Results for “cell analysis” — Page 67

DOE OSTI2015

SMITHERS: An object-oriented modular mapping methodology for MCNP-based neutronic–thermal hydraulic multiphysics

A novel object-oriented modular mapping methodology for externally coupled neutronics–thermal hydraulics multiphysics simulations was developed. The Simulator using MCNP with Integrated Thermal-Hydraulics for Exploratory Reactor Studies (SMITHERS) code performs on-the-fly mapping of material-wise power distribution tallies implemented by MCNP-based neutron transport/depletion solvers for use in estimating coolant temperature and density distributions with a separate thermal-hydraulic solver. The key development of SMITHERS is that it reconstructs the hierarchical geometry structure of the material-wise power generation tallies from the depletion solver automatically, with only a modicum of additional information required from the user. In addition, it performs the basis mapping from the combinatorial geometry of the depletion solver to the required geometry of the thermal-hydraulic solver in a generalizable manner, such that it can transparently accommodate varying levels of thermal-hydraulic solver geometric fidelity, from the nodal geometry of multi-channel analysis solvers to the pin-cell level of discretization for sub-channel analysis solvers.

42 ENGINEERING↗

DOE OSTI2014

Role of isothiocyanate conjugate of pterostilbene on the inhibition of MCF-7 cell proliferation and tumor growth in Ehrlich ascitic cell induced tumor bearing mice

Naturally occurring pterostilbene (PTER) and isothiocyanate (ITC) attract great attention due to their wide range of biological properties, including anti-cancer, anti-leukemic, anti-bacterial and anti-inflammatory activities. A novel class of hybrid compound synthesized by introducing an ITC moiety on PTER backbone was evaluated for its anti-cancer efficacy in hormone-dependent breast cancer cell line (MCF-7) in vitro and Ehrlich ascitic tumor bearing mice model in vivo. The novel hybrid molecule showed significant in vitro anti-cancer activity (IC{sub 50}=25±0.38) when compared to reference compound PTER (IC{sub 50}=65±0.42). The conjugate molecule induced both S and G2/M phase cell cycle arrest as indicated by flow cytometry analysis. In addition, the conjugate induced cell death was characterized by changes in cell morphology, DNA fragmentation, activation of caspase-9, release of cytochrome-c into cytosol and increased Bax: Bcl-2 ratio. The conjugate also suppressed the phosphorylation of Akt and ERK. The conjugate induced cell death was significantly increased in presence of A6730 (a potent Akt1/2 kinase inhibitor) and PD98059 (a specific ERK inhibitor). Moreover, the conjugated PTER inhibited tumor growth in Ehrlich ascitic cell induced tumor bearing mice as observed by reduction in tumor volume compared to untreated animals. Collectively, the pro-apoptotic effect of conjugate is mediated through the activation of caspases, and is correlated with the blockade of the Akt and ERK signaling pathways in MCF-7 cells. - Highlights: • Conjugate was prepared by appending isothiocyanate moiety on pterostilbene backbone. • Conjugate showed anticancer effects at comparatively lower dose than pterostilbene. • Conjugate caused blockage of the Akt and ERK signaling pathways in MCF-7 cells. • Conjugate significantly reduced solid tumor volume as compared to pterostilbene.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

Low cost back contact heterojunction solar cells on thin c-Si wafers. Integrating laser and thin film processing for improved manufacturability

