gebhart/patrepeval huggingface dataset:
Effective slip and friction reduction in nanograted superhydrophobic microchannels (2006)

Enabled by a technology to fabricate well-defined nanogrates over a large area (2×2cm2), we report the effect of such a surface, in both hydrophilic and hydrophobic conditions, on liquid slip and the corresponding friction reduction in microchannels. The grates are designed to be dense (∼230nm pitch) but deep (∼500nm) in order to sustain a large amount of air in the troughs when the grates are hydrophobic, even under pressurized liquid flow conditions (e.g., more than 1bar). A noticeable slip (i.e., slip length of 100–200nm, corresponding to 20%–30% reduction of pressure drop in a ∼3μm high channel) is observed for water flowing parallel over the hydrophobic nanogrates; this is believed to be an “effective” slip generated by the nanostrips of air in the grate troughs under the liquid. The effective slip is clearer and larger in flows parallel to the nanograting patterns than in transverse, suggesting that the nanograted superhydrophobic surfaces would not only reduce friction in liquid flows under pressure but also enable directional control of the slip. This paper is the first to use nanoscale grating patterns and to measure their effect on liquid flows in microchannels.
The evolution of interconnection technology at IBM (1995)

Advances in interconnection technology have played a key role in allowing continued improvements in integrated circuit density, performance, and cost. ibm contributions to interconnection technology over approximately the last ten generations of semiconductor products are reviewed. the development of a planar, back-end-of-line (beol) technology, used in ibm dram, bipolar, and cmos logic products since 1988, has led to a threefold increase in the number of wiring levels, aggressive wiring pitches at all interconnection levels, and high-leverage design options such as stacked contacts and vias. possible future beol technologies are also discussed, with emphasis on the use of higher-conductivity wiring and lower-dielectric-constant insulators. it is expected that their use will result in higher performance and reliability. applications include future, lower-power devices as well as more cost-effective, higher-performance versions of present-day designs.
Studies on Some New Indazole and Benzimidazole Derivatives (1966)

Abstract Alkylation of 5‐nitroindazole (I) with dimethyl sulphate and/or diethyl sulphate in presence of sodium hydroxide yields mixtures containing more 2‐alkylated than 1‐alkylated products. The action of diazomethane on 5‐nitro (I) and 6‐nitro‐indazole (IV) was investigated. Reduction of nitroindazoles with hydrogen on Pd/charcoal proceeds smoothly. The synthesis of several new benzimidazole and indazole dye intermediates is also described.
INTERACTION BETWEEN AIRGUNS* (1984)

A bstract In the design of linear airgun arrays the interaction between the airguns is usually neglected. We review the different formulae which have been proposed for the minimum separation between airguns at which the interaction is negligible. These formulae can all be approximated by a linear function of a single variable. We have analyzed a large number of measurements in order to establish the amount of interaction between two airguns of various volumes at different pressures and depths. The resulting far‐field signature has been measured and compared with the sum of the signatures from the two airguns measured in the same experimental situation. The changes in primary pulse amplitude, bubble period and primary/bubble peak‐to‐peak amplitude ratio were computed from the measurement data as a function of airgun separation, chamber volume, chamber pressure and airgun depth. The influence of a waveshape kit was investigated, and the effects of interaction and the effects of using a waveshape kit were compared.
Antigen Specificity of Serum Antibody in A. actinomycetemcomitans-infected Periodontitis Patients (1995)

