gebhart/patrepeval huggingface dataset:
Electrochemical Windows of Room-Temperature Ionic Liquids from Molecular Dynamics and Density Functional Theory Calculations (2011)

We investigated the cathodic and anodic limits of six room-temperature ionic liquids (ILs) formed from a combination of two common cations, 1-butyl-3-methylimidazolium (BMIM) and N,N-propylmethylpyrrolidinium (P13), and three common anions, PF6, BF4, and bis(trifluoromethylsulfonyl)imide (TFSI), using an approach that combines molecular dynamics (MD) simulations and density functional theory (DFT) calculations. All interion interactions were taken into account by explicitly modeling the entire liquid structure using classical MD, followed by DFT computations of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies. The relative cathodic and anodic limits of BMIM PF6, BMIM BF4, BMIM TFSI, and P13 TFSI obtained from our approach are in fairly good agreement with existing experimental data. From our DFT calculations, we also obtained the cation- and anion-projected density of states (DOS), which provide information on the likely species contributing to reductive and oxidative decomposition. Our predictions support Howlett et al.’s earlier finding(1) that the TFSI anion is less stable than the P13 cation against reduction. In addition, our results provide surprising evidence of possible cation anodic instability; we predict the aromatic BMIM cation to be less stable against oxidation than the respective anions in BMIM PF6 and BMIM BF4, and the P13 cation to be less stable against oxidation than the PF6 anion in P13 PF6. We also present a comparison of the predictions of our approach with that of simpler approximations based on in vacuo or polarizable continuum model calculations.
An FPGA implementation architecture for decoding of polar codes (2011)

Polar codes are a class of codes versatile enough to achieve the Shannon bound in a large array of source and channel coding problems. For that reason it is important to have efficient implementation architectures for polar codes in hardware. Motivated by this fact we propose a belief propagation (BP) decoder architecture for an increasingly popular hardware platform; Field Programmable Gate Array (FPGA). The proposed architecture supports any code rate and is quite flexible in terms of hardware complexity and throughput. The architecture can also be extended to support multiple block lengths without increasing the hardware complexity a lot. Moreover various schedulers can be adapted into the proposed architecture so that list decoding techniques can be used with a single block. Finally the proposed architecture is compared with a convolutional turbo code (CTC) decoder for WiMAX taken from a Xilinx Product Specification and seen that polar codes are superior to CTC codes both in hardware complexity and throughput.
Thrombus Formation on Atherosclerotic Plaques: Pathogenesis and Clinical Consequences (2001)

Long-term treatment with potent antithrombotic drugs, such as tissue factor or factor Xa inhibitors, that effectively block thrombosis without causing bleeding complications could help reduce death from cardiovascular disease.
Sobre la defensa mediática de un juez (2010)

En este trabajo el autor analiza el auto de la Sala Segunda del Tribunal Supremo, de 3 de febrero de 2010, mediante el cual se deniega el sobreseimiento de la causa especial instruida contra el juez titular del Juzgado Central num. 5 y se imputa al Juez encausado el delito de prevaricacion por haber iniciado y prolongado un procedimiento penal por delitos que habian prescrito y estaban amnistiados y que, ademas, no eran de su competencia.
Eccentric exercise effect on blood oxidative-stress markers and delayed onset of muscle soreness (2002)

LEE, J., A. H. GOLDFARB, M. H. RESCINO, S. HEGDE, S. PATRICK, and K. APPERSON. Eccentric exercise effect on blood oxidative-stress markers and delayed onset of muscle soreness. Med. Sci. Sports Exerc., Vol. 34, No. 3, pp. 443–448, 2002. Purpose This study examined the effects of a single bout of high-intensity eccentric exercise (EE) on blood protein carbonyls, glutathione status, and muscle damage indicators to ascertain whether blood markers of oxidative stress are elevated at the time delayed onset of muscle soreness (DOMS) occurs. Methods Eight healthy men (26.5 ± 1.5 yr) performed 60 eccentric contractions at ∼135-150% dominant arm maximum isometric force (MIF) using their nondominant arm elbow flexors. DOMS, range of motion (ROM), MIF, and blood were obtained before, immediately after, and 24, 48, 72, and 96 h after the EE. Blood samples were analyzed for plasma creatine kinase (CK) activity, and protein carbonyls (PC), and erythrocyte glutathione status. Results A significant decrease in MIF occurred at all times after the EE. ROM decreased from 24 to 96 h, and DOMS increased 24 to 72 h in the nondominant arm as indicated by a repeated measure ANOVA. Plasma CK activity peaked at 72 h (1620 ± 500 IU·L−1) compared with baseline (154 ± 27 IU·L−1). Erythrocyte-reduced glutathione (GSH) concentration was not significantly affected by the EE but tended to decrease 23% by 24 h and continued at this level for 96 h. Oxidized glutathione (GSSG) and total glutathione were unchanged over time. A significant increase in plasma PC occurred at 24 and 48 h after eccentric exercise. Conclusions The results suggest that 60 EE at 135–150% MIF can result in DOMS, with decreased muscle function and increases in plasma PC at 24 and 48 h without alterations in blood glutathione status.
Heparin Binding Nanostructures to Promote Growth of Blood Vessels (2006)

