gebhart/patrepeval huggingface dataset:
Physics and chemistry of silicon wafer bonding investigated by infrared absorption spectroscopy (1996)

Silicon wafer bonding is achieved by joining two particle-free silicon wafers and annealing to elevated temperatures (∼1100 °C). We have used multiple internal transmission infrared absorption spectroscopy to probe the interface between the wafers upon initial joining and also during subsequent annealing steps. For atomically flat hydrophobic wafers (H passivated), we observe a pronounced shift in the Si–H stretching frequency due to the physical interaction (van der Waals attraction) that occurs when the surfaces come into intimate contact. The hydrogen eventually disappears at high temperatures (1000 °C) and Si–Si bonds are formed between the two surfaces. For hydrophilic wafers (oxide passivated), we initially observe three to five monolayers of water at the interface (providing the initial attraction through H bonding), as well as the presence of hydroxyl groups that terminate the oxide at low temperature. Upon moderate heating (&amp;lt;400 °C), the water trapped at the interface dissociates and leads to the formation of additional oxide. Between 400 and 800 °C, the hydroxyl groups disappear, resulting in a corresponding increase in oxide and the formation of Si–O–Si bridging linkages across the two surfaces.
Comparative analysis of the structures of the outer membrane protein P1 genes from major clones of Haemophilus influenzae type b (1989)

P1 outer membrane proteins from Haemophilus influenzae type b are heterogeneous antigenically and with respect to apparent molecular weight in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. For determination of the molecular basis for the differences in the P1 proteins, the genes for the P1 proteins from strain 1613, representative of outer membrane protein subtype 3L, and strain 8358, representative of outer membrane protein subtype 6U, were cloned, sequenced, and compared with the previously reported gene for the P1 protein from strain MinnA, a strain with the outer membrane protein subtype 1H. These prototype strains are representatives of the three major clonal families of H. influenzae type b responsible for invasive disease in diverse areas of the world. The nucleotide sequences of the P1 genes from strains 1613 and 8358 were 94 and 90% identical to the MinnA sequence, respectively. The derived amino acid sequences were 91 and 86% identical, respectively. Heterogeneity between the MinnA and 1613 proteins was largely localized to two short variable regions; the protein from strain 8538 contained a third variable region not observed in the other P1 proteins. Thus, the outer membrane protein P1 genes are highly conserved; the variable regions may code for the previously demonstrated strain-specific antigenic determinants.
The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome (2012)

Drosophila melanogaster now has the most extensive genomic deletion coverage and breakpoint subdivision as well as the most comprehensive inventory of haploinsufficient genes of any multicellular organism. The improved selection of chromosomal deletion strains will be useful to nearly all Drosophila researchers.
Using a CMOS camera sensor for visible light communication (2012)

In this paper, a novel scheme for data reception in a mobile phone using visible light communications (VLC) is proposed. The camera of the smartphone is used as a receiver in order to capture the continuous changes in state (on-off) of the light, which are invisible to the human eye. The information is captured in the camera in the form of light and dark bands which are then decoded by the smartphone and the received message is displayed. By exploiting the rolling shutter effect of CMOS sensors, a data rate much higher than the camera frame rate is achieved.
Interleukin-1 receptor antagonist haplotype associated with prostate cancer risk (2005)

