gebhart/patrepeval huggingface dataset:
Abstract 4056: Fluorescence labeling of different live cell populations and subsequent analysis by flow and imaging cytometry (2011)

Abstract Relative to conventional antibody-based immunohistological methods employing fixed and permeabilized cells, live cell imaging has presented challenges due to the lack of availability of compatible fluorescent probes. Additionally, instrument-dependent complications arise, such as the requirement that adherent cells be detached into a single cell suspension for flow cytometry, which can impact physiological response. A novel noncovalent fluorescence, long-term labeling technology was employed to stably incorporate green, red, or mixtures of green and red fluorescent dyes into the plasma membranes of different live cell populations. The dyes were well retained for up to 96 hours, faithfully transferred to daughter cells upon mitosis, yet displayed no tendency for nonspecific transfer to adjacent unlabeled cell populations. Since the described dyes do not covalently modify proteins within the cells, normal physiological responses are well preserved. Labeled cell populations were analyzed by conventional flow cytometry as well as with a novel imaging cytometer, the Cellometer Vision, incorporating inexpensive disposable counting chambers. Using a combination of bright-field and fluorescent images, the imaging system automates cell image acquisition and processing using novel counting algorithms for accurate and consistent measurement of cell concentration, fluorescent intensities and percentages of fluorescent positive cells. Results achieved using the imaging cytometer showed excellent correlation with those achieved by flow cytometry, but required 25-fold lower sample per analysis. As many as four cell subpopulations could be determined simultaneously. The described workflow provides a powerful, yet economic, approach applicable to long-term cell viability, cytotoxicity, cell adhesion, cell migration, lineage tracing and cell-cell fusion analysis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4056. doi:10.1158/1538-7445.AM2011-4056
TCAD Investigation of Abnormal Degradation of Inhibited Cells in NAND Flash Structures (2009)

In this paper, we propose to investigate the abnormal degradation on inhibited cells in NAND structures when cycling the addressed cell. The impact of the electric field is first explored and shows that the electric field isn't the main source of degradation. Then we try to identify the phenomenon occurring in the inhibition phase called "channel boosting". To visualize the potential in the channel area, a 2D TCAD simulation, emulating a 3D behavior by taking into account parasitic capacitances in the array, is developed and calibrated. We succeed in reproducing the bias conditions in the inhibited cell and to observe the emergence of a source/drain bias during the rising of potentials.
Ski is a component of the histone deacetylase complex required for transcriptional repression by Mad and thyroid hormone receptor (1999)

The N-CoR/SMRT complex containing mSin3 and histone deacetylase (HDAC) mediates transcriptional repression by nuclear hormone receptors and Mad. The proteins encoded by the ski proto-oncogene family directly bind to N-CoR/SMRT and mSin3A, and forms a complex with HDAC. c-Ski and its related gene product Sno are required for transcriptional repression by Mad and thyroid hormone receptor (TRbeta). The oncogenic form, v-Ski, which lacks the mSin3A-binding domain, acts in a dominant-negative fashion, and abrogates transcriptional repression by Mad and TRbeta. In ski-deficient mouse embryos, the ornithine decarboxylase gene, whose expression is normally repressed by Mad-Max, is expressed ectopically. These results show that Ski is a component of the HDAC complex and that Ski is required for the transcriptional repression mediated by this complex. The involvement of c-Ski in the HDAC complex indicates that the function of the HDAC complex is important for oncogenesis.
Synaptic dynamics at the neuromuscular junction: Mechanisms and models (1990)