An interdigitated back contact (IBC) Si wafer solar cell with deposited a-Si heterojunction (HJ) emitter and contacts is considered the ultimate single junction Si solar cell design. This was confirmed in 2014 by both Panasonic and Sharp Solar producing IBC-HJ cells breaking the previous record Si solar cell efficiency of 25%. But manufacturability at low cost is a concern for the complex IBC-HJ device structure. In this research program, our goals were to addressed the broad industry need for a high-efficiency c-Si cell that overcomes the dominant module cost barriers by 1) developing thin Si wafers synthesized by innovative, kerfless techniques; 2) integrating laser-based processing into most aspects of solar cell fabrication, ensuring high speed and low thermal budgets ; 3) developing an all back contact cell structure compatible with thin wafers using a simplified, low-temperature fabrication process; and 4) designing the contact patterning to enable simplified module assembly. There were a number of significant achievements from this 3 year program. Regarding the front surface, we developed and applied new method to characterize critical interface recombination parameters including interface defect density Dit and hole and electron capture cross-section for use as input for 2D simulation of the IBC cell to guide design and loss analysis. We optimized the antireflection and passivation properties of the front surface texture and a-Si/a-SiN/a-SiC stack depositions to obtain a very low (< 6 mA/cm2) front surface optical losses (reflection and absorption) while maintaining excellent surface passivation (SRV<5 cm/s). We worked with kerfless wafer manufacturers to apply defect-engineering techniques to improve bulk minority-carrier lifetime of thin kerfless wafers by both reducing initial impurities during growth and developing post-growth gettering techniques. This led insights about the kinetics of nickel, chromium, and dislocations in PV-grade silicon and to achieving millisecond lifetimes in kerfless silicon materials. Laser fired contacts to n-Si were developed for the first time using a Al/Sb/Ti metal stack giving contact resistances < 5 mOhm-cm2 when fired through several different dielectric layers. A new 2 step laser+chemical etch isolation technique was developed using a sacrificial top coating which avoids laser damage to Si passivation. Regarding the heterojunction emitter, analysis of front FHJ (1D) and IBC (2D) cells with range of p-layer conditions found that a 2-stage high/low doped p-layer was optimum: the low doped region has lower defects giving higher Voc and the high doped region gave a better contact to the metal. A significant effort was spent studying the patterning process and its contribution to degradation of passivation and reproducibility. Several promising new cleaning, contact and deposition patterning and processing approaches were implemented leading to fabrication of several runs with cells having 19-20% efficiency which were stable over several months. This program resulted in the training and support of 12 graduate students, publication of 21 journal papers and 14 conference papers.

14 SOLAR ENERGY↗

DOE OSTI2015

Low cost back contact heterojunction solar cells on thin c-Si wafers. integrating laser and thin film processing for improved manufacturability

An interdigitated back contact (IBC) Si wafer solar cell with deposited a-Si heterojunction (HJ) emitter and contacts is considered the ultimate single junction Si solar cell design. This was confirmed in 2014 by both Panasonic and Sharp Solar producing IBC-HJ cells breaking the previous record Si solar cell efficiency of 25%. But manufacturability at low cost is a concern for the complex IBC-HJ device structure. In this research program, our goals were to addressed the broad industry need for a high-efficiency c-Si cell that overcomes the dominant module cost barriers by 1) developing thin Si wafers synthesized by innovative, kerfless techniques; 2) integrating laser-based processing into most aspects of solar cell fabrication, ensuring high speed and low thermal budgets ; 3) developing an all back contact cell structure compatible with thin wafers using a simplified, low-temperature fabrication process; and 4) designing the contact patterning to enable simplified module assembly. There were a number of significant achievements from this 3 year program. Regarding the front surface, we developed and applied new method to characterize critical interface recombination parameters including interface defect density Dit and hole and electron capture cross-section for use as input for 2D simulation of the IBC cell to guide design and loss analysis. We optimized the antireflection and passivation properties of the front surface texture and a-Si/a-SiN/a-SiC stack depositions to obtain a very low (< 6 mA/cm2) front surface optical losses (reflection and absorption) while maintaining excellent surface passivation (SRV<5 cm/s). We worked with kerfless wafer manufacturers to apply defect-engineering techniques to improve bulk minority-carrier lifetime of thin kerfless wafers by both reducing initial impurities during growth and developing post-growth gettering techniques. This led insights about the kinetics of nickel, chromium, and dislocations in PV-grade silicon and to achieving millisecond lifetimes in kerfless silicon materials. Laser fired contacts to n-Si were developed for the first time using a Al/Sb/Ti metal stack giving contact resistances < 5 mOhm-cm2 when fired through several different dielectric layers. A new 2 step laser+chemical etch isolation technique was developed using a sacrificial top coating which avoids laser damage to Si passivation. Regarding the heterojunction emitter, analysis of front FHJ (1D) and IBC (2D) cells with range of p-layer conditions found that a 2-stage high/low doped p-layer was optimum: the low doped region has lower defects giving higher Voc and the high doped region gave a better contact to the metal. A significant effort was spent studying the patterning process and its contribution to degradation of passivation and reproducibility. Several promising new cleaning, contact and deposition patterning and processing approaches were implemented leading to fabrication of several runs with cells having 19-20% efficiency which were stable over several months. This program resulted in the training and support of 12 graduate students, publication of 21 journal papers and 14 conference papers.

