gebhart/patrepeval huggingface dataset:
BHK cell proteins that bind to the 3' stem-loop structure of the West Nile virus genome RNA (1995)

The first 83 3' nucleotides of the genome RNA of the flavivirus West Nile encephalitis virus (WNV) form a stable stem-loop (SL) structure which is followed in the genome by a smaller SL. These 3' structures are highly conserved among divergent flaviviruses, suggesting that they may function as cis-acting signals for RNA replication and as such might specifically bind to cellular or viral proteins. Cellular proteins from uninfected and WNV-infected BHK-21 S100 cytoplasmic extracts formed three distinct complexes with the WNV plus-strand 3' SL [(+)3'SL] RNA in a gel mobility shift assay. Subsequent competitor gel shift analyses showed that two of these RNA-protein complexes, complexes 1 and 2, contained cell proteins that specifically bound to the WNV (+)3'SL RNA. UV-induced cross-linking and Northwestern blotting analyses detected WNV (+)3'SL RNA-binding proteins of 56, 84, and 105 kDa. When the S100 cytoplasmic extracts were partially purified by ion-exchange chromatography, a complex that comigrated with complex 1 was detected in fraction 19, while a complex that comigrated with complex 2 was detected in fraction 17. UV-induced cross-linking experiments indicated that an 84-kDa cell protein in fraction 17 and a 105-kDa protein in fraction 19 bound specifically to the WNV (+)3'SL RNA. In addition to binding to the (+)3'SL RNA, the 105-kDa protein bound to the SL structure located at the 3' end of the WNV minus-strand RNA. Initial mapping studies indicated that the 84- and 105-kDa proteins bind to different regions of the (+)3'SL RNA. The 3'-terminal SL RNA of another flavivirus, dengue virus type 3, specifically competed with the WNV (+)3'SL RNA in gel shift assays, suggesting that the host proteins identified in this study are flavivirus specific.
Vertical Sleeve Gastrectomy Is Effective in Two Genetic Mouse Models of Glucagon-Like Peptide 1 Receptor Deficiency (2013)

Glucagon-like peptide 1 (GLP-1) is a peptide hormone that is released from the gut in response to nutrient ingestion and that has a range of metabolic effects, including enhancing insulin secretion and decreasing food intake. Postprandial GLP-1 secretion is greatly enhanced in rats and humans after some bariatric procedures, including vertical sleeve gastrectomy (VSG), and has been widely hypothesized to contribute to reduced intake, weight loss, and the improvements in glucose homeostasis after VSG. We tested this hypothesis using two separate models of GLP-1 receptor deficiency. We found that VSG-operated GLP-1 receptor-deficient mice responded similarly to wild-type controls in terms of body weight and body fat loss, improved glucose tolerance, food intake reduction, and altered food selection. These data demonstrate that GLP-1 receptor activity is not necessary for the metabolic improvements induced by VSG surgery.
Ubiquitin conjugation by the N-end rule pathway and mRNAs for its components increase in muscles of diabetic rats (1999)

Insulin deficiency (e.g., in acute diabetes or fasting) is associated with enhanced protein breakdown in skeletal muscle leading to muscle wasting. Because recent studies have suggested that this increased proteolysis is due to activation of the ubiquitin-proteasome (Ub-proteasome) pathway, we investigated whether diabetes is associated with an increased rate of Ub conjugation to muscle protein. Muscle extracts from streptozotocin-induced insulin-deficient rats contained greater amounts of Ub-conjugated proteins than extracts from control animals and also 40-50% greater rates of conjugation of 125 I-Ub to endogenous muscle proteins. This enhanced Ub-conjugation occurred mainly through the N-end rule pathway that involves E2 14k and E3. A specific substrate of this pathway, -lactalbumin, was ubiquitinated faster in the diabetic extracts, and a dominant negative form of E2 14k inhibited this increase in ubiquitination rates. Both E2 14k and E3 were shown to be rate-limiting for Ub conjugation because adding small amounts of either to extracts stimulated Ub conjugation. Furthermore, mRNA for E2 14k and E3 (but not E1) were elevated 2-fold in muscles from diabetic rats, although no significant increase in E2 14k and E3 content could be detected by immunoblot or activity assays. The simplest interpretation of these results is that small increases in both E2 14k and E3 in muscles of insulin-deficient animals together accelerate Ub conjugation and protein degradation by the N-end rule pathway, the same pathway activated in cancer cachexia, sepsis, and hyperthyroidism.
Assignment of Rfp-Y to the chicken major histocompatibility complex/NOR microchromosome and evidence for high-frequency recombination associated with the nucleolar organizer region. (1996)

