Whole-genome methylation analysis of benign and malignant colorectal tumours

Changes in DNA methylation, whether hypo- or hypermethylation, have been shown to be associated with the progression of colorectal cancer. Methylation changes substantially in the progression from normal mucosa to adenoma and to carcinoma. This phenomenon has not been studied extensively and studies have been restricted to individual CpG islands, rather than taking a whole-genome approach. We aimed to study genome-wide methylation changes in colorectal cancer. We obtained 10 fresh-frozen normal tissue-cancer sample pairs, and five fresh-frozen adenoma samples. These were run on the lllumina HumanMethylation27 whole-genome methylation analysis system. Differential methylation between normal tissue, adenoma and carcinoma was analysed using Bayesian regression modelling, gene set enrichment analysis (GSEA) and hierarchical clustering (HC). The highest-rated individual gene for differential methylation in carcinomas versus normal tissue and adenomas versus normal tissue was GRASP (padjusted  = 1.59 × 10(-5) , BF = 12.62, padjusted  = 1.68 × 10(-6) , BF = 14.53). The highest-rated gene when comparing carcinomas versus adenomas was ATM (padjusted  = 2.0 × 10(-4) , BF = 10.17). Hierarchical clustering demonstrated poor clustering by the CIMP criteria for methylation. GSEA demonstrated methylation changes in the Netrin-DCC and SLIT-ROBO pathways. Widespread changes in DNA methylation are seen in the transition from adenoma to carcinoma. The finding that GRASP, which encodes the general receptor for phosphoinositide 1-associated scaffold protein, was differentially methylated in colorectal cancer is interesting. This may be a potential biomarker for colorectal cancer

Benzobisoxazole cruciforms: a tunable, cross-conjugated platform for the generation of deep blue OLED materials

Four new cross-conjugated small molecules based on a central benzo[1,2-d:4,5-d′]bisoxazole moiety possessing semi-independently tunable HOMO and LUMO levels were synthesized and the properties of these materials were evaluated experimentally and theoretically. The molecules were thermally stable with 5% weight loss occurring well above 350 °C. The cruciforms all exhibited blue emission in solution ranging from 433–450 nm. Host–guest OLEDs fabricated from various concentrations of these materials using the small molecule host 4,4′-bis(9-carbazolyl)-biphenyl (CBP) exhibited deep blue-emission with Commission Internationale de L'Eclairage (CIE) coordinates of (0.15 ≤ x ≤ 0.17, 0.05 ≤ y ≤ 0.11), and maximum luminance efficiencies as high as ∼2 cd A−1. These results demonstrate the potential of benzobisoxazole cruciforms as emitters for developing high-performance deep blue OLEDs.We would like to thank Dr Sarah Cady, Dr Kamel Harrata and Mr Steven Veysey of Iowa State University (ISU) Chemical Instrumentation Facility for compound analysis. We thank Eeshita Manna for technical assistance. We also thank the National Science Foundation (CHE-1413173) for financial support of this work. RK and JS were partially supported by Basic Energy Sciences, Division of Materials Science and Engineering, USDOE. Ames Laboratory is operated by Iowa State University for the US Department of Energy (USDOE) under Contract No. DE-AC 02-07CH11358. Computational resources were provided in part by the MERCURY consortium (http://mercuryconsortium.org/) under NSF grants CHE-0116435, CHE-0521063, CHE-0849677, and CHE-1229354. (CHE-1413173 - National Science Foundation; Basic Energy Sciences, Division of Materials Science and Engineering, USDOE; DE-AC 02-07CH11358 - Iowa State University for the US Department of Energy (USDOE); CHE-0116435 - MERCURY consortium under NSF; CHE-0521063 - MERCURY consortium under NSF; CHE-0849677 - MERCURY consortium under NSF; CHE-1229354 - MERCURY consortium under NSF)http://pubs.rsc.org/en/Content/ArticleLanding/2016/TC/C5TC03622D#!divAbstractPublished versio

The Late Quaternary tephrostratigraphy of annually laminated sediments from Meerfelder Maar, Germany

© 2015 Elsevier Ltd.The record of Late Quaternary environmental change within the sediments of Meerfelder Maar in the Eifel region of Germany is renowned for its high precision chronology, which is annually laminated throughout the Last Glacial to Interglacial transition (LGIT) and most of the Holocene. Two visible tephra layers are prominent within the floating varve chronology of Meerfelder Maar. An Early Holocene tephra layer, the Ulmener Maar Tephra (~11,000 varve years BP), provides a tie-line of the Meerfelder Maar record to the varved Holocene record of nearby Lake Holzmaar. The Laacher See Tephra provides another prominent time marker for the late Allerød, ~200 varve years before the transition into the Younger Dryas at 12,680 varve years BP. Further investigation has now shown that there are also 15 cryptotephra layers within the Meerfelder Maar LGIT-Holocene stratigraphy and these layers hold the potential to make direct comparisons between the Meerfelder Maar record and other palaeoenvironmental archives from across Europe and the North Atlantic. Most notable is the presence of the Vedde Ash, the most widespread Icelandic eruption known from the Late Quaternary, which occurred midway through the Younger Dryas. The Vedde Ash has also been found in the Greenland ice cores and can be used as an isochron around which the GICC05 and Meerfelder Maar annual chronologies can be compared. Near the base of the annual laminations in Meerfelder Maar a cryptotephra is found that correlates to the Neapolitan Yellow Tuff, erupted from Campi Flegrei in southern Italy, 1200km away. This is the furthest north that the Neapolitan Yellow Tuff has been found, highlighting its importance in the construction of a European-wide tephrostratigraphic framework. The co-location of cryptotephra layers from Italian, Icelandic and Eifel volcanic sources, within such a precise chronological record, makes Meerfelder Maar one of the most important tephrostratotype records for continental Europe during the Last Glacial to Interglacial transition