14 SOLAR ENERGY↗

NASA NTRS1975

Vertical velocity structure and geometry of clear air convective elements

The paper discusses observations of individual convective elements with a high-power narrow-beam scanning radar, an FM-CW radar, and an acoustic sounder, including the determination of the vertical air velocity patterns of convective structures with the FM-CW radar and acoustic sounder. Data are presented which link the observed velocity structure and geometrical patterns to previously proposed models of boundary layer convection. It is shown that the high-power radar provides a clear three-dimensional picture of convective cells and fields over a large area with a resolution of 150 m, where the convective cells are roughly spherical. Analysis of time-height records of the FM-CW radar and acoustic sounder confirms the downdraft-entrainment mechanism of the convective cell. The Doppler return of the acoustic sounder and the insect-trail slopes on FM-CW radar records are independent but redundant methods for obtaining the vertical velocity patterns of convective structures.

Rowland, J. R.↗

NASA NTRS1984

Bioprocessing in space

Attachment to a substrate and survival of human embryonic kidney cells (HEK) was tested in an incubator installed in the flight-deck of the space shuttle Challenger. The HEK cells produce the enzyme urokinase and are candidates for electrophoretic separation. Attachment of the cells to a substrate is mandatory for survival. Analysis of the samples shows that cells adhere, spread and survive in 0 g conditions as well as the ground controls at 1 g.

Tschopp, A.↗

NASA NTRS1991

Pilot production of 4 sq cm ITO/InP photovoltaic solar cells

Experimental results of a pilot production of 32 4-sq cm indium tin oxide (ITO)InP space solar cells are presented. The discussion includes analysis of the device performance of the best cells produced as well as the performance range of all production cells. The experience gained from the production is discussed, indicating other issues that may be encountered when large-scale productions are initiated. Available data on a 4-sq cm ITO/InP cell that was flown on the UoSAT-5 satellite is reported.

Gessert, T. A.↗

NASA NTRS1995

On the Finite Element Implementation of the Generalized Method of Cells Micromechanics Constitutive Model

The Generalized Method of Cells (GMC), a micromechanics based constitutive model, is implemented into the finite element code MARC using the user subroutine HYPELA. Comparisons in terms of transverse deformation response, micro stress and strain distributions, and required CPU time are presented for GMC and finite element models of fiber/matrix unit cell. GMC is shown to provide comparable predictions of the composite behavior and requires significantly less CPU time as compared to a finite element analysis of the unit cell. Details as to the organization of the HYPELA code are provided with the actual HYPELA code included in the appendix.

Wilt, T. E.↗

DOE OSTI2015

Microfluidic Cell-based Assays in Stem Cell and Other Rare Cell Type Research

Microfluidics is a technology defined by the engineered precise manipulation of minute amount of liquids through channels with dimensions in the micron scale. Much of microfluidic devices used for biomedical purposes are produced in the form of so called “lab-on-a-chip” format, where multiple steps of conventional biochemical analyses such as staining, washing, and signal collection are miniaturized and integrated into chips fabricated from polymer or glass. Cell-based microfluidic lab-on-achip technology provides some obvious advantages: 1) drastically reduced sample and reagent requirement, and 2) separation and detection with improved sensitivity due to fluid properties at the microscale, i.e. laminar flow. Based on these two advantages, the obvious place where microfluidic cell assays will provide the most benefit is wherescientists must gather much information from precious little sample. Stem cells and other precious cell types such as circulating tumor cells (CTCs), and rare immune subsets are the perfect match for microfluidic multiplex assays. The recent demonstration that multiple cellular changes such as surface receptor activation, protein translocation, long and short RNA, and DNA changes can all be extracted from intact single cells paves the way to systems level understanding of cellular states during development or disease. Finally, with the ability to preserve cell integrity in a microfluidic device during multiplexed analysis, one also preserves the single cell resolution, where information regarding the cell-to-cell heterogeneity during differentiation or response to stimuli is vitally important.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Development of a Fluorescence-Activated Cell Sorting Method Coupled with Whole Genome Amplification To Analyze Minority and Trace Dehalococcoides Genomes in Microbial Communities

