gebhart/patrepeval huggingface dataset:
A Common Variant on Chromosome 9p21 Affects the Risk of Myocardial Infarction (2007)

The global endemic of cardiovascular diseases calls for improved risk assessment and treatment. Here, we describe an association between myocardial infarction (MI) and a common sequence variant on chromosome 9p21. This study included a total of 4587 cases and 12,767 controls. The identified variant, adjacent to the tumor suppressor genes CDKN2A and CDKN2B, was associated with the disease with high significance. Approximately 21% of individuals in the population are homozygous for this variant, and their estimated risk of suffering myocardial infarction is 1.64 times as great as that of noncarriers. The corresponding risk is 2.02 times as great for early-onset cases. The population attributable risk is 21% for MI in general and 31% for early-onset cases.
New Thionitrites: Synthesis, Stability, and Nitric Oxide Generation (1994)

International audience
Exosome platform for diagnosis and monitoring of traumatic brain injury (2014)

We have previously demonstrated the release of membranous structures by cells into their extracellular environment, which are termed exosomes, microvesicles or extracellular vesicles depending on specific characteristics, including size, composition and biogenesis pathway. With activation, injury, stress, transformation or infection, cells express proteins and RNAs associated with the cellular responses to these events. The exosomes released by these cells can exhibit an array of proteins, lipids and nucleic acids linked to these physiologic events. This review focuses on exosomes associated with traumatic brain injury, which may be both diagnostic and a causative factor in the progression of the injury. Based on current data, exosomes play essential roles as conveyers of intercellular communication and mediators of many of the pathological conditions associated with development, progression and therapeutic failures and cellular stress in a variety of pathologic conditions. These extracellular vesicles express components responsible for angiogenesis promotion, stromal remodelling, signal pathway activation through growth factor/receptor transfer, chemoresistance, immunologic activation and genetic exchange. These circulating exosomes not only represent a central mediator of the pro-inflammatory microenvironment linked with secondary brain injury, but their presence in the peripheral circulation may serve as a surrogate for biopsies, enabling real-time diagnosis and monitoring of neurodegenerative progression.
A film bulk acoustic resonator-based high-performance pressure sensor integrated with temperature control system (2017)

This paper presented a high-performance pressure sensor based on a film bulk acoustic resonator (FBAR). The support film of the FBAR chip was made of silicon nitride and the part under the resonator area was etched to enhance the sensitivity and improve the linearity of the pressure sensor. A micro resistor temperature sensor and a micro resistor heater were integrated in the chip to monitor and control the operating temperature. The sensor chip was fabricated, and packaged in an oscillator circuit for differential pressure detection. When the detected pressure ranged from −100 hPa to 600 hPa, the sensitivity of the improved FBAR pressure sensor was −0.967 kHz hPa−1, namely −0.69 ppm hPa−1, which was 19% higher than that of existing sensors with a complete support film. The nonlinearity of the improved sensor was less than ±0.35%, while that of the existing sensor was ±5%. To eliminate measurement errors from humidity, the temperature control system integrated in the sensor chip controlled the temperature of the resonator up to 75 °C, with accuracy of ±0.015 °C and power of 20 mW.
Increased DNA Vaccine Delivery and Immunogenicity by Electroporation In Vivo (2000)

DNA vaccines have been demonstrated to be potent in small animals but are less effective in primates. One limiting factor may be inefficient uptake of DNA by cells in situ. In this study, we evaluated whether cellular uptake of DNA was a significant barrier to efficient transfection in vivo and subsequent induction of immune responses. For this purpose, we used the technique of electroporation to facilitate DNA delivery in vivo. This technology was shown to substantially increase delivery of DNA to cells, resulting in increased expression and elevated immune responses. The potency of a weakly immunogenic hepatitis B surface Ag DNA vaccine was increased in mice, as seen by a more rapid onset and higher magnitude of anti-hepatitis B Abs. In addition, the immunogenicity of a potent HIV gag DNA vaccine was increased in mice, as seen by higher Ab titers, a substantial reduction in the dose of DNA required to induce an Ab response, and an increase in CD8+ T cell responses. Finally, Ab responses were enhanced by electroporation against both components of a combination HIV gag and env DNA vaccine in guinea pigs and rabbits. Therefore, cellular uptake of DNA is a significant barrier to transfection in vivo, and electroporation appears able to overcome this barrier.
The structural and optical behaviors of K-doped ZnO∕Al2O3(0001) films (2004)

