gebhart/patrepeval huggingface dataset:
New insights into the determination of HDL structure by apolipoproteins (2012)

Apolipoprotein (apo)A-I is the principal protein component of HDL, and because of its conformational adaptability, it can stabilize all HDL subclasses. The amphipathic α-helix is the structural motif that enables apoA-I to achieve this functionality. In the lipid-free state, the helical segments unfold and refold in seconds and are located in the N-terminal two thirds of the molecule where they are loosely packed as a dynamic, four-helix bundle. The C-terminal third of the protein forms an intrinsically disordered domain that mediates initial binding to phospholipid surfaces, which occurs with coupled α-helix formation. The lipid affinity of apoA-I confers detergent-like properties; it can solubilize vesicular phospholipids to create discoidal HDL particles with diameters of approximately 10 nm. Such particles contain a segment of phospholipid bilayer and are stabilized by two apoA-I molecules that are arranged in an anti-parallel, double-belt conformation around the edge of the disc, shielding the hydrophobic phospholipid acyl chains from exposure to water. The apoA-I molecules are in a highly dynamic state, and they stabilize discoidal particles of different sizes by certain segments forming loops that detach reversibly from the particle surface. The flexible apoA-I molecule adapts to the surface of spherical HDL particles by bending and forming a stabilizing trefoil scaffold structure. The above characteristics of apoA-I enable it to partner with ABCA1 in mediating efflux of cellular phospholipid and cholesterol and formation of a heterogeneous population of nascent HDL particles. Novel insights into the structure-function relationships of apoA-I should help reveal mechanisms by which HDL subclass distribution can be manipulated.
Synthesis, bacterial expression, and mutagenesis of the gene coding for mammalian cytochrome b5. (1986)

We have totally synthesized a gene that codes for rat hepatic cytochrome b5. The 5' flanking region was designed for efficient expression of this gene in Escherichia coli by incorporating an optimum ribosome binding site and spacer region. Both a soluble form, analogous to the protease-treated microsomal protein, as well as the complete cytochrome with hydrophobic membrane anchor, was constructed and expressed. Transformants with the gene for the soluble protein overproduce authentic cytochrome b5 to a level of 8% of the total cell protein. The complete cytochrome is expressed to a lesser extent with most of the protein found in the cell membrane fraction. This represents complete synthesis and bacterial expression of a mammalian metalloprotein gene. Cytochrome b5 is normally a six-coordinate low spin heme protein with histidine-39 and histidine-63 as axial ligands. We have replaced histidine-63 with a methionine residue by cassette mutagenesis, utilizing specific restriction enzyme sites engineered into the synthetic gene. The resultant protein has histidine-39 as sole axial ligand and is five-coordinate high spin in the ferric resting state, as indicated by optical and electron spin resonance spectroscopy. The ability to generate mutant cytochrome b5 in high yield is a crucial step in understanding heme protein folding, protein-protein recognition and binding, and biological electron transfer processes.
Technical challenges for cognitive radio in the TV white space spectrum (2009)

The FCC recently issued the regulatory rules for cognitive radio use of the TV white space spectrum. These new rules provide an opportunity but they also introduce a number of technical challenges. The challenges require development of cognitive radio technologies like spectrum sensing as well as new wireless PHY and MAC layer designs. These challenges include spectrum sensing of both TV signals and wireless microphone signals, frequency agile operation, geo-location, stringent spectral mask requirements, and of course the ability to provide reliable service in unlicensed and dynamically changing spectrum. After describing these various challenges we will describe some of the possible methods for meeting these challenges.
The Sleep Disorders Questionnaire I: Creation and Multivariate Structure of SDQ (1994)

The development of the Sleep Disorders Questionnaire (SDQ) from the Sleep Questionnaire and Assessment of Wakefulness (SQAW) of Stanford University is described in detail. The extraction of the best question items from the SQAW and their subsequent rewording in the SDQ to insure greater completion rates are described. Two item test-retest reliability studies are reported on 71 controls and on 130 sleep-disorder patients, which confirmed adequate reliability. To create multivariate scoring scales, SDQ was then given in a multicenter study to 519 persons, 435 of whom were sleep-disorder patients with full polysomnography. Canonical Discriminant Function Analysis was employed, which resulted in four clinical-diagnostic scales: SA for sleep apnea, NAR for narcolepsy, PSY for psychiatric sleep disorder and PLM for periodic limb movement disorder. Each was adjusted for male and female responses and transformed to a percentile using the observed distribution of raw scores. Using Receiver Operating Characteristics analysis, cutoff points were determined for each scale to maximize its sensitivity and specificity. Positive and negative predictive values were also calculated. The SA and NAR scales proved to be the most discriminating.
Allophanate Hydrolase, Not Urease, Functions in Bacterial Cyanuric Acid Metabolism (2005)

