gebhart/patrepeval huggingface dataset:
Distinct steps in the penetration of adenylate cyclase toxin of Bordetella pertussis into sheep erythrocytes. Translocation of the toxin across the membrane. (1992)

Adenylate cyclase (AC) toxin from Bordetella pertussis penetrates eukaryotic cells and upon activation by calmodulin generates unregulated levels of intracellular cAMP. The process of toxin penetration into sheep erythrocytes was resolved into three consecutive steps including insertion, translocation, and intracellular cleavage. Insertion of the toxin into the cell membrane occurred over a wide temperature range (4-36 degrees C). In contrast, translocation of the toxin, i.e. transfer of the NH2-terminal catalytically active fragment across the membrane, occurred only above 20 degrees C and was highly temperature-dependent. While a single exposure of the toxin to Ca2+ was sufficient for its insertion into the plasma membrane, toxin translocation required exogenous Ca2+ at mM concentrations. Translocation was not affected by pretreatment of cells with trypsin, N-ethylmaleimide, and sodium carbonate at alkaline pH. The NH2-terminal fragment of the toxin was cleaved in the cell releasing the 45-kDa active AC into the cytosol. The cleavage was blocked by treatment of cells with N-ethylmaleimide. It is hypothesized that the COOH-terminal portion of the toxin creates in the membrane a channel through which the NH2-terminal fragment is translocated.
Text segmentation with multiple surface linguistic cues (1998)

In general, a certain range of sentences in a text, is widely assumed to form a coherent unit which is called a discourse segment. Identifying the segment boundaries is a first step to recognize the structure of a text. In this paper, we describe a method for identifying segment boundaries of a Japanese text with the aid of multiple surface linguistic cues, though our experiments might be small-scale. We also present a method of training the weights for multiple linguistic cues automatically without the overfitting problem.
The role of nitric oxide in innate immunity (2000)

Type 2 nitric oxide synthase (iNOS or NOS2) was originally described as an enzyme that is expressed in activated macrophages, generates nitric oxide (NO) from the amino acid L-arginine, and thereby contributes to the control of replication or killing of intracellular microbial pathogens. Since interferon (IFN)-gamma is the key cytokine for the induction of NOS2 in macrophages and the prototypic product of type 1 T-helper cells, high-level expression of NOS2 has been regarded to be mostly restricted to the adaptive phase of the immune response. In this review, we summarize data that demonstrate a prominent role of NOS2/NO also during innate immunity. During the early phase of infection with the intracellular pathogen Leishmania major, focally expressed NOS2/NO not only exerts antimicrobial activities but also controls the function of natural killer cells and the expression of cytokines such as IFN-gamma or transforming growth factor-beta. Some of these effects result from the function of NOS2/NO as an indispensable co-factor for the activation of Tyk2 kinase and, thus, for interleukin-12 and IFN-alpha/beta signaling in natural killer cells.
A Review of Antimicrobial Peptides and Their Therapeutic Potential as Anti-Infective Drugs (2005)

While AMPs are recognized as essential components of natural host innate immunity against microbial challenge, their usefulness as a new class of antimicrobial drugs still remains to be proven.
Studies on the Structure and Function of Glycosylated and Nonglycosylated neu Differentiation Factors (1995)

Comparative analyses of both glycosylated and nonglycosylated neu differentiation factor (NDF) isoforms revealed significant similarities and differences of their overall structures and functions. Biophysical analyses confirmed that all NDF isoforms are monomeric, but have an extended ellipsoidal shape in solution. All full-length NDFs are similar in secondary and tertiary structures and they contain no alpha-helix but are abundant in beta-strand structures. A small NDF fragment containing only the epidermal growth factor domain is also rich in beta-strand structures, but exhibits tertiary structure different from the long NDF forms. Monoclonal antibodies that selectively recognize epidermal growth factor domains of human NDF-alpha and -beta can specifically bind the respective NDF-alpha and -beta isoforms independent of NDF origins. Western blot analysis and quantitative binding assays further identify that an NDF preparation produced naturally from Rat1-EJ cells contains both alpha and beta isoforms in a 3 to 2 ratio. In receptor-binding competition experiments, human and rat NDF-beta isoforms have higher affinity than NDF-alpha isoforms. NDF-beta isoforms can dramatically enhance the stimulation of DNA synthesis for transfected NIH3T3 cells that overexpress HER-3 and HER-4 receptors, while NDF-alpha isoforms can only stimulate proliferation of HER-4-transfected cells with lower activity. Taken together, NDF-alpha and -beta isoforms share similar gross protein conformations but are biologically distinct.
The magnitude of radiation force on ultrasound contrast agents (2002)

