gebhart/patrepeval huggingface dataset:
The influence of membrane ion-permselectivity on electrokinetic concentration enrichment in membrane-based preconcentration units (2008)

The performance of nanoporous hydrogel microplugs with varying surface charge density is described in concentrating charged analytes electrokinetically in a microfluidic device. A neutral hydrogel plug with a mean pore size smaller than the size of charged analytes acts as a simple size-exclusion membrane. The presence of fixed charges on the backbone of a nanoporous hydrogel creates ion-permselectivity which results in charge-selective transport through the hydrogel. This leads to the development of concentration polarization (CP) in the adjoining bulk electrolyte solutions under the influence of an applied electrical field. CP strongly affects the distribution of the local electrical field strength, in particular, in the vicinity of the hydrogel plug which can significantly reduce the concentration enrichment factors compared to the neutral hydrogel. A theoretical model and simulations are presented, together with experimental data, to explain the interplay of hydrogel or membrane cation-selectivity, electrical field-induced CP, and the distribution of the local electrical field strength with respect to concentration enrichment of negatively charged analytes at the cathodic membrane-solution interface.
Covalent Heparin Cofactor II-Heparin and Heparin Cofactor II-Dermatan Sulfate Complexes (1998)

Heparin cofactor II is a naturally occurring anticoagulant that acts by specifically inhibiting thrombin and is facilitated by the binding of glycosaminoglycans such as heparin and dermatan sulfate. In vivo, heparin cofactor II-glycosaminoglycan complexes dissociate, leaving the inhibitor less active in its ability to function as a component of the anticoagulation pathway. We have produced permanently activated heparin cofactor II molecules by covalent linkage to either heparin or dermatan sulfate. Covalent heparin cofactor II-heparin and heparin cofactor II-dermatan sulfate complexes had catalytic antithrombin activities similar to those of the corresponding starting heparin and dermatan sulfate (86% and 110% of standard heparin and dermatan sulfate activity, respectively). Both heparin cofactor II-heparin and heparin cofactor II-dermatan sulfate had fast bimolecular rate constants of 1.4 x 10(7) M-1 s-1 and 1.3 x 10(7) M-1 s-1, respectively, for reaction with thrombin. The intravenous half-life of the covalent complexes in rabbits was significantly longer than that of free heparin or dermatan sulfate (4.4, 3.4, 0.33, and 0.50 h for heparin cofactor II-heparin, heparin cofactor II-dermatan sulfate, heparin, and dermatan sulfate, respectively). Given their unique properties, these conjugates may have a clinical application for long term, selective inhibition of thrombin.
Single-Dose Pharmacokinetics of Madopar HBS in Patients and Effect of Food and Antacid on the Absorption of Madopar HBS in Volunteers (1987)

Pharmacokinetic studies in parkinsonian patients and healthy volunteers have shown that Madopar HBS behaves as a slow-release formulation of L-dopa and benserazide. In comparison with standard Madopar the rate of absorption is reduced, providing lower peak concentrations of L-dopa. The drug is released and absorbed over a period of 4-5 h, thus maintaining substantial plasma concentrations for 6-8 h after dosing. Although the bioavailability after oral dosing is reduced as compared with standard Madopar (60-70%), this difference seems to be due to incomplete absorption rather than altered disposition of the drug. The presence or absence of food in the stomach has no effect on the absorption of L-dopa from Madopar HBS, but administration of antacids further reduces the bioavailability (45%).
Therapeutic Potential of Mesenchymal Stem Cells Producing Interferon-α in a Mouse Melanoma Lung Metastasis Model (2008)

