gebhart/patrepeval huggingface dataset:
Tepidibacter thalassicus gen. nov., sp. nov., a novel moderately thermophilic, anaerobic, fermentative bacterium from a deep-sea hydrothermal vent (2003)

A moderately thermophilic, anaerobic, endospore-forming bacterium (strain SC 562T) was isolated from a hydrothermal vent chimney located at 13 degrees N on the East-Pacific Rise at a depth of 2650 m. Cells of strain SC 562T were straight to slightly curved rods, which were 0.7-0.9 microm in diameter and 3.5-6.0 microm in length with peritrichous flagella. Strain SC 562T formed round, refractile endospores in terminally swollen sporangia. The temperature range for growth was 33-60 degrees C, with an optimum at 50 degrees C. The pH range for growth was 4.8-8.5, with an optimum at pH 6.5-6.8. Growth of strain SC 562T was observed at NaCl concentrations ranging from 1.5 to 6% (w/v). The substrates utilized by strain SC 562T included casein, peptone, albumin, yeast extract, beef extract, alanine plus proline and starch. Glucose, maltose, pyruvate, valine and arginine each slightly stimulated growth in the presence of yeast extract. The products of glucose fermentation were ethanol, acetate, H2 and CO2. Strain SC 562T reduced elemental sulfur to hydrogen sulfide. The G + C content of the DNA of strain SC 562T was 24 mol%. 16S rDNA sequence analysis revealed that the isolated organism belonged to cluster XI of the Clostridium subphylum. On the basis of its physiological properties and phylogenetic analyses, it is proposed that strain SC 562T represents the sole species of a novel genus, Tepidibacter; the name Tepidibacter thalassicus is proposed for strain SC 562T (=DSM 15285T=UNIQEM 215T).
[Durene derivates. IV. N-((2,3,5,6-tetramethylbenzoyl)alkyl)imidazoles and N-((beta-(2,3,5,6-tetramethylphenyl)-beta-hydroxy)ethyl)imidazoles with anticonvulsant activity]. (1981)

A series of N-[(2,3,4,6-tetramethylbenzoyl)alkyl]imidazoles and of N-([beta-(2,3,5,6-tetramethylphenyl)-beta-hydroxy]ethyl)imidazoles has been synthesized. All compounds were tested in mice for anticonvulsant activity against electroshock and pentylenetetrazole convulsions. These durene-derivatives showed good activity, whereas the corresponding benzene-derivatives were inactive.
Selection, Fabrication and Failure Behavior of Sic Monofilament-Reinforced Glass Composites (2008)

Unidirectional Sic monofilament-reinforced borosilicate glass composites were fabricated. Matrix materials were evaluated on the basis of optical clarity, thermo-elastic compatibility, and process ability. Preliminary observations of failure modes of these composites are discussed. Severe matrix cracking was found to be the predominant failure mode.
Systemic Insulin-like Growth Factor-1 Reverses Hypoalgesia and Improves Mobility in a Mouse Model of Diabetic Peripheral Neuropathy (2008)

Peripheral neuropathy is a particularly debilitating complication of both type 1 and type 2 diabetes characterized by sensory and motor neuron damage and decreased circulating levels of insulin-like growth factor 1 (IGF-1). Quite often, an early hyperalgesia is followed by hypoalgesia and muscle weakness. Hypoalgesia can lead to significant morbidity for which there is no current treatment. Hyperglycemic, streptozotocin (STZ)-induced rodent models reproduce these symptoms. We investigated whether increasing systemic IGF-1 could improve neuronal function in hyper- and hypoalgesic STZ-treated mice. Increased circulating levels of IGF-1 were achieved by delivering a plasmid or adeno-associated viral (AAV) vector bearing mouse IGF-1 to the liver. Treating mice in the hyperalgesia stage prevented later hypoalgesia. Treating mice in the hypoalgesia stage reversed existing hypoalgesia. This latter effect could be seen by merely restoring IGF-1 serum levels to normalcy, which was possible to achieve by IGF-1 gene therapy or insulin treatment. Sensory nerve functional correction was seen to be correlated with attenuated Schwann cell vacuolization and demyelination in peripheral sensory nerve fibers. A further increase in serum IGF-1 levels with gene therapy also improved motor function, consistent with the observed prevention of both muscle atrophy and peripheral motor nerve fiber demyelination. These results suggest that the restoration of systemic levels of IGF-1 may prove to be a highly effective therapeutic modality for treating diabetic peripheral neuropathy.
Expression in Escherichia coli, purification and functional activity of recombinant human chaperonin 10 (1995)

