Non-specific filtering of beta-distributed data.

BackgroundNon-specific feature selection is a dimension reduction procedure performed prior to cluster analysis of high dimensional molecular data. Not all measured features are expected to show biological variation, so only the most varying are selected for analysis. In DNA methylation studies, DNA methylation is measured as a proportion, bounded between 0 and 1, with variance a function of the mean. Filtering on standard deviation biases the selection of probes to those with mean values near 0.5. We explore the effect this has on clustering, and develop alternate filter methods that utilize a variance stabilizing transformation for Beta distributed data and do not share this bias.ResultsWe compared results for 11 different non-specific filters on eight Infinium HumanMethylation data sets, selected to span a variety of biological conditions. We found that for data sets having a small fraction of samples showing abnormal methylation of a subset of normally unmethylated CpGs, a characteristic of the CpG island methylator phenotype in cancer, a novel filter statistic that utilized a variance-stabilizing transformation for Beta distributed data outperformed the common filter of using standard deviation of the DNA methylation proportion, or its log-transformed M-value, in its ability to detect the cancer subtype in a cluster analysis. However, the standard deviation filter always performed among the best for distinguishing subgroups of normal tissue. The novel filter and standard deviation filter tended to favour features in different genome contexts; for the same data set, the novel filter always selected more features from CpG island promoters and the standard deviation filter always selected more features from non-CpG island intergenic regions. Interestingly, despite selecting largely non-overlapping sets of features, the two filters did find sample subsets that overlapped for some real data sets.ConclusionsWe found two different filter statistics that tended to prioritize features with different characteristics, each performed well for identifying clusters of cancer and non-cancer tissue, and identifying a cancer CpG island hypermethylation phenotype. Since cluster analysis is for discovery, we would suggest trying both filters on any new data sets, evaluating the overlap of features selected and clusters discovered

Development of laser pulse sampled DC voltammetry and its application to the determination of glucose

ArticleBUNSEKI KAGAKU. 57(1): 61-65 (2008)journal articl

Successful Endoscopic Management of Fish Bone Embedded into the Bladder Wall

We report a case of a pyogenous vesical abscess resulting from an ingested fish bone embedded in the bladder wall that was treated endoscopically in an asymptomatic man. Computed tomography of the abdomen showed a linear radiopaque structure in the thickened left anterolateral wall of the bladder. Cystoscopy revealed a protruding mass, covered with normal-appearing mucosa, with outflow of pus from a shallow recess. Histopathological findings indicated that the transurethrally removed linear structure, located in the submucosa, was compatible with fish bone. A high index of suspicion should be maintained for the correct diagnosis to be made

Synthesis and circularly polarized luminescence properties of BINOL-derived bisbenzofuro[2,3-b:3′,2′-e]pyridines (BBZFPys)

A series of optically active bisbenzofuro[2,3-b:3′,2′-e]pyridine (BBZFPy) derivatives was synthesized starting with the readily available (S)- and (R)-1,1′-bi-2-naphthols through a palladium-catalyzed multiple intramolecular C-H/C-H coupling as the key ring-closure step. The effect of terminal tert-butyl substituents on the BBZFPy skeleton was systematically investigated to uncover a unique aggregation-induced enhancement of CPL characteristics in the solid state. The crystal structures of the coupling products were also evaluated by single crystal X-ray analysis and the well-ordered intermolecular stacking arrangements appeared to be responsible for the enhanced CPL.Beilstein J. Org. Chem. 2020, 16, 325–336. doi:10.3762/bjoc.16.3

Projeto Democratização: Relato de Experiência com adolescentes Acolhidos na Cidade de Campo Grande - MS