Adult stem cells represent a potential source for cell-based therapy of cancer. The present study evaluated the potential of bone marrow-derived mesenchymal stem cells (MSC), genetically modified to express interferon (IFN)-alpha, for the treatment of lung metastasis in an immunocompetent mouse model of metastatic melanoma. A recombinant adeno-associated virus (rAAV) 6 vector encoding IFN-alpha was used to transduce mouse bone marrow-derived MSC ex vivo. Expression and bioactivity of the transgenic protein from rAAV-transduced MSC were confirmed prior to in vivo studies. A lung metastasis model of melanoma was developed by i.v. injection of B16F10 cells into 8-week-old C57BL/6 mice. Ten days later, MSC transduced with rAAV-IFN-alpha or green fluorescent protein were intravenously injected. One cohort of mice was sacrificed to determine the effects of the therapy at an earlier time point, and another cohort was observed for long-term survival. Results indicated that systemic administration of MSC producing IFN-alpha reduced the growth of B16F10 melanoma cells and significantly prolonged survival. Immunohistochemistry analysis of the tumors from MSC-IFN-alpha-treated animals indicated an increase in apoptosis and a decrease in proliferation and blood vasculature. These data demonstrate the potential of adult MSC constitutively producing IFN-alpha to reduce the growth of lung metastasis in melanoma.
Lime (2010)

The halt in clock frequency scaling has forced architects and language designers to look elsewhere for continued improvements in performance. We believe that extracting maximum performance will require compilation to highly heterogeneous architectures that include reconfigurable hardware. We present a new language, Lime, which is designed to be executable across a broad range of architectures, from FPGAs to conventional CPUs. We present the language as a whole, focusing on its novel features for limiting side-effects and integration of the streaming paradigm into an object- oriented language. We conclude with some initial results demonstrating applications running either on a CPU or co- executing on a CPU and an FPGA.
Blocking ovarian cancer progression by targeting tumor microenvironmental leukocytes (2010)

Current therapies for metastatic ovarian carcinoma are based on surgical debulking followed by chemotherapy. After more than three decades implementing treatments that selectively target the tumor cell, the 5-year survival rate for metastatic ovarian cancer patients is still lower than 30%. Novel strategies are therefore urgently needed to complement classical treatments for this malignancy. Recently, leukocytes in the ovarian cancer microenvironment such as regulatory T cells and immature pro-angiogenic/tolerogenic myeloid cells have been demonstrated to play a fundamental role in tumor progression. This review focuses on our recent understanding of the potential of eliminating and/or modulating the phenotype of these leukocytes in vivo and in situ as a novel intervention to complement standard ovarian cancer treatments. The significant effects of targeting these crucial microenvironmental players on cancer vascularization, local tumor growth, distal metastatic spreading and spontaneous anti-tumor immune responses are discussed.
Homology of mecA gene in methicillin-resistant Staphylococcus haemolyticus and Staphylococcus simulans to that of Staphylococcus aureus (1990)

A penicillin-binding protein of molecular weight 76,000 inducible by beta-lactams was detected in methicillin-resistant Staphylococcus haemolyticus and Staphylococcus simulans. DNA from these strains hybridized to the mecA gene from Staphylococcus aureus; however, the chromosomal HindIII fragments containing the mecA genes were 3.4 kilobases in S. haemolyticus and 4.3 kilobases in S. simulans.
Effects of Phosphatidylcholine and Phosphatidylinositol on Acetic-Acid-lnduced Colitis in the Rat (1992)

The therapeutic effects of exogenous phosphatidylcholine and phosphatidylinositol on acetic acid-induced colitis in rats were evaluated. A uniform colitis developed 4 days after instillation of 4% acetic acid for 15 s in an excluded colonic segment, also resulting in a 6-fold increase in mucosal permeability. Instillation of 12.5 mg phosphatidylcholine once daily from the day after acetic acid instillation and for the following 2 days prevented partially the development of colitis causing partial mucosal restoration. By increasing the phosphatidylcholine dose to 25 and 50 mg, a better preventive effect was achieved. By starting the phosphatidylcholine instillation immediately after the acetic acid exposure, almost complete prevention of the colitis could be obtained. Similarly, 50 mg phosphatidylinositol in each instillation with the first administration immediately after acetic acid administration resulted in complete prevention of the colitis and a significant decrease in mucosal permeability expressed as a plasma exudation into the colonic lumen. Similar results were obtained when phosphatidylcholine was administered immediately after acetic acid, but the drug then had to be applied twice daily. In contrast, a single application of the same total dose (150 mg) of the two different phospholipids, either 30 min before or immediately after acetic acid administration, could not prevent the development of colitis. It is concluded that both phosphatidylcholine and phosphatidylinositol have a therapeutic effect on the development of acetic acid-induced colitis in the rat.
Nanometer molecular lithography (1986)