Rfp-Y is a second region in the genome of the chicken containing major histocompatibility complex (MHC) class I and II genes. Haplotypes of Rfp-Y assort independently from haplotypes of the B system, a region known to function as a MHC and to be located on chromosome 16 (a microchromosome) with the single nucleolar organizer region (NOR) in the chicken genome. Linkage mapping with reference populations failed to reveal the location of Rfp-Y, leaving Rfp-Y unlinked in a map containing &gt;400 markers. A possible location of Rfp-Y became apparent in studies of chickens trisomic for chromosome 16 when it was noted that the intensity of restriction fragments associated with Rfp-Y increased with increasing copy number of chromosome 16. Further evidence that Rfp-Y might be located on chromosome 16 was obtained when individuals trisomic for chromosome 16 were found to transmit three Rfp-Y haplotypes. Finally, mapping of cosmid cluster III of the molecular map of chicken MHC genes (containing a MHC class II gene and two rRNA genes) to Rfp-Y validated the assignment of Rfp-Y to the MHC/NOR microchromosome. A genetic map can now be drawn for a portion of chicken chromosome 16 with Rfp-Y, encompassing two MHC class I and three MHC class II genes, separated from the B system by a region containing the NOR and exhibiting highly frequent recombination.
Regioselective Protection of Triols to Cyclic Carbonates (1994)

Abstract Regioselective protection of 1,2,3-,1,2,4-, and 1,2,5-triols to 5-membered cyclic carbonates with triphosgene, dimethyl carbonate, or carbonyldiimidazole is described.
Single photon emission from site-controlled pyramidal quantum dots (2004)

We demonstrate that a single photoexcited InGaAs semiconductor quantum dot (QD) grown by organo-metallic chemical vapor deposition on prepatterned substrates emits one photon at a time, with no uncontrolled background photon emission, making it an excellent single photon emitter. Moreover, our fabrication technique offers complete site control and small inhomogeneous broadening of QD arrays, which is essential for the practical implementation of QDs in efficient solid-state single photon emitting devices.
Characterization of cell lines that inducibly express the adeno-associated virus Rep proteins (1994)

The replication (rep) gene of adeno-associated virus (AAV) is involved in AAV DNA replication, gene regulation, and inhibition of cellular transformation induced by various oncogenes. To study the rep gene's antiproliferative effects, we have developed cell lines which express the replication proteins under the control of an inducible mouse metallothionein transcription promoter. The Rep78 protein produced in these cell lines binds to the AAV terminal repeat sequences in vitro and supports AAV DNA replication and trans activation of the AAV p40 transcription promoter in vivo. These cell lines are capable of assembling infectious viruses containing a mutant rep gene or a vector bearing a heterologous gene. Growth rate and colony formation efficiency assays indicated that rep gene expression substantially altered cellular proliferation. Long-term induction of the cell lines followed by removal of the inducing agent suggested that constitutive expression of the Rep proteins does not necessarily result in cell death and that the cells can recover from the cytostatic effects. Flow cytometry analysis indicated that the presence of the Rep proteins increased the population of cells in the S phase of the cell cycle. Thus the rep gene's antiproliferative effects may be realized by interference with cellular DNA replication.
Electrical Percolation Behavior in Silver Nanowire–Polystyrene Composites: Simulation and Experiment (2010)