High-speed photography of insonified bubbles with a time resolution of 10 ns allows observations of translation due to radiation force, in addition to the visualization of radial oscillations. A modified version of the Rayleigh-Plesset equation is used to estimate the radius-time behavior of insonified microbubbles, and the accuracy of this model is verified experimentally. The translation of insonified microbubbles is calculated using a differential equation relating the acceleration of the bubble to the forces due to acoustic radiation and the drag imposed by the fluid. Simulations and experiments indicate that microbubbles translate significant distances with clinically relevant parameters. A 1.5 micron radius contrast agent can translate over 5 microns during a single 20-cycle, 2.25 MHz, 380 kPa acoustic pulse, achieving velocities over 0.5 m/s. Therefore, radiation force should be considered during an ultrasonic examination because of the possibility of influencing the position and flow velocity of the contrast agents with the interrogating acoustic beam.
<title>Near-infrared absorption and scattering spectra of tissues in vivo</title> (1999)

Tissue inhomogeneity is often neglected in the analysis of the spectral data collected in tissues. We have measured the absorption and reduced scattering spectra of the human forearm in the wavelength range 633-841 nm, and in the range of source-detector separations 0.7-3.3 cm. We found that the layered tissue structure due to the skin and adipose layers may have a significant effect not only on the data collected at different distances, but also on the data at 633 nm, where the optical absorbance is significantly higher than at the longer wavelengths considered. We conclude that the dependence of the optical penetration depth on the absorption and reduced scattering coefficients should be carefully considered in the quantitative analysis of the optical spectra of tissues.
Chemoselective Covalent Coupling of Oligonucleotide Probes to Self-Assembled Monolayers (2005)

A chemoselective route to routinely and rapidly attach oligonucleotide probes to well-defined surfaces is presented. Cu(I) tris(benzyltriazolylmethyl)amine-catalyzed coupling of terminal acetylenes to azides on a self-assembled monolayer is used instead of traditional nucleophilic-electrophilic coupling reactions. The reaction proceeds well even in the presence of purposely introduced nucleophilic and electrophilic impurities. The density of oligonucleotide probes can be controlled by controlling the amount of azide functionality. Although most of our work was done on gold surfaces, this technique should be readily applicable to any surface on which an azide-containing monolayer can be assembled as we have preliminarily demonstrated by derivatizing azidotrimethoxysilane-modified glass slides with fluorescein-containing oligonucleotides.
Silsesquioxane Models for Geminal Silica Surface Silanol Sites. A Spectroscopic Investigation of Different Types of Silanols (2002)

The incompletely condensed monosilylated silsesquioxanes (c-C5H9)7Si7O9(OSiRR'2)(OH)2 (SiRR'2 = SiMe3, SiMe2C(H)CH2, SiMePh2) were reacted with SiCl(4) in the presence of an amine which yielded the dichloro compounds (c-C5H9)7Si7O9(OSiRR'2)O2SiCl2 (1-3). These compounds could be hydrolyzed into the corresponding silsesquioxanes containing geminal silanols, (c-C5H9)7Si7O9(OSiRR'2)O2Si(OH)2 (4-6). At elevated temperatures, the geminal silsesquioxanes 4 and 5 undergo condensation reactions and form the closed-cage silsesquioxane monosilanol, (c-C5H9)7Si8O12(OH). The more sterically hindered geminal silsesquioxane 6 undergoes in solution intermolecular dehydroxylation, yielding the thermodynamically stable dimeric disilanol, [(c-C5H9)7Si7O9(OSiMePh2)(O2Si(OH)-)]2-(mu-O) (7). NMR and FT-IR studies show that the two silanols of the geminal silsesquioxanes 4-6 are different from each other with respect to hydrogen bonding, both in solution and in the solid state. Hydrogen bonding of the geminal silanol-containing silsesquioxanes was examined and compared to hydrogen bonding in silsesquioxanes possessing vicinal or isolated silanol groups. The relative Brønsted acidity of the geminal silanols was determined using pK(ip) (ion-pair acidity) measurements in THF with UV-vis. These acidities were compared with those of other silsesquioxanes containing silanol groups. Acidities of 4-6 were found to be among the lowest known for silsesquioxanes.
DNA Fuel for Free-Running Nanomachines (2003)

