Editorial História e Cultura, v.4, n.3

Texto do editorial da Revista Discente História e Cultura, v.4, n.3 

Cytogenetic complexity in chronic lymphocytic leukemia: definitions, associations and clinical impact

Recent evidence suggests that complex karyotype (CK) defined by the presence of 653 chromosomal aberrations (structural and/or numerical) identified by chromosome banding analysis (CBA) may be relevant for treatment decision-making in chronic lymphocytic leukemia (CLL). However, many challenges towards routine clinical application of CBA remain. In a retrospective study of 5290 patients with available CBA data, we explored both clinicobiological associations and the clinical impact of CK in CLL. We found that patients with 655 abnormalities, defined as high-CK, exhibit uniformly dismal clinical outcome, independently of clinical stage, TP53 aberrations (deletion of chromosome 17p and or TP53 mutations, TP53abs) and the expression of somatically hypermutated (M-CLL) or unmutated (U-CLL) immunoglobulin heavy variable genes (IGHV). Thus, they contrasted CK cases with 3 or 4 aberrations (low-CK and intermediate-CK, respectively) who followed aggressive disease courses only in the presence of TP53abs. At the other end of the spectrum, patients with CK and +12,+19 displayed an exceptionally indolent profile. Building upon CK, TP53abs and IGHV gene somatic hypermutation status, we propose a novel hierarchical model where patients with high-CK exhibit the worst prognosis, while M-CLL lacking CK or TP53abs as well as CK with +12,+19 show the longest overall survival. In conclusion, CK should not be axiomatically considered unfavorable in CLL, representing a heterogeneous group with variable clinical behavior. High-CK with 655 chromosomal aberrations emerges as prognostically adverse, independently of other biomarkers. Prospective clinical validation is warranted before finally incorporating high-CK in risk stratification of CLL

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Gamasoidosis (bird mite dermatitis): dermanyssus gallinae in a young boy

Submitted by Janaína Nascimento ([email protected]) on 2019-01-14T12:13:43Z No. of bitstreams: 1 ve_Sousa_Marcos_e_Bernardes_Filho_Fred_INI_2018.pdf: 311287 bytes, checksum: 6a4fed8105bfc2e9abe28be4210c0d57 (MD5)Approved for entry into archive by Janaína Nascimento ([email protected]) on 2019-01-14T13:48:53Z (GMT) No. of bitstreams: 1 ve_Sousa_Marcos_e_Bernardes_Filho_Fred_INI_2018.pdf: 311287 bytes, checksum: 6a4fed8105bfc2e9abe28be4210c0d57 (MD5)Made available in DSpace on 2019-01-14T13:48:53Z (GMT). No. of bitstreams: 1 ve_Sousa_Marcos_e_Bernardes_Filho_Fred_INI_2018.pdf: 311287 bytes, checksum: 6a4fed8105bfc2e9abe28be4210c0d57 (MD5) Previous issue date: 2018Fundação Oswaldo Cruz. Instituto Nacional de Infectologia Evandro Chagas Rio de Janeiro, RJ, Brazil.University of São Paulo. Ribeirão Preto Medical School. Department of Medical Clinics. Dermatology Division. Ribeirão Preto, Brazil

Automated detection of synapses in serial section transmission electron microscopy image stacks.

We describe a method for fully automated detection of chemical synapses in serial electron microscopy images with highly anisotropic axial and lateral resolution, such as images taken on transmission electron microscopes. Our pipeline starts from classification of the pixels based on 3D pixel features, which is followed by segmentation with an Ising model MRF and another classification step, based on object-level features. Classifiers are learned on sparse user labels; a fully annotated data subvolume is not required for training. The algorithm was validated on a set of 238 synapses in 20 serial 7197×7351 pixel images (4.5×4.5×45 nm resolution) of mouse visual cortex, manually labeled by three independent human annotators and additionally re-verified by an expert neuroscientist. The error rate of the algorithm (12% false negative, 7% false positive detections) is better than state-of-the-art, even though, unlike the state-of-the-art method, our algorithm does not require a prior segmentation of the image volume into cells. The software is based on the ilastik learning and segmentation toolkit and the vigra image processing library and is freely available on our website, along with the test data and gold standard annotations (http://www.ilastik.org/synapse-detection/sstem)

EDITORIAL HISTÓRIA E CULTURA , v.4, n.2, 2015

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Editorial História e Cultura, v.4, n.2, 2015

Texto do editorial da Revista Discente História e Cultura, v.4, n.2, 201

Quantification of phytoplankton bloom dynamics by citizen scientists in urban and peri-urban environments

Freshwater ecosystems are severely threatened by urban development and agricultural intensification. Increased occurrence of algal blooms is a main issue, and the identification of local dynamics and drivers is hampered by a lack of field data. In this study, data from 13 cities (250 water bodies) were used to examine the capacity of trained community members to assess elevated phytoplankton densities in urban and peri-urban freshwater ecosystems. Coincident nutrient concentrations and land use observations were used to examine possible drivers of algal blooms. Measurements made by participants showed a good relationship to standard laboratory measurements of phytoplankton density, in particular in pond and lake ecosystems. Links between high phytoplankton density and nutrients (mainly phosphate) were observed. Microscale observations of pollution sources and catchment scale estimates of land cover both influenced the occurrence of algal blooms. The acquisition of environmental data by committed and trained community members represents a major opportunity to support agency monitoring programmes and to complement field campaigns in the study of catchment dynamics