gebhart/patrepeval huggingface dataset:
A quasi‐Newton reconstruction algorithm for a complex microwave imaging scanner environment (2003)

An iterative complex permittivity reconstruction technique for two‐dimensional near‐field imaging is presented. A particular feature of the algorithm is that it takes into account the complicated environment of a circular 434 MHz microwave imaging scanner, which was developed to conduct biomedical imaging experiments. This is accomplished in a computationally efficient way by means of an embedding technique. The reconstruction technique is further based on a quasi‐Newton optimization scheme with approximate line search, in which the Hessian matrix is iteratively updated with the Broyden–Fletcher–Goldfarb–Shanno (BFGS) formula. This way, second derivative information is exploited to a large extent. The technique is illustrated with complex permittivity reconstructions of homogeneous and inhomogeneous lossy dielectric cylinders of moderate and high contrast from simulated data.
Transmission electron microscopy of silicides nucleated in Y–Si reaction system (1999)

The nucleation of silicides was examined by transmission electron microscopy in a Y–Si reaction system, in which the Y layer was deposited on the Si substrate at 330 °C. It was revealed that the amorphization due to alloying took place and the concentration gradient was formed over the alloying layer during deposition. A hexagonal YSi2 phase and a cubic Y5Si3 metastable phase were observed at the layer adjoining the Si substrate and at the midmost region of the alloying layer, respectively. This result was interpreted in the light of the proposed phenomenological theory that the silicide phases were nucleated from the amorphous alloys with suitable compositions within the formed concentration gradient.
Fast Molecular Beacon Hybridization in Organic Solvents with Improved Target Specificity (2010)

DNA hybridization is of tremendous importance in biology, bionanotechnology, and biophysics. Molecular beacons are engineered DNA hairpins with a fluorophore and a quencher labeled on each of the two ends. A target DNA can open the hairpin to give an increased fluorescence signal. To date, the majority of molecular beacon detections have been performed only in aqueous buffers. We describe herein DNA detection in nine different organic solvents, methanol, ethanol, isopropanol, acetonitrile, formamide, dimethylformamide (DMF), dimethyl sulfoxide (DMSO), ethylene glycol, and glycerol, varying each up to 75% (v/v). In comparison with detection in water, the detection in organic solvents showed several important features. First, the molecular beacon hybridizes to its target DNA in the presence of all nine solvents up to a certain percentage. Second, the rate of this hybridization was significantly faster in most organic solvents compared with water. For example, in 56% ethanol, the beacon showed a 70-fold rate enhancement. Third, the ability of the molecular beacon to discriminate single-base mismatch is still maintained. Lastly, the DNA melting temperature in the organic solvents showed a solvent concentration-dependent decrease. This study suggests that molecular beacons can be used for applications where organic solvents must be involved or organic solvents can be intentionally added to improve the molecular beacon performance.
Separation and growth of human CD4+ and CD8+ tumor-infiltrating lymphocytes and peripheral blood mononuclear cells by direct positive panning on covalently attached monoclonal antibody-coated flasks. (1990)

A direct positive panning technique was developed in order to achieve highly purified CD4+ and CD8+ cells. Fresh peripheral blood mononuclear cells or tumor-infiltrating lymphocytes derived from bulk cultures were applied to modified polystyrene surfaces to which anti-CD4 or anti-CD8 monoclonal antibodies were covalently attached. Adherent cells were allowed to grow in the original flask and were then harvested and cultured in IL-2-containing medium. This positive immunoselection technique resulted in CD4+ and CD8+ cell subsets with high cell viability and a high degree of purity. In several samples, the isolated cell subsets were subsequently subjected to a negative immunomagnetic bead selection in order to remove reciprocal cell subset contamination or double-positive CD4+/CD8+ cells. The isolated cells maintained their ability to proliferate, kept their phenotypic profiles, and remained functionally intact after long-term growth in culture without the further addition of mitogenic or allogeneic cell stimulation. This approach is a simple, rapid, and reproducible technique that might be useful on a large scale to isolate and to grow T-cell subsets for research and for clinical use.
Negative substrate bias enhanced breakdown hardness in ultra-thin oxide pMOSFETs (2003)