Growth substrates containing an s-triazine ring are typically metabolized by bacteria to liberate 3 mol of ammonia via the intermediate cyanuric acid. Over a 25-year period, a number of original research papers and reviews have stated that cyanuric acid is metabolized in two steps to the 2-nitrogen intermediate urea. In the present study, allophanate, not urea, was shown to be the 2-nitrogen intermediate in cyanuric acid metabolism in all the bacteria examined. Six different experimental results supported this conclusion: (i) synthetic allophanate was shown to readily decarboxylate to form urea under acidic extraction and chromatography conditions used in previous studies; (ii) alkaline extraction methods were used to stabilize and detect allophanate in bacteria actively metabolizing cyanuric acid; (iii) the kinetic course of allophanate formation and disappearance was consistent with its being an intermediate in cyanuric acid metabolism, and no urea was observed in those experiments; (iv) protein extracts from cells grown on cyanuric acid contained allophanate hydrolase activity; (v) genes encoding the enzymes AtzE and AtzF, which produce and hydrolyze allophanate, respectively, were found in several cyanuric acid-metabolizing bacteria; and (vi) TrzF, an AtzF homolog found in Enterobacter cloacae strain 99, was cloned, expressed in Escherichia coli, and shown to have allophanate hydrolase activity. In addition, we have observed that there are a large number of genes homologous to atzF and trzF distributed in phylogenetically distinct bacteria. In total, the data indicate that s-triazine metabolism in a broad class of bacteria proceeds through allophanate via allophanate hydrolase, rather than through urea using urease.
Helium field ion source for application in a 100 keV focused ion beam system (1992)

A He gas-phase ion source having a three-electrode acceleration lens that can change the acceleration energy and magnification independently was developed. This source allows application of acceleration voltages up to 100 kV and extraction voltages up to 30 kV. This source is a component of our final objective of development, a nanometer lithography system with a beam diameter of 10 nm and a beam energy of 100 keV. In the present experiment, by using this source, the characteristics of He ion current emitted from W (111) emitter cooled by liquid N2 or liquid He was obtained. Maximum angular intensities of 40 nA/sr and 2.2 μA/sr were obtained at emitter temperatures of ∼100 and 20 K, respectively. In addition, the increase of the gas-phase ion current by emitter treatment (field-emission treatment or field-evaporation treatment) was ascertained.
Antibody-dependent enhancement and vaccine development (2006)

The development of protective antibodies has long been the basis for vaccine development against a large range of infective agents. However, the discovery of the phenomena of antibody-dependent enh...
Identification of Nore1 as a Potential Ras Effector (1998)

The small GTP-binding protein Ras is pivotal in transmitting growth and differentiation signals downstream of cell surface receptors. Many observations have indicated that Ras transmits signals from cell surface receptors into multiple pathways via direct interaction with different effectors in mammalian cells. We have identified a novel potential Ras effector or target named Nore1. Nore1 has no significant sequence similarity to known mammalian proteins and lacks an identifiable catalytic domain, but contains sequence motifs that predict DAG_PE binding and SH3 domain binding. We show that Nore1 directly interacts with Ras in vitro in a GTP-dependent manner, and the interaction requires an intact Ras effector domain. Nore1 becomes associated with Ras in situ following activation of epidermal growth factor receptor in COS-7 and in KB cells.
Development and functional specialization of CD103+ dendritic cells (2010)

