gebhart/patrepeval huggingface dataset:
Elevated circulating free fatty acid levels impair endothelium-dependent vasodilation. (1997)

We have recently shown that insulin-resistant obese subjects exhibit impaired endothelial function. Here, we test the hypothesis that elevation of circulating FFA to levels seen in insulin-resistant subjects can impair endothelial function. We studied leg blood flow responses to graded intrafemoral artery infusions of the endothelium-dependent vasodilator methacholine chloride (Mch) or the endothelium-independent vasodilator sodium nitroprusside during the infusion of saline and after raising systemic circulating FFA levels exogenously via a low- or high-dose infusion of Intralipid plus heparin or endogenously by an infusion of somatostatin (SRIF) to produce insulinopenia in groups of lean healthy humans. After 2 h of infusion of Intralipid plus heparin, FFA levels increased from 562+/-95 to 1,303+/-188 micromol, and from 350+/-35 to 3,850+/-371 micromol (P < 0.001) vs. saline for both low- and high-dose groups, respectively. Mch-induced vasodilation relative to baseline was reduced by approximately 20% in response to the raised FFA levels in both groups (P < 0.05, saline vs. FFA, ANOVA). In contrast, similar FFA elevation did not change leg blood flow responses to sodium nitroprusside. During the 2-h SRIF infusion, insulin levels fell, and FFA levels rose from 474+/-22 to 1,042+/-116 micromol (P < 0.01); Mch-induced vasodilation was reduced by approximately 20% (P < 0.02, saline vs. SRIF, ANOVA). Replacement of basal insulin levels during SRIF resulted in a fall of FFA levels from 545+/-47 to 228+/-61 micromol, and prevented the impairment of Mch-induced vasodilation seen with SRIF alone. In conclusion, (a) elevated circulating FFA levels cause endothelial dysfunction, and (b) impaired endothelial function in insulin-resistant humans may be secondary to the elevated FFA concentrations observed in these patients.
Parallel capillaries for high throughput in electrophoretic separations and electroosmotic drug discovery systems (2002)

Electrophoresis microstructures are known to be up to 100-fold faster than today's analytical instruments. In some cases, even higher throughput is required or there is an inherent limitation to separation speed. Therefore, parallel processing becomes very important. Injections into parallel capillaries are feasible using one introduction channel to feed the sample. This allows one to control up to 80 channels using 4-electrodes only.
High‐resolution light microscopy using luminescent nanoparticles (2010)

This review presents recent progress in the development of the luminescent nanoparticles for confocal and multiphoton microscopy. Four classes of nanomaterials are discussed: (1) silica-based nanoparticles doped with fluorescent molecules, (2) gold nanoparticles, (3) semiconductor nanocrystals (quantum dots/rods), and (4) nanophosphors. Special considerations are given to recently developed imaging nanoprobes, such as (1) organically modified silica (ORMOSIL) nanoparticles doped with two-photon absorbing fluorophores, which exhibit aggregation-enhanced fluorescence (AEF), and (2) nanophosphors (ceramic nanoparticles containing luminescent lanthanoid ions). Advantages and disadvantages of every class of nanomaterials and their specific applications are briefly discussed.
A review of actively moving polymers in textile applications (2010)

Actively moving polymers being developed rapidly have drawn wide attention. A review is presented to highlight the most important areas and directions in textile applications. The molecular structure of actively moving polymers is introduced firstly. The textile applications of actively moving polymers are then summarized from the fibre spinning (including wet spinning, melt spinning and electro-spinning), fabric manufacturing, shape memory finishing technologies and water vapor permeability investigation. Additionally, the challenges of actively moving polymers in textile applications are pointed out and some research directions are suggested.
Uterine arterial embolization for the management of leiomyomas: quality-of-life assessment and clinical response. (1998)

Uterine arterial embolization is an effective therapy in the management of symptomatic leiomyomas and may prove to be a valuable alternative to myomectomy, hysterectomy, or other surgical procedures. Further investigation is warranted.
Tailoring in Vitro Selection for a Picomolar Affinity Human Antibody Directed against Vascular Endothelial Growth Factor Receptor 2 for Enhanced Neutralizing Activity (2003)

