gebhart/patrepeval huggingface dataset:
Superparamagnetic microbead inductive detector (2005)

We developed an inductive system to measure the surface concentration of superparamagnetic microbeads resulting from a bioassay. Our tabletop apparatus, tested with Dynal MyOne™ microbeads, has a detection limit of about 1000beads∕Hz1∕2 (i.e., about 2×1010Bohr magnetons). The system can measure surface concentrations from 0.01% to 100% over the 6mm2 sensitive area with an integration time of 1s.
Precise Recovery of Latent Vectors from Generative Adversarial Networks (2017)

Generative adversarial networks (GANs) transform latent vectors into visually plausible images. It is generally thought that the original GAN formulation gives no out-of-the-box method to reverse the mapping, projecting images back into latent space. We introduce a simple, gradient-based technique called stochastic clipping. In experiments, for images generated by the GAN, we precisely recover their latent vector pre-images 100% of the time. Additional experiments demonstrate that this method is robust to noise. Finally, we show that even for unseen images, our method appears to recover unique encodings.
Hepatic mRNA levels for the LDL receptor and HMG-CoA reductase show coordinate regulation in vivo. (1992)

A sensitive solution hybridization assay using autologous cRNA probes was developed with the aim to study the simultaneous regulation of hepatic mRNA levels, on a quantitative basis, for the LDL receptor (LDLr), HMG-CoA reductase, and cholesterol 7 alpha-hydroxylase (Cho-7-hx) in C57BL/6J mice. With the purpose to suppress and stimulate transcript levels respectively, animals received established high fat diets, cholesterol-enriched diets, and a diet supplemented with mevinolin and colestipol. One hundred nineteen animals were investigated in six separate experiments. In spite of an eightfold increase in hepatic cholesterol induced by a high fat diet, the LDLr and the HMG-CoA reductase mRNA levels were only reduced to 60-70% and 25-50% of control values, respectively. When the data from all animals were analyzed, a strong positive correlation was obtained between the mRNA levels for the LDLr and HMG-CoA reductase (r = 0.79, P less than 0.001). A significant relation remained when control animals only were analyzed (n = 42, r = 0.59, P less than 0.001). Cho-7-hx mRNA showed a regulatory pattern that differed from that of the LDLr and HMG-CoA reductase; feeding cholesterol at 1.7% and 5% but not at 0.4% elevated the mRNA levels for Cho-7-hx while the LDLr and HMG-CoA reductase mRNA levels were maximally suppressed already at 0.4% of dietary cholesterol. The results show that the mRNA levels for the LDLr and HMG-CoA reductase are regulated in parallel in the liver in vivo during various metabolic perturbations as well as at normal physiologic conditions.(ABSTRACT TRUNCATED AT 250 WORDS)
The role of complement in atherosclerosis (2008)

The articles that have emerged over the last year highlight the relevance of the complement system to the atherosclerosis field.
Open questions in ferredoxin‐NADP<sup>+</sup> reductase catalytic mechanism (2003)

Ferredoxin (flavodoxin)-NADP(H) reductases (FNR) are ubiquitous flavoenzymes that deliver NADPH or low potential one-electron donors (ferredoxin, flavodoxin) to redox-based metabolisms in plastids, mitochondria and bacteria. The plant-type reductase is also the basic prototype for one of the major families of flavin-containing electron transferases that display common functional and structural properties. Many aspects of FNR biochemistry have been extensively characterized in recent years using a combination of site-directed mutagenesis, steady-state and transient kinetic experiments, spectroscopy and X-ray crystallography. Despite these considerable advances, various key features in the enzymology of these important reductases remain yet to be explained in molecular terms. This article reviews the current status of these open questions. Measurements of electron transfer rates and binding equilibria indicate that NADP(H) and ferredoxin interactions with FNR result in a reciprocal decrease of affinity, and that this induced-fit step is a mandatory requisite for catalytic turnover. However, the expected conformational movements are not apparent in the reported atomic structures of these flavoenzymes in the free state or in complex with their substrates. The overall reaction catalysed by FNR is freely reversible, but the pathways leading to NADP+ or ferredoxin reduction proceed through entirely different kinetic mechanisms. Also, the reductases isolated from various sources undergo inactivating denaturation on exposure to NADPH and other electron donors that reduce the FAD prosthetic group, a phenomenon that might have profound consequences for FNR function in vivo. The mechanisms underlying this reductive inhibition are so far unknown. Finally, we provide here a rationale to interpret FNR evolution in terms of catalytic efficiency. Using the formalism of the Albery-Knowles theory, we identified which parameter(s) have to be modified to make these reductases even more proficient under a variety of conditions, natural or artificial. Flavoenzymes with FNR activity catalyse a number of reactions with potential importance for biotechnological processes, so that modification of their catalytic competence is relevant on both scientific and technical grounds.
Human/robot interaction via the transfer of power and information signals. I. Dynamics and control analysis (2003)

