gebhart/patrepeval huggingface dataset:
SDF-1 alone and in co-operation with HGF regulates biology of human cervical carcinoma cells. (2006)

Stromal Derived Factor-1 (SDF-1)-CXCR4 axis plays a pivotal role in biology and metastasis of several tumors. The aim of this study was to see if SDF-1 alone or in combination with Hepatocyte Growth Factor (HGF) affects biology of human cervical carcinoma (HCC) cells. We found that HCC cell lines investigated in our study highly express CXCR4 on their surface. CXCR4 was also expressed on tumor cells in tissue sections derived from cervical cancer patients. At the same time normal cervical epithelium was negative for CXCR4 expression what suggests a strong correlation between CXCR4 and malignant cell phenotype. Subsequently, we studied a potential role of the SDF-1-CXCR4 axis in HCC and noticed that SDF-1 (i) chemoattracted HCC cells, (ii) enhanced their scattering, (iii) stimulated nuclear localization of beta-catenins and upregulated their target gene cyclin D1 and (iv) at the molecular level induced calcium flux and activated RAS-MAPK, PI3-AKT and JAK-STAT pathways. SDF-1-mediated functions were additionally enhanced in the presence of HGF. Thus, our data show that the SDF-1-CXCR4 axis affects biology of HCC cells. Furthermore, we postulate that this axis might become a potential target to prevent progression of cervical cancer.
Three-dimensional optical coherence tomography of Barrett’s esophagus and buried glands beneath neosquamous epithelium following radiofrequency ablation (2009)

We report three-dimensional (3D) endoscopic microscopy findings in Barrett's esophagus, using an endoscopic optical coherence tomography (OCT) system in one patient before and in one patient after radiofrequency ablation (RFA). Findings were compared with those in a normal patient without Barrett's esophagus. In the normal patient,findings were of regular flat squamous mucosa with small subepithelial vessels and glands. In the Barrett's esophagus patient, findings were of large, densely packed glands with distortion of mucosal architecture. In the post-RFA case, findings were of a small number of isolated glands buried beneath 300-500 microm of neosquamous epithelium and lamina propria. Neosquamous epithelium is a marker of successful ablative therapy, while buried glands may have potential for dysplastic progression and are difficult to detect using conventional methods. These results indicate a potential role of 3D-OCT endoscopic microscopy for follow-up, including subsurface assessment, of ablative treatments for Barrett's esophagus.
End-to-end and end-to-middle interhelical interactions: new classes of interacting helix pairs in protein structures (2009)

Helix-helix interactions are important for the structure, stability and function of alpha-helical proteins. Helices that either cross in the middle or show extensive contacts between each other, such as coiled coils, have been investigated in previous studies. Interactions between two helices can also occur only at the terminal regions or between the terminal region of one helix and the middle region of another helix. Examples of such helix pairs are found in aquaporin, H(+)/Cl(-) transporter and Bcl-2 proteins. The frequency of the occurrence of such ;end-to-end' (EE) and ;end-to-middle' (EM) helix pairs in protein structures is not known. Questions regarding the residue preferences in the interface and the mode of interhelical interactions in such helix pairs also remain unanswered. In this study, high-resolution structures of all-alpha proteins from the PDB have been systematically analyzed and the helix pairs that interact only in EE or EM fashion have been extracted. EE and EM helix pairs have been categorized into five classes (N-N, N-C, C-C, N-MID and C-MID) depending on the region of interaction. Nearly 13% of 5725 helix pairs belonged to one of the five classes. Analysis of single-residue propensities indicated that hydrophobic and polar residues prefer to occur in the C-terminal and N-terminal regions, respectively. Hydrophobic C-terminal interacting residues and polar N-terminal interacting residues are also highly conserved. A strong correlation exists between some of the residue properties (surface area/volume and length of side chains) and their preferences for occurring in the interface of EE and EM helix pairs. In contrast to interacting non-EE/EM helix pairs, helices in EE and EM pairs are farther apart. In these helix pairs, residues with large surface area/volume and longer side chains are preferred in the interfacial region.
Prevention of endotoxin-induced acute lethality in Propionibacterium acnes-primed rabbits by an antibody to leukocyte integrin beta 2 with concomitant reduction of cytokine production (1995)

