gebhart/patrepeval huggingface dataset:
The Effect of HCl and Cl[sub 2] on the Thermal Oxidation of Silicon (1972)

The addition of a few mole per cent of or to the oxidizing atmosphere has been found to significantly improve the electrical stability of dry‐grown films. The results reported here were obtained with 30 min oxidation at 1150°C. The process not only decreases the mobile ion contamination originating from the furnace tube, but to a large extent also passivates the films against ionic instabilities caused by contaminated metallization. The use of or apparently also reduces the number of surface states at the interface. No significant change between standard and or oxides was observed in oxide charge, dielectric strength, dielectric constant and index of refraction, but the oxidation rate of Si is considerably increased in the presence of or . The mixture of and dry was also found to be very effective for the "cleaning" of quartz furnace tubes.
The Metal−Ligand Bifunctional Catalysis:  A Theoretical Study on the Ruthenium(II)-Catalyzed Hydrogen Transfer between Alcohols and Carbonyl Compounds (2000)

The ternary system consisting of [RuCl2(η6-benzene)]2, N-tosylethylenediamine or ethanolamine, and KOH (Ru:amine:KOH = 1:1:2 molar ratio) catalyzes reversible hydrogen transfer between alcohols and carbonyl compounds. The use of chiral amine auxiliaries effects asymmetric transformation. The theoretical calculations using methanol/formaldehyde transformation as the model indicates the operation of a novel metal−ligand bifunctional catalysis, which is contrary to currently accepted putative pathways. The results reveal that: (1) KOH is necessary for the generation of a formal 16-electron Ru complex, Ru(NHCH2CH2Y)(η6-benzene) (Y = O or NH) (catalyst), from an 18-electron Ru chloride, RuCl(NH2CH2CH2Y)(η6-benzene) (precatalyst), by a Dcb elimination of HCl, and not for increasing alkoxide concentration; (2) Ru alkoxides do not intervene in transfer hydrogenation; (3) the Ru alkoxide, even if formed, serves merely as a reservoir of the 16-electron catalyst; (4) the key 18-electron Ru hydride, RuH(NH2CH2CH2Y)(η6-benzene) (reducing intermediate), is generated by dehydrogenation of methanol with coordinatively unsaturated Ru(NHCH2CH2Y)(η6-benzene); (5) this process and reverse hydrogen delivery from RuH(NH2CH2CH2Y)(η6-benzene) to formaldehyde take place by a pericyclic mechanism via a six-membered transition structure; (6) neither carbonyl oxygen nor alcoholic oxygen interacts with Ru throughout the hydrogen transfer; (7) the carbonyl oxygen atom interacts with NH on Ru and the hydroxy function with the amido nitrogen via hydrogen bonding; (8) the Ru center and nitrogen ligand simultaneously participate in both forward and reverse steps of the hydrogenation transfer. The ethanolamine- and ethylenediamine-based complexes behave similarly. In the asymmetric transformation catalyzed by chiral Ru complexes, the stereochemical bias originates primarily from the chirality of the heteroatom-based five-membered chelate rings in the transition structure. The calculated mechanism explains a range of experimental observations including the ligand acceleration effect, the structural characteristics of the isolated Ru(II) complexes, the role of the NH or NH2 end of auxiliaries, the effect of a strong base cocatalyst, the kinetic profile, the reactivities of hydrogen donors and acceptors, the CO vs CC chemoselectivity, and the origin of enantioselection. This metal−ligand bifunctional catalysis is in sharp contrast to many other metal-centered catalyses.
Isolation of High-Affinity Single-Chain Antibodies against Mycobacterium avium subsp. paratuberculosis Surface Proteins from Sheep with Johne's Disease (2006)

