gebhart/patrepeval huggingface dataset:
Quality Control of Cell Processing and Cord Blood Storage Using HALO To Measure Proliferative Potential of Stem and Progenitor Cells. (2004)

Abstract Prior to the introduction of flow cytometry to detect and measure CD34+ cells in the early 1980s, quality control of stem cell transplants was performed using the granulocyte-macrophage colony-forming assay (GM-CFC). The major disadvantages of this growth potential assay are that progenitor and not stem cells are detected and the assay takes too long to perform. Yet, measurement of the growth potential of proliferating cell populations in vitro is the only technique that guarantees the presence of stem cells after cell processing and may predict engraftment and reconstitution. There are no assays presently that exhibit these characteristics in real-time. However, it is now possible to measure the proliferative potential of stem and progenitor cells after cell processing and/or storage in half the time required by the classical colony-forming assay (CFA). Originally developed for hemotoxicity testing for all stages of drug development, HALO (Hematopoietic/Hemotoxicity Assays via Luminescence Output) can be used as an in-line stem cell processing quality control procedure as well as a method to ensure the growth potential of processed and stored umbilical cord blood. HALO sensitively measures small numbers of proliferating cells and because cell differentiation is not detected, manual enumeration of colonies is not required. The assay is based on the CFA procedure. However, as cells proliferate in response to growth factors, there is a proportional increase in the intracellular ATP concentration. The assay is performed in a 96-well plate and release of intracellular ATP drives a luciferin/luciferase reaction to produce bioluminescence in the form of light measured in a plate luminometer. The kinetics of most hematopoietic proliferating populations, including mature stem cells, allows results to be obtained after 6–7 days in culture. Measurement of luminescence for all 96 well cultures takes about 5 minutes. An ATP standard dose response performed prior to sample measurement not only provides quality control of the reagents used, but intra- and interlaboratory comparison of results. Due to the rapid and easy set-up procedure with high-throughput capability, the proliferative capacity of several stem and progenitor cell populations from either single or large numbers of samples from bone marrow, peripheral blood or cord blood can be analyzed simultaneously. Rapid assay turnaround and multiparameter capability should therefore allow an increased safety factor for patients undergoing stem cell transplantation. Additional studies are underway to further validate this approach.
Maternal control of seed size by <i>EOD3/CYP78A6</i> in <i>Arabidopsis thaliana</i> (2012)

Seed size in higher plants is coordinately determined by the growth of the embryo, endosperm and maternal tissue, but relatively little is known about the genetic and molecular mechanisms that set final seed size. We have previously demonstrated that Arabidopsis DA1 acts maternally to control seed size, with the da1-1 mutant producing larger seeds than the wild type. Through an activation tagging screen for modifiers of da1-1, we have identified an enhancer of da1-1 (eod3-1D) in seed size. EOD3 encodes the Arabidopsis cytochrome P450/CYP78A6 and is expressed in most plant organs. Overexpression of EOD3 dramatically increases the seed size of wild-type plants, whereas eod3-ko loss-of-function mutants form small seeds. The disruption of CYP78A9, the most closely related family member, synergistically enhances the seed size phenotype of eod3-ko mutants, indicating that EOD3 functions redundantly with CYP78A9 to affect seed growth. Reciprocal cross experiments show that EOD3 acts maternally to promote seed growth. eod3-ko cyp78a9-ko double mutants have smaller cells in the maternal integuments of developing seeds, whereas eod3-1D forms more and larger cells in the integuments. Genetic analyses suggest that EOD3 functions independently of maternal factors DA1 and TTG2 to influence seed growth. Collectively, our findings identify EOD3 as a factor of seed size control, and give insight into how plants control their seed size.
Modification of existing chip layout for yield and reliability improvement by computer-aided design tools (2003)

A CAD flow has been developed to modify an existing large scale chip layout to reinforce the redundant via design rules to improve the yield and reliability. The flow operates on each metal-via pair from bottom up to correct the redundant via rule violations. It divides a large complex design into cells, so that multiple process can work concurrently as if every process were working on the top level to reach the goal in a reasonable time.
Acid-gas bioconversion favors sulfur production (1982)