Controlling new blood vessel formation is of interest in regenerative medicine and cancer treatment. Heparin, a biopolymer that binds to angiogenic growth factors, was used to nucleate the self-assembly of nanostructures from designed peptide amphiphile molecules. This process yields rigid nanofibers that display heparin chains to orient proteins for cell signaling. In vivo, the nanostructures stimulated extensive new blood vessel formation using nanogram amounts of growth-factor proteins that by themselves did not induce any detectable angiogenesis.
A discussion of methods for measuring low-amplitude jitter (2002)

There is an escalating need in current designs to control and measure the stability of critically timed signals, most notably clocks. The success of any design methods which attempt to ensure such stability hinge on the suitability and quality of the timing data upon which the design decisions are based. For clock signals, there are a variety of metrics of stability (peak, cycle-to-cycle, etc.). Furthermore, the widespread use of PLL devices for the distribution and reception of clocks necessitates other measurement types, such as modulation spectrum. This paper presents a comparative discussion of methods of measuring low-amplitude jitter, and other related behavior such as modulation spectrum. It compares "front-panel" oscilloscope-based methods, and time-interval analyzer and counter-based methods. It then describes a method of post-processing oscilloscope data in ways that are more accurate and useful to the design process than is possible from the scope's front panel.
Conversion of cellular sialic acid expression from N-acetyl- to N-glycolylneuraminic acid using a synthetic precursor, N-glycolylmannosamine pentaacetate: inhibition of myelin-associated glycoprotein binding to neural cells (2000)

Sialic acids are prominent termini of mammalian glycoconjugates and are key binding determinants for cell-cell recog-nition lectins. Binding of the sialic acid-dependent lectin, myelin-associated glycoprotein (MAG), to nerve cells is implicated in the inhibition of nerve regeneration after injury. Therefore, blocking MAG binding to nerve cell sialoglycoconjugates might enhance nerve regeneration. Previously, we reported that certain sialoglycoconjugates bearing N-acetylneuraminic acid (NeuAc) but not N-glycolylneuraminic acid (NeuGc) support MAG binding (Collins et al., 1997a). We now report highly efficient conversion of sialic acids on living neural cells from exclusively NeuAc to predominantly NeuGc using a novel synthetic metabolic precursor, N-glycolylmannosamine pentaacetate (Man-NGc-PA). When NG108-15 neuroblastoma-glioma hybrid cells, which normally express only NeuAc (and bind to MAG), were cultured in the presence of 1 mM ManNGcPA, they expressed 80-90% of their sialic acid precursor pool as NeuGc within 24 h. Within 5 days, 80% of their ganglioside-associated sialic acids and 70% of their glycoprotein-associated sialic acids were converted to NeuGc. Consistent with this result, treatment of NG108-15 cells with ManNGcPA resulted in nearly complete abrogation of MAG binding. These results demonstrate that ManNGcPA treatment efficiently alters the sialic acid structures on living cells, with a commensurate change in recognition by a physiologically important lectin.
Restricted Receptor Segregation into Membrane Microdomains Occurs on Human T Cells During Apoptosis Induced by Galectin-1 (1999)