Vascular endothelial growth factor (VEGF) and its receptors have been implicated in promoting solid tumor growth and metastasis via stimulating tumor-associated angiogenesis. We previously identified several fully human neutralizing anti-VEGF receptor 2 (or kinase inserting domain-containing receptor (KDR)) antibodies from a large antibody phage display library. These antibodies bind specifically to KDR, block VEGF/KDR interaction, and inhibit VEGF-induced proliferation of human endothelial cells and migration of KDR+ leukemia cells. Three of these antibodies, interestingly, share an identical heavy chain variable (VH) sequence. In this report, we constructed a new library comprising the single VH paired with the variable light chain (VL) repertoire obtained from the original naïve human library. Initial in vitro selection revealed that the single VH could pair with a number of different VL while retaining its specificity for KDR. However, a consensus VH/VL pair, clone 1121, was identified after three or four rounds of selection by tailoring the stringency of the panning conditions. Clone 1121 showed a >30-fold higher binding affinity to KDR (Kd, 100 pm) because of improvement on both association and dissociation constants and blocked VEGF/KDR interaction with an IC50 of approximately 1 nm, compared with that of 3-4 nm for the parent Fab fragments. Further, clone 1121 was more potent in inhibiting VEGF-stimulated KDR phosphorylation in endothelial cells. A binding epitope mapping study on clone 1121 and one of the parent clones, 2C6, demonstrated that both antibodies interacted with the third immunoglobulin domain within the extracellular region of KDR. Several peptide phage display libraries were utilized to further examine the fine binding specificities of the two antibodies. All of the 2C6-binding peptides are cysteine-constrained, whereas clone 1121 binds to both cysteine-constrained and linear peptides. It is noteworthy that most of the 2C6-binding peptides also cross-react with clone 1121, but none of the clone 1121-specific peptides binds to 2C6, indicating that clone 1121 retained part of the original binding epitope(s) of 2C6 while gaining new binding specificity. Taken together, our observation suggests that clone 1121 may have great clinical potential in anti-angiogenesis therapy. It further underscores the efforts to identify antibodies of high affinity for enhanced biological activities.
An Integrated ISFET Sensor Array (2009)

A monolithically integrated ISFET sensor array and interface circuit are described. A new high-density, low-power source-drain follower was developed for the sensor array. ISFETs were formed by depositing Au/Ti extended-gate electrodes on standard MOSFETs, then thin silicon nitride layers using catalytic chemical vapor deposition and/or SU-8 protective layers were formed on the extended-gate electrodes. Applications for the array include: (1) pH detection by statistical distribution observing time and space fluctuations; (2) DNA detection using thiol-modified or silane-coupled oligonucleotides; (3) bio-image sensing by converting photons to electrons using Photosystem I of Thermosynechococcus elongatus, and sensing the converted electric charges by ISFETs.
A taxonomy of computer worms (2003)

To understand the threat posed by computer worms, it is necessary to understand the classes of worms, the attackers who may employ them, and the potential payloads. This paper describes a preliminary taxonomy based on worm target discovery and selection strategies, worm carrier mechanisms, worm activation, possible payloads, and plausible attackers who would employ a worm.
Fluorescence studies of the intra-cellular distribution of zinc bis(thiosemicarbazone) complexes in human cancer cells (2005)

The uptake of zinc bis(thiosemicarbazone) complexes in human cancer cells has been studied by fluorescence microscopy and the cellular distribution established, including the degree of uptake in the nucleus.
Epitope mapping of monoclonal antibodies to the paired helical filaments of Alzheimer's disease: identification of phosphorylation sites in tau protein (1994)

Tau is a neuronal phosphoprotein the expression of which is developmentally regulated. A single tau isoform is expressed in fetal human brain but six isoforms are expressed in adult human brain, with the fetal isoform corresponding to the shortest adult isoform. Phosphorylation is also developmentally regulated, as fetal tau is phosphorylated at more sites than adult tau. In Alzheimer's disease, the six adult tau isoforms become hyperphosphorylated and form the paired helical filament (PHF), the major fibrous component of the neurofibrillary lesions. One way to identify phosphorylated sites in tau is to use antibodies that recognize phosphorylated residues within a specific amino acid sequence. We here characterize the two novel phosphorylation-dependent anti-tau antibodies AT270 and AT180 and identify their epitopes as containing phosphorylated Thr-181 and Thr-231 respectively. With these antibodies we show that these two threonine residues are partially phosphorylated in fetal and adult tau and almost fully phosphorylated in PHF tau. This result contrasts with previous studies of Ser-202 and Ser-396 which are partially phosphorylated in fetal tau, unphosphorylated in adult tau but almost fully phosphorylated in PHF tau.
A molecular mechanics/grid method for evaluation of ligand–receptor interactions (1995)