We demonstrate a three-step parallel process for the fabrication of a 1-nm-thick metal (Ta/W) film with 15-nm-diam holes periodically arranged on a triangular lattice of parameter 22 nm. In this process, a two-dimensional crystalline protein monolayer is deposited on a smooth substrate, metal coated by evaporation, and then ion milled. Under ion milling this protein-metal heterostructure exhibits differential metal removal and rearrangement which varies on a protein molecular length scale. The spatial ordering of the resulting holes has the same nanometer periodicity as the protein lattice.
On the importance of image formation optics in the design of infrared spectroscopic imaging systems (2014)

Infrared spectroscopic imaging provides micron-scale spatial resolution with molecular contrast. While recent work demonstrates that sample morphology affects the recorded spectrum, considerably less attention has been focused on the effects of the optics, including the condenser and objective. This analysis is extremely important, since it will be possible to understand effects on recorded data and provides insight for reducing optical effects through rigorous microscope design. Here, we present a theoretical description and experimental results that demonstrate the effects of commonly-employed cassegranian optics on recorded spectra. We first combine an explicit model of image formation and a method for quantifying and visualizing the deviations in recorded spectra as a function of microscope optics. We then verify these simulations with measurements obtained from spatially heterogeneous samples. The deviation of the computed spectrum from the ideal case is quantified via a map which we call a deviation map. The deviation map is obtained as a function of optical elements by systematic simulations. Examination of deviation maps demonstrates that the optimal optical configuration for minimal deviation is contrary to prevailing practice in which throughput is maximized for an instrument without a sample. This report should be helpful for understanding recorded spectra as a function of the optics, the analytical limits of recorded data determined by the optical design, and potential routes for optimization of imaging systems.
A literature review: robots in medicine (1991)

Robotic systems employed in the laboratory, in rehabilitation, and in surgery are reviewed. The advantages of using a robot system over manual procedures in the laboratory to prepare samples is discussed, and some of the obstacles are noted. A typical laboratory robot is described. Rehabilitative applications in the major research areas of tactile sensors, assistive devices for the blind, prosthetics, and orthotics are examined. Manipulators that can help a disabled individual with important everyday tasks and other assistive robotic systems in rehabilitation are described. A variety of robots that assist or perform surgery is surveyed. These applications include positioning in stereotactic neurosurgery, patient manipulation, an in vivo spinal kinematic instrument, and robotic radial keratotomy, among others.
Processor hardware counter statistics as a first-class system resource (2007)

Today’s processors provide a rich source of statistical information on program execution characteristics through hardware counters. However, traditionally, operating system (OS) support for and utilization of the hardware counter statistics has been limited and ad hoc. In this paper, we make the case for direct OS management of hardware counter statistics. First, we show the utility of processor counter statistics in CPU scheduling (for improved performance and fairness) and in online workload modeling, both of which require online continuous statistics (as opposed to ad hoc infrequent uses). Second, we show that simultaneous system and user use of hardware counters is possible via time-division multiplexing. Finally, we highlight potential counter misuses to indicate that the OS should address potential security issues in utilizing processor counter statistics. 1
Tissue factor controls the balance of angiogenic and antiangiogenic properties of tumor cells in mice. (1994)

Meth-A sarcoma cells were stable transfected to overexpress (sense construct) or underexpress (antisense construct) tissue factor. In vitro, there was no difference in plating efficiency or growth between these cell lines. In vivo, tumor cells transfected to overexpress tissue factor grew more rapidly, and established larger and more vascularized tumors than control transfectants. Antisense transfectants grew the slowest and were the least vascularized. Anticoagulation of mice with warfarin did not alter the difference between these tumor lines. Tumor cells over-expressing tissue factor released more (compared with control transfectants) mitogenic activity for endothelial cells in parallel with enhanced transcription of vascular permeability factor/vascular endothelial cell growth factor (VEGF/VPF), and diminished transcription of thrombospondin (TSP2), a molecule with anti-angiogenic properties. Antisense tissue factor transfectants, while releasing the lowest amount of mitogenic activity, had increased thrombospondin and decreased VEGF/VPF transcription compared with control transfectants or wild-type cells. Experiments with these sense, antisense, truncated sense, or vector tumor lines gave comparable results in complete medium, serum free medium or in the presence of hirudin, indicating that the activation of the coagulation mechanism was not likely to be responsible for changes in tumor cell properties. These results suggest that tissue factor regulates angiogenic properties of tumor cells by altering the production of growth regulatory molecules of endothelium by a mechanism distinct from tissue factor activation of the coagulation mechanism.
Gα15 and Gα16 Couple a Wide Variety of Receptors to Phospholipase C (1995)

