Deciphering tectonic controls on fluvial sedimentation within the Barmer Basin, India: The lower cretaceous Ghaggar-Hakra formation

The Cretaceous of NW India is poorly known from sparse outcrops in Rajasthan and Gujarat. Here, we describe the stratigraphy and sedimentology of outcrops of the Ghaggar-Hakra Formation of probable Lower Cretaceous age from the Sarnoo Hills, eastern Barmer Basin, Rajasthan and correlate them with equivalent sediments in core from the subsurface of the Barmer Basin. At outcrop the Ghaggar-Hakra Formation contains three fluvial sandstone sequences of varying depositional type and geometry interbedded with associated floodplain deposits. At the base of the exposure the Darjaniyon-ki Dhani Sandstone is composed of compositionally mature, granule-grade quartzitic conglomerates that form braid bars. The deposits represent a poorly-developed braided system. Subsequently, the Sarnoo Sandstone constitutes medium- to very coarse-grained, cross-bedded sandstones, that fine upwards into fine-grained rippled and laminated sandstones, forming in-channel bars and point bars, implying the development of a meandering system. Lastly, capping the exposed sequence, the Nosar Member is composed of very coarse- to medium-grained, planar and trough cross-bedded quartz-arenites. These deposits represent in-channel dunes that display evidence of braiding, indicating the establishment of a well-developed braided system. The intervening mudrocks are characteristic of floodplain deposits, which are mottled, with vertical fractures, soil slickenlines and a pedogenic nature.Within the core the sequence differs from outcrop as there are two separate environments a braided system with associated floodplain deposits and a lacustrine system. The braided river comprises of very coarse- to fine-grained cross-bedded and rippled sandstones. The associated floodplain deposits are mottled, rooted, fractured and have rizoliths within. The detrital composition of the braidplain sandstones does not vary greatly from the outcrop as the minerals are quartz, lithics, heavy minerals and clays. However, the authigenic minerals do vary, as in the subsurface we see kaolinite clays, quartz overgrowths, siderite, pyrite and chlorite cements, whereas at the surface there are quartz overgrowths, calcite, dolomite and haematite cements with kaolinite clays. It is likely that the braided river in core is the same sequence as seen at outcrop. We interpret the successions here into a single fluvial system that has been affected by regional tectonics from the separation of Madagascar (Aptian) from the Indian continent and the continent drifting northwards. This heavily influenced the localised tectonics, which alludes to why there is a significant change in fluvial style from the Sarnoo Sandstone (meandering) to the Nosar Member (braided)

Nanoporous aluminosilicate-catalyzed telescoped acetalization-direct aldol reactions of acetals with 1,3-dicarbonyl compounds

Nanoporous aluminosilicate materials, synthesized by an evaporation-induced self-assembly process, catalyze the direct aldol reaction of acyclic acetals with a range of 1,3-dicarbonyl compounds to produce the corresponding aldol addition products in high yield, rather than the expected Knoevenagel elimination products. By carrying out the reaction in the presence of either dimethoxy propane or the corresponding orthoester, it is possible to capitalize on the ability of these aluminosilicate materials to catalyze the corresponding acetalization reaction leading to the development of novel telescoped, acetalization-direct aldol addition reaction protocols

Preparation of Biomass-Derived Furfuryl Acetals by Transacetalization Reactions Catalyzed by Nanoporous Aluminosilicates

Nanoporous aluminosilicate materials efficiently catalyze the formation of furaldehyde dimethyl acetal directly from methanol in high yields and in short reaction times. The facile nature of this reaction has led to the development of a telescoped protocol in which the acyclic acetal is produced in situ and subsequently functions as a substrate for a transacetalization reaction with glycerol to produce the corresponding dioxane and dioxolane products, which are potentially useful biofuel additives. These products are generated in high yield without the requirement for high reaction temperatures of prolonged reaction times, and the aluminosilicate catalysts are operationally simple to produce, are effective with either purified furaldehyde or crude furaldehyde, and are fully recyclable

