gebhart/patrepeval huggingface dataset:
Targeting HER-2/ neu in Early Breast Cancer Development Using Dendritic Cells with Staged Interleukin-12 Burst Secretion (2007)

Overexpression of HER-2/neu (c-erbB2) is associated with increased risk of recurrent disease in ductal carcinoma in situ (DCIS) and a poorer prognosis in node-positive breast cancer. We therefore examined the early immunotherapeutic targeting of HER-2/neu in DCIS. Before surgical resection, HER-2/neu(pos) DCIS patients (n = 13) received 4 weekly vaccinations of dendritic cells pulsed with HER-2/neu HLA class I and II peptides. The vaccine dendritic cells were activated in vitro with IFN-gamma and bacterial lipopolysaccharide to become highly polarized DC1-type dendritic cells that secrete high levels of interleukin-12p70 (IL-12p70). Intranodal delivery of dendritic cells supplied both antigenic stimulation and a synchronized preconditioned burst of IL-12p70 production directly to the anatomic site of T-cell sensitization. Before vaccination, many subjects possessed HER-2/neu-HLA-A2 tetramer-staining CD8(pos) T cells that expressed low levels of CD28 and high levels of the inhibitory B7 ligand CTLA-4, but this ratio inverted after vaccination. The vaccinated subjects also showed high rates of peptide-specific sensitization for both IFN-gamma-secreting CD4(pos) (85%) and CD8(pos) (80%) T cells, with recognition of antigenically relevant breast cancer lines, accumulation of T and B lymphocytes in the breast, and induction of complement-dependent, tumor-lytic antibodies. Seven of 11 evaluable patients also showed markedly decreased HER-2/neu expression in surgical tumor specimens, often with measurable decreases in residual DCIS, suggesting an active process of "immunoediting" for HER-2/neu-expressing tumor cells following vaccination. DC1 vaccination strategies may therefore have potential for both the prevention and the treatment of early breast cancer.
The developmentally regulated type X collagen gene contains a long open reading frame without introns. (1986)

Type X collagen is a recently discovered product of hypertrophic chondrocytes that is localized to presumptive mineralization zones of hyaline cartilage. Thus, in the epiphyseal growth plate of long bones it is present only in the zone of hypertrophic chondrocytes and absent in the resting and rapidly growing cartilage and in bone. Type X collagen represents, therefore, a transient and developmentally regulated collagen which is synthesized by a subpopulation of chondrocytes. We report here the isolation and characterization of cDNA and genomic clones specific for the chicken protein. The results demonstrate that the polypeptide chains of this collagen contain three distinct domains: a short non-collagenous, amino-terminal region, a collagenous domain of 460 amino acid residues, and a non-collagenous, carboxyl-terminal domain of 170 amino acid residues. The nucleotide sequence of the gene shows that these domains are encoded by a long open reading frame that is not interrupted by introns. Examination of the amino acid sequence derived from this nucleotide sequence reveals the presence of a hydrophobic segment localized 10 amino acid residues upstream from the translational stop codon. The length and sequence characteristics of this segment raise the intriguing possibility that Type X collagen polypeptides may contain a transmembrane segment.
Disruption of the neuronal PAS3 gene in a family affected with schizophrenia (2003)

Schizophrenia and its subtypes are part of a complex brain disorder with multiple postulated aetiologies. There is evidence that this common disease is genetically heterogeneous, with many loci involved. In this report, we describe a mother and daughter affected with schizophrenia, who are carriers of a t(9;14)(q34;q13) chromosome. By mapping on flow sorted aberrant chromosomes isolated from lymphoblast cell lines, both subjects were found to have a translocation breakpoint junction between the markers D14S730 and D14S70, a 683 kb interval on chromosome 14q13. This interval was found to contain the neuronal PAS3 gene (NPAS3), by annotating the genomic sequence for ESTs and performing RACE and cDNA library screenings. The NPAS3 gene was characterised with respect to the genomic structure, human expression profile, and protein cellular localisation to gain insight into gene function. The translocation breakpoint junction lies within the third intron of NPAS3, resulting in the disruption of the coding potential. The fact that the bHLH and PAS domains are disrupted from the remaining parts of the encoded protein suggests that the DNA binding and dimerisation functions of this protein are destroyed. The daughter (proband), who is more severely affected, has an additional microdeletion in the second intron of NPAS3. On chromosome 9q34, the translocation breakpoint junction was defined between D9S752 and D9S972 and no genes were found to be disrupted. We propose that haploinsufficiency of NPAS3 contributes to the cause of mental illness in this family.
Access to Heterogeneous Atom-Transfer Radical Polymerization (ATRP) Catalysts Based on Dipyridylamine and Terpyridine via Ring-Opening Metathesis Polymerization (ROMP) (2001)