The murine G-protein alpha-subunit G alpha 15 and its human counterpart G alpha 16 are expressed in a subset of hematopoietic cells, and they have been shown to regulate beta-isoforms of inositide-specific phospholipase C. We studied the ability of a variety of receptors to interact with G alpha 15 and G alpha 16 by cotransfecting receptors and G-protein alpha-subunits in COS-7 cells. Activation of beta 2 adrenergic and muscarinic M2 receptors in cells expressing the receptors alone or together with G alpha q, G alpha 11, or G alpha 14 led to a very small stimulation of endogenous phospholipase C. However, when the receptors were coexpressed with G alpha 15 and G alpha 16, addition of appropriate ligands caused a severalfold increase in inositol phosphate production which was time- and dose-dependent. A similar activation of phospholipase C was observed when several other receptors which were previously shown to couple to members of the Gi and Gs family were coexpressed with G alpha 15/16. In addition, stimulation of inositol phosphate formation via receptors naturally coupled to phospholipase C was enhanced by cotransfection of G alpha 15 and G alpha 16. These data demonstrate that G alpha 15 and G alpha 16 are unique in that they can be activated by a wide variety of G-protein-coupled receptors. The ability of G alpha 15 and G alpha 16 to bypass the selectivity of receptor G-protein interaction can be a useful tool to understand the mechanism of receptor-induced G-protein activation. In addition, the promiscuous behavior of G alpha 15 and G alpha 16 toward receptors may be helpful in finding ligands corresponding to orphan receptors whose signaling properties are unknown.
Structural and magnetic properties and tunnel magnetoresistance for Co2(Cr,Fe)Al and Co2FeSi full-Heusler alloys (2006)

We have investigated the structure and magnetization of Co2(Cr1−xFex)Al (0 ≤ x ≤ 1) and Co2FeSi full-Heusler alloy films deposited on thermally oxidized Si (SiO2) and MgO (001) single crystal substrates by ultra-high vacuum sputtering at various temperatures. The films were also post-annealed after deposition at room temperature (RT). Magnetic tunnel junctions with a full-Huesler alloy electrode were fabricated with a stacking structure of Co2YZ (20 nm)/Al (1.2 nm)-oxide/Co75Fe25 (3 nm)/IrMn (15 nm)/Ta (60 nm) and microfabricated using electron beam lithography and Ar ion etching with a 102 µm2 junction area, where Co2YZ stands for Co2(Cr1−xFex)Al or Co2FeSi. The tunnel barriers were formed by the deposition of 1.2 nm Al, followed by plasma oxidization in the chamber. The x-ray diffraction revealed the A2 or B2 structure depending on heat treatment conditions and the substrate, but not L21 structure for the Co2(Cr1−xFex)Al (0 ≤ x ≤ 1) films. The L21 structure, however, was obtained for the Co2FeSi films when deposited on a MgO (001) substrate at elevated temperatures above 473 K. The maximum tunnelling magnetoresistance (TMR) was obtained with 52% at RT and 83% at 5 K for a junction using a Co2(Cr0.4Fe0.6)Al electrode. While the junction using a Co2FeSi electrode with the L21 structure exhibited the TMR of 41% at RT and 60% at 5 K, which may be improved by using a buffer layer for reducing the lattice misfit between the Co2FeSi and MgO (001) substrate.
Immunization of cancer patients with autologous cancer-derived heat shock protein gp96 preparations: A pilot study (2000)