We hypothesized that serum antibody with selected antigen specificities would relate to infection and disease in the patients and, thus, describe the characteristics of potential protective antibody. This study used serum samples from 24 periodontitis patients with subgingival infection and elevated serum IgG antibody to A. actinomycetemcomitans to define the antigenic specificities of IgG, IgM, IgA, and IgG1-4 antibody to A. actinomycetemcomitans strain Y4 outer membrane antigens (OMA). Uniform IgG antibody (> 70% of the patients) was noted to antigens with M(r) of 65, 38, 29, and 17 kDa. Both IgA and IgM specificities reflected those shown for IgG in each patient. IgG1 and IgG2 antibody reacted with several OMA bands in each patient, while IgG3 antibodies were directed to numerous OMA bands in many patients and represented the most broad-based response. The IgG4 response patterns were limited to a few OMA bands. We noted a prominent occurrence of IgG reactions with OMA bands that were characteristic for individual patients. The frequency of responses to OMA of higher M(r) (i.e., > 80 kDa) and to the 34-, 31-, and 24-kDa antigens was positively related to the total IgG antibody levels. Antibody reactive with OMA bands at 65-, 38-, 29-, 17-, 15-, and 11-kDa antigens was detected in patients with few to many teeth infected with A. actinomycetemcomitans. Furthermore, patients with a high percentage of teeth with > or = 6 mm pockets had a decreased frequency of responses to the high-M(r) antigens (i.e. > 90 kDa) as well as to the 58-kDa antigen.(ABSTRACT TRUNCATED AT 250 WORDS)
The systems biology markup language (SBML): a medium forrepresentation and exchange of biochemical network models (2003)

The specification of SBML Level 1 is freely available from http://www.sbml.org/
Insulin-stimulated Protein Kinase B Phosphorylation on Ser-473 Is Independent of Its Activity and Occurs through a Staurosporine-insensitive Kinase (2001)

Full activation of protein kinase B (PKB, also called Akt) requires phosphorylation on two regulatory sites, Thr-308 in the activation loop and Ser-473 in the hydrophobic C-terminal regulatory domain (numbering for PKB alpha/Akt-1). Although 3'-phosphoinositide-dependent protein kinase 1 (PDK1) has now been identified as the Thr-308 kinase, the mechanism of the Ser-473 phosphorylation remains controversial. As a step to further characterize the Ser-473 kinase, we examined the effects of a range of protein kinase inhibitors on the activation and phosphorylation of PKB. We found that staurosporine, a broad-specificity kinase inhibitor and inducer of cell apoptosis, attenuated PKB activation exclusively through the inhibition of Thr-308 phosphorylation, with Ser-473 phosphorylation unaffected. The increase in Thr-308 phosphorylation because of overexpression of PDK1 was also inhibited by staurosporine. We further show that staurosporine (CGP 39360) potently inhibited PDK1 activity in vitro with an IC(50) of approximately 0.22 microm. These data indicate that agonist-induced phosphorylation of Ser-473 of PKB is independent of PDK1 or PKB activity and occurs through a distinct Ser-473 kinase that is not inhibited by staurosporine. Moreover, our results suggest that inhibition of PKB signaling is involved in the proapoptotic action of staurosporine.
More on the sequencing of the human genome (2003)

The international Human Genome Project (HGP) and Celera Genomics published articles last year on the sequence of the human genome (1, 2). In a recent article (3), we analyzed aspects of the Celera article.
The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in  Arabidopsis (1997)

APETALA2 (AP2) plays an important role in the control of Arabidopsis flower and seed development and encodes a putative transcription factor that is distinguished by a novel DNA binding motif referred to as the AP2 domain. In this study we show that the AP2 domain containing or RAP2 (related to AP2) family of proteins is encoded by a minimum of 12 genes in Arabidopsis. The RAP2 genes encode two classes of proteins, AP2-like and EREBP-like, that are defined by the number of AP2 domains in each polypeptide as well as by two sequence motifs referred to as the YRG and RAYD elements that are located within each AP2 domain. RAP2 genes are differentially expressed in flower, leaf, inflorescence stem, and root. Moreover, the expression of at least three RAP2 genes in vegetative tissues are controlled by AP2. Thus, unlike other floral homeotic genes, AP2 is active during both reproductive and vegetative development.
A differential effect of C5a and C5a des Arg in the induction of pulmonary inflammation. (1980)