Johne's disease, caused by infection with Mycobacterium avium subsp. paratuberculosis, causes significant economic losses to the livestock farming industry. Improved investigative and diagnostic tools-necessary to understand disease processes and to identify subclinical infection-are much sought after. Here, we describe the production of single-chain antibodies with defined specificity for M. avium subsp. paratuberculosis surface proteins. Single-chain antibodies (scFv) were generated from sheep with Johne's disease by cloning heavy-chain and lambda light-chain variable regions and expressing these in fusion with gene III of filamentous phages. Two scFv clones (designated SurfS1.2 and SurfS2.2) were shown to be immunoreactive against M. avium subsp. paratuberculosis surface targets by flow cytometry, and immunoblotting identified specificity for a 34-kDa proteinase-susceptible determinant. Both antibodies were cross-reactive against Mycobacterium avium subsp. avium but nonreactive against Mycobacterium bovis or Mycobacterium phlei cells and were shown to be capable of enriching M. avium subsp. paratuberculosis cells by a factor of approximately 10(6)-fold when employed in magnetic bead separation of mixed Mycobacterium sp. cultures. Further, magnetic bead separation using SurfS1.2 and SurfS2.2 was capable of isolating as few as 10(3) M. avium subsp. paratuberculosis cells from ovine fecal samples, indicating the diagnostic potential of these reagents. Finally, inclusion of SurfS1.2 or SurfS2.2 in in vitro broth culture with M. avium subsp. paratuberculosis indicated that surface binding activity did not impede bacterial growth, although colony clumping was prevented. These results are discussed in terms of the potential use of single-chain phage display monoclonal antibodies as novel diagnostic reagents.
Ligand-dependent Differences in the Internalization of Endothelin A and Endothelin B Receptor Heterodimers (2004)

Endothelin-1 (ET-1) is a potent vasoactive peptide that acts on endothelin A (ET(A)) and endothelin B (ET(B)) receptors. Although both receptor subtypes are co-expressed in numerous cells, little is known about their ability to form heterodimers. Here we show that both receptors were co-immunoprecipitated with an ET(B)-specific antibody using extracts from HEK293 cells stably co-expressing a fusion protein consisting of a myc-tagged ET(A) receptor and CFP (ET(A)myc.CFP) and a fusion protein consisting of an ET(B) receptor and YFP (ET(B).YFP). Co-immunoprecipitation was also observed with extracts from HEK293 cells transiently co-expressing FLAG-tagged ET(B) and myc-tagged ET(A) receptors, thereby excluding that heterodimerization is mediated by the CFP/YFP moieties. Heterodimerization was further confirmed in fluorescence resonance energy transfer (FRET) analysis of HEK293 cells transiently co-expressing ET(A)myc.CFP and ET(B).YFP receptors. FRET efficiencies were between 12 and 18% in untreated and antagonist- or ET-1-treated cells, indicating constitutive heterodimerization. Prolonged stimulation (30 min) with the ET(B) receptor-selective agonist BQ3020 decreased FRET efficiency by 50%. This decrease was not observed when internalization was inhibited by co-expression of dominant-negative K44A.dynamin I or incubation with 450 mm sucrose. Enzyme-linked immunosorbent assay and laser scanning microscopy of cell clones stably co-expressing ET(A)myc.CFP/ET(B)flag.YFP receptors revealed a slower sequestration of the ET(B)flag.YFP receptors upon stimulation with ET-1 than with BQ3020. No difference in ET-1 or BQ3020-mediated sequestration was observed with cell clones expressing ET(B)flag.YFP receptors alone. The data suggest that ET(A) and ET(B) receptors form constitutive heterodimers, which show a slower sequestration upon stimulation with ET-1 than with BQ3020. Heterodimer dissociation along the endocytic pathway only occurs upon ET(B)-selective stimulation.
Effect of human chorionic gonadotropin on duration of estrous cycle and fertility of normally cycling, nonlactating mares. (1974)

The effect of a single dose (3300IU) of human chorionic gonadotropin (HCG) given on Day 1 or 2 of estrus on the duration of estrus and fertility of normally cycling nonlactating mares was studied. 36 mares received HCG 24 hours prior to the first insemination and 36 mares served as controls. During Cycle 1. treated mares had a shorter (p < .01) estrus than did untreated mares. The duration of diestrus was not affected and the duration of the estrous cycle was shortened slightly (18.8 vs 21.4 days). There were only slight differences in Cycle 2 and no differences in Cycle 3. HCG did not affect the pregnancy rate (61.6% vs. 63.9%) during Cycle 1 but more (p < .5) treated mares became pregnant during the 3 cycles studied than did the untreated (94.4% vs. 80.6%).
Multiplex Reverse Transcriptase PCR Assay for Simultaneous Detection of Three Fish Viruses (1999)

ABSTRACT A multiplex reverse transcriptase (RT)-PCR assay was developed for the simultaneous detection of three different fish viruses: infectious pancreatic necrosis virus (IPNV), infectious hematopoietic necrosis virus (IHNV), and viral hemorrhagic septicemia virus (VHSV). The sensitivity levels of the multiplex RT-PCR assay were 100, 1, and 32 50% tissue culture infective doses/ml for IPNV, IHNV, and VHSV, respectively.
Human Genome Project: Discovery of New Drugs (2000)

