Accurate detection of uniparental disomy and microdeletions by SNP array analysis in myelodysplastic syndromes with normal cytogenetics.

Progress in the management of patients with myelodysplastic syndromes (MDS) has been hampered by the inability to detect cytogenetic abnormalities in 40-60% of cases. We prospectively analyzed matched pairs of bone marrow and buccal cell (normal) DNA samples from 51 MDS patients by single nucleotide polymorphism (SNP) arrays, and identified somatically acquired clonal genomic abnormalities in 21 patients (41%). Among the 33 patients with normal bone marrow cell karyotypes, 5 (15%) had clonal, somatically acquired aberrations by SNP array analysis, including 4 with segmental uniparental disomies (UPD) and 1 with three separate microdeletions. Each abnormality was detected more readily in CD34+ cells than in unselected bone marrow cells. Paired analysis of bone marrow and buccal cell DNA from each patient was necessary to distinguish true clonal genomic abnormalities from inherited copy number variations and regions with apparent loss of heterozygosity. UPDs affecting chromosome 7q were identified in two patients who had a rapidly deteriorating clinical course despite a low-risk International Prognostic Scoring System score. Further studies of larger numbers of patients will be needed to determine whether 7q UPD detected by SNP array analysis will identify higher risk MDS patients at diagnosis, analogous to those with 7q cytogenetic abnormalities

Accreting Black Holes

This chapter provides a general overview of the theory and observations of black holes in the Universe and on their interpretation. We briefly review the black hole classes, accretion disk models, spectral state classification, the AGN classification, and the leading techniques for measuring black hole spins. We also introduce quasi-periodic oscillations, the shadow of black holes, and the observations and the theoretical models of jets.Comment: 41 pages, 18 figures. To appear in "Tutorial Guide to X-ray and Gamma-ray Astronomy: Data Reduction and Analysis" (Ed. C. Bambi, Springer Singapore, 2020). v3: fixed some typos and updated some parts. arXiv admin note: substantial text overlap with arXiv:1711.1025

Foundations of Black Hole Accretion Disk Theory

This review covers the main aspects of black hole accretion disk theory. We begin with the view that one of the main goals of the theory is to better understand the nature of black holes themselves. In this light we discuss how accretion disks might reveal some of the unique signatures of strong gravity: the event horizon, the innermost stable circular orbit, and the ergosphere. We then review, from a first-principles perspective, the physical processes at play in accretion disks. This leads us to the four primary accretion disk models that we review: Polish doughnuts (thick disks), Shakura-Sunyaev (thin) disks, slim disks, and advection-dominated accretion flows (ADAFs). After presenting the models we discuss issues of stability, oscillations, and jets. Following our review of the analytic work, we take a parallel approach in reviewing numerical studies of black hole accretion disks. We finish with a few select applications that highlight particular astrophysical applications: measurements of black hole mass and spin, black hole vs. neutron star accretion disks, black hole accretion disk spectral states, and quasi-periodic oscillations (QPOs).Comment: 91 pages, 23 figures, final published version available at http://www.livingreviews.org/lrr-2013-

2021 roadmap on lithium sulfur batteries

Batteries that extend performance beyond the intrinsic limits of Li-ion batteries are among the most important developments required to continue the revolution promised by electrochemical devices. Of these next-generation batteries, lithium sulfur (Li–S) chemistry is among the most commercially mature, with cells offering a substantial increase in gravimetric energy density, reduced costs and improved safety prospects. However, there remain outstanding issues to advance the commercial prospects of the technology and benefit from the economies of scale felt by Li-ion cells, including improving both the rate performance and longevity of cells. To address these challenges, the Faraday Institution, the UK's independent institute for electrochemical energy storage science and technology, launched the Lithium Sulfur Technology Accelerator (LiSTAR) programme in October 2019. This Roadmap, authored by researchers and partners of the LiSTAR programme, is intended to highlight the outstanding issues that must be addressed and provide an insight into the pathways towards solving them adopted by the LiSTAR consortium. In compiling this Roadmap we hope to aid the development of the wider Li–S research community, providing a guide for academia, industry, government and funding agencies in this important and rapidly developing research space