K-doped ZnO films were prepared on Al2O3(0001) substrates by solution deposition. For the prepared thin films of Zn1−xKxO (x=0.002, 0.01, 0.02, 0.05, 0.1), we carried out x-ray diffraction, transmittance spectroscopy, photoluminescence, Hall measurement and x-ray photoemission spectroscopy study, and found that properties like the crystallinity, optical band gap, carrier concentrations and chemical binding states changed at a K doping concentration of 2mol%. From these results, we suggest that the doped K in ZnO films processed by the sol–gel method plays a different role at K doping concentrations below 2mol% and above 2mol%.
On the Computation of All Global Minimizers Through Particle Swarm Optimization (2004)

This paper presents approaches for effectively computing all global minimizers of an objective function. The approaches include transformations of the objective function through the recently proposed deflection and stretching techniques, as well as a repulsion source at each detected minimizer. The aforementioned techniques are incorporated in the context of the particle swarm optimization (PSO) method, resulting in an efficient algorithm which has the ability to avoid previously detected solutions and, thus, detect all global minimizers of a function. Experimental results on benchmark problems originating from the fields of global optimization, dynamical systems, and game theory, are reported, and conclusions are derived.
Subclincal Disease as Surrogate Endpoint of Cardiovascular Disease Events: Ankle-brachial Index as an Example (2005)

protein (a) was reported to be associated with abnormal ABI. 4 More important, the ABI was associated with cardiovascular morbidity and there was dose-response gradient for cardiovascular mortality. 5 In the paper, the authors also demonstrate that ABI less than 0.9 can be an independent factor for cardiovascular events in the setting of outpatient clinic.
Anti-Human Immunodeficiency Virus Type 1 (HIV-1) Antibodies 2F5 and 4E10 Require Surprisingly Few Crucial Residues in the Membrane-Proximal External Region of Glycoprotein gp41 To Neutralize HIV-1 (2004)

The conserved membrane-proximal external region (MPER) of human immunodeficiency virus type 1 (HIV-1) gp41 is a target of two broadly neutralizing human monoclonal antibodies, 2F5 and 4E10, and is an important lead for vaccine design. However, immunogens that bear MPER epitopes so far have not elicited neutralizing antibodies in laboratory animals. One explanation is that the immunogens fail to recreate the proper molecular environment in which the epitopes of 2F5 and 4E10 are presented on the virus. To explore this molecular environment, we used alanine-scanning mutagenesis across residues 660 to 680 in the MPER of a pseudotyped variant of HIV-1(JR-FL), designated HIV-1(JR2), and examined the ability of 2F5 and 4E10 to neutralize the Ala mutant viruses. The results show that the only changes to produce neutralization resistance to 2F5 occurred in residue D, K, or W of the core epitope (LELDKWANL). Likewise, 4E10 resistance arose by replacing one of three residues; two (W and F) were in the core epitope, and one (W) was seven residues C-terminal to these two (NWFDISNWLW). Importantly, no single substitution resulted in resistance of virus to both 2F5 and 4E10. Surprisingly, 8 out of 21 MPER Ala mutants were more sensitive than the parental pseudovirus to 2F5 and/or 4E10. At most, only small differences in neutralization sensitivity to anti-gp120 monoclonal antibody b12 and peptide T20 were observed with the MPER Ala mutant pseudoviruses. These data suggest that MPER substitutions can act locally and enhance the neutralizing activity of antibodies to this region and imply a distinct role of the MPER of gp41 during HIV-1 envelope-mediated fusion. Neutralization experiments showing synergy between and T20 and 4E10 against HIV-1 are also presented. The data presented may aid in the design of antigens that better present the MPER of gp41 to the immune system.
Apolipoprotein E modulates low density lipoprotein retention by lipoprotein lipase anchored to the subendothelial matrix (1993)

