gebhart/patrepeval huggingface dataset:
FinFET design considerations based on 3-D simulation and analytical modeling (2002)

Design considerations of the FinFET have been investigated by three-dimensional (3-D) simulation and analytical modeling in this paper. Short-channel effects (SCE) of the FinFET can be reasonably controlled by reducing either silicon fin height or fin thickness. Analytical solution of 3-D Laplace's equation is employed to establish the design equations for the subthreshold behavior in the fully depleted silicon fins. Based on the 3-D analytical electrostatic potential in the subthreshold region, the threshold voltage (V/sub th/) roll-off and the subthreshold swing (S) are estimated by considering the source barrier changes in the most leaky channel path. V/sub th/ roll-off is an exponential function of the ratio of effective channel length to drain potential decay length, which can then be expressed as a function of the fin thickness, the fin height and the gate oxide thickness. The drain-potential decay lengths of single-gate fully depleted SOI MOSFET (FDFET), double-gate MOSFET (DGFET), rectangular surrounding-gate MOSFET (SGFET), and FinFET are compared. The drain potential scaling length and V/sub th/ roll-off can be included into a universal relation for convenient comparison.
Cooperative Conservation - Interagency Volunteer Program Quarterly Progress Report: Period Ending September 30, 2004 (2004)

Collaboration with Interagency Team\nAlthough the task agreement formally commenced June 30, 2004, the agreement was not fully executed by both parties until July 29, 2004. In the first three months of this agreement, UNLV representatives have met with or communicated via email with the Interagency Volunteer Team on numerous occasions. At the first meeting on July 13, 2004, Government Technical Representative Bobbie Antonich and UNLV Public Lands Initiative Director Nancy Flagg met with the interagency team to discuss the overall goals for the Interagency Volunteer Program (IVP). The team was brought up-to-date on the status of the task agreement, UNLV’s role in fulfilling the agreement, and provided with a draft position announcement for review and comment. Final feedback was received from the Interagency Team via e-mail prior to the posting of the announcement. At the July 13 meeting, team lead Nancy Bernard of the National Park Service noted that it would be ideal to have a new data system in place by the start of the October 1 fiscal year. Another goal noted was to have volunteer events planned on an annual basis. The team also discussed UNLV’s proposal to hire an interim project coordinator while a search for a permanent project manager is ongoing.
Anandamide Amidohydrolase Activity in Rat Brain Microsomes (1995)

An amidohydrolase activity present in rat brain microsomes catalyzes the hydrolysis of N-arachidonoyl-[3H]ethanolamine ([3H]anandamide), an endogenous cannabimimetic substance, forming [3H]ethanolamine and arachidonic acid. Amidohydrolase activity is maximal at pH 6 and 8, is independent of divalent cations, has an apparent Km for [3H]anandamide of 12.7 +/- 1.8 microM, and has a Vmax of 5630 +/- 200 pmol/min/mg of protein. Phenylmethylsulfonyl fluoride, a serine protease inhibitor, and p-bromophenacyl bromide, a histidine-alkylating reagent, inhibit the activity, whereas N-ethylmaleimide and various nonselective peptidase inhibitors (EDTA, o-phenanthroline, bacitracin) have no effect. Brain amidohydrolase activity exhibits high substrate specificity for [3H]anandamide; N-gamma-linolenoyl-, N-homo-gamma-linolenoyl-, and N-11,14-eicosadienoyl- are hydrolyzed at markedly slower rates. Moreover, N-11-eicosaenoyl- and N-palmitoyl-[3H]ethanolamine are not hydrolyzed. [3H]Anandamide hydrolysis is inhibited competitively by nonradioactive anandamide and by other N-acylethanolamines with the following rank order of potency: anandamide > N-linoleoyl- = N-cis-linolenoyl- = N-gamma-linolenoyl- = N- homo-gamma-linolenoyl- > N-11,14-eicosadienoyl- > N-oleoyl- > N- docosahexaenoyl- > N-docosatetraenoyl > N-linoelaidoyl- > N-eicosaenoyl- > N- palmitoyl > or = N-elaidoyl- = N-eicosanoyl-ethanolamine = no effect. Amidohydrolase activity is high in liver and brain and low in heart, kidney, intestine, stomach, lung, spleen, and skeletal muscle. Within the central nervous system, highest activity is found in globus pallidus and hippocampus, two regions rich in cannabinoid receptors, and lowest activity is found in brainstem and medulla, where cannabinoid receptors are sparse. The results, showing that brain amidohydrolase activity is selective for anandamide and enriched in areas of the central nervous system with high density of cannabinoid receptors, suggest that this activity may participate in the inactivation of anandamide at its sites of action.
Involvement of the YneS/YgiH and PlsX proteins in phospholipid biosynthesis in both Bacillus subtilis and Escherichia coli (2007)

