gebhart/patrepeval huggingface dataset:
Reduced expression of the liver/beta-cell glucose transporter isoform in glucose-insensitive pancreatic beta cells of diabetic rats. (1990)

Rats injected with a single dose of streptozocin at 2 days of age develop non-insulin-dependent diabetes 6 weeks later. The pancreatic beta islet cells of these diabetic rats display a loss of glucose-induced insulin secretion while maintaining sensitivity to other secretagogues such as arginine. We analyzed the level of expression of the liver/beta-cell glucose transporter isoform in diabetic islets by immunofluorescence staining of pancreas sections and by Western blotting of islet lysates. Islets from diabetic animals have a reduced expression of this beta-cell-specific glucose transporter isoform and the extent of reduction is correlated with the severity of hyperglycemia. In contrast, expression of this transporter isoform in liver is minimally modified by the diabetes. Thus a decreased expression of the liver/beta-cell glucose transporter isoform in beta cells is associated with the impaired glucose sensing characteristic of diabetic islets; our data suggest that this glucose transporter may be part of the beta-cell glucose sensor.
Thirty-Cycle Temperature Optimization of a Closed-Cycle Capillary PCR Machine (2002)

The performance of a novel thermal cycler has been characterized in a 30-cycle PCR. The device consists of a microcapillary equipped with bidirectional pressure-driven flow and in situ optical position sensors. A 1-μL droplet of reaction mixture moves between three heat zones in a 1-mm i.d., oilfilled capillary using a multi-element scattered light detector and active feedback. The design permits time and number of cycles to be changed without hardware modification, unlike other flow-in-capillary PCR systems. Temperature optimization has been performed on the three PCR heat steps. The optimal denaturation temperature is 94°C–96°C, which is identical to commercial machines. The optimal extension temperature of 62°C–66°C is lower than reported for Taq DNA polymerase (70°C–80°C) because of the high enzyme concentration and/or the absence of detergent in the PCR mixture. The optimal annealing temperature seems to be the same as the optimal extension temperature. This is because extension occurs when the sample is inside of the annealing heat zone. Annealing takes place as the sample travels between heat zones. Device speed (23 min for 30 cycles without time optimization) is competitive with other rapid PCR designs for efficiencies comparable to a commercial machine.
The PRP4 (RNA4) protein of Saccharomyces cerevisiae is associated with the 5' portion of the U4 small nuclear RNA. (1990)

We have combined oligonucleotide-directed RNase H degradation and immunoprecipitation in a study of the association of the Saccharomyces cerevisiae PRP4 protein with the U4-U6 complex. We have found that three oligonucleotides were able to direct nearly to completion the RNase H-specific cleavage of the target RNA molecules as they exist in splicing extracts. Immunoprecipitation of the degradation products with PRP4 antibody showed that the 5' portion of U4 small nuclear RNA (snRNA) and the 3' portion of U6 snRNA coimmunoprecipitated with the PRP4 protein. Micrococcal nuclease protection experiments confirmed further that the 5' portion and 3' end of U4 snRNA were very resistant to nuclease digestion, whereas the 3' portion of U6 snRNA was protected to only a very small extent. We conclude that the PRP4 protein of S. cerevisiae is associated primarily with the 5' portion of U4 snRNA in the U4-U6 small nuclear ribonucleoprotein (snRNP).
Core-Shell Hydrogel Particles Harvest, Concentrate and Preserve Labile Low Abundance Biomarkers (2009)

We envision the application of harvesting core-shell nanoparticles to whole blood for concentration and immediate preservation of low abundance and labile analytes at the time of venipuncture.
Single, antigen-specific B cells used to generate Fab fragments using CD40-mediated amplification or direct PCR cloning. (1995)

A simple procedure for the generation of human antibody fragments directly from single B cells or B-cell clones is described here. The procedure is based on antigen-specific selection of single human B cells, using antigen-coated magnetic beads and a cellular amplification step based on a culture system involving both EL-4 thymoma cells and anti-CD40 antibodies, presented by CD32-expressing fibroblasts. Nested PCR was applied to rescue V-regions from both single B cells and B-cell clones obtained using the cellular amplification step. This amplification step both increased the cell number as well as activated the cells that amplified mRNA levels, thereby facilitating immortalization by cloning. The V-regions were cloned and expressed as Fab fragments and characterized by biosensor analysis. This approach allowed us to bypass cumbersome hybridoma technology and to obtain human antibody fragments that retained the original VH/VL pairing, a feature of importance when studying, e.g., the V-gene usage in various human diseases and in normal B-cell repertoires.
Unexpected synergism between Tetrodotoxin and μ-conotoxin in blocking voltage-gated sodium channels (2009)