IL1-RN is an important anti-inflammatory cytokine that modulate the inflammation response by binding to IL1 receptors, and as a consequence inhibits the action of proinflammatory cytokines IL1alpha and IL1beta. In this study, we hypothesise that sequence variants in the IL1-RN gene are associated with prostate cancer risk. The study population, a population-based case-control study in Sweden, consisted of 1383 prostate cancer case patients and 779 control subjects. We first selected 18 sequence variants covering the IL1-RN gene and genotyped these single-nucleotide polymorphisms (SNPs) in 96 control subjects. Gene-specific haplotypes of IL1-RN were constructed and four haplotype-tagging single-nucleotide polymorphisms (htSNPs) were identified (rs878972, rs315934, rs3087263 and rs315951) that could uniquely describe >95% of the haplotypes. All study subjects were genotyped for the four htSNPs. No significant difference in genotype frequencies between cases and controls were observed for any of the four SNPs based on a multiplicative genetic model. Overall there was no significant difference in haplotype frequencies between cases and controls; however, the prevalence of the most common haplotype (ATGC) was significantly higher among cases (38.7%) compared to controls (33.5%) (haplotype-specific P = 0.009). Evaluation of the prostate cancer risk associated with carrying the 'ATGC' haplotype revealed that homozygous carriers were at significantly increased risk (odds ratio (OR) = 1.6, 95% confidence interval (CI) = 1.2-2.2), compared to noncarriers, while no significant association was found among subjects heterozygous for the haplotype (OR = 1.0, 95% CI = 0.8-1.2). Restricting analyses to advanced prostate cancer strengthened the association between the 'ATGC' haplotype and disease risk (OR for homozygous carriers vs noncarriers 1.8, 95% CI = 1.3-2.5). In conclusion, the results from this study support the hypothesis that inflammation has a role of in the development of prostate cancer, but further studies are needed to identify the causal variants in this region and to elucidate the biological mechanism for this association.
Stochastic functional fourier series, Volterra series, and nonlinear systems analysis (1979)

A functional Fourier series is developed with emphasis on applications to the nonlinear systems analysis. In analogy to Fourier coefficients, Fourier kernels are introduced and can be determined through a cross correlation between the output and the orthogonal basis function of the stochastic input. This applies for the class of strict-sense stationary white inputs, except for a singularity problem incurred with inputs distributed at quantized levels. The input may be correlated if it is zero-mean Gaussian. The Wiener expansion is treated as an example corresponding to the white Gaussian input and this modifies the Lee-Schetzen algorithm for Wiener kernel estimation conceptually and computationally. The Poisson-distributed white input is dealt with as another example. Possible links between the Fourier and Volterra series expansions are investigated. A mutual relationship between the Wiener and Volterra kernels is presented for a subclass of analytic nonlinear systems. Connections to the Cameron-Martin expansion are examined as well The analysis suggests precautions in the interpretation of Wiener kernel data from white-noise identification experiments.
Gene transfer of endothelial nitric oxide synthase but not Cu/Zn superoxide dismutase restores nitric oxide availability in the SHRSP (2000)

Objective: Previous studies from our group have shown a deficit in nitric oxide (NO) bioavailability and an excess production of the 2 superoxide anion (O ) in the stroke prone spontaneously hypertensive rat (SHRSP) compared to the normotensive Wistar Kyoto (WKY) 2 strain. This present study has investigated whether adenoviral-mediated gene transfer of human eNOS or Cu / ZnSOD can alter the 2 NO / O balance, thereby improving endothelial function. Methods: A recombinant adenovirus, Ad / Hu / eNOS, containing the human 2 eNOS cDNA fragment was generated by homologous recombination in 293 cells. Ad / Hu / eNOS or Ad / Cu / ZnSOD was delivered into 9 1 0
Twenty years of antibiotic sensitivity testing of dental infections. Part 2. A review, 1966–1986 (1988)

Abstract A review spanning the years 1966–1986 has been made of the bacteria isolated from pyogenic dental infections and their antibiotic sensitivity patterns. Changes in the type of bacteria isolated from these infections and their antibiotic sensitivities have been identified. Antibiotic regimens aimed at reducing the emergence of antibiotic resistant bacteria have been suggested.
Characterization of the Receptors for Peptide-YY and Avian Pancreatic Polypeptide in Chicken and Pig Brains* (1990)