Dehalococcoides mccartyi are functionally important bacteria that catalyze the reductive dechlorination of chlorinated ethenes. However, these anaerobic bacteria are fastidious to isolate, making downstream genomic characterization challenging. In order to facilitate genomic analysis, a fluorescence-activated cell sorting (FACS) method was developed in this study to separate D. mccartyi cells from a microbial community, and the DNA of the isolated cells was processed by whole genome amplification (WGA) and hybridized onto a D. mccartyi microarray for comparative genomics against four sequenced strains. First, FACS was successfully applied to a D. mccartyi isolate as positive control, and then microarray results verified that WGA from 10 6 cells or &sim;1 ng of genomic DNA yielded high-quality coverage detecting nearly all genes across the genome. As expected, some inter- and intrasample variability in WGA was observed, but these biases were minimized by performing multiple parallel amplifications. Subsequent application of the FACS and WGA protocols to two enrichment cultures containing &sim;10% and &sim;1% D. mccartyi cells successfully enabled genomic analysis. As proof of concept, this study demonstrates that coupling FACS with WGA and microarrays is a promising tool to expedite genomic characterization of target strains in environmental communities where the relative concentrations are low.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Gastight Hydrodynamic Electrochemistry: Design for a Hermetically Sealed Rotating Disk Electrode Cell

Rotating disk electrodes (RDEs) are widely used in electrochemical characterization to analyze the mechanisms of various electrocatalytic reactions. RDE experiments often make use of or require collection and quantification of gaseous products. The combination of rotating parts and gaseous analytes makes the design of RDE cells that allow for headspace analysis challenging due to gas leaks at the interface of the cell body and the rotator. In this manuscript we describe a new, hermetically sealed electrochemical cell that allows for electrode rotation while simultaneously providing a gastight environment. Electrode rotation in this new cell design is controlled by magnetically coupling the working electrode to a rotating magnetic driver. Calibration of the RDE using a tachometer shows that the rotation speed of the electrode is the same as that of the magnetic driver. To validate the performance of this cell for hydrodynamic measurements, limiting currents from the reduction of a potassium ferrocyanide (K 4 [Fe(CN) 6 ]·3H 2 O) were measured and shown to compare favorably with calculated values from the Levich equation and with data obtained using more typical, nongastight RDE cells. Faradaic efficiencies of ~95% were measured in the gas phase for oxygen evolution in alkaline media at an Inconel 625 alloy electrocatalyst during rotation at 1600 rpm. These data verify that a gastight environment is maintained even during rotation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

The RNA-binding protein Modulo promotes neural stem cell maintenance in Drosophila

A small population of stem cells in the developing Drosophila central nervous system generates the large number of different cell types that make up the adult brain. To achieve this, these neural stem cells (neuroblasts, NBs) divide asymmetrically to produce non-identical daughter cells. The balance between stem cell self-renewal and neural differentiation is regulated by various cellular machinery, including transcription factors, chromatin remodelers, and RNA-binding proteins. The list of these components remains incomplete, and the mechanisms regulating their function are not fully understood, however. Here, we identify a role for the RNA-binding protein Modulo (Mod; nucleolin in humans) in NB maintenance. We employ transcriptomic analyses to identify RNA targets of Mod and assess changes in global gene expression following its knockdown, results of which suggest a link with notable proneural genes and those essential for neurogenesis. Mod is expressed in larval brains and its loss leads to a significant decrease in the number of central brain NBs. Stem cells that remain lack expression of key NB identity factors and exhibit cell proliferation defects. Mechanistically, our analysis suggests these deficiencies arise at least in part from altered cell cycle progression, with a proportion of NBs arresting prior to mitosis. Overall, our data show that Mod function is essential for neural stem cell maintenance during neurogenesis.

Parra, Amalia S.↗

NASA NTRS1984

The structure and function of fungal cells

The structure and function of fungal cell walls were studied with particular emphasis on dermatophytes. Extraction, isolation, analysis, and observation of the cell wall structure and function were performed. The structure is described microscopically and chemically.

