gebhart/patrepeval huggingface dataset:
Febrile infections and malignant melanoma (1992)

Several reports have described an inverse relationship between the frequency of infections and various malignancies. In this paper results of a hospital-based case control study on 139 melanoma patients and 271 suitable selected controls are presented, addressing the question of whether this relationship exists with respect to malignant melanoma while simultaneously controlling for the effects of other risk factors. Data on childhood diseases (group I), febrile diseases of adulthood (group II) and common febrile infections within a 5-year period prior to the diagnosis of melanoma (group III) were collected using a standardized interview. Group I diseases did not show a marked influence on the risk of malignant melanoma. Considering group II diseases, a significant protective effect was determined for chronic infectious diseases (OR = 0.32) and also for wound infections, abscesses and furunculosis (OR = 0.21). In group III, herpes simplex infections (OR = 0.45) and influenza/common cold (OR = 0.32) substantially reduced the melanoma risk. This effect was less pronounced for gastroenteritis (OR = 0.52). Analysis of the cumulative influence of infections pointed to a strong dose-response relationship between the frequency of febrile infections in adulthood and malignant melanoma. In particular, the risk reduction was striking when two or more febrile infections were compared to no febrile infections in group II (OR = 0.09) and group III (OR = 0.20). The study confirms the hypothesis that an inverse relationship exists between febrile infections and malignant melanoma, but these results have to be interpreted cautiously due to the inherent limitations of the case-control design.(ABSTRACT TRUNCATED AT 250 WORDS)
Cell Separation on Microfabricated Electrodes Using Dielectrophoretic/Gravitational Field-Flow Fractionation (1999)

Dielectrophoretic/gravitational field-flow fractionation (DEP/G-FFF) was used to separate cultured human breast cancer MDA-435 cells from normal blood cells mixed together in a sucrose/dextrose medium. An array of microfabricated, interdigitated electrodes of 50 microns widths and spacings, and lining the bottom surface of a thin chamber (0.42 mm H x 25 mm W x 300 mm L), was used to generate DEP forces that levitated the cells. A 10-microL cell mixture sample containing approximately 50,000 cells was introduced into the chamber, and cancerous and normal blood cells were levitated to different heights according to the balance of DEP and gravitational forces. The cells at different heights were transported at different velocities under the influence of a parabolic flow profile that was established in the chamber and were thereby separated. Separation performance depended on the frequency and voltage of the applied DEP field and the fluid-flow rate. It took as little as 5 min to achieve cell separation. An analysis of the DEP/G-FFF results revealed that the separation exploited the difference in dielectric and density properties between cell populations. The DEP/G-FFF technique is potentially applicable to many biological and biomedical problems, especially those related to microfluidic systems.
A vertical cavity longwave infrared SiGe/Si photodetector using a buried silicide mirror (2002)

We describe the fabrication, modelling and performance of a resonant cavity detector using epitaxial p-type SiGe/Si quantum wells grown over a high reflectance tungsten silicide layer. The device operates in the 8-12 /spl mu/m band in normal incidence and has a black body responsivity comparable to current n-GaAs/AlGaAs detectors at /spl sim/1 V, making it suitable for integration in a monolithic Si-based focal plane array. Ways to improve the design are discussed.
Power-aware network swapping for wireless palmtop PCs (2006)

Virtual memory is considered to be an unlimited resource in desktop or notebook computers with high storage capabilities. However, in wireless mobile devices, like palmtops and personal digital assistants (PDAs), storage memory is limited or absent due to weight, size, and power constraints, so that swapping over remote memory devices can be considered as a viable alternative. However, power-hungry wireless network interface cards (WNICs) may limit the battery lifetime and application performance if not efficiently exploited. In this paper, we study performance and energy of network swapping in comparison with swapping on local microdrives and flash memories. We report the results of extensive experiments conducted on different WNICs and local swapping devices, using both synthetic and natural benchmarks. Our study points out that remote swapping over power-manageable WNICs can be more efficient than local swapping, especially in bursty workload conditions. Such conditions can be forced where possible by reshaping swapping requests to increase energy efficiency and performance.
Complementation of the Arabidopsispds1Mutation with the Gene Encodingp-Hydroxyphenylpyruvate Dioxygenase (1998)