CdCl2 treatment related diffusion phenomena in Cd1xZnxS/CdTe solar cells

Utilisation of wide bandgap Cd1_xZnxS alloys as an alternative to the CdS window layer is an attractive route to enhance the performance of CdTe thin film solar cells. For successful implementation, however, it is vital to control the composition and properties of Cd1_xZnxS through device fabrication processes involving the relatively high-temperature CdTe deposition and CdCl2 activation steps. In this study, cross-sectional scanning transmission electron microscopy and depth profiling methods were employed to investigate chemical and structural changes in CdTe/Cd1_xZnxS/CdS superstrate device structures deposited on an ITO/boro-aluminosilicate substrate. Comparison of three devices in different states of completion—fully processed (CdCl2 activated), annealed only (without CdCl2 activation), and a control (without CdCl2 activation or anneal)—revealed cation diffusion phenomena within the window layer, their effects closely coupled to the CdCl2 treatment. As a result, the initial Cd1_xZnxS/CdS bilayer structure was observed to unify into a single Cd1_xZnxS layer with an increased Cd/Zn atomic ratio; these changes defining the properties and performance of the Cd1_xZnxS/CdTe device

Classification Performance of Neural Networks Versus Logistic Regression Models: Evidence From Healthcare Practice

Machine learning encompasses statistical approaches such as logistic regression (LR) through to more computationally complex models such as neural networks (NN). The aim of this study is to review current published evidence for performance from studies directly comparing logistic regression, and neural network classification approaches in medicine. A literature review was carried out to identify primary research studies which provided information regarding comparative area under the curve (AUC) values for the overall performance of both LR and NN for a defined clinical healthcare-related problem. Following an initial search, articles were reviewed to remove those that did not meet the criteria and performance metrics were extracted from the included articles. Teh initial search revealed 114 articles; 21 studies were included in the study. In 13/21 (62%) of cases, NN had a greater AUC compared to LR, but in most the difference was small and unlikely to be of clinical significance; (unweighted mean difference in AUC 0.03 (95% CI 0-0.06) in favour of NN versus LR. In the majority of cases examined across a range of clinical settings, LR models provide reasonable performance that is only marginally improved using more complex methods such as NN. In many circumstances, the use of a relatively simple LR model is likely to be adequate for real-world needs but in specific circumstances in which large amounts of data are available, and where even small increases in performance would provide significant management value, the application of advanced analytic tools such as NNs may be indicated

METRIC-EF: magnetic resonance enterography to predict disabling disease in newly diagnosed Crohn's disease-protocol for a multicentre, non-randomised, single-arm, prospective study

INTRODUCTION: Crohn's disease (CD) is characterised by discontinuous, relapsing enteric inflammation. Instituting advanced therapies at an early stage to suppress inflammation aims to prevent future complications such as stricturing or penetrating disease, and subsequent surgical resection. Therapeutics are effective but associated with certain side-effects and relatively expensive. There is therefore an urgent need for robust methods to predict which newly diagnosed patients will develop disabling disease, to identify patients who are most likely to benefit from early, advanced therapies. We aim to determine if magnetic resonance enterography (MRE) features at diagnosis improve prediction of disabling CD within 5 years of diagnosis. METHODS AND ANALYSIS: We describe the protocol for a multicentre, non-randomised, single-arm, prospective study of adult patients with newly diagnosed CD. We will use patients already recruited to the METRIC study and extend their clinical follow-up, as well as a separate group of newly diagnosed patients who were not part of the METRIC trial (MRE within 3 months of diagnosis), to ensure an adequate sample size. Follow-up will extend for at least 4 years. The primary outcome is to evaluate the comparative predictive ability of prognostic models incorporating MRE severity scores (Magnetic resonance Enterography Global Score (MEGS), simplified MAgnetic Resonance Index of Activity (sMaRIA) and Lémann Index) versus models using standard characteristics alone to predict disabling CD (modified Beaugerie definition) within 5 years of new diagnosis. ETHICS AND DISSEMINATION: This study protocol achieved National Health Service Research Ethics Committee (NHS REC), London-Hampstead Research Ethics Committee approval (IRAS 217422). Our findings will be disseminated via conference presentations and peer-reviewed publications. TRIAL REGISTRATION NUMBER: ISRCTN76899103

Nanoporous aluminosilicate catalyzed Friedel–Crafts alkylation reactions of indoles with aldehydes and acetals

