Knowledge Based Gene Set analysis (KB-GSA): A novel method for gene expression analysis

Abstract Microarray technology allows measurement of the expression levels o

Projecting picosecond lattice dynamics through x-ray topography

A method for time-resolved x-ray diffraction studies has been demonstrated. As a test case, coherent acoustic phonon propagation into crystalline InSb is observed using a laser plasma x-ray source. An extended x-ray topogram of the semiconductor's surface was projected onto a high spatial resolution x-ray detector and acoustic phonons were excited by rapidly heating the crystal's surface with a femtosecond laser pulse. A correlation between the spatial position on the x-ray detector and the time of arrival of the laser pulse was encoded into the experimental geometry by tilting the incident laser pulse with an optical grating. This approach enabled a temporal window of 200 ps to be sampled in a single topogram, thereby negating the disadvantages of pulse-to-pulse fluctuations in the intensity and spectrum of the laser-plasma source. (C) 2002 American Institute of Physics

Coherent phonon control.

http://dx.doi.org

Artificial Intelligence Supports Automated Characterization of Differentiated Human Pluripotent Stem Cells

Revolutionary advances in AI and deep learning in recent years have resulted in an upsurge of papers exploring applications within the biomedical field. Within stem cell research, promising results have been reported from analyses of microscopy images to, that is, distinguish between pluripotent stem cells and differentiated cell types derived from stem cells. In this work, we investigated the possibility of using a deep learning model to predict the differentiation stage of pluripotent stem cells undergoing differentiation toward hepatocytes, based on morphological features of cell cultures. We were able to achieve close to perfect classification of images from early and late time points during differentiation, and this aligned very well with the experimental validation of cell identity and function. Our results suggest that deep learning models can distinguish between different cell morphologies, and provide alternative means of semi-automated functional characterization of stem cell cultures

Levosimendan versus Milrinone for Inotropic Support in Pediatric Cardiac Surgery: Results from a Randomized Trial

Objective : We aimed to determine the differential effects of intra-operative administration of milrinone versus levosimendan on myocardial function after pediatric cardiac surgery. Transthoracic echocardiography was employed for myocardial function evaluation, utilizing biventricular longitudinal strain with two-dimensional speckle tracking echocardiography in addition to conventional echocardiographic variables. Design : A secondary analysis of a randomized, prospective, double-blinded clinical drug trial Setting : Two pediatric tertiary university hospitals Participants : Infants between 1-12 months of age diagnosed with ventricular septal defect, complete atrioventricular septal defect, or tetralogy of Fallot who were scheduled for corrective surgery with cardiopulmonary bypass. Interventions : The patients were randomized to receive an infusion of milrinone or levosimendan at the start of cardiopulmonary bypass and for 26 consecutive hours. Measurements and main results : Biventricular longitudinal strain and conventional echocardiographic variables were measured preoperatively, on the first postoperative morning and prior to hospital discharge. The association between perioperative parameters and postoperative myocardial function was also investigated. Images were analyzed for left ventricular (n=67) and right ventricular (n=44) function. The day after surgery, left ventricular longitudinal strain was deteriorated in both the milrinone and levosimendan groups; 33% and 39%, respectively. The difference was not significant. The corresponding deterioration in right ventricular longitudinal strain was 42% and 50% (non-significant difference). For both groups, biventricular longitudinal strain approached their preoperative values at hospital discharge. Preoperative N-terminal pro-brain natriuretic peptide could predict the left ventricular strain on postoperative day one (p=0.014). Conclusions : Levosimendan was comparable to milrinone for left and right ventricular inotropic support in pediatric cardiac surgery.Peer reviewe

Human Embryonic Stem Cell Derived Hepatocyte-Like Cells as a Tool for In Vitro Hazard Assessment of Chemical Carcinogenicity

Hepatocyte-like cells derived from the differentiation of human embryonic stem cells (hES-Hep) have potential to provide a human relevant in vitro test system in which to evaluate the carcinogenic hazard of chemicals. In this study, we have investigated this potential using a panel of 15 chemicals classified as noncarcinogens, genotoxic carcinogens, and nongenotoxic carcinogens and measured whole-genome transcriptome responses with gene expression microarrays. We applied an ANOVA model that identified 592 genes highly discriminative for the panel of chemicals. Supervised classification with these genes achieved a cross-validation accuracy of > 95%. Moreover, the expression of the response genes in hES-Hep was strongly correlated with that in human primary hepatocytes cultured in vitro. In order to infer mechanistic information on the consequences of chemical exposure in hES-Hep, we developed a computational method that measures the responses of biochemical pathways to the panel of treatments and showed that these responses were discriminative for the three toxicity classes and linked to carcinogenesis through p53, mitogen-activated protein kinases, and apoptosis pathway modules. It could further be shown that the discrimination of toxicity classes was improved when analyzing the microarray data at the pathway level. In summary, our results demonstrate, for the first time, the potential of human embryonic stem cell--derived hepatic cells as an in vitro model for hazard assessment of chemical carcinogenesis, although it should be noted that more compounds are needed to test the robustness of the assay

Projecting picosecond lattice dynamics through x-ray topography

A method for time-resolved x-ray diffraction studies has been demonstrated. As a test case, coherent acoustic phonon propagation into crystalline InSb is observed using a laser plasma x-ray source. An extended x-ray topogram of the semiconductor's surface was projected onto a high spatial resolution x-ray detector and acoustic phonons were excited by rapidly heating the crystal's surface with a femtosecond laser pulse. A correlation between the spatial position on the x-ray detector and the time of arrival of the laser pulse was encoded into the experimental geometry by tilting the incident laser pulse with an optical grating. This approach enabled a temporal window of 200 ps to be sampled in a single topogram, thereby negating the disadvantages of pulse-to-pulse fluctuations in the intensity and spectrum of the laser-plasma source. (C) 2002 American Institute of Physics