During development, the neuromuscular junction passes through a stage of extensive polyinnervation followed by a period of wholesale synapse elimination. In this report we discuss mechanisms and interactions that could mediate many of the key aspects of these important developmental events. Our emphasis is on (1) establishing an overall conceptual framework within which the role of many distinct cellular interactions and molecular factors can be evaluated, and (2) generating computer simulations that systematically test the adequacy of different models in accounting for a wide range of biological data. Our analysis indicates that several relatively simple mechanisms are each capable of explaining a variety of experimental observations. On the other hand, no one mechanism can account for the full spectrum of experimental results. Thus, it is important to consider models that are based on interactions among multiple mechanisms. A potentially powerful combination is one based on (1) a scaffold within the basal lamina or in the postsynaptic membrane which is induced by nerve terminals and which serves to stabilize terminals by a positive feedback mechanism; (2) a sprouting factor whose release by muscle fibers is down-regulated by activity and perhaps other factors; and (3) an intrinsic tendency of motor neurons to withdraw some connections while allowing others to grow.
Label-free multicolor imaging flow cytometry with stimulated Raman scattering (2019)

By combining the strength of flow cytometry with optical imaging and digital image analysis, imaging flow cytometry is a powerful tool in diverse fields of biology and medicine [1]. However, its applications are constrained by its requirement of fluorescent labeling for phenotyping.
Comparative Dispersion Study of Dry Powder Aerosols of Albuterol Sulfate/Lactose Monohydrate and Disodium Cromoglycate/Lactose Monohydrate Delivered by Standardized Entrainment Tubes (2008)

Attrition milling of drug, followed by geometric dilution and Turbula mixing with the lactose carriers. Malvern laser diffraction for volume particle size distribution (PSD). Particle morphology was characterized by scanning electron microscopy. Thermodynamic phase behavior, molecular interaction, and long range/short range order were evaluated by differential scanning calorimetry (DSC) and X-ray powder diffraction (XRPD) before and after blending. The blends were prepared at 2% (w/w) concentration.
Sensitivity Analysis of Electric Energy Consumption in Battery Electric Vehicles with Different Electric Motors (2023)

In the last decade, a number of research works in electrified vehicles have been devoted to the analysis of the electric consumption of battery electric vehicles and the evaluation of the main influencing factors. The literature analysis reveals that the electric motor size, efficiency, and driving condition substantially affect the electric energy stored in the vehicle battery. This paper studies the degree of sensitivity of energy consumption to electric motor size and to its efficiency map characteristics. In order to accomplish this task, three electric motors whose parameters are re-scaled to fit the maximum power torque and speed with different efficiency maps are simulated by installing them on two commercially available battery electric vehicles. This allows for isolating the influence of the efficiency map on electricity consumption. The original characteristics of the motors are then used to evaluate the influence on the electricity consumption of both the size and the efficiency characteristics. The results of the simulation revealed that the influences of the efficiency map and the electric motor size can be around 8–10% and 2–11%, respectively. When both factors are taken into account, the overall difference in electricity consumption can be around 10–21%.
Submodularity on a tree: Unifying $L^\\natural$-convex and bisubmodular\n functions (2010)

We introduce a new class of functions that can be minimized in polynomial\ntime in the value oracle model. These are functions $f$ satisfying\n$f(x)+f(y)\\ge f(x \\sqcap y)+f(x \\sqcup y)$ where the domain of each variable\n$x_i$ corresponds to nodes of a rooted binary tree, and operations\n$\\sqcap,\\sqcup$ are defined with respect to this tree. Special cases include\npreviously studied $L^\\natural$-convex and bisubmodular functions, which can be\nobtained with particular choices of trees. We present a polynomial-time\nalgorithm for minimizing functions in the new class. It combines Murota's\nsteepest descent algorithm for $L^\\natural$-convex functions with bisubmodular\nminimization algorithms.\n
Feedback Control of Computing Systems (2004)

Preface. PART I: BACKGROUND. 1. Introduction and Overview. PART II: SYSTEM MODELING. 2. Model Construction. 3. Z-Transforms and Transfer Functions. 4. System Modeling with Block Diagrams. 5. First-Order Systems. 6. Higher-Order Systems. 7. State-Space Models. PART III: CONTROL ANALYSIS AND DESIGN. 8. Proportional Control. 9. PID Controllers. 10. State-Space Feedback Control. 11. Advanced Topics. Appendix A: Mathematical Notation. Appendix B: Acronyms. Appendix C: Key Results. Appendix D: Essentials of Linear Algebra. Appendix E: MATLAB Basics. References. Index.
New Generation of Air Cooled Heat Exchanger 1 kW Module Design Optimization (2012)

