gebhart/patrepeval huggingface dataset:
Cell Chromatography: Biocompatible chromatographic separation and interrogation of microbial cells (2022)

Abstract The isolation of pure, single colonies lies at the heart of experimental microbiology. However, a microbial colony typically contains around one million cells at all stages of the life cycle. Here we describe a novel, cell chromatography method that facilitates the capture, purification and interrogation of microbial cells from both single and mixed cultures. The method described relies on, but is not limited to, differences in surface charge to separate bacterial strains. The method is fully biocompatible, leading to no significant loss of cell viability,. The chromatographic capture of cells, combined with selective elution methods facilitates a greater level of experimental control over the sample inputs required for downstream high throughput and high sensitivity, analytical methods. The application of the method for interrogating the antibiotic resistance of bacterial strains and for the separation of bacteria from environmental samples is illustrated.
Autopsy Study Defines Composition and Dynamics of the HIV-1 Reservoir after Allogeneic Hematopoietic Stem Cell Transplantation with CCR5Δ32/Δ32 Donor Cells (2022)

Allo-HSCT with CCR5Δ32/Δ32 donor cells is the only curative HIV-1 intervention. We investigated the impact of allo-HSCT on the viral reservoir in PBMCs and post-mortem tissue in two patients. IciS-05 and IciS-11 both received a CCR5Δ32/Δ32 allo-HSCT. Before allo-HSCT, ultrasensitive HIV-1 RNA quantification; HIV-1-DNA quantification; co-receptor tropism analysis; deep-sequencing and viral characterization in PBMCs and bone marrow; and post-allo-HSCT, ultrasensitive RNA and HIV-1-DNA quantification were performed. Proviral quantification, deep sequencing, and viral characterization were done in post-mortem tissue samples. Both patients harbored subtype B CCR5-tropic HIV-1 as determined genotypically and functionally by virus culture. Pre-allo-HSCT, HIV-1-DNA could be detected in both patients in bone marrow, PBMCs, and T-cell subsets. Chimerism correlated with detectable HIV-1-DNA LTR copies in cells and tissues. Post-mortem analysis of IciS-05 revealed proviral DNA in all tissue biopsies, but not in PBMCs. In patient IciS-11, who was transplanted twice, no HIV-1-DNA could be detected in PBMCs at the time of death, whereas HIV-1-DNA was detectable in the lymph node. In conclusion, shortly after CCR5Δ32/Δ32, allo-HSCT HIV-1-DNA became undetectable in PBMCs. However, HIV-1-DNA variants identical to those present before transplantation persisted in post-mortem-obtained tissues, indicating that these tissues play an important role as viral reservoirs.
BMP2 is Superior to BMP4 for Promoting Human Muscle-Derived Stem Cell-Mediated Bone Regeneration in a Critical-Sized Calvarial Defect Model (2013)

Muscle-derived cells have been successfully isolated using a variety of different methods and have been shown to possess multilineage differentiation capacities, including an ability to differentiate into articular cartilage and bone in vivo; however, the characterization of human muscle-derived stem cells (hMDSCs) and their bone regenerative capacities have not been fully investigated. Genetic modification of these cells may enhance their osteogenic capacity, which could potentially be applied to bone regenerative therapies. We found that hMDSCs, isolated by the preplate technique, consistently expressed the myogenic marker CD56, the pericyte/endothelial cell marker CD146, and the mesenchymal stem cell markers CD73, CD90, CD105, and CD44 but did not express the hematopoietic stem cell marker CD45, and they could undergo osteogenic, chondrogenic, adipogenic, and myogenic differentiation in vitro. In order to investigate the osteoinductive potential of hMDSCs, we constructed a retroviral vector expressing BMP4 and GFP and a lentiviral vector expressing BMP2. The BMP4-expressing hMDSCs were able to undergo osteogenic differentiation in vitro and exhibited enhanced mineralization compared to nontransduced cells; however, when transplanted into a calvarial defect, they failed to regenerate bone. Local administration of BMP4 protein and cell pretreatment with N-acetylcysteine (NAC), which improves cell survival, did not enhance the osteogenic capacity of the retro-BMP4-transduced cells. In contrast, lenti-BMP2-transduced hMDSCs not only exhibited enhanced in vitro osteogenic differentiation but also induced robust bone formation and nearly completely healed a critical-sized calvarial defect in CD-1 nude mice 6 weeks following transplantation. Herovici's staining of the regenerated bone demonstrated that the bone matrix contained a large amount of type I collagen. Our findings indicated that the hMDSCs are likely mesenchymal stem cells of muscle origin and that BMP2 is more efficient than BMP4 in promoting the bone regenerative capacity of the hMDSCs in vivo.
P1434 Evolution of coronary wall shear stress following implantation of bioabsorbable vascular scaffolds - first results of a 1-year follow-up pilot study (2020)