Both plsX and yneS are essential for 1-acyl-G3P synthesis in B. subtilis, in agreement with recent reports on their biochemical functions. In E. coli, PlsB plays a principal role in 1-acyl-G3P synthesis and is also essential for bacterial growth. PlsX and YgiH also, however, play important roles in E. coli growth, possibly by regulating the intracellular concentration of acyl-ACP. These proteins are therefore important targets for development of new antibacterial agents.
Design, expression, and renaturation of a lesion-targeted recombinant epidermal growth factor-von Willebrand factor fusion protein: efficacy in an animal model of experimental colitis. (2000)

In the present study, the mature epidermal growth factor (EGF) protein was engineered to incorporate a high affinity collagen-binding domain (CBD) derived from co-agulation von Willebrand factor, to specifically target EGF to colonic lesions. The fusion protein was expressed in an E. coli bacterial expression system, purified by metal chelate chromatography, and renatured by oxidative refolding into a soluble biologically active growth factor. The EGF-CBD fusion protein bound tightly to collagen matrices under conditions in which native non-targeted EGF was washed away. In biologic assays, the EGF-CBD fusion protein stimulated NIH3T3 cell proliferation with near wild-type biological activity. In vivo binding studies showed that the collagen-targeted EGF, but not the non-targeted EGF, accumulated at areas of exposed collagen on the luminal surface of the inflamed colon. Finally, a single colonic instillation of the collagen-targeted EGF-induced a more rapid regeneration of intestinal crypts 24 h after treatment (no. of crypts = 89.2+/-8.1) compared to the non-targeted EGF (no. of crypts = 52.2+/-29.8; p=0.027), and the PBS control (no. of crypts = 24. 0+/-22.9; p=0.001). Taken together, these findings indicate that intracolonic delivery of collagen-targeted EGF represents a potentially effective therapeutic strategy for acute or chronic inflammatory bowel disease.
Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation (2005)

Diverse point mutations in the enzyme Cu, Zn superoxide dismutase (SOD1) are linked to its aggregation in the familial form of the disease amyotrophic lateral sclerosis. The disease-associated mutations are known to destabilize the protein, but the structural basis of the aggregation of the destabilized protein and the structure of aggregates are not well understood. Here, we investigate in silico the sequence and structural determinants of SOD1 aggregation: (1) We identify sequence fragments in SOD1 that have a high aggregation propensity, using only the sequence of SOD1, and (2) we perform molecular dynamics simulations of the SOD1 dimer folding and misfolding. In both cases, we identify identical regions of the protein as having high propensity to form intermolecular interactions. These regions correspond to the N- and C-termini, and two crossover loops and two beta-strands in the Greek-key native fold of SOD1. Our results suggest that the high aggregation propensity of mutant SOD1 may result from a synergy of two factors: the presence of highly amyloidogenic sequence fragments ("hot spots"), and the presence of these fragments in regions of the protein that are structurally most likely to form intermolecular contacts under destabilizing conditions. Therefore, we postulate that the balance between the self-association of aggregation-prone sequences and the specific structural context of these sequences in the native state determines the aggregation propensity of proteins.
MCAM is a novel metastasis marker and regulates spreading, apoptosis and invasion of ovarian cancer cells (2012)

Melanoma cell adhesion molecule (MCAM) is a cell adhesion molecule that is abnormally expressed in a variety of tumours and is closely associated with tumour metastasis. The role of MCAM in ovarian cancer development has not been fully studied. In this study, through immunohistochemical staining of ovarian cancer tissue samples and RNA interference to silence MCAM in ovarian cancer cells, we examined the impact of MCAM on the biological functions of ovarian cancer cells and attempted to reveal the role of MCAM in ovarian cancer development. Our results showed that MCAM expression was particularly high in metastatic ovarian cancers compared with other pathological types of ovarian epithelial tissues. After MCAM silencing in the MCAM high-expression ovarian cancer cell line SKOV-3, the cell apoptosis was increased, whereas the cell spreading and invasion were significantly reduced, which may be related with dysregulation of small RhoGTPase (RhoA and Cdc42).These results suggest that MCAM expression in ovarian cancer is highly correlated with the metastatic potential of the cancer. MCAM is likely to participate in the regulation of the Rho signalling pathway to protect ovarian cancer cells from apoptosis and promote their malignant invasion and metastasis. Therefore, MCAM can be used not only as a molecular marker to determine the prognosis of ovarian cancer but also as a therapeutic target in metastatic ovarian cancer.
Dextromethorphan reduces neocortical ischemic neuronal damage in vivo (1988)