The objective of this paper is to evaluate and optimize the performance of 1 kW integrated heat exchanger module for new generations of air cooled heat exchangers. The first objective is to minimize the ratio of the header frontal area to the entire heat exchanger frontal which will help to reduce the header size. The second objective is to minimize the pressure drop for the entire heat exchanger, i.e., inside the inlet and outlet headers in addition to pressure drop inside the tubes. A three step approach is proposed. First step involves selecting the header design based on previous header optimization studies and then simulating the header using a new 3D CFD simulation approach. Second step includes solving the heat exchanger using information from the header simulation that accounts for the variation in refrigerant mass flow rate inside the tubes and obtain the performance for the entire heat exchanger. Finally, a solver is used to evaluate the overall module performance. Three different headers are investigated with different header height and size ratio. Then parametric studies are conducted to explore the effect of header size ratio on the optimum designs. Lastly, design guidelines to optimize the integrated heat exchange module are provided based on the study results.
Computation of Compressible Multiphase Flows (2003)

A computational model capable of capturing fully compressible multiphase flow including energy conservation is presented. The model is a finite volume form based on the Reynolds Averaged Navier-Stokes Equations and is capable of considering fully general equations of state. The preconditioning matrix is presented and ensures a well conditioned eigensystem, essential for efficient and accurate multiphase computations. Solutions are given representing both the utility of the preconditioning method as well as the ability of the model to capture highly compressible multiphase flow fields. When considering compressible flows where thermal effects are significant and a general equation of state is necessary, energy conservation in a multiphase flow field is shown to be a requirement.
Liquid crystalline glycosteroids and acyl steroid glycosides (ASG) (2017)

As part of our studies on glycolipidic liquid crystals, we have investigated some molecules comprising a steroid moiety. These systems can exhibit several types of structures depending on their polarity pattern based on the number of polar and non-polar moieties and their resulting molecular shape. Therefore, to aid describing such systems, we have proposed a specific classification based on this polarity pattern. Many compounds in this family are natural products, which possess important biological properties. Some of the compounds have bolaphilic structures, with both a steroid and a fatty alkyl chain attached to the carbohydrate moiety, such as either the β-galactoside BbGL-1 or the α-glucoside α-CAG that are found in the membranes of the pathogens Borrelia burgdorferi and Helicobacter pylori, respectively. In this account, after a brief introduction on liquid crystalline glycolipids, we focus on carbohydrate–steroid hybrids, summarising our previous work on glycosteroids prepared by the CMGL-synthon strategy, and reporting our preliminary results on the thermotropic behaviour of acyl steroid glycosides (ASG), namely cholesteryl 6-O-acyl-β-gluco- and -galacto-pyranosides.
Titanium Coating of the Boston Keratoprosthesis (2016)

This approach may improve adhesion with donor corneas in humans.
The infrared emission of the Galactic center (1978)

Ground-based and airborne infrared observations of the Galactic center near Sgr A are presented. The principal results include: (1) A map at 56 microns (28-arcsec beam FWHM) which shows a ridge of emission in which are immersed two peaks, one at the infrared cluster and another 1 arcmin to the southwest. Early-type stars may produce much of the luminosity seen as thermally reradiated far-infrared flux. (2) A map of the infrared cluster at 34 microns (8.5-arcsec beam) which indicates that the distribution at this wavelength is similar to that at 21 microns, with most of the compact sources which emit at wavelengths shorter than 20 microns emitting relatively weakly at 34 microns. (3) A map at 10 microns which combines observations obtained with 1.5-, 2.3-, 3-, 5.5-, and 20-arcsec beams and shows for the first time the extended 10-micron structure, including the southwestern component, in relation to the cluster of compact sources. Most of the compact 10-micron sources have the structure and spectra to be expected if a luminous object is embedded in a tenuous dust cloud.
Structural inversion in 3-D hexagonal organization of coil–rod–coil molecule (2005)

