gebhart/patrepeval huggingface dataset:
Mechanism for hydrogen compensation of shallow-acceptor impurities in single-crystal silicon (1985)

Experimental results are presented which identify the following chemical reaction as being responsible for compensation of shallow-acceptor impurities when single-crystal silicon is exposed to monatomic hydrogen: ${A}^{\ensuremath{-}}+{h}^{+}+{\mathrm{H}}^{0}\ensuremath{\leftrightarrow}{(A\mathrm{H})}^{0}$, where ${A}^{\ensuremath{-}}$ represents an ionized shallow acceptor, ${h}^{+}$ is a (positively charged) free hole, and ${\mathrm{H}}^{0}$ is a neutral hydrogen atom. Infrared absorption spectroscopy on boron-doped silicon, combined with recent defect-model calculations, reveals that the hydrogen atom forms a Si-H bond at the site of a substitutional boron atom; the absorption band for the stretch mode appears at 1870 ${\mathrm{cm}}^{\ensuremath{-}1}$. Measurements by secondary-ion mass spectrometry of impurity profiles in deuterated silicon reveal that shallow-acceptor passivation is suppressed by counter doping to produce $n$-type conductivity. These new results identify both the defect complex responsible for hydrogen compensation of shallow acceptors and the essential role of free holes, or equivalently neutral acceptors, in the chemical reaction.
Possible Involvement of Leaf Gibberellins in the Clock-Controlled Expression of XSP30, a Gene Encoding a Xylem Sap Lectin, in Cucumber Roots (2003)

Root-produced organic compounds in xylem sap, such as hormones and amino acids, are known to be important in plant development. Recently, biochemical approaches have revealed the identities of several xylem sap proteins, but the biological functions and the regulation of the production of these proteins are not fully understood. XYLEM SAP PROTEIN 30 kD (XSP30), which is specifically expressed in the roots of cucumber (Cucumis sativus), encodes a lectin and is hypothesized as affecting the development of above-ground organs. In this report, we demonstrate that XSP30 gene expression and the level of XSP30 protein fluctuate in a diurnal rhythm in cucumber roots. The rhythmic gene expression continues for at least two or three cycles, even under continuous light or dark conditions, demonstrating that the expression of this gene is controlled by a circadian clock. Removal of mature leaves or treatment of shoots with uniconazole-P, an inhibitor of gibberellic acid (GA) biosynthesis, dampens the amplitude of the rhythmic expression; the application of GA negates these effects. These results suggest that light signals perceived by above-ground organs, as well as GA that is produced, possibly, in mature leaves, are important for the rhythmic expression of XSP30 in roots. This is the first demonstration of the regulation of the expression of a clock-controlled gene by GA.
The Chondrocyte: Biology and Clinical Application (2006)

Chondrocyte is a unique cell type in articular cartilage tissue and is essential for cartilage formation and functionality. It arises from mesenchymal stem cells (MSCs) and is regulated by a series of cytokine and transcription factor interactions, including the transforming growth factor-beta super family, fibroblast growth factors, and insulin-like growth factor-1. To understand the biomechanisms of the chondrocyte differentiation process, various cellular model systems have been employed, such as primary chondrocyte culture, clonal normal cell lines (HCS-2/8, Ch-1, ATDC5, CFK-2, and RCJ3.1C5.18), and transformed clonal cell lines (T/C-28a2, T/C-28a4, C-28/I2, tsT/AC62, and HPV-16 E6/E7). Additionally, cell culture methods, including conventional monolayer culture, three-dimensional scaffold culture, bioreactor culture, pellet culture, and organ culture, have been established to create stable environments for the expansion, phenotypic maintenance, and subsequent biological study of chondrocytes for clinical application. Knowledge gained through these study systems has allowed for the use of chondrocytes in orthopedics for the treatment of cartilage injury and epiphyseal growth plate defects using tissue-engineering approaches. Furthermore, the potential of chondrocyte implantation for facial reconstruction, the treatment of long segmental tracheal defects, and urinary incontinence and vesicoureteral reflux are being investigated. This review summarizes the present study of chondrocyte biology and the potential uses of this cell in orthopedics and other disciplines.
Cetuximab, a Monoclonal Antibody Targeting the Epidermal Growth Factor Receptor, in Combination With Gemcitabine for Advanced Pancreatic Cancer: A Multicenter Phase II Trial (2004)