We have previously identified the peptide-YY (PYY) receptor on porcine brain membranes as a 50-kDa protein after chemical cross-linking. PYY receptors are discretely distributed in the brain of various mammals, to which neuropeptide-Y (NPY), but not pancreatic polypeptide (PP), bind with great specificity. The present study was carried out in order 1) to identify and characterize the PYY receptor in the avian brain, 2) to compare it with the APP receptor that had been demonstrated in the cerebellum, and 3) to examine [125I]APP-binding activity in the porcine brain. [125I]PYY was bound to chicken brain membranes via high affinity (Kd = 2.19 x 10(-10) M) and low affinity (Kd = 1.93 x 10(-7) M) components. The binding sites were highly specific for PYY and APP as well as for NPY and PPP, coupled to a guanine nucleotide regulatory protein, and distributed in various brain areas, including the cerebellum. The C-terminal fragments of PYY, PYY-(17-36) and PYY-(24-36), exhibited low potency in inhibiting binding, but behaved like full agonists. Porcine brain membranes, on the other hand, possessed two orders of the APP-binding sites, a high affinity component (Kd = 4.24 x 10(-9) M) and a low affinity component (Kd = 3.08 x 10(-7) M). APP binding showed a high specificity for APP, but not for PPP, NPY, or PYY. The binding activity was highest in the pituitary gland, followed by the hippocampus, amygdala, cerebral cortex, hypothalamus, and cerebellum. Guanosine 5'-O-thiotriphosphate, a nonhydrolyzable GTP analog, did not inhibit the binding of [125I]APP to porcine or chicken brain membranes, which ran counter to the results of PYY receptors in both species. Cross-linking studies have demonstrated that receptor-bound [125I]APP is cross-linked to a protein of 67 kDa without disulfide-linked subunits in both porcine and chicken brain membranes. In the latter species, [125I]PYY and [125I]NPY were also cross-linked to the same 67-kDa proteins, which were different from the receptor proteins (50 kDa) in mammalian species. These results indicate that chicken brain has receptors specific for PYY and NPY, as was found in mammalian brains, and that PYY, NPY, and PP act in the brain through interaction at multiple receptor sites, which are similar to and shared by other members of the PP family. Furthermore, the finding that APP-binding sites in porcine brain are more specific than those in avian brain suggests that an endogenous peptide similar to APP may exist in porcine brain.
A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells (2011)

Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization, and turnover rates, on a whole proteome level remains a major challenge in the postgenome era. Quantitative methods for measuring mRNA expression do not reliably predict corresponding protein levels and provide little or no information on other protein properties. Here we describe a combined pulse-labeling, spatial proteomics and data analysis strategy to characterize the expression, localization, synthesis, degradation, and turnover rates of endogenously expressed, untagged human proteins in different subcellular compartments. Using quantitative mass spectrometry and stable isotope labeling with amino acids in cell culture, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualized using specialized software tools developed in PepTracker. Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear, and nucleolar compartments. Expression levels of endogenous HeLa proteins varied by up to seven orders of magnitude. The average turnover rate for HeLa proteins was ~20 h. Turnover rate did not correlate with either molecular weight or net charge, but did correlate with abundance, with highly abundant proteins showing longer than average half-lives. Fast turnover proteins had overall a higher frequency of PEST motifs than slow turnover proteins but no general correlation was observed between amino or carboxyl terminal amino acid identities and turnover rates. A subset of proteins was identified that exist in pools with different turnover rates depending on their subcellular localization. This strongly correlated with subunits of large, multiprotein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.
Polysaccharides in fungi. XIII. Antitumor activity of various polysaccharides isolated from Dictyophora indusiata, Ganoderma japonicum, Cordyceps cicadae, Auricularia auricula-judae, and Auricularia species. (1983)

A mannan and water-soluble glucans from Dictyophora indusiata, a water-insoluble glucan from Ganoderma japonicum, a galactomannan from Cordyceps cicadae, and acidic heteroglycans from Auricularia auricula-judae and Auricularia species (Yu er), whose structural features have been reported in our previous papers of this series, were tested for antitumor activity against subcutaneously implanted sarcoma 180 in mice by intraperitoneal administration. Considerable antitumor activity was observed with partially O-acetylated (1→3)-α-D-mannan (T-2-HN) at doses of 10 mg·kg-1·d-1×10, water-soluble (1→3)-β-D-glucans having β-1→6 linked D-glucosyl side chains (T-4-N and T-5-N) at doses 5 or 10 mg·kg-1·d-1×10, and a glucuronoxyloglucomannan (U-3-A) at doses of 25 mg·kg-1·d-1×10.
Patterned metal polyhedra using calixarenes as organizational scaffolds: Ir4-based cluster assemblies (2010)

