gebhart/patrepeval huggingface dataset:
SIP Caller Preferences and Callee Capabilities (1999)

This document describes a set of extensions to SIP which allow a caller to express preferences about request handling in servers. It also extends the SIP Contact header to allow users to describe their communications capabilities and characteristics.
Prevention of Mucosal Escherichia coli Infection by FimH-Adhesin-Based Systemic Vaccination (1997)

Virtually all uropathogenic strains of Escherichia coli, the primary cause of cystitis, assemble adhesive surface organelles called type 1 pili that contain the FimH adhesin. Sera from animals vaccinated with candidate FimH vaccines inhibited uropathogenic E. coli from binding to human bladder cells in vitro. Immunization with FimH reduced in vivo colonization of the bladder mucosa by more than 99 percent in a murine cystitis model, and immunoglobulin G to FimH was detected in urinary samples from protected mice. Furthermore, passive systemic administration of immune sera to FimH also resulted in reduced bladder colonization by uropathogenic E. coli. This approach may represent a means of preventing recurrent and acute infections of the urogenital mucosa.
Remediation of Line Edge Roughness in Chemical Nanopatterns by the Directed Assembly of Overlying Block Copolymer Films (2010)

Block copolymer structures have been directed to assemble on chemically patterned surfaces with the domain interfaces oriented perpendicular to the substrate. Such methods have been pursued for lithographic applications to achieve long-range order in the assembled structures and, potentially more important, provide nanometer-level control over the interfaces between structures. The chemically striped surfaces used for the directed assembly of lamellae are patterned by top-down lithographic techniques and thus often have rough edges between the regions of different chemistry. Here we quantitatively characterize, using experiments and molecular-level simulations, the propagation of line edge roughness from the chemically patterned surfaces into the interfaces between domains of block copolymer lamellae as a function of the wavelength, amplitude, and geometry of the roughness. Two geometries of surface pattern roughness are considered with oscillatory neighboring interfaces that are either in-phase or out-of-phase. Block copolymer lamellae of poly(styrene-block-methyl methacrylate) effectively self-corrected surface patterns with small wavelength in-phase and out-of-phase roughness such that little or no memory of the substrate pattern roughness could be observed at the top surface of a 40 nm thin film. Larger wavelength in-phase roughness, and to a lesser extent larger wavelength out-of-phase roughness, propagated farther from the surface pattern such that the domain interfaces between block copolymer lamellae maintained the roughness throughout the film. These self-healing capabilities of block copolymers will be essential for lithographic applications with tight tolerances on line edge roughness and line width control, e.g., in patterning transistor gates.
Clinical Impact of Different Classes of Infiltrating T Cytotoxic and Helper Cells (Th1, Th2, Treg, Th17) in Patients with Colorectal Cancer (2011)

The tumor microenvironment includes a complex network of immune T-cell subpopulations. In this study, we systematically analyzed the balance between cytotoxic T cells and different subsets of helper T cells in human colorectal cancers and we correlated their impact on disease-free survival. A panel of immune related genes were analyzed in 125 frozen colorectal tumor specimens. Infiltrating cytotoxic T cells, Treg, Th1, and Th17 cells were also quantified in the center and the invasive margin of the tumors. By hierarchical clustering of a correlation matrix we identified functional clusters of genes associated with Th17 (RORC, IL17A), Th2 (IL4, IL5, IL13), Th1 (Tbet, IRF1, IL12Rb2, STAT4), and cytotoxicity (GNLY, GZMB, PRF1). Patients with high expression of the Th17 cluster had a poor prognosis, whereas patients with high expression of the Th1 cluster had prolonged disease-free survival. In contrast, none of the Th2 clusters were predictive of prognosis. Combined analysis of cytotoxic/Th1 and Th17 clusters improved the ability to discriminate relapse. In situ analysis of the density of IL17+ cells and CD8+ cells in tumor tissues confirmed the results. Our findings argue that functional Th1 and Th17 clusters yield opposite effects on patient survival in colorectal cancer, and they provide complementary information that may improve prognosis.
Human immunodeficiency virus encephalitis in SCID mice. (1996)

