gebhart/patrepeval huggingface dataset:
Electrochemical and Spectroscopic Characterization of Surface Sol−Gel Processes (2004)

(3-Mercaptopropyl)trimethoxysilane (MTS) forms a unique film on a platinum substrate by self-assembly and sol-gel cross-linking. The gelating and drying states of the self-assembled MTS sol-gel films were probed by use of electrochemical and spectroscopic methods. The thiol moiety was the only active group within the sol-gel network. Gold nanoparticles were employed to detect the availability of the thiol group and their interaction further indicated the physicochemical states of the sol-gel inner structure. It was found that the thiol groups in the open porous MTS aerogel matrix were accessible to the gold nanoparticles while thiol groups in the compact MTS xerogel network were not accessible to the gold nanoparticles. The characteristics of the sol-gel matrix change with time because of its own irreversible gelating and drying process. The present work provides direct evidence of gold nanoparticle binding with thiol groups within the sol-gel structures and explains the different permeability of "aerogel" and "xerogel" films of MTS on the basis of electrochemical and spectroscopic results. Two endogenous species, hydrogen peroxide and ascorbic acid, were used to test the permeability of the self-assembled sol-gel film in different states. The MTS xerogel film on the platinum electrode was extremely selective against ascorbic acid while maintaining high sensitivity to hydrogen peroxide in contrast to the relatively high permeability of ascorbic acid in the MTS aerogel film. This study showed the potential of the MTS sol-gel film as a nanoporous material in biosensor development.
False Discovery Rates and Related Statistical Concepts in Mass Spectrometry-Based Proteomics (2007)

Development of statistical methods for assessing the significance of peptide assignments to tandem mass spectra obtained using database searching remains an important problem. In the past several years, several different approaches have emerged, including the concept of expectation values, target-decoy strategy, and the probability mixture modeling approach of PeptideProphet. In this work, we provide a background on statistical significance analysis in the field of mass spectrometry-based proteomics, and present our perspective on the current and future developments in this area.
A modified terminology for cervical intraepithelial neoplasia. (1990)

Recent data are consistent with the concept that human papillomavirus (HPV) is etiologically important in the causation of cervical squamous cell cancer. There appear to be certain important events in the process of HPV infection and neoplasia. It is suggested that the terminology of the HPV-related precursor lesions be modified and that two terms, rather than three, would best satisfy the requirements of both science and clinical care. The "early" lesions should be referred to as "low-grade cervical intraepithelial neoplasia (CIN) with HPV-related changes" and the lesions that have the features of cancer precursors as "high-grade CIN."
<title>Tracking speckle patterns with optical correlation</title> (1993)

It has been shown that tracking small particle motion can be accomplished by tracking the speckle pattern is produces. This paper describes various methods of real-time tracking of speckle patterns obtained from ultrasonic flow imaging of blood and tissue motion using optical correlation. Results obtained from a gray scale joint transform correlator utilizing a twisted nematic liquid crystal spatial light modulator and from Sandia Lab's acousto-optical correlator are presented. The experimental results demonstrate the feasibility of real-time tracking with accuracy comparable to that of template matching algorithms currently being implemented in digital hardware.
Genetic Regulation of Platelet Receptor Expression and Function (2010)

Understanding genetic contributions to platelet function could have profound clinical ramifications for personalizing platelet-directed pharmacotherapy, by providing insight into the risks and possible benefits associated with specific genotypes. This article represents an integrated summary of presentations related to genetic regulation of platelet receptor expression and function given at the Fifth Annual Platelet Colloquium in January 2010. It is supplemented with additional highlights from the literature covering (1) approaches to determining and evidence for the associations of genetic variants with platelet hypo- and hyperresponsive phenotypes, (2) the ramifications of these polymorphisms with regard to clinical responses to antiplatelet therapies, and (3) the role of platelet function/genetic testing in guiding antiplatelet therapy.
Immunogenicity of Multiple Gene and Clade Human Immunodeficiency Virus Type 1 DNA Vaccines (2003)

