gebhart/patrepeval huggingface dataset:
Species and ecological diversity within the Cladosporium cladosporioides complex (Davidiellaceae, Capnodiales) (2010)

The genus Cladosporium is one of the largest genera of dematiaceous hyphomycetes, and is characterised by a coronate scar structure, conidia in acropetal chains and Davidiella teleomorphs. Based on morphology and DNA phylogeny, the species complexes of C. herbarum and C. sphaerospermum have been resolved, resulting in the elucidation of numerous new taxa. In the present study, more than 200 isolates belonging to the C. cladosporioides complex were examined and phylogenetically analysed on the basis of DNA sequences of the nuclear ribosomal RNA gene operon, including the internal transcribed spacer regions ITS1 and ITS2, the 5.8S nrDNA, as well as partial actin and translation elongation factor 1-α gene sequences. For the saprobic, widely distributed species Cladosporium cladosporioides, both a neotype and epitype are designated in order to specify a well established circumscription and concept of this species. Cladosporium tenuissimum and C. oxysporum, two saprobes abundant in the tropics, are epitypified and shown to be allied to, but distinct from C. cladosporioides. Twenty-two species are newly described on the basis of phylogenetic characters and cryptic morphological differences. The most important phenotypic characters for distinguishing species within the C. cladosporioides complex, which represents a monophyletic subclade within the genus, are shape, width, length, septation and surface ornamentation of conidia and conidiophores; length and branching patterns of conidial chains and hyphal shape, width and arrangement. Many of the treated species, e.g., C. acalyphae, C. angustisporum, C. australiense, C. basiinflatum, C. chalastosporoides, C. colocasiae, C. cucumerinum, C. exasperatum, C. exile, C. flabelliforme, C. gamsianum, and C. globisporum are currently known only from specific hosts, or have a restricted geographical distribution. A key to all species recognised within the C. cladosporioides complex is provided.
The efferent connections of the feline lateral cervical nucleus : a light and electron microscopic study (1985)

The efferent connections of the feline lateral cervical nucleus : a light and electron microscopic study
Intelligent video smoother for multimedia communications (2002)

Multimedia communications often require intra-media synchronization for video data to prevent potential playout discontinuity resulting from network delay variation while still achieving satisfactory playout throughput. We propose a neural-network-based intra-video synchronization mechanism, called the intelligent video smoother (IVS), operating at the application layer of the receiving end system. The IVS is composed of a neural network (NN) traffic predictor, an NN window determinator, and a window-based playout smoothing algorithm. The NN traffic predictor employs an on-line-trained backpropagation neural network (BPNN) to periodically predict the characteristics of traffic modelled by a generic interrupted Bernoulli process (IBP) over a future fixed time period. With the predicted traffic characteristics, the NN window determinator determines the corresponding optimal window by means of an off-line-trained BPNN in an effort to achieve a maximum of the playout quality (Q) value. The window-based playout smoothing algorithm then dynamically adopts various playout rates according to the window and the number of packets in the buffer. Finally, we show via simulation results that, compared to two other playout approaches, the IVS achieves a high-throughput and low-discontinuity playout under a mixture of IBP arrivals.
Effective models to predict customers' responses to interactive audio advertisements (2015)

XAPPmedia provides an interactive audio advertising service that allows customers to connect with advertisers by speaking prompted phases in their audio advertisement. In order to provide better services for their advertisers, XAPPmedia needs to determine key components that influence advertising performance. We developed an Ad Effectiveness model that coaches advertisers to optimize their XAPP advertising configurations for maximum ROI (Return on Investment), and it can also forecast expected advertising performance in the future. In this project, we implemented logistic regression and decision tree models to determine significant variables and the relationship between predictive variables and the voice response rates. We adopt log loss function and accuracy to evaluate model performance. Logistic regression with higher accuracy and smaller loss is a better model for our data than the decision tree.
Prognostic DNA Methylation Marker in Serum of Cancer Patients (2004)