CD103 (alpha(E)) integrin expression distinguishes a population of dendritic cells (DCs) that can be found in many if not all lymphoid and non-lymphoid organs. CD103(+) DCs display distinct functional activities. Migratory CD103(+) DCs derived from skin, lung, and intestine efficiently present exogenous antigens in their corresponding draining lymph nodes to specific CD8(+) T cells through a mechanism known as cross-presentation. On the T cells they prime, intestinal CD103(+) DCs can drive the induction of the chemokine receptor CCR9 and alpha(4)beta(7) integrin, both known as gut-homing receptors. CD103(+) DCs also contribute to control inflammatory responses and intestinal homeostasis by fostering the conversion of naive T cells into induced Foxp3(+) regulatory T cells, a mechanism that relies on transforming growth factor-beta and retinoic acid signaling. This review discusses recent findings that identify murine CD103(+) DCs as important regulators of the immune response.
Molecular Dissection of the Mechanism by Which Potexvirus Triple Gene Block Proteins Mediate Cell-to-Cell Transport of Infectious RNA (1998)

The triple gene block (TGB; consisting of proteins TGB1–3) and coat protein (CP) of white clover mosaic potexvirus (WClMV) are required for cell-to-cell movement of viral RNA. Cell-to-cell spread of WClMV mutants in which the TGB open reading frames had been mutated was rescued in transgenic plants expressing specific TGB proteins (TGBPs). This indicated that there are no requirements for the synthesis in cis of viral TGBPs. These transgenic plants provided an experimental framework to explore the roles performed by the TGBPs and CP in cell-to-cell movement of WClMV RNA. Microinjection experiments established that TGB1 functions as the WClMV cell-to-cell movement protein (MP). Furthermore, combined microinjection and dual-channel confocal laser scanning microscopy provided direct evidence that infectious transcripts of WClMV move cell to cell as a ribonucleoprotein complex, consisting of single-stranded RNA, TGB1, and CP. Movement of this ribonucleoprotein complex displayed an absolute requirement for the presence of both TGB2 and TGB3. A model consistent with these findings is presented.
Self-Organised Beamforming and Opportunistic Scheduling in an OFDM-based Cellular Network (2006)

In this paper, a system concept is proposed and investigated for the downlink of a cellular network which combines a self-organised beamforming approach with an opportunistic scheduling concept. In the considered OFDM-based system, different beams or grids of beams are formed in time and frequency and the available space-time-frequency resources are allocated by intelligent scheduling algorithms to those mobile terminals with high instantaneous signal-to-interference-and-noise ratios (SINRs). Analysing the impact of various design criteria, such as the type of beamforming, scheduling concepts and frequency reuse factors, the performance in the cellular network regarding throughput and fairness is assessed
New advances in Clostridium difficile infection: changing epidemiology, diagnosis, treatment and control (2008)

CDAD is an increasing health problem throughout the United States, Canada and Europe with rising mortality rate. Occurrence of CDAD outside of healthcare settings and in pediatric populations represents newly emerging problems. New treatments are needed.
Increased population of high fluorescence 1F7 (CD26) antigen on T cells in synovial fluid of patients with rheumatoid arthritis. (1996)

Our results indicate that SF of patients with RA contains activated T cells, and suggest that T cells with high levels of CD26 antigen may preferentially migrate into the rheumatoid synovium to induce inflammation and tissue destruction.
0.2V adiabatic NC-FinFET with 0.6mA/&#x00B5;m I<inf>ON</inf> and 0.1nA/&#x00B5;m I<inf>OFF</inf> (2015)

We present for the first time a Negative Capacitance (NC) FinFET. Simulation shows 0.2V operation with 0.6mA/µm on-current and 100pA/µm leakage current. A simple model guides the optimization of the ferroelectric film and the FinFET in the NC-FinFET. Our finding that a weak ferroelectric material is preferable greatly increases the candidate material classes and we report the target properties to search for. Counterintuitively, the gate to S/D capacitance and a thicker EOT both reduce the required V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DD</inf> . NC-FinFET is good for high performance and very low power applications.
Quantitative PCR: the determination of template copy numbers by temperature gradient gel electrophoresis (TGGE) (1990)

Journal Article Quantitative PCR: the determination of template copy numbers by temperature gradient gel electrophoresis (TGGE) Get access K. Henco, K. Henco * DIAGEN GmbHNiederheider Str. 3, 4000 Düsseldorf 13, FRG *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar M. Heibey M. Heibey DIAGEN GmbHNiederheider Str. 3, 4000 Düsseldorf 13, FRG Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 22, 25 November 1990, Pages 6733–6734, https://doi.org/10.1093/nar/18.22.6733 Published: 25 November 1990 Article history Received: 11 October 1990 Published: 25 November 1990
A placebo‐controlled multi‐centred evaluation of an anaesthetic gel (Oraqix®) for periodontal therapy (2003)

