gebhart/patrepeval huggingface dataset:
Conversion of Waste Agriculture Biomass to Bioethanol by Recombinant <i>Saccharomyces cerevisiae</i> (2010)

Agricultural waste biomass has already been transferred to bioethanol and used as energy related products, although many issues such as efficiency and productivity still to be overcome. In this study, the protein engineering was applied to generate enzymes with completely reversed coenzyme specificity and developed recombinant yeasts containing those engineered enzymes for construction of an efficient biomass-ethanol conversion system. Recombinant yeasts were constructed with the genes encoding a wild type xylose reductase (XR) and the protein engineered xylitol dehydrogenase (XDH) (with NADP) of Pichia stipitis. These recombinant yeasts were characterized based on the enzyme activity and fermentation ability of xylose to ethanol. The protein engineered enzymes were expressed significantly in Saccharomyces cerevisiae as judged by the enzyme activity in vitro. Ethanol fermentation was measured in batch culture under anaerobic conditions. The significant enhancement was found in Y-ARS strain, in which NADP+-dependent XDH was expressed; 85% decrease of unfavorable xylitol excretion with 26% increased ethanol production, when compared with the reference strain expressing the wild-type XDH. Keywords: Agricultural waste biomass; Protein engineering; Xylitol dehydrogenase; Xylose-fermentation; Eethanol production. © 2010 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. DOI: 10.3329/jsr.v2i2.2882 J. Sci. Res. 2 (2), 351-361 (2010)
Osteopetrosis (1998)

Osteopetrosis describes a heterogeneous group of congenital bone disorders characterized by a generalized increase in skeletal mass resulting from a primary reduction in osteoclast-mediated bone resorption. The pathogenetic heterogeneity is due to differences in the mutated gene that adversely affect the development or activation of the osteoclast. There are numerous naturally occurring and induced osteopetrotic mutations in animals; likewise, children afflicted with this disease also fall into various subgroups. The molecular basis for the disease has been determined in some animal mutations, but little is known concerning the etiology of osteopetrosis in most forms in humans. This review will focus on the genetic defects associated with osteopetrosis that have been identified to date and will demonstrate how experimental studies in animal models of osteopetrosis have led to the use of bone marrow transplantation and other alternative strategies to treat osteopetrosis in humans. The clinical outcomes of these therapeutic strategies and potential therapies for use in the future will be discussed. From this review it should become evident that studies of osteopetrosis in animals will continue to identify the molecular causes for other forms of the disease and to provide information that will help develop new strategies for treatment. In addition, the information gained from these experimental studies is likely to shed additional light on osteoclast biology as well as on broader aspects of skeletal diseases such as inflammation-mediated bone loss and osteoporosis.
DQDB networks with and without bandwidth balancing (1992)

It is explained why long distributed queue dual bus (DQDB) networks without bandwidth balancing can have fairness problems when several nodes are performing large file transfers. The problems arise because the network control information is subject to propagation delays that are much longer than the transmission time of a data segment. Bandwidth balancing is then presented as a simple solution. By constraining each node to take only a certain fraction of the transmission opportunities offered to it by the basic DQDB protocol, bandwidth balancing gradually achieves a fair allocation of bandwidth among simultaneous file transfers. Two ways to extend this procedure effectively to multipriority traffic are proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Superconducting Pulse Conserving Logic and Josephson-SRAM (2023)

Superconducting digital Pulse-Conserving Logic (PCL) and Josephson SRAM (JSRAM) memory together enable scalable circuits with energy efficiency 100x beyond leading-node CMOS. Circuit designs support high throughput and low latency when implemented in an advanced fabrication stack with high-critical-current-density Josephson junctions of 1000$μ$A/$μ$m$^2$. Pulse-conserving logic produces one single-flux-quantum output for each input, and includes a three-input, three-output gate producing logical or3, majority3 and and3. Gate macros using dual-rail data encoding eliminate inversion latency and produce efficient implementations of all standard logic functions. A full adder using 70 Josephson junctions has a carry-out latency of 5ps corresponding to an effective 12 levels of logic at 30 GHz. JSRAM (Josephson SRAM) memory uses single-flux-quantum signals throughout an active array to achieve throughput at the same clock rate as the logic. The unit cell has eight Josephson junctions, signal propagation latency of 1ps, and a footprint of 2$μ$m$^2$. Projected density of JSRAM is 4 MB/cm$^2$, and computational density of pulse-conserving logic is on par with leading node CMOS accounting for power densities and clock rates.
Masitinib for treatment of severely symptomatic indolent systemic mastocytosis: a randomised, placebo-controlled, phase 3 study (2017)