Acute lethality was induced in rabbits by the sequential injection of Propionibacterium acnes and lipopolysaccharide (LPS). P. acnes induced the infiltration of inflammatory cells into the liver lobules during the early phase, and LPS in the late phase caused death in association with pathological changes mimicking hepatocellular necrosis or degeneration around infiltrated mononuclear cells and fibrin deposition in the liver, lung, and kidney, suggestive of a systemic Schwartzman-like reaction. These pathological changes were accompanied by the elevation of plasma tumor necrosis factor (TNF) and interleukin-8 (IL-8) levels. A neutralizing antibody to a leukocyte adhesion molecule, integrin beta 2 (CD18), administered at the time of LPS challenge, prevented reduced the elevation of plasma TNF and IL-8 levels. An anti-TNF alpha antibody but not an anti-IL-8 mediator in this model. These results indicate that CD18 is critically involved in vivo in activating leukocytes to produce cytokines in response to LPS.
A highly conserved repeated DNA element located in the chromosome ofStreptococcus pneumoniae (1992)

We report the discovery of a group of highly conserved DNA sequences located, in those cases studied, within intergenic regions of the chromosome of the Gram positive Streptococcus pneumoniae. The S. pneumoniae genome contains about 25 of these elements called BOX. From 5' to 3', BOX elements are composed of three subunits (boxA, boxB, and boxC) which are 59, 45 and 50 nucleotides long, respectively. BOX elements containing one, two and four copies of boxB have been observed; boxB alone was also detected in one instance. These elements are unrelated to the two most thoroughly documented families of repetitive DNA sequences present in the genomes of enterobacteria. BOX sequences have the potential to form stable stem-loop structures and one of these, at least, is transcribed. Most of these elements are located in the immediate vicinity of genes whose product has been implicated at some stage in the process of genetic transformation or in virulence of S. pneumoniae. This location raises the intriguing possibility that BOX sequences are regulatory elements shared by several coordinately controlled genes, including competence-specific and virulence-related genes.
IDA-intrusion detection alert (2003)

The author provides an overview of the IDA (intrusion detection alert) knowledge-based system project. This project involves the development of a prototype knowledge based system to analyze mainframe security audit trail data. Various aspects of the IDA knowledge-based system prototyping effort, including project management, design, and development are discussed. Highlights of IDA features are described. The use of knowledge based system technology to address the increased importance of securing corporate data and information systems, a critical and valuable company asset, is the primary focus.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ME1 and GE1: Basic Helix – Loop – Helix Transcription Factors Expressed at High Levels in the Developing Nervous System and in Morphogenetically Active Regions (1993)

Several class A basic helix-loop-helix (bHLH) transcription factors have been cloned from the developing mouse and chick nervous system. The cloned cDNAs (ME1, ME2, ME3, ME4, in the mouse and GE1, GE2 in the chick) have HLH coding regions highly homologous to other known class A bHLH genes. The genes corresponding to ME1 and GE1 are abundantly expressed during development of the central nervous system. ME1 and GE1 are expressed in proliferating neuroblasts and in cells at the initial stages of differentiation (for example in the external granule cell layer of the cerebellum and in the lateral region of the ventricular zone in the developing neural tube and cortex). They are also expressed at high levels in morphogenetically active regions such as limb buds, somites and mesonephric tubules. The expression of ME1 and GE1 decreases once cellular differentiation is over. Based on the expression of ME1 and GE1 in regions of active cellular proliferation and differentiation and on the known role of other bHLH factors in development, we suggest that ME1 and GE1 play important roles during development of the nervous system as well as in other organ systems.
Water-Induced Disproportionation of Superoxide Ion in Aprotic Solvents (1996)

The water-induced disproportionation of the electrogenerated superoxide ion (O2-) in acetonitrile, dimethylformamide, and dimethyl sulfoxide media containing various concentrations of water as a Brønsted acid has been examined by UV−vis spectroscopy. Analysis of the kinetics as a function of O2- and water concentrations and of the measurement time demonstrated that the disproportionation of O2- by water in these media obeys a common mechanism: O2- + H2O ⇄ HO2• + OH- (k1, k-1) HO2• + O2- → HO2- + O2 (k2) (HO2•, hydroperoxyl radical; HO2-, hydrogen peroxide anion). The solvent dependence of the obtained kinetic parameters of (k1/k-1)k2, k1 and k-1/k2 is discussed in terms of the solvation of O2- and H2O as well as the effective acidities of H2O in different aprotic solvents.
Substance Abuse Vaccines (2008)