Cetuximab in combination with gemcitabine showed promising activity against advanced pancreatic cancer. Further clinical investigation is warranted.
The Mismatch Repair System Reduces Meiotic Homeologous Recombination and Stimulates Recombination-Dependent Chromosome Loss (1996)

Efficient genetic recombination requires near-perfect homology between participating molecules. Sequence divergence reduces the frequency of recombination, a process that is dependent on the activity of the mismatch repair system. The effects of chromosomal divergence in diploids of Saccharomyces cerevisiae in which one copy of chromosome III is derived from a closely related species, Saccharomyces paradoxus, have been examined. Meiotic recombination between the diverged chromosomes is decreased by 25-fold. Spore viability is reduced with an observable increase in the number of tetrads with only two or three viable spores. Asci with only two viable spores are disomic for chromosome III, consistent with meiosis I nondisjunction of the homeologs. Asci with three viable spores are highly enriched for recombinants relative to tetrads with four viable spores. In 96% of the class with three viable spores, only one spore possesses a recombinant chromosome III, suggesting that the recombination process itself contributes to meiotic death. This phenomenon is dependent on the activities of the mismatch repair genes PMS1 and MSH2. A model of mismatch-stimulated chromosome loss is proposed to account for this observation. As expected, crossing over is increased in pms1 and msh2 mutants. Furthermore, genetic exchange in pms1 msh2 double mutants is affected to a greater extent than in either mutant alone, suggesting that the two proteins act independently to inhibit homeologous recombination. All mismatch repair-deficient strains exhibited reductions in the rate of chromosome III nondisjunction.
Re-evaluation of Conditions for Plant Regeneration and Agrobacterium-Mediated Transformation from Tomato (Lycopersicon esculentum) (1993)

Conditions for plant regeneration from explants of tomato (Lycopersicon esculentum) cv. UC82B were studied for optimizing transformation procedure. The best regeneration rate was obtained from cotyledon explants from 8–10-d-old seedlings on a modified Murashige and Skoog medium (1962) with 0·5 mg dm−3 zeatin and 0·5 mg dm−3 indolylacetic acid. Tomato cultivars (UC82B, Castone, Fl Ferline, Monalbo) and a Lycopersicon peruvkmum ‘CMV sel. INRA’ were studied. The cultivarUC82B and the wild Lycopersicon species showed an efficient shoot regeneration potential. Early events in the transformation of tomato cotyledons were analysed using an Agrobacterium tumefaciens strain carrying a binary vector with an nptII (pnos) gene and a reporter GUS-intron (p35S) chimeric gene. Two days after infection, GUS activity appeared specifically at the cut surface. Subepidermal cells were more susceptible to transformation than epidermal cells. When selection for kanamycin resistance was applied 2 d after inoculation, transformed cells were efficiently recovered. Preculture with feeder cells stimulated cell transformation, but reducedregeneration capacity from transformed cells. The optimal transformation rate was observed witha time of preculture of 1 and 2 d. Transformation events for two tomato cultivars (UC82B and Monalbo) occurred at the same rate as 55% of the inoculated explants developed kanamycin resistant calli. However, transformed plants were obtained at different rates of 8% and 14% for cv. Monalbo and cv. UC82B.
Drug resistance to targeted therapies: Déjà vu all over again (2014)

A major limitation of targeted anticancer therapies is intrinsic or acquired resistance. This review emphasizes similarities in the mechanisms of resistance to endocrine therapies in breast cancer and those seen with the new generation of targeted cancer therapeutics. Resistance to single-agent cancer therapeutics is frequently the result of reactivation of the signaling pathway, indicating that a major limitation of targeted agents lies in their inability to fully block the cancer-relevant signaling pathway. The development of mechanism-based combinations of targeted therapies together with non-invasive molecular disease monitoring is a logical way forward to delay and ultimately overcome drug resistance development.
Integral imaging with large depth of field using an asymmetric phase mask (2007)

We propose to improve the depth of field of Integral Imaging systems by combining an array of phase masks with the traditional lenslet array. We show that obtained elemental images are sharp over a larger range than with a regular lenslet array. We further increase the quality of elemental images by a digital restauration. Computer simulations of pickup and reconstruction are presented.
Action pattern of polysaccharide lyases on glycosaminoglycans (1994)

