversity as a function of volume and shape similarity is surprisingly uniform. Given the distribution of chemicals in PubChem versus what is theoretically synthetically possible, the results from this analysis should be considered a conservative estimate to the true diversity of shape space.</p

PubChem3D: Similar conformers

<p>Abstract</p> <p>Background</p> <p>PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.</p> <p>Results</p> <p>The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST) of 0.8 or greater and a color Tanimoto (CT) of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds") for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs), despite limited PubChem 2-D similarity.</p> <p>In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average count of conformer neighbors per conformer increases rather slowly as a function of diverse conformers considered, with only a 70% increase for a ten times growth in conformers per compound (a 68-fold increase in the conformer pairs considered).</p> <p>Neighboring 3-D conformers on the scale performed, if implemented naively, is an intractable problem using a modest sized compute cluster. Methodology developed in this work relies on a series of filters to prevent performing 3-D superposition optimization, when it can be determined that two conformers cannot possibly be a neighbor. Most filters are based on Tanimoto equation volume constraints, avoiding incompatible conformers; however, others consider preliminary superposition between conformers using reference shapes.</p> <p>Conclusion</p> <p>The "Similar Conformers" 3-D neighboring relationship locates similar small molecules of biological interest that may go unnoticed when using traditional 2-D chemical structure graph-based methods, making it complementary to such methodologies. The computational cost of 3-D similarity methodology on a wide scale, such as PubChem contents, is a considerable issue to overcome. Using a series of efficient filters, an effective throughput rate of more than 150,000 conformers per second per processor core was achieved, more than two orders of magnitude faster than without filtering.</p

PubChem3D: a new resource for scientists

<p>Abstract</p> <p>Background</p> <p>PubChem is an open repository for small molecules and their experimental biological activity. PubChem integrates and provides search, retrieval, visualization, analysis, and programmatic access tools in an effort to maximize the utility of contributed information. There are many diverse chemical structures with similar biological efficacies against targets available in PubChem that are difficult to interrelate using traditional 2-D similarity methods. A new layer called PubChem3D is added to PubChem to assist in this analysis.</p> <p>Description</p> <p>PubChem generates a 3-D conformer model description for 92.3% of all records in the PubChem Compound database (when considering the parent compound of salts). Each of these conformer models is sampled to remove redundancy, guaranteeing a minimum (non-hydrogen atom pair-wise) RMSD between conformers. A diverse conformer ordering gives a maximal description of the conformational diversity of a molecule when only a subset of available conformers is used. A pre-computed search per compound record gives immediate access to a set of 3-D similar compounds (called "Similar Conformers") in PubChem and their respective superpositions. Systematic augmentation of PubChem resources to include a 3-D layer provides users with new capabilities to search, subset, visualize, analyze, and download data.</p> <p>A series of retrospective studies help to demonstrate important connections between chemical structures and their biological function that are not obvious using 2-D similarity but are readily apparent by 3-D similarity.</p> <p>Conclusions</p> <p>The addition of PubChem3D to the existing contents of PubChem is a considerable achievement, given the scope, scale, and the fact that the resource is publicly accessible and free. With the ability to uncover latent structure-activity relationships of chemical structures, while complementing 2-D similarity analysis approaches, PubChem3D represents a new resource for scientists to exploit when exploring the biological annotations in PubChem.</p

Clinical practice: The bleeding child. Part II: Disorders of secondary hemostasis and fibrinolysis

Bleeding complications in children may be caused by disorders of secondary hemostasis or fibrinolysis. Characteristic features in medical history and physical examination, especially of hemophilia, are palpable deep hematomas, bleeding in joints and muscles, and recurrent bleedings. A detailed medical and family history combined with a thorough physical examination is essential to distinguish abnormal from normal bleeding and to decide whether it is necessary to perform diagnostic laboratory evaluation. Initial laboratory tests include prothrombin time and activated partial thromboplastin time. Knowledge of the classical coagulation cascade with its intrinsic, extrinsic, and common pathways, is useful to identify potential defects in the coagulation in order to decide which additional coagulation tests should be performed

Measuring common mental disorders in women in Ethiopia: Reliability and construct validity of the comprehensive psychopathological rating scale

BACKGROUND: There is a dearth of methodological studies critically evaluating reliability, validity and feasibility of measures of common mental disorders (CMD) in low-income countries.METHODS: Test-retest and inter-rater reliability of categorisation of CMD caseness, according to locally agreed criteria using the Comprehensive Psychopathological Rating Scale (CPRS), was measured in 99 women from out-patient clinics (inter-rater) and 99 women from a primary healthcare centre (test-retest) in Ethiopia. The construct validity of CMD as measured with CPRS was assessed with exploratory factor analysis using maximum likelihood with varimax rotation.RESULTS: Test-retest reliability was fair (kappa = 0.29). Subsequent assessment of inter-rater reliability found excellent agreement (kappa = 0.82). The construct of CMD appeared unidimensional, combining depressive, anxiety and somatic symptoms.CONCLUSIONS: Detection of socioculturally meaningful cases of CMD in Ethiopia can be reliably achieved with local psychiatrist assessment using CPRS, although thorough training is essential

Depressive symptoms and suicide in 56,000 older Chinese: a Hong Kong cohort study

Objective: To examine dose-response associations between depressive symptoms and suicide and modification effects of sex, age and health status in older Chinese. Methods: We used the Chinese version of the 15-item Geriatric Depression Scale (GDS) to measure depressive symptoms (GDS score ≥ 8) and Cox regression to examine association with suicide mortality in a population-based cohort of 55,946 individuals, aged 65 years or above, enrolled from July 1998 to December 2000 at one of 18 Elderly Health Centres of Hong Kong Department of Health. The cohort was followed up for suicide mortality till 31 March 2009 (mean follow-up 8.7 years). Results: Depressive symptoms were associated with suicide in men [hazard ratio (HR) 2.03, 95% confidence interval (CI) 0.96-4.29] and women (HR = 2.36, 95% CI 1.31-4.24) after adjusting for age, education, monthly expenditure, smoking, alcohol drinking, physical activity, body mass index, health status, and self-rated health. There was no threshold for GDS score and suicide in either sex. Age, sex and health status did not modify the association. Conclusions: Depressive symptoms predict higher suicide risk in older Chinese in a dose-response pattern. These associations were not attenuated by adjustment for health status, suggesting that depressive symptoms in older people are likely to be an independent causal factor for suicide. The GDS score showed no threshold in predicting suicide risk, suggesting that older people with low GDS scores deserve further attention and those with very high scores need urgent intervention. © 2011 The Author(s).published_or_final_versionSpringer Open Choice, 21 Feb 201