gebhart/patrepeval huggingface dataset:
Electrophoresis of proteins and nucleic acids: I--Theory. (1989)

Electrophoresis is used extensively in both routine clinical chemistry and biomedical research as a rapid method to separate macromolecules. The high reso- lution of proteins or nucleic acids that can be achieved by electrophoresis makes it an indispensable tool in the research laboratory. The separation of complex mix- tures of either protein or nucleic acid polymers is most conveniently achieved with electrophoresis; indeed, often the separations obtained by electrophoresis can- not be achieved by any other method. By contrast, the separation of smaller molecules such as amino acids, nucleotides, sugars, or drugs is best achieved by high performance liquid chromatography. Hence electro- phoresis and high performance liquid chromatography are generally considered to be complementary in their applications.
A radial basis classifier for the automatic detection of aspiration in children with dysphagia (2006)

The proposed aspiration classification algorithm provides promising accuracy for aspiration detection in children. The classifier is conducive to hardware implementation as a non-invasive, portable "aspirometer". Future research should focus on further enhancement of accuracy rates by considering other signal features, classifier methods, or an augmented variety of training samples. The present study is an important first step towards the eventual development of wearable intelligent intervention systems for the diagnosis and management of aspiration.
Sex separation strategies: past experience and new approaches (2009)

The success of the sterile insect technique (SIT) and other genetic strategies designed to eliminate large populations of insects relies on the efficient inundative releases of competitive, sterile males into the natural habitat of the target species. As released sterile females do not contribute to the sterility in the field population, systems for the efficient mass production and separation of males from females are needed. For vector species like mosquitoes, in which only females bite and transmit diseases, the thorough removal of females before release while leaving males competent to mate is a stringent prerequisite. Biological, genetic and transgenic approaches have been developed that permit efficient male-female separation for some species considered for SIT. However, most sex separation methods have drawbacks and many of these methods are not directly transferable to mosquitoes. Unlike genetic and transgenic systems, biological methods that rely on sexually dimorphic characters, such as size or development rate, are subject to natural variation, requiring regular adjustment and re-calibration of the sorting systems used. The yield can be improved with the optimization of rearing, but the scale of mass production places practical limits on what is achievable, resulting in a poor rearing to output ratio. High throughput separation is best achieved with scalable genetic or transgenic approaches.
The dyskerin ribonucleoprotein complex as an OCT4/SOX2 coactivator in embryonic stem cells (2014)

Acquisition of pluripotency is driven largely at the transcriptional level by activators OCT4, SOX2, and NANOG that must in turn cooperate with diverse coactivators to execute stem cell-specific gene expression programs. Using a biochemically defined in vitro transcription system that mediates OCT4/SOX2 and coactivator-dependent transcription of the <i>Nanog</i> gene, we report the purification and identification of the dyskerin (DKC1) ribonucleoprotein complex as an OCT4/SOX2 coactivator whose activity appears to be modulated by a subset of associated small nucleolar RNAs (snoRNAs). The DKC1 complex occupies enhancers and regulates the expression of key pluripotency genes critical for self-renewal in embryonic stem (ES) cells. Depletion of DKC1 in fibroblasts significantly decreased the efficiency of induced pluripotent stem (iPS) cell generation. This study thus reveals an unanticipated transcriptional role of the DKC1 complex in stem cell maintenance and somatic cell reprogramming.
Assessment of control loop performance (1989)

Abstract For processes described by linear transfer functions with additive disturbances, the best possible control in the mean square sense is realized when a minimum variance controller is implemented. It is shown that an estimate of the best possible control can be obtained by fitting a univariate time series to process data collected under routine control. No ‘identifiabüity’ constraints need be imposed. The use of this technique is demonstrated with pilot plant and production data.
Water Soluble Nanoparticles from PEG-Based Cationic Hyperbranched Polymer and RNA That Protect RNA from Enzymatic Degradation (2006)