We describe kinetic control of DNA hybridization: loop complexes are used to inhibit the hybridization of complementary oligonucleotides; rationally designed DNA catalysts are shown to be effective in promoting their hybridization. This is the basis of a strategy for using DNA as a fuel to drive free-running artificial molecular machines.
A newly identifiedMAGE-3-derived epitope recognized by HLA-A24-restricted cytotoxic T lymphocytes (1999)

Five MAGE-3-derived peptides carrying an HLA-A24-binding motif were synthesized. Binding capacity of these peptides was analyzed by an HLA-class-I stabilization assay. Two of the 5 peptides bound to HLA-A*2402 molecule with high affinity, and 3 peptides with low affinity. Peripheral-blood mononuclear cells (PBMC) depleted of CD4+T cells were stimulated with the peptides to determine whether these peptides would induce cytotoxic T lymphocytes (CTL) from PBMCs obtained from 7 healthy HLA-A*2402+ donors. Peptide M3-p97 (TFPDLESEF; corresponding to amino-acid residues 97-105 of MAGE-3), with high binding capacity to the HLA-A*2402 molecule, elicited the peptide-specific and HLA-A24-restricted CD8+CTL lines in 2 of the 7 donors, while none of the 4 other peptides induced CTL specific for the corresponding peptide in any of the donors. CTL lines induced by stimulation with peptide M3-p97 exhibited cytolytic activities against HLA-A*2402 transfectant cell lines (C1R-A*2402) in the presence of peptide M3-p97, but not in unloaded or irrelevant peptide-pulsed C1R-A*2402 cells. The CTL lines and a cloned CD8+CTL isolated from one of the bulk populations by limiting dilution could lyse MAGE-3+/HLA-A*2402+ squamous-cell-carcinoma(SCC) lines but neither MAGE-3-/HLA-A*2402+ nor MAGE-3+/HLA-A*2402- SCC lines, indicating that M3-p97 can be naturally processed and presented on the tumor-cell surface in association with HLA-A*2402 molecules. Combined with the 4 currently reported CTL epitopes derived from MAGE-3 and presented by HLA-A1, HLA-A2, HLA-A24 or HLA-B44, identification of this CTL epitope presented by the HLA-A*2402 molecule will extend the application of MAGE-3-derived peptides for immunotherapy for cancer patients.
Short Paper: Analyzing Metadata Schemas for Buildings (2015)

Commercial buildings account for a large amount of delivered energy in the U.S., nearly 42% of which is consumed in buildings with digital control systems {EIA}. These buildings are a ripe venue to deploy novel applications because of (a) access to sensors and actuators that are used in their digital control systems, (b) deployed wireless sensor networks, and (c) the advent of smart "internet-of-things" sensors. However, these novel applications face a fundamental scalability challenge because the sensor metadata across buildings do not follow any common schema. In this paper, we quantify the shortcomings of three metadata schemas which have gained traction in modeling the contextual, spatial and functional relationships between sensors in the built environment: (1) Project Haystack, (2) Industry Foundation Classes (3) and Semantic Sensor Web against three commercial buildings and an extensive list of smart-building applications.
Progress in orientation-patterned GaP for next-generation nonlinear optical devices (2013)