Chemical acid-gas conversion systems are available for converting H/sub 2/S to S/sup 0/. These include the Claus and Stretford processes. a photosynthetic anaerobic bioprocess for acid-gas removal has been developed which utilizes carbon dioxide instead of O/sub 2/ as the final electron acceptor. The carbohydrate produced by this reaction is of the general formula (CH/sub 2/O)/sub n/ and the photoautotrophic microorganism which catalyzes acid-gas bioconversion is Chlorobium thiosulfatophilum. Although orthorhombic sulfur is excreted by Chlorobium, the production of oxidized sulfur compounds decreases the yield of elemental sulfur from H/sub 2/S, and it is therefore desirable to control this side reaction. This article describes how the production of sulfate may be retarded. The factors studied were the effect of H/sub 2/S molar flow rate on the conversion of H/sub 2/S to SO/sub 4//sup -2/ and the effect of space velocity on the percentage conversion of H/sub 2/S to SO/sub 4//sup -2/. A higher percentage H/sub 2/S conversion to sulfate was associated with lower H/sub 2/S gas inflow rates; and at low space-velocity, a high conversion of H/sub 2/S to SO/sub 4//sup -2/ was achieved. 3 figures. (DP)
<title>Optimization of Q factor in optical nanocavities based on free-standing membranes</title> (2002)

We express the quality factor of a mode in terms of the Fourier transforms of its field components, and prove that the reduction in radiation loss can be achieved by suppressing the mode's wave-vector components within the light cone. Although this is intuitively clear, our analytical proof gives us insight into how to achieve the Q factor optimization, without the mode delocalization. We focus on the dipole defect mode in free standing membrane and achieve Q > 10<SUP>4</SUP>, while preserving the mode volume of the order of one half of cubic wavelength in material. The derived expressions and conclusions can be used in optimization of Q factor for any type of defect in planar photonic crystals.
Limited feedback design for interference alignment on MIMO interference networks with asymmetric path loss and spatial correlations (2012)

Interference alignment (IA) is degree of freedom (DoF) optimal on K-user MIMO interference channels and many previous works have studied the transceiver design of IA. However, these works predominantly focus on networks with perfect channel state information at the transmitters (CSIT) and symmetrical interference topology. In this paper, we consider a limited feedback system with heterogeneous path loss and spatial correlations, and investigate how the dynamics of the interference topology can be exploited to improve the feedback efficiency. We propose a novel spatial codebook design with low complexity, and perform dynamic quantization via bit allocations to adapt to the asymmetry of the interference topology. We also derive a lower bound of the system throughput under this proposed scheme. Both analytical and simulation results show that the proposed scheme can capture the heterogeneity of path loss and spatial correlations to enhance feedback efficiency.
Comparative transcriptomics of hepatic differentiation of human pluripotent stem cells and adult human liver tissue (2017)

Hepatocytes derived from human pluripotent stem cells (hPSC-HEP) have the potential to replace presently used hepatocyte sources applied in liver disease treatment and models of drug discovery and development. Established hepatocyte differentiation protocols are effective and generate hepatocytes, which recapitulate some key features of their in vivo counterparts. However, generating mature hPSC-HEP remains a challenge. In this study, we applied transcriptomics to investigate the progress of in vitro hepatic differentiation of hPSCs at the developmental stages, definitive endoderm, hepatoblasts, early hPSC-HEP, and mature hPSC-HEP, to identify functional targets that enhance efficient hepatocyte differentiation. Using functional annotation, pathway and protein interaction network analyses, we observed the grouping of differentially expressed genes in specific clusters representing typical developmental stages of hepatic differentiation. In addition, we identified hub proteins and modules that were involved in the cell cycle process at early differentiation stages. We also identified hub proteins that differed in expression levels between hPSC-HEP and the liver tissue controls. Moreover, we identified a module of genes that were expressed at higher levels in the liver tissue samples than in the hPSC-HEP. Considering that hub proteins and modules generally are essential and have important roles in the protein-protein interactions, further investigation of these genes and their regulators may contribute to a better understanding of the differentiation process. This may suggest novel target pathways and molecules for improvement of hPSC-HEP functionality, having the potential to finally bring this technology to a wider use.
Automotive Mixed Flow Fan with Guide Vanes on Blade Surfaces (1980)