The ability to elicit an immune response to a spectrum of human immunodeficiency virus type 1 (HIV-1) gene products from divergent strains is a desirable feature of an AIDS vaccine. In this study, we examined combinations of plasmids expressing multiple HIV-1 genes from different clades for their ability to elicit humoral and cellular immune responses in mice. Immunization with a modified Env, gp145DeltaCFI, in combination with a Gag-Pol-Nef fusion protein plasmid elicited similar CD4(+) and CD8(+) cellular responses to immunization with either vector alone. Further, when mice were immunized with a mixture of Env from three clades, A, B, and C, together with Gag-Pol-Nef, the overall potency and balance of CD4(+)- and CD8(+)-T-cell responses to all viral antigens were similar, with only minor differences noted. In addition, plasmid mixtures elicited antibody responses comparable to those from individual inoculations. These findings suggest that a multigene and multiclade vaccine, including components from A, B, and C Env and Gag-Pol-Nef, can broaden antiviral immune responses without immune interference. Such combinations of immunogens may help to address concerns about viral genetic diversity for a prospective HIV-1 vaccine.
CMOS continuous-time current-mode filters for high-frequency applications (1993)

Design considerations for high-frequency CMOS continuous-time current-mode filters are presented. The basic building block is a differential current integrator with its gain constant set by a small-signal transconductance and a gate capacitance. A prototype fifth-order low-pass ladder filter implemented in a standard digital 2 mu m n-well CMOS process achieved a -3 dB cutoff frequency (f/sub 0/) of 42 MHz; f/sub 0/ was tunable from 24 to 42 MHZ by varying a reference bias current from 50 to 150 mu A. Using a single 5 V power supply with a nominal reference current of 100 mu A, the five-pole filter dissipated 25.5 mW. The active filter area was 0.056 mm/sup 2//pole. With the minimum input signal defined as the input-referred noise integrated over a 40 MHz bandwidth, and the maximum input signal defined at the 1% total intermodulation distortion (TIMD) level, the measured dynamic range was 69 dB. A third-order elliptic low-pass ladder filter was also integrated in the 2 mu m n-well CMOS process to verify the implementation of finite transmission zeros.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Securing web application code by static analysis and runtime protection (2004)

Security remains a major roadblock to universal acceptance of the Web for many kinds of transactions, especially since the recent sharp increase in remotely exploitable vulnerabilities have been attributed to Web application bugs. Many verification tools are discovering previously unknown vulnerabilities in legacy C programs, raising hopes that the same success can be achieved with Web applications. In this paper, we describe a sound and holistic approach to ensuring Web application security. Viewing Web application vulnerabilities as a secure information flow problem, we created a lattice-based static analysis algorithm derived from type systems and typestate, and addressed its soundness. During the analysis, sections of code considered vulnerable are instrumented with runtime guards, thus securing Web applications in the absence of user intervention. With sufficient annotations, runtime overhead can be reduced to zero. We also created a tool named.WebSSARI (Web application Security by Static Analysis and Runtime Inspection) to test our algorithm, and used it to verify 230 open-source Web application projects on SourceForge.net, which were selected to represent projects of different maturity, popularity, and scale. 69 contained vulnerabilities. After notifying the developers, 38 acknowledged our findings and stated their plans to provide patches. Our statistics also show that static analysis reduced potential runtime overhead by 98.4%.
Death deflected: IL‐15 inhibits TNF‐α‐mediated apoptosis in fibroblasts by TRAF2 recruitment to the IL‐15Rα chain (1999)

Interleukin-15 (IL-15) is a potent inhibitor of several apoptosis pathways. One prominent path toward apoptosis is the ligand-induced association of TNF receptor 1 (TNFR1) with death domain adaptor proteins. Studying if and how IL-15 blocks TNFR1-mediated apoptosis in a murine fibroblast cell line (L929), we show here that IL-15 blocks TNFR1-induced apoptosis via IL-15Ralpha chain signaling. The intracellular tail of IL-15Ralpha shows sequence homologies to the TRAF2 binding motifs of CD30 and CD40. Most important, binding of IL-15 to IL-15Ralpha successfully competes with the TNFR1 complex for TRAF2 binding, which may impede assembly of key adaptor proteins to the TNFR1 complex, and induces IkappaBalpha phosphorylation. Thus, IL-15Ralpha chain stimulation is a powerful deflector of cell death very early in the apoptosis signaling cascade, while TNF-alpha and IL-15 surface as major opponents in apoptosis control.
Ganglioside embedded in reconstituted lipoprotein binds cholera toxin with elevated affinity (2010)

