Advances in aquatic insect systematics and biodiversity in the Neotropics: introduction

The Neotropical Region or Neotropics, contains vast expanses of rain forest and river systems representing some of the most biologically diverse ecosystems on Earth, but much of its resident biota remains undescribed and undocumented, and some of it is at risk of extirpation and extinction. Anthropogenic disturbances, especially deforestation, urbanization, and climate change, threaten the integrity of the Neotropics and its biodiversity. In the Neotropics, freshwater habitats are particularly susceptible to environmental stressors and freshwater species throughout the Neotropics have experienced marked declines greater than those of other groups when compared to marine and terrestrial systems. Advances in taxonomic descriptions, preparation of keys, and faunal assessments will aid future studies as well as conservation efforts

Emergence of phlebotomine sandflies (Diptera: Psychodidade) in non-flooded forest floor in Central Amazon, Brazil: a modified emergence trap model

Information concerning the potential natural breeding sites of phlebotomine sandflies are of high epidemiological importance. However, few studies have been conducted on the subject. This is due especially to the difficulties in finding as well as extracting immature sandflies that develop in the soil and organic matter of the forest floor. In the present study, a modified emergence trap model was tested in order to find potential breeding sites. This model was tested in the Pitinga Village, situated in the Presidente Figueredo municipality, in the State of Amazonas. Twenty-seven individuals belonging to nine species (Lutzomyia umbratilis,L. monstruosa,L. ayrozai,L. anduzei,L. trichopyga,L. davisi,L. geniculata,L. georgii e L. saulensis.) were collected. Lutzomyia umbratilis showed the highest number of individuals (37.1%) of all species captured in the area. The phlebotomine productivity was estimated as 2.2 sandflies per 100 m²/day. September showed the highest density of individuals, with a productivity of 5.8.Informações acerca de potenciais criadouros naturais de flebotomíneos sempre foram de fundamental interesse epidemiológico. Contudo, são poucas as informações advindas dos diversos estudos realizados até o momento. Isto se deve principalmente às dificuldades de localização e extração dos imaturos que se desenvolvem no solo e matéria orgânica do chão de florestas. No presente estudo o modelo modificado de armadilha de emergência foi testado na Vila do Pitinga, município de Presidente Figueiredo, Estado do Amazonas, a fim de localizar potenciais criadouros naturais. Vinte e sete indivíduos de nove espécies (Lutzomyia umbratilis,L. monstruosa,L. ayrozai,L. anduzei,L. trichopyga,L. davisi,L. geniculata,L. georgii e L. saulensis) foram coletados. Lutzomyia umbratilis foi a espécie com maior número de indivíduos, 10, representando 37,1% do total. A produção de flebotomíneos foi estimada em 2,2 flebotomíneos por 100 m² por dia. Em setembro, mês com maior número de indivíduos, esta produção foi de 5,8

Measurement of the B0-anti-B0-Oscillation Frequency with Inclusive Dilepton Events

The $B^0$-$\bar B^0$ oscillation frequency has been measured with a sample of 23 million \B\bar B pairs collected with the BABAR detector at the PEP-II asymmetric B Factory at SLAC. In this sample, we select events in which both B mesons decay semileptonically and use the charge of the leptons to identify the flavor of each B meson. A simultaneous fit to the decay time difference distributions for opposite- and same-sign dilepton events gives $\Delta m_d = 0.493 \pm 0.012{(stat)}\pm 0.009{(syst)}$ ps$^{-1}$.Comment: 7 pages, 1 figure, submitted to Physical Review Letter

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Functional mechanisms underlying pleiotropic risk alleles at the 19p13.1 breast-ovarian cancer susceptibility locus

A locus at 19p13 is associated with breast cancer (BC) and ovarian cancer (OC) risk. Here we analyse 438 SNPs in this region in 46,451 BC and 15,438 OC cases, 15,252 BRCA1 mutation carriers and 73,444 controls and identify 13 candidate causal SNPs associated with serous OC (P=9.2 × 10-20), ER-negative BC (P=1.1 × 10-13), BRCA1-associated BC (P=7.7 × 10-16) and triple negative BC (P-diff=2 × 10-5). Genotype-gene expression associations are identified for candidate target genes ANKLE1 (P=2 × 10-3) and ABHD8 (P<2 × 10-3). Chromosome conformation capture identifies interactions between four candidate SNPs and ABHD8, and luciferase assays indicate six risk alleles increased transactivation of the ADHD8 promoter. Targeted deletion of a region containing risk SNP rs56069439 in a putative enhancer induces ANKLE1 downregulation; and mRNA stability assays indicate functional effects for an ANKLE1 3′-UTR SNP. Altogether, these data suggest that multiple SNPs at 19p13 regulate ABHD8 and perhaps ANKLE1 expression, and indicate common mechanisms underlying breast and ovarian cancer risk

Measurement of the CP-Violating Asymmetry Amplitude sin2β\beta

We present results on time-dependent CP-violating asymmetries in neutral B decays to several CP eigenstates. The measurements use a data sample of about 88 million Y(4S) --> B Bbar decays collected between 1999 and 2002 with the BABAR detector at the PEP-II asymmetric-energy B Factory at SLAC. We study events in which one neutral B meson is fully reconstructed in a final state containing a charmonium meson and the other B meson is determined to be either a B0 or B0bar from its decay products. The amplitude of the CP-violating asymmetry, which in the Standard Model is proportional to sin2beta, is derived from the decay-time distributions in such events. We measure sin2beta = 0.741 +/- 0.067 (stat) +/- 0.033 (syst) and |lambda| = 0.948 +/- 0.051 (stat) +/- 0.017 (syst). The magnitude of lambda is consistent with unity, in agreement with the Standard Model expectation of no direct CP violation in these modes

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

Somatic Mutational Landscape of Splicing Factor Genes and Their Functional Consequences across 33 Cancer Types

Hotspot mutations in splicing factor genes have been recently reported at high frequency in hematological malignancies, suggesting the importance of RNA splicing in cancer. We analyzed whole-exome sequencing data across 33 tumor types in The Cancer Genome Atlas (TCGA), and we identified 119 splicing factor genes with significant non-silent mutation patterns, including mutation over-representation, recurrent loss of function (tumor suppressor-like), or hotspot mutation profile (oncogene-like). Furthermore, RNA sequencing analysis revealed altered splicing events associated with selected splicing factor mutations. In addition, we were able to identify common gene pathway profiles associated with the presence of these mutations. Our analysis suggests that somatic alteration of genes involved in the RNA-splicing process is common in cancer and may represent an underappreciated hallmark of tumorigenesis