The dextrorotatory morphinan dextromethorphan (DM), a clinically tested antagonist of the N-methyl-D-aspartate (NMDA) receptor-channel complex, was tested in an in vivo model of acute transient focal cerebral ischemia. Rabbits were randomly assigned to pretreatment with a 20 mg/kg i.v. bolus followed by 10 mg/kg/h of 0.4% DM in normal saline (NS), or with an equivalent volume of NS alone. They then underwent 1 h occlusion of the left internal carotid artery an anterior cerebral artery followed by 4 h of reperfusion. DM-treated animals showed a significant decrease in the percentage of severe neocortical ischemic neuronal damage (10.5%), as compared to NS-treated animals (49.6%).
Oxygen-Independent Alkane Formation by Non-Heme Iron-Dependent Cyanobacterial Aldehyde Decarbonylase: Investigation of Kinetics and Requirement for an External Electron Donor (2011)

Cyanobacterial aldehyde decarbonylase (cAD) is, structurally, a member of the di-iron carboxylate family of oxygenases. We previously reported that cAD from Prochlorococcus marinus catalyzes the unusual hydrolysis of aldehydes to produce alkanes and formate in a reaction that requires an external reducing system but does not require oxygen [Das et al. (2011) Angew. Chem. 50, 7148-7152]. Here we demonstrate that cADs from divergent cyanobacterial classes, including the enzyme from N. puntiformes that was reported to be oxygen dependent, catalyze aldehyde decarbonylation at a much faster rate under anaerobic conditions and that the oxygen in formate derives from water. The very low activity (<1 turnover/h) of cAD appears to result from inhibition by the ferredoxin reducing system used in the assay and the low solubility of the substrate. Replacing ferredoxin with the electron mediator phenazine methosulfate allowed the enzyme to function with various chemical reductants, with NADH giving the highest activity. NADH is not consumed during turnover, in accord with the proposed catalytic role for the reducing system in the reaction. With octadecanal, a burst phase of product formation, k(prod) = 3.4 ± 0.5 min(-1), is observed, indicating that chemistry is not rate-determining under the conditions of the assay. With the more soluble substrate, heptanal, k(cat) = 0.17 ± 0.01 min(-1) and no burst phase is observed, suggesting that a chemical step is limiting in the reaction of this substrate.
Self-Association and Complexation of the Anti-Cancer Drug Doxorubicin with PEGylated Hyperbranched Polyesters in an Aqueous Environment (2013)

Fully atomistic molecular dynamics simulations were employed in order to examine in detail the self-assembly characteristics and the complexation behavior of the anticancer drug doxorubicin with PEGylated hyperbranched polyesters in an aqueous environment. We have examined two variants of the polymeric compound by altering the length of the hydrophilic poly(ethylene glycol) arms attached to the hydrophobic hyperbranched core. By comparing the clustering properties of the drug molecules in a polymer-free system to those in the polymer-containing models, we were able to assess the effects related to the presence and to the structural features of the polymer moiety. In addition, we have distinguished the effects associated with the neutral and protonated drug molecules separately. It was found that, in the presence of the polymeric material, the drug molecules formed clusters preferentially close to the polymer's periphery, the characteristics of which depended on the structural details of the polymeric host and on the charge of the drug molecules. Hydrogen bonding was found to contribute to the polymer/drug complexation, with the nature of the prevailing donor/acceptor pairs depending on the charge of the drug. Dynamic analysis of the drugs' motion revealed that in the polymer-containing systems the drug molecules experienced a larger degree of confinement within the formed clusters compared to that describing their polymer-free analogues, while the structural coherence of the clusters was found to be more persistent in the system with the larger poly(ethylene glycol) arms. The results described in this work, through the monitoring of both static and dynamic aspects of the self-association and the complexation behavior of the neutral and charged molecules of doxorubicin with the polymeric host, may help toward the elucidation of the key parameters that are involved in the formation of effective polymer-based carriers for drug molecules of the anthracycline family used in cancer chemotherapy.
Poly(m-aminobenzene sulfonic acid) functionalized single-walled carbon nanotubes based gas sensor (2007)