Plastoquinone and tocopherols are the two major quinone compounds in higher plant chloroplasts and are synthesized by a common pathway. In previous studies we characterized two loci in Arabidopsis defining key steps of this biosynthetic pathway. Mutation of the PDS1 locus disrupts the activity of p-hydroxyphenylpyruvate dioxygenase (HPPDase), the first committed step in the synthesis of both plastoquinone and tocopherols in plants. Although plants homozygous for the pds1 mutation could be rescued by growth in the presence of homogentisic acid, the product of HPPDase, we were unable to determine if the mutation directly or indirectly disrupted HPPDase activity. This paper reports the isolation of a cDNA, pHPPD, encoding Arabidopsis HPPDase and its functional characterization by expression in both plants and Escherichia coli. pHPPD encodes a 50-kD polypeptide with homology to previously identified HPPDases, including 37 highly conserved amino acid residues clustered in the carboxyl region of the protein. Expression of pHPPD in E. coli catalyzes the accumulation of homogentisic acid, indicating that it encodes a functional HPPDase enzyme. Mapping of pHPPD and co-segregation analysis of the pds1 mutation and the HPPD gene indicate tight linkage. Constitutive expression of pHPPD in a pds1 mutant background complements this mutation. Finally, comparison of the HPPD genomic sequences from wild type and pds1 identified a 17-bp deletion in the pds1 allele that results in deletion of the carboxyterminal 26 amino acids of the HPPDase protein. Together, these data conclusively demonstrate that pds1 is a mutation in the HPPDase structural gene.
Theory of Mind (2005)

Abstract Theory of mind refers to the everyday psychology that we use to understand and explain our own and others' actions by reference to mental states, such as ‘desiring’, ‘knowing’ and ‘believing’.
HIV-1 Gag Processing Intermediates Trans-dominantly Interfere with HIV-1 Infectivity (2009)

Protease inhibitors (PI) act by blocking human immunodeficiency virus (HIV) polyprotein processing, but there is no direct quantitative correlation between the degree of impairment of Gag processing and virion infectivity at low PI concentrations. To analyze the consequences of partial processing, virus particles were produced in the presence of limiting PI concentrations or by co-transfection of wild-type proviral plasmids with constructs carrying mutations in one or more cleavage sites. Low PI concentrations caused subtle changes in polyprotein processing associated with a pronounced reduction of particle infectivity. Dissection of individual stages of viral entry indicated a block in accumulation of reverse transcriptase products, whereas virus entry, enzymatic reverse transcriptase activity, and replication steps following reverse transcription were not affected. Co-expression of low amounts of partially processed forms of Gag together with wild-type HIV generally exerted a trans-dominant effect, which was most prominent for a construct carrying mutations at both cleavage sites flanking the CA domain. Interestingly, co-expression of low amounts of Gag mutated at the CA-SP1 cleavage site also affected processing activity at this site in the wild-type virus. The results indicate that low amounts (<5%) of Gag processing intermediates can display a trans-dominant effect on HIV particle maturation, with the maturation cleavage between CA and SP1 being of particular importance. These effects are likely to be important for the strong activity of PI at concentrations achieved in vivo and also bear relevance for the mechanism of action of the antiviral drug bevirimat.
A synthetic peptide mimicking the HLA-DR β2-binding site for CD4 inhibits antigen-independent CD4+ T cell adhesion to B cells and CD4+ T cell activation (1996)

We studied the ability of a peptide mimicking the major binding site of HLA-DR beta 2 for CD4 (i.e. amino acids 134-148) to inhibit the adhesion of CD4+ T cells to B cells and ICAM-1-DR-expressing fibroblasts, as well as the proliferation of TCR-CD3-triggered CD4+ T cells. Peptide DR134-148 blocked CD4+ T cell (but not CD8+ T cell) binding to B cells and to DR+ ICAM-1+ fibroblasts in a concentration-dependent manner. A peptide composed of randomly associated identical amino acid residues had no effect. This inhibitory activity was not additive with the effect of an anti-CD4 antibody, peptide DR35-46 (mimicking another potential binding site of HLA-DR beta 1 to CD4) or an anti-LFA-1 antibody. Adhesion of a T cell line (HUT78) expressing a mutated form of CD4 unable to bind p56lck cytosine kinase was not inhibited by peptide DR134-148. In addition, herbimycin A, a tyrosine kinase inhibitor, abrogated the inhibitory activity of DR134-148. Since CD4-MHC class II interactions have been shown to play no detectable role in mediating antigen-independent adhesion in this assay, peptide interactions with CD4 may trigger an off signal down-regulating LFA-1-mediated adhesion. Indeed, adhesion of CD4+ T cells to ICAM-1- fibroblasts was not inhibited by peptide DR134-148, while the same peptide inhibited antigen (protein-pure derivative)- and anti-CD3 antibody-induced CD4 T cell proliferation. These findings suggest that the major sequence involved in the MHC class II interaction with CD4 is sufficient to induce a downstream negative regulatory signal that is mediated by p56lck, independently of antigen-specific TCR triggering.
Role of Phosphoenolpyruvate in the NADP-Isocitrate Dehydrogenase and Isocitrate Lyase Reaction in Escherichia coli (2006)