Extenders, a class of robot manipulators worn by humans to increase human mechanical strength while the wearer's intellect remains the central intelligent control system for manipulating the extender, are characterized, with a focus on the issues of the dynamics and control of human-machine interaction in the sense of the transfer of power and information signals. General models of the human, the extender, and the interaction between the human and the extender are developed. Unstructured modeling is chosen to include all the dynamics in the systems and to avoid specific models. The stability of the system of human, extender, and object being manipulated is analyzed, and the conditions for stable maneuvers derived. An expression for the performance of the extender is defined as a means to quantify the force augmentation. The tradeoff between stability and performance is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Functional Screening of Intracellular Proteins in Single Cells and in Patterned Cell Arrays Using Electroporation (2002)

A tool for detection and characterization of intracellular enzyme-substrate and receptor-ligand interactions inside the cytoplasm of single targeted cells or small confined groups of cells is presented. Fluorogenic enzyme substrates and receptor ligands were rapidly delivered by electroosmosis and internalized by electroporation in cells using an electrolyte-filled capillary (EFC) biased at a high voltage. Specifically, alkaline phosphatase and proteases were detected in single NG108-15 cells using fluorescein diphosphate and casein BODIPY FL, respectively. The intracellular 1,4,5-inositol triphosphate (IP3) and ryanodine receptors were detected after EFC introduction of the selective receptor agonists IP3 and cyclic adenosine diphosphate ribose (cADPr), respectively. Receptor activation in both cases resulted in increased cytosolic concentrations of free calcium ions that were measured using the calcium-ion-selective probe, fluo-3. The effect of cADPr could be blocked by coadministration of the ryanodine receptor antagonist ruthenium red. Furthermore, electroporation of a plurality of cells grown in microwell structures (100 x 100 x 45 microm) molded in PDMS is demonstrated. The methods and systems described using an EFC for electroporation and delivery of protein markers, ligands, and substrates might be useful in high-throughput screening of intracellular targets, with applications in proteomics and phenotype profiling, as well as in drug discovery.
Activation of Caspase-1 in the Nucleus Requires Nuclear Translocation of Pro-caspase-1 Mediated by Its Prodomain (1998)

The interleukin-1beta-converting enzyme-like protease precursor, pro-caspase-1, has an N-terminal prodomain that is removed during cleavage activation of the protease. Here we show that tumor necrosis factor treatment of HeLa cells induced apoptosis without detectable proteolytic activation of caspase-1 in the cytosol. Instead, tumor necrosis factor induced the translocation of pro-caspase-1 to the nucleus where it was proteolytically activated, releasing the intact prodomain. We identified a nuclear localization signal in the prodomain, which was required for translocation of both pro-caspase-1 as well as its prodomain to the nucleus. Surprisingly, transfected MCF-7 carcinoma or embryonic kidney 293T cells expressing the prodomain alone underwent apoptosis. These results show that death signal-induced nuclear targeting is a novel activity of a caspase prodomain and indicate that caspase-1 and its prodomain may have hitherto unsuspected nuclear functions in apoptosis.
Ca2+-induced Ca2+ Release in Sensory Neurons (2005)