Orientation-patterned GaP is a promising nonlinear material for frequency conversion in the mid and longwave IR (2-5 μm and 8-12 &mu;m) by quasi-phase matching. As an alternative to OPGaAs, OPGaP has the advantage of having lower two-photon absorption in the convenient pumping range 1 – 1.7 &mu;m. We report recent results on development of thick QPM GaP for high power tunable laser sources radiating in the mid IR. Two are the major challenges to producing OPGaP: development of simple techniques for preparation of patterned templates and a technology for fast epitaxial growth of thick, high quality GaP on these templates. The focus was to adapt/simplify the wafer fusion process for OPGaP template preparation. Then increase the growth rate and layer thickness of regrown material, while maintaining vertical domain propagation. The growth experiments were conducted in a horizontal quartz reactor, using a standard hydride vapor phase epitaxial process. The growth was performed on: (i) plain (100) GaP; (ii) half-patterned (HP) and (iii) orientation-patterned (OP) templates, fabricated on (100) GaP. Up to 370 &mu;m thick layers with high crystal and optical quality were reproducibly grown on plain material. Growth on HP templates resulted in up to 470 &mu;m thick layers with rectangular mesa‟s shape. These results were used to determine the optimal substrate and pattern orientations. HVPE growth on OP templates achieved stable growth rates of 50-70 &mu;m/h with domain walls propagating vertically, following the periodicity of the initial pattern, and resulted in the first 350 &mu;m thick device quality OPGaP.
Enhanced proliferative potential in culture of cells from p53-deficient mice. (1993)

Normal somatic cells are endowed with limited doubling potential in culture, and the process of immortalization is an inevitable step in neoplastic transformation of the cells. To examine the roles of p53 in this process, the cells of p53-deficient mice were examined for doubling potential. Fibroblast-like cells from a variety of tissues of these mice proliferated continuously without showing aging or crisis. The aneuploid cells overcome the population with passage, but cloning experiment indicated that chromosomal changes were not essential to this process. The enhanced proliferative potential in culture of cells from the p53-deficient mice was also observed in epithelial cells of lens, mammary glands and seminal vesicles and in neural precursor cells. Proliferation of bone marrow cells in response to stem cell factor was enhanced in long term culture, but not in in vitro colony assay; no permanent cell lines could be obtained. No effects of p53-deficiency were found in proliferation of cardiac muscle cells or hepatocytes.
[Sensitivity to fosfomycin of multiresistant serotype 012 Pseudomonas aeruginosa. Multicenter study]. (1997)

In a multicentric study including 214 strains of Pseudomonas aeruginosa, we observed that serotype O12 is more frequently sensitive to fosfomycine than other serotypes strains (72% vs 13.2%, p < 0.000001). Time killing experiments demonstrated that combination of ceftazidime-fosfomycine and amikacine-fosfomycine have usually bactericidal and synergistic activities and could be used for the treatment of multiresistant Pa O12 infections. However, an antagonism between beta-lactams and fosfomycin in disk diffusion needs an adequate concentration of both antibiotics in the site of infection.
Tissue Microarray: A rapidly evolving diagnostic and research tool (2009)

Tissue microarray is a recent innovation in the field of pathology. A microarray contains many small representative tissue samples from hundreds of different cases assembled on a single histologic slide, and therefore allows high throughput analysis of multiple specimens at the same time. Tissue microarrays are paraffin blocks produced by extracting cylindrical tissue cores from different paraffin donor blocks and re-embedding these into a single recipient (microarray) block at defined array coordinates. Using this technique, up to 1000 or more tissue samples can be arrayed into a single paraffin block. It can permit simultaneous analysis of molecular targets at the DNA, mRNA, and protein levels under identical, standardized conditions on a single glass slide, and also provide maximal preservation and use of limited and irreplaceable archival tissue samples. This versatile technique, in which data analysis is automated, facilitates retrospective and prospective human tissue studies. It is a practical and effective tool for high-throughput molecular analysis of tissues that is helping to identify new diagnostic and prognostic markers and targets in human cancers, and has a range of potential applications in basic research, prognostic oncology and drug discovery. This article summarizes the technical aspects of tissue microarray construction and sectioning, advantages, application, and limitations.
Pressure-Driven Enzyme Entrapment in Siliceous Mesocellular Foam (2006)

A pressure-driven method was employed to immobilize enzymes on hydrophobic mesoporous silica supports. This approach gave rise to higher enzyme loading and reduced enzyme leaching, compared to conventional methods. Candida antarctica lipase B (CALB) was successfully entrapped in the cagelike pores of siliceous mesocellular foam using this method. The resulting supported enzyme catalyst demonstrated reusability and thermal stability superior to those of the commercial immobilized CALB catalyst, Novozyme 435.
Metal-Free Atom Transfer Radical Polymerization (2014)