Tetrodotoxin (TTX) is the quintessential ligand of voltage-gated sodium channels (NaVs). Like TTX, mu-conotoxin peptides are pore blockers, and both toxins have helped to define the properties of neurotoxin receptor Site 1 of NaVs. Here, we report unexpected results showing that the recently discovered mu-conotoxin KIIIA and TTX can simultaneously bind to Site 1 and act in concert. Results with saturating concentrations of peptide applied to voltage-clamped Xenopus oocytes expressing brain NaV1.2, and single-channel recordings from brain channels in lipid bilayers, show that KIIIA or its analog, KIIIA[K7A], block partially, with a residual current that can be completely blocked by TTX. In addition, the kinetics of block by TTX and peptide are each affected by the prior presence of the other toxin. For example, bound peptide slows subsequent binding of TTX (an antagonistic interaction) and slows TTX dissociation when both toxins are bound (a synergistic effect on block). The overall functional consequence resulting from the combined action of the toxins depends on the quantitative balance between these opposing actions. The results lead us to postulate that in the bi-liganded NaV complex, TTX is bound between the peptide and the selectivity filter. These observations refine our view of Site 1 and open new possibilities in NaV pharmacology.
Obesity research continues to spring leaks. (1997)

Recent discoveries about the roles of 2 uncoupling proteins are changing the way we view obesity and its treatment. The author is also a coauthor of a recent Nature report that mice deficient in uncoupling protein 1 (UCP1) did not become fat, as anticipated, but lean. She found that the other uncoupling protein (UCP2) was up-regulated in the brown adipose tissue (BAT) of these mice, compensating, at least in part, for the lack of UCP1 and preventing obesity. Researchers have known for 40 years that the function of BAT is heat production. In 1978, researchers discovered UCP1, the protein responsible for this function. Subsequent investigation focused on the role of this protein in staving off obesity in animal models. In the early 1990s, surprising evidence from tissues other than BAT show that 20% to 40% of resting cellular energy expenditure is used to counter a proton leak down the electrochemical gradient across the mitochondrial inner membrane. This leak was found to be related to metabolic rate; the search for the mechanism of the leak led to the discovery of UCP2. Both uncoupling proteins have been found to act as leaks in mitochondrial inner membranes, allowing the dissipation of proton motive force. These findings could lead to new treatments for obesity and non-insulin-dependent diabetes mellitus.
Improving Vector Space Word Representations Using Multilingual Correlation (2014)

The distributional hypothesis of Harris (1954), according to which the meaning of words is evidenced by the contexts they occur in, has motivated several effective techniques for obtaining vector space semantic representations of words using unannotated text corpora. This paper argues that lexico-semantic content should additionally be invariant across languages and proposes a simple technique based on canonical correlation analysis (CCA) for incorporating multilingual evidence into vectors generated monolingually. We evaluate the resulting word representations on standard lexical semantic evaluation tasks and show that our method produces substantially better semantic representations than monolingual techniques.
Nano Nickel-Tin Interconnects and Electrodes for Next Generation 15 Micron Pitch Embedded Bio Fluidic Sensors in FR4 Substrates (2006)