<div class="section abstract"><div class="htmlview paragraph">We have developed a simple and lower cost mixed air flow fan with guide vanes on the blade surfaces for use in automotive engine cooling. Through investigation of the fan performance and flow visualization, the axial and radial flow produced by this fan proved to be most suitable and efficient for engine cooling. The improved efficiency and increased air flow provided by this fan contribute to reduction of specific noise level and power consumption as compared to conventional fans. It is moreover possible to reduce the size and dimensions of the fan while maintaining its cooling performance. It is also useful for eliminating heat dwelling and high temperature problems from the exhaust pipe and carburetor in the engine room.</div></div>
Single-Photon Detector at Telecommunication Wavelengths Using an Analog Integrator for Ultra Small Avalanche Discrimination (2013)

The afterpulse effect is one of the major bottlenecks limiting the performances of InGaAs/InP single-photon avalanche photodiodes (SPADs) for high-speed operation. In this paper, we present a practical and easy way to implement an afterpulse suppression scheme. Using an analog integrator circuit to discriminate small avalanche signals, we reduced drastically the afterpulse noise of the detector. At a repetition frequency of 25 MHz, the overall afterpulse probability is 1.48% with a detection efficiency of 15.6% and a dark count probability of 1.3×10-5. In addition, the detector features a maximum count rate of 25 MHz.
Synthesis of Metal Phthalocyanine Sheet Polymers (1986)

New method for synthesizing metal phthalocyanine tetracarboxylic acids (MPTCA's) yields high purity end product. In addition, high-purity metal phthalocyanine sheet polymers synthesized from compounds. Monomer formed into sheet polymer by heating. Units of polymer linked in manner similar to phenyl-group linkages in biphenyl: Conjugation extends throughout macromolecule, thereby increasing delocalization of TT-electrons. Increases conductivity and thermal stability of polymer.
SU-FF-T-169: Search for IMRT Inverse Plans with Piece-Wise Constant Fluence Maps Using Compressed Sensing Techniques (2009)

Purpose: An intensity modulated radiation therapy (IMRT) field is composed of a series of segmented beams. It is practically important to reduce the number of segments while maintaining the conformality of the final dose distribution. In this paper we quantify the complexity of an IMRT fluence map by introducing the concept of sparsity of fluence maps and formulate the inverse planning problem into a framework of compressing sensing. Method and Materials: In this approach, the treatment planning is modeled as a multi-objective optimization problem, with one objective on the dose performance and the other on the sparsity of the resultant fluence maps. A Pareto frontier is calculated, and the achieved dose distributions associated with the Pareto efficient points are evaluated using clinical acceptance criteria. The clinically acceptable dose distribution with the smallest number of segments is chosen as the final solution. Results: The method is demonstrated in the application of fixed-gantry IMRT on a prostate patient. The result shows that the total number of segments is greatly reduced while a satisfactory dose distribution is still achieved. Conclusion: A compressed sensing based inverse planning technique is proposed for IMRT planning. The main features of the approach include (1) the inclusion of a sparsity objective; and (2) the use of a convex optimization algorithm. Without compromising the dose performance, IMRT solutions with piece-wise constant fluence maps can be easily obtained using the proposed approach. The reduction of the number of segments in IMRT delivery reduces the total treatment time and therefore increases the dose delivery accuracy and the clinical throughput. With the focus on the sparsity of the optimal solution, the proposed method is distinct from the existing beamlet or segment-based optimization algorithms.
Temperature- and wavelength-insensitive parametric amplification enabled by noncollinear achromatic phase-matching (2016)