Abstract We present a computational method for prediction of the conformation of a ligand when bound to a macromolecular receptor. The method is intended for use in systems in which the approximate location of the binding site is known and no large‐scale rearrangements of the receptor are expected upon formation of the complex. The ligand is initially placed in the vicinity of the binding site and the atomic motions of the ligand and binding site are explicitly simulated, with solvent represented by an implicit solvation model and using a grid representation for the bulk of the receptor protein. These two approximations make the method computationally efficient and yet maintain accuracy close to that of an all‐atom calculation. For the benzamidine/trypsin system, we ran 100 independent simulations, in many of which the ligand settled into the low‐energy conformation observed in the crystal structure of the complex. The energy of these conformations was lower than and well‐separated from that of others sampled. Extensions of this method are also discussed. © 1995 by John Wiley &amp; Sons, Inc.
MicroRNA-126 inhibits invasion in bladder cancer via regulation of ADAM9 (2014)

In this study we describe the role of miR-126 in bladder cancer progression, identifying miR-126 and ADAM9 as potential clinical biomarkers of disease aggressiveness.
The Rx Gene from Potato Controls Separate Virus Resistance and Cell Death Responses (1999)

Rx-mediated extreme resistance against potato virus X in potato does not involve a necrotic hypersensitive response at the site of initial infection and thereby differs from the more usual type of disease resistance in plants. However, the Rx protein is structurally similar to products of disease resistance genes conferring the hypersensitive response. We show in both Nicotiana spp and potato that Rx has the potential to initiate a cell death response but that extreme resistance is separate and epistatic to necrosis. These data indicate that cell death and pathogen arrest are separate disease resistance responses in plants.
"Avoid the crush": hazards of medication administration in patients with dysphagia or a feeding tube (2005)

CASE 1: A 70-year-old woman is admitted with an acute dysphagic stroke. A pureed and thickened liquid diet is started during her hospital stay. Efforts at rehabilitation are hampered by severe knee pain from chronic osteoarthritis. Her pain is initially managed with a short-acting preparation of
Postsynaptic Calcineurin Activity Downregulates Synaptic Transmission by Weakening Intracellular Ca2+Signaling Mechanisms in Hippocampal CA1 Neurons (1997)

Protein phosphorylation and dephosphorylation are believed to functionally couple neuronal activity and synaptic plasticity. Our previous results indicated that postsynaptic Ca2+/calmodulin (CaM) signaling pathways play an important role in setting synaptic strength, and calcineurin (CaN) activity limits synaptic responses during basal synaptic transmission and long-term potentiation expression. The inhibition of postsynaptic CaN activity by FK-506 or an autoinhibitory peptide induced synaptic potentiation in hippocampal slices, which occludes tetanus-induced LTP. FK-506-induced synaptic potentiation was expressed in adult but not young rats. To elucidate mechanisms underlying CaN-inhibited synaptic potentiation, we co-injected certain agents affecting Ca2+ signaling pathways with CaN inhibitors into CA1 neurons. Synaptic potentiation induced by FK-506 was significantly attenuated by co-injecting BAPTA, heparin/dantrolene (inhibitors of intracellular Ca2+ release), a CaM-binding peptide, or CaM-KII/PKC pseudosubstrate peptides. These results indicate that postsynaptic CaN activity can downregulate evoked synaptic transmission by weakening intracellular Ca2+ signals and downstream protein kinase activities.
Purification of human marrow progenitor cells and demonstration of the direct action of macrophage colony-stimulating factor on colony-forming unit-macrophage (1991)