Abstract The design and preparation of isotropic silver nanowire‐polystyrene composites is described, in which the nanowires have finite L/D (&lt; 35) and narrow L/D distribution. These model composites allow the L/D dependence of the electrical percolation threshold, ϕ c , to be isolated for finite‐ L/D particles. Experimental ϕ c values decrease with increasing L/D , as predicted qualitatively by analytical percolation models. However, quantitative agreement between experimental data and both soft‐core and core–shell analytical models is not achieved, because both models are strictly accurate only in the infinite‐ L/D limit. To address this analytical limitation, a soft‐core simulation method to calculate ϕ c and network conductivity for cylinders with finite L/D are developed. Our simulated ϕ c results agree strongly with our experimental data, suggesting i) that the infinite‐aspect‐ratio assumption cannot safely be made for experimental networks of particles with L/D &lt; 35 and ii) in predicting ϕ c , the soft‐core model makes a less significant assumption than the infinite‐ L/D models do. The demonstrated capability of the simulations to predict ϕ c in the finite‐ L/D regime will allow researchers to optimize the electrical properties of polymer nanocomposites of finite‐ L/D particles.
Vibration welding of thermoplastics. Part III: Strength of polycarbonate butt welds (1988)

Abstract In vibration welding of thermoplastics, frictional work done by vibrating two parts under pressure, along their common interface, is used to generate heat to effect a weld. The main process parameters are the weld frequency, the amplitude of the vibratory motion, the weld pressure, and the weld time or weld penetration; The effects of these parameters on weld quality were systematically studied by first butt‐welding polycarbonate specimens under controlled conditions over a wide range of process parameters, and by then determining the strengths and ductilities of these welds by tensile tests, A significant result is the apparent existence of a weld‐penetration threshold above which high weld strengths are attained, but below which the strength drops off. Under the right conditions, the strengths of polycarbonate butt welds are shown to equal the strength of the virgin polymer.
Spirulina, the edible microorganism (1983)

Isolement, morphologie et taxonomie, physiologie, biochimie, composition chimique, production, nutrition et toxicologie, conclusions et prospectives concernant l'utilisation de Spirulina pour l'alimentation
Differentiation-Linked Leukemogenesis in Lymphocytes (1986)

Most human lymphoid malignancies preserve a pattern of gene expression reflecting their proliferative activity and the developmental level of clonal expansion and maturation arrest. Characteristics of leukemia and other cancer cells frequently considered to reflect aberrant differentiation may more often reflect clonal selection of cell types that are normally infrequent and transitory. The differentiation status of progenitor or mature lymphoid cells influences which genetic elements are at risk of being exploited, via mutation, recombination, or deletion, for clonal advantage. These alterations may frequently arise spontaneously as a consequence of the unique developmental and functional programs of lymphoid cells and have as a major phenotypic consequence the stabilization of transitory cellular phenotypes.
Ingestive Behaviour and Physiology of the Medicinal Leech (1988)

Ingestion lasts 25 min in Hirudo medicinalis and is characterized by pharyngeal peristalsis which fills the crop. This peristalsis has an initial rate of 2.4 Hz which decays smoothly to 1.2 Hz at termination of ingestion. During ingestion, the leech body wall undergoes peristalsis which appears to aid in filling the crop diverticula. Body peristalsis begins at a rate of 10 min-1 and decreases linearly to 2 min-1 at termination. The body also undergoes dorsoventral flexions when blood flow is occluded. Blood meal size increases slightly with leech size: 8.4 g for 1-g leeches and 9.7 g for 2-g leeches. However, relative meal size decreases markedly with increasing animal size; from 8.15 times body mass for 1-g to 4.80 times for 2-g leeches. When intact leeches were exposed to micromolar concentrations of serotonin, there was an increase in the rate of pharyngeal peristalsis and the size of the blood meals. Leeches excrete the plasma from their ingested blood meals. Excretion is activated during ingestion, which increases feeding efficiency by increasing the proportion of blood cells in the ingestate. Excretion continues for 4-6 days following ingestion, removing all the remaining plasma from the ingestate. Leech ingestion comprises stereotyped muscular movements, secretion of saliva and excretion of plasma. A strikingly similar feeding physiology is seen in the blood-sucking insect Rhodnius, and we suggest that efficient sanguivory may require the convergent evolution of similar ingestive mechanisms.
Vertically Oriented Sub-10-nm Plasmonic Nanogap Arrays (2010)