Earlier studies have shown that C5 fragments induce an inflammatory reaction when instilled into the rabbit lung. Because C5a is rapidly converted to C5a des Arg in vivo, experiments were performed to determine which fragment was most effective in producing pulmonary inflammation in this animal model. C5a des Arg consistently produced marked inflammation. This was characterized by neutrophil accumulation, edema, hemorrhage, fibrin formation, and damage to alveolar epithelium. The time course of the inflammatory reaction initiated by C5a des Arg showed pulmonary vascular sequestration of neutrophils with no intra-alveolar migration at 30 minutes after injection. By 2 hours, interstitial and alveolar neutrophils were numerous, with the accumulation of neutrophils in the alveoli increasing to a maximum at 6 hours. At 24 and 48 hours, the predominant cells were mononuclear (macrophages). By 120 hours, the lesions were resolving. In contrast, at all doses examined, a similar instillation of C5a induced either no inflammation or a milder, more focal response than C5a des Arg. This inability of C5a to initiate inflammation was not apparently due to the generation of inhibitors, since mixtures of C5a and C5a des Arg were phlogistic. A prolonged, intrapulmonary infusion of C5a (20 minutes), in contrast to a bolus instillation (1 minute), did initiate an inflammatory response, which may reflect the conversion of the C5a to C5a des Arg in the lung. This study points out the inflammatory potential of products of complement activation, particularly of the C5 fragment C5a des Arg, when applied to the airway side of the lungs. This inflammatory response raises the possibility that cleavage of intrapulmonary C5 may play an important role in the initiation of pulmonary inflammation.
Regulation of ZAP-70 Intracellular Localization: Visualization with the Green Fluorescent Protein (1997)

To investigate the cellular dynamics of ZAP-70, we have studied the distribution and regulation of its intracellular location using a ZAP-70 green fluorescent protein chimera. Initial experiments in epithelial cells indicated that ZAP-70 is diffusely located throughout the quiescent cell, and accumulates at the plasma membrane upon cellular activation, a phenotype enhanced by the coexpression of Lck and the initiation of ZAP-70 kinase activity. Subsequent studies in T cells confirmed this phenotype. Intriguingly, a large amount of ZAP-70, both chimeric and endogenous, resides in the nucleus of quiescent and activated cells. Nuclear ZAP-70 becomes tyrosine phosphorylated upon stimulation via the T cell receptor, indicating that it may have an important biologic function.
Electric Vehicle User Behavior Prediction Using Hybrid Kernel Density Estimator (2018)

This paper proposes a hybrid kernel density estimator (HKDE) that uses both Gaussian- and Diffusion-based KDE (GKDE and DKDE) to predict the stay duration and charging demand of electric vehicles (EVs), which are essential parameters for optimizing EV charging schedule. While DKDE has higher accuracy in general, GKDE tends to result in better estimation for users who charge the EV irregularly. Therefore, the HKDE evaluates and categorizes the charging pattern regularity of a user, and determines which KDE to use by a novelty detection method based on the user's historical data. The estimations are then applied to an optimal EV charging algorithm to minimize load variance in an EV charging infrastructure and reduce EV charging cost. Real data is used for the numerical simulation to show the effectiveness of the proposed approach for predicting EV user behavior and scheduling EV charging load.
The Chirality of the Cholesteric Phases of DNA and G-Wires: Its Connection to their Molecular Structures (2000)

While the handedness of the cholesteric phases formed by assembled guanosine derivatives (G-wires) follow the correlation right-handed helices-->right-handed cholesterics (left-handed -->left-handed), the cholesteric phase formed by B-DNA (right-handed helix) is left-handed. This apparent discrepancy is overcome by considering pitch (p) variations with temperature. Plots of p(-1) versus T(-1) have, in fact, the same trend (positive intercept and negative slope) in the case of right-handed G-wires and B-DNA, while for the left-handed G-wire of deoxyguanosine monophosphate (dGMP), the opposite behavior is observed (negative intercept and positive slope). Therefore, the relation between molecular handedness and cholesteric helicity cannot, in general, be assessed by using measurements based on a single temperature; hence the temperature variation of the cholesteric parameters should be investigated. In all cases there is no remarkable salt effect on the cholesteric parameters.
Asymmetric Synthesis of Tetrabenazine and Dihydrotetrabenazine (2009)