Lead free solder bumping requirements have challenged researchers to develop technologies to achieve fine pitch interconnects. ITRS has predicts that by 2017 the industry require 70 micron pitch area array lead free interconnects for flip chips. This paper describes bumping, assembly and reliability evaluation of a nano composite 15 micron pitch interconnect technology. Nanoparticles are the most common building blocks in several applications of nanotechnology. Beside, the enormous increase of their surface area, the high surface to volume ratio of the nano particles results in extraordinary high reactivity, and unusual physical properties (optical, magnetic, etc.). Several types of nanostructures (nano particles, nano-wires and nano-rods) can be fabricated. Dispersed nano particles are used in several important applications, e.g., catalysis, biomedical applications, nano coatings and nanocomposites. Nanostructured materials, prepared by consolidating nanoparticles with a very high density of grain boundary, have been shown to lead to dramatically improved mechanical and physical properties. Lead free interconnect reliability has been a concern due tin pest (whiskers), intermetallics and high temperature reflow problems. This problem becomes even more pronounced when the pitch of the flip chip reduces to 100 microns or lesser. This paper proposes a nano metal composite for fine pitch lead free interconnect as an alternative to solder for fine pitch flip chip interconnect as presented in R. R. Tummala (2001) and W. D. Brown (1999). This paper describes design, process, fabrication and reliability test for composite interconnects fabricated using Ni nano particles distributed in a tin core. A wafer level process is developed for flip chip having 15 micron pitch composite nano structured interconnect. The composition and intermetallics formed at the chip-to- interconnect-interface are evaluated when sent through 4 reflow cycles. Composition of the intermetallics is evaluated to study the distribution Ni3Sn4, Cu6Sn5 and Cu3Sn. Shear test on interconnects provide bump adhesion strength and fatigue resistance information. The failure mode associated with shear test is also presented. The chip is thermally cycled in a oven from -55degC to 125degC and after every 100 cycles is evaluated for defects using x-ray and Sonoscan techniques. A cross section is made and the composition at interface is also evaluated for intermetalic diffusion. The paper provides optimized data for next generation nano composite interconnect for fine pitch flip chip to achieve high reliability. The paper also describes a process to fabricate substrates with nano lines and embedded fluidic channels
Qualitative Determination of Specific Protein Glycation Products by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Peptide Mapping (2002)

The nonenzymatic reaction between reducing sugars and proteins, known as the Maillard reaction, has received increased recognition from nutritional science and medical research. The development of new analytical techniques for the detection of protein-bound Maillard products is therefore crucial. In this study, we applied peptide mapping by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry to investigate the formation of structurally specific Maillard products on glycated lysozyme (AGE-lysozyme), produced upon incubation with D-glucose. In parallel, we synthesized N(epsilon)-(carboxymethyl)lysine-modified lysozyme (CML-lysozyme) and N(epsilon)-(carboxyethyl)lysine-modified lysozyme, two well-described glycation products, as model substances. 3-Deoxyglucosone-modified lysozyme and methylglyoxal-modified lysozyme were prepared as examples of glycation products incubated with dicarbonyl compounds. We were able to detect specific modifications on AGE-lysozyme, which were assigned to CML, imidazolone A, and the Amadori product.
Structural requirements for lysosomal targeting of the prosaposin precursor protein (2003)

Although the Man-6-P-independent lysosomal sorting of prosaposin, a precursor of four saposins (A, B, C, and D) is not understood, a protein/lipid interaction is considered. Immunocytochemical analysis revealed that each single saposin linked to the C-terminus of prosaposin and to secretory albumin, drives the chimeric protein to lysosomes in COS-7 cells. Quantitative image analysis demonstrated that saposins are targeted with different efficiency (P<0.05) and in a less smooth manner than the precursor. Despite a very close homology, the charge distribution at the surface of 3D comparative models between saposins appeared different. Western blotting monitored prosaposin in cells also as a di- or trimeric form, whereas the chimeric saposins as monomeric. This implies that each amphipathic saposin-like motif may be a part of the overall structural requirements for binding of the precursor to the membrane lipids of transport vesicle. The crystal structure of saposin B demonstrating two dimeric units for lipid binding supports current findings.
A Comprehensive Understanding of the Erase of TANOS Memories Through Charge Separation Experiments and Simulations (2011)

We investigate and quantify the role played by electrons and holes during the erase operation of TANOS memories by means of charge separation experiments and physics-based simulations. Results demonstrate that electron emission via trap-to-band tunneling dominates the first part of the erase operation, whereas hole injection prevails in the remaining part of the transient. In addition, we show that the efficiency of the erase operation is high and constant mainly because of the high energy offset between nitride and alumina valence bands. Our results clearly identify the physical mechanisms responsible for TANOS erase and allow deriving some important guidelines for the optimization of this operation.
Learning Therapy in a Technology-Supported Instructional Environment (2003)

