gebhart/patrepeval huggingface dataset:
Emission reabsorption laser induced fluorescence (ERLIF) film thickness measurement (2001)

This paper presents a unique optical technique that utilizes the reabsorption and emission of two fluorescent dyes to accurately measure film thickness while minimizing errors caused by variations in illumination intensity and surface reflectivity. Combinations of dyes are selected that exhibit a high degree of emission reabsorption and each dye concentration is adjusted to create an optically thick system where emission reabsorption is intrinsic to the fluorescence of the film being measured. Film thickness information as well as excitation and dye response characteristics are all imbedded in the emission intensities of the dyes. Errors normally associated with laser induced fluorescence based film thickness measurements, including those due to optical distortion, variations in surface reflectivity and excitation non-uniformities, are minimized by observing the ratio of the dye emissions. The principle and constitutive equations characterizing emission reabsorption laser induced fluorescence (ERLIF) film thickness measurement are presented. In addition, film thickness measurements from 5 to 400 µm with 1% accuracy are demonstrated.
Advances in genosensor research. (1995)

Microfabricated devices containing arrays of nucleic acid hybridization sites, known as genosensors, are being developed for a variety of uses in genomic analysis. A great deal of the overall genosensor development effort involves optimization of experimental conditions in the actual use of genosensors. Here we describe a "low-tech" form of genosensor technology, involving arrays of oligonucleotides on glass microscope slides, which can be used to define optimal operating conditions and to develop applications of hybridization arrays in genome mapping and sequencing. In addition, we describe a porous silicon genosensor, which can be operated in a flowthrough mode, and discuss its advantages over current flat-surface designs. Porous silicon genosensors containing arrays of DNA fragments offer several unique capabilities in genome analysis.
A novel multimedia synchronization model and its applications in multimedia systems (1995)

A synchronization problem, which always arises when sound, video, motion pictures and other media are brought together and integrated into a computer system, is one of the most important issues in multimedia communications and applications. In a time-sharing and multi-process environment such as the UNIX operating system, the traditional synchronization mechanism results in two fatal defects, namely, audio discontinuity and out of synchronization between the audio and video signals. A novel media synchronization model in a multi-process environment is proposed. Based on this model, a continuous media playback module was implemented and served as the key component of the two multimedia systems developed in the Communication and Multimedia Laboratory of National Taiwan University. One is the multimedia authoring system which provides interactive VCR-like operations and audio/video editing facilities. The other is a prototype of the VOD (video on demand) system which provides video browsing facility. Both systems show that the performance of the proposed synchronization model is quite satisfactory.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Anti-aminoacyl tRNA synthetase immune responses: insights into the pathogenesis of the idiopathic inflammatory myopathies (2003)

The striking association between the inflammatory myopathies and anti-ARS antibodies implies a role for the ARS molecules in the pathogenesis of these syndromes. Recent data suggest that ARS molecules and their proteolytic fragments generated during the cell death process may be responsible for priming and sustaining a specific immune response in situ in myositis. How these molecules become altered and access the immune system in the disease microenvironment is an area of ongoing investigation.
Posttraumatic Osteoarthritis: A First Estimate of Incidence, Prevalence, and Burden of Disease (2006)

Although posttraumatic osteoarthritis (OA) is a common and important entity in orthopedic practice, no data presently exist regarding its prevalence or its relative burden of disease. A population-based estimate was formulated, based on one large institution's experience in terms of its fraction of patients with OA presenting to lower-extremity adult reconstructive clinics with OA of posttraumatic origin. The relative proportion of these patients undergoing total joint replacement provided a basis for extrapolating institutional experience with posttraumatic OA to a populationwide estimate because the numbers of lower-extremity total joint arthroplasty procedures performed were reliably tabulated both within the institution and populationwide. By this methodology, approximately 12% of the overall prevalence of symptomatic OA is attributable to posttraumatic OA of the hip, knee, or ankle. This corresponds to approximately 5.6 million individuals in the United States being affected by posttraumatic OA sufficiently severe to have caused them to present for care by an orthopedic lower-extremity adult reconstructive surgeon. Further, based on the relative prevalence of OA versus rheumatoid arthritis, and their relative impacts as assessed by the SF-36 (Short-Form 36) lower-extremity physical composite scores, about 85.5% of the societal costs of arthritis are attributable to OA. The corresponding aggregate financial burden specifically of posttraumatic OA is Dollars 3.06 billion annually, or approximately 0.15% of the total U.S. health care direct cost outlay.
A guideline for designing chalcogenide-based glasses for threshold switching characteristics (1997)