We have demonstrated a NH3, NO2 and water vapour sensor based on poly(m-aminobenzene sulfonic acid) functionalized single-walled carbon nanotube (SWNT–PABS) networks. The SWNT–PABS based sensors were fabricated by simple dispersion of SWNT–PABS on top of pre-fabricated gold electrodes. SWNT–PABS sensors showed excellent sensitivity with ppbv level detection limits (i.e., 100 ppbv for NH3 and 20 ppbv for NO2) at room temperature. The response time was short and the response was totally reversible. The sensitivity could be tuned by adjusting the sensor initial resistance. The sensors were also suitable for monitoring relative humidity in air.
Elevated Carbon Dioxide Improves Plant Iron Nutrition through Enhancing the Iron-Deficiency-Induced Responses under Iron-Limited Conditions in Tomato (2009)

The increases in atmospheric carbon dioxide (CO(2)) concentrations can enhance plant growth and change their nutrient demands. We report that when tomato (Lycopersicon esculentum 'Zheza 809') plants were grown in iron (Fe)-limited medium (with hydrous ferric iron oxide) and elevated CO(2) (800 microL L(-1)), their biomass and root-to-shoot ratio were greater than plants grown in ambient CO(2) (350 microL L(-1)). Furthermore, the associated increase in Fe concentrations in the shoots and roots alleviated Fe-deficiency-induced chlorosis. Despite the improved nutrient status of plants grown in Fe-limited medium under elevated CO(2), the Fe-deficiency-induced responses in roots, including ferric chelate reductase activity, proton secretion, subapical root hair development, and the expression of FER, FRO1, and IRT genes, were all greater than plants grown in the ambient CO(2). The biomass of plants grown in Fe-sufficient medium was also increased by the elevated CO(2) treatment, but changes in tissue Fe concentrations and Fe deficiency responses were not observed. These results suggest that the improved Fe nutrition and induction of Fe-deficient-induced responses in plants grown in Fe-limited medium under elevated CO(2) are caused by interactions between elevated CO(2) and Fe deprivation. Elevated CO(2) also increased the nitric oxide (NO) levels in roots, but treatment with the NO scavenger cPTIO inhibited ferric chelate reductase activity and prevented the accumulation of LeFRO1, LeIRT1, and FER transcripts in roots of the Fe-limited plants. These results implicate some involvement of NO in enhancing Fe-deficiency-induced responses when Fe limitation and elevated CO(2) occur together. We propose that the combination of elevated CO(2) and Fe limitation induces morphological, physiological, and molecular responses that enhance the capacity for plants to access and utilize Fe from sparingly soluble sources, such as Fe(III)-oxide.
Alzheimer's Disease: Role of Aging in Pathogenesis (2002)

Alzheimer's disease (AD) is characterized by intraneuronal fibrillary tangles, plaques, and cell loss. Brain lesions in both sporadic AD (SAD) and familial AD (FAD) are the same, and in the same distribution pattern, as those in individuals with Down syndrome (DS) and in smaller numbers in nondemented older individuals. Dementia onset is around 40 years for DS, 40-60 years for FAD, and usually over 60 years for SAD. The different categories of AD may be due to processes that augment to different degrees the innate cellular aging rate, that is, mitochondrial superoxide radical (SO) formation. Thus, they increase the rate of accumulation of AD lesions. This lowers the age of onset into the dementia ranges associated with DS, FAD, and SAD, and concomitantly shortens life spans. Faster aging lowers AD onset age by decreasing the onset age for neurofibrillary tangle formation and neuronal loss, and the age when brain intercellular H2O2 can activate microglial cells. The early AD onset in DS is attributed to a defective mitochondrial complex 1. The proteins associated with FAD and their normal counterparts undergo proteolytic processing in the endoplasmic reticulum (ER). The mutated compounds increase the ratio of betaA42 to betaA40 and likely also down-regulate the ER calcium (Ca2+) buffering activity. Decreases in ER Ca2+ content should increase the mitochondrial Ca2+ pool, thus enhancing SO formation. SAD may be due to increased SO formation caused by mutations in the approximately 1000 genes involved in mitochondrial biogenesis and function. The hypothesis suggests measures to prevent and treat.
Extracellular Protons Both Increase the Activity and Reduce the Conductance of Capsaicin- Gated Channels (2000)