The enantioselective synthesis of (+)-tetrabenazine (TBZ) and (+)-dihydrotetrabenazine (DTBZ), agents of significant interest for therapeutic and molecular imaging applications, has been completed in 21% (TBZ) and 16% (DTBZ) overall yield and in >97% ee from the starting dihydroisoquinoline. The synthesis utilizes Sodeoka's palladium-catalyzed asymmetric malonate addition to set the initial stereocenter followed by a number of diastereoselective transformations to incorporate the remaining asymmetric centers.
The importance of dominant negative effects of amino acid side chain substitution in peptide-MHC molecule interactions and T cell recognition (1993)

Previous studies on the role of specific residues of the peptide or MHC molecule in Ag presentation have revealed the sensitivity of this complex system to even small changes in structure. In our study, we have analyzed the effect of amino acid substitution in a major CD4+ T cell determinant (T1) of HIV-1 gp160 on binding and recognition in the context of various E alpha E beta MHC class II molecules. Individual alanine substitutions at all but three positions had little or no negative effect on either MHC binding or recognition by a specific T hybridoma, whereas substitutions with larger side chains often diminished reactivity. A poly-alanine peptide containing only four of the original residues was an effective MHC class II binder and in vivo immunogen, although lacking the ability to stimulate the hybridoma. Replacement of a glutamic acid in T1 with alanine or a size-conservative, uncharged glutamine, but not a negatively charged aspartic acid produced a peptide at least 100-fold more potent than the parent peptide, indicating an inhibitory effect of the negative charge. Conversely, substitution of a glutamic acid for valine at position 29 in the floor of the peptide binding site of the E alpha E beta molecule decreased functional presentation of this peptide by more than 2 logs. However, these two effects of glutamic acid were not complementary and were mediated by distinct mechanisms, as the change in the peptide altered the extent of binding to class II, but the change in the MHC molecule decreased recognition without inhibiting peptide binding. Taken together, the data all suggest the conclusion that changes in side-chains of peptides and MHC molecules affect Ag presentation and T cell stimulation most often by introducing dominant negative or interfering groups that prevent or alter the pattern of binding events primarily mediated by a very limited number of other residues in the Ag or presenting molecule. These results have important implications for understanding the biochemistry of peptide-MHC-TCR interactions and for the possible design of vaccines both more potent and less subject to allele-specific limitations on immunogenicity.
Cardiac-Specific Overexpression of GLUT1 Prevents the Development of Heart Failure Attributable to Pressure Overload in Mice (2002)

We found that increasing insulin-independent glucose uptake and glycolysis in adult hearts does not compromise cardiac function. Furthermore, we demonstrate that increasing glucose utilization in hypertrophied hearts protects against contractile dysfunction and LV dilation after chronic pressure overload.
Amino Acid Residues in the Fusion Peptide Pocket Regulate the pH of Activation of the H5N1 Influenza Virus Hemagglutinin Protein (2009)

The receptor specificity and cleavability of the hemagglutinin (HA) protein have been shown to regulate influenza A virus transmissibility and pathogenicity, but little is known about how its pH of activation contributes to these important biological properties. To identify amino acid residues that regulate the acid stability of the HA protein of H5N1 influenza viruses, we performed a mutational analysis of the HA protein of the moderately pathogenic A/chicken/Vietnam/C58/04 (H5N1) virus. Nineteen HA proteins containing point mutations in the HA2 coiled-coil domain or in an HA1 histidine or basic patch were generated. Wild-type and mutant HA plasmids were transiently transfected in cell culture and analyzed for total protein expression, surface expression, cleavage efficiency, pH of fusion, and pH of conformational change. Four mutations to residues in the fusion peptide pocket, Y23H and H24Q in the HA1 subunit and E105K and N114K in the HA2 subunit, and a K58I mutation in the HA2 coiled-coil domain significantly altered the pH of activation of the H5 HA protein. In some cases, the magnitude and direction of changes of individual mutations in the H5 HA protein differed considerably from similar mutations in other influenza A virus HA subtypes. Introduction of Y23H, H24Q, K58I, and N114K mutations into recombinant viruses resulted in virus-expressed HA proteins with similar shifts in the pH of fusion. Overall, the data show that residues comprising the fusion peptide pocket are important in triggering pH-dependent activation of the H5 HA protein.
Isolation and characterization of cells from rat adipose tissue developing into adipocytes. (1978)