The action pattern of polysaccharide lyases on glycosaminoglycan substrates was examined using viscosimetric measurements and gradient polyacrylamide gel electrophoresis (PAGE). Heparin lyase I (heparinase, EC 4.2.2.7) and heparin lyase II (no EC number) both acted on heparin in a random endolytic fashion. Heparin lyase II showed an ideal endolytic action pattern on heparan sulphate, while heparin lyase I decreased the molecular weight of heparan sulphate more slowly. Heparin lyase III (heparitinase, EC 4.2.2.8) acted endolytically only on heparan sulphate and did not cleave heparin. Chondroitin ABC lyase (chondroitinase ABC, EC 4.2.2.4) from Proteus vulgaris acted endolytically on chondroitin-6-sulphate (chondroitin sulphate C) and dermatan sulphate at nearly identical initial rates, but acted on chondroitin-4-sulphate (chondroitin sulphate A) at a reduced rate, decreasing its molecular weight much more slowly. Two chondroitin AC lyases (chondroitinase AC, both EC 4.2.2.5) were examined towards chondroitin-4- and -6-sulphates. The exolytic action of chondroitin AC lyase A from Arthrobacter aurescens on both chondroitin-4- and -6-sulphates was demonstrated viscosimetrically and confirmed using both gradient PAGE and gel permeation chromatography. Chondroitin AC lyase F from Flavobacterium heparinum (Cytophagia heparinia) acted endolytically on the same substrates. Chondroitin B lyase (chondroitinase B, no EC number) from F.heparinum acted endolytically on dermatan sulphate giving a nearly identical action pattern as observed for chondroitin ABC lyase acting on dermatan sulphate.
Theiler's Virus Infection: a Model for Multiple Sclerosis (2004)

Both genetic background and environmental factors, very probably viruses, appear to play a role in the etiology of multiple sclerosis (MS). Lessons from viral experimental models suggest that many different viruses may trigger inflammatory demyelinating diseases resembling MS. Theiler's virus, a picornavirus, induces in susceptible strains of mice early acute disease resembling encephalomyelitis followed by late chronic demyelinating disease, which is one of the best, if not the best, animal model for MS. During early acute disease the virus replicates in gray matter of the central nervous system but is eliminated to very low titers 2 weeks postinfection. Late chronic demyelinating disease becomes clinically apparent approximately 2 weeks later and is characterized by extensive demyelinating lesions and mononuclear cell infiltrates, progressive spinal cord atrophy, and axonal loss. Myelin damage is immunologically mediated, but it is not clear whether it is due to molecular mimicry or epitope spreading. Cytokines, nitric oxide/reactive nitrogen species, and costimulatory molecules are involved in the pathogenesis of both diseases. Close similarities between Theiler's virus-induced demyelinating disease in mice and MS in humans, include the following: major histocompatibility complex-dependent susceptibility; substantial similarities in neuropathology, including axonal damage and remyelination; and paucity of T-cell apoptosis in demyelinating disease. Both diseases are immunologically mediated. These common features emphasize the close similarities of Theiler's virus-induced demyelinating disease in mice and MS in humans.
A design for the ICARUS architecture (1991)

We describe our designs for ICARUS, an integrated architecture for controlling an intelligent agent in a complex physical environment. By navigating between locations and manipulating other objects, the agent influences the world and achieves its goals. The architecture includes components for perceiving the environment, for generating plans to solve problems, and for executing the plans generated. A fourth component manages the agent's long-term memory. Our assessment of the design suggests that it is general, versatile, scales well to larger problems, and is consistent with a variety of psychological results.
DMAPS: a database of multiple alignments for protein structures (2005)

The database of multiple alignments for protein structures (DMAPS) provides instant access to pre-computed multiple structure alignments for all protein structure families in the Protein Data Bank (PDB). Protein structure families have been obtained from four distinct classification methods including SCOP, CATH, ENZYME and CE, and multiple structure alignments have been built for all families containing at least three members, using CE-MC software. Currently, multiple structure alignments are available for 3050 SCOP-, 3087 CATH-, 664 ENZYME- and 1707 CE-based families. A web-based query system has been developed to retrieve multiple alignments for these families using the PDB chain ID of any member of a family. Multiple alignments can be viewed or downloaded in six different formats, including JOY/html, TEXT, FASTA, PDB (superimposed coordinates), JOY/postscript and JOY/rtf. DMAPS is accessible online at http://bioinformatics.albany.edu/~dmaps.
Characterization of the human melanoma nerve growth factor receptor. (1985)