The hybrid plant concept: Combining direct and indirect coal liquefaction processes

The objective of this study is to assess the technical and economic impacts of siting direct two-stage coal liquefaction and indirect liquefaction, using slurry Fischer-Tropsch (F-T) reactors, at the same location. The incentives for this co-siting include the sharing of the large number of common unit process operations and the potential blending of the very different, but complementary, products from the two processes, thereby reducing the refining required to produce specification transportation fuels. Both direct and indirect coal liquefaction share a large number of unit operations. This paper reports on the results of a study that attempts to quantify the extent of these potential synergisms by estimating the costs of transportation fuels produced by direct liquefaction, indirect liquefaction, and by combined direct and indirect hybrid plant configuration under comparable conditions. The technical approach used was to combine the MITRE computer simulated coal liquefaction models for the direct and indirect systems into one integrated model. An analysis of refining and blending of the raw product streams to produce specification diesel and gasoline fuels was included in the direct, indirect and hybrid models so that comparable product slates could be developed. 8 refs., 8 figs., 2 tabs

Clarifying the distal to proximal tephrochronology of the Millennium (B–Tm) eruption, Changbaishan Volcano, northeast China

Tephra dispersed during the Millennium eruption (ME), Changbaishan Volcano, NE China provides one of the key stratigraphic links between Asia and Greenland for the synchronization of palaeoenvironmental records. However, controversy surrounds proximal-distal tephra correlations because (a) the proposed proximal correlatives of the distal ME tephra (i.e. B-Tm) lack an unequivocal chronostratigraphic context, and (b) the ME tephra deposits have not been chemically characterized for a full spectrum of element using grain-specific techniques. Here we present grain-specific glass chemistry, including for the first time, single grain trace element data, for a composite proximal sequence and a distal tephra from Lake Kushu, northern Japan (ca. 1100 km away from Changbaishan). We demonstrate a robust proximal-distal correlation and that the Kushu tephra is chemically associated with the ME/B-Tm. We propose that three of the proximal pyroclastic fall units were erupted as part of the ME. The radiocarbon chronology of the Kushu sedimentary record has been utilised to generate a Bayesian age-depth model, providing an age for the Kushu tephra which is consistent with high resolution ages determined for the eruption and therefore supports our geochemical correlation. Two further Bayesian age-depth models were independently constructed each incorporating one of two ice-core derived ages for the B-Tm tephra, providing Bayesian modelled ages of 933-949 and 944-947 cal AD (95.4%) for the Kushu tephra. The high resolution ice-core tephra ages imported into the deposition models help test and ultimately constrain the radiocarbon chronology in this interval of the Lake Kushu sedimentary record. The observed geochemical diversity between proximal and distal ME tephra deposits clearly evidences the interaction of two compositionally distinct magma batches during this caldera forming eruption

Satellite Retrievals of Karenia brevis Harmful Algal Blooms in the West Florida Shelf Using Neural Networks and Comparisons with Other Techniques

We describe the application of a Neural Network (NN) previously developed by us, to the detection and tracking, of Karenia brevis Harmful Algal Blooms (KB HABs) that plague the coasts of the West Florida Shelf (WFS) using Visible Infrared Imaging Radiometer Suite (VIIRS) satellite observations. Previous approaches for the detection of KB HABs in the WFS primarily used observations from the Moderate Resolution Imaging Spectroradiometer Aqua (MODIS-A) satellite. They depended on the remote sensing reflectance signal at the 678 nm chlorophyll fluorescence band (Rrs678) needed for both the normalized fluorescence height (nFLH) and Red Band Difference algorithms (RBD) currently used. VIIRS which has replaced MODIS-A, unfortunately does not have a 678 nm fluorescence channel so we customized the NN approach to retrieve phytoplankton absorption at 443 nm (aph443) using only Rrs measurements from existing VIIRS channels at 486, 551 and 671 nm. The aph443 values in these retrieved VIIRS images, can in turn be correlated to chlorophyll-a concentrations [Chla] and KB cell counts. To retrieve KB values, the VIIRS NN retrieved aph443 images are filtered by applying limiting constraints, defined by (i) low backscatter at Rrs 551 nm and (ii) a minimum aph443 value known to be associated with KB HABs in the WFS. The resulting filtered residual images, are then used to delineate and quantify the existing KB HABs. Comparisons with KB HABs satellite retrievals obtained using other techniques, including nFLH, as well as with in situ measurements reported over a four year period, confirm the viability of the NN technique, when combined with the filtering constraints devised, for effective detection of KB HABs