The human immunodeficiency virus (HIV) is neuroinvasive and commonly causes cognitive and motor deficits during the later stages of viral infection. (referred to as HIV dementia). The mechanism(s) for disease revolves around secretory products produced from immune-activated brain macrophages/microglia. Recently, we developed an animal model system for HIV dementia that contains xenografts of HIV-1-infected cells inoculated into brains of mice with severe combined immunodeficiency (SCID). This animal system was used to quantitatively evaluate HIV-induced neuropathology. Xenografts of HIV-1-infected human monocytes (placed into the putamen and cortex of SCID mice) remained viable for 5 weeks. HIV-1 p24 antigen expression in mouse brain was persistent. Progressive inflammatory responses (including astrogliosis and cytokine production), which began at 3 days, peaked at day 12. The range of astrocyte proliferative reactions exceeded the inoculation site by > 1000 microns. Brains with virus-infected monocytes showed a > or = 1.6-fold increase in glial fibrillary acidic protein (staining distribution and intensity) as compared with similarly inoculated brains with uninfected control monocytes. These findings paralleled the accumulation and activation of murine microglia (increased branching of cell processes, formation of microglial nodules, interleukin (IL)-1 beta and IL-6 expression). An inflammatory reaction of human monocytes (as defined by HLA-DR, IL-1 beta, IL-6, and tumor necrosis factor-alpha expression) and neuronal injury (apoptosis) also developed after virus-infected monocyte xenograft placement into mouse brain tissue. These data, taken together, demonstrate that this SCID mouse model of HIV-1 neuropathogenesis can reproduce key aspects of disease (virus-infected macrophages, astrocytosis, microglial activation, and neuronal damage). This model may serve as an important means for therapeutic development directed toward improving mental function in HIV-infected subjects with cognitive and motor dysfunction.
Stress and immune competence in feedlot cattle. (1993)

For both scientific and commercial reasons there is an urgent need for informed scussion and further research on the relationship between stress and immune jmpetence of cattle in feedlots. As the Australian feedlot industry is in a period of rapid rOwth, considerable attention is being given to issues of public concern such as waste management, odour, disease (including usage of antibiotic drugs) and animal welfare. he recent Report of the Senate Standing Committee on Rural and Regional Affairs ntitled Be4 Cattle FeedEots in Australia (1992), highlights the importance of these issues. ‘hus, the commercial viability of the Australian feedlot industry in the future will lepend on researchers, and indeed the industry itself, satisfactorily addressing such ssues. In the scientific context, there is a growing recognition of the nexus between the zentral nervous system, the endocrine system and the immune system (Moberg 1985). [mpairment of immune competence as a consequence of stress should not be seen as a phenomenon restricted to cells or molecules of the immune system, rather as a problem for the whole animal, with neuroendocrine implications (Griffin 1989; Kelley and Dantzer 1990). Furthermore, there is an obvious link between stress, impaired immune competence and animal welfare. The relationship between stress and compromised immune competence therefore has important implications for the feedlot industry ranging from public perception/consumer resistance through to improved profitability associated with more efficient disease control. Of course, the point should be made that the stress/immune competence interaction is an issue not only for the feedlot sector. The beef cattle industry has other forms of intensification such as grain supplementation in the paddock and “finishing” steers on irrigated, improved pastures. In these situations, during transportation and, indeed, in all other examples of intensification of livestock production systems, the link between animal stress and reduced immune competence is important. In this paper we shall: (a) briefly describe some of the important disease problems in feedlot cattle in Australia; (b) provide some preliminary results of new research on stress in feedlot cattle; (c) outline the research program on Animal Health and Welfare in the Cattle and Beef Industry Cooperative Research Centre (CRC).
Functionally different T lymphocyte subpopulations determined by their sensitivity to complement-dependent cell lysis with the monoclonal antibody 4A. (1982)