A series of dipyridylamine and terpyridine derivatives, norborn-2-ene-5-di(pyrid-2-yl)carbamide (1), 4′-(norborn-2-ene-5-ylmethyleneoxy)terpyridine (2), di-(pyrid-2-yl)acetamide (3) and bis(4′-(norborn-2-ene-5-ylmethyleneoxy)-2,2′:6′,2″-terpyridine)iron(II) hexafluorophosphate (4) have been synthesized. Linear homopolymers, poly-1 and poly-2, as well as grafted and coated silica- and PS-DVB-based polymer supports have been prepared therefrom via ring-opening metathesis polymerization (ROMP). Monomer 3, poly-1, poly-2 have been loaded with Cu (I), Cu (II), Fe (II) as well as Hg (II) salts, respectively. These metal complexes as well as metal loaded supports based on compounds 1, 2 and 4 have subsequently been used for homogeneous and heterogeneous atom-transfer radical polymerization (ATRP) of styrene. Systems based on poly-2 coated silica loaded with Cu (I) were found to work best. Under optimum conditions, polystyrene was obtained in 30% yield with polydispersity indices < 1.6 within 2 h and with a remaining metal content in the ng/g (ppb)-range.
Evaluation of Fungicides and Surfactants for Control of Fairy Rings Caused by Marasmius oreades (Bolt ex. Fr.) Fr. (1997)

Marasmius oreades , a causal agent of fairy rings, is one of the most important pathogens of turfgrass in the Great Plains region of North America. Following in vitro and greenhouse screening of surfactants and fungicides, two organosilicone surfactants, Silwet L-77 and Sylgard, together with the fungicide chlorothalonil, were evaluated in the field. Treatments were applied to healthy and infested turfgrass ( Poa pratensis L., Festuca rubra L.) in either 1992, 1993, or in both years. Plots were sampled for grass production, canopy cover, mushroom production, grass chlorophyll content, soil water content, and phytotoxicity. Typically, there were no significant fungicide effects, fungicide by surfactant interactions or differences between Silwet L-77 and Sylgard. Relative to the water control, surfactants caused an approximate 3-fold increase in grass productivity on infested plots in the year of application. However, the difference in canopy cover between organosilicone-treated and control plots tended to be much less. Applying the surfactants to diseased plots in two successive years decreased the canopy cover but had no significant effect on grass production. Chlorophyll content tended to decrease in response to surfactants regardless of whether the turf was infested or healthy. Surfactants almost completely eliminated mushroom production and greatly reduced the occurrence of mycelium. Both organosilicones increased soil water content in infested areas; differences were detectable 2 years after application. Acute phytotoxicity from the surfactants was detected in infested but not in healthy plots. There was no direct evidence of chronic phytotoxicity. Organosilicone surfactants appear to have considerable potential for the management of fairy rings. Chemical names used: oxyalkylenemethylsiloxane (Silwet L-77); 2-(3-hydroxypropyl)-heptamethyltrisiloxane (Sylgard); tetrachloroisopthalonitrile (chlorothalonil).
Tertiary amine N-oxides as bioreductive drugs: DACA N-oxide, nitracrine N-oxide and AQ4N. (1996)