Capsaicin evokes a membrane current in trigeminal ganglion neurons that is increased substantially in a moderately acidic extracellular environment. Using excised outside-out membrane patches, we studied the mechanism by which protons enhance the sustained response to capsaicin. In the absence of capsaicin, extracellular exposure to a moderately acidic physiological solution (pH 6.6) did not result in sustained channel openings in any capsaicin-sensitive outside-out patches. When co-applied with capsaicin, the acidic extracellular solution greatly increased the probability of capsaicin-gated channels being in the open state. In addition, acidic extracellular solution appeared to increase the number of channels available to be opened by capsaicin. The amplitude of the unitary currents was reduced by the acidic extracellular solution. These results show that the proton enhancement of the capsaicin-evoked whole-cell excitatory current is attributable to proton-receptive site(s) causing a marked increase in the activity of capsaicin-gated channels.
Nanometer-size hard magnetic ferrite exhibiting high optical-transparency and nonlinear optical-magnetoelectric effect (2015)

Development of nanometer-sized magnetic particles exhibiting a large coercive field (Hc) is in high demand for densification of magnetic recording. Herein, we report a single-nanosize (i.e., less than ten nanometers across) hard magnetic ferrite. This magnetic ferrite is composed of ε-Fe2O3, with a sufficiently high Hc value for magnetic recording systems and a remarkably high magnetic anisotropy constant of 7.7 × 10(6) erg cm(-3). For example, 8.2-nm nanoparticles have an Hc value of 5.2 kOe at room temperature. A colloidal solution of these nanoparticles possesses a light orange color due to a wide band gap of 2.9 eV (430 nm), indicating a possibility of transparent magnetic pigments. Additionally, we have observed magnetization-induced second harmonic generation (MSHG). The nonlinear optical-magnetoelectric effect of the present polar magnetic nanocrystal was quite strong. These findings have been demonstrated in a simple iron oxide, which is highly significant from the viewpoints of economic cost and mass production.
A new look at hardware maze routing (2002)

This paper describes a new design for a hardware accelerator to support grid-based Maze Routing. Based on the direct mapped approach of Breuer and Shamsa [3], this work refines their design to substantially reduce the hardware requirements of each processing element while at the same time adding support for mulitilayer routing and fast iterative routing. An RTL implementation has been developed for this design in VHDL, and initial results show promise for its realization using ASIC, custom, or FPGA technology.
Discovering and predicting user routines by differential analysis of social network traces (2013)

The study of human activity patterns traditionally relies on the continuous tracking of user location. We approach the problem of activity pattern discovery from a new perspective which is rapidly gaining attention. Instead of actively sampling increasing volumes of sensor data, we explore the participatory sensing potential of multiple mobile social networks, on which users often disclose information about their location and the venues they visit. In this paper, we present automated techniques for filtering, aggregating, and processing combined social networking traces with the goal of extracting descriptions of regularly-occurring user activities, which we refer to as “user routines”. We report our findings based on two localized data sets about a single pool of users: the former contains public geotagged Twitter messages, the latter Foursquare check-ins that provide us with meaningful venue information about the locations we observe. We analyze and combine the two datasets to highlight their properties and show how the emergent features can enhance our understanding of users' daily schedule. Finally, we evaluate and discuss the potential of routine descriptions for predicting future user activity and location.
Expression of the Mouse Dihydrofolate Reductase Complementary Deoxyribonucleic Acid in Simian Virus 40 Vectors (1981)

A mouse complementary deoxyribonucleic acid segment coding for the enzyme dihydrofolate reductase has been cloned in two general classes of vectors containing simian virus 40 deoxyribonucleic acid: (i) those that can be propagated as virions in permissive cells and (ii) those that can be introduced into and maintained stably in various mammalian cells. Both types of vectors express the mouse dihydrofolate reductase by using signals supplied by simian virus 40 deoxyribonucleic acid sequences. Moreover, plasmid vectors carrying the complementary deoxyribonucleic acid segment can complement Chinese hamster ovary cells lacking dihydrofolate reductase.