In Virto

Seven new 3-alkyl(aryl)-4-(2-thienymethylenamino)-4,5-dihydro-1H-1,2,4-triazol-5-ones (2) were synthesized by the reactions of 3-alkyl(aryl)-4-amino-4,5-dihydro-1H-1,2,4-triazol-5-ones (1) with thiophene-2-carbaldehyde. In addition, N-acetyl derivatives of compounds 2d-2g were also prepared. The structures of eleven new compounds synthesized were determined by elemental analysis as well as IR, NMR and UV spectral data. In addition, compounds 2a-g and 3a, 3b, 3d-f were also screened for their antioxidant activities and 2a-g were potentiometrically titrated with tetrabutylammonium hydroxide (TBAH) in four nonaqueous solvents (isopropyl alcohol, t-butyl alcohol, acetonitrile and N,N-dimethyl formamide). Also half-neutralization potential values and the corresponding pKa values were determined in all cases

CalibFPA: A Focal Plane Array Imaging System based on Online Deep-Learning Calibration

Compressive focal plane arrays (FPA) enable cost-effective high-resolution (HR) imaging by acquisition of several multiplexed measurements on a low-resolution (LR) sensor. Multiplexed encoding of the visual scene is typically performed via electronically controllable spatial light modulators (SLM). An HR image is then reconstructed from the encoded measurements by solving an inverse problem that involves the forward model of the imaging system. To capture system non-idealities such as optical aberrations, a mainstream approach is to conduct an offline calibration scan to measure the system response for a point source at each spatial location on the imaging grid. However, it is challenging to run calibration scans when using structured SLMs as they cannot encode individual grid locations. In this study, we propose a novel compressive FPA system based on online deep-learning calibration of multiplexed LR measurements (CalibFPA). We introduce a piezo-stage that locomotes a pre-printed fixed coded aperture. A deep neural network is then leveraged to correct for the influences of system non-idealities in multiplexed measurements without the need for offline calibration scans. Finally, a deep plug-and-play algorithm is used to reconstruct images from corrected measurements. On simulated and experimental datasets, we demonstrate that CalibFPA outperforms state-of-the-art compressive FPA methods. We also report analyses to validate the design elements in CalibFPA and assess computational complexity

PathwayMapper: A collaborative visual web editor for cancer pathways and genomic data

Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene. Results: To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers. It can be used for viewing pre-curated cancer pathways, or as a graphical editor for creating new pathways, with the ability to overlay genomic alteration data from cBioPortal. In addition, a collaborative mode is available that allows scientists to co-operate interactively on constructing pathways, with support for concurrent modifications and built-in conflict resolution. © 2017 The Author. Published by Oxford University Press. All rights reserved

Collaborative workspaces for pathway curation

We present a web based visual biocuration workspace, focusing on curating detailed mechanistic pathways. It was designed as a flexible platform where multiple humans, NLP and AI agents can collaborate in real-time on a common model using an event driven API. We will use this platform for exploring disruptive technologies that can scale up biocuration such as NLP, human-computer collaboration, crowd-sourcing, alternative publishing and gamification. As a first step, we are designing a pilot to include an author-curation step into the scientific publishing, where the authors of an article create formal pathway fragments representing their discovery- heavily assisted by computer agents. We envision that this "microcuration" use-case will create an excellent opportunity to integrate multiple NLP approaches and semi-automated curation. © 2016, CEUR-WS. All rights reserved

A Multifaceted Analysis of Immune-Endocrine-Metabolic Alterations in Patients with Pulmonary Tuberculosis

Our study investigated the circulating levels of factors involved in immune-inflammatory-endocrine-metabolic responses in patients with tuberculosis with the aim of uncovering a relation between certain immune and hormonal patterns, their clinical status and in vitro immune response. The concentration of leptin, adiponectin, IL-6, IL-1β, ghrelin, C-reactive protein (CRP), cortisol and dehydroepiandrosterone (DHEA), and the in vitro immune response (lymphoproliferation and IFN-γ production) was evaluated in 53 patients with active untreated tuberculosis, 27 household contacts and 25 healthy controls, without significant age- or sex-related differences. Patients had a lower body mass index (BMI), reduced levels of leptin and DHEA, and increased concentrations of CRP, IL-6, cortisol, IL-1β and nearly significant adiponectin values than household contacts and controls. Within tuberculosis patients the BMI and leptin levels were positively correlated and decreased with increasing disease severity, whereas higher concentrations of IL-6, CRP, IL-1β, cortisol, and ghrelin were seen in cases with moderate to severe tuberculosis. Household contacts had lower DHEA and higher IL-6 levels than controls. Group classification by means of discriminant analysis and the k-nearest neighbor method showed that tuberculosis patients were clearly different from the other groups, having higher levels of CRP and lower DHEA concentration and BMI. Furthermore, plasma leptin levels were positively associated with the basal in vitro IFN-γ production and the ConA-driven proliferation of cells from tuberculosis patients. Present alterations in the communication between the neuro-endocrine and immune systems in tuberculosis may contribute to disease worsening