We have recently reported the cloning of a cDNA coding for a stress inducible human chaperonin 10. The protein was shown to possess 100% identity with the bovine homologue and a single amino acid replacement (glycine to serine at position 52) compared to rat chaperonin 10. Here we report the heterologous expression of human chaperonin 10 in Escherichia coli, its purification and its functional characterization. The recombinant protein was purified to homogeneity as judged by different analytical techniques, and mass spectrometry analysis showed a MW of 10,801 Da in agreement with the predicted sequence. This molecular weight accounts for a protein which is not modified post-translationally. In fact, natural rat chaperonin 10 has been shown to be acetylated at the N-terminus, a feature suggested to be important for targeting and functional activity. Here we show that recombinant human chaperonin 10 is fully active in assisting the chaperonin 60 GroEL in the refolding of denatured yeast enolase, thereby showing that, at least in the present system, post-translational acetylation is not necessary for its activity.
Physical wave propagation modeling for real-time synthesis of natural sounds (2002)

This thesis proposes banded waveguide synthesis as an approach to real-time sound synthesis based on the underlying physics. So far three main approaches have been widely used: digital waveguide synthesis, modal synthesis and finite element methods. Digital waveguide synthesis is efficient and realistic and captures the complete dynamics of the underlying physics but is restricted to instruments that are well-described by the one-dimensional string equation. Modal synthesis is efficient and realistic yet abandons complete dynamical description and hence cannot used for certain types of performance interactions like bowing. Finite element methods are realistic and capture the behavior of the constituent physical equations but on current commodity hardware does not perform in real-time. 
Banded waveguides offer efficient simulations for cases for which modal synthesis is appropriate but traditional digital waveguide synthesis is not applicable. The key realization is that the dynamic behavior of traveling waves, which is being used in waveguide synthesis, can be applied to individual modes and that the efficient computational structure can be utilized to achieve an approximate dynamical description in the neighborhood of modes. Secondly this realization is connected to related work on the theory of asymptotics and periodic orbits and hence shown to apply to higher dimensions also. 
This theoretical approach is studied in applications to bowed bar percussion instruments, complex stroke patterns on Indian Tabla drums as well as rubbed wine glasses and Tibetan singing bowls. None of these instruments and performance types has been synthesized efficiently before. The simulations are compared to experiments.
Welding Behavior of Semicrystalline Polymers. 1. The Effect of Nonequilibrium Chain Conformations on Autoadhesion of UHMWPE (1998)

The effect of the overall crystallinity and the initial crystal morphology on the welding behavior of semicrystalline polymers was investigated by means of T-peel testing above and below the melting point using ultrahigh-molecular-weight polyethylene (UHMWPE) as a model polymer. Different crystal morphologies were generated by either crystallizing UHMWPE from the melt or from dilute solutions. The initial crystal morphology was found to have a large influence on the adhesive fracture energy as measured above the melting temperature. In the case of two melt-crystallized films, the adhesive fracture energy above the melting temperature, , developed only slowly, and did not reach the fracture energy of the bulk material, even after 65 h of welding at 145 °C. However, welding two (completely wetted) solution-cast films above the melting temperature resulted in an almost instantaneous increase of to the level of the fracture energy of the bulk material. The adhesive fracture energy at room temperature increased almost instantaneously to the fracture energy of the bulk material upon welding above the melting point, irrespective of crystal morphology.
Figure S4 from AZD4320, A Dual Inhibitor of Bcl-2 and Bcl-x<sub>L</sub>, Induces Tumor Regression in Hematologic Cancer Models without Dose-limiting Thrombocytopenia (2023)

&lt;p&gt;Figure S4&lt;/p&gt;
He I Photoelectron Spectra and Gas-Phase Electronic Structures of End-Functionalized [3]- and [5]-Ladderanes (2008)