Heat shock protein (HSP)-peptide complexes isolated from murine cancers elicit protective immunity and T lymphocytes specific for the cancer from which the HSPs are isolated. A pilot study was designed to test the feasibility, immunogenicity and toxicity of such treatment in cancer patients. Sixteen patients with assorted advanced malignancies, which had become refractory to established therapies, were recruited. The gp96 vaccine was prepared for each patient from tumor obtained from that patient. Anti-tumor immune responses were evaluated using Elispot assays of T cells in peripheral blood after minimal in vitro stimulation. No unacceptable vaccine-related toxicities or auto-immune reactions were observed. Immunization with autologous gp96 elicited MHC I-restricted, tumor-specific CD8(+) T lymphocytes in 6/12 patients immunized. In addition, expansion of the NK cell population was seen in 8/13 of patients immunized. These observations are entirely consistent with the murine experience and form a firm basis for future trials with clinical end points, using autologous, patient-specific HSP-peptide vaccines.
Safety and tolerability of intravenous ferric carboxymaltose in patients with iron deficiency anemia (2009)

There is limited safety information about ferric carboxymaltose (FCM), a new intravenous iron preparation. This randomized, crossover study compared the safety and tolerability of double-blinded intravenous doses of FCM or placebo in patients with iron deficiency anemia. Subjects (559) with iron deficiency anemia received a dose of either FCM (15 mg/kg, maximum 1000 mg) over 15 minutes or placebo on day 0. On day 7, subjects received the other agent. Safety evaluations were performed on days 7 and 14. The primary endpoint was the incidence of treatment-emergent adverse events during each 7-day study period. During the first 24 hours and during the 7-day treatment period, at least one treatment-emergent adverse event was experienced by 15.0% and 29.3% of subjects after FCM and 11.4% and 19.7% after placebo, respectively. Most were classified as Grade 1 or 2. Six subjects had Grade 3 treatment-emergent adverse events after FCM and 9 subjects after placebo. One subject had a Grade 4, and 1 subject had a Grade 5 treatment-emergent adverse event, but neither was considered study drug-related. During the first 24 hours of the treatment period, drug-related adverse events were reported in 9.3% of subjects receiving FCM and 4.8% receiving placebo. Of drug-related Grade 3 events, 4 subjects received FCM and 5 subjects received placebo. Administration of FCM (15 mg/kg, maximum of 1000 mg) over 15 minutes was well tolerated and associated with minimal risk of adverse reactions in patients with iron deficiency anemia.
A high-speed clamped bit-line current-mode sense amplifier (1991)

A clamped bit-line current-mode sense amplifier that maintains a low-impedance fixed potential on the bit lines is introduced. Using a general model for active-drive memory cells that include the two-transistor (2T) and three-transistor (3T) dynamic cells and the four-transistor/two-resistor (4T-2R) and six-transistor (6T) static cells, the new sense amplifier is shown to have a response speed that is insensitive to bit-line capacitance. This is achieved by relocating the large bit-line capacitance to a node within the sense amplifier that has only a minimal effect on the speed of the circuit. Bit-line clamping also minimizes inter-bit-line voltage noise coupling.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Construction of a Novel Redox Protein by Rational Design:  Conversion of a Disulfide Bridge into a Mononuclear Iron−Sulfur Center (1998)

A mononuclear iron-sulfur center, capable of reversible electron transfer, has been introduced into thioredoxin, a protein devoid of such sites, using an automated, structure-based design algorithm. One of the sites predicted by the Dezymer computer program to introduce a tetrahedral tetrathiolate iron center included the intrinsic Cys32-Cys35 disulfide of wild-type thioredoxin and two additional mutants, Trp28Cys and Ile75Cys, thereby converting a disulfide into a metal-based redox center. This designed protein forms a 1:1 monomeric complex with FeIII, whose electronic absorption and EPR spectra closely resemble those of the rubredoxins, as intended. CoII spectra provided further confirmation of tetrahedral tetrathiolate metal coordination. The designed protein is capable of undergoing successive cycles of oxidation and reduction. The computer-generated design only took into account the geometry of the primary coordination shell around the metal. We have therefore demonstrated that simple geometrical considerations can be sufficient to reproduce the dominant electronic structure and reactivity of a simple metal-based redox center.