Risk and Resilience of Somali Children in the Context of Climate Change, Famine, and Conflict

Climate change is an existential threat to all of humanity. Its impact on the children of Somalia provides insights into the severity of risks posed by climate change to current and future generations. Globally, there has been a continuous increase in mean annual temperatures since 1991 and scientists anticipate an increase of up to 4.3 degrees Celsius by the end of the century. Concomitantly, Somalia has experienced a decrease in annual rainfall, resulting in recurrent droughts. According to the UN’s emergency aid coordination office, these droughts have grown in frequency and intensity over the past three decades, fueling increased frequency of famine and contributing to internal conflict and civil war. In this article, the impact of climate change on children, exemplified by the plight of Somali children, is viewed through the lens of cumulative adversity and related consequences of poverty on malnutrition, illness, disruptions of family systems, and displacement, with a diaspora around the globe. The paper promotes a multi-systems resilience framework that guides strategies for addressing the complex, cascading crises that accompany climate change, exploring the construct of resilience from the individual/interpersonal level through family systems and communities, including a reframing of the Somali diaspora. The paper concludes with a series of global transnational policy recommendations based on children’s rights, the promotion of resilience, and approaching climate change from a child sensitive perspective, encouraging youth engagement and leadership, along with peace-building

A STUDY OF THE STATISTICAL PROPERTIES OF TWO MEASURES OF COMPETITION

In competition studies, two species are studied, generally in ratios of 1:0, 3:1, 1:1, 1:3,and 0: 1. The standard measure of competition is the Relative Crowding Coefficient (RCC)..

First Detection of c-C3H2 in a Circumstellar Disk

We report the first detection of c-C3H2 in a circumstellar disk. The c-C3H2 J = 6-5 line (217.882 GHz) is detected and imaged through Atacama Large Millimeter Array (ALMA) Science Verification observations toward the disk around the Herbig Ae star HD 163296 at 0.''8 resolution. The emission is consistent with that arising from a Keplerian rotating disk. Two additional c-C3H2 transitions are also tentatively detected, bolstering the identification of this species, but with insufficient signal-to-noise ratio to constrain the spatial distribution. Using a previously developed model for the physical structure of this disk, we fit a radial power-law distribution model to the c-C3H2 6-5 emission and find that c-C3H2 is present in a ring structure from an inner radius of about 30 AU to an outer radius of about 165 AU. The column density is estimated to be 1012-1013 cm–2. The clear detection and intriguing ring structure suggest that c-C3H2 has the potential to become a useful probe of radiation penetration in disks.Astronom

RNA-seq: technical variability and sampling

<p>Abstract</p> <p>Background</p> <p>RNA-seq is revolutionizing the way we study transcriptomes. mRNA can be surveyed without prior knowledge of gene transcripts. Alternative splicing of transcript isoforms and the identification of previously unknown exons are being reported. Initial reports of differences in exon usage, and splicing between samples as well as quantitative differences among samples are beginning to surface. Biological variation has been reported to be larger than technical variation. In addition, technical variation has been reported to be in line with expectations due to random sampling. However, strategies for dealing with technical variation will differ depending on the magnitude. The size of technical variance, and the role of sampling are examined in this manuscript.</p> <p>Results</p> <p>In this study three independent Solexa/Illumina experiments containing technical replicates are analyzed. When coverage is low, large disagreements between technical replicates are apparent. Exon detection between technical replicates is highly variable when the coverage is less than 5 reads per nucleotide and estimates of gene expression are more likely to disagree when coverage is low. Although large disagreements in the estimates of expression are observed at all levels of coverage.</p> <p>Conclusions</p> <p>Technical variability is too high to ignore. Technical variability results in inconsistent detection of exons at low levels of coverage. Further, the estimate of the relative abundance of a transcript can substantially disagree, even when coverage levels are high. This may be due to the low sampling fraction and if so, it will persist as an issue needing to be addressed in experimental design even as the next wave of technology produces larger numbers of reads. We provide practical recommendations for dealing with the technical variability, without dramatic cost increases.</p

C/o and Snowline Locations in Protoplanetary Disks: The Effect of Radial Drift and Viscous Gas Accretion