Optical parametric chirped-pulse amplification (OPCPA) has been demonstrated to be a promising approach for pushing femtosecond pulses towards ultra-high peak powers. However, the future success of OPCPA strongly relies on the ability to manipulate its phase-matching (PM) configuration. When a high average power pump laser is involved, the thermal effects in nonlinear crystals induce phase-mismatch distortions that pose an inherent limitation on the conversion efficiency. Here, we demonstrate that the noncollinear configuration previously adopted for wavelength-insensitive PM can be employed for temperature-insensitive PM when the noncollinear angle is properly reset. Simultaneous temperature- and wavelength-insensitive PM is realized for the first time by imposing such a temperature-insensitive noncollinear configuration with an angularly dispersed seed signal. Based on the lithium triborate crystal, the proposed noncollinear achromatic PM has a thermal acceptance 6 times larger than that of the conventional wavelength-insensitive noncollinear PM and has a sufficient spectral acceptance to support pulse durations of ~20 fs at 800 nm. These achievements open new possibilities for generating ultra-high peak power lasers with high average power.
Online Parameterization of Lumped Thermal Dynamics in Cylindrical Lithium Ion Batteries for Core Temperature Estimation and Health Monitoring (2012)

Lithium ion batteries should always be prevented from overheating and, hence, thermal monitoring is indispensable. Since only the surface temperature of the battery can be measured, a thermal model is needed to estimate the core temperature of the battery, which can be higher and more critical. In this paper, an online parameter identification scheme is designed for a cylindrical lithium ion battery. An adaptive observer of the core temperature is then designed based on the online parameterization methodology and the surface temperature measurement. A battery thermal model with constant internal resistance is explored first. The identification algorithm and the adaptive observer is validated with experiments on a 2.3Ah 26650 lithium iron phosphate/graphite battery. The methodology is later extended to address temperature-dependent internal resistance with nonuniform forgetting factors. The ability of the methodology to track the long-term variation of the internal resistance is beneficial for battery health monitoring.
Motorized actuation system to perform droplet operations on printed plastic sheets (2016)

We developed an open microfluidic system to dispense and manipulate discrete droplets on planar plastic sheets. Here, a superhydrophobic material is spray-coated on commercially-available plastic sheets followed by the printing of hydrophilic symbols using an inkjet printer. The patterned plastic sheets are taped to a two-axis tilting platform, powered by stepper motors, that provides mechanical agitation for droplet transport. We demonstrate the following droplet operations: transport of droplets of different sizes, parallel transport of multiple droplets, merging and mixing of multiple droplets, dispensing of smaller droplets from a large droplet or a fluid reservoir, and one-directional transport of droplets. As a proof-of-concept, a colorimetric assay is implemented to measure the glucose concentration in sheep serum. Compared to silicon-based digital microfluidic devices, we believe that the presented system is appealing for various biological experiments because of the ease of altering design layouts of hydrophilic symbols, relatively faster turnaround time in printing plastic sheets, larger area to accommodate more tests, and lower operational costs by using off-the-shelf products.
Use of Transmitochondrial Cybrids To Assign a Complex I Defect to the Mitochondrial DNA-Encoded NADH Dehydrogenase Subunit 6 Gene Mutation at Nucleotide Pair 14459 That Causes Leber Hereditary Optic Neuropathy and Dystonia (1996)