Phosphoenolpyruvate inhibited Escherichia coli NADP-isocitrate dehydrogenase allosterically (Ki of 0.31 mM) and isocitrate lyase uncompetitively (Ki' of 0.893 mM). Phosphoenolpyruvate enhances the uncompetitive inhibition of isocitrate lyase by increasing isocitrate, which protects isocitrate dehydrogenase from the inhibition, and contributes to the control through the tricarboxylic acid cycle and glyoxylate shunt.
SYSTEMIC RESISTANCE INDUCED BY RHIZOSPHERE BACTERIA (1998)

Nonpathogenic rhizobacteria can induce a systemic resistance in plants that is phenotypically similar to pathogen-induced systemic acquired resistance (SAR). Rhizobacteria-mediated induced systemic resistance (ISR) has been demonstrated against fungi, bacteria, and viruses in Arabidopsis, bean, carnation, cucumber, radish, tobacco, and tomato under conditions in which the inducing bacteria and the challenging pathogen remained spatially separated. Bacterial strains differ in their ability to induce resistance in different plant species, and plants show variation in the expression of ISR upon induction by specific bacterial strains. Bacterial determinants of ISR include lipopolysaccharides, siderophores, and salicylic acid (SA). Whereas some of the rhizobacteria induce resistance through the SA-dependent SAR pathway, others do not and require jasmonic acid and ethylene perception by the plant for ISR to develop. No consistent host plant alterations are associated with the induced state, but upon challenge inoculation, resistance responses are accelerated and enhanced. ISR is effective under field conditions and offers a natural mechanism for biological control of plant disease.
Maximum Likelihood Inference of Phylogenetic Trees, with Special Reference to a Poisson Process Model of DNA Substitution and to Parsimony Analyses (1990)

Maximum likelihood inference is discussed, and some of its advantages and disadvantages are noted. The application of maximum likelihood inference to phylogenetics is examined, and a simple Poisson process model of DNA substitution is used as one example. Further examples follow from the clarification of implicit models underlying traditional “parsimony” and “compatibility” analyses. From the elucidation of these models and analyses, it is seen that Poisson process analysis gives a statistically consistent estimate of phylogeny, and that parsimony methods do indeed have a maximum likelihood foundation but give potentially incorrect estimates of phylogeny. The maximum likelihood formulation provides a common framework within which these analyses are discussed and compared.
Registration of clinical volumes to beams‐eye‐view images for real‐time tracking (2014)

Through the combination of EPID/4DCT registration and relative tracking, a necessary step toward the clinical implementation of BEV tracking has been completed. The knowledge of tumor volumes relative to the treatment field is important for future applications like real-time motion management, adaptive radiotherapy, and delivered dose calculations.
Sacral nerve stimulation for voiding dysfunction: One institution's 11‐year experience (2006)

SNS is an effective method for treating certain types of voiding dysfunction. Although 53% of patients experienced at least one RE, 97% were mild-to-moderate and did not appear to affect the continued use of this therapy. With improved technology, such as percutaneous tined leads, the RE rate is decreasing. Further analyses of subsets of this population are currently underway.
Lisinopril Overdose and Management with Intravenous Angiotensin II (1994)