Genomics will surpass the recombinant DNA era for generating therapeutic product opportunities. It will also be a key core technological competency for all therapeutic area. To determine biological functions of novel genes and to develop the therapeutic drugs for human diseases, we have applied various techniques and discovered the potential drugs. In my talk, I will give two examples how we determined the biological functions of the novels genes. Osteoprotegerin (OPG) is a novel molecule isolated from the human genome (EST) project. This molecule shares homology with tumor necrosis factor receptor. In vivo, over expression of OPG in the transgenic mice results in a profond osteopetrosis, coincident with a decrease in later stage of osteoclast differentiation. These same effects are observed upon administration of recombinant OPG into normal mice. In vitro, osteoclast differentiation from precursor cells is blocked in a dose-dependent manner by recombinant OPG. Furthermore, OPG blocks ovariectomy-associated bone loss in rat. These data show that OPG can act as a soluble factor in the regulation of bone loss and imply a utility for OPG in the treatment of osteoporosis. Currently, OPG has been in the phase III clinical trial for osteoporosis. NNT-1/BSF-3 is another novel molecule isolated from cDNA library of the activated T lymphoma cells. It is novel member of the IL-6 cytokine family. Over expression of the gene in transgenic mice induced proliferation of lymphoid tissue particularly in the speen and lymph node. It also increased blood B cells number in transgenic mice. In vitro study showed that NNT-1/BSF-3 also supported differentiation of chicken embryonic motor and sympathetic neurons. In vivo, it potentiated the induction by IL-1 of corticosterone and IL-6. Administration of the recombinant protein to the mice also induced b cells hyperplasia with serum IgG and IgM increase showing the same effect as in the transgenic mice. Currently, we are in the process of isolating several other novel growth factors and cytokine receptors. These molecules may have some relation with cancer biology, bone formation or wound healing. Determination of their biological functions and further development of potential drug are in progress. In summary, these studies demonstrate that human genome project is a good source for the discovery of potential drugs. Functional genomics will not only give us a revolutionary influence in understanding the biology of the novel genes but also greatly facilitate the development of new drugs for therapeutics in the 21th century.
A demon of our own design: markets, hedge funds, and the perils of financial innovation (2008)

Preface. Acknowledgments. About the Author. CHAPTER 1 ~ Introduction: The Paradox of Market Risk. CHAPTER 2 ~ The Demons of '87. CHAPTER 3 ~ A New Sheriff in Town. CHAPTER 4 ~ How Salomon Rolled the Dice and Lost. CHAPTER 5 ~ They Bought Salomon, Then They Killed It. CHAPTER 6 ~ Long-Term Capital Management Rides the Leverage Cycle to Hell. CHAPTER 7 ~ Colossus. CHAPTER 8 ~ Complexity, Tight Coupling, and Normal Accidents. CHAPTER 9 ~ The Brave New World of Hedge Funds. CHAPTER 10 ~ Cockroaches and Hedge Funds. CHAPTER 11 ~ Hedge Fund Existential. Conclusion: Built to Crash? Notes. Index.
Cardiac Steatosis in Diabetes Mellitus (2007)

In humans, impaired glucose tolerance is accompanied by cardiac steatosis, which precedes the onset of type 2 diabetes mellitus and left ventricular systolic dysfunction. Thus, lipid overstorage in human cardiac myocytes is an early manifestation in the pathogenesis of type 2 diabetes mellitus and is evident in the absence of heart failure.
ADM-LDA: An aspect detection model based on topic modelling using the structure of review sentences (2014)

Probabilistic topic models are statistical methods whose aim is to discover the latent structure in a large collection of documents. The intuition behind topic models is that, by generating documents by latent topics, the word distribution for each topic can be modelled and the prior distribution over the topic learned. In this paper we propose to apply this concept by modelling the topics of sentences for the aspect detection problem in review documents in order to improve sentiment analysis systems. Aspect detection in sentiment analysis helps customers effectively navigate into detailed information about their features of interest. The proposed approach assumes that the aspects of words in a sentence form a Markov chain. The novelty of the model is the extraction of multiword aspects from text data while relaxing the bag-of-words assumption. Experimental results show that the model is indeed able to perform the task significantly better when compared with standard topic models.
Intra‐amygdaloid projections of the lateral nucleus in the cat: PHA‐L anterograde labeling combined with postembedding GABA and glutamate immunocytochemistry (1994)