The VAS pain scores showed that the anaesthetic gel 5% was statistically more effective than the placebo in reducing pain during periodontal debridement.
Hydrogen Storage in Single-Walled Carbon Nanotubes at Room Temperature (1999)

Masses of single-walled carbon nanotubes (SWNTs) with a large mean diameter of about 1.85 nanometers, synthesized by a semicontinuous hydrogen arc discharge method, were employed for hydrogen adsorption experiments in their as-prepared and pretreated states. A hydrogen storage capacity of 4.2 weight percent, or a hydrogen to carbon atom ratio of 0.52, was achieved reproducibly at room temperature under a modestly high pressure (about 10 megapascal) for a SWNT sample of about 500 milligram weight that was soaked in hydrochloric acid and then heat-treated in vacuum. Moreover, 78.3 percent of the adsorbed hydrogen (3.3 weight percent) could be released under ambient pressure at room temperature, while the release of the residual stored hydrogen (0.9 weight percent) required some heating of the sample. Because the SWNTs can be easily produced and show reproducible and modestly high hydrogen uptake at room temperature, they show promise as an effective hydrogen storage material.
Development of Poly(Lactic Acid)/Chitosan Co-Matrix Microspheres: Controlled Release of Taxol-Heparin for Preventing Restenosis (2001)

Smooth muscle cell proliferation plays a major role in the genesis of restenosis after angioplasty or vascular injury. Controlled release of appropriate drugs alone and in combinations is one approach for treating coronary obstructions, balloon angioplasty, restenosis associated with thrombosis, and calcification. We demonstrated the possibility of encapsulating taxol-loaded polylactic acid (PLA) microspheres within heparin-chitosan spheres to develop a prolonged release co-matrix form. The in vitro release profile of taxol and heparin from this co-matrix system was monitored in phosphate buffered saline pH 7.4, using an ultraviolet spectrophotometer. The amount of taxol/heparin release was initially much higher, followed by a constant slow release profile for a prolonged period. The initial burst release of taxol (15.8%) and heparin (32.7%) from the co-matrix was modified with polyethylene glycol coatings (13.5% and 25.4%, respectively, for 24 hr). From scanning electron microscopy studies, it appears that these drugs diffuse out slowly to the dissolution medium through the micropores of the co-matrix. However, the surface micropores were modified with polyethylene glycol (PEG) coatings for a constant slow release profile. This PEG-coated PLA/chitosan co-matrix may target drug combinations having synergestic effects for prolonged periods to treat restenosis.
siRNA Delivery into Human T Cells and Primary Cells with Carbon‐Nanotube Transporters (2007)

Special delivery: Functionalized single-walled nanotubes (SWNT) can be used as molecular transporters to shuttle short interfering RNA (siRNA) into human T cells and primary cells and silence the expression of HIV-specific cell-surface receptors and coreceptors (see picture; scale bars 40 μm). This silencing effect, known to block HIV viral entry and reduce infection, is superior to that observed with conventional liposome-based nonviral delivery agents.
Biosynthesis of anabasine in transformed root cultures of Nicotiana species (1990)

The biosynthesis of 3-(2-piperidyl)pyridine (anabasine)(6) has been studied in transformed root cultures of Nicotiana rustica and N. tabacum using cadaverine precursors selectively labelled with deuterium. The labelling pattern in anabasine (6) derived biosynthetically from [2,2,4,4-2H4]-cadaverine in N. tabacum could not be established by 2H NMR spectroscopy because of the closeness of the chemical shifts of the labelled 2H atoms. However, the complete labelling pattern for the tetradeuteriated anabasine (10) was established by 1H NMR spectroscopy, because of the very high incorporation of 2H4 species (dilution in anabasine ca. 1). Two AB systems were observed for the protons at C-4′ and C-6′, and a singlet for the C-2′ proton in anabasine (10). No deuterium was incorporated into the nicotinic acid portion of anabasine. The labelling patterns in anabasine derived biosynthetically from (S)- and (R)-[1-2H]cadaverine in N. rustica were determined by 2H NMR spectroscopy. These labelling patterns, due to mixtures of species (11) and (12) and (13)–(16), respectively, show that the pro-R hydrogen of cadaverine is retained and the pro-S hydrogen is lost at the position which becomes C-2′ of anabasine. In addition, the labelling patterns are consistent with formation of equal amounts of (R)- and (S)-anabasine.
Hypothermia after cardiac arrest: Expanding the therapeutic scope (2009)