Monoclonal antibodies to the human nerve growth factor receptor have been used to biochemically characterize the receptor in the human melanoma cell line A875. Labeling of A875 cell proteins by culture with [35S]cysteine or labeling of cell surface proteins with 125I followed by immunoprecipitation with anti-nerve growth factor receptor antibody reveals a receptor protein with an apparent Mr of 70,000-75,000 and an isoelectric point of 4.9-5.2. Incorporation of [3H]glucosamine into this species indicates it is a glycoprotein. The receptor becomes phosphorylated on serine residues in intact cells and in isolated membranes incubated with [gamma-32P]ATP. The receptor appears to exist, at least partially, in the form of a disulfide-linked oligomer (probably a dimer) of Mr = 75,000 subunits. Kinetic [35S]cysteine labeling studies reveal an Mr = 59,000 core protein which is glycosylated via N-linked and probably also O-linked sugar moieties to produce the mature (Mr = 70,000-75,000) receptor.
Reduction of mispriming in amplification reactions with restricted PCR. (1995)

A simple method is described for reducing nonspecific background, which is caused by mispriming during PCR. Besides the standard pair of primers, 3'-dideoxy-terminated competitor oligonucleotides were added to the amplification. Sequences to those of the primers which had identical base. In this way enhanced specificity was achieved. The competitor oligonucleotides may act by masking possible sites of nonspecific primer-template interaction, thus excluding undesired chain extensions. This technique is generally applicable when highly degenerate primers are used and therefore expands the potential of "restricted" PCR.
Localization of Antibody-Combining Sites within the Variable Portions of Heavy and Light Chains (1972)

The Fab'-fragment of a mouse IgA-myeloma (protein-315) was split by pepsin to yield a smaller fragment that retained the anti-2,4-dinitrophenyl activity of the intact protein. This fragment, which we call Fv, has a molecular weight of about 30,000 (half that of Fab'), and is composed of two polypeptide chains (molecular weight 14,000) held together by noncovalent bonds. The N-terminal sequence of Fv suggests that it is composed of the N-terminal half of Fab', and consists of the variable portions of the heavy and light chains. Since Fv has about one binding site with the same association constant as Fab', this experiment provides direct evidence that the antibody site in this protein is contained entirely in the variable portion, and is independent of the constant portion, of the molecule.
Peroxynitrite-mediated DNA strand breakage activates poly-adenosine diphosphate ribosyl synthetase and causes cellular energy depletion in macrophages stimulated with bacterial lipopolysaccharide (1996)

The inducible isoform of nitric oxide (NO) synthase produces large quantities of NO, a cytotoxic free radical. Recent studies show that treatment with exogenous NO produces DNA strand breaks, activating the nuclear repair enzyme poly(ADP)ribosyltransferase (PARS), which results in ADP ribosylation, NAD+ consumption, and exhaustion of intracellular energy stores. Here we have characterized the cytotoxic effect of endogenous NO and peroxynitrite, a reactive oxidant formed from NO and superoxide. Immunostimulation of J774.2 macrophages with endotoxin resulted in the generation of superoxide (within 1 h) and NO (after 8 h). NO production paralleled an increase in peroxynitrite formation and DNA strand breakage, and a decrease in intracellular NAD+ content and mitochondrial respiration. Inhibition of NO synthase by NG-methyl-L-arginine or S-methyl-isothiourea or inhibition of PARS activity by 3-aminobenzamide or nicotinamide prevented the decrease in mitochondrial respiration and the depletion of NAD+. A similar pattern of free radical formation and cytotoxicity was observed in peritoneal macrophages from endotoxemic rats (formation of NO, superoxide, peroxynitrite, and DNA strand breaks). In vivo treatment with 3-aminobenzamide preserved mitochondrial respiration, NAD+, and ATP. Our data suggest that inflammatory cell injury involved DNA strand breakage and PARS, triggering an energy-consuming, futile repair cycle leading to cellular energy depletion. The active species responsible for the development of DNA strand breaks is peroxynitrite, rather than NO, since exogenous peroxynitrite, but not NO, induces DNA strand breaks. Inhibition of PARS may improve cellular energy homeostasis in patho-physiologic conditions associated with peroxynitrite generation.
Production of Wnt Inhibitors by Myeloma Cells: Potential Effects on Canonical Wnt Pathway in the Bone Microenvironment (2007)