Recent advances in understanding biological systems have proven that RNA is not merely the carrier of genetic information, but also a key molecule in regulation of gene expression and other crucial metabolic processes. Therefore, it is being considered as an ideal therapeutic candidate both for metabolic and genetic disorders. However, research involving RNA molecules faces a practical limitation since RNA is highly labile. We have developed a novel method to protect RNA from cleavage by complexing it with a hyperbranched cationic polymer. It was found that total cellular RNA isolated from yeast spontaneously interacts with the positively charged polymer to form a spherical nanoparticle morphology. This interaction protects the RNA against enzymatic degradation. This methodology can be easily adapted for long-term storage of RNA, long distance transfer of RNA, and genetic engineering using RNA as a building block.
Nonenzymatic Free Radical-catalyzed Generation of Thromboxane-like Compounds (Isothromboxanes) in Vivo (1996)

The isoprostanes (IsoPs) are novel bioactive prostaglandin-like compounds produced in vivo by free radical-catalyzed peroxidation of arachidonyl-containing lipids. Previously, we have identified IsoPs containing F-type and D- and E-type prostane rings that are formed by reduction and rearrangement of IsoP endoperoxide intermediates, respectively. We now explore whether thromboxane B2 (TxB2)-like compounds, termed B2-isothromboxanes (B2-IsoTxs), are formed by rearrangement of IsoP endoperoxides. Detection of these compounds was carried out using a stable isotope dilution mass spectrometric assay originally developed for quantification of cyclooxygenase-derived TxB2. Incubations of arachidonic acid with Fe/ADP/ascorbate for 30 min in vitro generated a series of peaks representing putative B2-IsoTx at levels of 62.4 +/- 21.0 ng/mg arachidonate. Using various chemical modification and derivatization approaches, it was determined that these compounds contained hemiacetal ring structures and two double bonds, as would be expected for B2-IsoTx. Analysis of the compounds by electron ionization mass spectrometry yielded multiple mass spectra similar to those of TxB2. B2-IsoTxs are also formed esterified to phospholipids; oxidation of arachidonyl-containing phosphatidylcholine in vitro followed by hydrolysis resulted in the release of large amounts of these compounds. To explore whether B2-IsoTxs are also formed in vivo, a well characterized animal model of lipid peroxidation consisting of orogastric administration of CCl4 to rats was used. Levels of B2-IsoTx esterified in lipids in the liver increased 41-fold from 2.5 +/- 0.5 to 102 +/- 30 ng/g of liver. In addition, circulating levels of free compounds increased from undetectable (<5 pg/ml) to 185 +/- 30 pg/ml after CCl4, a 37-fold increase. Thus, we have provided evidence that IsoTxs constitute another novel class of eicosanoids produced in vivo nonenzymatically by free radical-catalyzed lipid peroxidation. These studies thus expand our understanding of products of lipid peroxidation formed in vivo from the free radical-catalyzed peroxidation of arachidonic acid.
Acute ultrastructural effects of MPTP on the nigrostriatal pathway of the C57BL/6 adult mouse: Evidence of compensatory plasticity in nigrostriatal neurons (2000)

Acute doses of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) elicited degenerative and apparently compensatory changes in the nigrostriatum of injected animals within 1 day of treatment. In the substantia nigra pars compacta (SNc), low-dose (20 mg/kg) administration elicited early degeneration of mitochondria in the absence of other effects. In the striatum, a low MPTP dose resulted in myelin unwinding, demyelination, cytoplasmic shrinkage, and disturbance of synaptic communication, as evinced by a profound reduction in synaptic vesicle production. High-dose (40 mg/kg) administration generated more drastic axonal degeneration leading to cell elimination in the striatum. At neither dose was mitochondrial disturbance evident in the striatum. Evidence is presented that darkened synaptic boutons, visible at this level of MPTP administration, were part of healthy enlarged axons with an elevated number of synaptic contacts. These spared neuronal processes, therefore, were hypothesized to compensate for the MPTP-induced death of dopaminergic neurons by adaptive structural modifications that would serve to enhance their functional capability. J. Neurosci. Res. 59:126–135, 2000 © 2000 Wiley-Liss, Inc.
Individual protein-binding domains of the insulin gene enhancer positively activate beta-cell-specific transcription. (1989)

A beta-cell-specific enhancer is located in the 5'-flanking DNA of the rat insulin 1 gene. Two homologous 8-base-pair sequences in the enhancer (IEB1 and IEB2) significantly stimulated transcription from a heterologous promoter (two- to fourfold) in a cell-specific fashion. When the elements were combined or duplicated, more than 50% of the activity of the intact enhancer was obtained. These two cis-acting elements appear to play a dominant role in the positive control of beta-cell-specific transcription of the insulin gene.
SYNTHESIS AND BIOLOGICAL ACTIVITY OF 4′-C-HYDROXYMETHYL-2′-FLUORO-D-ARABINOFURANOSYLPURINE NUCLEOSIDES (2001)