Ca(2+)-induced Ca(2+) release (CICR) is a ubiquitous mechanism by which Ca(2+) release from the endoplasmic reticulum amplifies the trigger Ca(2+) entry and generates propagating Ca(2+) waves. To elucidate the mechanisms that control this positive feedback, we investigated the spatial and temporal kinetics and measured the gain function of CICR in small sensory neurons from mammalian dorsal root ganglions (DRGs). We found that subsurface Ca(2+) release units (CRUs) are under tight local control by Ca(2+) entry, whereas medullar CRUs as a "common pool" system are recruited by inwardly propagating CICR. Active CRUs often displayed repetitive Ca(2+) sparks, conferring the ability to encode a "memory" of neuronal activity well beyond the duration of an action potential. Store Ca(2+) reserve was able to support all CRUs each to fire approximately 15 sparks, excluding use-dependent inactivation or store depletion as the major CICR termination mechanism. Importantly, CICR in DRG neurons operated in a low gain, linear regime (gain = 0.54), which conferred intrinsic stability to CICR. Combined with high Ca(2+) current density (-156 pA/pF at -10 mV), such a low gain CICR system generated large intracellular Ca(2+) transients without jeopardizing the stability. These findings provide the first demonstration that CICR operating in a low gain regime can be harnessed to provide a robust and graded amplification of Ca(2+) signal in the absence of counteracting inhibitory mechanism.
Generating large non-singular matrices over an arbitrary field with blocks of full rank (2002)

This note describes a technique for generating large non-singular matrices with blocks of full rank. Our motivation to construct such matrices arises in the white-box implementation of cryptographic algorithms with S-boxes.
Interpretation of Galileo's Io plasma and field observations: I0, I24, and I27 flybys and close polar passes (2002)

We interpret plasma and magnetic field observations taken during the Galileo spacecraft Io flybys I0 in December 1995, I24 in October 1999, and I27 in February 2000, and we give predictions for a generic pass over Io's northern pole with a three‐dimensional, two‐fluid plasma model. We show that all previous field and plasma observations by the Galileo spacecraft can be explained without the assumption of an internal magnetic field of Io in contrast to claims by Kivelson et al. [1996a , 1996b ] and Khurana et al. [1997] . We are also able to reproduce both the magnitude and the structure of the double‐peak magnetic field signature of the I0 flyby. The origin of this structure can be attributed to diamagnetic and inertia currents. Observations by a polar flyby should answer Io's internal magnetic field question decisively. We also study the effect of different neutral atmosphere models on Io's electrodynamic interaction. Our analysis suggests that Io's atmosphere is longitudinally asymmetric with the scale height on the upstream side smaller than on the downstream side due to the drag force of the flowing plasma on Io's atmosphere. We also show how the Hall effect in Io's ionosphere generates rotated Alfvén wings. In addition, the high‐energy electrons observed by Williams et al. [1996 , 1999 ] and Frank and Paterson [1999] might play an important role for the formation of Io's downstream wake.
Pharmacological characterization of CP-547,632, a novel vascular endothelial growth factor receptor-2 tyrosine kinase inhibitor for cancer therapy. (2003)

Signaling through vascular endothelial growth factor (VEGF) receptors (VEGFRs) is a key pathway initiating endothelial cell proliferation and migration resulting in angiogenesis, a requirement for human tumor growth and metastasis. Abrogation of signaling through VEGFR by a variety of approaches has been demonstrated to inhibit angiogenesis and tumor growth. Small molecule inhibitors of VEGFR tyrosine kinase have been shown to inhibit angiogenesis, inhibit tumor growth, and prevent metastases. Our goal was to discover and characterize an p.o. active VEGFR-2 small molecule inhibitor. A novel isothiazole, CP-547,632, was identified as a potent inhibitor of the VEGFR-2 and basic fibroblast growth factor (FGF) kinases (IC(50) = 11 and 9 nM, respectively). It is selective relative to epidermal growth factor receptor, platelet-derived growth factor beta, and other related TKs. It also inhibits VEGF-stimulated autophosphorylation of VEGFR-2 in a whole cell assay with an IC(50) value of 6 nM. After oral administration of CP-547,632 to mice bearing NIH3T3/H-ras tumors, VEGFR-2 phosphorylation in tumors was inhibited in a dose-dependent fashion (EC(50) = 590 ng/ml). These plasma concentrations correlated well with the observed concentrations of the compound necessary to inhibit VEGF-induced corneal angiogenesis in BALB/c mice. A sponge angiogenesis assay was used to directly compare the inhibitory activities of CP-547,632 against FGF receptor 2 or VEGFR-2; this compound potently inhibits both basic FGF and VEGF-induced angiogenesis in vivo. The antitumor efficacy of this agent was evaluated after once daily p.o. administration to athymic mice bearing human xenografts and resulted in as much as 85% tumor growth inhibition. CP-547,632 is a well-tolerated, orally-bioavailable inhibitor presently under clinical investigation for the treatment of human malignancies.
Clinical Experience with CD3 X CD19 Bispecific Antibodies in Patients with B Cell Malignancies (1995)

