gebhart/patrepeval huggingface dataset:
A Prospective Study of the Risk of Tuberculosis among Intravenous Drug Users with Human Immunodeficiency Virus Infection (1989)

To determine the risk of active tuberculosis associated with human immunodeficiency virus (HIV) infection, we prospectively studied 520 intravenous drug users enrolled in a methadone-maintenance program. Tuberculin skin testing and testing for HIV antibody were performed in all subjects. Forty-nine of 217 HIV-seropositive subjects (23 percent) and 62 of 303 HIV-seronegative subjects (20 percent) had a positive response to skin testing with purified protein derivative (PPD) tuberculin before entry into the study. The rates of conversion from a negative to a positive PPD test were similar for seropositive subjects (15 of 131; 11 percent) and seronegative subjects (26 of 202; 13 percent) who were retested during the follow-up period (mean, 22 months). Active tuberculosis developed in eight of the HIV-seropositive subjects (4 percent) and none of the seronegative subjects during the study period (P less than 0.002). Seven of the eight cases of tuberculosis occurred in HIV-seropositive subjects with a prior positive PPD test (7.9 cases per 100 person-years, as compared with 0.3 case per 100 person-years among seropositive subjects without a prior positive PPD test; rate ratio, 24.0; P less than 0.0001). We conclude that, although the prevalence and incidence of tuberculous infection were similar for both HIV-seropositive and HIV-seronegative intravenous drug users, the risk of active tuberculosis was elevated only for seropositive subjects. These data also suggest that in HIV-infected persons tuberculosis most often results from the reactivation of latent tuberculous infection; our results lend support to recommendations for the aggressive use of chemoprophylaxis against tuberculosis in patients with HIV infection and a positive PPD test.
Grayscale transparent metasurface holograms (2016)

In this paper, we demonstrate transparent metaholograms based on silicon metasurfaces that allow high-resolution grayscale images to be encoded. Finally, the holograms feature the highest diffraction and transmission efficiencies, and operate over a broad spectral range.
Lack of the extracellular 19-kilodalton fibrinogen-binding protein from Staphylococcus aureus decreases virulence in experimental wound infection (1996)

A mutant deficient for the 19-kDa extracellular fibrinogen-binding protein (Fib) from Staphylococcus aureus has been constructed. The gene was inactivated by allele replacement. A 2.0-kb fragment from transposon Tn4001 carrying the gene for gentamicin resistance was inserted into the gene encoding Fib (fib). The genotype was verified by PCR analysis, and the loss of Fib was demonstrated by Western blotting (immunoblotting). The mutation has not altered the ability of the strain to bind to fibrinogen or fibronectin compared with that of the isogenic parental strain, FDA486. The mutant, designated K4.3, was compared with strain FDA486 in a wound infection model in rats. Sixty-eight percent of the rats challenged with parental strain FDA486 developed severe clinical signs of wound infection, whereas only 29% of the animals challenged with isogenic mutant K4.3 showed severe symptoms (P < 0.01). The weight loss of animals infected with the wild type was also significantly different from that of animals infected with the mutant strain. The result demonstrates that the extracellular 19-kDa fibrinogen-binding protein from S. aureus contributes to the virulence in wound infection and delays the healing process.
DNA REPAIR IN EUKARYOTES (1996)

Eukaryotic cells have multiple mechanisms for repairing damaged DNA. O6-methylguanine-DNA methyltransferase directly reverses some simple alkylation adducts. However, most repair strategies excise lesions from DNA. Two major pathways are base excision repair (BER), which eliminates single damaged-base residues, and nucleotide excision repair (NER), which excises damage within oligomers that are 25-32 nucleotides long. The specialized DNA glycosylases and AP endonucleases of BER act on spontaneous and induced DNA alterations caused by hydrolysis, oxygen free radicals, and simple alkylating agents. NER utilizes many proteins (including the XP proteins in humans) to remove the major UV-induced photoproducts from DNA, as well as other types of modified nucleotides. Different DNA polymerases and ligases are used to complete the separate pathways. Some organisms have alternative schemes, which include the use of photolyases and a specific UV-endonuclease for repairing UV damage to DNA. Finally, double-strand breaks in DNA are repaired by mechanisms that involve recombination proteins and, in mammalian cells, a DNA protein kinase.
Cellular immune response in multiple sclerosis plaques. (1990)

Multiple sclerosis plaques were immunohistochemically stained to exhibit cells expressing immune-system antigens. Human leukocyte antigen (HLA)-DR-positive cells formed dense rings around all plaque regions. The majority were reactive microglia/macrophages. Counterstaining with oil red O revealed heavy myelin debris within these cells. They were distinct from astrocytes, which were identified with an antibody to glial fibrillary acidic protein (GFAP) and which did not contain oil red O myelin debris. Numerous leukocytes and microglia were stained with antibody to leukocyte common antigen (LCA). Lymphocytes in cuffs around vessels, along the margins of capillary walls, and, sparingly, in the tissue matrix of affected areas, were stained with antibodies to CD4 (T-helper/inducer) and CD8 (T-cytotoxic/suppressor). In experimental allergic encephalomyelitis (EAE) induced in Lewis rats, a similar proliferation of Ia-positive (OX6, OX17) cells displaying reactive microglia/macrophage morphology was observed. These Ia-positive cells also were easily distinguished from GFAP-positive astrocytes. The results suggest that macrophages/reactive microglia, and not astrocytes, express class II MHC antigens in multiple sclerosis and EAE plaques.
Identification and characterization of the Vibrio vulnificus rtxA essential for cytotoxicity in vitro and virulence in mice. (2007)