Tertiary amine N-oxides of DNA intercalators with alkylamino sidechains are a new class of bioreductive drugs. N-oxidation masks the cationic charge of the amines, forming prodrugs with low DNA binding affinity and low toxicity which can be activated selectively by metabolic reduction under hypoxic conditions. This study compares three intercalator N-oxides (NC-NO, DACA-NO and AQ4N), which, respectively, give nitracrine (NC), DACA and AQ4 on reduction. In aerobic cell culture all three N-oxide were much less toxic than the corresponding amines, and showed large increases in cytotoxicity under hypoxia. The topoisomerase poisons DACA and AQ4 (and their N-oxides) were less active against non-cycling than cycling cells. However, only AQ4N was active against the mouse mammary tumour MDAH-MCa-4. This dialkylaminoanthraquinone-di-N-oxide has activity at least as great as the reference bioreductive drug RB 6145 against this tumour, both with and without radiation and when combined with the tumour blood flow inhibitor 5,6-dimethylxanthenone-4-acetic acid (DMXAA). It is suggested that the high in vivo activity of AQ4N relative to the other topoisomerase-targeted N-oxide, DACA-NO, may be in part due to release in hypoxic cells of an intracalator with sufficiently high DNA binding affinity that it is retained long enough to kill non-cycling cells when they eventually re-enter the cell cycle.
Reactive Silver Inks for Patterning High-Conductivity Features at Mild Temperatures (2012)

Reactive silver inks for printing highly conductive features (>10(4) S/cm) at room temperature have been created. These inks are stable, particle-free, and suitable for a wide range of patterning techniques. Upon annealing at 90 °C, the printed electrodes exhibit an electrical conductivity equivalent to that of bulk silver.
Object representation for multimedia document interchange (2002)

In order to investigate how high bandwidth communication systems will deal with multimedia documents, a detailed study of the representation of these documents must first be accomplished. The author presents an overview of the various techniques used to represent multimedia information. This includes the representation of the logical and physical structures of the different types of information objects composing multimedia documents. Issues concerning the relationship between these objects in the time domain (such as synchronization) are emphasized. The techniques used for coding and storing the contents of these objects are also discussed. Current standardization efforts in the area of multimedia document interchange are also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Segregation Analysis of Prostate Cancer in Sweden: Support for Dominant Inheritance (1997)

Several epidemiologic studies have shown familial aggregation of prostate cancer. To assess the nature of familial clustering of prostate cancer, a complex segregation analysis was performed on a population-based sample of 2,857 nuclear families ascertained through an affected father diagnosed with prostate cancer in Sweden during 1959-1963. The segregation analysis, using a large, unselected population of prostate cancer families, revealed that the observed clustering of prostate cancer was best explained by a high risk allele inherited in a dominant mode, with a high population frequency (1.67%) and a moderate lifetime penetrance (63%). This study confirms the result from one earlier published segregation analysis and provides the context for interpreting the recently published linkage of hereditary prostate cancer families to chromosome 1q 24-25 (HPC1).
FireDock: Fast interaction refinement in molecular docking (2007)

Abstract Here, we present FireDock, an efficient method for the refinement and rescoring of rigid‐body docking solutions. The refinement process consists of two main steps: (1) rearrangement of the interface side‐chains and (2) adjustment of the relative orientation of the molecules. Our method accounts for the observation that most interface residues that are important in recognition and binding do not change their conformation significantly upon complexation. Allowing full side‐chain flexibility, a common procedure in refinement methods, often causes excessive conformational changes. These changes may distort preformed structural signatures, which have been shown to be important for binding recognition. Here, we restrict side‐chain movements, and thus manage to reduce the false‐positive rate noticeably. In the later stages of our procedure (orientation adjustments and scoring), we smooth the atomic radii. This allows for the minor backbone and side‐chain movements and increases the sensitivity of our algorithm. FireDock succeeds in ranking a near‐native structure within the top 15 predictions for 83% of the 30 enzyme‐inhibitor test cases, and for 78% of the 18 semiunbound antibody‐antigen complexes. Our refinement procedure significantly improves the ranking of the rigid‐body PatchDock algorithm for these cases. The FireDock program is fully automated. In particular, to our knowledge, FireDock's prediction results are comparable to current state‐of‐the‐art refinement methods while its running time is significantly lower. The method is available at http://bioinfo3d.cs.tau.ac.il/FireDock/. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Disturbance of Tunneling Coherence by Oxygen Vacancy in EpitaxialFe/MgO/FeMagnetic Tunnel Junctions (2008)

Oxygen vacancies in the MgO barriers of epitaxial Fe/MgO/Fe magnetic tunnel junctions are observed to introduce symmetry-breaking scatterings and hence open up channels for noncoherent tunneling processes that follow the normal WKB approximation. The evanescent waves inside the MgO barrier thus experience two-step tunneling, the coherent followed by the noncoherent process, and lead to lower tunnel magnetoresistance, higher junction resistance, as well as increased bias and temperature dependence. The characteristic length of the symmetry scattering process is determined to be about 1.6 nm.
Selected Properties of Cs$_{2}$LiYCl$_{6}$, Cs$_{2}$LiLaCl$_{6}$, and Cs$_{2}$LiLaBr$_{6}$ Scintillators (2011)