Conventional substance-abuse treatments have only had limited success for drugs such as cocaine, nicotine, methamphetamine, and phencyclidine. New approaches, including vaccination to block the effects of these drugs on the brain, are in advanced stages of development. Although several potential mechanisms for the effects of antidrug vaccines have been suggested, the most straightforward and intuitive mechanism involves binding of the drug by antibodies in the bloodstream, thereby blocking entry and/or reducing the rate of entry of the drug into the central nervous system. The benefits of such antibodies on drug pharmacodynamics will be influenced by both the quantitative and the qualitative properties of the antibodies. The sum of these effects will determine the success of the clinical applications of antidrug vaccines in addiction medicine. This review will discuss these issues and present the current status of vaccine development for nicotine, cocaine, methamphetamine, phencyclidine, and morphine.
Treatment of Femoropopliteal Stenoses by Means of Self-expandable Endoprostheses: Midterm Results (1989)

An endovascular mechanical support that can be introduced percutaneously could be an attractive approach to preventing acute occlusion and restenosis following angioplasty. The self-expandable metallic endoprosthesis is characterized by its flexibility and elasticity. The authors report the results of 40 femoropopliteal implantations in 36 patients; the follow-up period was greater than 6 months in all patients. Lesion length exceeded 7 cm in 25% of cases and was 3-7 cm in 75%. Thirty percent of lesions were total occlusions. At hemodynamic and angiographic study, two types of complications were noted. In patients not receiving orally administered anticoagulants, six thromboses occurred early; no early thromboses were noted in the nine patients treated with acenocoumarol. Restenosis occurred in 10% of cases (maximum follow-up, 2 years) and was noted even in long lesions (greater than 7 cm). The authors believe that placement of this type of prosthesis is an attractive approach to preventing postangioplasty restenosis, provided that the conditions of anticoagulation are well controlled.
Micropthalmia transcription factor: a new prognostic marker in intermediate-thickness cutaneous malignant melanoma. (2000)

Micropthalmia transcription factor (Mitf) is involved in melanocyte development and differentiation. The current study was undertaken to determine whether there is a relationship between Mitf expression and survival in patients with intermediate-thickness (1.0-4.0 mm) melanoma. Original paraffin blocks or slides of the primary tumor were accessible in 63 such patients. Mitf expression was evaluated by immunocytochemistry and analyzed visually. Slides were graded as follows according to the percentage of cells whose nuclei stained positive for Mitf: (a) 0, 0%; (b) +1, 1-25%; (c) +2, 26-50%; (d) +3, 51-75%; and (e) +4, > 75%. Median follow-up was 50 months. Mean thickness was 2.2 +/- 0.7 mm. Mean overall survival was 171.90 +/- 13.12 months. Mean disease-free survival was 168.53 +/- 13.96 months. Fifty-two melanomas (82.5%) stained positive for Mitf. By univariate analysis, mean overall survival and disease-free survival in patients whose melanomas did not express Mitf were 80.89 +/- 17.98 months (median, 51 months) and 71.36 +/- 19.87 months (median, 40 months), respectively. This compares with 187.90 +/- 13.41 months (median, not reached) and 186.78 +/- 13.84 months (median, not reached), respectively, for patients whose melanomas expressed Mitf (P = 0.0086 and P = 0.0054). These findings persisted in multivariate analysis. In addition, patients with > 50% Mitf expression had significantly fewer nodal metastases after node dissection than patients with < or = 50% Mitf expression (P = 0.04). Our data suggest that Mitf may be a new molecular prognostic marker in patients with intermediate-thickness melanoma.
ChemInform Abstract: Synthesis of Functionally Substituted Alcohols Containing a CF3 Group by Condensation of Aryl and Heteroaryl Trifluoromethyl Ketones with Carbon Acids. (1991)