Lipoprotein lipase (lipase), a key enzyme in lipoprotein triglyceride metabolism, has been shown to markedly increase low density lipoprotein (LDL) retention by subendothelial matrix. In the present study we assessed the role that lipoprotein and matrix components play in retention of LDL by lipase anchored to the subendothelial matrix. Lipase addition to subendothelial matrix increased LDL retention by 66-fold. Scatchard analysis of LDL binding to lipase-containing matrix yielded an association constant of 12 nM. Exogenous addition of the matrix components, heparan sulfate and dermatan sulfate (i.e. chondroitin sulfate B), reduced LDL retention by greater than 90%. These glycosaminoglycans (GAGs) also reduced lipolytic activity associated with the matrix, suggesting that lipase was released from its binding sites on the matrix. In contrast, other matrix components (collagen, fibronectin, vitronectin, and chondroitin sulfate A) neither affected LDL release nor matrix lipolytic activity. Thus, heparan sulfate and dermatan sulfate function to anchor lipase to the subendothelial cell matrix. The effects of apolipoprotein E (apoE) and apoA-I were also examined. Preincubation of the subendothelial matrix with apoE, followed by washing, did not affect subsequent lipase binding to the matrix nor its ability to retain LDL. However, the direct addition of apoE alone or in combination with phospholipid liposomes decreased lipase-mediated LDL retention in a concentration-dependent fashion. Addition of apoA-I had no effect. Thus, in these studies apoE functions to displace LDL bound to lipase, but not lipase anchored to the matrix. To further examine the physiologic implications of this process, we assessed the ability of human apoE-rich and apoE-poor high density lipoproteins (HDL) to displace LDL from matrix-anchored lipase. ApoE-rich HDL reduced LDL retention dramatically (86% at 2.5 micrograms/ml). In contrast, apoE-poor HDL, at the highest concentration evaluated (400 micrograms/ml), decreased LDL retention by only 32%. Overall, these data suggest apoE and specifically apoE-containing HDL reduce the lipase-mediated retention of LDL by subendothelial matrix. This observation, in part could explain the protective effects of apoE and apoE-containing HDL against atherosclerosis.
Hyperpolarized 13 C allows a direct measure of flux through a single enzyme-catalyzed step by NMR (2007)

(13)C NMR is a powerful tool for monitoring metabolic fluxes in vivo. The recent availability of automated dynamic nuclear polarization equipment for hyperpolarizing (13)C nuclei now offers the potential to measure metabolic fluxes through select enzyme-catalyzed steps with substantially improved sensitivity. Here, we investigated the metabolism of hyperpolarized [1-(13)C(1)]pyruvate in a widely used model for physiology and pharmacology, the perfused rat heart. Dissolved (13)CO(2), the immediate product of the first step of the reaction catalyzed by pyruvate dehydrogenase, was observed with a temporal resolution of approximately 1 s along with H(13)CO(3)(-), the hydrated form of (13)CO(2) generated catalytically by carbonic anhydrase. In hearts presented with the medium-chain fatty acid octanoate in addition to hyperpolarized [1-(13)C(1)]pyruvate, production of (13)CO(2) and H(13)CO(3)(-) was suppressed by approximately 90%, whereas the signal from [1-(13)C(1)]lactate was enhanced. In separate experiments, it was shown that O(2) consumption and tricarboxylic acid (TCA) cycle flux were unchanged in the presence of added octanoate. Thus, the rate of appearance of (13)CO(2) and H(13)CO(3)(-) from [1-(13)C(1)]pyruvate does not reflect production of CO(2) in the TCA cycle but rather reflects flux through pyruvate dehydrogenase exclusively.
Patterns in Hydrogen Bonding: Functionality and Graph Set Analysis in Crystals (1995)