A bstract : Changes in the status of DNA methylation are among the most common molecular alterations in human neoplasia. Recent demonstrations of tumor‐derived methylated DNA in the blood stream of cancer patients allow the use of these epigenetic markers for risk assessment in cancer patients. We were interested in evaluating the prognostic value of several methylated genes in the serum of cancer patients. Using MethyLight, a high‐throughput DNA methylation assay, we analyzed 215 serum samples from patients with cervical ( n = 93 ) or breast cancer ( n = 122 ) for DNA methylation changes. In cervical cancer, hypermethylation of three genes ( MYOD1 , CDH1 , and CDH13 ) in pretreatment sera was statistically significantly associated with a poorer disease outcome. Additionally, for the first time we used a so‐called gene evaluation set to identify the most important DNA methylation changes in the serum of breast cancer patients from a long list of candidate genes. In the gene evaluation set, we detected five genes ( ESR1, APC, HSD17B4, HIC1 , and RASSF1A ) using our criteria for further analysis. Finally, two of the evaluated genes ( APC and RASSF1A ) proved to be independent prognostic parameters in breast cancer patients. In summary, we detected several prognostic DNA methylation markers in the serum of cervical and breast cancer patients. This finding indicates great potential for the use of these epigenetic markers in clinical, routine risk assessment in patients with various malignancies.
MBT-0206 enhances the anti-tumor treatment in a highly metastatic human pancreatic cancer mouse model (2004)

Proc Amer Assoc Cancer Res, Volume 45, 2004

4104 

Treatment of pancreatic cancer is still an unsolved problem because of the limited efficacy of systemic chemotherapy. MBT-0206 is a new anti-cancer agent which targets the neovascular endothelial cells of the tumor vasculature1,2. It is composed of paclitaxel bound to a cationic lipid complex, which has been shown to preferentially accumulate in endothelial cells of pancreatic tumor vessels in transgenic RIP-Tag2 mice3. In the current study we investigated the anti-cancer potential of a combination therapy of MBT-0206 with the standard chemotherapeutic drug gemcitabine against highly metastatic human pancreatic cancer (L3.6pl) growing orthotopically in nude mice. In order to evaluate the biodistribution of MBT-0206, fluorescently labeled cationic lipid complexes (LipoRed™) were injected systemically. For therapeutic studies, animals bearing a L3.6pl tumor were treated for 19 days either by i.v. injected MBT-0206 (5 mg paclitaxel/kg) three times a week, by i.p. injected gemcitabine (100 mg/kg) two times a week or by a combination of both treatments. The biodistribution of fluorescently labeled cationic lipid complexes (LipoRed™) revealed a highly selective accumulation in the tumor vessels compared to surrounding normal pancreas. Administration of the paclitaxel encapsulating MBT-0206 resulted in a strong growth inhibition of primary pancreatic tumors with a tumor size of 46% of the control size at the end of the treatment, which was similar to the efficacy of gemcitabine (47%). Combination therapy led to a strong enhancement of the anti-tumor activity, resulting in a tumor size of only 21% of untreated control tumors. In addition, MBT-0206 alone markedly inhibited the formation of liver metastases and reduced both liver and lymph node metastases when combined with gemcitabine. Interestingly, a dose reduction of gemcitabine by 50% (50 mg/kg) resulted in a comparable therapeutic efficacy and better tolerability of the combination therapy. In summary, these data demonstrate a strong anti-tumor activity of the anti-neovascular targeting agent MBT-0206. Furthermore, the efficacy of MBT-0206 is enhanced when used in combination with gemcitabine. Our results suggest that MBT-0206 as an anti-neovascular agent is a promising candidate for the treatment of pancreatic cancer. 1Kunstfeld R. et al., J Invest Dermatol 120: 476-482, 2003 2Schmitt-Sody M. et al., Clin Cancer Res 9: 2335-2341, 2003 3Thurston et al., J Clin Invest 101:1401-13, 1998
Influence of the gas mixture flow on the processing parameters of hollow cathode discharge iron sintering (2007)

A study was made to verify the influence of the gas mixture flow on the iron sintering process with simultaneous surface enrichment of alloying elements by hollow cathode discharge. In this process, two independent cathodes formed an annular discharge: (1) a pressed cylindrical sample of iron powder, acting as the central cathode, was placed concentrically inside an external (hollow) cathode; (2) the external cathode, machined from a AISI 310 steel bar, acted both to confine the geometry of the plasma and as a source of alloying elements (Cr and Ni). The sintering was carried out at 1423 K, for a period of 7.2 × 103 s, under a gas mixture of 80% Ar + 20% H2 and a pressure of 399 Pa, at flow rates of 2 × 10−6, 5 × 10−6, and 8 × 10−6 m3 s−1, with an inter-cathode radial space of 5.8 mm. The discharge was generated using a pulsed voltage power source with a 200 µs period. The gas mixture flow plays an important role both in the cleanliness of the sintering atmosphere (reflected in the electric power utilized to maintain the sample's temperature) and in the amount of metallic atoms deposited on the sample's surface (as a result of the sputtering and the oxidation/reduction process on the cathode surfaces).
Tim-3 mediates phagocytosis of apoptotic cells and cross-presentation (2009)