Spatial distribution of heavy metals in the middle nile delta of Egypt

Heavy metal contamination in the El-Gharbia Governorate (District) of Egypt was identified by using remote sensing, Geographical Information Systems (GIS), and X-ray fluorescence (XRF) spectrometry as the main research tools. Digital Elevation Model (DEM), Landsat 8 and contour map images were used to map the landforms. Different physiographic units in the study area are represented by nine soil profiles. X-ray fluorescence spectrometry (XRF) was used for geochemical analysis of 33 soil samples. Vanadium (V), nickel (Ni), chromium (Cr), copper (Cu) and zinc (Zn) concentrations were measured and they all exceeded the average global concentrations identified by Wedepohl (1995). Ni and Cr concentrations exceeded recommended values in all soil profile horizons (Canadian Soil Quality Guidelines, 2007), while Cu had a variable distribution. Zn concentrations are under recommended concentration limits in most soil samples. Contamination Factor, Pollution Load Index and Degree of Contamination indices were used to assess the environmental risks of heavy metal contamination from the soils. All analysed metals pose some potential hazard and pollution levels were particularly high near industrial and urban areas.Open Access funded by International Research and Training Center on Erosion and Sedimentation and China Water and Power Pres

Evaluating the impact of fluorination on the electro-optical properties of cross-conjugated benzobisoxazoles

Published as part of The Journal of Physical Chemistry virtual special issue “William M. Jackson Festschrift”.Six 2,4,6,8-tetrarylbenzo[1,2-d:4,5-d′]bisoxazoles (BBOs) were synthesized: three bearing phenyl substituents at the 2- and 6-positions and three bearing perfluorophenyl groups at those positions. The influence of perfluoro-aryl group substitution on the physical, optical, and electronic properties of 2,4,6,8-tetrarylbenzo[1,2-d:4,5-d′]bisoxazoles (BBO) was evaluated using both experimental and theoretical methods. The density functional theory (DFT) model was found to be well-matched to the experimental optical data, as evidenced by the UV–vis spectra. Both cyclic voltammetry (CV) and ultraviolet photoelectron spectroscopy (UPS) were used to determine the position of the HOMO with varying results. The values obtained by CV were deeper than those obtained via UPS and correlated well with the theoretical calculations. However, the UPS values were more consistent with the expected outcomes for a system with segregated frontier molecular orbitals (FMOs). The UPS results are also supported by the electrostatic potential maps, which indicate that the electron density within the LUMO and HOMO is nearly completely localized along the 2,6- or 4,8-axis, respectively. The summation of the results indicates that strongly electron-withdrawing groups can be used to selectively tune the LUMO level with minor perturbation of the HOMO, something that is challenging to accomplish in typical donor–acceptor systems.We thank Dr. Norman Lee, Stephon Betts, and Dr. Paul Ralifo from the Chemical Instrumentation Facility at Boston University for compound analysis. We also thank Margaret Chern from the Dennis Lab at Boston University for assistance in obtaining fluorescence lifetimes and quantum yields. Next, we thank Volodimyr Duzhko at the Center for Electronic Materials and Devices at the University of Massachusetts-Amherst. We also thank the National Science Foundation (CHE-141373, CHE-1640298, and CHE-1413207) as well a supercomputer allocation by the Extreme Science and Engineering Discovery Environment (XSEDE) for the Comet supercomputer cluster provided by the San Diego Supercomputing Center (DMR-160146) for supporting this work. (CHE-141373 - National Science Foundation; CHE-1640298 - National Science Foundation; CHE-1413207 - National Science Foundation)Accepted manuscrip

Setting Priorities in Child Health Research Investments for South Africa

Nearly 100,000 children under 5 years die annually in South Africa. This paper defines health research priorities to address this unacceptably high mortality rate

Synthesis, characterization and photovoltaic properties of poly(thiophenevinylene-alt-benzobisoxazole)swz

Herein we report the synthesis of two solution processible, conjugated polymers containing the benzobisoxazole moiety. The polymers were characterized using 1 H NMR, UV-Vis and fluorescence spectroscopy. Thermal gravimetric analysis shows that the polymers do not exhibit significant weight loss until approximately 300 1C under nitrogen. Cyclic voltammetry shows that the polymers have reversible reduction waves with estimated LUMO levels at À3.02 and À3.10 eV relative to vacuum and optical bandgaps of 2.04-2.17 eV. Devices based on blends of the copolymers and [6,6]-phenyl C61 butyric acid methyl ester (PCBM) exhibited modest power conversion efficiencies. Theoretical models reveal that there is poor electron delocalization along the polymer backbone, leading to poor performance. However, the energy levels of these polymers indicate that the incorporation of benzobisoxazoles into the polymer backbone is a promising strategy for the synthesis of new materials