Nanometric gaps in noble metals can harness surface plasmons, collective excitations of the conduction electrons, for extreme subwavelength localization of electromagnetic energy. Positioning molecules within such metallic nanogaps dramatically enhances light-matter interactions, increasing absorption, emission, and, most notably, surface-enhanced Raman scattering (SERS). However, the lack of reproducible high-throughput fabrication techniques with nanometric control over the gap size has limited practical applications. Here we show sub-10-nm metallic nanogap arrays with precise control of the gap's size, position, shape, and orientation. The vertically oriented plasmonic nanogaps are formed between two metal structures by a sacrificial layer of ultrathin alumina grown using atomic layer deposition. We show increasing local SERS enhancements of up to 10(9) as the nanogap size decreases to 5 nm. Because these sub-10-nm gaps can be fabricated at high densities using conventional optical lithography over an entire wafer, these results will have significant implications for spectroscopy and nanophotonics.
Direct writing of microlenses in polycarbonate with excimer laser ablation (2003)

A method for fabricating microlenses in polycarbonate material is reported. Using a direct-write technique based on scanning excimer laser ablation with a circular beam, we can etch an arbitrary shape in the polymer material. The beam is obtained by imaging a circular aperture onto the polymer surface, and scanning is realized by the translation stage carrying the sample, which makes successive contours with well-chosen diameters and scan velocities. Afterward, to smooth the ablated surface and release it from debris, a large beam aperture covering the full lens area is used to ablate the lens deeper into the substrate. The fabrication process and the characterization method are described, including calculation of the contour set for a desired lens shape. The optical performance is evaluated by Mach-Zehnder interferometry, showing that aberrations below lambda/10 are possible for slow lenses.
Calibration and linearity issues for an adaptive antenna system (2002)

Adaptive antennas are among the favourite techniques to help the current systems evolve towards third generation mobile communication systems. However, among the major concerns for adaptive antenna systems are the calibration process and the non-linearity effects of the RF-IF chains upon the performance of the beamforming network. This article investigates these issues based on experimental results produced with the adaptive antenna testbed that was developed under the RACE TSUNAMI project. Results highlight the sensitivity of the system on both the linearisation and the calibration processes employed.
Per-phase DQ control of a three-phase battery inverter in a diesel hybrid mini-grid supplying single-phase loads (2011)

Electricity in remote communities is usually provided by diesel power plants at relatively high costs. This issue can be addressed with the addition of renewable energy sources such as wind and PV. However, due to the intermittent and fluctuating characteristics of the power produced by these sources, the dispatch of the diesel gensets for operation with variable (droop-based) frequency, high efficiency and reduced unit cycling becomes more difficult. A battery energy storage system (BESS) with a suitable control strategy can simplify this task and improve the power quality. This paper discusses the operation of a hybrid system with a three-phase diesel power plant and a single-phase distribution network with intermittent sources. The per-phase dq control scheme used in the BESS allows energy management with superior power quality for operation with variable frequencies.
Conjugation of an anti–transferrin receptor IgG3-avidin fusion protein with biotinylated saporin results in significant enhancement of its cytotoxicity against malignant hematopoietic cells (2007)

We have previously developed an antibody fusion protein composed of a mouse/human chimeric IgG3 specific for the human transferrin receptor genetically fused to avidin (anti-hTfR IgG3-Av) as a universal delivery system for cancer therapy. This fusion protein efficiently delivers biotinylated FITC into cancer cells via TfR-mediated endocytosis. In addition, anti-hTfR IgG3-Av alone exhibits intrinsic cytotoxic activity and interferes with hTfR recycling, leading to the rapid degradation of the TfR and lethal iron deprivation in certain malignant B-cell lines. We now report on the cytotoxic effects of a conjugate composed of anti-hTfR IgG3-Av and biotinylated saporin 6 (b-SO6), a toxin derived from the plant Saponaria officinalis that inhibits protein synthesis. Conjugation of anti-hTfR IgG3-Av with b-SO6 enhances the cytotoxic effect of the fusion protein in sensitive cells and also overcomes the resistance of malignant cells that show low sensitivity to the fusion protein alone. Our results show for the first time that loading anti-hTfR IgG3-Av with a biotinylated toxin enhances the cytotoxicity of the fusion protein alone. These results suggest that anti-hTfR IgG3-Av has great potential as a therapeutic agent for a wide range of applications due to its intrinsic cytotoxic activity plus its ability to deliver biotinylated molecules into cancer cells.
Stimulated-emission-depletion microscopy with a multicolor stimulated-Raman-scattering light source (2008)