[3]- and [5]-ladderanes obtained by way of template-controlled syntheses conducted in the organic solid state have been characterized via He I photoelectron (PE) spectroscopy. The results provide a first correlation with X-ray crystallographic structure data and establish the reliability of quantum chemical DFT (B3LYP/6-31G*) and ab initio HF calculations in predicting geometrical and electronic structures of molecular ladder frameworks.
Test and evaluation of chip-to-chip attachment of MEMS devices (2002)

In the IC industry, the bond layer serves as the foundation and often the weak link in the reliability of chip packages. MEMS packages are likely to have a greater number of bond layers with more stringent requirements. The additional bond layers arise from multiple interfaces inside the package. The bond layers in MEMS devices often must maintain precise component or chip alignment. In addition, the bond layers may have to withstand loading from both the macroenvironment and loading within the package. This paper presents the bond requirements for a MEMS based Safety and Arming (S&A) device. The S&A system requires precise alignment between a micromachined silicon chip, a patterned Alumina ceramic chip, and a deflection delimiter. Several candidate designs were subjected to a series of environmental tests including thermal cycling, accelerated stress tests, mechanical shock, and combinations of the above conditions. A Scanning Acoustic Microscope (SAM) is utilized to measure initial delamination and to identify incremental damage due to environmental exposure. The tests are ultimately used to rank the suitability of the bond layer material for chip-to-chip attachment with large coefficient of expansion differences. Tested bond materials include epoxy, thermoplastic, and solder.
ChemInform Abstract: 3‐Aryl‐1,2‐diacetamidopropane Derivatives as Novel and Potent NK‐1 Receptor Antagonists. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Role of Ras Isoforms in the Stimulated Proliferation of Human Renal Fibroblasts in Primary Culture (2000)

The proliferation of renal fibroblasts is implicated in the pathophysiologic processes of renal fibrosis. Many of the growth factors involved in proliferation are known to activate intracellular signaling pathways that converge on Ras monomeric GTPases. Although three ras family genes exist, their functional specificity is not yet known. Using antisense oligonucleotides, a role for Kirsten (Ki)-Ras in the stimulated proliferation of a primate renal fibroblast cell line was previously demonstrated. This study examines Ras in primary cultures of adult human renal fibroblasts. Using reverse transcription-PCR, mRNA for Harvey (Ha)-ras, Ki(4B)-ras, and neural (N)-ras, but not Ki(4A)-ras, were detected. Antisense oligonucleotides targeting Ha-, Ki-, and N-ras mRNA, which were used for liposomal transfection at 100 to 200 nM, were demonstrated to be active and isoform-specific in quantitative reverse transcription-PCR assays. Cellular Ras protein levels, as estimated using isoform-specific monoclonal antibodies, indicated that Ki-Ras was the predominantly expressed isoform (>95% of total Ras protein) under both serum-containing and serum-free conditions, with N- and Ha-Ras being detected in small amounts. Consistent with this finding, the antisense oligonucleotide directed against Ki-Ras reduced total cellular Ras levels by >70%, whereas Ha-Ras, N-Ras, and control oligonucleotides had no significant effect. Proliferation of oligonucleotide-transfected cells was measured using epidermal growth factor (EGF) and serum stimulation. The Ki-Ras oligonucleotide at 100 nM reduced serum-stimulated proliferation by >50% and EGF-stimulated proliferation by 25%, compared with data obtained with the control oligonucleotide (P: < 0. 01). The N-Ras oligonucleotide was not active, compared with the control oligonucleotide. The Ha-Ras oligonucleotide was not significantly active at 100 nM but reduced serum-stimulated proliferation by 13% and EGF-stimulated growth by 40% at 200 nM (P: < 0.01). These results demonstrate that Ki-Ras(4B) is the predominantly expressed Ras isoform in human renal fibroblasts in primary culture and is important for both serum- and EGF-stimulated proliferation. Ha-Ras appears to be expressed at low levels but may also play a distinct role in stimulated proliferation.
Vasopressin-independent targeting of aquaporin-2 by selective E-prostanoid receptor agonists alleviates nephrogenic diabetes insipidus (2011)