Overcoming the challenge of metal contamination in traditional ATRP systems, a metal-free ATRP process, mediated by light and catalyzed by an organic-based photoredox catalyst, is reported. Polymerization of vinyl monomers are efficiently activated and deactivated with light leading to excellent control over the molecular weight, polydispersity, and chain ends of the resulting polymers. Significantly, block copolymer formation was facile and could be combined with other controlled radical processes leading to structural and synthetic versatility. We believe that these new organic-based photoredox catalysts will enable new applications for controlled radical polymerizations and also be of further value in both small molecule and polymer chemistry.
Tissue factor activity in patients with systemic lupus erythematosus: association with disease activity. (2000)

Arthritis, previous thrombosis, and use of NSAID significantly modified TF activity in patients with SLE. Unlike previous reports, we found no association between aCL titer and TF activity, which may be due to our adjusting for other important clinical factors.
Bi-specific and tri-specific antibodies- the next big thing in solid tumor therapeutics (2018)

Antibody-based therapy has revitalized the world of cancer therapeutics since rituximab was first approved for the treatment of Non-Hodgkin's Lymphoma. Monoclonal antibodies against cancer antigens have been successful strategies for only a handful of cancer types due to many reasons including lack of antibody specificity and complex nature of tumor milieu which interfere with antibody efficacy. Polyspecific antibodies are promising class of anti-cancer agents which can be directed at multiple tumor antigens to eradicate tumor cells more precisely and effectively. They may overcome some of these limitations and have already changed treatment landscape for some malignancies such as B cell acute lymphoblastic leukemia. Pre-clinical studies and early phase clinical trials have demonstrated that this approach may be an effective strategy even for solid tumors. This review focuses on the development of bispecific and trispecific antibody therapy for the treatment of solid tumor malignancies and highlights the potential they hold for future therapies to come.
Evidence for long‐term survival and function of dopaminergic grafts in progressive Parkinson's disease (1994)

Two patients with idiopathic Parkinson's disease (Patients 3 and 4 in our series) were followed up to 3 years after grafting of human embryonic dopamine-rich mesencephalic tissue unilaterally into the putamen. During the first postoperative year both patients showed significant amelioration of parkinsonian symptoms and increased 6-L-[18F]-fluorodopa uptake in the grafted putamen, as assessed with positron emission tomography. Three years after grafting the patients still exhibited increased fluorodopa uptake in the grafted putamen and significant clinical improvements, evidenced by a reduction of the severity of symptoms and of the time spent in the "off" phase, and by a prolongation of the effect of a single dose of L-dopa. Between 1 and 3 years after surgery, Patient 3 showed only minor changes of parkinsonian symptoms on the side contralateral to the graft, whereas there was a worsening on the ipsilateral side. Fluorodopa uptake decreased in the nongrafted putamen but was unchanged in the grafted putamen. Patient 4 continued to improve after the first postoperative year and L-dopa was withdrawn after 32 months. The reduction of parkinsonian symptoms on the side contralateral to the graft became more pronounced between 1 and 3 years after surgery. Fluorodopa uptake further increased in the grafted putamen, whereas no change was detected on the non-grafted side. These results indicate that grafts of embryonic dopamine neurons can survive, grow, and exert functional effects up to at least 3 years after surgery in the parkinsonian brain, despite an ongoing disease process leading to degeneration of the intrinsic dopamine system.
Insertion and Management of Central Venous Catheters (2011)

The indications for placement of central venous catheters are continually expanding. The rapid growth of hemodialysis services, transplantation programs, and oncologic centers has contributed to the need for maintaining patients who require parenteral nutrition, hemodialysis, plasmapheresis, blood transfusion, blood sampling, and longterm chemotherapy for various neoplastic and infections disease. There are three basic categories of venous catheters: non-tunneled catheters, tunneled catheters and implantable ports. Each category of non-tunneled and tunneled catheter divided to infusion and high flow hemodialysis catheter. Peripherally inserted central catheter is a unique long non-tunneled catheter inserted through an arm vein. All physicians should have a deep understanding of each central venous catheters and ability to select the most appropriate one for each patient. Central venous catheteri-zation should be performed by experts with imaging guidance. The high failure rate and high complication rate in the landmark bedside technique was revealed due to anatomical variance of veins. Appropriate management of the catheter is one of the most important parts should be understood by nurses as well as physician in central venous catheterization.