Background:Indolent systemic mastocytosis, including the subvariant of smouldering systemic mastocytosis, is a lifelong condition associated with reduced quality of life. Masitinib inhibits KIT and LYN kinases that are involved in indolent systemic mastocytosis pathogenesis. We aimed to assess safety and efficacy of masitinib versus placebo in severely symptomatic patients who were unresponsive to optimal symptomatic treatments.Methods:In this randomised, double-blind, placebo-controlled, phase 3 study, we enrolled adults (aged 18–75 years) with indolent or smouldering systemic mastocytosis, according to WHO classification or documented mastocytosis based on histological criteria, at 50 centres in 15 countries. We excluded patients with cutaneous or non-severe systemic mastocytosis after a protocol amendment. Patients were centrally randomised (1:1) to receive either oral masitinib (6 mg/kg per day over 24 weeks with possible extension) or matched placebo with minimisation according to severe symptoms. The primary endpoint was cumulative response (≥75% improvement from baseline within weeks 8–24) in at least one severe baseline symptom from the following: pruritus score of 9 or more, eight or more flushes per week, Hamilton Rating Scale for Depression of 19 or more, or Fatigue Impact Scale of 75 or more. We assessed treatment effect using repeated measures methodology for rare diseases via the generalised estimating equation model in a modified intention-to-treat population, including all participants assigned to treatment minus those who withdrew due to a non-treatment-related cause. We assessed safety in all patients who received at least one dose of study drug. This trial is registered with ClinicalTrials.gov, number NCT00814073. Findings: Between Feb 19, 2009, and July 15, 2015, 135 patients were randomly assigned to masitinib (n=71) or placebo (n=64). By 24 weeks, masitinib was associated with a cumulative response of 18·7% in the primary endpoint (122·6 responses of 656·5 possible responses [weighted generalised estimating equation]) compared with 7·4% for placebo (48·9 of 656·5; difference 11·3%; odds ratio 3·6; 95% CI 1·2–10·8; p=0·0076). Frequent severe adverse events (&gt;4% difference from placebo) were diarrhoea (eight [11%] of 70 in the masitinib group vs one [2%] of 63 in the placebo group), rash (four [6%] vs none), and asthenia (four [6%] vs one [2%]). The most frequent serious adverse events were diarrhoea (three patients [4%] vs one [2%]) and urticaria (two [3%] vs none), and no life-threatening toxicities occurred. One patient in the placebo group died (unrelated to study treatment). Interpretation:These study findings indicate that masitinib is an effective and well tolerated agent for the treatment of severely symptomatic indolent or smouldering systemic mastocytosis. Funding: AB Science (Paris, France)
Structural Relationship Between Human Salivary Histatins (1990)

Histatins are a group of electrophoretically distinct histidine-rich polypeptides with microbicidal activity found in human parotid and submandibular gland secretions. Recently, we have shown that histatins 1, 3, and 5 are homologous proteins that consist of 38, 32, and 24 amino acid residues, respectively, and that these polypeptides kill the pathogenic yeast, Candida albicans. We now describe the isolation and structural characterization of histatins 2, 4, 6, and 7-12, the remaining members of this group of polypeptides. Histatin 2 was found to be identical to the carboxyl terminal 26 residues of histatin 1; histatin 4 was found to be identical to the carboxyl terminal 20 residues of histatin 3; and histatin 6 was found to be identical to histatin 5, but contained an additional carboxyl terminal arginine residue. The amino acid sequences of histatins 7-12 formally correspond to residues 12-24, 13-24, 12-25, 13-25, 5-11, and 5-12, respectively, of histatin 3, but could also arise proteolytically from histatin 5 or 6. These results establish, for the first time, the complete structural relationships between all members of this group of microbicidal proteins in human parotid saliva. The relationship of histatins to one another is discussed in the context of their genetic origin, biosynthesis and secretion into the oral cavity, and potential as reagents in anti-candidal studies.
Induction of Opsonic Antibodies to Pseudomonas aeruginosa Mucoid Exopolysaccharide by an Anti-idiotypic Monoclonal Antibody (1991)

