gebhart/patrepeval huggingface dataset:
Interferon Action against Human Parainfluenza Virus Type 3: Involvement of a Novel Antiviral Pathway in the Inhibition of Transcription (2001)

Interferon (IFN)-induced 2'-5' oligoadenylate synthetase (2-5A synthetase)/RNase L, PKR, and Mx proteins are considered to be the principal antiviral protein pathways through which IFN induces an antiviral state. It was previously reported that human parainfluenza virus type 3 (HPIV3) multiplication was inhibited by IFN-alpha in human lung epithelial cells A549 and that MxA was found to contribute to the inhibition process (Zhao et al., Virology 220:330-338, 1996). Viral primary transcription was dramatically inhibited in A549 cells after IFN-alpha treatment, but a step following primary transcription was inhibited in U87-MxA cells constitutively expressing MxA. Here we have investigated the role of MxA, believed to be cell type specific, and other antiviral pathways in the inhibition of viral primary transcription. Our data indicate that a novel IFN-induced pathway(s) is involved in the inhibition of primary transcription. This is based on the following findings: (i) IFN-alpha inhibited viral primary transcription in U87-MxA and other cell types including cells lacking MxA; (ii) cells constitutively expressing 2-5A synthetase had no antiviral effect against HPIV3; and (iii) primary transcription occurred in the absence of protein synthesis, a step of PKR target. The novel antiviral pathway(s) was induced by both IFN-alpha and IFN-gamma to establish an effective antiviral state against HPIV3. By using IFN-alpha-signaling mutant cells, we found that IFN-gamma could elicit antiviral effect against HPIV3 without cross talk with the IFN-alpha-signaling pathway. These data provide the first evidence that a novel antiviral pathway(s) contributes to the antiviral action of IFN against a nonsegmented negative-strand RNA virus by targeting the primary transcription.
TTAnalyze: A Tool for Analyzing Malware (2006)

Malware analysis is the process of determining the purpose and functionality of a given malware sample (such as a virus, worm, or Trojan horse). This process is a necessary step to be able to develop effective detection techniques for malicious code. In addition, it is an important prerequisite for the development of removal tools that can thoroughly delete malware from an infected machine. Traditionally, malware analysis has been a manual process that is tedious and time-intensive. Unfortunately, the number of samples that need to be analyzed by security vendors on a daily basis is constantly increasing. This clearly reveals the need for tools that automate and simplify parts of the analysis process. In this paper, we present...
Genomic Cloning of 18 kDa Oleosin and Detection of Triacylglycerols and Oleosin Isoforms in Maturing Rice and Postgerminative Seedlings (1998)

Oleosins are hydrophobic proteins localized abundantly in the oil bodies of plant seeds. Two distinct oleosin isoforms of molecular masses 18 and 16 kDa are present in rice oil bodies. These isoforms were found in similar ratio in rice embryos and aleurone layers. To survey potential DNA sequences involved in the activation of oleosin genes, a genomic clone of rice 18 kDa oleosin was sequenced, and its 5'-flanking region was compared with that of the known rice 16 kDa oleosin gene. Corresponding mRNAs of the two rice oleosin isoforms appeared seven days after pollination and vanished in mature seeds. Triacylglycerols and oleosins were accumulated concomitantly in maturing rice reeds in accord with the active assembly of oil bodies, and partly mobilized in postgerminative seedlings. Approximately 60% of the stored triacylglycerols in rice were not utilized: while the majority of oil bodies in embryos were mobilized in five days after imbibition, those in aleurone layers remained intact in postgerminative seedlings.
Inhibition of Breast Cancer Metastasis and Angiogenesis by Antiosteopontin Single-Chain Fv-Fc Fusion Protein (2009)