A series of 4′-C-hydroxymethyl-2′-fluoro-D-arabinofuranosylpurine nucleosides was prepared and evaluated for cytotoxicity in human tumor cell lines. A convenient synthesis of the carbohydrate precursor 4-C-hydroxymethyl-3,5-di-O-benzoyl-2-fluoro-α-D-arabinofuranosyl bromide (13) was developed. Coupling of 13 with the sodium salt of 2,6-dichloropurine led to five target purine nucleosides.
Synthesis, Structure, Characterization, and Redox Properties of the Porous MIL‐68(Fe) Solid (2010)

Abstract A new porous Fe III ‐based MOF, formulated Fe(OH)(BDC) · (dmf) x with x ≈ 1.1 and presenting the MIL‐68 topology, was prepared by reaction of an iron(III) salt and terephthalic acid (H 2 BDC) in N , N′ ‐dimethylformamide (dmf) under acidic conditions. The structure and properties of this solid were studied by means of X‐ray diffraction, thermogravimetric analysis, nitrogen sorption, 57 Fe Mössbauer spectrometry, and electrochemical lithium insertion.
Implications of Emerging 3D GPU Architecture on the Scan Primitive (2015)

Analytic database workloads are growing in data size and query complexity. At the same time, computer architects are struggling to continue the meteoric increase in performance enabled by Moore's Law. We explore the impact of two emerging architectural trends which may help continue the Moore's Law performance trend for analytic database workloads, namely 3D die-stacking and tight accelerator-CPU integration, specifically GPUs. GPUs have evolved from fixed-function units, to programmable discrete chips, and now are integrated with CPUs in most manufactured chips. Past efforts to use GPUs for analytic query processing have not had widespread practical impact, but it is time to re-examine and re-optimize database algorithms for massively data-parallel architectures. We argue that high-throughput data-parallel accelerators are likely to play a big role in future systems as they can be easily exploited by database systems and are becoming ubiquitous. Using the simple scan primitive as an example, we create a starting point for this discussion. We project the performance of both CPUs and GPUs in emerging 3D systems and show that the high-throughput data-parallel architecture of GPUs is more efficient in these future systems. We show that if database designers embrace emerging 3D architectures, there is possibly an order of magnitude performance and energy efficiency gain.
Partial purification of Golgi-bound arabinosyltransferase and two isoforms of xylosyltransferase from French bean (Phaseolus vulgaris L.) (1992)

The purification of glycosyltransferases involved in wall matrix polysaccharide synthesis has been attempted. A number of activities readily demonstrated in isolated Golgi membranes are lost following detergent solubilization. However, solubilization releases pyrophosphorylases and phosphatases that hydrolyse the substrate in enzyme assays, whether UDP-glucose, -arabinose or -xylose is used. This hydrolysis, which cannot be completely inhibited, appears to be the major factor in the apparent loss of activity. Separation of this hydrolytic activity during further purification by ion-exchange and gel exclusion leads to recovery of glycosyltransferase activity. Thus two xylosyltransferases and one arabinosyltransferase could be partially purified. These appeared to be differentially expressed. The arabinosyltransferase of apparent M(r) 70,000 on size-exclusion chromatography was isolated from cells undergoing rapid growth and division. A xylosyltransferase of apparent M(r) 38,000 on size-exclusion chromatography was associated with cell expansion and primary wall synthesis. A second xylosyltransferase, which was purified to near homogeneity with M(r) 40,000, showed a peak of activity during the period of maximum secondary wall synthesis.
N- and P-type SiGe/Si superlattice coolers (2002)