Mucoid strains of Pseudomonas aeruginosa are the major pulmonary pathogens for cystic fibrosis patients. Opsonizing antibodies to the mucoid exopolysaccharide (MEP) antigen may protect animals and some cystic fibrosis patients from infection. However, MEP does not readily elicit opsonic antibodies either during chronic infection or after vaccination. To evaluate alternative means to induce opsonic antibodies, a murine monoclonal anti-idiotypic antibody directed to an opsonic monoclonal antibody specific to MEP was produced. The anti-idiotypic antibody bound to F(ab')2 fragments of the opsonic antibody, blocked binding to MEP, bound to cross-reactive idiotopes on human opsonic antibodies to MEP, and elicited MEP-specific antibodies in syngeneic and allogeneic mice. These anti-idiotype-induced, MEP-specific antibodies fixed complement to mucoid P. aeruginosa cells and opsonized them for phagocytic killing by human leukocytes. These studies demonstrate the potential utility of anti-idiotypic monoclonal antibody for generating protective immunity against bacterial polysaccharides.
Research and Development of an Efficient Process for the Construction of the 2,4,5-Substituted Pyridines of NK-1 Receptor Antagonists (2006)

Roche has identified a 2,4,5-trisubstituted pyridine template for a new class of potent NK1 receptor antagonists. Previous strategies for construction of the pyridine core of these NK-1 receptor antagonists involved functionalization of a 2,5-disubstituted pyridine. We now report on construction of the pyridine core from commodity components. Shestopalov reported the synthesis of trans-4‘-aryl-5‘-cyano-1‘,2‘,3‘,4‘-tetrahydro-6‘-hydroxy-2‘-oxo-1,3‘-bipyridinium inner salts from 1-(2-amino-2-oxoethyl)pyridinium chloride, aromatic aldehydes, and ethyl cyanoacetate in the presence of a base. Reaction of these salts with phosphorus oxychloride affords 4-aryl-3-cyano-2,6-dichloropyridines. These are efficiently converted to nicotinamide precursors of the Roche NK-1 receptor antagonists by regioselective displacement of one chlorine by an amine, hydrogenolysis of the remaining chlorine, and nitrile hydrolysis.
A Panel of Monoclonal Antibodies to Cytoplasmic GW Bodies and the mRNA Binding Protein GW182 (2003)

GW182 is a mRNA binding protein characterized by 60 repeats of glycine (G):tryptophan (W) motifs and is localized in cytoplasmic structures referred to as GW bodies (GWBs). Current evidence suggests that this unique protein plays a role in mRNA processing. To enable a more detailed study of GW182 and GWBs in cells and tissues, including their role in mRNA processing, we developed four monoclonal antibodies (MAbs) that bind the human recombinant GW182 protein. These MAbs can be used for Western blot analysis and indirect immunofluorescence (IIF) on cultured cells and tissues. Of special interest, one of the MAbs, 2D6, can be used to identify GW182 and GWBs in formalin-fixed and paraffin-embedded tissues after using an antigen retrieval method (ARM). All the MAbs described in this study immunoprecipitate the GW182 protein. Epitope mapping using overlapping 15-mer peptides representing the full-length GW182 showed that the major antibody-binding domains of these MAbs are distinct. These MAbs are valuable tools for cell biologists and pathologists to study the location and function of the novel GW182 protein in tissue culture cells, as well as cryopreserved or archived tissues.
A Non-peptide Mimetic of Ras-CAAX: Selective Inhibition of Farnesyltransferase and Ras Processing (1995)