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.
Overview of Fine‐Scale Piezoelectric Ceramic/Polymer Composite Processing (1995)

In the past two decades, piezoelectric ceramic/polymer composites with different connectivities have been developed for transducer applications such as hydrophones, biomedical imaging, nondestructive testing, and air imaging. Recently, much attention has been given to fine‐scale piezoelectric ceramic/polymer composites. These composites allow higher operating frequencies, and thus increased resolution, in medical imaging transducers. In this review, methods for processing fine‐scale piezoelectric ceramic/polymer composites are discussed. The current capabilities, strengths, and weaknesses of each method are compared. The importance of spatial scale in composite performance is also reviewed. Several of the processing methods have demonstrated composites with fine‐scale ceramic phases (&lt;50 μm), and others have potential to form composites with a ceramic scale of under 20 μm.
Stoichiometry of G Protein Subunits Affects the Saccharomyces cerevisiae Mating Pheromone Signal Transduction Pathway (1990)

The Saccharomyces cerevisiae GPA1, STE4, and STE18 genes encode products homologous to mammalian G-protein alpha, beta, and gamma subunits, respectively. All three genes function in the transduction of the signal generated by mating pheromone in haploid cells. To characterize more completely the role of these genes in mating, we have conditionally overexpressed GPA1, STE4, and STE18, using the galactose-inducible GAL1 promoter. Overexpression of STE4 alone, or STE4 together with STE18, generated a response in haploid cells suggestive of pheromone signal transduction: arrest in G1 of the cell cycle, formation of cellular projections, and induction of the pheromone-inducible transcript FUS1 25- to 70-fold. High-level STE18 expression alone had none of these effects, nor did overexpression of STE4 in a MATa/alpha diploid. However, STE18 was essential for the response, since overexpression of STE4 was unable to activate a response in a ste18 null strain. GPA1 hyperexpression suppressed the phenotype of STE4 overexpression. In addition, cells that overexpressed GPA1 were more resistant to pheromone and recovered more quickly from pheromone than did wild-type cells, which suggests that GPA1 may function in an adaptation response to pheromone.
Limited T cell antigen receptor repertoire in tumor-infiltrating lymphocyte and inhibition of experimental lung metastasis of murine melanoma by anti-TCR antibody. (1995)

We analyzed the variability of T cell Ag receptor in tumor-infiltrating lymphocytes in primary and metastatic melanomas. Using a very sensitive inverse/double step PCR, we found the preferential V alpha usage of TCR in tumor-infiltrating lymphocytes in which some TCR sequences were homogenous. However, the profile of TCR V alpha expression was different in primary and metastatic melanomas. V alpha 8+, V alpha 2+, V alpha 4+, and V alpha 3+ TCR were the most dominant repertoires in primary melanoma, whereas V alpha 3+ and V alpha 4+ TCR dominated metastatic melanoma. Depletion of V alpha 3 T cells by the injection of tumor-bearing mice with anti-V alpha 3 Ab resulted in protection against experimental lung metastasis, indicating that V alpha 3+ regulatory T cells exist in the tumor site and help metastatic tumor growth.
Locating the other in an online world: trolling Islam in 'American sniper' (2017)

As the online realm continues to become more important in the United States, questions of identity become increasingly difficult to parse, while still remaining at the forefront of US political discussions. In seeking to understand how identity construction is intertwined with a text's online circulation, I've focused on Clint Eastwood's American Sniper as an act of online trolling. In looking at articles written about the film, along with comments accompanying both the film and articles, I've found a pattern which centers on deeply-held orientalist beliefs about the Middle East. Additionally, the online circulation of these texts reveals a strawman-styled othering process in which rhetors, ranging from Eastwood himself to anonymous online contributors, define themselves not by what they believe, but by what they are not. Ultimately, this analysis exposes the paradoxical element of rhizomatic communities: in an online world, where there is often no discernable connection to a static, geographic place, users create their identities by denigrating perceived 'other' ideologies. Instead of focusing on what makes them (in this case) American, users condemn the opposing political side, and then attribute all the remaining positive qualities to themselves.
A Novel Multipurpose Monoclonal Antibody for Evaluating Human c-Met Expression in Preclinical and Clinical Settings (2008)