Research on the implication of the amygdala in classical fear conditioning suggests that the central amygdaloid nucleus is the output station of the amygdala for conditioned fear responses, while the lateral nucleus acts as the input nucleus, at least for auditory conditioned stimuli. However, the nature and locus of the plastic changes taking place between these two nuclei are unknown partly because the neurotransmitter(s) used by intra-amygdaloid projections of the lateral nucleus has not been identified. To address this issue in cats, anterograde tracing with Phaseolus vulgaris-leucoagglutinin (PHA-L) was combined with postembedding immunocytochemistry for gamma-aminobutyric acid (GABA) and glutamate. Two sectors can be recognized in the lateral nucleus of the cat: a shell located laterally along the external capsule, and a core. Iontophoretic injections of PHA-L in these two sectors revealed that they have nonoverlapping intra-amygdaloid targets with the exception of a common projection to the central lateral nucleus. The core projects mainly to itself and to the basomedial nucleus, whereas the shell contributes a massive projection to the basolateral nucleus. No projection of the lateral nucleus to the central medial nucleus was found. Electron microscopically, PHA-L-labeled axon terminals in the lateral, basomedial, basolateral, and central lateral nuclei as well as in the perirhinal and insular cortices formed asymmetric synapses (100%; n = 289) with dendritic spines (77-100%). Moreover, postembedding immunocytochemistry revealed that PHA-L-labeled axon terminals are immunoreactive for glutamate but not GABA. Since most amygdaloid projections to the brainstem originate in the central medial nucleus, these results suggest that intra-amygdaloid targets of the lateral nucleus are involved in the transmission of auditory conditioned stimuli to the central medial nucleus. Moreover, these findings imply that intra-amygdaloid projections of the lateral nucleus use glutamate but not GABA as a neurotransmitter.
Interleukin 1, a potential regulator of fibroblast proliferation. (1982)

Abstract Secondary mixed lymphocyte reaction (MLR) supernatants contain factors that stimulate fibroblast proliferation in vitro. Biochemical analysis of secondary MLR supernatants using gel filtration chromatography and isoelectrofocusing (IEF) demonstrated that the fibroblast proliferation factors have apparent m.w. of 75,000 and 13,000 and isoelectric points (pi) of 6.8 to 7.2, 5.8 to 6.2, and 5.2 to 5.4, values similar to those previously reported for human interleukin 1 (IL 1). To further explore the relationship between the MLR-derived fibroblast proliferation factors and IL 1, the following experiments were performed. First, the fractions obtained from gel filtration and IEF were assayed for both thymocyte proliferation activity, a measure of IL 1 activity, and fibroblast proliferation activity, and superimposable activity profiles were obtained. Second, to confirm that the observed thymocyte proliferation activity was in fact due to IL 1 and not interleukin 2 (IL 2) or novel factors, the IEF fractions containing peak thymocyte and fibroblast proliferation activity (i.e., fractions having pi of 6.8, 6.0, and 5.3, respectively) were demonstrated to stimulate IL 2 production by a murine T lymphoma line, a specific measure of IL 1 activity. Third, IL 1 and the fibroblast proliferation factors were co-purified through a three-step, 200-plus-fold purification protocol consisting of ammonium sulfate precipitation, gel filtration chromatography, and IEF. Fourth, partially purified human IL 1 made in another laboratory and highly purified murine IL 1, but not human and murine IL 2, stimulated fibroblast proliferation. These results demonstrate that the fibroblast proliferation factors found in secondary MLR supernatants have several functional and biochemical properties in common with human IL 1. These findings raise the possibility that IL 1 may regulate fibroblast proliferation and that the local production of IL 1 by infiltrating mononuclear cells may contribute to the fibrosis observed in chronic inflammatory disease states.
Intermediates in Amino Acid Biosynthesis (1955)

This chapter contains sections titled: Introduction Criteria for Establishing a Normal Biosynthetic Intermediate Glutamic Acid, Nitrogen Assimilation, and Transamination Glutamic Acid Group; Glutamine, Proline, Hydroxyproline, and Arginine Four-Carbon Group: Aspartic Acid, Asparagine, Threonine, and Methionine Short-Chain Amino Acids: Alanine, Serine, Glycine, and Cystine Isoleucine, Valine, and Leucine Aromatic Amino Acids: Tyrosine, Phenylalanine, and Tryptophane. Lysine and Histidine General Considerations
Low-density parity-check codes for digital subscriber lines (2003)