Galectin-1 induces apoptosis of human thymocytes and activated T cells by an unknown mechanism. Apoptosis is a novel function for a mammalian lectin; moreover, given the ubiquitous distribution of the oligosaccharide ligand recognized by galectin-1, it is not clear how susceptibility to and signaling by galectin-1 is regulated. We have determined that galectin-1 binds to a restricted set of T cell surface glycoproteins, and that only CD45, CD43, and CD7 appear to directly participate in galectin-1-induced apoptosis. To determine whether these specific glycoproteins interact cooperatively or independently to deliver the galectin-1 death signal, we examined the cell surface localization of CD45, CD43, CD7, and CD3 after galectin-1 binding to human T cell lines and human thymocytes. We found that galectin-1 binding resulted in a dramatic redistribution of these glycoproteins into segregated membrane microdomains on the cell surface. CD45 and CD3 colocalized on large islands on apoptotic blebs protruding from the cell surface. These islands also included externalized phosphatidylserine. In addition, the exposure of phosphatidylserine on the surface of galectin-1-treated cells occurred very rapidly. CD7 and CD43 colocalized in small patches away from the membrane blebs, which excluded externalized phosphatidylserine. Receptor segregation was not seen on cells that did not die in response to galectin-1, including mature thymocytes, suggesting that spatial redistribution of receptors into specific microdomains is required for triggering apoptosis.
Methods for NEURAL ENSEMBLE RECORDINGS (1998)

Neuroscientists have long recognized the importance of understanding the underlying principles of information processing by large populations of neurons. Methods for Neural Ensemble Recordings explores methods for using electrophysiological techniques for monitoring the concurrent activity of ensembles of single neurons. Since current methods allow
Visually controlled graphics (1993)

Interactive graphics systems that are driven by visual input are discussed. The underlying computer vision techniques and a theoretical formulation that addresses issues of accuracy, computational efficiency, and compensation for display latency are presented. Experimental results quantitatively compare the accuracy of the visual technique with traditional sensing. An extension to the basic technique to include structure recovery is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunization of chimpanzees with tumor antigen MUC1 mucin tandem repeat peptide elicits both helper and cytotoxic T-cell responses. (1999)

CTLs and antibody responses to the tumor-associated antigen MUC1 mucin can be detected in patients with adenocarcinomas of the breast, pancreas, colon, and ovary. However, neither response is generally effective at controlling disease. Methods to augment immunity to MUC1 are being designed, with the expectation that this will lead to an antitumor response. The key to eliciting potent immunity to tumor MUC1 may be in generating MUC1-specific T-helper cell responses, which, to date, have not been reported in cancer patients. We have recently demonstrated that a synthetic vaccine representing five copies of the MUC1 tandem repeat peptide can be used to prime MUC1-specific human CD4+ T cells in vitro. Here, we extend these studies to test the immunogenicity and safety of the tandem repeat peptide in the chimpanzee, which has the identical MUC1 tandem repeat sequence to the human. To promote induction of Th1-type responses, we used the novel adjuvant LeIF, a Leishmania-derived protein that is known to stimulate human peripheral blood mononuclear cells (PBMCs) and antigen-presenting cells, to produce a Th1-type cytokine profile. We found that MUC1 tandem repeat peptide administered with LeIF elicited positive, albeit transient, proliferative T-cell responses to MUC1 in the PBMCs from four of four chimpanzees. Immunization induced MUC1-specific IFN-gamma but not interleukin 4 expression in CD4+ T cells from PBMCs and draining lymph nodes. MUC1-specific CTLs were also generated that did not induce detectable autoimmune dysfunction during the 1 year of observation. We conclude that the MUC1 tandem repeat peptide can be used to elicit both T-helper and cytotoxic cell responses to MUC1 in the primate and holds promise as a safe and effective cancer vaccine.
Structural Features of MicroRNA (miRNA) Precursors and Their Relevance to miRNA Biogenesis and Small Interfering RNA/Short Hairpin RNA Design (2004)

We have established the structures of 10 human microRNA (miRNA) precursors using biochemical methods. Eight of these structures turned out to be different from those that were computer-predicted. The differences localized in the terminal loop region and at the opposite side of the precursor hairpin stem. We have analyzed the features of these structures from the perspectives of miRNA biogenesis and active strand selection. We demonstrated the different thermodynamic stability profiles for pre-miRNA hairpins harboring miRNAs at their 5'- and 3'-sides and discussed their functional implications. Our results showed that miRNA prediction based on predicted precursor structures may give ambiguous results, and the success rate is significantly higher for the experimentally determined structures. On the other hand, the differences between the predicted and experimentally determined structures did not affect the stability of termini produced through "conceptual dicing." This result confirms the value of thermodynamic analysis based on mfold as a predictor of strand section by RNAi-induced silencing complex (RISC).
The Putative Pore-Forming Domain of Bax Regulates Mitochondrial Localization and Interaction with Bcl-XL (2000)