Este relato tem por objetivo apresentar a experiência do projeto de extensão Democratização: construindo valores, da Universidade Católica Dom Bosco (UCDB), que está em andamento desde o ano de 2021. A extensão universitária vem para cumprir o papel social da universidade, auxiliando nas soluções de demandas e atendendo aos interesses da população. A partir da necessidade das instituições de atendimento socioassistencial e dando escuta às necessidades local, o projeto tem por finalidade desenvolver atividades de apoio sociopedagógico que favoreçam o fortalecimento dos vínculos familiares e comunitários, educação financeira, desenvolvimento do autoconhecimento, formação para convivência, ética, cidadania, autoconfiança e resiliência, a fim de contribuir com o projeto de vida de adolescentes acolhidos, por meio de metodologias ativas como gamificação, dinâmicas de grupo, dentre outras. Na sua execução, esta proposta se compromete com as diretrizes conceituais da extensão, tendo como foco seus pilares e dentre eles, a dialogicidade. As ações ocorrem em parceria entre o projeto de extensão e a Instituição atendida, isto é, a Unidade de Acolhimento Institucional de adolescentes masculina vinculada à Secretaria Municipal de Assistência Social de Campo Grande - MS.  As atividades são interdisciplinares e ocorrem com acompanhamento e supervisão docente. Sob a vertente dialógica, a proposta procura levar em consideração a pluralidade e a diversidade, marcas intrínsecas da democracia com pauta na escuta, escolha, coautoria e corresponsabilidade. Espera-se que as ações conjuntas resultem em atitudes individuais e coletivas, que poderão impactar positivamente a realidade dos adolescentes atendidos, diminuindo as desigualdades sociais, na construção de novos valores

Ethyl (E)-2-methoxy­imino-2-(4-nitro­benzo­yl)acetate

The title mol­ecule, C12H12N2O6, features an E conformation about the oxime group. The methoxy­imino and ester residues are effectively coplanar with each other (r.m.s. deviation for the nine non-H atoms = 0.127 Å) and almost orthogonal [with dihedral angles of 99.44 (13) and −77.85 (13)°, respectively] to the carbonyl and nitro­phenyl groups which lie to either side of this central plane. The crystal structure is consolidated by C—H⋯O contacts

Analysis of the Association between CIMP and BRAFV600E in Colorectal Cancer by DNA Methylation Profiling

A CpG island methylator phenotype (CIMP) is displayed by a distinct subset of colorectal cancers with a high frequency of DNA hypermethylation in a specific group of CpG islands. Recent studies have shown that an activating mutation of BRAF (BRAFV600E) is tightly associated with CIMP, raising the question of whether BRAFV600E plays a causal role in the development of CIMP or whether CIMP provides a favorable environment for the acquisition of BRAFV600E. We employed Illumina GoldenGate DNA methylation technology, which interrogates 1,505 CpG sites in 807 different genes, to further study this association. We first examined whether expression of BRAFV600E causes DNA hypermethylation by stably expressing BRAFV600E in the CIMP-negative, BRAF wild-type COLO 320DM colorectal cancer cell line. We determined 100 CIMP-associated CpG sites and examined changes in DNA methylation in eight stably transfected clones over multiple passages. We found that BRAFV600E is not sufficient to induce CIMP in our system. Secondly, considering the alternative possibility, we identified genes whose DNA hypermethylation was closely linked to BRAFV600E and CIMP in 235 primary colorectal tumors. Interestingly, genes that showed the most significant link include those that mediate various signaling pathways implicated in colorectal tumorigenesis, such as BMP3 and BMP6 (BMP signaling), EPHA3, KIT, and FLT1 (receptor tyrosine kinases) and SMO (Hedgehog signaling). Furthermore, we identified CIMP-dependent DNA hypermethylation of IGFBP7, which has been shown to mediate BRAFV600E-induced cellular senescence and apoptosis. Promoter DNA hypermethylation of IGFBP7 was associated with silencing of the gene. CIMP-specific inactivation of BRAFV600E-induced senescence and apoptosis pathways by IGFBP7 DNA hypermethylation might create a favorable context for the acquisition of BRAFV600E in CIMP+ colorectal cancer. Our data will be useful for future investigations toward understanding CIMP in colorectal cancer and gaining insights into the role of aberrant DNA hypermethylation in colorectal tumorigenesis