Cysteine farnesylation of the carboxyl-terminal tetrapeptide CAAX (C = Cys, A = Leu, Ile, or Val, X = Met or Ser) of the oncogene product Ras is required for its malignant transformation activity. As a consequence farnesyltransferase (FTase), the enzyme responsible for this lipid modification, has become one of the most sought-after targets for anticancer drug development. We have recently designed peptide mimics of the COOH-terminal Cys-Val-Ile-Met of KB-Ras where the dipeptide Val-Ile was replaced by aminobenzoic acid derivatives. Although these peptidomimetics are potent inhibitors of FTase in vitro, they retain several undesirable peptide features that hamper their use in vivo. We report here the design, synthesis, and biological activity of the first non-peptide mimetics of CAAX where the tripeptide AAX was replaced by biphenyl derivatives. (R)-4-[N-(3-mercapto-2-aminopropyl)]amino-3'- carboxybiphenyl, where the cysteine is linked to the biphenyl derivative through a secondary amine, contains no amino acids, lacks peptidic features, and has no hydrolyzable bonds. This peptidomimetic is a potent inhibitor of FTase in vitro (IC50 = 50-150 nM) and disrupts Ras processing in whole cells. Furthermore, this non-peptide mimetic of CAAX is highly selective for FTase (666-fold) relative to the closely related geranylgeranyltransferase I. This selectivity is also respected in vivo since the processing of Ras but not the geranylgeranylated Rap1A was disrupted in whole cells. Structure activity relationship studies revealed that FTase recognition and inhibitory potency of CAAX peptidomimetics require free thiol and carboxylate groups separated by a hydrophobic moiety, and that precise positioning of these functional groups must correspond to that of the parent CAAX. The true CAAX peptidomimetic described in this manuscript has several desirable features for further development as a potential anticancer agent. It is not metabolically inactivated by FTase, does not require a pro-drug strategy for inhibition in vivo, and is selective for farnesylation relative to geranylgeranylation.
Expression of Follicle-Stimulating Hormone Receptor in Tumor Blood Vessels (2011)

The follicle-stimulating hormone (FSH) receptor is expressed in adult humans and animals almost exclusively in the testicular Sertoli cells and the ovarian granulosa cells; low levels are expressed in the endothelial cells of the ovary and testis. Previous studies using immunohistochemical methods detected the FSH receptor in the tumor cells of prostate adenocarcinomas. It has been suggested that the FSH receptor is expressed in proliferating tumor cells. A number of studies have found more intense proliferation of tumor cells in variety of human cancers at the tumor periphery. Expression of FSH receptor by endothelial cells may be associated with their proliferation in this specific location. If intravenously administered antibodies to the FSH receptor were able to detect tumor cells on the endothelial cell surface in a wide range of tumors, such tumor-specific endothelial receptors for FSH could be a specific target for tumor imaging and therapy. This study was designed to assess endothelial-cell expression of the FSH receptor in blood vessels of a wide range of human cancers. The FSH receptor was detected in surgical samples from 1336 patients with a wide range of tumors by use of immunohistochemical and immunoblotting techniques, involving 4 monoclonal FSH-receptor antibodies specific for different FSH-receptor epitopes, and by use of in situ hybridization techniques. Immunoelectron microscopy was used to detect the FSH receptor in mice with xenograft tumors. Surgical specimens were obtained from tumors located in the prostate, breast, lung, liver, colon, pancreas, stomach, testis, ovary, urinary bladder, and kidney. The FSH receptor was expressed by endothelial cells of tumor blood vessels in all 1336 patients among all grades including early T1 tumors. The FSH receptor was not expressed in the normal tissues located more than 10-mm outside the tumors in specimens obtained during surgery. Lymphatic vessels in tumors did not express the FSH receptor. Endothelial cells expressing the FSH receptor were found only at the periphery of the tumors in a layer with a thickness of about 10 mm that extended a few millimeters both inside and outside the tumor. After intravenous perfusion of mice bearing the xenograft tumors with anti-FSH-receptor antibodies coupled to colloidal gold, the FSH receptor was exposed on the luminal endothelial surface and could bind and internalize circulating ligands. In contrast, there was only rare binding of anti-FSH-receptor antibodies after perfusion in endothelial cells of normal organs obtained from the same animals. These findings demonstrate the selective expression of the FSH receptor on the endothelial surface of blood vessels in a wide range of tumors in the human beings. The data suggest that tumor-specific endothelial receptors for FSH could be a specific target for tumor imaging and therapy.
Biometric open protocol standard (2017)