Osteopontin (OPN) is associated with many diseases, and its role in tumor growth and metastasis has been studied in breast cancers. Previous studies have described anti-OPN antibodies that could inhibit tumor cell adhesion and invasion in vitro, but until now, there are no systematic studies on antitumor effects of anti-OPN antibodies in vivo. In the present study, we have raised several anti-OPN single-chain variable fragments from phage antibody library and expressed them as single-chain variable fragment-constant region fragment fusion proteins in Chinese hamster ovary cells. Of them, two antibodies (1A12 and 2H8) were able to inhibit MDA-MB-435s breast cancer cell attachment, invasion, migration, and colony formation in soft agar. Furthermore, 1A12 and 2H8 inhibited the anti-apoptotic and prosurvival functions of OPN in human umbilical vein endothelial cell. In human umbilical vein endothelial cell capillary tube formation, chicken chorioallantoic membrane assay, and rabbit corneal micropocket assay, the two antibodies showed markedly inhibitory effects toward angiogenesis. We investigated antitumor effects of anti-OPN antibodies in nude mice by assessing xenograft tumor growth and lung metastasis potential. The results showed that the two antibodies were capable of delaying primary tumor growth and reducing spontaneous lung metastasis. Epitope mappings of these two anti-OPN antibodies were performed, and a new binding site of 1A12 was revealed. In summary, the present study has demonstrated the roles of anti-OPN antibodies in blocking the function of OPN, suggesting that they may have the potential to be developed for future clinical use.
Insulin biosynthesis in neuronal progenitors derived from adult hippocampus and the olfactory bulb (2011)

In the present study, we demonstrated that insulin is produced not only in the mammalian pancreas but also in adult neuronal cells derived from the hippocampus and olfactory bulb (OB). Paracrine Wnt3 plays an essential role in promoting the active expression of insulin in both hippocampal and OB-derived neural stem cells. Our analysis indicated that the balance between Wnt3, which triggers the expression of insulin via NeuroD1, and IGFBP-4, which inhibits the original Wnt3 action, is regulated depending on diabetic (DB) status. We also show that adult neural progenitors derived from DB animals retain the ability to give rise to insulin-producing cells and that grafting neuronal progenitors into the pancreas of DB animals reduces glucose levels. This study provides an example of a simple and direct use of adult stem cells from one organ to another, without introducing additional inductive genes.
Analysis of the idiotypic network in tumor immunity. (1987)

Herein we have analyzed the expression of idiotopes associated with a monoclonal anti-tumor-associated antigen (TAA) antibody in DBA/2 mice which have progressively growing tumors or resist tumor growth. A panel of eight monoclonal antiidiotypic antibodies raised against a monoclonal antibody which reacts with a mouse mammary tumor virus cross-reactive qp52 envelope protein (TAA) of the L1210/GZL lymphoma was used to measure the expression of idiotopes in sera from different treatment groups. Significant correlations between the expression of certain idiotopes and the growth of the tumor or the establishment of anti-tumor immunity are seen. 1) Idiotypes detected by anti-idiotype D11 are high in anti-idiotype immunized progressor or tumor-susceptible mice and low or absent in regressor mice, i.e., the mice immunized with the protective 2F10 anti-idiotype; 2) the 3A4-detected idiotypes are less frequent or absent in irradiated tumor-immunized regressor mice than in untreated mice challenged with live tumor or progressor mice; 3) no difference in the anti-TAA titers is seen in mice in which the tumor growth is inhibited and in mice in which the tumor grows; 4) no difference in 11C1 idiotype + anti-TAA titer was observed between regressor and progressor mice; and 5) mice with normal or accelerated tumor growth have higher titers of idiotypes detected by a polyclonal anti-idiotype. These findings provide evidence for a regulatory idiotype network induced by the growing L1210/GZL tumor or by anti-idiotypic immunization. The titer of anti-TAA antibody does not correlate with the biology of tumor growth, but certain idiotopes correlate with either progressive or regressive tumor behavior. Therefore, the target of the idiotype regulation is likely to be anti-tumor T effector cells. Effective idiotype therapy of tumors must deal with the complexity of idiotype regulation induced by the tumor itself and is unlikely to be successful if anti-idiotypes are used only as internal mimicry of a TAA.
Contractile Properties of Early Human Embryonic Stem Cell-Derived Cardiomyocytes: Beta-Adrenergic Stimulation Induces Positive Chronotropy and Lusitropy but Not Inotropy (2012)