Isolated and patterned assemblies of Ir(4)-based metal polyhedra are described, in which a coordinated calixarene phosphine ligand enforces the desired cluster organization. The compounds are characterized by single-crystal X-ray diffraction and infrared spectroscopy.
Direct conversion of patient fibroblasts demonstrates non-cell autonomous toxicity of astrocytes to motor neurons in familial and sporadic ALS (2013)

Amyotrophic lateral sclerosis (ALS) causes motor neuron degeneration, paralysis, and death. Accurate disease modeling, identifying disease mechanisms, and developing therapeutics is urgently needed. We previously reported motor neuron toxicity through postmortem ALS spinal cord-derived astrocytes. However, these cells can only be harvested after death, and their expansion is limited. We now report a rapid, highly reproducible method to convert adult human fibroblasts from living ALS patients to induced neuronal progenitor cells and subsequent differentiation into astrocytes (i-astrocytes). Non-cell autonomous toxicity to motor neurons is found following coculture of i-astrocytes from familial ALS patients with mutation in superoxide dismutase or hexanucleotide expansion in C9orf72 (ORF 72 on chromosome 9) the two most frequent causes of ALS. Remarkably, i-astrocytes from sporadic ALS patients are as toxic as those with causative mutations, suggesting a common mechanism. Easy production and expansion of i-astrocytes now enables rapid disease modeling and high-throughput drug screening to alleviate astrocyte-derived toxicity.
Effects of a combined drug regimen on tumour necrosis factor and plasma kallikrein activity in experimental endotoxaemia. (1994)

Endotoxin affects several mediators, but combination treatment can prevent some of these effects.
The final acylation step in Taxol biosynthesis: Cloning of the taxoid C13-side-chain N -benzoyltransferase from Taxus (2002)

The formation of several acyl groups and an amide group of Taxol is catalyzed by regioselective CoA thioester-dependent acyltransferases. Several full-length acyltransferase sequences, obtained from a cDNA library constructed from mRNA isolated from Taxus cuspidata cells induced for Taxol production with methyl jasmonate, were individually expressed in Escherichia coli, from which a cDNA clone encoding a 3'-N-debenzoyl- 2'-deoxytaxol N-benzoyltransferase was identified. This recombinant enzyme catalyzes the stereoselective coupling of the surrogate substrate N-debenzoyl-(3'RS)-2'-deoxytaxol with benzoyl-CoA to form predominantly one 3'-epimer of 2'-deoxytaxol. The product 2'-deoxytaxol was confirmed by radio-HPLC,(1)H-NMR, and chemical ionization-MS. This enzymatic reaction constitutes the final acylation in the Taxol biosynthetic pathway. The full-length cDNA coding for the N-benzoyltransferase has an ORF of 1,323 nucleotides and encodes a 441-residue protein with a calculated molecular weight of 49,040. The recombinant enzyme expressed in E. coli has a pH optimum at 8.0, a k(cat) approximately 1.5 +/- 0.3 s(-1) and K(m) values of 0.42 mM and 0.40 mM for the N-deacylated taxoid and benzoyl-CoA, respectively. In addition to improving the production yields of Taxol in genetically engineered host systems, this enzyme provides a means of attaching modified aroyl groups to taxoid precursors for the purpose of improving drug efficacy.
Functional analysis of the flagellar genes in the fliD operon of Salmonella typhimurium (1995)

The fliD genes of Salmonella typhimurium and Escherichia coli encode the filament-cap protein of the flagellar apparatus, which facilitates the polymerization of endogenous flagellin at the tips of the growing filaments. Previous sequence analysis of this operon in both organisms has revealed that the fliD gene constitutes an operon together with two additional genes, fliS and fliT. Based on the gene-disruption experiment in E. coli, both the fliS and fliT genes have been postulated to be necessary for flagellation. In the present study, we constructed S. typhimurium mutants in which either fliS or fliT on the chromosome was specifically disrupted. Both mutants were found to produce functional flagella, indicating that these genes are dispensable for motility development in S. typhimurium. However, flagellar filaments produced by the fliS mutant were much shorter than those produced by the wild-type strain. This indicates that the fliS mutation affects the elongation step of filament assembly. The excretion efficiency of flagellin was examined in the fliD-mutant background, where the exported flagellin molecules cannot assemble onto the hooks, resulting in their excretion into the culture media. We found that the amount of flagellin excreted was much reduced by the fliS mutation. Based on these results, we conclude that FliS facilitates the export of flagellin through the flagellum-specific export pathway.
New treatment of ulcerative colitis with K-76 (1992)