To identify cells developing into adipocytes by accumulation of triglyceride, rat epididymal fat pad cells from small rats were exposed to (3)H-labeled chylomicron fatty acids in vivo and then liberated with collagenase. Tissue remnants were removed by filtration and mature fat cells by flotation. Aggregating cells were then removed by filtration through a 25- micro m nylon screen. Further purification of cells labeled in vivo was obtained by removing floating cells from those adhering to the bottom of a culture dish. The adhering cells multiplied to a confluent monolayer when cultured in Medium 199 containing serum, glucose, insulin, and a triglyceride emulsion. The cells then gradually enlarged due to granulation of the cytoplasm by a lipid-staining material. After about 2 weeks these granules had coalesced forming mature adipocytes of typical signet-ring appearance. Free adipocytes could then be recovered from the cultures by collagenase treatment. After about 2 weeks of culture these cells had the same size (about 30 micro m) as adipocytes recovered in the original collagenase preparation of the rat epididymal fat pad. They contained triglyceride lipase activity and incorporated glucose into triglycerides to the same extent as cells developed in vivo but had higher lipoprotein lipase activity. In vitro, heparin in a low concentration, prostaglandin E(1), isobutylmethylxanthine, and cholera toxin markedly promoted the development of these cells into adipocytes. This could be shown to occur almost completely indicating that this fraction of cells was homogeneous and consisted of cells with the capacity to form adipocytes. The duplication time was about 2 days and did not change with subculturing. Preadipocytes could be obtained by density gradient centrifugation, isolating triglyceride-containing cells either directly from the pad or after 3 days in culture. All of these cells developed into adipocytes as described above but did not multiply as readily. It was concluded that cells from the epididymal fat pad from small rats can be isolated in a homogenous fraction that develops in culture into cells of identical morphology and function as adipocytes formed in vivo. The differentiation of these cells into adipocytes may be manipulated in vitro.
Mobile Terminated SMS Billing &amp;#8212; Exploits and Security Analysis (2006)

This paper analyses mobile terminated (MT) SMS billing, an area of mobile commerce which has undergone massive growth with the maturation of mobile content delivery on 2.5G mobile networks. Although the short message service for GSM devices was never designed to be a facilitator for micropayments, premium SMS services have been embraced by many network operators worldwide. We investigate its inherent insecurity as a payment solution and show how existing systems can be used for fraud or to deceive users. From a UK perspective, we see how the standardisation of mobile platforms with J2ME combined with WAP delivery have enabled the rise of the mobile content industry, with premium SMS as the most method common of billing. Threats to the established business models are addressed, with particular attention paid to the potential for severe disruption from mobile (SMS) spam. Furthermore, we present attacks on MT SMS systems, showing how a malicious attacker could damage the mobile content industry by undermining consumer confidence in premium rate SMS payment solutions
Novel developments with selective, non-peptidic kappa-opioid receptor agonists (1997)

Despite the recent introduction of a number of new compounds, there has of late been a cooling of interest by pharmaceutical companies in the development of centrally-active, selective kappa opioid agonists for therapeutic purposes. This is reflected in the discontinuation of a number of clinical trials, for reasons that are often not completely clear to outside observers. Spiradoline and enadoline have apparently been abandoned as potential analgesics because they induce dose-limiting central side-effects (i.e., dysphoria) in models of post-surgical pain. The development of niravoline as an aquaretic for the treatment of cirrhosis with ascites and other hyponatraemic disorders has also been halted. Enadoline may yet find some application against ischaemic stroke and severe head injury, presumably in comatose patients in whom psychiatric side-effects are taken to be immaterial, while apadoline and TRK 820 remain in Phase II clinical testing against cancer pain. The peripherally-selective kappa agonists, asimadoline, and the atypical compound, fedotozine, are well-tolerated in man. Results of Phase III trials of fedotozine against irritable bowel syndrome and dyspepsia have, however, ultimately been disappointing, whereas asimadoline is currently in Phase II clinical trials against pain of rheumatic and osteoarthritic origin. The results of these trials are eagerly awaited.