Chalcogenide-based switching materials have potential applications in power control and information storage. In this work, an approach has been suggested to design chalcogenide-based amorphous materials for threshold or memory switching characteristics. Using this guideline, glasses have been formed in a new chalcogenide Al-Ge-As-Te system. All the samples studied have been found to exhibit threshold switching characteristics, which proves the validity of the suggested guideline.
OKT3 prevents xenogeneic GVHD and allows reliable xenograft initiation from unfractionated human hematopoietic tissues (2014)

Immunodeficient mice are now readily engrafted with human hematopoietic cells. However, these mice are susceptible to graft-versus-host disease (GVHD) induced by the engraftment and rapid expansion of coinjected human T cells. Therefore, highly purified sample populations must be used, adding significant time, expense, and effort. Here, we have explored in vivo and in vitro methods utilizing anti-T-cell antibodies to circumvent this problem. Intraperitoneal injection of the antibody within 48 hours prevented GVHD. Alternatively, short-term in vitro incubation of cells with antibody immediately before transplant was equally effective. Although in vitro antithymocyte globulin treatment resulted in a dramatic loss of SCID-repopulating cells (SRCs), treatment with OKT3 or UCHT1 abrogated GVHD risk and preserved engraftment potential. Leukemia samples that presented with substantial human T-cell contamination were effectively rescued from GVHD. In addition, OKT3 treatment of unfractionated cord blood resulted in robust engraftment of primary and secondary mice that was indistinguishable from grafts obtained using purified CD34(+) cells. Limiting dilution analysis of unfractionated blood demonstrated a SRC frequency of 1 in 300 to 500 CD34(+) cells, similar to that of purified hematopoietic stem and progenitor cells. This protocol streamlines xenograft studies while significantly reducing the cost and time of the procedure.
Dysregulation of Src Family Kinases in Mast Cells from Epilepsy-Resistant ASK versus Epilepsy-Prone EL Mice (2007)

Abstract EL mice have been used as a model of epilepsy, whereas ASK mice are an epilepsy-resistant variant originating from a colony of EL mice. Mast cell-dependent anaphylaxis is easily inducible by stimulation with IgE and Ag in ASK mice, whereas EL mice are resistant to such stimuli. In this study we have characterized mast cells derived from these two strains. ASK mast cells proliferated more vigorously than EL cells in response to IL-3 and stem cell factor. Although ASK mast cells degranulated less vigorously than EL mast cells upon stimulation with IgE and Ag, ASK cells produced and secreted several-fold more TNF-α and IL-2 than EL cells. Consistent with the similarities of these ASK and EL mast cell responses with phenotypes of lyn−/− and wild-type mast cells, respectively, Lyn activity was reduced in ASK cells. In addition to the impaired Lyn activity, ASK cells just like lyn−/− cells exhibited reduced Syk activity, prolonged activation of ERK and JNK, and enhanced activation of Akt. Furthermore, the lipid raft-resident transmembrane adaptor protein Cbp/PAG that associates with Lyn was hypophosphorylated in ASK cells. Importantly, similar to lyn−/− cells, Fyn was hyperactivated in ASK cells. Therefore, these results are consistent with the notion that Lyn-dependent phosphorylation of Cbp/PAG negatively regulates Src family kinases. This study also suggests that reduced activity of Lyn, a negative regulator of mast cell activation, underlies the susceptibility of ASK mice to anaphylaxis and implies that dysregulation of Lyn and other Src family kinases contributes to epileptogenesis.
A 5‐year (2000–2004) epidemiological survey of Candida and non‐Candida yeast species causing vulvovaginal candidiasis in Graz, Austria (2006)