There has been an explosion of interest in virtual education in recent years. Learning in a technology-supported instructional environment has meant a shift in the way we conceptualize how trainees are taught and how they learn. This article describes how the principles of a systems-oriented intervention model inspired the development of a step-by-step pedagogical strategy to guide the design and implementation of an effective technology-supported learning environment to train human service professionals for working with troubled youth and their families.
Immunocytochemical localization of peptidylarginine deiminase in human eosinophils and neutrophils (2001)

Peptidylarginine deiminase, registered as PAD V in the DDBJ/GenBank/EMBL data banks, is expressed in HL-60 cells differentiated into granulocytes or monocytes. We analyzed PAD activities in density-fractionated human peripheral blood cell fractions. PAD activity with similar substrate specificity to that of PAD V was found in the eosinophil and neutrophil fractions, which showed single bands comigrating with authentic PAD V on immunoblotting with an anti-PAD V antibody. Both the biochemical and immunoblotting analyses showed marked enrichment of PAD V in the eosinophil fraction. Its immunoreactivity appeared to localize in eosinophilic granules at high density and in myeloperoxidase-negative cytoplasmic granules of neutrophils at low density, as determined by confocal laser-scanning microscopy. Possible roles of PAD V in myeloid differentiation and granulocyte function are discussed. In addition, we present evidence for the presence of PAD(s) that are antigenically different from PAD V in monocytes and lymphocytes.
Efficient Chemoenzymatic Synthesis of O-Linked Sialyl Oligosaccharides (2002)

The tumor associated Tn (GalNAcalpha(1-1)-Thr/Ser)- and T (Galbeta(1-3)-GalNAcalpha(1-1)Thr/Ser)-antigens and their sialylated derivatives are present on the surface of many cancer cells. Preparative synthesis of these sialylated T- and Tn-structures has been achieved mainly from a chemical synthetic approach due to the lack of the required glycosyltransferases. We demonstrate a flexible and efficient chemoenzymatic approach for using recombinant sialyltransferases including a chicken GalNAcalpha2,6-sialyltransferase (chST6GalNAc I) and a porcine Galbeta(1-3)GalNAcalpha-2,3-sialyltransferase (pST3Gal I). Using these enzymes, the common O-linked sialosides Neu5Acalpha(2-6)GalNAcalpha(1-1)Thr, Galbeta(1-3)[Neu5Acalpha(2-6)]GalNAcalpha(1-1)Thr, Neu5Acalpha(2-3)Galbeta(1-3)GalNAcalpha(1-1)Thr, and Neu5Acalpha(2-3)Galbeta(1-3)[Neu5Acalpha(2-6)]GalNAcalpha(1-1)Thr were readily prepared at preparative scale. The chST6GalNAc I was found to require at least one amino acid (Thr/Ser) for optimal activity, and is thus an ideal catalyst for synthesis of synthetic glycopeptides and glycoconjugates with O-linked glycans.
Measurement of intracellular pH using flow cytometry with carboxy‐SNARF‐1 (1993)

The new intracellular pH (pH(i)) dye carboxy-seminaphthorhodafluor (SNARF-1) was compared to the established dye 2,3-dicyanohydroquinone (DCH) using flow cytometry. Both dyes give high-resolution pH(i) measurements. SNARF-1 remains trapped within cells much longer than DCH, so that pH(i) can be monitored during and after treatments with chemicals or hyperthermia. The toxicity of the dyes is similar, and both dyes can be used at concentrations that result in low toxicity to cells. Adequate staining of cells with SNARF-1 is dependent on the cell concentration. The absolute pHi values indicated by SNARF-1 are higher than values measured with DCH. However, the trends measured by both dyes are consistent, and both are useful for making pH(i) measurements.
Growth of Ultrasmooth Octadecyltrichlorosilane Self-Assembled Monolayers on SiO2 (2003)

Ultrasmooth octadecyltrichlorosilane (OTS) monolayers (2.6 ± 0.2 nm thick, RMS roughness ∼1.0 Å) can be obtained reproducibly by exposing clean native SiO2 surfaces to a dry solution of OTS in Isopar-G. A clean room is not required. Atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), contact angle data, and ellipsometry show that film formation occurs through a “patch expansion” process and terminates once a single monolayer is formed, after about 2 days. These monolayers are suitable as substrates for high-resolution electron beam and AFM or STM lithography. Further observations highlight the importance of controlling water content during deposition of siloxane self-assembled monolayers. OTS covers the surface much faster when there is a little water in the OTS solution; contact angle and ellipsometry data indicate formation of a hydrophobic, 2.6 nm thick film after about 2 h. However, these OTS films have a totally different growth mechanism than films grown from dry solutions and are not really monolayers. The OTS forms platelike islands that then adsorb onto the surface; the resulting overlayers have RMS roughness of more than 3 Å. Continued exposure to the OTS solution results in continued island deposition and increased roughness.
The recycling of apolipoprotein E in macrophages (2005)