Homeland security applications often require detection of both neutron and gamma radiation. A combination of two detectors registering neutrons and gammas separately is typically used. Recently, a number of scintillators from the elpasolite crystal family were proposed, that provide detection of both types of radiation. The most promising are Cs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> LiYCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> , Cs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> LiLaCl <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> , and Cs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> LiLaBr <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> . All are doped with Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> . They are capable of providing very high energy resolution. The best values achieved for each material are 3.9%, 3.4%, and 2.9% at 662 keV (FWHM), respectively. Since <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> Li has an acceptable cross-section for thermal neutron capture, these materials also detect thermal neutrons. In the energy spectra, the full energy thermal neutron peak typically appears above 3 MeV gamma equivalent energy. Thus very effective pulse height discrimination can be implemented with these materials. The CLLC and CLYC emissions consist of two main components: Core-to-Valence Luminescence (CVL; 220 nm to 320 nm) and Ce emission (350 to 500 nm). The former is of particular interest since it appears only under gamma excitation. It is also very fast and decays with less than 2 ns time constant. The CVL provides a significant difference to temporal responses under gamma and neutron excitation thus it may be used for effective pulse shape discrimination.
The folding pathway of reduced lysozyme. (1976)

Studies on the mechanism of the glutathione regeneration (Saxena, V.P., and Wetlaufer, D.B. (1970) Biochemistry 9, 5015-5023) of hen egg lysozyme have been carried out. The first two stoichiometric disulfides in lysozyme are formed about 8 times more rapidly than the second two. Almost no enzymic activity is regained until the first two disulfides are formed, thus ruling out an all-or-none mechanism. The disulfide peptides formed early in the regeneration have been isolated and identified. The results show a limited search of folding intermediates, and outline a folding pathway. The early disulfides involve cysteinyl residues III, IV, V, and VI. At the same time cysteinyl residues I, II, VII, and VIII are still reduced, as demonstrated by their isolation as S-alkylated derivatives. At slightly later times a peptide is found which contains the (native) disulfide between cysteinyl residues II and VII. It is likely, but as yet unproven, that formation of disulfide I-VIII completes the cross-linking of lysozyme.
A yeast artificial chromosome-based map of the region of chromosome 20 containing the diabetes-susceptibility gene, MODY1, and a myeloid leukemia related gene. (1996)

We have generated a physical map of human chromosome bands 20q11.2-20q13.1, a region containing a gene involved in the development of one form of early-onset, non-insulin-dependent diabetes mellitus, MODY1, as well as a putative myeloid tumor suppressor gene. The yeast artificial chromosome contig consists of 71 clones onto which 71 markers, including 20 genes, 5 expressed sequence tags, 32 simple tandem repeat DNA polymorphisms, and 14 sequence-tagged sites have been ordered. This region spans about 18 Mb, which represents about 40% of the physical length of 20q. Using this physical map, we have refined the location of MODY1 to a 13-centimorgan interval (approximately equal to 7 Mb) between D20S169 and D20S176. The myeloid tumor suppressor gene was localized to an 18-centimorgan interval (approximately equal to 13 Mb) between RPN2 and D20S17. This physical map will facilitate the isolation of MODY1 and the myeloid tumor suppressor gene.
Synthesis and Acetylcholinesterase/Butyrylcholinesterase Inhibition Activity of 4-Amino-2, 3-diaryl-5, 6, 7, 8-tetrahydrofuro(and thieno)[2, 3-b]-quinolines, and 4-Amino-5, 6, 7, 8, 9-pentahydro-2, 3-diphenylcyclohepta[e]furo(and thieno)-[2, 3-b]pyridines (2002)

The acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE) inhibition activities of a series of 4-amino-2, 3-diaryl-5, 6, 7, 8-tetrahydrofuro[2, 3-b]quinolines (10-12)/4-amino-5, 6, 7, 8-tetrahydro-2, 3-diphenylthieno[2, 3-b]quinoline (14) and 4-amino-5, 6, 7, 8, 9-pentahydro-2, 3-diphenylcyclohepta[e]furo[2, 3-b]pyridine (13)/4-amino-5, 6, 7, 8, 9-pentahydro-2, 3-phenylcyclohepta[e]thieno[2, 3-b]pyridine (15) are described. These compounds are tacrine (THA) analogues which have been prepared either from readily available 2-amino-3-cyano-4, 5-diarylfurans (16-18) or from 2-amino-3-cyano-4, 5-diphenylthiophene (19), via Friedländer condensation with cyclohexanone or cycloheptanone. These compounds are competitive inhibitors for acetylcholinesterase, the more potent being compound (13) which is three-fold less active than tacrine. The butyrylcholinesterase inhibition activity is significant only in compounds 10 and133, which are ten-fold less active than tacrine. It is found that the products 11 and 12 strongly inhibit acetylcholinesterase, and show excellent selectivity regarding butyrylcholinesterase.
Gold nanoparticle-based colorimetric assay for selective detection of aluminium cation on living cellular surfaces (2009)

A colorimetric assay based on pentapeptide (CALNN) functionalized gold nanoparticles exhibits high sensitivity and selectivity for detection of aluminium cation (Al(3+)) both in aqueous solution and on living cellular surfaces under physiological condition.
Expression, Purification, and Characterization of Interferon-tau Produced in Pichia pastoris Grown in a Minimal Medium (1999)

Interferon-tau (IFN-tau) is a novel type I IFN that was originally identified as a pregnancy recognition hormone. IFN-tau shares all of the biological properties of other type I IFNs including antiviral activity and antiproliferative activity through induction of the cell cycle inhibitor gene product p21WAF1. It is a promising therapy for cancers, viral infections, and for autoimmune disorders such as multiple sclerosis, without the adverse side effects associated with IFN-alpha and IFN-beta. Here, we describe novel growth and induction conditions for the expression of functionally active and uniformly 15N-labeled IFN-tau from Pichia pastoris in a minimal media for use in initial 2D- and 3D-NMR studies in solution. Purified 15N-IFN-tau was homogenous, as determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and MALDI-TOF mass spectrometer (MS), and retained full biological activity. MS analysis confirmed uniform isotopic labeling of IFN-tau with 15N incorporation exceeding 99%. Circular dichroism (CD) as well as 1D-NMR and 15N-1H heteronuclear single quantum coherence (HSQC) spectra confirmed that purified 15N-labeled IFN-tau has a stable secondary structure. Besides providing a route for isotope labeling of IFN-tau, our procedure may be useful for the expression and purification of other proteins that are difficult to obtain in Pichia pastoris grown in minimal media.
An Angiogenic Extract from Skeletal Muscle Stimulates Monocyte and Endothelial Cell Chemotaxis In Vitro (1991)

The purpose of this study was to determine whether the extraction of skeletal muscle with a combination of ethanol and hydrochloric acid yields a product capable of stimulating angiogenesis. The resulting extract stimulated inflammation in the rabbit corneal assay, which was followed by capillary formation. In order to determine whether the observed angiogenesis was stimulated by a factor(s) acting directly on the endothelial cells versus a factor(s) recruiting macrophages that in turn release factors acting on endothelial cells, the muscle extract was tested for endothelial cell and monocyte chemotaxis activity in vitro. The muscle extract stimulated significant endothelial cell chemotaxis at concentrations between 94 and 750 micrograms of protein/ml and significant monocyte chemotaxis at concentrations between 8 and 75 micrograms of protein/ml. Polyacrylamide gel electrophoresis suggests that basic fibroblast growth factor and transforming growth factor-beta may be present in this acid/ethanol extract of skeletal muscle.
Closed-form inverse kinematic solution for fluoroscopic C-arms (2007)

Abstract This paper presents a closed-form solution to the inverse kinematic problem for general fluoroscopic C-arms. The resulting algorithm determines the necessary joint parameters for imaging a given point of interest p→ from a given direction z→. The existence and uniqueness of the solution is proven for all p→ and z→. The inverse kinematics lays the basis for a completely robotized C-arm. The paper describes some applications for such an automatized device and presents the first results. Keywords: INVERSE KINEMATICSROBOTIZED FLUOROSCOPIC C-ARMDIGITAL SUBTRACTION ANGIOGRAPHYCOMPUTED TOMOGRAPHY