A human T lymphocyte antigen 4A (40,000 daltons) is defined by a monoclonal, complement- (C) fixing, hybridoma-produced antibody (moAb 4A). This antigen, which is identical to the previously reported antigen 3A 1, is expressed at quantitatively different levels on functional subsets of peripheral T lymphocytes as determined by the cell sensitivity to antibody and C. Peripheral T lymphocytes can be divided into two populations: 4A high-density T cells (4A increases), which are killed in vitro by moAb 4A + C, and 4A low-density T cells (4A decreases), which are not affected in vitro by moAb 4A + C treatment. The helper/inducer T cell lineage, defined by moAb Leu 3a, and the cytotoxic/suppressor T cell lineage, defined by moAb Leu 2A, contain both 4A increases and 4A decreases T cell populations. Functional studies by moAb 4A + C treatment show that 1) the 4A increases T cell population contains T helper cells, which are necessary for in vitro antibody production against red cell-bound determinant; 2) the 4A decreases T cell population contains the precursor T cells, which proliferate in vitro in MLC, and the precursor T cells, which are necessary for the in vitro generation of the alloreactive cytotoxic T cells; and 3) the cytotoxic activity of alloreactive T cells generated in CML assay is abrogated by moAb 4A + C treatment; 4) the activation of T cells by PHA and Con A increases the quantitative expression of 4A antigen.
Lysins: the arrival of pathogen-directed anti-infectives (2013)

Lysins represent a novel class of anti-infectives derived from bacteriophage. Lysins are bacterial cell-wall hydrolytic enzymes that selectively and rapidly kill (≥3 log c.f.u. in 30 min) specific Gram-positive bacteria providing a targeted therapeutic approach with minimal impact on unrelated commensal flora. The potential for bacterial resistance to lysins is considered low due to targeting of highly conserved peptidoglycan components. Through cutting-edge genetic engineering, lysins can be assembled into large libraries of anti-infective agents tailored to any bacterium of interest including drug-resistant Gram-positive pathogens such as meticillin- and vancomycin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecalis and Enterococcus faecium, and penicillin-resistant Streptococcus pneumoniae. Lysins can eliminate bacteria systemically and topically from mucosal surfaces and biofilms, as evidenced by experimental models of sepsis, endocarditis, pneumonia, meningitis, and nasopharyngeal, skin and vaginal decolonization. Furthermore, lysins can act synergistically with antibiotics and, in the process, resensitize bacteria to non-susceptible antibiotics. Clinical trials are being prepared to assess the safety and pharmacokinetic properties of lysins in humans.
In silico Methods for Design of Kinase Inhibitors as Anticancer Drugs (2020)

Rational drug design implies usage of molecular modeling techniques such as pharmacophore modeling, molecular dynamics, virtual screening and molecular docking, to explain activity of biomolecules, define molecular determinants for interaction with the drug target and design more efficient drug candidates. Kinases play essential role in cell function and therefore are extensively studied targets in drug design and discovery. Kinase inhibitors are clinically very important and widely used antineoplastic drugs. In this review, computational methods used in rational drug design of kinase inhibitors are discussed and compared, considering some representative case studies.
Fluorescence In Situ Hybridization Using Peptide Nucleic Acid Probes for Rapid Detection of Mycobacterium avium subsp. avium and Mycobacterium avium subsp. paratuberculosis in Potable-Water Biofilms (2006)

Here, we present for the first time a high-affinity peptide nucleic acid (PNA) oligonucleotide sequence for detecting Mycobacterium avium bacteria, including the opportunistically pathogenic subspecies M. avium subsp. avium, M. avium subsp. paratuberculosis, and M. avium subsp. silvaticum, by the fluorescence in situ hybridization (FISH) method. There is evidence that M. avium subsp. avium especially is able to survive and grow in drinking-water biofilms and possibly transmit via drinking water. The designed PNA probe (MAV148) specificity was tested with several bacterial species, including other mycobacteria and mycolic acid-containing bacteria. From the range of bacterial strains tested, only M. avium subsp. avium and M. avium subsp. paratuberculosis strains were hybridized. The PNA FISH method was applied successfully to detect M. avium subsp. avium spiked in water samples and biofilm established within a Propella biofilm reactor fed with potable water from a distribution supply.
The synthesis of a new benzothiazine derivative, related to oxicams, synthesized from natural safrole (1992)