In the kidney, the actions of vasopressin on its type-2 receptor (V2R) induce increased water reabsorption alongside polyphosphorylation and membrane targeting of the water channel aquaporin-2 (AQP2). Loss-of-function mutations in the V2R cause X-linked nephrogenic diabetes insipidus. Treatment of this condition would require bypassing the V2R to increase AQP2 membrane targeting, but currently no specific pharmacological therapy is available. The present study examined specific E-prostanoid receptors for this purpose. In vitro, prostaglandin E2 (PGE2) and selective agonists for the E-prostanoid receptors EP2 (butaprost) or EP4 (CAY10580) all increased trafficking and ser-264 phosphorylation of AQP2 in Madin-Darby canine kidney cells. Only PGE2 and butaprost increased cAMP and ser-269 phosphorylation of AQP2. Ex vivo, PGE2, butaprost, or CAY10580 increased AQP2 phosphorylation in isolated cortical tubules, whereas PGE2 and butaprost selectively increased AQP2 membrane accumulation in kidney slices. In vivo, a V2R antagonist caused a severe urinary concentrating defect in rats, which was greatly alleviated by treatment with butaprost. In conclusion, EP2 and EP4 agonists increase AQP2 phosphorylation and trafficking, likely through different signaling pathways. Furthermore, EP2 selective agonists can partially compensate for a nonfunctional V2R, providing a rationale for new treatment strategies for hereditary nephrogenic diabetes insipidus.
A Dynamic Multivariable State-Space Model for Bidirectional Inductive Power Transfer Systems (2012)

Bidirectional inductive power transfer (IPT) systems facilitate contactless power transfer between two sides, which are separated by an air gap, through weak magnetic coupling. Typical bidirectional IPT systems are essentially high-order resonant circuits and, therefore, difficult to both design and control without an accurate mathematical model, which is yet to be reported. This paper presents a dynamic model, which provides an accurate insight into the behavior of bidirectional IPT systems. The proposed state-space-based model is developed in a multivariable framework and mapped into frequency domain to compute the transfer function matrix of eight-order bidirectional IPT systems. The interaction between various control variables and degree of controllability of the system are analyzed from the relative gain array and singular values of the system. The validity of the proposed dynamic model is demonstrated by comparing the predicted behavior with that measured from a 1 kW prototype bidirectional IPT system under various operating conditions. Experimental results convincingly indicate that the proposed model accurately predicts the dynamical behavior of bidirectional IPT systems and can, therefore, be used as a valuable tool for transient analysis and optimum controller design.
A7 Drug discovery approach for rare neurological diseases: using novel zinc finger protein technology to develop potential therapy for huntington’s disease (2016)

<h3></h3> There are approximately 7000 known rare and orphan diseases, over a third of which affect the central nervous system, virtually all do not have adequate treatment options. Shire is committed to developing innovative medicines to treat the fundamental biochemical abnormalities that result in pathologies caused by lysosomal storage disorders and other rare neurological diseases by selecting the right biological target based on extensive knowledge of disease pathophysiology and the right therapeutic modality from our array of technology platforms that includes antibodies, modified RNA, small molecules, gene therapy and protein therapeutics. This approach is particularly relevant for Huntington’s disease (HD), a rare and fatal neurodegenerative disease caused by a CAG trinucleotide repeat expansion in exon 1 of one copy of the Huntingtin (Htt) gene, resulting in expression of an aggregation-prone mutant protein. As this mutant protein is believed to be a primary cause of the pathophysiology in HD, Htt-lowering approaches are being explored using various technologies. Here, we will describe the use of an engineered zinc-finger protein transcription factor (ZFP TF) that preferentially down-regulates expression from the disease-causing copy of the Htt gene relative to the normal, unexpanded copy of the gene in both in vitro and in vivo HD models. Results presented here support the further development of allele-specific ZFP TFs as a potential therapy for HD.
In vitro antitumor activity of TAS-103 against freshly-isolated human colorectal cancer. (2002)