The ability of apolipoprotein E (apoE) to be spared degradation in lysosomes and to recycle to the cell surface has been demonstrated by our group and others, but its physiologic relevance is unknown. In this study, we characterized apoE recycling in primary murine macrophages and probed the effects of HDL and apoA-I on this process. In cells pulsed with (125)I.apoE bound to VLDL, intact apoE was found in the chase medium for up to 24 h after the pulse. Approximately 27 +/- 5% of the apoE internalized during the pulse was recycled after 4 h of chase. Addition of apoA-I and HDL increased apoE recycling to 45 +/- 3% and 46 +/- 3%, respectively, similar to the amount of apoE recycled after pulsing the cells with (125)I.apoE.HDL. In addition, apoA-I-producing macrophages from transgenic mice showed increased apoE recycling at 4 h (38 +/- 3%). Increased ABCA1 expression potentiated apoE recycling, suggesting that recycling occurs via ABCA1. Finally, in the presence of apoA-I, recycled apoE exited the cells on HDL-like particles. These results suggest that apoE recycling in macrophages may be part of a larger signaling loop activated by HDL and directed at maximizing cholesterol losses from the cell.
Targeted radionuclide therapy (2008)

Targeted radionuclide therapy (TRT) seeks molecular and functional targets within patient tumor sites. A number of agents have been constructed and labeled with beta, alpha, and Auger emitters. Radionuclide carriers spanning a broad range of sizes; e.g., antibodies, liposomes, and constructs such as nanoparticles have been used in these studies. Uptake, in percent-injected dose per gram of malignant tissue, is used to evaluate the specificity of the targeting vehicle. Lymphoma (B-cell) has been the primary clinical application. Extension to solid tumors will require raising the macroscopic absorbed dose by several-fold over values found in present technology. Methods that may effect such changes include multistep targeting, simultaneous chemotherapy, and external sequestration of the agent. Toxicity has primarily involved red marrow so that marrow replacement can also be used to enhance future TRT treatments. Correlation of toxicities and treatment efficiency has been limited by relatively poor absorbed dose estimates partly because of using standard (phantom) organ sizes. These associations will be improved in the future by obtaining patient-specific organ size and activity data with hybrid SPECT/CT and PET/CT scanners.
A simple statistical model for depicting the cdc-15 synchronized yeast cell cycle-regulated gene expression data (2002)

Abstract: Microarrays are used for identifying cell-cycle regulated genes by Spell-man et al. (1998). In one experiment, a strain of yeast (cdc15-2) was incubated at a high temperature (35oC) for a long time, causing cdc15 arrest. Cells were then shifted back to a low temperature (23oC) and the monitoring of gene expression is taken every 10 min for 300 min, using cDNA microarrays. The data are available from their web site
Novel Inhibitors for PRMT1 Discovered by High-Throughput Screening Using Activity-Based Fluorescence Polarization (2012)

Protein arginine methyltransferases (PRMTs) catalyze the posttranslational methylation of arginine using S-adenosylmethionine (SAM) as a methyl-donor. The PRMT family is widely expressed and has been implicated in biological functions such as RNA splicing, transcriptional control, signal transduction, and DNA repair. Therefore, specific inhibitors of individual PRMTs have potentially significant research and therapeutic value. In particular, PRMT1 is responsible for >85% of arginine methyltransferase activity, but currently available inhibitors of PRMT1 lack specificity, efficacy, and bioavailability. To address this limitation, we developed a high-throughput screening assay for PRMT1 that utilizes a hyper-reactive cysteine within the active site, which is lacking in almost all other PRMTs. This assay, which monitors the kinetics of the fluorescence polarization signal increase upon PRMT1 labeling by a rhodamine-containing cysteine-reactive probe, successfully identified two novel inhibitors selective for PRMT1 over other SAM-dependent methyltransferases.