Negative substrate bias enhanced breakdown hardness in ultra-thin oxide (1.4 nm) pMOS is observed. This result is believed to be due to the increase of hole stress current during breakdown progression via breakdown induced carrier heating. Numerical analysis of the substrate bias effect on hole tunneling current is performed to support the proposed theory. This phenomenon is particularly significant to gate oxide reliability in floating substrate (PD-SOI) or forward-biased substrate devices.
Thermal Stability of a RuO<sub>2</sub> Electrode Prepared by DC Reactive Sputtering (2000)

RuO 2 films were deposited by reactive DC sputtering, and the formation process and the thermal stability were investigated. In the RuO 2 /Ti/SiO 2 structure, the Ti surface was preferentially oxidized at the initial stage of RuO 2 growth. Insertion of Ru and TiN layers between the RuO 2 and Ti layers can suppress the oxygen diffusion toward the Ti layer during the film growth. However, when the RuO 2 /Ru/TiN/Ti/Si structure was heat-treated, the RuO 2 was partially reduced to form RuO 2- X and the TiN was oxidized to TiO 2 while generating N 2 and O 2 gases, resulting in voids formation at the RuO 2 /Ru interface, regardless of the heat-treatment atmosphere. We found this was caused by internal oxygen diffusion within the stacked layers. This reaction is governed by the transference of oxygen to the TiN and Ti layers by the difference in the Gibbs' formation free energy, and by the oxygen diffusion enhancement.
Integrated Flight Path Planning System and Flight Control System for Unmanned Helicopters (2011)

This paper focuses on the design of an integrated navigation and guidance system for unmanned helicopters. The integrated navigation system comprises two systems: the Flight Path Planning System (FPPS) and the Flight Control System (FCS). The FPPS finds the shortest flight path by the A-Star (A*) algorithm in an adaptive manner for different flight conditions, and the FPPS can add a forbidden zone to stop the unmanned helicopter from crossing over into dangerous areas. In this paper, the FPPS computation time is reduced by the multi-resolution scheme, and the flight path quality is improved by the path smoothing methods. Meanwhile, the FCS includes the fuzzy inference systems (FISs) based on the fuzzy logic. By using expert knowledge and experience to train the FIS, the controller can operate the unmanned helicopter without dynamic models. The integrated system of the FPPS and the FCS is aimed at providing navigation and guidance to the mission destination and it is implemented by coupling the flight simulation software, X-Plane, and the computing software, MATLAB. Simulations are performed and shown in real time three-dimensional animations. Finally, the integrated system is demonstrated to work successfully in controlling the unmanned helicopter to operate in various terrains of a digital elevation model (DEM).
Peripheral Blood Stem Cell Transplantations: Past, present and future (1993)

Since the first successful attempt in 1985, peripheral blood stem cell transplants are increasingly performed worldwide and should now be considered as an essential therapeutic weapon against onco-hematological diseases. Their development has benefited greatly from a rapid concomitant advance of experimental knowledge regarding the nature of hematopoietic progenitor cells. For this reason and also for technical ones, until now these transplants generally have been autotransplants. Although one of the main reasons to use blood rather than bone marrow-derived stem cells was that they might carry less risk of relapse than autologous bone marrow cells, the lack of clinical randomized trials and/or the short follow-up make conclusions difficult so far in terms of disease-free and overall survival. Probably the risk of relapse also depends on the type of disease, on prior chemotherapies, on the type of peripheral stem cell mobilization regimen and on the number of blood-derived cells transplanted. Nevertheless, there are several major clinical indications for autologous blood stem cell transplant: acute nonlymphoblastic leukemias (ANLL), low-grade non-Hodgkin's lymphomas, multiple myeloma, some solid tumors, and even chronic myeloid leukemia. Now well-demonstrated advantages add a socioeconomic interest to this technique. The speed of post-transplant hematopoietic recovery induces a briefer hospitalization and a lower cost of the procedure, which represents "per se" important progress. Furthermore, the increasing use of hematopoietic growth factor(s) at time of blood-derived cell mobilization should increase the safety of the procedure. Also new trends are currently being developed: autotransplants with purified peripheral CD34+ cells; addition of adjuvant immunotherapy to induce graft-versus-tumor effect, which is lacking in autotransplant; and transplants using allogenic umbilical cord blood progenitors. Allogenic blood cell transplants might also be developed, provided that blood cells would be less likely to cause graft-versus-host disease (GVHD) than bone marrow, which is still not verified. Finally, the use of blood-derived cells as a vehicle for gene therapy should develop greatly in the near future.
Checking that finite state concurrent programs satisfy their linear specification (1985)