Oncogenic Signaling Pathways in The Cancer Genome Atlas

Genetic alterations in signaling pathways that control cell-cycle progression, apoptosis, and cell growth are common hallmarks of cancer, but the extent, mechanisms, and co-occurrence of alterations in these pathways differ between individual tumors and tumor types. Using mutations, copy-number changes, mRNA expression, gene fusions and DNA methylation in 9,125 tumors profiled by The Cancer Genome Atlas (TCGA), we analyzed the mechanisms and patterns of somatic alterations in ten canonical pathways: cell cycle, Hippo, Myc, Notch, Nrf2, PI-3-Kinase/Akt, RTK-RAS, TGFb signaling, p53 and beta-catenin/Wnt. We charted the detailed landscape of pathway alterations in 33 cancer types, stratified into 64 subtypes, and identified patterns of co-occurrence and mutual exclusivity. Eighty-nine percent of tumors had at least one driver alteration in these one alteration potentially targetable by currently available drugs. Thirty percent of tumors had multiple targetable alterations, indicating opportunities for combination therapy

Bone mineral density in patients with endogenous subclinical hyperthyroidism

The aim of our study was to elucidate whether endogenous subclinical hyperthyroidism due to an autonomously functioning thyroid nodule affects bone metabolism and is a risk factor for osteoporosis and if so, whether it differs according to sex and menopausal status. In this cross-sectional study measurements of bone mineral density (BMD) were performed in 9 premenopausal, 12 post-menopausal women and it 7 men who had all endogenous subclinical hyperthyroidism due to an autonomously functioning thyroid nodule. Neither of them had a past history of hyperthyroidism not had been treated for any thyroid disorder. All of them were euthryroid by clinical and laboratory evaluation. They had single or multiple solid nodules or ultrasound and single or multiple autonomous (suppressing the surrounding tissue) nodules or scintigraphy. Lumbar spine BMD was measured by quantitative computerized tomography. The levels of triiodothyronine (T3), tetraiodothyronine (T4), free T3 (fT3), free T4 (fT4), thyrotropin (TSH), parathyroid hormone (PTH), serum calcium (Ca), alkaline phosphatase (ALP), cholesterol, ferritin, osteocalcin (OC) and urine calcium-creatinine ratios were determined. The results were compared with the age and sex matched controls in each subgroup (premenopausal, post-menopausal females and males). Bone mineral density of premenopausal females did not show any difference in comparison with age and sex matched controls. It was found to be significantly (p < 0.05) lower in post-menopausal females and insignificantly low in males when compared with age and sex matched controls. A statistically significant increase was found in OC levels in each of the three subgroup when compared with controls (p < 0.05). In conclusion, the results of our study revealed that endogenous subclinical hyperthyroidism due to an autonomously functioning thyroid nodule may affect bone metabolism and may be an additional risk factor for osteoporosis especially in post-menopausal females

Correlation between serum lipoprotein(a) and angiographic coronary artery disease in non-insulin-dependent diabetes mellitus.

Objectives, To examine the impact of diabetic state on the concentrations of lipoprotein(a) [Lp(a)] in patients with non-insulin-dependent diabetes mellitus (NIDDM) and the correlation between angiographic coronary artery disease (CAD) and serum Lp(a) concentrations in NIDDM

PathwayMapper: A collaborative visual web editor for cancer pathways and genomic data

Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene. Results: To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers. It can be used for viewing pre-curated cancer pathways, or as a graphical editor for creating new pathways, with the ability to overlay genomic alteration data from cBioPortal. In addition, a collaborative mode is available that allows scientists to co-operate interactively on constructing pathways, with support for concurrent modifications and built-in conflict resolution. © 2017 The Author. Published by Oxford University Press. All rights reserved