The ability to exogenously present cell-surface receptors in high-affinity conformations in a synthetic system offers an opportunity to provide host cells with protection from pathogenic toxins. This strategy requires improvement of the synthetic receptor binding affinity against its native counterpart, particularly with polyvalent toxins where clustering of membrane receptors can hinder binding. Here we demonstrate that reconstituted lipoprotein, nanometer-sized discoidal lipid bilayers bounded by apolipoprotein and functionalized by incorporation of pathogen receptors, provides a means to enhance toxin-receptor binding through molecular-level control over the receptor microenvironment (specifically, its rigidity, composition, and heterogeneity). Using a Foerster Resonance Energy Transfer (FRET)-based assay, we found that reconstituted lipoprotein incorporating low concentrations of ganglioside monosialotetrahexosylganglioside (GM1) binds polymeric cholera toxin with significantly higher affinity than liposomes or supported lipid bilayers, most likely a result of the enhanced control over receptor clustering provided by the lipoprotein platform. Using wide-area epifluorescence, we found that this enhanced binding capacity can be effectively utilized to divert cholera toxin away from populations of healthy mammalian cells. In summary, we found that reconstitutions of high-density lipoprotein can be engineered to include specific pathogen receptors; that their pathogen binding affinity is altered, presumably due to attenuation of receptor aggregation; and that these assemblies are effective at protecting cells from biological toxins.
Defective Myotilin Homodimerization Caused by a Novel Mutation in MYOT Exon 9 in the First Japanese Limb Girdle Muscular Dystrophy 1A Patient (2009)

Myotilin is a muscle-specific Z disk protein. Several missense mutations in the myotilin gene (MYOT) have been identified in limb girdle muscular dystrophy (LGMD), myofibrillar myopathy, and distal myopathy patients. All previously reported pathogenic MYOT mutations have been identified only in Exon 2. We sequenced MYOT in 138 patients diagnosed as having LGMD, myofibrillar myopathy, or distal myopathy, and identified a novel MYOT mutation in Exon 9 encoding the second immunoglobulin-like domain in 1 patient with clinically typical LGMD. By light microscopy, there were scattered fibers with rimmed vacuoles and myofibrillary disorganization in the patient's muscle biopsy; accumulation of Z disk proteins was observed by immunohistochemistry. Immunoblot analysis demonstrated that the amount of myotilin monomer was increased in the patient muscle, but that the myotilin homodimeric band was decreased. Functional analysis of the myotilin mutation using a yeast 2-hybrid system revealed defective homodimerization of the mutant myotilin and decreased interaction between mutant myotilin and alpha-actinin. The homodimerization defect was further demonstrated by immunoprecipitation. This is the first MYOT mutation outside of Exon 2 in an LGMD type 1A patient and the first MYOT mutation identified in the Japanese population. This mutation in the second immunoglobulin-like domain impairs myotilin dimerization and alters the binding between myotilin and alpha-actinin, which is known to be important for actin bundling.
A novel transgenic chimaeric mouse system for the rapid functional evaluation of genes encoding secreted proteins (2005)