DNA topoisomerases (Topo) are enzymes that relieve the secondary twist on the DNA strand in the process of DNA synthesis and transcription; therefore they are unique targeting molecules for the chemotherapy of colorectal cancer. TAS-103 (6-[[2-(dimethylamino)ethyl]amino]-3-hydroxy-7H-in-deno [2,1-c]quinolin-7-one dihydrochloride, MW; 406.31), a novel quinoline derivative, has recently been established as a Topo I and Topo II inhibitor. The aim of the present study was to investigate the antitumor activity of TAS-103 by the MTT assay in human highly-purified and freshly-isolated colorectal cancer cells. To our knowledge, this is the first data concerning the antitumor activity of TAS-103 in highly-purified and isolated human colorectal cancer cells. TAS-103 showed the strongest antitumor activity among the conventional anticancer agents for colorectal cancer (p<0.05). The combination with CDDP augmented the antitumor activity of TAS-103 (p<0.05), indicating that CDDP is one of the most potent candidates to be used in combination with TAS-103. To predict the clinical effect of TAS-103, the expressions of Topo I and Topo II were measured by quantitative PCR. However, a correlation between the expression of Topo and the antitumor activity of TAS-103 was not established. In conclusion, according to this data, TAS-103 may be useful in the chemotherapy of colorectal cancer.
The phosphohydrolase component of the hepatic microsomal glucose-6-phosphatase system is a 36.5-kilodalton polypeptide. (1988)

The phosphohydrolase component of the microsomal glucose-6-phosphatase system has been identified as a 36.5-kDa polypeptide by 32P-labeling of the phosphoryl-enzyme intermediate formed during steady-state hydrolysis. A 36.5-kDa polypeptide was labeled when disrupted rat hepatic microsomes were incubated with three different 32P-labeled substrates for the enzyme (glucose-6-P, mannose-6-P, and PPi) and the reaction terminated with trichloroacetic acid. Labeling of the phosphoryl-enzyme intermediate with [32P]glucose-6-P was blocked by several well-characterized competitive inhibitors of glucose-6-phosphatase activity (e.g. Al(F)-4 and Pi) and by thermal inactivation, and labeling was not seen following incubations with 32Pi and [U-14C]glucose-6-P. In agreement with steady-state dictates, the amount of [32P]phosphoryl intermediate was directly and quantitatively proportional to the steady-state glucose-6-phosphatase activity measured under a variety of conditions in both intact and disrupted hepatic microsomes. The labeled 36.5-kDa polypeptide was specifically immunostained by antiserum raised in sheep against the partially purified rat hepatic enzyme, and the antiserum quantitatively immunoprecipitated glucose-6-phosphatase activity from cholate-solubilized rat hepatic microsomes. [32P]Glucose-6-P also labeled a similar-sized polypeptide in hepatic microsomes from sheep, rabbit, guinea pig, and mouse and rat renal microsomes. The glucose-6-phosphatase enzyme appears to be a minor protein of the hepatic endoplasmic reticulum, comprising about 0.1% of the total microsomal membrane proteins. The centrifugation of sodium dodecyl sulfate-solubilized membrane proteins was found to be a crucial step in the resolution of radiolabeled microsomal proteins by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Synergistic clinical efficacy of niraparib in combination with pembrolizumab in patients with recurrent platinum-resistant ovarian carcinoma (2019)

Ovarian cancer is the most common cause of gynecologic cancer death in the United States with 22,530 newly diagnosed cases and 13,980 deaths annually. There has been a miniscule, approximately 2.3% decrease, each year in the death rates from ovarian cancer over the past few decades (1). Although most patients with advanced ovarian cancer respond to initial platinum-based chemotherapy, 70% will relapse and ultimately become resistant, refractory, or unable to receive platinum-based chemotherapy owing to cumulative toxic effects (2,3). This has led to a paradigm shift in the approach to the treatment of ovarian cancer with precision medicine and additional targeted therapies becoming part of the standard treatment regimen.
Cutting Edge: Hormonal Milieu, Not Antigenic Specificity, Determines the Mature Phenotype of Autoreactive B Cells (2006)

Although both marginal zone and follicular B cells produce anti-DNA Abs in murine models of systemic lupus erythematosus, it has been unclear whether these distinct B cell subsets make identical or different Abs. Single-cell analysis demonstrates that the same DNA-reactive B cells can mature to either subset, depending on the hormonal environment. Anti-DNA B cells in estradiol-treated mice become marginal zone cells while identical cells from prolactin-treated mice become follicular cells. The B cell receptor signaling pathway is influenced by hormonal milieu. Thus, hormonal milieu and perhaps B cell receptor signaling, but not antigenic specificity, correlates with the differentiation pathway. These observations have implications for the pathogenesis and treatment of autoimmune disease.