Osteoblast impairment occurs within multiple myeloma cell infiltration into the bone marrow. Canonical Wnt signaling activation in osteoprogenitor cells is involved in osteoblast formation through the stabilization of dephosphorylated beta-catenin and its nuclear translocation. The effects of multiple myeloma cells on Wnt signaling in human mesenchymal/osteoprogenitor cells are unclear. In 60 multiple myeloma patients checked, we found that among the Wnt inhibitors, Dickkopf-1 and secreted frizzled-related protein-3 were produced by multiple myeloma cells. However, although multiple myeloma cells or multiple myeloma bone marrow plasma affected expression of genes in the canonical Wnt signaling and inhibited beta-catenin stabilization in murine osteoprogenitor cells, they failed to block the canonical Wnt pathway in human mesenchymal or osteoprogenitor cells. Consistently, Wnt3a stimulation in human osteoprogenitor cells did not blunt the inhibitory effect of multiple myeloma cells on osteoblast formation. Consequently, despite the higher Wnt antagonist bone marrow levels in osteolytic multiple myeloma patients compared with nonosteolytic ones, beta-catenin immunostaining was not significantly different. Our results support the link between the production of Wnt antagonists by multiple myeloma cells and the presence of bone lesions in multiple myeloma patients but show that myeloma cells do not inhibit canonical Wnt signaling in human bone microenvironment.
Mito-DCA: A Mitochondria Targeted Molecular Scaffold for Efficacious Delivery of Metabolic Modulator Dichloroacetate (2014)

Tumor growth is fueled by the use of glycolysis, which normal cells use only in the scarcity of oxygen. Glycolysis makes tumor cells resistant to normal death processes. Targeting this unique tumor metabolism can provide an alternative strategy to selectively destroy the tumor, leaving normal tissue unharmed. The orphan drug dichloroacetate (DCA) is a mitochondrial kinase inhibitor that has the ability to show such characteristics. However, its molecular form shows poor uptake and bioavailability and limited ability to reach its target mitochondria. Here, we describe a targeted molecular scaffold for construction of a multiple DCA loaded compound, Mito-DCA, with three orders of magnitude enhanced potency and cancer cell specificity compared to DCA. Incorporation of a lipophilic triphenylphosphonium cation through a biodegradable linker in Mito-DCA allowed for mitochondria targeting. Mito-DCA did not show any significant metabolic effects toward normal cells but tumor cells with dysfunctional mitochondria were affected by Mito-DCA, which caused a switch from glycolysis to glucose oxidation and subsequent cell death via apoptosis. Effective delivery of DCA to the mitochondria resulted in significant reduction in lactate levels and played important roles in modulating dendritic cell (DC) phenotype evidenced by secretion of interleukin-12 from DCs upon activation with tumor antigens from Mito-DCA treated cancer cells. Targeting mitochondrial metabolic inhibitors to the mitochondria could lead to induction of an efficient antitumor immune response, thus introducing the concept of combining glycolysis inhibition with immune system to destroy tumor.
A Phase I clinical and pharmacological evaluation of sodium phenylbutyrate on an 120-h infusion schedule. (2001)

The DLT in this Phase I study for infusional PB given for 5 days every 21 days is neuro-cortical in nature. The recommended Phase II dose is 410 mg/kg/day for 120 h.
Syntheses, Characterization, and Photophysics Studies of Photoactive Chromophore 2-Naphthyl-Labeled [n]-Ladderanes (1996)

The syntheses and characterization of a series of saturated ladderanes 3, oligomers of 1,3-cyclobutadiene-1,2-dicarboxylate diesters with pendant 2-naphthyl groups, are described. Absorption and fluorescence spectra provide evidence for a ground state through-space interchromophore interaction that becomes stronger with an increasing number of pendant aryl groups. A new fluorescence band (λmax = 303 nm) observed in the tetramer (3c) and pentamer (3d) as blue-shifted from the monomer (λmax = 335 nm) was assigned as emission from an imperfectly stacked chromophore array. Nonexponential fluorescence decays of all four oligomers, obtained by single photon counting, are accommodated well by conformations attained from a molecular mechanics geometry optimization. In the solid state, the monomeric precursor of the family, tricarbonyl[di-2-naphthylmethyl 1,2,3,4-η-1,3-cyclobutadiene-1,2-dicarboxylate]iron (2), exists as highly stable channel solvate under ambient conditions.