Although only a few cases of ACE inhibitor overdose have been reported, it is possible that with widespread use of these agents, overdose may become a more common problem. Management of ACE inhibitor overdose should include general supportive care, gut decontamination when possible, intravenous fluids, and vasopressors if necessary. Intravenous angiotensin II may be effective in situations in which traditional vasopressors fail, and is a physiologically rational treatment.
Site-specific integration of Agrobacterium T-DNA in Arabidopsis thaliana mediated by Cre recombinase (1998)

In this study Agrobacterium tumefaciens transferred DNA (T-DNA) was targeted to a chromosomally introduced lox site in Arabidopsis thaliana by employing the Cre recombinase system. To this end, Arabidopsis target lines were constructed which harboured an active chimeric promoter-lox-cre gene stably integrated in the plant genome. A T-DNA vector with a promoterless lox -neomycin phosphotransferase (nptII) fusion was targeted to this genomic lox site with an efficiency of 1.2-2.3% of the number of random events. Cre-catalyzed site-specific recombination resulted in restoration of nptII expression by translational fusion of the lox-nptII sequence in the integration vector with the transcription and translation initiation sequences present at the target site, allowing selective enrichment on medium containing kanamycin. Simultaneously, the coding sequence of the Cre recombinase was disconnected from these same transcription and translation initiation signals by displacement, aimed at preventing the efficient reversible excision reaction. Of the site-specific recombinants, 89% were the result of precise integration. Furthermore, approximately 50% of these integrants were single copy transformants, based on PCR analysis. Agrobacterium T-DNA, which is transferred to plant cells as a single-stranded linear DNA structure, is in principle incompatible with Cre-mediated integration. Nevertheless, the results presented here clearly demonstrate the feasibility of the Agrobacterium -mediated transformation system, which is generally used for transformation of plants, to obtain site-specific integration.
Development of an SU-8 fabry-perot blood pressure sensor (2005)

This paper presents the fabrication method and testing of an interferometric pressure sensor designed for intravascular blood pressure measurements. A cap containing a pressure-sensing diaphragm was mounted onto the end of a fiber optic cable. The Fabry-Perot interferometer, formed between the reflective diaphragm and the fiber's end, measured the diaphragm deflection. Microfabricated from the biocompatible polymer, SU-8, the device is fast, simple, and inexpensive to manufacture. Its small dimensions (<300/spl mu/m outer diameter) reduce the risk of infection and thrombosis and allow for its insertion into small vessels. The sensor showed a linear response to pressure from 0 to 125 mmHg with approximately 1-2 mmHg resolution. The use of an optical displacement transducer allowed a series of careful measurements of drift and hysteresis of SU-8 materials in different environments. This data may be valuable to other researchers working with SU-8.
An analogue of the erythroid membrane skeletal protein 4.1 in nonerythroid cells. (1984)

Protein 4.1 is a crucial component of the erythrocyte membrane skeleton. Responsible for the amplification of the spectrin-actin interaction, its presence is required for the maintenance of erythrocyte integrity. We have demonstrated a 4.1-like protein in nonerythroid cells. An antibody was raised to erythrocyte protein 4.1 purified by KCl extraction (Tyler, J. M., W. R. Hargreaves, and D. Branton, 1979, Proc. Natl. Acad. Sci. USA, 76:5192-5196), and used to identify a serologically cross-reactive protein in polymorphonuclear leukocytes, platelets, and lymphoid cells. The cross-reactive protein(s) were localized to various regions of the cells by immunofluorescence microscopy. Quantitative adsorption studies indicated that at least 30-60% of the anti-4.1 antibodies reacted with this protein, demonstrating significant homology between the erythroid and nonerythroid species. A homologous peptide doublet was observed on immunopeptide maps, although there was not complete identity between the two proteins. When compared with erythrocyte protein 4.1, the nonerythroid protein(s) displayed a lower molecular weight--68,000 as compared with 78,000-and did not bind spectrin or the nonerythroid actin-binding protein filamin. There was no detectable cross-reactivity between human acumentin or human tropomyosin-binding protein, which are similarly sized actin-associated proteins, and erythrocyte protein 4.1. The possible origin and significance of 4.1-related protein(s) in nonerythroid cells are discussed.
Transformation ofLactobacillus caseiby electroporation (1987)