A major challenge of the post-genomic era is the functional characterization of anonymous open reading frames (ORFs) identified by the Human Genome Project. In this context, there is a strong requirement for the development of technologies that enhance our ability to analyze gene functions at the level of the whole organism. Here, we describe a rapid and efficient procedure to generate transgenic chimaeric mice that continuously secrete a foreign protein into the systemic circulation. The transgene units were inserted into the genomic site adjacent to the endogenous immunoglobulin (Ig) kappa locus by homologous recombination, using a modified mouse embryonic stem (ES) cell line that exhibits a high frequency of homologous recombination at the Igkappa region. The resultant ES clones were injected into embryos derived from a B-cell-deficient host strain, thus producing chimaerism-independent, B-cell-specific transgene expression. This feature of the system eliminates the time-consuming breeding typically implemented in standard transgenic strategies and allows for evaluating the effect of ectopic transgene expression directly in the resulting chimaeric mice. To demonstrate the utility of this system we showed high-level protein expression in the sera and severe phenotypes in human EPO (hEPO) and murine thrombopoietin (mTPO) transgenic chimaeras.
A Large Labeled Corpus for Online Harassment Research (2017)

A fundamental part of conducting cross-disciplinary web science research is having useful, high-quality datasets that provide value to studies across disciplines. In this paper, we introduce a large, hand-coded corpus of online harassment data. A team of researchers collaboratively developed a codebook using grounded theory and labeled 35,000 tweets. Our resulting dataset has roughly 15% positive harassment examples and 85% negative examples. This data is useful for training machine learning models, identifying textual and linguistic features of online harassment, and for studying the nature of harassing comments and the culture of trolling.
Using latent semantic indexing to filter spam (2003)

Past research has explored the effectiveness of a Naïve Bayesian classifier when filtering unsolicited bulk email (spam). Results have shown that the degree of precision of this approach is generally superior to the degree of recall. This study evaluates the effectiveness of a classifier incorporating Latent Semantic Indexing (LSI) to filter spam email on corpus used in previous studies. Results show that email classifiers using LSI to filter spam enjoy a very high degree of both recall and precision, no matter if the corpus is treated using a stop list or a lemmatizer. While using LSI leads to precision roughly equal to that of using a Naïve Bayesian approach, the LSI technique has a substantially higher recall and is more effective under certain conditions.Results show that incorporating LSI into an anti-spam filter is viable, particularly in implementations when misclassified legitimate messages are not arbitrarily deleted. Other inferences are drawn to the applicability of this method to other text mining tasks.
Structural and Immunological Characterization of the Intracellular Forms of an Abundant 68000 Mr Human Cytomegalovirus Protein (1987)

SUMMARY Murine monoclonal antibodies and polyvalent monospecific antisera reactive with an abundant 68000 M r (p68) human cytomegalovirus (CMV) virion protein were used to characterize this protein within CMV-infected cells. The protein was found to partition within the nucleus and cytoplasm of infected cells. Pulse-chase analysis indicated the p68 was degraded into three proteins of 52000, 51000 and 50000 M r which were found only within infected cells. Both cellular forms as well as the virion p68 were phosphorylated but non-glycosylated. The p68 was synthesized shortly after infection and in the presence of cytosine arabinoside, an inhibitor of viral DNA replication. Studies with monospecific antisera and a panel of monoclonal antibodies specific for the p68 suggested that this protein was not expressed on the surface of infectious virions or infected cells.
Health risk appraisal: the estimation of risk. (1980)

describes a person's chances of becoming ill or dying from selected diseases. The procedure generates a statement of probability, not a diagnosis. Identifying the variables known to influence individual risk, quantifying their effect and interaction, and constructing algorithms to estimate risk are fundamental to risk appraisal. The accurate estimation of risk presents a challenge to both research workers and clinicians. Existing risk-appraisal instruments have been reviewed elsewhere, for example, by Hettler and coauthors (1) and in a 1978 survey of health promotion conducted by the Washington [D.C.] Business Group on Health. We treat here the methodological and research issues relating to the current state and future development of risk estimation. Risk Estimation If one can accurately estimate a person's risk of (a) getting specific diseases, both physical and mental (for example, having a myocardial infarction), (b) dying from certain diseases (for example, from breast cancer), and (c) dying within a defined period (for example, within 10 years), then it is appropriate to ask of what use these estimates are. To adequately answer this question, it is essential to recognize the underlying hypotheses that require substantiation.
ras gene Amplification and Malignant Transformation (1985)