Vulvovaginal candidasis (VVC) is a common disease. The majority of cases is caused by Candida albicans, but in recent years an increase has been observed in the frequency of non-albicans Candida infections, especially due to C. glabrata and C. tropicalis. The aim of the study was to assess the prevalence of non-albicans Candida infections in patients suffering from VVC. Therefore, the statistical data of culture-confirmed VVC ascertained at the Institute of Hygiene (Medical University Graz) have been studied. Altogether, 10,463 samples from patients with vulvovaginal complaints were analysed in the years 2000-2004, a number of 3184 proved to be culture-positive for yeast. Candida albicans was the most prevalent cause in 87.9% of all cases. Non-albicans Candida yeast were detected in 12.1%, mainly C. glabrata and Saccharomyces cerevisiae. During a 1-year period 185 patients showed more than one episode of VVC. Patients aged 21-40 years were significantly more prone to suffer from VVC compared with other age-related groups.
High-resolution optical diffraction microscopy (2003)

In an optical diffraction microscopy experiment, one measures the phase and amplitude of the field diffracted by the sample and uses an inversion algorithm to reconstruct its map of permittivity. We show that with an iterative procedure accounting for multiple scattering, it is possible to visualize details smaller than λ/4 with relatively few illumination and observation angles. The roles of incident evanescent waves and noise are also investigated.
HIV-1 Vpr interacts with a human 34-kDa mov34 homologue, a cellular factor linked to the G 2 /M phase transition of the mammalian cell cycle (1998)

Several important and possibly interrelated functions have been identified for the HIV-1 accessory gene product Vpr. These include import of the HIV reverse transcription complex into the nucleus of nondividing cells, cellular differentiation including cell cycle arrest at the G2/M phase border, immune suppression, and enhancement of virus replication. We have cloned a candidate Vpr ligand, termed human Vpr interacting protein (hVIP/MOV34), by using a yeast two-hybrid assay. This gene is homologous to a simultaneously identified 34-kDa human mov34 homologue. The MOV34 family includes proteins that function as transcriptional and proteolytic regulators of cell growth and differentiation. We demonstrate direct interactions between the putative ligand hVIP/MOV34 and Vpr in vitro and in vivo. hVIP/MOV34 localizes to the nucleus and appears to function as a component of the cell cycle cascade. We observe an association between the induction of cell cycle arrest at the G2/M phase border by Vpr and a change in the subcellular localization of hVIP/MOV34 from a nuclear to a perinuclear localization. This was further associated with the inhibition of maturation promoting factor-associated histone H1 kinase activity. We conclude that hVIP/MOV34 is involved in the regulation of the cell cycle and a likely cellular cofactor for HIV-1 Vpr.
Cytotoxic T lymphocytes in HIV-induced disease: implications for therapy and vaccination. (1989)

The immune response to HIV in infected humans leads to the production of HIV-specific cytotoxic T lymphocytes (CTL) which circulate in high frequencies. The presence of these CTL and their eventual protective activities have been studied by various laboratories, and correlations have been made with certain immunopathological manifestations of HIV infections. It seems probable that HIV-immune CTL participate in the induction of certain disorders by initiating inflammatory reactions in the lungs, central nervous system and lymph nodes. Various virus antigens recognized by HIV-immune CTL on the surface of the infected cell have been identified, and molecular definition of the epitopes recognized is well under way. Likewise, numerous HLA transplantation antigens that regulate HIV antigen recognition by CTL have been identified. These data are discussed with regard to the eventual development of a vaccine and of functional immunotherapies.
DigSig: Runtime Authentication of Binaries at Kernel Level (2004)

This paper presents a Linux kernel module, DigSig, which helps system administrators control Executable and Linkable Format (ELF) binary execution and library loading based on the presence of a valid digital signature. By preventing attackers from replacing libraries and sensitive, privileged system daemons with malicious code, DigSig increases the difficulty of hiding illicit activities such as access to compromised systems.DigSig provides system administrators with an efficient tool which mitigates the risk of running malicious code at run time. This tool adds extra functionality previously unavailable for the Linux operating system: kernel level RSA signature verification with caching and revocation of signatures.
Inactivation of Clostridium botulinum type A neurotoxin by trypsin and purification of two tryptic fragments (1985)