The paper investigates the application of low-density parity-check (LDPC) codes to digital subscriber-line (DSL) transmission systems that employ discrete multitone modulation. A family of linear-time encodable binary LDPC codes that are well-suited for DSL transmission is introduced. Encoding and symbol mapping for multilevel modulation are described. Simulation results show that even under tight latency constraints good net coding gains can be achieved. Implementation complexity is analyzed and compared with that of trellis-coded modulation as employed in current asymmetric DSL transceivers. The incorporation of powerful LDPC coding techniques into next-generation DSL modems appears to be possible with reasonable increase in transceiver complexity.
RETRACTED: Characterization of capsaicin synthase and identification of its gene ( csy1 ) for pungency factor capsaicin in pepper ( Capsicum sp.) (2006)

Capsaicin is a unique alkaloid of the plant kingdom restricted to the genus Capsicum. Capsaicin is the pungency factor, a bioactive molecule of food and of medicinal importance. Capsaicin is useful as a counterirritant, antiarthritic, analgesic, antioxidant, and anticancer agent. Capsaicin biosynthesis involves condensation of vanillylamine and 8-methyl nonenoic acid, brought about by capsaicin synthase (CS). We found that CS activity correlated with genotype-specific capsaicin levels. We purified and characterized CS ( approximately 35 kDa). Immunolocalization studies confirmed that CS is specifically localized to the placental tissues of Capsicum fruits. Western blot analysis revealed concomitant enhancement of CS levels and capsaicin accumulation during fruit development. We determined the N-terminal amino acid sequence of purified CS, cloned the CS gene (csy1) and sequenced full-length cDNA (981 bp). The deduced amino acid sequence of CS from full-length cDNA was 38 kDa. Functionality of csy1 through heterologous expression in recombinant Escherichia coli was also demonstrated. Here we report the gene responsible for capsaicin biosynthesis, which is unique to Capsicum spp. With this information on the CS gene, speculation on the gene for pungency is unequivocally resolved. Our findings have implications in the regulation of capsaicin levels in Capsicum genotypes.
A DDS-based middleware for scalable tracking, communication and collaboration of mobile nodes (2013)

Applications such as transportation management and logistics, emergency response, environmental monitoring and mobile workforce management employ mobile networks as a means of enabling communication and coordination among a possibly very large set of mobile nodes. The majority of those systems may thus require real-time tracking of the nodes and interaction with all participant nodes as well as a means of adaptability in a very dynamic scenario. In this paper, we present a middleware communication service based on the OMG DDS standard that supports on-line tracking and unicast, groupcast and broadcast with several thousand mobile nodes. We then show a Fleet Tracking and Management application built using or middleware, and present the performance results in LAN and WAN settings to evaluate our middleware in terms of scalability and robustness.
A short adaptive path from DNA to RNA polymerases (2012)

DNA polymerase substrate specificity is fundamental to genome integrity and to polymerase applications in biotechnology. In the current paradigm, active site geometry is the main site of specificity control. Here, we describe the discovery of a distinct specificity checkpoint located over 25 Å from the active site in the polymerase thumb subdomain. In Tgo, the replicative DNA polymerase from Thermococcus gorgonarius, we identify a single mutation (E664K) within this region that enables translesion synthesis across a template abasic site or a cyclobutane thymidine dimer. In conjunction with a classic "steric-gate" mutation (Y409G) in the active site, E664K transforms Tgo DNA polymerase into an RNA polymerase capable of synthesizing RNAs up to 1.7 kb long as well as fully pseudouridine-, 5-methyl-C-, 2'-fluoro-, or 2'-azido-modified RNAs primed from a wide range of primer chemistries comprising DNA, RNA, locked nucleic acid (LNA), or 2'O-methyl-DNA. We find that E664K enables RNA synthesis by selectively increasing polymerase affinity for the noncognate RNA/DNA duplex as well as lowering the K(m) for ribonucleotide triphosphate incorporation. This gatekeeper mutation therefore identifies a key missing step in the adaptive path from DNA to RNA polymerases and defines a previously unknown postsynthetic determinant of polymerase substrate specificity with implications for the synthesis and replication of noncognate nucleic acid polymers.