Bax is a proapoptotic member of the Bcl-2 family of proteins which localizes to and uses mitochondria as its major site of action. Bax normally resides in the cytoplasm and translocates to mitochondria in response to apoptotic stimuli, and it promotes apoptosis in two ways: (i) by disrupting mitochondrial membrane barrier function by formation of ion-permeable pores in mitochondrial membranes and (ii) by binding to antiapoptotic Bcl-2 family proteins via its BH3 domain and inhibiting their functions. A hairpin pair of amphipathic alpha-helices (alpha5-alpha6) in Bax has been predicted to participate in membrane insertion and pore formation by Bax. We mutagenized several charged residues in the alpha5-alpha6 domain of Bax, changing them to alanine. These substitution mutants of Bax constitutively localized to mitochondria and displayed a gain-of-function phenotype when expressed in mammalian cells. Furthermore, substitution of 8 out of 10 charged residues in the alpha5-alpha6 domain of Bax resulted in a loss of cytotoxicity in yeast but a gain-of-function phenotype in mammalian cells. The enhanced function of this Bax mutant was correlated with increased binding to Bcl-X(L), through a BH3-independent mechanism. These observations reveal new functions for the alpha5-alpha6 hairpin loop of Bax: (i) regulation of mitochondrial targeting and (ii) modulation of binding to antiapoptotic Bcl-2 proteins.
Guaranteed Response Times in a Hard-Real-Time Environment (1980)

This paper describes a scheduling algorithm for a set of tasks that guarantees the time within which a task, once started, will complete. A task is started upon receipt of an external signal or the completion of other tasks. Each task has a rxed set of requirements in processor time, resources, and device operations needed for completion of its various segments. A worst case analysis of task performance is carried out. An algorithm is developed for determining the response times that can be guaranteed for a set of tasks. Operating system overhead is also accounted for.
Somatostatin analogues inhibit growth of pancreatic cancer by stimulating tyrosine phosphatase. (1989)

Several analogues of somatostatin were examined in the Mia PaCa-2 human pancreatic cancer cell line for their ability to promote tyrosine phosphatase activity affecting the receptors for the epidermal growth factor. The inhibition of growth of the Mia PaCa-2 cells in culture was also evaluated to determine the mechanism of action of somatostatin analogues and their relative effectiveness in inhibiting cancer growth. Of the analogues tested D-Phe-Cys-Tyr-D-Trp-Lys-Val-Cys-Trp-NH2 (RC-160) caused the greatest stimulation of tyrosine phosphatase activity. Analogue D-Phe-Cys-Tyr-D-Trp-Lys-Val-Cys-Thr-NH2 (RC-121) had less effect but was more potent than somatostatin-14. Analogue D-Phe-Cys-Phe-D-Trp-Lys-Thr-Cys-Thr(ol) (SMS 201-995) produced no significant dephosphorylation. The analogues displayed the same order of activity in assays on growth inhibition of Mia PaCa-2 cells in cultures. Analogue (SMS-201-995) caused virtually no tyrosine phosphatase stimulation or growth inhibition in this cancer cell line, although it possesses a much higher antisecretory activity than somatostatin-14 in normal tissues. These observations indicate that somatostatin and some of its analogues can act as growth inhibitors in cancer cells through the activation of tyrosine phosphatase. These data reinforce the view that somatostatin analogue RC-160 and related compounds could be used for treatment of pancreatic cancer.
The Effects of Physiological Stress on Tactile Communication (2006)

The researcher-constructed tactile display prototype has been used to conduct a variety of laboratory studies that have demonstrated positive results for tactile signaling and communication. This prototype display that uses precision tactors and skilled placement of them exhibits potential for superior reception of the vibration in the appropriate skin receptors. The purpose of this study was to determine if this prototype tactile display could still produce accurate reception of tactile localization and messaging under physiological stress. Results showed that USMA cadets running on a treadmill had almost error free performance, demonstrating that messaging and localization of tactile signals seemed to be unaffected by physiological arousal or stress.
Adenoviral Gene Transfer of FGF-5 to Hibernating Myocardium Improves Function and Stimulates Myocytes to Hypertrophy and Reenter the Cell Cycle (2005)