We present an algorithm for checking satisfiability of a linear time temporal logic formula over a finite state concurrent program. The running time of the algorithm is exponential in the size of the formula but linear in the size of the checked program. The algorithm yields also a formal proof in case the formula is valid over the program. The algorithm has four versions that check satisfiability by unrestricted, impartial, just and fair computations of the given program.
Interactive SQL query suggestion: Making databases user-friendly (2011)

SQL is a classical and powerful tool for querying relational databases. However, it is rather hard for inexperienced users to pose SQL queries, as they are required to be proficient in SQL syntax and have a thorough understanding of the underlying schema. To give users gratification, we propose SQLSUGG, an effective and user-friendly keyword-based method to help various users formulate SQL queries. SQLSUGG suggests SQL queries as users type in keywords, and can save users' typing efforts and help users avoid tedious SQL debugging. To achieve high suggestion effectiveness, we propose queryable templates to model the structures of SQL queries. We propose a template ranking model to suggest templates relevant to query keywords. We generate SQL queries from each suggested template based on the degree of matchings between keywords and attributes. For efficiency, we propose a progressive algorithm to compute top-k templates, and devise an efficient method to generate SQL queries from templates. We have implemented our methods on two real data sets, and the experimental results show that our method achieves high effectiveness and efficiency.
Functional prostate-specific membrane antigen is enriched in exosomes from prostate cancer cells (2014)

Developing simple and effective approaches to detect tumor markers will be critical for early diagnosis or prognostic evaluation of prostate cancer treatment. Prostate‑specific membrane antigen (PSMA) has been validated as an important tumor marker for prostate cancer progression including angiogenesis and metastasis. As a type II membrane protein, PSMA can be constitutively internalized from the cell surface into endosomes. Early endosomes can fuse with multivesicular bodies (MVB) to form and secrete exosomes (40-100 nm) into the extracellular environment. Herein, we tested whether some of the endosomal PSMA could be transferred to exosomes as an extracellular resource for PSMA. Using PSMA-positive LNCaP cells, the secreted exosomes were collected and isolated from the cultured media. The vesicular structures of exosomes were identified by electron microscopy, and exosomal marker protein CD9 and tumor susceptibility gene (TSG 101) were confirmed by western blot analysis. Our present data demonstrate that PSMA can be enriched in exosomes, exhibiting a higher content of glycosylation and partial proteolysis in comparison to cellular PSMA. An in vitro enzyme assay further confirmed that exosomal PSMA retains functional enzymatic activity. Therefore, our data may suggest a new role for PSMA in prostate cancer progression, and provide opportunities for developing non-invasive approaches for diagnosis or prognosis of prostate cancer.
Weatherman: Automated, Online and Predictive Thermal Mapping and Management for Data Centers (2006)

Recent advances have demonstrated the potential benefits of coordinated management of thermal load in data centers, including reduced cooling costs and improved resistance to cooling system failures. A key unresolved obstacle to the practical implementation of thermal load management is the ability to predict the effects of workload distribution and cooling configurations on temperatures within a data center enclosure. The interactions between workload, cooling and temperature are dependent on complex factors that are unique to each data center, including physical room layout, hardware power consumption and cooling capacity; this dictates an approach that formulates management policies for each data center based on these properties. We propose and evaluate a simple, flexible method to infer a detailed model of thermal behavior within a data center from a stream of instrumentation data. This data - taken during normal data center operation - includes continuous readings taken from external temperature sensors, server instrumentation and computer room air conditioning units. Experimental results from a representative data center show that automatic thermal mapping can predict accurately the heat distribution resulting from a given workload distribution and cooling configuration, thereby removing the need for static or manual configuration of thermal load management systems. We also demonstrate how our approach adapts to preserve accuracy across changes to cluster attributes that affect thermal behavior - such as cooling settings, workload distribution and power consumption.
A Ca<sup>2+</sup> binding cyclic peptide derived from the α‐subunit of LFA‐1: inhibitor of ICAM‐1 /LFA‐1‐mediated T‐cell adhesion (1999)