Phagocytes such as macrophages and dendritic cells (DCs) engulf apoptotic cells to maintain peripheral immune tolerance. However, the mechanism for the recognition of dying cells by phagocytes is not fully understood. Here, we demonstrate that T-cell immunoglobulin mucin-3 (Tim-3) recognizes apoptotic cells through the FG loop in the IgV domain, and is crucial for clearance of apoptotic cells by phagocytes. Whereas Tim-4 is highly expressed on peritoneal resident macrophages, Tim-3 is expressed on peritoneal exudate macrophages, monocytes, and splenic DCs, indicating distinct Tim-mediated phagocytic pathways used by different phagocytes. Furthermore, phagocytosis of apoptotic cells by CD8(+) DCs is inhibited by anti-Tim-3 mAb, resulting in a reduced cross-presentation of dying cell-associated antigens in vitro and in vivo. Administration of anti-Tim-3 as well as anti-Tim-4 mAb induces autoantibody production. These results indicate a crucial role for Tim-3 in phagocytosis of apoptotic cells and cross-presentation, which may be linked to peripheral tolerance.
Asparaginyl endopeptidase of jack bean seeds. Purification, characterization, and high utility in protein sequence analysis. (1993)

Asparaginyl endopeptidase was highly purified from mature seeds of the jack bean (Canavalia ensiformis). The final enzyme preparation showed a single peak in high-performance liquid chromatography on a reversed-phase column, and the material in the peak gave the following NH2-terminal amino acid sequence on Edman degradation for 25 cycles: H-Glu-Val-Gly-Thr-Arg-Trp-Ala-Val-Leu-Val-Ala-Gly-Ser-Asn-Gly-Tyr-Gly-Asn-Tyr- Arg-His-Gln-Ala-Asp-Val-. Behavior of the enzyme toward various protease inhibitors suggested that it belongs to a family of cysteine proteases. Strict substrate specificity of this enzyme was verified by the use of 14 polypeptide substrates including those derived from proteins. Almost all the peptide bonds on the carboxyl side of Asn residues were susceptible to the enzyme. The exceptions were cases where the residue was at the NH2 terminus or the second position from the NH2 terminus of substrates and where it was N-glycosylated Asn. Peptide bonds on the carboxyl side of any other amino acid residues were not cleaved. These properties promise the high utility of this novel endopeptidase in protein sequence analysis. Identity of jack bean asparaginyl endopeptidase with a processing enzyme responsible for maturation of concanavalin A from its precursor is also discussed.
Diblock Copolymer Thin Film Melts on Striped, Heterogeneous Surfaces:  Parallel, Perpendicular and Mixed Lamellar Morphologies (1999)

We consider the problem of a diblock copolymer melt thin film on a striped surface. Because of the different surface energies, the different stripes have different preferences for each of the blocks, while the upper free surface may also prefer one of the blocks. As a result of a combination of factors such as the surface tensions and chain stretching, a number of morphologies may appear. We allow for perpendicular, parallel, and mixed type lamellae and study the resulting phase diagrams. These diagrams should provide a crude guide for experimental studies on such systems. Our main conclusions are 2-fold. First the phase diagram is intricate and complicated. Second, to produce a single crystal oriented along the stripes, it is best to use thin films and a diblock lamellar size equal to or larger than the stripe width.
Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells (2014)

Phenotypic screening provides a means to discover small molecules that perturb cell biological processes. Discerning the proteins and biochemical pathways targeted by screening hits, however, remains technically challenging. We recently described the use of small molecules bearing photoreactive groups and latent affinity handles as fully functionalized probes for integrated phenotypic screening and target identification. The general utility of such probes, or, for that matter, any small-molecule screening library, depends on the scope of their protein interactions in cells, a parameter that remains largely unexplored. Here, we describe the synthesis of an ~60-member fully functionalized probe library, prepared from Ugi-azide condensation reactions to impart structural diversity and introduce diazirine and alkyne functionalities for target capture and enrichment, respectively. In-depth mass spectrometry-based analysis revealed a diverse array of probe targets in human cells, including enzymes, channels, adaptor and scaffolding proteins, and proteins of uncharacterized function. For many of these proteins, ligands have not yet been described. Most of the probe-protein interactions showed well-defined structure-activity relationships across the probe library and were blocked by small-molecule competitors in cells. These findings indicate that fully functionalized small molecules canvas diverse segments of the human proteome and hold promise as pharmacological probes of cell biology.
A Method of Reducing the Irrelevant Events in a Fault Tree (1996)