SiGe is a good thermoelectric material for high temperature applications. In this paper the fabrication and characterization of single-element SiGe/Si superlattice coolers of both n- and p-type devices are described for room temperature applications. Superlattice structures were used to enhance the device performance by reducing the thermal conductivity between the hot and the cold junctions, and by providing selective removal of hot carriers through thermionic emission. The structure of the samples consisted of a 3 /spl mu/m thick symmetrically strained Si/sub 0.7/Ge/sub 0.3//Si superlattice grown on a buffer layer designed so that the in-plane lattice constant is approximately that of relaxed Si/sub 0.9/Ge/sub 0.1/. Cooling by 1.7 K for n-type device and by 1.9 K for p-type device at room temperature was measured, corresponding to cooling power densities of hundreds of watts per square centimeter. The results show that the packaged devices of both n and p coolers can work together in similar optimal conditions. This paves the road to fabricate n- and p-type superlattice coolers in an array format electrically in series and thermally in parallel, similar to conventional thermoelectric devices, and thus achieve large cooling capacities with relatively small currents.
A Cleavable N-Terminal Signal Peptide Promotes Widespread Olfactory Receptor Surface Expression in HEK293T Cells (2013)

Olfactory receptors (ORs) are G protein-coupled receptors that detect odorants in the olfactory epithelium, and comprise the largest gene family in the genome. Identification of OR ligands typically requires OR surface expression in heterologous cells; however, ORs rarely traffic to the cell surface when exogenously expressed. Therefore, most ORs are orphan receptors with no known ligands. To date, studies have utilized non-cleavable rhodopsin (Rho) tags and/or chaperones (i.e. Receptor Transporting Protein, RTP1S, Ric8b and G(αolf)) to improve surface expression. However, even with these tools, many ORs still fail to reach the cell surface. We used a test set of fifteen ORs to examine the effect of a cleavable leucine-rich signal peptide sequence (Lucy tag) on OR surface expression in HEK293T cells. We report here that the addition of the Lucy tag to the N-terminus increases the number of ORs reaching the cell surface to 7 of the 15 ORs (as compared to 3/15 without Rho or Lucy tags). Moreover, when ORs tagged with both Lucy and Rho were co-expressed with previously reported chaperones (RTP1S, Ric8b and G(αolf)), we observed surface expression for all 15 receptors examined. In fact, two-thirds of Lucy-tagged ORs are able to reach the cell surface synergistically with chaperones even when the Rho tag is removed (10/15 ORs), allowing for the potential assessment of OR function with only an 8-amino acid Flag tag on the mature protein. As expected for a signal peptide, the Lucy tag was cleaved from the mature protein and did not alter OR-ligand binding and signaling. Our studies demonstrate that widespread surface expression of ORs can be achieved in HEK293T cells, providing promise for future large-scale deorphanization studies.
Characterization of Three Novel H3F3A-mutated Giant Cell Tumor Cell Lines and Targeting of Their Wee1 Pathway (2019)

The giant cell tumor of bone (GCTB) is a locally aggressive primary bone tumor that is composed of mononuclear stroma cells, scattered macrophages, and multinucleated osteoclast-like giant cells which cause pathologic osteolysis. The stroma cells represent the neoplastic population of the tumor and are characterized by the H3F3A mutation G34W. This point mutation is regarded as the driver mutation of GCTB. We have established three new stable H3F3A mutated GCTB cell lines: U-GCT1, U-GCT2, and U-GCT3M. MK-1775 is a Wee1-kinase inhibitor which has been used for blocking of sarcoma growth. In the cell lines we detected Wee1, Cdk1, Cyclin B1, H3K36me3, and Rrm2 as members of the Wee1 pathway. We analyzed the effect of MK-1775 and gemcitabine, alone and in combination, on the growth of the cell lines. The cell lines showed a significant reduction in cell proliferation when treated with MK-1775 or gemcitabine. The combination of both agents led to a further significant reduction in cell proliferation compared to the single agents. Immunohistochemical analysis of 13 GCTB samples revealed that Wee1 and downstream-relevant members are present in GCTB tissue samples. Overall, our work offers valuable new tools for GCTB studies and presents a description of novel biomarkers and molecular targeting strategies.
Anion-Directed Self-Assembly of Coordination Polymer into Tunable Secondary Structure (2004)