In extensive preclinical testing, a CD3 x CD19 bispecific antibody (BsAb) induced killing of malignant B cells by resting T cells even in an autologous situation. In a 14 day clonogenic assay using a CD19+ pre-B cell line (REH), BsAb required repeated administration together with IL-2 to achieve a 5 log kill by resting peripheral blood T cells. Intravenously administered BsAb in an intrapatient dose escalation study of 3 patients with B cell non-Hodgkin's lymphoma showed limited toxicity (WHO grade II fever and chills) due to tumor necrosis factor-alpha (TNF-alpha) release by T cells. Pharmacokinetics with 2.5 mg BsAb showed peak levels of 200-300 micrograms/ml and a t1/2 of 10.5 h. The next patient, with chronic lymphocytic leukemia (CLL), received 0.6 mg BsAb/m2 as an i.v. infusion preceded by 1 MU IL-2/m2 s.c. Improved T cell activation was noted, as indicated by an increase in IFN-gamma, IL-6, IL-8, and IL-10, in addition to high TNF-alpha increases. TNF-alpha increases were highest on the first day. Toxicity remained restricted to grade II fever and chills, observed every day after the infusion of BsAb. No clear clinical effects were seen in this chemotherapy-resistant CLL patient with a high tumor burden. If subsequent patients also show limited toxicity, treatment of patients with a lower tumor load seems to be warranted to evaluate the efficacy of CD3 x CD19 BsAb therapy.
Phorbol Ester-mediated Down-regulation of an Interferon-inducible Gene (1989)

Interferons (IFNs) induce the expression of a variety of cellular RNAs and inhibit phorbol ester induction of other genes. Experiments reported here indicate that phorbol esters can also specifically inhibit the expression of an IFN-induced RNA (IFN-IND-1). Phorbol esters exert their effects by inhibiting IFN-induced transcription of the gene that encodes IFN-IND-1 (ISG-54K); inhibitors of protein synthesis reverse the effects of these compounds. The actions of phorbol esters are only seen in those types of cultured cells where cycloheximide in the presence of IFN prevents long term IFN treatment of cells from inducing a "desensitized state." In desensitized cells, IFN is not able to reinduce the transcription of the RNA. Our results indicate that a protein kinase C-dependent pathway requiring protein synthesis may be one mechanism by which IFN is able to down regulate the transcription of genes whose expression it initially induces.
Trust and etiquette in high-criticality automated systems (2004)

article Share on Trust and etiquette in high-criticality automated systems Authors: Raja Parasuraman The Catholic University of America, Washington, D.C. The Catholic University of America, Washington, D.C.View Profile , Christopher A. Miller Smart Information Flow Technologies (SIFT) Inc., Minneapolis, MN Smart Information Flow Technologies (SIFT) Inc., Minneapolis, MNView Profile Authors Info & Claims Communications of the ACMVolume 47Issue 4April 2004pp 51–55https://doi.org/10.1145/975817.975844Published:01 April 2004Publication History 214citation3,141DownloadsMetricsTotal Citations214Total Downloads3,141Last 12 Months117Last 6 weeks11 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Functional Recovery in Traumatic Spinal Cord Injury after Transplantation of Multineurotrophin-Expressing Glial-Restricted Precursor Cells (2005)