We report an unusual example of supramolecular structural inversion in coil-rod-coil molecules, from organized coil perforations in a rod layers to organized discrete rod-bundles in a coil matrix, while maintaining a 3-D hexagonal superlattice.
Real-Time Adaptive suppression of MR gradient Artifacts on Electorcardiograms using a new 3D Hall Probe (2009)

International audience
A comparison of detection methods in the presence of nonlinearities (1998)

In this paper we evaluate the detectability of nonlinear signals characteristic of high-density, magnetic recording channels read by a magneto-resistive (MR) head. We first introduce a signal model which performs nonlinear superposition of experimentally-collected MR-head transition responses. Feeding signals synthesized from this model through a detection simulator, we compare the performance of Decision Feedback Equalization (DFE), RAM DFE, Partial Response Maximum-likelihood detection with PR4, EPR4, and E/sup 2/PR4 targets, and Fixed Delay Tree Search with Decision Feedback (FDTS/DF) in the presence of time and amplitude nonlinearities. Signals are generated at a variety of signal-to-noise ratios (SNRs) and densities with runlength constraints of (0,3) and (1,7). We found that the most detrimental nonlinearities come from amplitude asymmetry characteristic of poorly biased MR heads, and such nonlinearities cause a loss of between 0.5 and 1 orders of magnitude in bit error rate. We found that of the schemes, FDTS/DF provided the great robustness against all nonlinearities in the presence of RLL(1,7) coding, and EPR4ML and E/sup 2/PR4ML preformed the best with RLL(0,3) coding.
Intracellular Polyphosphate Length Characterization in Polyphosphate Accumulating Microorganisms (PAOs): Implications in PAO Phenotypic Diversity and Enhanced Biological Phosphorus Removal Performance (2021)

Polyphosphate (polyP) accumulating organisms (PAOs) are the key agent to perform enhanced biological phosphorus removal (EBPR) activity, and intracellular polyP plays a key role in this process. Potential associations between EBPR performance and the polyP structure have been suggested, but are yet to be extensively investigated, mainly due to the lack of established methods for polyP characterization in the EBPR system. In this study, we explored and demonstrated that single-cell Raman spectroscopy (SCRS) can be employed for characterizing intracellular polyPs of PAOs in complex environmental samples such as EBPR systems. The results, for the first time, revealed distinct distribution patterns of polyP length (as Raman peak position) in PAOs in lab-scale EBPR reactors that were dominated with different PAO types, as well as among different full-scale EBPR systems with varying configurations. Furthermore, SCRS revealed distinctive polyP composition/features among PAO phenotypic sub-groups, which are likely associated with phylogenetic and/or phenotypic diversity in EBPR communities, highlighting the possible resolving power of SCRS at the microdiversity level. To validate the observed polyP length variations via SCRS, we also performed and compared bulk polyP length characteristics in EBPR biomass using conventional polyacrylamide gel electrophoresis (PAGE) and solution 31P nuclear magnetic resonance (31P-NMR) methods. The results are consistent with the SCRS findings and confirmed the variations in the polyP lengths among different EBPR systems. Compared to conventional methods, SCRS exhibited advantages as compared to conventional methods, including the ability to characterize in situ the intracellular polyPs at subcellular resolution in a label-free and non-destructive way, and the capability to capture subtle and detailed biochemical fingerprints of cells for phenotypic classification. SCRS also has recognized limitations in comparison with 31P-NMR and PAGE, such as the inability to quantitatively detect the average polyP chain length and its distribution. The results provided initial evidence for the potential of SCRS-enabled polyP characterization as an alternative and complementary microbial community phenotyping method to facilitate the phenotype-function (performance) relationship deduction in EBPR systems.
Evolutionary segmentation of financial time series into subsequences (2002)