To facilitate the investigation of the direct interaction between hematopoietic progenitors and colony-stimulating factors, we have developed a method to purify human marrow progenitor cells. Using density centrifugation, negative panning with concanavalin A coated plates, positive selection of CD34-positive cells with immunomagnetic microspheres, overnight adherence to a plastic dish, negative selection with a panel of monoclonal antibodies, and density centrifugation, human marrow progenitor cells were purified from 1.5% to 53.2%, a 42- fold purification, with a 4.8% yield. The purified cells consisted of 38% erythroid, 9% colony forming unit-granulocyte (CFU-G), 29% CFU- macrophage (CFU-M), 12% CFU-eosinophil/basophil (CFU-Eo/Ba), and 4% CFU- mix. The purified cells cultured in serum-free fibrin clots with recombinant human macrophage colony-stimulating factor (rM-CSF) for 14 days developed a pure population of CFU-M colonies. An appearance of CFU-M colonies was present after the addition of 1 U/mL of rM-CSF and the maximum stimulation was found at 100 U/mL. When the purified cells were cultured in serum-free medium with rM-CSF in a limiting dilution assay and the percentage of nonresponder wells for CFU-M colonies was plotted against cell concentration, serum-free cultures yielded a straight line through the origin, indicating that CFU-M development did not depend on accessory cells and that rM-CSF acted directly on the CFU- M.
Highly sensitive feature detection for high resolution LC/MS (2008)

The new feature detection algorithm meets the requirements of current metabolomics experiments. centWave can detect close-by and partially overlapping features and has the highest overall recall and precision values compared to the other algorithms, matchedFilter (the original algorithm of XCMS) and the centroidPicker from MZmine. The centWave algorithm was integrated into the Bioconductor R-package XCMS and is available from (http://www.bioconductor.org/).
Role of BkdR, a Transcriptional Activator of the SigL-Dependent Isoleucine and Valine Degradation Pathway in Bacillus subtilis (1999)

A new gene, bkdR (formerly called yqiR), encoding a regulator with a central (catalytic) domain was found in Bacillus subtilis. This gene controls the utilization of isoleucine and valine as sole nitrogen sources. Seven genes, previously called yqiS, yqiT, yqiU, yqiV, bfmBAA, bfmBAB, and bfmBB and now referred to as ptb, bcd, buk, lpd, bkdA1, bkdA2, and bkdB, are located downstream from the bkdR gene in B. subtilis. The products of these genes are similar to phosphate butyryl coenzyme A transferase, leucine dehydrogenase, butyrate kinase, and four components of the branched-chain keto acid dehydrogenase complex: E3 (dihydrolipoamide dehydrogenase), E1alpha (dehydrogenase), E1beta (decarboxylase), and E2 (dihydrolipoamide acyltransferase). Isoleucine and valine utilization was abolished in bcd and bkdR null mutants of B. subtilis. The seven genes appear to be organized as an operon, bkd, transcribed from a -12, -24 promoter. The expression of the bkd operon was induced by the presence of isoleucine or valine in the growth medium and depended upon the presence of the sigma factor SigL, a member of the sigma 54 family. Transcription of this operon was abolished in strains containing a null mutation in the regulatory gene bkdR. Deletion analysis showed that upstream activating sequences are involved in the expression of the bkd operon and are probably the target of bkdR. Transcription of the bkd operon is also negatively controlled by CodY, a global regulator of gene expression in response to nutritional conditions.
Overlapping Destinations for Two Dual Targeted Glycyl-tRNA Synthetases in Arabidopsis thaliana and Phaseolus vulgaris (2001)

In plant mitochondria, some of the tRNAs are encoded by the mitochondrial genome and resemble their prokaryotic counterparts, whereas the remaining tRNAs are encoded by the nuclear genome and imported from the cytosol. Generally, mitochondrial isoacceptor tRNAs all have the same genetic origin. One known exception to this rule is the group of tRNA(Gly) isoacceptors in dicotyledonous plants. A mitochondrion-encoded tRNA(Gly) and at least one nucleus-encoded tRNA(Gly) coexist in the mitochondria of these plants, and both are required to allow translation of all four GGN glycine codons. We have taken advantage of this atypical situation to address the problem of tRNA/aminoacyl-tRNA synthetase coevolution in plants. In this work, we show that two different nucleus-encoded glycyl-tRNA synthetases (GlyRSs) are imported into Arabidopsis thaliana and Phaseolus vulgaris mitochondria. The first one, GlyRS-1, is similar to human or yeast glycyl-tRNA synthetase, whereas the second, GlyRS-2, is similar to Escherichia coli glycyl-tRNA synthetase. Both enzymes are dual targeted, GlyRS-1 to mitochondria and to the cytosol and GlyRS-2 to mitochondria and chloroplasts. Unexpectedly, GlyRS-1 seems to be active in the cytosol but inactive in mitochondrial fractions, whereas GlyRS-2 is likely to glycylate both the organelle-encoded tRNA(Gly) and the imported tRNA(Gly) present in mitochondria.
Isolation, Structure, Synthesis, and Bioactivity of a Novel Putative Insulin Mediator. A Galactosamine chiro-Inositol Pseudo-Disaccharide Mn2+ Chelate with Insulin-like Activity (2003)