Demyelination contributes to the physiological and behavioral deficits after contusive spinal cord injury (SCI). Therefore, remyelination may be an important strategy to facilitate repair after SCI. We show here that rat embryonic day 14 spinal cord-derived glial-restricted precursor cells (GRPs), which differentiate into both oligodendrocytes and astrocytes, formed normal-appearing central myelin around axons of cultured DRG neurons and had enhanced proliferation and survival in the presence of neurotrophin 3 (NT3) and brain-derived neurotrophin factor (BDNF). We infected GRPs with retroviruses expressing the multineurotrophin D15A (with both BDNF and NT3 activities) and then transplanted them into the contused adult thoracic spinal cord at 9 d after injury. Expression of D15A in the injured spinal cord is five times higher in animals receiving D15A-GRP grafts than ones receiving enhanced green fluorescent protein (EGFP)-GRP or DMEM grafts. Six weeks after transplantation, the grafted GRPs differentiated into mature oligodendrocytes expressing both myelin basic protein (MBP) and adenomatus polyposis coli (APC). Ultrastructural analysis showed that the grafted GRPs formed morphologically normal-appearing myelin sheaths around the axons in the ventrolateral funiculus (VLF) of spinal cord. Expression of D15A significantly increased the percentage of APC+ oligodendrocytes of grafted GRPs (15-30%). Most importantly, 8 of 12 rats receiving grafts of D15A-GRPs recovered transcranial magnetic motor-evoked potential responses, indicating that conduction through the demyelinated VLF axons was restored. Such electrophysiological recovery was not observed in rats receiving grafts of EGFP-GRPs, D15A-NIH3T3 cells, or an injection of an adenovirus expressing D15A. Recovery of hindlimb locomotor function was also significantly enhanced only in the D15A-GRP-grafted animals at 4 and 5 weeks after transplantation. Therefore, combined treatment with neurotrophins and GRP grafts can facilitate functional recovery after traumatic SCI and may prove to be a useful therapeutic strategy to repair the injured spinal cord.
&lt;i&gt;In vitro&lt;/i&gt; Labelling of Platelets (1977)

Duplicate platelet survival studies, using autologous platelets labelled in vitro with radioactive sodium chromate, were carried out on 5 lymphoma patients who had been splenectomized 14–21 months earlier. In the first experiment plasma was employed as the incubation medium and in the second a Ringer-citrate-dextrose (RCD) solution. The uptake of chromate by the platelets was 2.0 times higher in the RCD as compared to the plasma experiments. An identical pattern for the immediate behaviour of infused labelled platelets was observed in the duplicate studies, and the recovery of platelet-bound radioactivity remained stable at the 90% level during 2 h after infusion. In these experiments the means for platelet mean life span were almost identical, 5.4 + 0.6 and 5.3 + 0.5 days, respectively, and significantly (p < 0.05) shorter than the mean for a control group consisting of 21 healthy males (6.9 + 0.3 days). It is concluded that RCD and plasma seem to serve equally well as incubation medium at the in vitro labelling of platelets
The use of modulated energy carried on a high frequency wave for the relief of intractable pain. (1993)

Ten volunteer patients with chronic neck/shoulder or back pain had been taking analgesics, and using conventional transcutaneous electrical nerve stimulation (TENS) with no significant pain relief. On entry to the trial, they were requested to stop taking their analgesics for two days prior to the study and for two days after starting to use the Liss Bipolar Body Stimulator for 20 min 3-5 times daily. Resumption of medication was then allowed. The stimulator (15,000 Hz carrier wave with a double modulation of 15 and 500 Hz) was connected to two adhesive electrodes placed so that the current field encompassed the trigger points, and used at a current that was just threshold for perception (1-4 mA). A visual analogue pain score was recorded before the study, and each evening of the month's study. The pain showed an overall highly significant rapid reduction of approximately 62% (p < 0.001), and all but two of the patients received substantial benefit throughout the study. We conclude that the Liss Bipolar Body Stimulator usually causes a substantial reduction of pain even in patients not helped by conventional TENS devices.
Photostability of UV Screeners in Polymers and Coatings (1996)

All major classes of commercially available UV screeners undergo photodegradation at quantum yields on the order of 1 X 10M-6 in polar matrices. The rates obey zero-order kinetics in the high-absorption range and are highly dependent on the nature of the matrix. Typical rates of photodegradation for screeners in cast polymethyl methacrylate films are on the order of 0.3 to 0.7 absorption units per year of outdoor exposure and 0.2 to 0.5 absorption units per 1000 h of xenon-arc or QUV exposure. Concentration of the screener appears to play little role. The presence of hindered amine light stabilizers and the nature of the light source might affect the rate of degradation of the matrix. Rapidly degrading matrices seem to cause rapid destruction of the screeners.
Optical fiber interferometers with [3×3] directional couplers: Analysis (1981)

All-guided wave interferometers using [3×3] directional couplers as beam splitters are analyzed in detail. The characteristics of such interferometers are compared with those of conventional interferometers using [2×2] beam splitters. It is shown that there are advantages in using [3×3] couplers instead of [2×2] couplers in the Mach-Zehnder interferometric sensors and the Sagnac rotation sensors (gyroscopes).