Abstract Whereas much of organic chemistry has classically dealt with the preparation and study of the properties of individual molecules, an increasingly significant portion of the activity in chemical research involves understanding and utilizing the nature of the interactions between molecules. Two representative areas of this evolution are supramolecular chemistry and molecular recognition. The interactions between molecules are governed by intermolecular forces whose energetic and geometric properties are much less well understood than those of classical chemical bonds between atoms. Among the strongest of these interactions, however, are hydrogen bonds, whose directional properties are better understood on the local level (that is, for a single hydrogen bond) than many other types of non‐bonded interactions. Nevertheless, the means by which to characterize, understand, and predict the consequences of many hydrogen bonds among molecules, and the resulting formation of molecular aggregates (on the microscopic scale) or crystals (on the macroscopic scale) has remained largely enigmatic. One of the most promising systematic approaches to resolving this enigma was initially developed by the late M. C. Etter, who applied graph theory to recognize, and then utilize, patterns of hydrogen bonding for the understanding and design of molecular crystals. In working with Etter's original ideas the power and potential utility of this approach on one hand, and on the other, the need to develop and extend the initial Etter formalism was generally recognized. It with that latter purpose that we originally undertook the present review.
Papulopustular rosacea, skin immunity and Demodex: pityriasis folliculorum as a missing link (2011)

Papulopustular rosacea (PPR) is a common facial skin disease, characterized by erythema, telangiectasia, papules and pustules. Its physiopathology is still being discussed, but recently several molecular features of its inflammatory process have been identified: an overproduction of Toll-Like receptors 2, of a serine protease, and of abnormal forms of cathelicidin. The two factors which stimulate the Toll-like receptors to induce cathelicidin expression are skin infection and cutaneous barrier disruption: these two conditions are, at least theoretically, fulfilled by Demodex, which is present in high density in PPR and creates epithelial breaches by eating cells. So, the major pathogenic mechanisms of Demodex and its role in PPR are reviewed here in the context of these recent discoveries. In this review, the inflammatory process of PPR appears to be a consequence of the proliferation of Demodex, and strongly supports the hypothesis that: (1) in the first stage a specific (innate or acquired) immune defect against Demodex allows the proliferation of the mite; (2) in the second stage, probably when some mites penetrate into the dermis, the immune system is suddenly stimulated and gives rise to an exaggerated immune response against the Demodex, resulting in the papules and the pustules of the rosacea. In this context, it would be very interesting to study the immune molecular features of this first stage, named "pityriasis folliculorum", where the Demodex proliferate profusely with no, or a low immune reaction from the host: this entity appears to be a missing link in the understanding of rosacea.
ChemInform Abstract: Synthesis of N,N′‐Carbonyl‐bis‐amino Acids and N,N′‐Carbonyl‐bis‐ peptides. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Activation tagging identifies a gene fromPetunia hybridaresponsible for the production of active cytokinins in plants (2002)

Cytokinins (CKs) are phytohormones that play an important role in plant growth and development. Although the first naturally produced CK, zeatin, was isolated almost four decades ago, no endogenous gene has been shown to produce active CKs in planta. In an activation tagging experiment we have identified a petunia line that showed CK-specific effects including enhanced shooting, reduced apical dominance and delayed senescence and flowering. This phenotype correlated with the enhanced expression of a gene we labelled Sho (Shooting). Sho, which encodes a protein with homology to isopentenyl transferases (IPTs), also causes CK-specific effects when expressed in other plant species. In contrast to the ipt gene from Agrobacterium, which primarily increases zeatin levels, Sho expression in petunia and tobacco especially enhances the levels of certain N6-(delta2-isopentenyl) adenosine (2iP) derivatives. Our data suggest that Sho encodes a plant enzyme whose activity is sufficient to produce active CKs in plants.
Laterally coupled BAW filters with 5% bandwidth (2010)

Lateral coupling between thin-film bulk acoustic wave resonators (LBAW) is a promising technology for fabrication of bandpass filters. Previously, narrow bandwidth of realized filters has been the main problem for the applicability of this technology. In this paper, solidly-mounted LBAW filters with different number of electrodes and passband width up to 5% are presented. Thin-film AlN is used as the piezoelectric material with a Mo bottom electrode and an Al top electrode. Filters consist of interdigital electrodes with varied electrode number, electrode width and gap between the electrodes. Acoustic coupling strength obtained at 2 GHz varies from 1%...1.5% for 2-electrode devices to 5% given by 31-electrode filters. With post-measurement matching to 120 Ω ∥ 5 nH, electrical frequency response obtained with 31-electrode LBAW shows a minimum insertion loss of 2...3 dB and a relative 3-dB bandwidth of 5% at 2 GHz. Effect of electrode number to filter passband is studied.
Combinatorial optimization for spacecraft scheduling (2003)