We isolated from beef liver a putative insulin mediator termed INS-2, 1. Its structure was determined to be a novel inositol glycan pseudo-disaccharide Mn(2+) chelate containing D-chiro-inositol 2a (as pinitol) and galactosamine. Purification methods were scaled up from those previously reported to isolate an inositol glycan with similar composition from rat liver.(1) Structure of the beef liver glycan was determined by degradative chemistry and 2D NMR spectroscopy and confirmed by chemical synthesis. Its structure is 4-O-(2-amino-2-deoxy-beta-D-galactopyranosyl)-3-O-methyl-D-chiro-inositol 1 (INS-2, Figure 1). Its role as an insulin mimetic was demonstrated by its action in vivo to decrease elevated blood glucose injected to low-dose streptozotocin diabetic rats in a stereospecific and dose-dependent manner. The pseudo-disaccharide also stimulated [(14)C]glucose incorporation into [(14)C]glycogen in a dose-dependent manner in H4IIE hepatoma cells in the presence of insulin, thus enhancing insulin action. Only when chelated to Mn(2+) did it activate pyruvate dehydrogenase phosphatase in vitro in a dose-dependent manner. To our knowledge, this is the first example of a beta-1,4-linked inositol glycan consisting of D-chiro-inositol and galactosamine isolated from animal tissues with insulin mimetic actions.
Freezing as a Path to Build Complex Composites (2006)

Materials that are strong, ultralightweight, and tough are in demand for a range of applications, requiring architectures and components carefully designed from the micrometer down to the nanometer scale. Nacre, a structure found in many molluscan shells, and bone are frequently used as examples for how nature achieves this through hybrid organic-inorganic composites. Unfortunately, it has proven extremely difficult to transcribe nacre-like clever designs into synthetic materials, partly because their intricate structures need to be replicated at several length scales. We demonstrate how the physics of ice formation can be used to develop sophisticated porous and layered-hybrid materials, including artificial bone, ceramic-metal composites, and porous scaffolds for osseous tissue regeneration with strengths up to four times higher than those of materials currently used for implantation.
Expression of firefly luciferase gene in Xenopus laevis oocyte. (1991)

Fusion plasmid pSV-Luc20 and pSV-Luc19 were constructed by using the larger BamHI restricted fragments of plasmid pDO432 containing the firefly luciferase (luc) gene and HindIII-BamHI restricted fragment of plasmid pSVK100 containing the SV-40 promoter as insert and vector, respectively. The fusion plasmid had different ligation orientations between the encoding sequence of luc gene and the SV-40 promoter, i.e., they were sense and antisense plasmid. When they were introduced into Xenopus oocyte by micro-injection, only pSV-Luc20 could be transcribed and translated into the enzymatic protein of luciferase with high biological activity. Therefore, firefly luciferase gene and Xenopus oocyte can be used as an excellent system for monitoring the activity of various promoters.
Potential Therapeutic Strategies to Overcome Acquired Resistance to BRAF or MEK Inhibitors in BRAF Mutant Cancers (2011)

Recent clinical trials with selective inhibitors of the BRAF and MEK kinases have shown promising results in patients with tumors harboring BRAF V600 mutations. However, as has been observed previously with similarly successful targeted therapies, acquired resistance to these agents is an emerging problem that limits their clinical benefit. Several recent studies from our laboratory and others have investigated the causes of acquired resistance to BRAF and MEK inhibitors, and multiple resistance mechanisms have been identified. Here, we review these mechanisms and suggest that they can be broadly grouped into two main classes: ERK-dependent and ERK-independent. We also propose distinct therapeutic strategies that might be employed to overcome each class of acquired resistance..
Designing and deploying an information awareness interface (2002)

The concept of awareness has received increasing attention over the past several CSCW conferences. Although many awareness interfaces have been designed and studied, most have been limited deployments of research prototypes. In this paper we describe Sideshow, a peripheral awareness interface that was rapidly adopted by thousands of people in our company. Sideshow provides regularly updated peripheral awareness of a broad range of information from virtually any accessible web site or database. We discuss Sideshow's design and the experience of refining and redesigning the interface based on feedback from a rapidly expanding user community.