Nozawa, Y.↗

NASA NTRS1993

Preconditioned domain decomposition scheme for three-dimensional aerodynamic sensitivity analysis

A preconditioned domain decomposition scheme is introduced for the solution of the 3D aerodynamic sensitivity equation. This scheme uses the iterative GMRES procedure to solve the effective sensitivity equation of the boundary-interface cells in the sensitivity analysis domain-decomposition scheme. Excluding the dense matrices and the effect of cross terms between boundary-interfaces is found to produce an efficient preconditioning matrix.

Eleshaky, Mohammed E.↗

DOE OSTI2021

Multiblock Discriminant Analysis of Integrative 18F-FDG-PET/CT Radiomics for Predicting Circulating Tumor Cells in Early-Stage Non-small Cell Lung Cancer Treated With Stereotactic Body Radiation Therapy

The main objective of the present study was to integrate {sup 18}F-FDG-PET/CT radiomics with multiblock discriminant analysis for predicting circulating tumor cells (CTCs) in early-stage non-small cell lung cancer (ES-NSCLC) treated with stereotactic body radiation therapy (SBRT).

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2015

Metabolic Adaptations of Azospirillum brasilense to Oxygen Stress by Cell-to-Cell Clumping and Flocculation

The ability of bacteria to monitor their metabolism and adjust their behavior accordingly is critical to maintain competitiveness in the environment. The motile microaerophilic bacterium Azospirillum brasilense navigates oxygen gradients by aerotaxis in order to locate low oxygen concentrations that can support metabolism. When cells are exposed to elevated levels of oxygen in their surroundings, motile A. brasilense cells implement an alternative response to aerotaxis and form transient clumps by cell-to-cell interactions. Clumping was suggested to represent a behavior protecting motile cells from transiently elevated levels of aeration. Using the proteomics of wild-type and mutant strains affected in the extent of their clumping abilities, we show that cell-to-cell clumping represents a metabolic scavenging strategy that likely prepares the cells for further metabolic stresses. Analysis of mutants affected in carbon or nitrogen metabolism confirmed this assumption. The metabolic changes experienced as clumping progresses prime cells for flocculation, a morphological and metabolic shift of cells triggered under elevated-aeration conditions and nitrogen limitation. The analysis of various mutants during clumping and flocculation characterized an ordered set of changes in cell envelope properties accompanying the metabolic changes. These data also identify clumping and early flocculation to be behaviors compatible with the expression of nitrogen fixation genes, despite the elevated-aeration conditions. Finally, cell-to-cell clumping may thus license diazotrophy to microaerophilic A. brasilense cells under elevated oxygen conditions and prime them for long-term survival via flocculation if metabolic stress persists.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1966

Synthesis of current-switching circuits with cell matching using p-n-p and n-p-n transistors

Logical circuit for analysis of switching circuits with cell matching using p-n-p and n-p-n transistors

TRANSISTOR↗

DOE OSTI2017

Automating cell detection and classification in human brain fluorescent microscopy images using dictionary learning and sparse coding

Background Immunofluorescence (IF) plays a major role in quantifying protein expression in situ and understanding cell function. It is widely applied in assessing disease mechanisms and in drug discovery research. Automation of IF analysis can transform studies using experimental cell models. However, IF analysis of postmortem human tissue relies mostly on manual interaction, often subjected to low-throughput and prone to error, leading to low inter and intra-observer reproducibility. Human postmortem brain samples challenges neuroscientists because of the high level of autofluorescence caused by accumulation of lipofuscin pigment during aging, hindering systematic analyses. We propose a method for automating cell counting and classification in IF microscopy of human postmortem brains. Our algorithm speeds up the quantification task while improving reproducibility. New method Dictionary learning and sparse coding allow for constructing improved cell representations using IF images. These models are input for detection and segmentation methods. Classification occurs by means of color distances between cells and a learned set. Results Our method successfully detected and classified cells in 49 human brain images. We evaluated our results regarding true positive, false positive, false negative, precision, recall, false positive rate and F1 score metrics. We also measured user-experience and time saved compared to manual countings. Comparison with existing methods We compared our results to four open-access IF-based cell-counting tools available in the literature. Lastly, our method showed improved accuracy for all data samples. Conclusion The proposed method satisfactorily detects and classifies cells from human postmortem brain IF images, with potential to be generalized for applications in other counting tasks.

59 BASIC BIOLOGICAL SCIENCES↗