The C/O ratio is a defining feature of both gas giant atmospheric and protoplanetary disk chemistry. In disks, the C/O ratio is regulated by the presence of snowlines of major volatiles at different distances from the central star. We explore the effect of radial drift of solids and viscous gas accretion onto the central star on the snowline locations of the main C and O carriers in a protoplanetary disk, H2O, CO2 and CO, and their consequences for the C/O ratio in gas and dust throughout the disk. We determine the snowline locations for a range of fixed initial particle sizes and disk types. For our fiducial disk model, we find that grains with sizes ∼0.5 cm . s . 7 m for an irradiated disk, and ∼0.001 cm . s . 7 m for an evolving and viscous disk, desorb at a size-dependent location in the disk, which is independent of the particle’s initial position. The snowline radius decreases for larger particles, up to sizes of ∼7 m. Compared to a static disk, we find that radial drift and gas accretion in a viscous disk move the H2O snowline inwards by up to 40 %, the CO2 snowline by up to 60 %, and the CO snowline by up to 50 %. We thus determine an inner limit on the snowline locations when radial drift and gas accretion are accounted for.Astronom

Discovery of ovarian cancer biomarkers in serum using NanoLC electrospray ionization TOF and FT-ICR mass spectrometry

Abstract. Treatment of cancer patients is greatly facilitated by detection of the cancer prior to metastasis. One of the obstacles to early cancer detection is the lack of availability of biomarkers with sufficient specificity. With modern differential proteomic techniques, the potential exists to identify high specificity cancer biomarkers. We have delineated a set of protocols for the isolation and identification of serum biomarkers for ovarian cancer that exist in the low molecular weight serum fraction. After isolation of the low molecular weight fraction by ultrafiltration, the potential biomarkers are separated by reversed phase nano liquid chromatography. Detection via TOF or FT-ICR yields a data set for each sample. We compared stage III/IV ovarian cancer serum with postmenopausal age-matched controls. Using bioinformatics tools developed at Mayo, we normalized each sample for intensity and chromatographic alignment. Normalized data sets are subsequently compared and potential biomarkers identified. Several candidate biomarkers were found. One of these contains the sequence of fibrinopeptide-A known to be elevated in many types of cancer including ovarian cancer. The protocols utilized will be examined and would be applicable to a wide variety of cancers or disease states

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

<p>Abstract</p> <p>Background</p> <p>Massive parallel sequencing has the potential to replace microarrays as the method for transcriptome profiling. Currently there are two protocols: full-length RNA sequencing (RNA-SEQ) and 3'-tag digital gene expression (DGE). In this preliminary effort, we evaluated the 3' DGE approach using two reference RNA samples from the MicroArray Quality Control Consortium (MAQC).</p> <p>Results</p> <p>Using Brain RNA sample from multiple runs, we demonstrated that the transcript profiles from 3' DGE were highly reproducible between technical and biological replicates from libraries constructed by the same lab and even by different labs, and between two generations of Illumina's Genome Analyzers. Approximately 65% of all sequence reads mapped to mitochondrial genes, ribosomal RNAs, and canonical transcripts. The expression profiles of brain RNA and universal human reference RNA were compared which demonstrated that DGE was also highly quantitative with excellent correlation of differential expression with quantitative real-time PCR. Furthermore, one lane of 3' DGE sequencing, using the current sequencing chemistry and image processing software, had wider dynamic range for transcriptome profiling and was able to detect lower expressed genes which are normally below the detection threshold of microarrays.</p> <p>Conclusion</p> <p>3' tag DGE profiling with massive parallel sequencing achieved high sensitivity and reproducibility for transcriptome profiling. Although it lacks the ability of detecting alternative splicing events compared to RNA-SEQ, it is much more affordable and clearly out-performed microarrays (Affymetrix) in detecting lower abundant transcripts.</p

Genome-Wide Transcriptional Profiling Reveals MicroRNA-Correlated Genes and Biological Processes in Human Lymphoblastoid Cell Lines