Abstract The synthesis of the new derivatives, 2‐methyl‐6,7‐methylenodioxy‐2 H ‐1,2‐benzothiazin‐3‐one‐4‐( N ‐phenyl)carboxamide 1,1‐dioxide ( 6a ) from natural safrole ( 5 ) is described. The principal feature of this route is brevity and the high overall yield, producing the new analogue in ca. 35% from the natural product.
Selective binding and local photophysics of the fluorescent cyanine dye PicoGreen in double-stranded and single-stranded DNA (2003)

The selectivity of binding of the unsymmetric monomethine cyanine dye PicoGreen (PG) to double-stranded (ds) and single-stranded (ss) DNA has been investigated by fluorescence and by circular dichroism spectroscopy, and the photophysical properties of individual binding modes have been determined for the first time. We demonstrate that binding of PG to dsDNA preferentially occurs by intercalation between alternating GC base pairs. Intercalation is also the most important association mode for other base-pair configurations, but in many cases, binding to the exterior of DNA efficiently competes with intercalation. Intercalated PG molecules are characterized by a monoexponential fluorescence decay rate constant of (0.23 ± 0.02) ns−1, which is independent of the base pairs surrounding the dye. Dye molecules in other configurations exhibit fluorescence decay rate constants of about (0.5–0.8) ns−1, and are observed at dye∶base pair ratios larger than 0.30 in calf thymus DNA. Fluorescence yields in ssDNA homopolymers are 0.18, 0.04, 0.008 and 0.003 in poly(dG), poly(dT), poly(dC), and poly(dA), respectively, but 0.30 in random-sequence ssDNA. These differences are explained by dimeric binding to poly(dG) and poly(dT), and comparatively loose association with poly(dA) and poly(dC). Fluorescence decay is multi-exponential in all types of ssDNA, none of its components depend on base redox properties or on stacking interactions. The dye binds as a monomer to heat-denatured ss calf-thymus DNA, and the dominant mode is intercalation between two different bases, one of them being G or T.
Discrimination of Prostate Cancer from Benign Disease by Plasma Measurement of Intact, Free Prostate-specific Antigen Lacking an Internal Cleavage Site at Lys145-Lys146 (2001)

The ratio fPSA-I/PSA-F is significantly higher in cancer compared with noncancer. The percentages of both fPSA-N/PSA-T and fPSA-I/PSA-F may provide interesting diagnostic enhancements alone or in combination with other markers and require further studies.
Clotrimazole, an inhibitor of epidermal benzo(a)pyrene metabolism and DNA binding and carcinogenicity of the hydrocarbon. (1984)

Clotrimazole, a topically applied imidazole antifungal agent widely used in dermatological practice, was shown to be a potent inhibitor of the epidermal metabolism of benzo(a)pyrene (BP) and its microsomal enzyme-mediated binding both to neonatal rat epidermal DNA in vivo and to calf thymus DNA in vitro. Varying concentrations of clotrimazole added to in vitro incubation systems resulted in a dose-dependent inhibition of cytochrome P-450-dependent microsomal aryl hydrocarbon hydroxylase (AHH) in control animals as well as in animals pretreated with topical application of known inducers of the enzyme. Inhibition of epidermal AHH by topically applied clotrimazole was time and dose dependent. The 50% inhibition of clotrimazole for epidermal AHH ranged from 0.12 to 0.25 microM, which suggests that clotrimazole is among the most potent inhibitors of epidermal AHH yet identified. Clotrimazole was also found to be a potent inhibitor of epoxide hydrolase activity in vitro with a 50% inhibition at 0.1 mM. High-pressure liquid chromatographic analysis of the metabolism of BP in rat epidermal microsomes revealed substantial inhibition of metabolite formation by clotrimazole. This occurred in microsomes prepared from untreated as well as animals pretreated with inducers of the enzyme. Furthermore, a single topical application of clotrimazole resulted in 80 and 30% induction of epidermal and hepatic glutathione S-transferase activity, respectively. Topical application of clotrimazole to the skin of BALB/c mice substantially increased the latent period for the development of skin tumors by 3-methylcholanthrene. These studies indicate that clotrimazole is an extremely potent inhibitor of epidermal BP metabolism and of the DNA-binding of polycyclic aromatic hydrocarbon (PAH) carcinogens, and is an enhancer of enzymes necessary for detoxification of the PAH. Clotrimazole also reduces the formation of carcinogenic and mutagenic metabolites of BP in vitro and in vivo and inhibits induction of skin tumors by the PAH. These data indicate that the imidazole antifungal clotrimazole offers promise as an agent useful for the modulation of PAH cancer risk in the skin.
The complete sequence of the coding region of the ATM gene reveals similarity to cell cycle regulators in different species (1995)