Fault tree analysis is NP-hard problem. In this paper, we present a method which reduces size of the fault tree by eliminating the irrelevant events. Irrelevant event is the event which has no contribution to the system failure. In a fault tree, the irrelevant events occur due to the existence of the replicated events. By investigating the structure of the replicated events we establish the conditions which characterize the irrelevant events. Based on these conditions we present the computational algorithm which eliminate the irrelevant events. Complexity of the algorithm is shown to be polynomial and so, this algorithm can be utilized efficiently in FTA.
The tissue factor/factor VIIa/factor Xa complex: A model built by docking and site‐directed mutagenesis (2003)

Factor X is activated to factor Xa (fXa) in the extrinsic coagulation pathway by the tissue factor (TF)/factor VIIa (fVIIa) complex. Upon activation, the fXa molecule remains associated with the TF/fVIIa complex, and this ternary complex is known to activate protease-activated receptors (PARs) 1 and 2. Activation of fVII in the TF complex by fXa is also seen at physiologic concentrations. The ternary complexes TF/fVII/fXa, TF/fVIIa/fX, and TF/fVIIa/fXa are therefore all physiologically relevant and of interest as targets for inhibition of both coagulation and cell-signaling pathways that are important in cardiovascular disease and inflammation. We therefore present a model of the TF/fVIIa/fXa complex, built with the use of the available structures of the TF/fVIIa complex and fXa by protein-protein docking calculations with the program Surfdock. The fXa model has an extended conformation, similar to that of fVIIa in the TF/fVIIa complex, with extensive interactions with TF and the protease domain of fVIIa. All four domains of fXa are involved in the interaction. The gamma-carboxyglutamate (Gla) and epithelial growth factor (EGF1 and EGF2) domains of fVIIa are not significantly involved in the interaction. Docking of the Gla domain of fXa to TF/fVIIa has been reported previously. The docking results identify potential interface residues, allowing rational selection of target residues for site-directed mutagenesis. This combination of docking and mutagenesis confirms that residues Glu51 and Asn57 in the EGF1 domain, Asp92 and Asp95 in the EGF2 domain, and Asp 185a, Lys 186, and Lys134 in the protease domain of factor Xa are involved in the interaction with TF/fVIIa. Other fX protease domain residues predicted to be involved in the interaction come from the 160s loop and the N-terminus of the fX protease domain, which is oriented in such a way that activation of both fVII by fXa, and the reciprocal fX activation by fVIIa, is possible.
Mechanistic Aspects of the Photocatalytic Oxidation of Phenol in Aqueous Solutions (1990)

A photo-catalytic oxidation process using photocatalyst TiO2 and ultra violet light to decompose phenol in aqueous solution was studied. The photocatalyst was thoroughly characterized for specific surface area (BET), surface charge (zeta potential), surface morphology (scanning electron microscopy, SEM) and surface composition (x-ray energy dispersion analysis, EDAX). Parameters such as oxygen, temperature, pH, concentration of photocatalyst, and phenol concentration that may affect the oxidation reaction were thoroughly examined. Results show that oxygen plays one of the most important roles in phenol photo-oxidation. Trace amounts of chloride can inhibit the phenol decomposition reaction while aluminum impurity enhances it. At high phenol concentrations, e.g. ca > 5 X10-2 M, hydroquinone and a biphenyl dimer are the major intermediates of the oxidation reaction. Free radicals such as hydroxyl and super oxide are keys to photo-oxidation of phenol.
Catalytic Nitrile-Alkyne Cross-Metathesis (2007)