Morphologic transformation of NIH 3T3 mouse cells occurs upon transfection of these cells with large amounts (greater than or equal to 10 micrograms) of recombinant DNA molecules carrying the normal human H-ras-1 proto-oncogene. We provide experimental evidence indicating that transformation of these NIH 3T3 cells results from the combined effect of multiple copies of the H-ras-1 proto-oncogene rather than from spontaneous mutation of one of the transfected H-ras-1 clones (E. Santos, E.P. Reddy, S. Pulciani, R.J. Feldman, and M. Barbacid, Proc. Natl. Acad. Sci. USA 80:4679-4683, 1983). Levels of H-ras-1 RNA and p21 expression are highly elevated in the NIH 3T3 transformants, and in those cases examined, these levels correlate with the malignant properties of these cells. We have also investigated the presence of amplified ras genes in a variety of human carcinomas. In 75 tumor biopsies, we found amplification of the human K-ras-2 locus in one carcinoma of the lung. These results indicate that ras gene amplification is an alternative pathway by which ras genes may participate in the development of human neoplasia.
Global gene expression analysis of early response to chemotherapy treatment in ovarian cancer spheroids (2008)

Most alterations in gene expression were directly related to mechanisms of the cytotoxics actions in OC spheroids. However, the induction of genes linked to mechanisms of DNA replication and repair in cisplatin- and topotecan-treated OC spheroids could be associated with immediate adaptive response to treatment. Similarly, overexpression of different tubulin genes upon exposure to paclitaxel could represent an early compensatory effect to this drug action. Finally, multicellular growth conditions that are known to alter gene expression (including cell adhesion and cytoskeleton organization), could substantially contribute in reducing the initial effectiveness of CT drugs in OC spheroids. Results described in this study underscore the potential of the microarray technology for unraveling the complex mechanisms of CT drugs actions in OC spheroids and early cellular response to treatment.
1,7‐Dideaza‐2′,3′‐dideoxyadenosine: Syntheses of Pyrrolo[2,3‐b]pyndine 2′,3′‐Dideoxyribofuranosides and Participation of Purine N(1) during HIV‐1 Reverse Transcriptase Inhibition (1991)

Abstract The syntheses of 1,7‐dideaza‐2′,3′‐dideoxyadenosine ( 1 ) and related pyrrolo[2,3‐ b ]pyridine 2′,3′‐dideoxyribi and 2′,3′‐didehydro‐2′,3′‐dideoxyribonucleosides (see 2–5 ) are described. As starting materials, 2′‐deoxyribo‐nucleosides 6 or 7 were used. The 3′‐OH group was removed by Barton deoxygenation or via mesylation follow by elimination and catalytic hydrogenation. Compound 1 was also obtained from the direct glycosylation of 4‐nitro‐1 H ‐pyrrolo[2,3‐ b ]pyridine ( 17 ) with the 2,3‐dideoxyribofuranosyl chloride 18. The triphosphate 25 of 1 showed only marginal activity against HIV‐1 reverse transcriptase, indicating that purine N(1) is required for the inhibitory activity of the parent 2′,3′‐dideoxyadenosine.
Acute Renal Failure in Pregnancy (1997)

From 1976 to 1994, 57 women were referred to the Centro de Nefrología, Montevideo, with obstetric acute renal failure (ARF). The main causes were hypertensive disorders such as preeclampsia (PE) in 27, acute pyelonephritis of pregnancy (APN) in 26, and idiopathic postpartum renal failure in 3. Severe preeclampsia superimposed on chronic hypertension and acute pyelonephritis of pregnancy complicated by sepsis accounted for more than 50% of the cases of ARF. Chronic renal failure developed in 6 patients: 2 had bilateral renal cortical necrosis, 1 had malignant nephrosclerosis, and 3 had idiopathic postpartum renal failure. Maternal mortality related to ARF was low in this group of patients (less than 2%). In contrast, perinatal mortality was strikingly high (40%).
CyberCash Credit Card Protocol Version 0.8 (1996)

CyberCash is developing a general payments system for use over the Internet.The structure and communications protocols of version 0.8 are described.This version includes credit card payments only.Additional capabilities are planned for future versions.