The objective of this work is to study the conformation of cyclic peptide (1), cyclo (1, 12) Pen1-Gly2-Val3-Asp4-Val5-Asp6-Gln7-+ ++Asp8-Gly9-Glu10-Thr11-Cys12, in the presence and absence of calcium. Cyclic peptide 1 is derived from the divalent cation binding sequence of the alpha-subunit of LFA-1. This peptide has been shown to inhibit ICAM-1-LFA-1 mediated T-cell adhesion. In order to understand the structural requirements for this biologically active peptide, its solution structure was studied by nuclear magnetic resonance (NMR), circular dichroism (CD) and molecular dynamics simulations. This cyclic peptide exhibits two types of possible conformations in solution. Structure I is a loop-turn-loop type of structure, which is suitable to bind cations such as EF hand proteins. Structure II is a more extended structure with beta-hairpin bend at Asp4-Val5-Asp6-Gln7. There is evidence that alterations in the conformation of LFA-1 upon binding to divalent cations cause LFA-1 to bind to ICAM-1. To understand this mechanism, the cation-binding properties of the peptide were studied by CD and NMR. CD studies indicated that the peptide binds to calcium and forms a 1 : 1 (peptide: calcium) complex at low calcium concentrations and multiple types of complexes at higher cation concentrations. NMR studies indicated that the conformation of the peptide is not significantly altered upon binding to calcium. The peptide can inhibit T-cell adhesion by directly binding to ICAM-1 or by disrupting the interaction of the alpha and beta-subunits of LFA-1 protein. This study will help us to understand the mechanism(s) of action of this peptide and will improve our ability to design a better inhibitor of T-cell adhesion.
Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells (2014)

Genetic alterations that reduce the function of the immunoregulatory cytokine IL-10 contribute to colitis in mouse and man. Myeloid cells such as macrophages (MΦs) and dendritic cells (DCs) play an essential role in determining the relative abundance of IL-10 versus inflammatory cytokines in the gut. As such, using small molecules to boost IL-10 production by DCs-MΦs represents a promising approach to increase levels of this cytokine specifically in gut tissues. Toward this end, we screened a library of well-annotated kinase inhibitors for compounds that enhance production of IL-10 by murine bone-marrow-derived DCs stimulated with the yeast cell wall preparation zymosan. This approach identified a number of kinase inhibitors that robustly up-regulate IL-10 production including the Food and Drug Administration (FDA)-approved drugs dasatinib, bosutinib, and saracatinib that target ABL, SRC-family, and numerous other kinases. Correlating the kinase selectivity profiles of the active compounds with their effect on IL-10 production suggests that inhibition of salt-inducible kinases (SIKs) mediates the observed IL-10 increase. This was confirmed using the SIK-targeting inhibitor HG-9-91-01 and a series of structural analogs. The stimulatory effect of SIK inhibition on IL-10 is also associated with decreased production of the proinflammatory cytokines IL-1β, IL-6, IL-12, and TNF-α, and these coordinated effects are observed in human DCs-MΦs and anti-inflammatory CD11c(+) CX3CR1(hi) cells isolated from murine gut tissue. Collectively, these studies demonstrate that SIK inhibition promotes an anti-inflammatory phenotype in activated myeloid cells marked by robust IL-10 production and establish these effects as a previously unidentified activity associated with several FDA-approved multikinase inhibitors.
Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display (2004)