Abstract Funding Acknowledgements This research has been funded by the research grant PlaqueImage, contract number 26/01.09.2016, SMIS code 103544, Project funded by the European Union Aims Coronary shear stress (CSS) has been recently recognized to play a significant role in coronary plaque progression and vulnerabilisation. However, the evolution of CSS after implantation of different types of coronary stents is still under investigation. The aim of this study was to assess the evolution of the CSS along the coronary lesions following implantation of bioabsorbable vascular scaffolds (BVS), to determine the impact of BVS on coronary flow haemodynamics. Methods and results This was a single center prospective pilot study which enrolled 15 patients (aged 58.35 +/- 7.79 years, 13 males) with coronary artery disease undergoing BVS implantation in a major epicardial vessel. In all patients, angio CT scanning (Siemens Somatom Sensation scanner, Erlangen, Germany) was performed prior to the BVS implantation and repeated after 12 months. Lumen information was extracted from the vessels of interest and coronary rest hemodynamics, including CSS, were calculated using a computational fluid dynamics solver. All shear stress calculations were performed at baseline and repeated after 1 year. Average CSS was determined proximally, distally, and at the level of the minimal lumen area (MLA). Average CSS along the stented segment significantly decreased after BVS implantation, from 2.87 +/- 1.64 Pa at baseline to 1.9 +/- 0.49 at 1 year (p = 0.0001). Maximum CSS along the segment also exhibited a significant decrease, from 11.78 +/- 10.06 Pa to 6.35 +/- 3.08 Pa (p = 0.0009). Proximally to the MLA, CSS significantly decreased after BVS implantation, from 3.39 +/- 1.93 Pa at baseline to 1.91 +/- 0.68 Pa at 1 year (p &amp;lt;0.0001). However, this decrease in CSS was not significant distally to the MLA (1.3 +/- 0.72 Pa vs 1.59 +/- 0.65 Pa, p = 0.9). Conclusions Implantation of BVS leads to a significant decrease of CSS after 1 year, especially within coronary segments located proximally to the stenosis. This underlines the role of BVS in re-establishing a physiological pattern of coronary flow in diseased coronary vessels. The feature (mentioned herein) is not commercially available. Due to regulatory reasons its future availability cannot be guaranteed.
Music Generation and Transformation with Moment Matching-Scattering Inverse Networks (2018)

We introduce a Moment Matching-Scattering Inverse Network (MM-SIN) to generate and transform musical sounds. The MM-SIN generator is similar to a variational autoencoder or an adversarial network. However, the encoder or the discriminator are not learned, but computed with a scattering transform defined from prior information on sparse time-frequency audio properties. The generator is trained by jointly minimizing the reconstruction loss of an inverse problem, and a generation loss which computes a distance over scattering moments. It has a similar causal architecture as a WaveNet and provides a simpler mathematical model related to time-frequency decompositions. Numerical experiments demonstrate that this MMSIN generates new realistic musical signals. It can transform low-level musical attributes such as pitch with a linear transformation in the embedding space of scattering coefficients.
Reductive methylation of lysine residues in acidic fibroblast growth factor: effect on mitogenic activity and heparin affinity (1988)