Human embryonic stem cell-derived cardiomyocytes (hESC-CMs) provide the unique opportunity to study the very early development of the human heart. The aim of this study was to investigate the effect of calcium and beta-adrenergic stimulation on the contractile properties of early hESC-CMs. Beating clusters containing hESC-CMs were co-cultured in vitro with noncontractile slices of neonatal murine ventricles. After 5-7 days, when beating clusters had integrated morphologically into the damaged tissue, isometric force measurements were performed during spontaneous beating as well as during electrical field stimulation. Spontaneous beating stopped when extracellular calcium ([Ca²⁺](ec)) was removed or after administration of the Ca²⁺ channel blocker nifedipine. During field stimulation at a constant rate, the developed force increased with incremental concentrations of [Ca²⁺](ec). During spontaneous beating, rising [Ca²⁺](ec) increased beating rate and developed force up to a [Ca²⁺](ec) of 2.5 mM. When [Ca²⁺](ec) was increased further, spontaneous beating rate decreased, whereas the developed force continued to increase. The beta-adrenergic agonist isoproterenol induced a dose-dependent increase of the frequency of spontaneous beating; however, it did not significantly change the developed force during spontaneous contractions or during electrical stimulation at a constant rate. Force developed by early hESC-CMs depends on [Ca²⁺](ec) and on the L-type Ca²⁺ channel. The lack of an inotropic reaction despite a pronounced chronotropic response after beta-adrenergic stimulation most likely indicates immaturity of the sarcoplasmic reticulum. For cell-replacement strategies, further maturation of cardiac cells has to be achieved either in vitro before or in vivo after transplantation.
Enzymatic function of nitric oxide synthases (1999)

Nitric oxide (NO) is synthesised from L-arginine by the enzyme NO synthase (NOS). The complex reaction involves the transfer of electrons from NADPH, via the flavins FAD and FMN in the carboxy-terminal reductase domain, to the haem in the amino-terminal oxygenase domain, where the substrate L-arginine is oxidised to L-citrulline and NO. The haem is essential for dimerisation as well as NO production. The pteridine tetrahydrobiopterin (BH4) is a key feature of NOS, affecting dimerisation and electron transfer, although its full role in catalysis remains to be determined. NOS can also catalyse superoxide anion production, depending on substrate and cofactor availability. There are three main isoforms of the enzyme, named neuronal NOS (nNOS), inducible NOS (iNOS), and endothelial NOS (eNOS), which differ in their dependence on Ca2+, as well as in their expression and activities. These unique features give rise to the distinct subcellular localisations and mechanistic features which are responsible for the physiological and pathophysiological roles of each isoform.
Nonalcoholic fatty liver disease and nonalcoholic steatohepatitis (2008)

Health care providers should not only focus on liver disease but also concentrate on aggressively modifying and treating their cardiovascular risk factors.
Interaction of the Cyclic Antimicrobial Cationic Peptide Bactenecin with the Outer and Cytoplasmic Membrane (1999)

Bactenecin, a 12-amino acid cationic antimicrobial peptide from bovine neutrophils, has two cysteine residues, which form one disulfide bond, making it a cyclic molecule. To study the importance of the disulfide bond, a linear derivative Bac2S was made and the reduced form (linear bactenecin) was also included in this study. Circular dichroism spectroscopy showed that bactenecin existed as a type I beta-turn structure regardless of its environment, while the reduced form and linear bactenecin adopted different conformations according to the lipophilicity of the environment. Bactenecin was more active against the Gram-negative wild type bacteria Escherichia coli, Pseudomonas aeruginosa, and Salmonella typhimurium than its linear derivative and reduced form, while all three peptides were equally active against the outer membrane barrier-defective mutants of the first two bacteria. Only the two linear peptides showed activity against the Gram-positive bacteria Staphylococcus epidermidis and Enterococcus facaelis. Bactenecin interacted well with the outer membrane and its higher affinity for E. coli UB1005 lipopolysaccharide and improved ability to permeabilize the outer membrane seemed to account for its better antimicrobial activity against Gram-negative bacteria. The interaction of bactenecin with the cytoplasmic membrane was determined by its ability to dissipate the membrane potential by using the fluorescence probe 3, 3-dipropylthiacarbocyanine and an outer membrane barrier-defective mutant E. coli DC2. It was shown that the linear derivative and reduced form were able to dissipate the membrane potential at much lower concentrations than bactenecin despite the similar minimal inhibitory concentrations of all three against this barrier-defective mutant.
ChemInform Abstract: The Catalyzed α‐Hydroxyalkylation and α‐Aminoalkylation of Activated Olefins (The Morita—Baylis—Hillman Reaction) (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Transmembrane Protein Insertion Orientation in Yeast Depends on the Charge Difference across Transmembrane Segments, Their Total Hydrophobicity, and Its Distribution (1998)