Nanoporous aluminosilicate materials efficiently catalyze Friedel-Crafts reactions of indoles to produce bisindolylalkane products. These reactions proceed rapidly and in high yields when acetals are used in place of the more commonly used carbonyl reagents. It is possible to capitalise on the large difference in the rates of reaction observed with aldehydes and acetals to develop a tandem acetalization-Friedel-Crafts protocol in which the acetal is generated in situ and undergoes subsequent reaction. © 2011 The Royal Society of Chemistry

Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: The Tasmanian devil (Sarcophilus harrisii) is currently under threat of extinction due to an unusual fatal contagious cancer called Devil Facial Tumour Disease (DFTD). DFTD is caused by a clonal tumour cell line that is transmitted between unrelated individuals as an allograft without triggering immune rejection due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils. RESULTS: Here we report the characterization of the genomic regions encompassing MHC Class I and Class II genes in the Tasmanian devil. Four genomic regions approximately 960 kb in length were assembled and annotated using BAC contigs and physically mapped to devil Chromosome 4q. 34 genes and pseudogenes were identified, including five Class I and four Class II loci. Interestingly, when two haplotypes from two individuals were compared, three genomic copy number variants with sizes ranging from 1.6 to 17 kb were observed within the classical Class I gene region. One deletion is particularly important as it turns a Class Ia gene into a pseudogene in one of the haplotypes. This deletion explains the previously observed variation in the Class I allelic number between individuals. The frequency of this deletion is highest in the northwestern devil population and lowest in southeastern areas. CONCLUSIONS: The third sequenced marsupial MHC provides insights into the evolution of this dynamic genomic region among the diverse marsupial species. The two sequenced devil MHC haplotypes revealed three copy number variations that are likely to significantly affect immune response and suggest that future work should focus on the role of copy number variations in disease susceptibility in this species

Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC

BACKGROUND The Tasmanian devil (Sarcophilus harrisii) is currently under threat of extinction due to an unusual fatal contagious cancer called Devil Facial Tumour Disease (DFTD). DFTD is caused by a clonal tumour cell line that is transmitted between unrelated individuals as an allograft without triggering immune rejection due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils. RESULTS Here we report the characterization of the genomic regions encompassing MHC Class I and Class II genes in the Tasmanian devil. Four genomic regions approximately 960 kb in length were assembled and annotated using BAC contigs and physically mapped to devil Chromosome 4q. 34 genes and pseudogenes were identified, including five Class I and four Class II loci. Interestingly, when two haplotypes from two individuals were compared, three genomic copy number variants with sizes ranging from 1.6 to 17 kb were observed within the classical Class I gene region. One deletion is particularly important as it turns a Class Ia gene into a pseudogene in one of the haplotypes. This deletion explains the previously observed variation in the Class I allelic number between individuals. The frequency of this deletion is highest in the northwestern devil population and lowest in southeastern areas. CONCLUSIONS The third sequenced marsupial MHC provides insights into the evolution of this dynamic genomic region among the diverse marsupial species. The two sequenced devil MHC haplotypes revealed three copy number variations that are likely to significantly affect immune response and suggest that future work should focus on the role of copy number variations in disease susceptibility in this species.This work was funded by an ARC Future Fellowship to KB (FT0992212), the Eric Guiler fund and the Tasmanian Department of Primary Industries, Parks, Water and the Environment. YC was supported by an Endeavour International Postgraduate Research Scholarship, KM by an Australian Postgraduate Award and an ARC Linkage Grant

Dehydrative etherification reactions of glycerol with alcohols catalyzed by recyclable nanoporous aluminosilicates: telescoped routes to glyceryl ethers

Catalytic strategies for the efficient transformation of abundant sustainable bioderived molecules, such as glycerol, into higher value more useful products is an important research goal. In this study, we demonstrate that atom efficient dehydrative etherification reactions of glycerol with activated alcohols are effectively catalyzed by nanoporous aluminosilicate materials in dimethylcarbonate (DMC) to produce the corresponding 1-substituted glyceryl ethers in high yield. By carrying out the reaction in acetone, it is possible to capitalize on the ability of these materials to catalyze the corresponding acetalization reaction, allowing for the development of novel, telescoped acetalization-dehydrative etherification reaction sequences to selectively produce protected solketal derivatives. These materials also catalyze the telescoped reaction of glycerol with <i>tert</i>-butanol (TBA) in acetone to produce the corresponding solketal mono <i>tert</i>-butyl ether product in high yield, providing a potential route to convert glycerol directly into a useful and sustainable fuel additive