Therapeutic hypothermia for 12 to 24 hrs following resuscitation from out-of-hospital cardiac arrest is now recommended by the American Heart Association for the treatment of neurological injury when the initial cardiac rhythm is ventricular fibrillation. However, the role of therapeutic hypothermia is uncertain when the initial cardiac rhythm is asystole or pulseless electrical activity, or when the cardiac arrest is primarily due to a noncardiac cause, such as asphyxia or drug overdose. Given that survival rate in these latter conditions is very low, it is unlikely that clinical trials will be undertaken to test the efficacy of therapeutic hypothermia in this setting because of the very large sample size that would be required to detect a significant difference in outcomes. Therefore, in patients with anoxic brain injury after nonventricular fibrillation cardiac arrest, clinicians will need to balance the possible benefit of therapeutic hypothermia with the possible side effects of this therapy. Given that the side effects of therapeutic hypothermia are generally easily managed in the critical care setting, and there is benefit for anoxic brain injury demonstrated in laboratory studies, consideration may be given to treat comatose post-cardiac arrest patients with therapeutic hypothermia in this setting. Because the induction of therapeutic hypothermia has become more feasible with the development of simple intravenous cooling techniques and specialized equipment for improved temperature control in the critical care unit, it is expected that therapeutic hypothermia will become more widely used in the management of anoxic neurological injury whatever the presenting cardiac rhythm.
Thematic review series: The Pathogenesis of Atherosclerosis. Effects of infection and inflammation on lipid and lipoprotein metabolism mechanisms and consequences to the host (2004)

Infection and inflammation induce the acute-phase response (APR), leading to multiple alterations in lipid and lipoprotein metabolism. Plasma triglyceride levels increase from increased VLDL secretion as a result of adipose tissue lipolysis, increased de novo hepatic fatty acid synthesis, and suppression of fatty acid oxidation. With more severe infection, VLDL clearance decreases secondary to decreased lipoprotein lipase and apolipoprotein E in VLDL. In rodents, hypercholesterolemia occurs attributable to increased hepatic cholesterol synthesis and decreased LDL clearance, conversion of cholesterol to bile acids, and secretion of cholesterol into the bile. Marked alterations in proteins important in HDL metabolism lead to decreased reverse cholesterol transport and increased cholesterol delivery to immune cells. Oxidation of LDL and VLDL increases, whereas HDL becomes a proinflammatory molecule. Lipoproteins become enriched in ceramide, glucosylceramide, and sphingomyelin, enhancing uptake by macrophages. Thus, many of the changes in lipoproteins are proatherogenic. The molecular mechanisms underlying the decrease in many of the proteins during the APR involve coordinated decreases in several nuclear hormone receptors, including peroxisome proliferator-activated receptor, liver X receptor, farnesoid X receptor, and retinoid X receptor. APR-induced alterations initially protect the host from the harmful effects of bacteria, viruses, and parasites. However, if prolonged, these changes in the structure and function of lipoproteins will contribute to atherogenesis.
Synthesis of Y chromosome-specific labeled DNA probes by in vitro DNA amplification. (1990)

We describe the use of in vitro DNA amplification for production of double-stranded, biotin-labeled DNA probes. Specifically, a 124 BP DNA segment of the Y chromosome-specific 3.4 KB repeat was amplified in preparations of human genomic DNA using the polymerase chain reaction (PCR) and a thermostable DNA polymerase. The PCR products were amplified further in the presence of a molar excess of biotin-11-dUTP. The resulting double-stranded DNA segments showed a high amount of incorporated biotin-11-dUTP. The probes were used in DNA-DNA hybridization experiments without further purification. When DNA sequences flanking the target region are known, probe generation by enzymatic amplification offers a rapid and efficient alternative to molecular cloning and nick translation.