Electroporation has been used to introduce DNA into both eucaryotic and procaryotic cells. Since current methods for the transfection and transformation of lactobacilli using protoplasts are slow, inefficient, and inconsistent, we evaluated electroporation as a simple alternative. In initial experiments, PL-1 phage DNA (40 kb) was transfected into untreated cells of Lactobacillus casei by electroporation. Approximately 50% of the CFU survived pulses of 5000 V/cm at 25 μF; conditions found to be optimal for the transfection process. The β-galactosidase-encoding plasmid, pLZ15 (28 kb), and the vectors pSA3 (Emr), pLP825 (Cmr) and pNZ12 (Cmr) transformed L. casei at efficiencies of 1.1–8.5 × 104 transformants/μg DNA. Plasmid DNA isolated from pNZ12 containing transformants was used to retransform L. casei and was indistinguishable from authentic preparations of pNZ12 by gel electrophoretic analysis.
A Proinflammatory Gut Microbiota Increases Systemic Inflammation and Accelerates Atherosclerosis (2019)

Introduction of the proinflammatory Casp1<sup>-/-</sup> microbiota into Ldlr<sup>-/-</sup> mice enhances systemic inflammation and accelerates atherogenesis.
[Stress-protective effect of neuropeptides in monkeys]. (1995)

The effects of endorphin and casomorphin on the behavior and function of steroid-producing glands were tested in 25 male baboons during free behavior and emotional stress caused by a single 2-hour immobilization. The stress-protective effect of peptide preparations was rated by the indices of the individual and social behavior of the monkeys, as well as by the level of corticosteroid and gonad systems. Exogenous opioids on the behavioral and neurohormonal manifestations of the stress-reaction in the baboons were found, which suggests that the use of regulatory peptides is promising as protective agents of emotional stress.
Preparation and Characterization of Oil-in-Water Type Poly (D, L-Lactic Acid) Microspheres Containing Testosterone Enanthate (1998)

Poly (D,L-lactic acid) (PLA) microspheres containing testosterone enanthate (ET) were prepared by using an oil-in-water (O/W) emulsion technique. The size distribution of the microspheres obtained could be explained by a log-normal distribution, and as a result, it was found that ET fully incorporates into microspheres even when the drug is loaded at up to 50%. On the other hand, the dissolution behavior of ET from microspheres was strongly dependent on particle size, suggesting that dissolution of the drug from microspheres can be easily controlled by controlling the preparative conditions.
An Introduction to Categorical Data Analysis (2006)

Two--Way Contingency Tables. Three--Way Contingency Tables. Generalized Linear Models. Logistic Regression. Loglinear Models for Contingency Tables. Building and Applying Logit and Loglinear Models. Multicategory Logit Models. Models for Matched Pairs. A Twentieth--Century Tour of Categorical Data Analysis. Appendix. Table of Chi--Squared Distribution Values for Various Right--Tail Probabilities. Bibliography. Indexes.
Improving land seismic repeatability with virtual source redatuming: synthetic case study (2012)

We apply virtual source redatuming to land seismic data with shallow buried receivers and evaluate potential improvements in post-stack repeatability associated with redatuming. In particular we focus on examining how redatuming can handle three typical sources of land seismic non-repeatability: changes in acquisition geometry, variable source coupling and daily/seasonal changes in the near surface. We use a synthetic model derived from log and well data and acquisition parameters inspired by a recent field experiment conducted in one of the onshore fields in Saudi Arabia. We demonstrate that, in all cases, the virtual source method improves repeatability of redatumed stacked images even when the density of virtual sources is substantially smaller than that of the surface sources.
Integration is essential for efficient gene expression of human immunodeficiency virus type 1 (1993)

A mutant of human immunodeficiency virus type 1 which carries a frameshift insertion in the integrase/endonuclease region of pol gene was constructed in vitro. Upon transfection into cells, although this mutant exhibited a normal phenotype with respect to expression of gag, pol, and env genes and to generation of progeny virions, no replication-competent virus in CD4-positive cells emerged. An assay for the single-step replication of a defective viral genome dependent on trans complementation by rev protein was established and used to monitor the early phase of viral infection process. Viral clones with a mutation in the vif, vpr, or vpu gene displayed no abnormality in the early phase. In contrast, the integrase mutant did not direct a marker gene expression after infection. Together with an observation that the mutant lacked the ability to integrate, these results indicated that the integration was required for efficient viral gene expression and productive infection of human immunodeficiency virus type 1.