Ataxia-telangiectasia (A-T) is an autosomal recessive disorder involving cerebellar degeneration, immunodeficiency radiation sensitivity, and cancer predisposition. A-T heterozygotes are moderately cancer prone. The A-T gene, designated ATM, was recently identified in our laboratory by positional cloning, and a partial cDNA clone was found to encode a polypeptide with a PI-3 kinase domain. We report here the molecular cloning of a cDNA contig spanning the complete open reading frame of the ATM gene. The predicted protein of 3056 amino acids shows significant sequence similarities to several large proteins in yeast, Drosophila and mammals, all of which share the PI-3 kinase domain. Many of these proteins are involved in the detection of DNA damage and the control of cell cycle progression. Mutations in their genes confer a variety of phenotypes with features similar to those observed in human A-T cells. The complete sequence of the ATM gene product provides useful clues to the function of this protein, and furthers understanding of the pleiotropic nature of the A-T mutations.
Myotonic dystrophy with no trinucleotide repeat expansion (1994)

We report 3 patients from 2 families with myotonic dystrophy who do not show an abnormal expansion of CTG trinucleotide repeats within the myotonic dystrophy gene. Characteristic features of myotonic dystrophy in these patients were frontal balding, cataracts, cardiac conduction abnormalities, and testicular atrophy with myotonia and muscle weakness. Results of muscle histopathology were consistent with myotonic dystrophy. Genetic analysis of leukocyte and muscle DNA showed a normal number of CTG repeats. The demonstration of normal CTG repeat number for the myotonic dystrophy gene does not exclude the diagnosis of myotonic dystrophy.
Biooxidations in Chiral Synthesis (2008)

This chapter contains sections titled: Introduction Oxidations of Alcohols and Amines Oxygenation of Nonactivated Carbon Centers Enzymatic Epoxidation Baeyer–Villiger Oxidations Heteroatom Oxidations Aryl Dihydroxylations Halogenation Reactions Summary and Outlook References
Water Adsorption in Porous Metal–Organic Frameworks and Related Materials (2014)

Water adsorption in porous materials is important for many applications such as dehumidification, thermal batteries, and delivery of drinking water in remote areas. In this study, we have identified three criteria for achieving high performing porous materials for water adsorption. These criteria deal with condensation pressure of water in the pores, uptake capacity, and recyclability and water stability of the material. In search of an excellently performing porous material, we have studied and compared the water adsorption properties of 23 materials, 20 of which are metal-organic frameworks (MOFs). Among the MOFs are 10 zirconium(IV) MOFs with a subset of these, MOF-801-SC (single crystal form), -802, -805, -806, -808, -812, and -841 reported for the first time. MOF-801-P (microcrystalline powder form) was reported earlier and studied here for its water adsorption properties. MOF-812 was only made and structurally characterized but not examined for water adsorption because it is a byproduct of MOF-841 synthesis. All the new zirconium MOFs are made from the Zr6O4(OH)4(-CO2)n secondary building units (n = 6, 8, 10, or 12) and variously shaped carboxyl organic linkers to make extended porous frameworks. The permanent porosity of all 23 materials was confirmed and their water adsorption measured to reveal that MOF-801-P and MOF-841 are the highest performers based on the three criteria stated above; they are water stable, do not lose capacity after five adsorption/desorption cycles, and are easily regenerated at room temperature. An X-ray single-crystal study and a powder neutron diffraction study reveal the position of the water adsorption sites in MOF-801 and highlight the importance of the intermolecular interaction between adsorbed water molecules within the pores.