Reductive methylation of bovine brain derived acidic fibroblast growth factor (aFGF) with formaldehyde and sodium cyanoborohydride reduces its capacity to stimulate mitogenesis in Balb/C 3T3 cells, and this correlates with the modification of less than 3 of its 12 lysine residues. Fractionation of methylated aFGF on immobilized heparin shows that the affinity of the modified mitogen for heparin is also decreased substantially. The capacity of methylated mitogen of low heparin affinity (LA-aFGF) to stimulate mitogenesis is also reduced, and this correlates with a reduced affinity for its cell surface receptor. Structural characterization of LA-aFGF using peptide mapping and sequencing procedures demonstrates that Lys-118 is the primary site of modification. The results indicate that in aFGF, Lys-118 plays an important role in heparin binding and suggest that this residue and its local environment are involved in the interaction of aFGF with both heparin and its cell surface receptor.
Preparación de moléculas orgánicas útiles como agentes surfactántes (2014)

Procedimiento de obtención de moléculas orgánicas&#13;\nque comprende, al menos, los siguientes pasos:&#13;\na) un primer paso de esterificación oxidativa selectiva&#13;\ndel grupo formil del HMF con metanol en presencia&#13;\nde, al menos, un catalizador metálico y un agente&#13;\noxidante;&#13;\nb) un segundo paso de eterificación selectiva del&#13;\ngrupo hidroximetil del compuesto obtenido en el&#13;\nprimer paso en presencia de, al menos, un compuesto&#13;\ncon estructura hidrocarbonada, y un catalizador ácido;&#13;\nc) un tercer paso de hidrólisis del grupo éster del&#13;\ncompuesto obtenido en el segundo paso en presencia&#13;\nde, al menos, una disolución acuosa básica
GATA-6 Induces p21Cip1 Expression and G1Cell Cycle Arrest (1998)

GATA transcription factors represent a family of highly conserved zinc finger proteins with tissue-specific expression patterns. Previous studies have shown that GATA-6 is expressed in vascular smooth muscle cells (VSMCs) and rapidly down-regulated when VSMCs are induced to proliferate. Here we investigated whether the GATA-6 transcription factor can modulate cellular proliferation. Transient transfection with a GATA-6 expression vector inhibited S-phase entry in VSMCs and in mouse embryonic fibroblasts (MEFs) lacking both p53 alleles. The GATA-6-induced growth arrest correlated with a marked increase in the expression of the general cyclin-dependent kinase (Cdk) inhibitor p21. In contrast to p53-deficient MEFs and VSMCs, MEFs null for both p21 alleles were refractory to the GATA-6-induced growth inhibition. These data demonstrate that elevated GATA-6 expression can promote the quiescent phenotype in VSMCs.
Cobaltporphyrin‐adsorbed carbon black: highly efficient electrocatalysts for oxygen reduction (2005)

Abstract meso ‐Substituted cobalt porphyrins adsorbed on carbon black were prepared as catalysts for the electroreduction of O 2 . The catalyst, which was prepared by using a homogenizer in mixing cobalt tetraethylporphyrin and carbon black, gave rise to electroreduction of O 2 at a remarkably positive potential ( E p = 0.45 V versus saturated calomel electrode (SCE)) and showed a high selectively for the four‐electron reduction ( n = 3.8). Electrochemical study and extended X‐ray absorption fine structure (EXAFS) analysis revealed that the adsorbed face‐to‐face dimeric aggregates of cobalt porphyrin molecules were highly efficient catalysts for electroreduction of O 2 . Copyright © 2005 John Wiley &amp; Sons, Ltd.
Parallel storage system with burst buffer appliance for storage of partitioned key-value store across a plurality of storage tiers (2023)

Parallel storage systems are provided with a burst buffer appliance for storage of a partitioned key-value store across a plurality of storage tiers. The burst buffer appliance is configured to store key-value data on first and second storage tiers comprising respective disjoint subsets of storage. One or more servers in the partitioned key-value store provide (i) an interface between one or more local key-value stores and one or more additional storage architectures, and/or (ii) a key value interface that provides access to at least one hardware key-value store. The local key-values are optionally sorted both locally by the local store and globally by the overall MDHIM framework. The local and global sorting can be leveraged to provide batch input/output (IO) operations that aggregate multiple requests into batch operations on one or more sorted ranges.
Decomposing global light transport using time of flight imaging (2012)