The complement inhibitor K-76 (Otsuka Pharmaceutical Co., Osaka, Japan) was clinically evaluated as a new drug for treatment of active stage ulcerative colitis (UC). As monotherapy, K-76 proved effective in four of five cases. Furthermore, in patients with active stage UC that continued despite administration of corticosteroid hormone and salicylazosulphapyridine (so-called refractory UC), concomitant administration of K-76 was effective in seven of 21 cases. Thus, we believe that the multifunctional agent K-76 will provide clinicians with a new therapeutic approach to inflammatory bowel diseases, including UC and Crohn's disease.
Preparation of 131I‐Asialo‐α1‐Acid Glycoprotein (1976)

Alpha1-Acid glycoprotein (orosomucoid) was prepared from a byproduct of the ethanol plasma fractionation by means of ion-exchange procedures. Immunoelectrophoresis suggested a high degree of purity; the purified protein contained 13.5% sialic acid and 17.8% hexose. The alpha1-acid glycoprotein was modified by removal of sialic acid with neuraminidase (EC 3.2.1.18) followed by iodination with 131I. The purpose of the preparation, its potential use as a pharmacon for liver function studies in nuclear medicine is the subject of further study.
Rejection of Renal Allografts: Specific Immunologic Suppression (1968)

Kidneys were transplanted across a major genetic barrier (Ag-B locus), from LewisxBN F(1) hybrid rats into bilaterally nephrectomized Lewis rats. Survival of grafts is prolonged (indefinite?) in rats treated with a combination of (i) intravenous injection of donor spleen cells 1 day before the graft, and (ii) passive immunization with antiserum prepared in rats of the recipient strain against donor spleen and lymph-node cells. The recipient's immune response to other antigens is not impaired.
The Influence of Multiple Piezoelectric Effects on Electromechanical Coupling Factor of Piezoelectric Crystals (2012)

In order to improve the electro-mechanical coupling property of piezoelectric sensors, the influence of multiple piezoelectric effects on electromechanical coupling factor(EMCF) of piezoelectric crystals is studied in this paper. Theoretical analysis shows that when multiple piezoelectric effects are taken into consideration, the energy of electro-mechanical transformation grows less. A PZT-5 stack is adopted to perform the experiment. By means of a capacitor in parallel with the PZT-5 stack, the experimental results of short-circuit electromechanical transformation are obtained. Then through contrasting them with the open-circuit results, the influence result of multiple piezoelectric effects on EMCF of the PZT-5 is obtained. The calculation result shows multiple piezoelectric effects make EMCF of the PZT-5 be improved by 18%. So EMCF defined by the open-circuit/short-circuit method may be modified. This paper provides a way to the further improvement of electro-mechanical coupling properties of piezoelectric products.
IPv6 Packet Classification Based on Flow Label, Source and Destination Addresses (2005)

Packet classification is important for supporting multi-field packet routing, quality of service (QoS), real-time data streaming applications and firewalls. Existing schemes in IPv4 uses the 5-tuple approach, giving much overhead in the dataplane processing. With the introduction of IPv6 flow label field which facilitates labeling of packets belonging to the same flow; classification can now be done using the 3-tuple approach. In this paper, we propose 3-tuple packet classification algorithm using hierarchical-trie data structure that has low storage requirement and optimum search speed. Packet filters are evaluated based on hierarchical approach, starting from flow label followed by source and destination addresses. A hashing model with collision resolution for addresses that minimizes memory consumption is also being described. The time complexity of the lookup process is bounded by the length of header fields and is independent of the trie size.