The inappropriate expression of the c-MET cell surface receptor in many human solid tumors necessitates the development of companion diagnostics to identify those patients who could benefit from c-MET targeted therapies. Tumor tissues are formalin fixed and paraffin embedded (FFPE) for histopathologic evaluation, making the development of an antibody against c-MET that accurately and reproducibly detects the protein in FFPE samples an urgent need. We have developed a monoclonal antibody (mAb), designated MET4, from a panel of MET-avid mAbs, based on its specific staining pattern in FFPE preparations. The accuracy of MET4 immunohistochemistry (MET4-IHC) was assessed by comparing MET4-IHC in FFPE cell pellets with immunoblotting analysis. The technical reproducibility of MET4-IHC possessed a percentage coefficient of variability of 6.25% in intra-assay and interassay testing. Comparison with other commercial c-MET antibody detection reagents demonstrated equal specificity and increased sensitivity for c-MET detection in prostate tissues. In cohorts of ovarian cancers and gliomas, MET4 reacted with ovarian cancers of all histologic subtypes (strong staining in 25%) and with 63% of gliomas. In addition, MET4 bound c-MET on the surfaces of cultured human cancer cells and tumor xenografts. In summary, the MET4 mAb accurately and reproducibly measures c-MET expression by IHC in FFPE tissues and can be used for molecular imaging in vivo. These properties encourage further development of MET4 as a multipurpose molecular diagnostics reagent to help to guide appropriate selection of patients being considered for treatment with c-MET-antagonistic drugs.
Effect of moisture absorption on the thermal properties ofBombyx mori silk fibroin films (1997)

Films of regenerated Bombyx mori silk are strongly affected by absorbed moisture, a phenomenon studied here by differential scanning calorimetry (DSC). Exposure of previously dried films to environments of controlled relative humidity produces test samples of well-defined equilibrium moisture content. Ultimate moisture uptake is as high as 20–23% (by weight) at 75% relative humidity. The glass transition temperature, Tg, drops by 40°C at moisture uptakes as low as 2%, and Tg depressions as large as 140°C are observed at higher relative humidity. The moisture-induced decrease of Tg is completely reversible, as a film remoistened and then redried possesses an unchanged Tg. Trends in Tg with water uptake correspond reasonably well to predictions of a classical thermodynamic theory, indicating that the plasticization effect of moisture on the combined silk-water system can be satisfactorily explained from macroscopic properties of the constituents without any reference to specific interactions. © 1997 John Wiley & Sons, Inc. J Appl Polym Sci 63: 401–410, 1997
Synthesis of a Fluorogenic Cyclooctyne Activated by Cu-Free Click Chemistry (2011)

Cyclooctyne-based probes that become fluorescent upon reaction with azides are important targets for real-time imaging of azide-labeled biomolecules. The concise synthesis of a coumarin-conjugated cyclooctyne, coumBARAC, that undergoes a 10-fold enhancement in fluorescence quantum yield upon triazole formation with organic azides is reported. The design principles embodied in coumBARAC establish a platform for generating fluorogenic cyclooctynes suited for biological imaging.
Electron Affinities of 1,1-Diaryl-2,3,4,5-tetraphenylsiloles:  Direct Measurements and Comparison with Experimental and Theoretical Estimates (2005)

We present a comprehensive experimental and theoretical characterization of the electronic structure of four 1,1-diaryl-2,3,4,5-tetraphenylsiloles (aryl = phenyl, 2-(9,9-dimethylfluorenyl), 2-thienyl, pentafluorophenyl). Solid-state electron affinities and ionization potentials of these siloles were measured using inverse-photoelectron spectroscopy (IPES) and photoelectron spectroscopy (PES), respectively; the density of electronic states obtained from calculations performed at the density functional theory (DFT) level corresponds very well to the PES and IPES data. The direct IPES measurements of electron affinity were then used to assess alternative estimates based on electrochemical and/or optical data. We also used DFT to calculate the reorganization energies for the electron-transfer reactions between these siloles and their radical anions. Additionally, optical data and ionization potential and electron affinity data were utilized to estimate the binding energies of excitons in these siloles.