Global light transport is composed of direct and indirect components. In this paper, we take the first steps toward analyzing light transport using high temporal resolution information via time of flight (ToF) images. The time profile at each pixel encodes complex interactions between the incident light and the scene geometry with spatially-varying material properties. We exploit the time profile to decompose light transport into its constituent direct, subsurface scattering, and interreflection components. We show that the time profile is well modelled using a Gaussian function for the direct and interreflection components, and a decaying exponential function for the subsurface scattering component. We use our direct, subsurface scattering, and interreflection separation algorithm for four computer vision applications: recovering projective depth maps, identifying subsurface scattering objects, measuring parameters of analytical subsurface scattering models, and performing edge detection using ToF images.
Cationic Peptide Exposure Enhances Pulsed-Electric-Field-Mediated Membrane Disruption (2014)

Exposure to cationic peptides reduced the PEF intensity required to induce rapid and irreversible membrane disruption. Critically, peptide exposure reduced the PEF intensities required to elicit irreversible membrane disruption at normally sub-electroporation intensities. We believe that these cationic peptides, when coupled with current advancements in cell targeting techniques will be useful tools in applications where targeted destruction of unwanted cell populations is desired.
Performance optimization of a high current dual active bridge with a wide operating voltage range (2006)

The main aim of this paper is to improve the performance of high current dual active bridge converters when operated over a wide voltage range. A typical application is for fuel cell vehicles where a bi-directional interface between a 12V battery and a high voltage DC bus is required. The battery side voltage ranges from 11V to 16V while the fuel cell is operated between 220V and 447V and the required power is typically 1kW. Careful analysis shows that the high currents on the battery side cause significant design issues in order to obtain a high efficiency. The standard phase shift modulation method can result in high conduction and switching losses. This paper proposes a combined triangular and trapezoidal modulation method to reduce losses over the wide operating range. Approximately, a 2% improvement in efficiency can be expected. An experimental system is used to verify the improved performance of the dual active bridge using the proposed advanced modulation method.
Mechanisms Underlying the Functional Cooperation Between PPARα and GRα to Attenuate Inflammatory Responses (2019)

Glucocorticoids (GCs) act via the glucocorticoid receptor (NR3C1, GRα) to combat overshooting responses to infectious stimuli, including lipopolysaccharide (LPS). As such, GCs inhibit the activity of downstream effector cytokines, such as tumor necrosis factor (TNF). PPARα (NR1C1) is a nuclear receptor described to function on the crossroad between lipid metabolism and control of inflammation. In the current work, we have investigated the molecular mechanism by which GCs and PPARα agonists cooperate to jointly inhibit NF-κB-driven expression in A549 cells. We discovered a nuclear mechanism that predominantly targets Mitogen- and Stress-activated protein Kinase-1 activation upon co-triggering GRα and PPARα. <i>In vitro</i> GST-pull down data further support that the anti-inflammatory mechanism may additionally involve a non-competitive physical interaction between the p65 subunit of NF-κB, GRα, and PPARα. Finally, to study metabolic effector target cells common to both receptors, we overlaid the effect of GRα and PPARα crosstalk in mouse primary hepatocytes under LPS-induced inflammatory conditions on a genome-wide level. RNA-seq results revealed lipid metabolism genes that were upregulated and inflammatory genes that were additively downregulated. Validation at the cytokine protein level finally supported a consistent additive anti-inflammatory response in hepatocytes.
<title>Static and dynamic characterization of polysilicon surface-micromachined actuators</title> (1999)

A measurement system for static and dynamic characterization of silicon micromachines was developed. The computer- controlled system, using a HeNe-laser at 633 nm and a two- dimensional position sensor, allows simultaneous measurements of optical beam motion on two axes. To demonstrate the flexibility and functionality of the setup, measurements on various polysilicon surface-micromachined mirrors were performed. These measurements included tilt-angle versus driving-voltage curves, frequency responses, and motion perpendicular to the primary scan axis.
Tight nanoscale clustering of Fcγ-receptors using DNA origami promotes phagocytosis (2021)