The first catalytic cross-metathesis reaction of an alkyne with a nitrile is described. The nitride complex N⋮W(OC(CF3)2CH3)3(DME) undergoes reversible triple-bond metathesis reactions with alkynes (RC⋮CR; R = Et, 4-C6H4OMe), forming the alkylidyne complexes RC⋮W(OC(CF3)2CH3)3(DME) (R = Et, 4-C6H4OMe) along with the corresponding nitrile RC⋮N. This has been exploited to effect catalytic cross-metathesis of nitriles with alkynes, in which the organic CR fragments of two nitriles are coupled to yield an alkyne. A simple “sacrificial” alkyne (3-hexyne) acts as the N-atom acceptor, forming two equivalents of nitrile byproduct (propionitrile).
Effect of Antioxidants on X-ray–induced γ-H2AX Foci in Human Blood Lymphocytes: Preliminary Observations (2012)

The tested formulation of antioxidants significantly reduced formation of γ-H2AX and 53BP1 foci after irradiation at a radiologic radiation dose typical for computed tomographic imaging; administration 60 minutes prior to irradiation seems to be appropriate and leads to a significant reduction in foci.
Autoxidation of 2,6-di-tert-butylphenol with cobalt Schiff base catalysts by oxygen in CO2-expanded liquids (2004)

CO2-expanded acetonitrile and methylene chloride have been used in this first detailed study of catalytic O2 oxidations in these remarkably effective reaction media. The autoxidation of 2,6-di-tert-butylphenol (DTBP) with the cobalt Schiff-base (Co(salen*) in these so-called CO2-expanded liquids (CXLs) has been extensively studied using precisely controlled and monitored batch reactions. The dependence of conversion, selectivity and turn-over-frequency on various reaction parameters, including temperature, [O2], [catalyst], and solvent composition has been evaluated. The rates of O2-oxidation in CXLs are typically 1–2 orders of magnitude greater than those obtained with either the neat organic solvent or supercritical CO2 as reaction media. In keeping with the proposed mechanism, the dependence of both the selectivity and conversion on O2 concentration and catalyst concentration indicates that the O2 adduct, and not free O2, serves as oxidant in two critical steps in these systems. The increase in conversion with increasing temperature supports formation of the phenoxy radical as the rate determining step. In contrast, the temperature independence of selectivity is as expected for two competing radical coupling reactions. The balance between O2 solubility and mixed-solvent dielectric constant determines some of the benefits of the CXLs. Because of the greatly increased solubility of O2 in CXLs, the conversion in those media is substantially greater than that in either scCO2 or the neat organic solvent. However, conversion eventually decreases with increasing CO2 content of the solvent because of the decreasing dielectric constant of the medium. The solubilities of O2 and Co(salen*) have been determined in CXLs based on methylene chloride.
Complement : a practical approach (1997)

1: The complement system: an introduction. 2: Haemolytic assays for whole complement activity and individual components. 3: Immunochemical methods for the detection of complement components and complement activation. 4: Identification, functional assessment, and quantitation of receptors and membrane regulatory proteins whose ligands are C3 and C4. 5: C1 inhibitor and HANe. 6: Formation and regulation of the membrane attack complex. 7: Purification of complement components. 8: The anaphylatoxins. 9: Complement genetics. 10: Biosynthesis of complement components. 11: Complement and immune complexes. 12: Non-human complement
Preferential pairing of T and B cells for production of antibodies without covalent association of T and B epitopes (1994)

T cell from H-2b mice recognize at least 12 sequence regions on the Torpedo acetylcholine receptor (TAChR) alpha, gamma and delta subunits. Immunization of C57BL/6 mice with individual synthetic TAChR sequences known to contain CD4+ epitopes resulted in most cases (10 out of 12 peptides) in anti-peptide antibody (Ab) production, indicating that short TAChR sequences contain both CD4+ and B epitopes. Immunization of C57BL/6 mice with a mixture of a CD4+ epitope peptide, from the TAChR or from an unrelated protein, plus another TAChR sequence forming a "pure" B epitope (T alpha 63-80), induced in most cases anti-peptide Ab and CD4+ cell sensitization only against the peptide containing the CD4+ epitope. However, when the T epitope peptide T alpha 360-378 was co-injected with the B epitope, Ab were also produced against the B epitope peptide. Injection of the individual peptides T alpha 360-378 and T alpha 63-80 at different and distant sites along the back of mice elicited sensitization of CD4+ cells and Ab production only against peptide T alpha 360-378. Therefore, when optimal cooperation between T and B cells occurs, spatial proximity but not covalent association of the B and the CD4+ epitope is necessary for production of Ab against the B epitope.