Fibroblast growth factors (FGFs) have diverse actions on the myocardium but the importance of stimulating angiogenesis versus direct effects of FGFs on cardiac myocytes is unclear. We used intracoronary injection of a replication-deficient adenoviral construct overexpressing FGF-5 (AdvFGF-5) to improve flow and function in swine with hibernating myocardium. Two-weeks after AdvFGF-5 (n=8), wall-thickening increased from 2.4+/-0.04 to 4.7+/-0.7 mm in hibernating LAD regions (P<0.05) whereas remote wall-thickening was unchanged (6.7+/-0.4 to 5.8+/-0.5 mm). This was associated with small increases in resting flow to dysfunctional myocardium, but flow during adenosine was unchanged (LAD 1.45+/-0.27 versus 1.46+/-0.23 mL/min per g and remote 4.84+/-0.23 versus 4.71+/-0.47 mL/min per g, P=NS). Unexpectedly, animals receiving AdvFGF-5 demonstrated a 29% increase in LV mass over the 2-week period (P<0.05 versus untreated animals with hibernating myocardium and normal shams). Histological analysis confirmed profound myocyte cellular hypertrophy in AdvFGF-5 treated myocardium (19.9+/-0.32 versus 15.2+/-0.92 microm in untreated, P<0.001). Myocytes in the proliferative phase of the cell cycle (Ki-67 staining) increased 7-fold after AdvFGF-5 (2,904+/-405 versus 409+/-233 per 10(6) myocyte nuclei in untreated, P<0.05). Myocyte nuclei in the mitotic phase (phosphorylated histone H3 staining) also increased after AdvFGF-5 (127+/-24 versus 35+/-13 per 10(6) myocyte nuclei in untreated, P<0.05). Thus, rather than angiogenesis, stimulation of hypertrophy and reentry of a small number of myocytes into the mitotic phase of the cell cycle are responsible for the effects of AdvFGF-5 on function. Although additional mechanisms may contribute to the improvement in wall-thickening, overexpression of AdvFGF-5 may afford a way to restore function in hibernating myocardium and ameliorate heart failure in chronic ischemic cardiomyopathy.
Hybrid memory cube (HMC) (2011)

This article consists of a collection of slides from the author's conference presentation on the special features, system design, system architectures; processing capabilities, and targeted markets for Micron's Hybrid Memory Cube (HMC).
Leucine Metabolism in the Black Bear (1987)

Ralph A. Nelson, James D. Jones, Leucine Metabolism in the Black Bear, Bears: Their Biology and Management, Vol. 7, A Selection of Papers from the Seventh International Conference on Bear Research and Management, Williamsburg, Virginia, USA, and Plitvice Lakes, Yugoslavia, February and March 1986 (1987), pp. 329-331
Determinants of Mg2+-Dependent Activities of Recombinant Human Immunodeficiency Virus Type 1 Integrase (2000)

The relationship between Mg(2+)-dependent activity and the self-assembly state of HIV-1 integrase was investigated using different protein preparations. The first preparations, IN(CHAPS) and IN(dial), were purified in the presence of detergent, but in the case of IN(dial), the detergent was removed during a final dialysis. The third preparation, IN(zn), was purified without any detergent. The three preparations displayed comparable Mn(2+)-dependent activities. In contrast, the Mg(2+)-dependent activity that reflects a more realistic view of the physiological activity strongly depended on the preparation. IN(CHAPS) was not capable of using Mg(2+) as a cofactor, whereas IN(zn) was highly active under the same conditions. In the accompanying paper [Deprez, E., et al. (2000) Biochemistry 39, 9275-9284], we used time-resolved fluorescence anisotropy to demonstrate that IN(CHAPS) was monomeric at the concentration of enzymatic assays. Here, we show that IN(zn) was homogeneously tetrameric under similar conditions. Moreover, IN(dial) that exhibited an intermediary Mg(2+)-dependent activity existed in a monomer-multimer equilibrium. The level of Mg(2+)- but not Mn(2+)-dependent activity of IN(dial) was altered by addition of detergent which plays a detrimental role in the maintenance of the oligomeric organization. Our results indicate that the ability of integrase to use Mg(2+) as a cofactor is related to its self-assembly state in solution, whereas Mn(2+)-dependent activity is not. Finally, the oligomeric IN(zn) was capable of binding efficiently to DNA regardless of the cationic cofactor, whereas the monomeric IN(CHAPS) strictly required Mn(2+). Thus, we propose that a specific conformation of integrase is a prerequisite for its binding to DNA in the presence of Mg(2+).