Limited treatment of Clostridium botulinum type A neurotoxin with trypsin resulted in the cleavage of the heavy (95000 Da) subunit at approximately the mid-position and a loss of toxic activity. The rate of toxicity loss was considerably faster than that of mid-chain cleavage; thus a loss of toxicity in excess of 90% was accompanied by only 30-35% mid-chain cleavage of the heavy subunit. A study of the binding of 125I-labelled neurotoxin to rat brain synaptosomes showed the loss of toxicity on trypsin treatment to be paralleled by a loss of toxin binding to rat brain synaptosomes suggesting the presence of at least two sites of tryptic action on the 95000-Da binding subunit. Prolonged treatment of the neurotoxin with trypsin resulted in the complete digestion of a 46000-Da fragment of the heavy subunit, leaving intact a soluble fragment of approximately 105000 Da containing the light subunit linked to the remaining (49000-Da) portion of the heavy subunit. This fragment exhibited less than 0.01% of the original toxicity and gave immunoprecipitation reactions indistinguishable from the native toxin. The 49000-Da portion of the heavy chain was purified from the 105000-Da fragment of the toxin and the sequence of the first 35 amino acids determined. The sequence of the first 10 residues was found to be identical to that previously reported for the heavy subunit showing that the 49000-Da fragment represents the NH2-terminal portion of the heavy chain and that this region is resistant to tryptic action. It is suggested that the primary site(s) of tryptic action on the heavy subunit of botulinum type A neurotoxin is close to the COOH terminus and that cleavage of the polypeptide chain in this region results in a loss of toxic activity mediated by the destruction of the neurotoxin-binding site.
A Novel Photometric Method for the Determination of Photoacid Generation Efficiencies Using Benzothiazole and Xanthene Dyes as Acid Sensors (1997)

We report here on a new photometric method for acid quantification in nonaqueous media which has been developed to facilitate quantification for photoacid generators (PAGs) employed in resist compositions for microlithography, but may find application in other fields. The method employs laser excitation of the PAG and is based on the acid-induced bathochromic shift in the absorption spectra of a selected organic dye such as rhodamine B (RB), fluorescein (Fl), coumarin 6 (C6), and 2-[4-(3,4-dimethoxyphenyl)-1,3-butadienyl]benzothiazole (DB). The differences in signal intensity of the protonated form of the sensor are used to evaluate the differences in acid generation efficiencies of the PAGs by relative actinometry. To test this methodology, we have determined the photoacid generation efficiencies of 2-methyl- (1), 2-(2‘-furyl ethylidene)- (2), and 2-(4‘-methoxystyryl)-4,6-bis(trichloromethyl)-1,3,5-triazine (3) in acetonitrile by laser flash photolysis, using direct 308 nm laser excitation for 2 and 3 and 355 nm excitation and various phenothiazine derivatives as sensitizers for 1. The values determined this way for 2 and 3 using the four different dyes coincide fairly well, and the absolute values are in good agreement with those determined independently with an established technique earlier. Under sensitized conditions, the efficiency of acid generation seems to equal the combined quenching efficiencies of the S1 and T1 state of the sensitizers. Experiments in thin polymer films indicate that the same technique could be used to perform in situ acid analysis on coated quartz wafers. This approach has a set of advantages over existing methods and should be applicable to virtually every photoacid generating system by simply selecting the sensor that meets the specific requirements of the PAG under investigation.
Organizational Forms of Matter: An Inorganic Super Fullerene and Keplerate Based on Molybdenum Oxide (1998)

Plato and Kepler would have been pleased. Despite the large number of atoms present the cluster anion 1 resembles an icosahedral-type structure. This represents definitively an unprecedented event in chemistry! The structure is made up of 12 {Mo<sub>11</sub> } fragments such that the fivefold symmetry axes are retained in the resulting spherical object. As an inscribed icosahedron can be recognized in the spherical shell of 1 (see picture), similarities with Kepler's famous shell model of the cosmos can be seen.
Production of a Monoclonal Antibody against an Epitope on HeLa Cells that Is the Functional Poliovirus Binding Site (1985)