The determinants of transmembrane protein insertion orientation at the endoplasmic reticulum have been investigated in Saccharomyces cerevisiae using variants of a Type III (naturally exofacial N terminus (Nexo)) transmembrane fusion protein derived from the N terminus of Ste2p, the alpha-factor receptor. Small positive and negative charges adjacent to the transmembrane segment had equal and opposite effects on orientation, and this effect was independent of N- or C-terminal location, consistent with a purely electrostatic interaction with response mechanisms. A 3:1 bias toward Nexo insertion, observed in the absence of a charge difference, was shown to reflect the Nexo bias conferred by longer transmembrane segments. Orientation correlated best with total hydrophobicity rather than length, but it was also strongly affected by the distribution of hydrophobicity within the transmembrane segment. The most hydrophobic terminus was preferentially translocated. Insertion orientation thus depends on integration of responses to at least three parameters: charge difference across a transmembrane segment, its total hydrophobicity, and its hydrophobicity gradient. Relative signal strengths were estimated, and consequences for topology prediction are discussed. Responses to transmembrane sequence may depend on protein-translocon interactions, but responses to charge difference may be mediated by the electrostatic field provided by anionic phospholipids.
The role of small RNAs in human diseases: Potential troublemaker and therapeutic tools (2005)

Small RNAs, including short interfering RNAs (siRNAs) and microRNAs (miRNAs), are ubiquitous, versatile repressors of gene expression in plants, animals, and many fungi. They can trigger destruction of homologous mRNA or inhibition of cognate mRNA translation and play an important role in maintaining the stable state of chromosome structure and regulating the expression of protein-coding genes. Furthermore, the recent research showed that there exists close relationship between small RNAs and human diseases. Several human diseases have surfaced in which miRNAs or their machinery might be implicated, such as some neurological diseases and cancers. The specificity and potency of small RNAs suggest that they might be promising as therapeutic agents. This article will review the role of small RNAs in some human diseases etiology and investigations of taking siRNAs as therapeutic tools for treating viral infection, cancer, and other diseases. We also discuss the potential of miRNAs in gene therapy.
Regulation of the Myeloid-Cell-Expressed Human gp91-phox Gene As Studied by Transfer of Yeast Artificial Chromosome Clones into Embryonic Stem Cells: Suppression of a Variegated Cellular Pattern of Expression Requires a Full Complement of Distant cis Elements (1997)

Identifying the full repertoire of cis elements required for gene expression in mammalian cells (or animals) is challenging, given the moderate sizes of many loci. To study how the human gp91-phox gene is expressed specifically in myeloid hematopoietic cells, we introduced yeast artificial chromosome (YAC) clones and derivatives generated in yeast into mouse embryonic stem cells competent to differentiate to myeloid cells in vitro or into mouse chimeras. Fully appropriate regulation was recapitulated with a 130-kb YAC containing 60 and 30 kb of 5' and 3' flanking sequences, respectively. Immunodetection of human gp91-phox protein revealed uniform expression in individual myeloid cells. The removal of upstream sequences led to decreased overall expression which reflected largely a variegated pattern of expression, such that cells were either "on" or "off," rather than pancellular loss of expression. The proportion of clones displaying marked variegation increased with progressive deletion. DNase I mapping of chromatin identified two hypersensitive clusters, consistent with the presence of multiple regulatory elements. Our findings point to cooperative interactions of complex regulatory elements and suggest that the presence of an incomplete set of elements reduces the probability that an open chromatin domain (or active transcriptional complex) may form or be maintained in the face of repressive influences of neighboring chromatin.
Electroreduction of Chlorine Gas at Platinum Electrodes in Several Room Temperature Ionic Liquids: Evidence of Strong Adsorption on the Electrode Surface Revealed by Unusual Voltammetry in Which Currents Decrease with Increasing Voltage Scan Rates (2008)