Time series data are difficult to manipulate. When they can be transformed into meaningful symbols, it becomes an easy task to query and understand them. While most recent works in time series query only concentrate on how to identify a given pattern from a time series, they do not consider the problem of identifying a suitable set of time points based upon which the time series can be segmented in accordance with a given set of pattern templates, e.g., a set of technical analysis patterns for stock analysis. On the other hand, using fixed length segmentation is only a primitive approach to such kind of problem and hence a dynamic approach is preferred so that the time series can be segmented flexibly and effectively. In view of the fact that such a segmentation problem is actually an optimization problem and evolutionary computation is an appropriate tool to solve it, we propose an evolutionary segmentation algorithm in this paper. Encouraging experimental results in segmenting the Hong Kong Hang Seng Index using 22 technical analysis patterns are reported.
C4 polymorphism and major histocompatibility complex haplotypes in IgA deficiency: association with C4A null haplotypes. (1991)

IgA-deficient individuals (n = 110) and six families comprising 9 cases of IgA deficiency were typed for HLA-A, -B, -DR, C4 and factor B. Phenotype frequencies were increased for HLA-B8 (p = 0.004), HLA-DR3 (p = 0.001) and homozygous C4AQ0 (p = 0.01) and decreased for HLA-B7 (p = 0.004), HLA-DR2 (p = 0.0001) and C4A3 (p = 0.00007) compared to controls. Homozygous C4A deficiency was found in 20% of IgA-deficient persons. As clearly suggested by investigation of families, the findings could be attributed to high prevalence of the extended major histocompatibility complex (MHC) haplotype [HLA-A1, B8, C4AQ0, C4B1, BfS, DR3] in IgA deficiency. All but 1 of the 9 IgA-deficient persons included in the family study carried this haplotype and 4 of them were homozygous. In the families, 3 persons with normal serum IgA concentrations had the same MHC haplotypes as their IgA-deficient relatives. The findings were also consistent with possible overrepresentation of other MHC haplotypes with aberrant C4 gene organization in IgA deficiency. As previously suggested, the presence of two MHC haplotypes associated with IgA deficiency appears to be a necessary but not sufficient requirement for manifestation of the condition. The putative existence of a recessive gene in the MHC with regulatory function with regard to IgA gene expression is consistent with the findings.
Data from Phase I Study Utilizing a Novel Antigen-Presenting Cell–Targeted Vaccine with Toll-like Receptor Stimulation to Induce Immunity to Self-antigens in Cancer Patients (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; The use of tumor-derived proteins as cancer vaccines is complicated by tolerance to these self-antigens. Tolerance may be broken by immunization with activated, autologous, &lt;i&gt;ex vivo&lt;/i&gt; generated and antigen-loaded, antigen-presenting cells (APC); however, targeting tumor antigen directly to APC &lt;i&gt;in vivo&lt;/i&gt; would be a less complicated strategy. We wished to test whether targeted delivery of an otherwise poorly immunogenic, soluble antigen to APC through their mannose receptors (MR) would induce clinically relevant immunity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Two phase I studies were conducted with CDX-1307, a vaccine composed of human chorionic gonadotropin beta-chain (hCG-β) fused to an MR-specific monoclonal antibody, administered either locally (intradermally) or systemically (intravenously) in patients with advanced epithelial malignancies. An initial dose escalation of single-agent CDX-1307 was followed by additional cohorts of CDX-1307 combined with granulocyte-macrophage colony-stimulating factor (GM-CSF) and the Toll-like receptor (TLR) 3 agonist polyinosinic-polycytidylic acid (poly-ICLC) and TLR7/8 agonist resiquimod to activate the APC.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; CDX-1307 induced consistent humoral and T-cell responses to hCG-β when coadministered with TLR agonists. Greater immune responses and clinical benefit, including the longest duration of stable disease, were observed with immunization combined with local TLR agonists. Immune responses were induced equally efficiently in patients with elevated and nonelevated levels of serum hCG-β. Antibodies within the serum of vaccinated participants had tumor suppressive function &lt;i&gt;in vitro&lt;/i&gt;. Toxicity consisted chiefly of mild injection site reactions.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; APC targeting and activation induce adaptive immunity against poorly immunogenic self-antigens which has implications for enhancing the efficacy of cancer immunotherapy. &lt;i&gt;Clin Cancer Res; 17(14); 4844–53. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;