A heteroplasmic G-to-A transition at nucleotide pair (np) 14459 within the mitochondrial DNA (mtDNA)-encoded NADH dehydrogenase subunit 6 (ND6) gene has been identified as the cause of Leber hereditary optic neuropathy (LHON) and/or pediatric-onset dystonia in three unrelated families. This ND6 np 14459 mutation changes a moderately conserved alanine to a valine at amino acid position 72 of the ND6 protein. Enzymologic analysis of mitochondrial NADH dehydrogenase (complex I) with submitochondrial particles isolated from Epstein-Barr virus-transformed lymphoblasts revealed a 60% reduction (P < 0.005) of complex I-specific activity in patient cell lines compared with controls, with no differences in enzymatic activity for complexes II plus III, III and IV. This biochemical defect was assigned to the ND6 np 14459 mutation by using transmitochondrial cybrids in which patient Epstein-Barr virus-transformed lymphoblast cell lines were enucleated and the cytoplasts were fused to a mtDNA-deficient (p 0) lymphoblastoid recipient cell line. Cybrids harboring the np 14459 mutation exhibited a 39% reduction (p < 0.02) in complex I-specific activity relative to wild-type cybrid lines but normal activity for the other complexes. Kinetic analysis of the np 14459 mutant complex I revealed that the Vmax of the enzyme was reduced while the Km remained the same as that of wild type. Furthermore, specific activity was inhibited by increasing concentrations of the reduced coenzyme Q analog decylubiquinol. These observations suggest that the np 14459 mutation may alter the coenzyme Q-binding site of complex I.
Bovine herpesvirus 1 attachment to permissive cells is mediated by its major glycoproteins gI, gIII, and gIV (1991)

A bovine herpesvirus 1 (BHV-1) gIII deletion mutant (gIII-) was produced by means of recombinant DNA that retained the ability to replicate in cell culture. However, the gIII- mutant was functionally defective, showing impaired attachment to permissive cells, a delay in virus replication, and reduced extracellular virus production. The attachment defect exhibited by the gIII- mutant is an indication of the role played by gIII in the normal infection process. This was shown by dramatically decreased binding of radiolabelled gIII- virus to permissive cells and a slower adsorption rate, as measured by plaque formation, than the wild-type (wt) virus. Furthermore, treatment of the gIII- virus with neomycin increased virus adsorption and plaque formation by severalfold, whereas neomycin treatment had no effect on the wt virus. This observation showed that the gIII- mutant was strictly defective in adsorption but fully competent to produce productive infections once induced to attach. The gIII- mutant showed greater sensitivities than did the wt virus to anti-gI and anti-gIV antibody-mediated neutralization. Analyses with panels of monoclonal antibodies to gI and gIV revealed that the epitopes gI-IV and gIV-III were the main targets for enhanced neutralization. This provided evidence that gI and gIV may also participate in virus attachment. Finally, when affinity-purified gI, gIII, and gIV were tested for their ability to inhibit virus adsorption, gIII had the most pronounced inhibitory effect, followed by gI and then gIV. gIII was able to completely inhibit wt virus adsorption, and at a high concentration, it also partially inhibited the gIII- mutant. gI and gIV inhibited wt and gIII- mutant adsorption to a comparable extent. Our results collectively indicate that gIII plays a predominant role in virus attachment, but gI and gIV also contribute to this process. In addition, a potential cooperative mechanism for virus attachment with these three proteins is presented.
Tilted-grating approach for scanning-mode X-ray phase contrast imaging (2014)

Among the existent X-ray phase-contrast modalities, grating interferometry appears as a very promising technique for commercial applications, since it is compatible with conventional X-ray tubes and is robust from a mechanical point of view. However, since applications such as medical imaging and homeland security demand covering a considerable field of view, the fabrication of large-area gratings, which is known to be challenging and expensive, would be needed. A scanning setup is a good solution for this issue, because it uses cheaper line instead of large-area 2D detectors and, therefore, would require smaller gratings. In such a setup, the phase-retrieval using the conventional phase-stepping approach would be very slow, so having a faster method to record the signals becomes fundamental. To tackle this problem, we present a scanning-mode grating interferometer design, in which a grating is tilted to form Moiré fringes perpendicular to the grating lines. The sample is then translated along the fringes, so each line detector records a different phase step for each slice of the sample. This new approach was tested both in a simulated scenario and in an experimental setting, and its performance was quantitatively satisfactory compared to the traditional phase-stepping method and another existing scanning-mode technique.