Voltammetry is reported for chlorine, Cl2, dissolved in various room temperature ionic liquids using platinum microdisk electrodes. A single reductive voltammetric wave is seen and attributed to the two-electron reduction of chlorine to chloride. Studies of the effect of voltage scan rate reveal uniquely unusual behavior in which the magnitude of the currents decrease with increasing scan rates. A model for this is proposed and shown to indicate the presence of strongly adsorbed species in the electrode reaction mechanism, most likely chlorine atoms, Cl•(ads).
Rrn3 Phosphorylation Is a Regulatory Checkpoint for Ribosome Biogenesis (2002)

Cycloheximide inhibits ribosomal DNA (rDNA) transcription in vivo. The mouse homologue of yeast Rrn3, a polymerase-associated transcription initiation factor, can complement extracts from cycloheximide-treated mammalian cells. Cycloheximide inhibits the phosphorylation of Rrn3 and causes its dissociation from RNA polymerase I. Rrn3 interacts with the rpa43 subunit of RNA polymerase I, and treatment with cycloheximide inhibits the formation of a Rrn3.rpa43 complex in vivo. Rrn3 produced in Sf9 cells but not in bacteria interacts with rpa43 in vitro, and such interaction is dependent upon the phosphorylation state of Rrn3. Significantly, neither dephosphorylated Rrn3 nor Rrn3 produced in Escherichia coli can restore transcription by extracts from cycloheximide-treated cells. These results suggest that the phosphorylation state of Rrn3 regulates rDNA transcription by determining the steady-state concentration of the Rrn3.RNA polymerase I complex within the nucleolus.
Anisotropic diffusion of surface normals for feature preserving surface reconstruction (2004)

For 3D surface reconstruction problems with noisy and incomplete range data measured from complex scenes with arbitrary topologies, a low-level representation, such as level set surfaces, is used. Such surface reconstruction is typically accomplished by minimizing a weighted sum of datamodel discrepancy and model smoothness terms. We introduce a new nonlinear model smoothness term for surface reconstruction based on variations of the surface normals. A direct solution requires solving a fourth-order partial differential equation (PDE), which is very difficult with; conventional numerical techniques. Our solution is based on processing the normals separately from the surface, which allows us to separate the problem into two second-order PDEs. The proposed method can smooth complex, noisy surfaces, while preserving sharp, geometric features, and it is a natural generalization of edge-preserving methods in image processing, such as anisotropic diffusion.
Síndrome de Sweet (2010)

A sindrome de Sweet, tambem conhecida como dermatose neutrofilica febril aguda, caracteriza-se pelo aparecimento de papulas e/ou placas eritematosas dolorosas, muitas vezes em surtos que duram cerca de duas semanas ou mais. Foram revisados caracteristicas clinicas, achados laboratoriais, doencas associadas, histopatologia e opcoes de tratamento da sindrome, assim como sua manifestacao em criancas
JAPANESE AND EUROPEAN WINTER MAINTENANCE TECHNOLOGY (1995)

Snow and ice control operations in the United States differ from those of other countries. A Winter Maintenance Scanning Panel visited Japan and Europe to study these differences. The visits were sponsored by the U.S. Department of Transportation's Federal Highway Administration's Office of International Outreach Programs, the American Association of State Highway and Transportation Officials, and the National Cooperative Highway Research Program of the Transportation Research Board. The panel consisted of six United States managers responsible for snow and ice control operations. They came from federal, state, county, and municipal authorities. General topics of interest to the panel included anti-icing operations, road weather information systems, weather forecasting services, equipment, public information systems, policy, roadway level-of-service criteria, visibility, and environmental issues. The panel visited Japan from March 12 to March 19, 1994, and Germany and Austria from March 20 to March 27, 1994. While in Austria the panel attended the 9th Permanent International Association of Road Congresses, the International Winter Road Congress, and the International Road Weather Conference. The panel proposes the development of a winter maintenance program to demonstrate, evaluate, and acceptance-test promising U.S. and foreign technologies. This program should be a joint effort of the federal, state, and local authorities with snow and ice control responsibilities.
Expression of interleukin‐22 in rheumatoid arthritis: Potential role as a proinflammatory cytokine (2005)

These data suggest that IL-22, produced by synovial fibroblasts and macrophages, promotes inflammatory responses in RA synovial tissues by inducing the proliferation and chemokine production of synovial fibroblasts.