Homologous recombination in yeast can be exploited to reliably generate libraries of >10(7) transformants from a pool of PCR products and a linearized plasmid vector. Homology in the PCR insertion products drives shuffling of these genes in vivo by yeast homologous recombination. Two scFvs that share 89.8% homology were shuffled in vivo by homologous recombination, and chimeric genes were generated regardless of whether or not one of the scFv PCR products lacked 5' homology to the cut vector and the second scFv PCR product lacked 3' homology to the cut vector, or both PCR products had both 5' and 3' homology to the cut vector. A majority of the chimeras had single crossovers; however, double and triple crossovers were isolated. Crossover points were evenly distributed in the hybrids created and homology of as little as two nucleotides was able to produce a chimeric clone. The numbers of clones isolated with a given number of crossovers was approximated well by a Poisson distribution. Transformation efficiencies for the chimeric libraries were of the order of 10(4)-10(5) transformants per microgram of insert, which is the same order of magnitude as when a single PCR product is inserted alone into the display vector by homologous recombination. This method eliminates ligation and Escherichia coli transformation steps of previous methods for generating yeast-displayed libraries, requires fewer PCR cycles than in vitro DNA shuffling and, unlike site-specific recombination methods, allows for recombination anywhere that homology exists between the genes to be recombined. This simple technique should prove useful for protein engineering in general and antibody engineering, specifically in yeast.
Harvesting Multiple Views for Marker-Less 3D Human Pose Annotations (2017)

Recent advances with Convolutional Networks (ConvNets) have shifted the bottleneck for many computer vision tasks to annotated data collection. In this paper, we present a geometry-driven approach to automatically collect annotations for human pose prediction tasks. Starting from a generic ConvNet for 2D human pose, and assuming a multi-view setup, we describe an automatic way to collect accurate 3D human pose annotations. We capitalize on constraints offered by the 3D geometry of the camera setup and the 3D structure of the human body to probabilistically combine per view 2D ConvNet predictions into a globally optimal 3D pose. This 3D pose is used as the basis for harvesting annotations. The benefit of the annotations produced automatically with our approach is demonstrated in two challenging settings: (i) fine-tuning a generic ConvNet-based 2D pose predictor to capture the discriminative aspects of a subjects appearance (i.e.,personalization), and (ii) training a ConvNet from scratch for single view 3D human pose prediction without leveraging 3D pose groundtruth. The proposed multi-view pose estimator achieves state-of-the-art results on standard benchmarks, demonstrating the effectiveness of our method in exploiting the available multi-view information.
Insulin-like Growth Factor I (IGF-I)-stimulated Pancreatic β-Cell Growth Is Glucose-dependent (1998)

Nutrients and certain growth factors stimulate pancreatic beta-cell mitogenesis, however, the appropriate mitogenic signal transduction pathways have not been defined. In the glucose-sensitive pancreatic beta-cell line, INS-1, it was found that glucose (6-18 mM) independently increased INS-1 cell proliferation (>20-fold at 15 mM glucose). Insulin-like growth factor I (IGF-I)-induced INS-1 cell proliferation was glucose-dependent only in the physiologically relevant concentration range (6-18 mM glucose). The combination of IGF-I and glucose was synergistic, increasing INS-1 cell proliferation >50-fold at 15 mM glucose + 10 nM IGF-I. Glucose metabolism and phosphatidylinositol 3'-kinase (PI 3'-kinase) activation were necessary for both glucose and IGF-I-stimulated INS-1 cell proliferation. IGF-I and 15 mM glucose increased tyrosine phosphorylation mediated recruitment of Grb2/mSOS and PI 3'-kinase to IRS-2 and pp60. Glucose and IGF-I also induced Shc association with Grb2/mSOS. Glucose (3-18 mM) and IGF-I, independently of glucose, activated mitogen-activated protein kinase but this did not correlate with IGF-I-induced beta-cell proliferation. In contrast, p70(S6K) was activated with increasing glucose concentration (between 6 and 18 mM), and potentiated by IGF-I in the same glucose concentration range which correlated with INS-1 cell proliferation rate. Thus, glucose and IGF-I-induced beta-cell proliferation were mediated via a signaling mechanism that was facilitated by mitogen-activated protein kinase but dependent on IRS-mediated induction of PI 3'-kinase activity and downstream activation of p70(S6K). The glucose dependence of IGF-I mediated INS-1 cell proliferation emphasizes beta-cell signaling mechanisms are rather unique in being tightly linked to glycolytic metabolic flux.