A bent-shaped bipyridine ligand containing a dendritic aliphatic side chain has been synthesized as a ligand and complexed with silver ion through a self-assembling process. The resulting complexes were observed to self-assemble into supramolecular structures that differ significantly as a function of the counteranion size in the solid state, as confirmed by 1-D and 2-D X-ray diffraction experiments. The secondary structure of a cationic coordination chain appears to be dependent on the size of the counteranion. As the size of anion increases, the secondary structure of the coordination chain changes, from a helical chain, via a dimeric cycle, to a zigzag chain in the solid state. Interestingly, dilute solutions of the complexes exhibiting a columnar structure in polar solvents undergo spontaneous gelation and the resulting gels display a significant Cotton effect in the chromophore of the aromatic unit. These results represent a significant example that small variation in the anion size can provide a useful strategy to manipulate the secondary structure of linear chain and thereby solid-state supramolecular structure.
Restructuring of deep neural network acoustic models with singular value decomposition (2013)

Recently proposed deep neural network (DNN) obtains significant accuracy improvements in many large vocabulary continuous speech recognition (LVCSR) tasks. However, DNN requires much more parameters than traditional systems, which brings huge cost during online evaluation, and also limits the application of DNN in a lot of scenarios. In this paper we present our new effort on DNN aiming at reducing the model size while keeping the accuracy improvements. We apply singular value decomposition (SVD) on the weight matrices in DNN, and then restructure the model based on the inherent sparseness of the original matrices. After restructuring we can reduce the DNN model size significantly with negligible accuracy loss. We also fine-tune the restructured model using the regular back-propagation method to get the accuracy back when reducing the DNN model size heavily. The proposed method has been evaluated on two LVCSR tasks, with context-dependent DNN hidden Markov model (CD-DNN-HMM). Experimental results show that the proposed approach dramatically reduces the DNN model size by more than 80% without losing any accuracy. Index Terms: deep neural network, singular value decomposition, model restructuring
Synthesis and Transfection Efficiencies of New Lipophilic Polyamines (2006)

A homologous series of lipophilic polyamines was synthesized and evaluated for DNA delivery and transfection efficiency. The series contained 1,4-butanediamine, 1,8-octanediamine, 2-[2-(2-amino-ethoxy)-ethoxy]-ethylamine, homospermidine, and homospermine covalently attached via their N1 terminus to a 3,4-bis(oleyloxy)-benzyl motif. In addition, homospermidine and homospermine were also attached via amide linkers. The homospermidine derivatives (i.e., benzyl tether 25 and benzamide tether 27) showed a 3-fold and 4-fold respective enhancement in delivery of AlexaFluor-488-labeled DNA over the butanediamine analogue 22. Homospermine derivative 26 was shown to inhibit 14C-spermine uptake (IC50 approximately 10 microM), which implied that 26 is able to compete effectively for polyamine recognition sites on the cell surface. This study demonstrated that the number and position of the positive charges along the polyamine scaffold plays a key role in DNA delivery and in determining the transfection efficiency.
Cellular and Humoral Immunity following Snow Mountain Virus Challenge (2005)

Little is known about the immune response to noroviruses. To elucidate the immunobiology of norovirus infection in humans, 15 volunteers were challenged with Snow Mountain virus (SMV), a genogroup 2 norovirus. We assessed the cellular and humoral immune response and infection by analyzing stool, serum, saliva, and peripheral blood mononuclear cell (PBMC) responses pre- and postchallenge. In contrast to Norwalk virus (NV), SMV infection was not dependent upon blood group secretor status. Nine of 15 volunteers were infected and showed a >/=4-fold increase over the prechallenge anti-SMV serum immunoglobulin G (IgG) titer, mostly subclass IgG1. Although serum IgG elicited by SMV infection was cross-reactive with Hawaii virus (HV), another genogroup 2 norovirus, salivary IgA was less cross-reactive. Neither SMV-elicited serum IgG nor salivary IgA cross-reacted with NV, a genogroup 1 norovirus. Significant increases in serum gamma interferon (IFN-gamma) and IL-2, but not IL-6 or IL-10, were noted on day 2 postchallenge. For the majority of volunteers, both infected and uninfected, PBMCs stimulated with norovirus virus-like particles secreted IFN-gamma and other Th1 cytokines, suggesting previous norovirus exposure in most volunteers. Like the IgG antibodies, the SMV-activated T cells were cross-reactive with HV but not NV. IFN-gamma production was dependent upon CD4(+) cells, consistent with a predominant, but not exclusive, Th1 response. To our knowledge, this is the first report characterizing T-cell and cytokine responses following live norovirus challenge.