Cell lines of primate origin carry receptors on their plasma membrane which are responsible for the specific binding of poliovirus. This paper describes the isolation and characterization of a monoclonal antibody reacting with the plasma membrane of HeLa cells. The antibody (D171) was selected for its protection of HeLa cells against the cytopathic effect of poliovirus type 1. This protection was found to extend to all three viral serotypes, while the replication of five other viruses in HeLa cells was not affected. The 125I-labelled purified antibody did not react with cell lines derived from pig, dog or rodents but bound specifically to all lines of human or primate origin. Immunoglobulin or Fab fragments of D171 prevented the binding of 35S-labelled poliovirus to HeLa cells. Conversely, nearly all binding sites of 125I-labelled D171 immunoglobulins or Fab fragments could be blocked after preincubation of HeLa cells with poliovirus. These results indicate that D171 recognizes the poliovirus receptor site on different susceptible cells and that practically all D171 binding sites are involved in the specific attachment of poliovirus to the plasma membrane. To determine whether the epitope recognized by D171 could be separated from the receptor for poliovirus, human-mouse cell hybrids were prepared and analysed. In all 40 clones tested, the susceptibility to poliovirus correlated with the binding of D171.
Contributions of Angular Momentum and Catting to the Twist Rotation in High Jumping (1997)

This project sought to break down high jump twist rotation into portions contributed by angular momentum and those contributed by rotational action and reaction ("catting"). Five male and 5 female high jumpers were studied with three-dimensional film/video analysis procedures. The hip twist angle at the peak was broken down into an initial twist angle at takeoff and the subsequent twist rotation accumulated between takeoff and the peak. The latter was in turn broken down into rotations contributed by the twisting component of angular momentum and rotations contributed by catting. It was found that the contribution of catting to the twist rotation was at least as large as that of the angular momentum. The important contribution of catting to the twist rotation introduces the possibility that defects in its execution might play a role in the problems that some high jumpers have with twist rotation.
Nuclear matrix proteins reflect cell type of origin in cultured human cells. (1988)

The low abundance proteins of the nuclear matrix (NM) were separated from the intermediate filament (IF) proteins and analyzed by two-dimensional gel electrophoresis. Three human breast carcinoma lines had virtually identical patterns of 37 NM proteins. In contrast, cell lines derived from diverse tissues had qualitatively different NM protein patterns. Together, the five cell types examined here had a total of 205 distinguishable NM proteins with 125 of these proteins unique to a single cell type. The remaining NM proteins were shared among cell types to different degrees. Polyclonal antisera, obtained by immunization with total NM proteins as antigens, preferentially stained the nuclear interior and not the exterior IF. These observations suggest that the NM proteins, localized to the interior of the nucleus, vary in a cell-type-specific manner.
Emergence of a Drug-Dependent Human Immunodeficiency Virus Type 1 Variant during Therapy with the T20 Fusion Inhibitor (2004)

The fusion inhibitor T20 belongs to a new class of anti-human immunodeficiency virus type 1 (HIV-1) drugs designed to block entry of the virus into the host cell. However, the success of T20 has met with the inevitable emergence of drug-resistant HIV-1 variants. We describe an evolutionary pathway taken by HIV-1 to escape from the selective pressure of T20 in a treated patient. Besides the appearance of T20-resistant variants, we report for the first time the emergence of drug-dependent viruses with mutations in both the HR1 and HR2 domains of envelope glycoprotein 41. We propose a mechanistic model for the dependence of HIV-1 entry on the T20 peptide. The T20-dependent mutant is more prone to undergo the conformational switch that results in the formation of the fusogenic six-helix bundle structure in gp41. A premature switch will generate nonfunctional envelope glycoproteins (dead spikes) on the surface of the virion, and T20 prevents this abortive event by acting as a safety pin that preserves an earlier prefusion conformation.