Biometric technologies provide consumers with a long-awaited convenience to securely enter cyberspace on the front end. The biometric open protocol standard (BOPS), developed by Hoyos Labs, protects digital assets and digital identities on the backend. BOPS is a biometrics-agnostic standard that opens an application programing interface (API) for registered developers. Entering as a game-changer, BOPS communication architecture enables two-way secure sockets layer (SSL) or transport layer security (TLS) connection over the encryption mechanism to the server, which employs an intrusion detection system (IDS). The IDS is an external system responsible for blacklisting devices that are violating the replay portion of this specification.
Coherent transistor (1993)

The high-frequency operation of an abrupt-heterojunction transistor with ballistic transport in the base is considered. The coherent regime arises at temperatures low enough compared to the injection energy that the injected minority carriers form a nearly collimated and monoenergetic beam. The coherent transistor can have both current gain and power gain at frequencies far above the conventional cutoff. The extended frequency of an intrinsic transistor is limited by the dispersion in the minority-carrier times of flight across the base, rather than the average time of flight itself. The unilateral gain U calculated for an exemplary heterostructure, including the parasitics, demonstrates an active behavior of the coherent transistor in extended frequency ranges.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On-Line Estimation of Laser Weld Penetration (1997)

High-power CO2 laser welding has been widely used in the industry because of its high productivity and excellent weld quality. In order to tap the potential of this process completely, it is important to have on-line weld quality inspection methods to improve the process productivity and reliability by achieving 100 percent weld inspection. Weld penetration is one of the most important factors critical to the quality of a laser weld. However, it is very difficult to directly measure the extent of penetration without sectioning the workpiece. In this paper a model-based penetration depth estimation technique suitable for the production environment is developed. The proposed model relates the temperature measured on the bottom surface of the workpiece, weld bead width, laser beam power and welding speed to penetration depth. The closed-loop depth estimator combines the model and a model-error compensator to compensate for the uncertainty in the measurement of the laser power and absorptivity. Other effects considered are the averaging due to the finite size of the sensor, delay based on the sensor location and the process and sensor dynamics. Several bead-on-plate and butt welds were made on low carbon steel plates to validate the static process models and the depth estimation scheme. Temperatures on the bottom surface of the workpiece during welding were measured using infrared thermocouples. The welds were sectioned longitudinally to obtain the penetration profile. The penetration profiles estimated by the depth estimator matched satisfactorily with the measured penetration profiles. The results validate the capability of the proposed depth estimator to estimate penetration depth and its ability to trace the dynamic changes in penetration depth.
Tailorable stimulated Brillouin scattering in nanoscale silicon waveguides (2013)

Nanoscale modal confinement is known to radically enhance the effect of intrinsic Kerr and Raman nonlinearities within nanophotonic silicon waveguides. By contrast, stimulated Brillouin-scattering nonlinearities, which involve coherent coupling between guided photon and phonon modes, are stifled in conventional nanophotonics, preventing the realization of a host of Brillouin-based signal-processing technologies in silicon. Here we demonstrate stimulated Brillouin scattering in silicon waveguides, for the first time, through a new class of hybrid photonic-phononic waveguides. Tailorable travelling-wave forward-stimulated Brillouin scattering is realized-with over 1,000 times larger nonlinearity than reported in previous systems-yielding strong Brillouin coupling to phonons from 1 to 18 GHz. Experiments show that radiation pressures, produced by subwavelength modal confinement, yield enhancement of Brillouin nonlinearity beyond those of material nonlinearity alone. In addition, such enhanced and wideband coherent phonon emission paves the way towards the hybridization of silicon photonics, microelectromechanical systems and CMOS signal-processing technologies on chip.
Role of frequency domain optical spectroscopy in the detection of neonatal brain hemorrhage ? A newborn piglet study (2000)

Clearly, frequency-domain spectroscopy cannot increase our ability to quantify the volume (size) or the oxygenation of the injected blood, especially in the case of IVH. However, the ability to quantify the baseline tissue absorption and scattering would significantly improve diagnostic performance, and may allow for early identification and treatment of neonatal brain hemorrhage.