Abstract Macrophages destroy pathogens and diseased cells through Fcγ receptor (FcγR)-driven phagocytosis of antibody-opsonized targets. Phagocytosis requires activation of multiple FcγRs, but the mechanism controlling the threshold for response is unclear. We developed a DNA origami-based engulfment system that allows precise nanoscale control of the number and spacing of ligands. When the number of ligands remains constant, reducing ligand spacing from 17.5 nm to 7 nm potently enhances engulfment, primarily by increasing efficiency of the engulfment-initiation process. Tighter ligand clustering increases receptor phosphorylation, as well as proximal downstream signals. Increasing the number of signaling domains recruited to a single ligand-receptor complex was not sufficient to recapitulate this effect, indicating that clustering of multiple receptors is required. Our results suggest that macrophages use information about local ligand densities to make critical engulfment decisions, which has implications for the mechanism of antibody-mediated phagocytosis and the design of immunotherapies.
IEEE Access Special Section Editorial: Trust Management in Pervasive Social Networking (TruPSN) (2018)

With the rapid growth of mobile computing and social networking, social networks have extended their popularity from the Internet to mobile domain. Pervasive Social Networking (PSN) ensures social communications at any time and in any place with a universal manner. It supports online and instant (i.e., pervasive) social activities based on heterogeneous networks, e.g., the Internet, mobile cellular networks or self-organized networks or other networking technologies. It is treated as one of the killer applications in the next generation mobile networks and wireless systems (i.e., 5G). There are various applications over PSN. Typical examples include social chatting, gaming, rescuing, recommending and information sharing. Because group mobility is very common in modern life, PSN has become valuable for mobile users, especially when they are familiar strangers and often appear in the same vicinity. PSN greatly extends our experiences of social communications.
Effects of Trace Layers and Joule Heating on the Temperature Distribution of Printed Circuit Boards: A Computational Study (2009)

A printed circuit board (PCB) is generally a multilayered board made of dielectric material and several layers of traces and vias. Performing detailed system-level computational fluid dynamics (CFD) simulations of PCBs including meshed trace and via geometries for each of the layers is impractical. In the present approach, the effects of the trace and via geometry are accurately modeled in the physical model by importing electronics computer aided-design data consisting of the trace and via layout of the board and computing locally varying orthotropic conductivity (kx, ky, and kz) on the printed circuit board using a background mesh. The spatially varying orthotropic conductivity is then mapped from the background mesh to the CFD mesh and used in a system-level simulation of the PCB with a minimal increase in the overall computational cost. On the other hand, as PCB component densities increase, the current densities increase thereby leading to regions of hot spots due to Joule heating. Hence, it is essential that the computational heat transfer simulations account for the heating due to the high current carrying traces. In order to accurately model the Joule heating of traces and vias, it is of essence to solve for the conservation of current in each of these traces. In this study, the effects of both trace layer nonhomogeneity and Joule heating are examined on a sample PCB with several components attached to it. The results are then compared with those from the conventional modeling techniques. It is demonstrated that there is considerable difference in the location of the hot spots and temperature values between two different methods.
Chord Recognition and Segmentation Using EM-trained Hidden Markov Models (2003)

An overview of work on chord recognition and EM-trained Hidden Markov Models.
Purine Metabolism in Normal and Thioguanine-Resistant Neuroblastoma (1973)

Purine metabolism has been examined in a clonal line of mouse neuroblastoma cells resistant to the cytotoxic effects of 6-thioguanine. Comparative studies in the resistant and parental lines indicate that the former cells have less than 1% of normal hypoxanthine phosphoribosyltransferase (EC 2.4.2.8) activity. The activities of other enzymes important in the de novo and salvage pathways of purine biosynthesis were not significantly different in the two lines. Hypoxanthine phosphoribosyltransferase deficiency in this neuroblastoma line was associated with increased intracellular concentrations of 5-phosphoribosyl-1-pyrophosphate, an increased rate of purine biosynthesis de novo, and failure to incorporate hypoxanthine, but not adenine, into nucleotides. There are essentially the same alterations in purine metabolism that occur in hypoxanthine phosphoribosyltransferase-deficient fibroblasts or lymphoblasts derived from individuals with the Lesch-Nyhan syndrome. Clonal lines of hypoxanthine phosphoribosyltransferase-deficient neuroblastoma cells may therefore be of use in elucidating the mechanisms by which the enzyme defect leads to the neurologic dysfunction seen in children with this disease.