Pathway Analysis for Genome-Wide Association Study of Basal Cell Carcinoma of the Skin

Recently, a pathway-based approach has been developed to evaluate the cumulative contribution of the functionally related genes for genome-wide association studies (GWASs), which may help utilize GWAS data to a greater extent.In this study, we applied this approach for the GWAS of basal cell carcinoma (BCC) of the skin. We first conducted the BCC GWAS among 1,797 BCC cases and 5,197 controls in Caucasians with 740,760 genotyped SNPs. 115,688 SNPs were grouped into gene transcripts within 20 kb in distance and then into 174 Kyoto Encyclopedia of Genes and Genomes pathways, 205 BioCarta pathways, as well as two positive control gene sets (pigmentation gene set and BCC risk gene set). The association of each pathway with BCC risk was evaluated using the weighted Kolmogorov-Smirnov test. One thousand permutations were conducted to assess the significance.Both of the positive control gene sets reached pathway p-values<0.05. Four other pathways were also significantly associated with BCC risk: the heparan sulfate biosynthesis pathway (p  =  0.007, false discovery rate, FDR  =  0.35), the mCalpain pathway (p  =  0.002, FDR  =  0.12), the Rho cell motility signaling pathway (p  =  0.011, FDR  =  0.30), and the nitric oxide pathway (p  =  0.022, FDR  =  0.42).We identified four pathways associated with BCC risk, which may offer new insights into the etiology of BCC upon further validation, and this approach may help identify potential biological pathways that might be missed by the standard GWAS approach

The cloud aerosol interaction and precipitation enhancement experiment (CAIPEEX): Overview and preliminary results

While the demand for enhancing rainfall through cloud seeding is strong and persistent in the country, considerable uncertainty exists on the success of such an endeavour at a given location. To understand the pathways of aerosol-cloud interaction through which this might be achieved, a national experiment named Cloud Aerosol Interaction and Precipitation Enhancement EXperiment (CAIPEEX) in two phases, was carried out. The rationale of CAIPEEX, the strategy for conducting the experiment, data quality and potential for path-breaking science are described in this article. Pending completion of quality control and calibration of the CAIPEEX phase-II data, here we present some initial results of CAIPEEX phase-I aimed at documenting the prevailing microphysical characteristics of aerosols and clouds and associated environmental conditions over different regions of the country and under different monsoon conditions with the help of an instrumented research aircraft. First-time simultaneous observations of aerosol, cloud condensation nuclei (CCN) and cloud droplet number concentration (CDNC) over the Ganges Valley during monsoon season show very high concentrations (&gt; 1000 cm-3) of CCN at elevated layers. Observations of elevated layers with high aerosol concentration over the Gangetic valley extending up to 6 km and relatively less aerosol concentration in the boundary layer are also documented. We also present evidence of strong cloud- aerosol interaction in the moist environments with an increase in the cloud droplet effective radius. Our observations also show that pollution increases CDNC and the warm rain depth, and delays its initiation. The critical effective radius for warm rain initiation is found to be between 10 and 12 μm in the polluted clouds and it is between 12 and 14 μm in cleaner monsoon clouds

Biocomposite films based on κ-carrageenan/locust bean gum blends and clays : physical and antimicrobial properties