We describe a subdiffraction-resolution far-field fluorescence microscope employing stimulated emission depletion (STED) with a light source consisting of a microchip laser coupled into a standard single-mode fiber, which, via stimulated Raman scattering (SRS), yields a comb-like spectrum of seven discrete peaks extending from the fundamental wavelength at 532 nm to 620 nm. Each of the spectral peaks can be used as STED light for overcoming the diffraction barrier. This SRS light source enables the simple implementation of multicolor STED and provides a spectral output with multiple available wavelengths from green to red with potential for further expansion.
Substrate Trenching Mechanism during Plasma and Magnetically Enhanced Polysilicon Etching (1991)

Plasma and magnetically enhanced reactive ion etching processes with chlorine gas have been developed for subhalf micron polysilicon gate electrode etching (1). In this paper, gate oxide trenching during polysilicon gate etching using chlorine‐based reactive ion etching (RIE) and magnetically enhanced reactive ion etching (MERIE) processes is studied in detail. The trenching mechanism was found to be a direct result of off‐angle ion bombardment and reflection from the partially etched polysilicon sidewall during plasma etching. The off‐angle ion bombardment is caused by the elastic collision between ions and neutrals as ions move across the plasma sheath. Monte Carlo simulation confirms the angular distribution of ions under most plasma processing conditions. A two‐step MERIE process, first with high etch rate and high anisotropy and second with high selectivity to the gate oxide, with low ion energy bombardment is also developed to minimize the trenching effect during polysilicon‐gate etching.
Acetoxymethyl esters of phosphates, enhancement of the permeability and potency of cAMP. (1993)

Acetoxymethyl esters of alkyl or aryl phosphates can be prepared by reacting their trialkylammonium or silver salts with acetoxymethyl bromide. Because acetoxymethyl esters are rapidly cleaved intracellularly, they facilitate the delivery of organophosphates into the cytoplasm without puncturing or disruption of the plasma membrane. In addition, acylation of free hydroxyls, for example with butyryl groups, is useful both for synthetic convenience and increased hydrophobicity of the permeant derivatives. The highly polar intracellular messengers cAMP and cGMP were thus converted into uncharged membrane-permeant derivatives. Extracellularly applied N6,2'-O-dibutyryl cAMP acetoxymethyl ester (Bt2cAMP/AM) is shown to simulate intracellular cAMP in three model systems, namely dissociation of cAMP-dependent protein kinase in fibroblasts, activation of Cl- secretion of monolayers of the human colon epithelial cell line T84, and dispersion of pigment granules in angel fish melanophores. Bt2cAMP/AM is effective at concentrations two or three orders of magnitude less than those required for commonly used membrane-permeant cAMP derivatives such as Bt2cAMP, 8-Br-cAMP, and 8-pCPT-cAMP lacking the acetoxymethyl ester. This methodology should be of general utility for the intracellular delivery of phosphate-containing second messengers.
Recent human-to-poultry host jump, adaptation, and pandemic spread of <i>Staphylococcus aureus</i> (2009)

The impact of globalization on the emergence and spread of pathogens is an important veterinary and public health issue. Staphylococcus aureus is a notorious human pathogen associated with serious nosocomial and community-acquired infections. In addition, S. aureus is a major cause of animal diseases including skeletal infections of poultry, which are a large economic burden on the global broiler chicken industry. Here, we provide evidence that the majority of S. aureus isolates from broiler chickens are the descendants of a single human-to-poultry host jump that occurred approximately 38 years ago (range, 30 to 63 years ago) by a subtype of the worldwide human ST5 clonal lineage unique to Poland. In contrast to human subtypes of the ST5 radiation, which demonstrate strong geographic clustering, the poultry ST5 clade was distributed in different continents, consistent with wide dissemination via the global poultry industry distribution network. The poultry ST5 clade has undergone genetic diversification from its human progenitor strain by acquisition of novel mobile genetic elements from an avian-specific accessory gene pool, and by the inactivation of several proteins important for human disease pathogenesis. These genetic events have resulted in enhanced resistance to killing by chicken heterophils, reflecting avian host-adaptive evolution. Taken together, we have determined the evolutionary history of a major new animal pathogen that has undergone rapid avian host adaptation and intercontinental dissemination. These data provide a new paradigm for the impact of human activities on the emergence of animal pathogens.