Expression level of many genes shows abundant natural variation in human populations. The variations in gene expression are believed to contribute to phenotypic differences. Emerging evidence has shown that microRNAs (miRNAs) are one of the key regulators of gene expression. However, past studies have focused on the miRNA target genes and used loss- or gain-of-function approach that may not reflect natural association between miRNA and mRNAs.To examine miRNA regulatory effect on global gene expression under endogenous condition, we performed pair-wise correlation coefficient analysis on expression levels of 366 miRNAs and 14,174 messenger RNAs (mRNAs) in 90 immortalized lymphoblastoid cell lines, and observed significant correlations between the two species of RNA transcripts. We identified a total of 7,207 significantly correlated miRNA-mRNA pairs (false discovery rate q<0.01). Of those, 4,085 pairs showed positive correlations while 3,122 pairs showed negative correlations. Gene ontology analyses on the miRNA-correlated genes revealed significant enrichments in several biological processes related to cell cycle, cell communication and signal transduction. Individually, each of three miRNAs (miR-331, -98 and -33b) demonstrated significant correlation with the genes in cell cycle-related biological processes, which is consistent with important role of miRNAs in cell cycle regulation.This study demonstrates feasibility of using naturally expressed transcript profiles to identify endogenous correlation between miRNA and miRNA. By applying this genome-wide approach, we have identified thousands of miRNA-correlated genes and revealed potential role of miRNAs in several important cellular functions. The study results along with accompanying data sets will provide a wealth of high-throughput data to further evaluate the miRNA-regulated genes and eventually in phenotypic variations of human populations

Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform

<p>Abstract</p> <p>Background</p> <p>The cDNA-mediated Annealing, extension, Selection and Ligation (DASL) assay has become a suitable gene expression profiling system for degraded RNA from paraffin-embedded tissue. We examined assay characteristics and the performance of the DASL 502-gene Cancer Panel^v1(1.5K) and 24,526-gene panel (24K) platforms at differentiating nine human epidermal growth factor receptor 2- positive (HER2+) and 11 HER2-negative (HER2-) paraffin-embedded breast tumors.</p> <p>Methods</p> <p>Bland-Altman plots and Spearman correlations evaluated intra/inter-panel agreement of normalized expression values. Unequal-variance <it>t</it>-statistics tested for differences in expression levels between HER2 + and HER2 - tumors. Regulatory network analysis was performed using Metacore (GeneGo Inc., St. Joseph, MI).</p> <p>Results</p> <p>Technical replicate correlations ranged between 0.815-0.956 and 0.986-0.997 for the 1.5K and 24K panels, respectively. Inter-panel correlations of expression values for the common 498 genes across the two panels ranged between 0.485-0.573. Inter-panel correlations of expression values of 17 probes with base-pair sequence matches between the 1.5K and 24K panels ranged between 0.652-0.899. In both panels, <it>erythroblastic leukemia viral oncogene homolog 2 </it>(<it>ERBB2</it>) was the most differentially expressed gene between the HER2 + and HER2 - tumors and seven additional genes had p-values < 0.05 and log2 -fold changes > |0.5| in expression between HER2 + and HER2 - tumors: <it>topoisomerase II alpha </it>(<it>TOP2A</it>), <it>cyclin a2 </it>(<it>CCNA2</it>), <it>v-fos fbj murine osteosarcoma viral oncogene homolog </it>(<it>FOS</it>), <it>wingless-type mmtv integration site family, member 5a </it>(<it>WNT5A</it>), <it>growth factor receptor-bound protein </it><it>7 </it>(<it>GRB7</it>), <it>cell division cycle 2 </it>(<it>CDC2</it>), <it>and baculoviral iap repeat-containing protein 5 </it>(<it>BIRC5</it>). The top 52 discriminating probes from the 24K panel are enriched with genes belonging to the regulatory networks centered around <it>v-myc avian myelocytomatosis viral oncogene homolog </it>(<it>MYC</it>), <it>tumor protein p53 </it>(<it>TP53</it>), and <it>estrogen receptor α </it>(<it>ESR1</it>). Network analysis with a two-step extension also showed that the eight discriminating genes common to the 1.5K and 24K panels are functionally linked together through <it>MYC</it>, <it>TP53</it>, and <it>ESR1</it>.</p> <p>Conclusions</p> <p>The relative RNA abundance obtained from two highly differing density gene panels are correlated with eight common genes differentiating HER2 + and HER2 - breast tumors. Network analyses demonstrated biological consistency between the 1.5K and 24K gene panels.</p