The aims of this work were to evaluate the physical and antimicrobial properties of biodegradable films composed of mixtures of κ-carrageenan (κ-car) and locust bean gum (LBG) when organically modified clay Cloisite 30B (C30B) was dispersed in the biopolymer matrix. Film-forming solutions were prepared by adding C30B (ranging from 0 to 16 wt.%) into the κ-car/LBG solution (40/60 wt.%) with 0.3 % (w/v) of glycerol. Barrier properties (water vapour permeability, P vapour; CO2 and O2 permeabilities), mechanical properties (tensile strength, TS, and elongation-at-break, EB) and thermal stability of the resulting films were determined and related with the incorporation of C30B. Also, X-ray diffraction (XRD) was done in order to investigate the effect of C30B in film structure. Antimicrobial effects of these films against Listeria monocytogenes, Escherichia coli and Salmonella enterica were also evaluated. The increase of clay concentration causes a decrease of P vapour (from 5.34 × 10−11 to 3.19 × 10−11 g (m s Pa)−1) and an increase of the CO2 permeability (from 2.26 × 10−14 to 2.91 × 10−14 g (m s Pa)−1) and did not changed significantly the O2 permeability for films with 0 and 16 wt.% C30B, respectively. Films with 16 wt.% clay exhibited the highest values of TS (33.82 MPa) and EB (29.82 %). XRD patterns of the films indicated that a degree of exfoliation is attained depending on clay concentration. κ-car/LBG–C30B films exhibited an inhibitory effect only against L. monocytogenes. κ-car/LBG–C30B composite films are a promising alternative to synthetic films in order to improve the shelf life and safety of food products.J. T. Martins, A. I. Bourbon, A. C. Pinheiro and M. A. Cerqueira gratefully acknowledge the Fundacao para a Ciencia e Tecnologia (FCT, Portugal) for their fellowships (SFRH/BD/32566/2006, SFRH/BD/73178/2010, SFRH/BD/48120/2008 and SFRH/BPD/72753/2010, respectively), and B. W. S. Souza acknowledges the Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES, Brazil)

The genesis of cerebellar interneurons and the prevention of neural DNA damage require XRCC1

Defective responses to DNA single strand breaks underlie various neurodegenerative diseases. However, the exact role of this repair pathway during the development and maintenance of the nervous system is unclear. Using murine neural-specific inactivation of Xrcc1, a factor that is critical for the repair of DNA single strand breaks, we found a profound neuropathology that is characterized by the loss of cerebellar interneurons. This cell loss was linked to p53-dependent cell cycle arrest and occurred as interneuron progenitors commenced differentiation. Loss of Xrcc1 also led to the persistence of DNA strand breaks throughout the nervous system and abnormal hippocampal function. Collectively, these data detail the in vivo link between DNA single strand break repair and neurogenesis and highlight the diverse consequences of specific types of genotoxic stress in the nervous system

Discovery and profiling of small RNAs responsive to stress conditions in the plant pathogen <i>Pectobacterium atrosepticum</i>

BACKGROUND: Small RNAs (sRNAs) have emerged as important regulatory molecules and have been studied in several bacteria. However, to date, there have been no whole-transcriptome studies on sRNAs in any of the Soft Rot Enterobacteriaceae (SRE) group of pathogens. Although the main ecological niches for these pathogens are plants, a significant part of their life cycle is undertaken outside their host within adverse soil environment. However, the mechanisms of SRE adaptation to this harsh nutrient-deficient environment are poorly understood. RESULTS: In the study reported herein, by using strand-specific RNA-seq analysis and in silico sRNA predictions, we describe the sRNA pool of Pectobacterium atrosepticum and reveal numerous sRNA candidates, including those that are induced during starvation-activated stress responses. Consequently, strand-specific RNA-seq enabled detection of 137 sRNAs and sRNA candidates under starvation conditions; 25 of these sRNAs were predicted for this bacterium in silico. Functional annotations were computationally assigned to 68 sRNAs. The expression of sRNAs in P. atrosepticum was compared under growth-promoting and starvation conditions: 68 sRNAs were differentially expressed with 47 sRNAs up-regulated under nutrient-deficient conditions. Conservation analysis using BLAST showed that most of the identified sRNAs are conserved within the SRE. Subsequently, we identified 9 novel sRNAs within the P. atrosepticum genome. CONCLUSIONS: Since many of the identified sRNAs are starvation-induced, the results of our study suggests that sRNAs play key roles in bacterial adaptive response. Finally, this work provides a basis for future experimental characterization and validation of sRNAs in plant pathogens. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-2376-0) contains supplementary material, which is available to authorized users