The application of combinatorial optimization techniques to the automatic spacecraft scheduling problem is described. The problem is to search over the candidate sequences of experiments for a sequence that maximizes the value of the science conducted while minimizing constraint conflicts. Exploratory computational results indicate that pseudorandom research techniques, such as simulated annealing, generate viable sequences in reasonable times.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Toll-like receptors 2 and 4 in ischemic stroke: Outcome and therapeutic values (2011)

Stroke triggers an intense inflammatory response that could be a consequence of Toll-like receptors (TLRs) activation. However, the clinical significance and the therapeutic possibilities of TLR in stroke is not completely clear. In this study, we analyze the association between the expression of TLR2 and TLR4, inflammatory molecules and endogenous ligands, and clinical outcome of ischemic stroke patients, and we test the potential of TLR2/TLR4 and their endogenous ligands as therapeutic targets. For this purpose, we included 110 patients with ischemic stroke finding that TLR2 and TLR4 are independently associated to poor outcome and correlated with higher serum levels of interleukin (IL)1β, IL6, tumor necrosis factor α, and VCAM1, and that TLR4 was independently associated to lesion volume. In addition, we have developed an in vitro model to test the potential therapeutic value of blocking TLR2/TLR4 or their endogenous ligands. Cultured cells (monocytes and human umbilical vein endothelial cells) were treated with serum from ischemic stroke patients, showing a strong inflammatory response that was blocked when TLR2/4 or cellular fibronectin (cFN) or HSP60 were blocked. In conclusion, TLR2 and TLR4 are associated to outcome in stroke patients and TLR2/4 or their endogenous ligands, cFN/HSP60 could be new therapeutic targets for ischemic stroke.
Immunomagnetic Manipulation of Hematopoietic Cells: A Review of Current Technology (1992)

During the last decade, immunomagnetic separation of cells has become popular due to the simplicity and speed of the technology. A variety of magnetic materials have been developed that have fundamentally different characteristics. Some of these act as true colloids and have the properties of solutions, while others are larger and are based on the polymerization of materials, such as styrene, in the presence of magnetite. In this article, the different magnetic matrices are discussed and reviewed with respect to their use for the separation of cells of the hematopoietic system. Additionally, a brief introduction into the field of immunomagnetic separation of nucleic acids is presented, as this technology may be used to perform investigations at the molecular level on hematopoietic cells.
Thyrocyte specific killer cell activity is decreased in patients with thyroid carcinoma (1987)

Natural killer cells (NK) are important in immune surveillance, and they have found to be decreased in the serum of patients with various types of malignancies. In patients with thyroid carcinoma, we investigated NK activity of peripheral lymphocytes directed against either a standard tumor cell target, K562, or against the clinically relevant target cell, the thyrocyte. Although NK-cell activity was normal when directed against K562 cell targets, NK-cell activity was reduced when labeled thyrocytes were used as target cells. At effector to target cell ratios of 100:1 and 20:1, there was 43 +/- 3% (n = 7) and 29 +/- 3% (n = 7) lyses of thyrocytes using normal lymphocytes, and 17 +/- 4% (n = 5) and 13 +/- 2% (n = 3) using lymphocytes from patients with thyroid carcinoma. These findings suggest that NK-cells have distinct subpopulations and that immune surveillance against specific thyrocyte target cells may be important in thyroid cancer.
Construction of an efficient expression vector for coupled transcription/translation in a wheat germ cell-free system (2000)

Using the expression vector, pEU, which we have constructed, highly efficient in vitro protein synthesis can be achieved: The system works for 150 hours and without further template addition once the reaction has started, yielding 5 mg of enzymatically active protein in a 1 ml reaction.
On the application of information theory to neural spike trains. (1998)

The nervous system represents time-dependent signals in sequences of discrete action potentials or spikes are identical so that information is carried only in the spike arrival times. We show how to quantify this information, in bits, free from any assumptions about which features of the spike train or input waveform are most important. We apply this approach to the analysis of experiments on a variety of systems, including some where we confront severe sampling problems, and discuss some to the results obtained and hopes for future extensions.