A mutant exhibiting decreased cytotoxic activity toward INT-407 intestinal epithelial cells and carrying a mutation in the rtx gene cluster that consists of rtxCA and rtxBDE operons was screened from a library of V. vulnificus mutants. The functions of the rtxA gene, assessed by constructing an isogenic mutant and evaluating its phenotypic changes, demonstrated that RtxA is essential for the virulence of V. vulnificus in mice as well as in tissue cultures.
Clinical Applications of Micro‐ and Nanoscale Biosensors (2007)

This chapter contains sections titled: Introduction Classes of Biosensors Types of In Vitro Diagnostics In Vivo Diagnostics Current and Emerging Clinical Applications of Micro- and Nanoscale Biosensors Conclusions Acknowledgments References
Synthesis of thioesters by reactions of carboxylic acids with tris(ethylthio)borane (1977)

Thioesters are obtained in high yield by reactions of carboxylic acids with tris(ethylthio)borane in a refluxing solvent. The reaction pathway is complex, involving initial production of carboxylic anhydrides and oxybis(diacyloxy-boranes), which are separately attacked by liberated ethanethiol or the excess of tris(ethylthio)borane.
Frequent alteration of the DF3 tumor-associated antigen gene in primary human breast carcinomas. (1989)

The gene for the human DF3 breast carcinoma-associated antigen contains a conserved (G + C)-rich 60-base pair tandem repeat and maps to chromosome 1q21-24. In the present study we isolated and characterized 1220 base pairs of nonrepetitive adjacent sequences. Multiple alleles were identified by fragment size. Signal intensity of hybrids with the tandem and unique sequence probes indicated that allelic variation is due to different numbers of repeats. Probes for both the tandem and the unique sequences were used to study the DF3 locus in human breast tumor DNAs. Seventy of 110 breast tumor DNAs were informative at the DF3 locus. Of these, 20 (29%) showed a loss of heterozygosity, while eight (11%) had an increased copy number of one allele. In some cases, the loss of heterozygosity or increased copy number did not extend to other markers on chromosome 1q or 1p. These data indicate that the chromosomal region around the DF3 locus is affected by mutations at high frequency.
Learning to Control a Brain–Machine Interface for Reaching and Grasping by Primates (2003)

Reaching and grasping in primates depend on the coordination of neural activity in large frontoparietal ensembles. Here we demonstrate that primates can learn to reach and grasp virtual objects by controlling a robot arm through a closed-loop brain-machine interface (BMIc) that uses multiple mathematical models to extract several motor parameters (i.e., hand position, velocity, gripping force, and the EMGs of multiple arm muscles) from the electrical activity of frontoparietal neuronal ensembles. As single neurons typically contribute to the encoding of several motor parameters, we observed that high BMIc accuracy required recording from large neuronal ensembles. Continuous BMIc operation by monkeys led to significant improvements in both model predictions and behavioral performance. Using visual feedback, monkeys succeeded in producing robot reach-and-grasp movements even when their arms did not move. Learning to operate the BMIc was paralleled by functional reorganization in multiple cortical areas, suggesting that the dynamic properties of the BMIc were incorporated into motor and sensory cortical representations.
Conditional gene expression by controlling translation with tetracycline-binding aptamers (2003)

We present a conditional gene expression system in Saccharomyces cerevisiae which exploits direct RNA-metabolite interactions as a mechanism of genetic control. We inserted preselected tetracycline (tc) binding aptamers into the 5'-UTR of a GFP encoding mRNA. While aptamer insertion generally reduces GFP expression, one group of aptamers displayed an additional, up to 6-fold, decrease in fluorescence upon tc addition. Regulation is observed for aptamers inserted cap-proximal or near the start codon, but is more pronounced from the latter position. Increasing the thermodynamic stability of the aptamer augments regulation but reduces expression of GFP. Decreasing the stability leads to the opposite effect. We defined nucleotides which influence the regulatory properties of the aptamer. Exchanging a nucleotide probably involved in tc binding only influences regulation, while mutations at another position alter expression in the absence of tc, without affecting regulation. Thus, we have developed and characterized a regulatory system which is easy to establish and controlled by a non-toxic, small ligand with good cell permeability.
Multistage Multiantigen Heterologous Prime Boost Vaccine forPlasmodium knowlesiMalaria Provides Partial Protection in Rhesus Macaques (2001)

A nonhuman primate model for malaria vaccine development allowing reliable, stringent sporozoite challenge and evaluation of both cellular and antibody responses is needed. We therefore constructed a multicomponent, multistage DNA vaccine for the simian malaria species Plasmodium knowlesi including two preerythrocytic-stage antigens, the circumsporozoite protein (PkCSP) and sporozoite surface protein 2 (PkSSP2), and two blood stage antigens, apical merozoite antigen 1 (PkAMA1) and merozoite surface protein 1 (PkMSP1p42), as well as recombinant canarypox viruses encoding the four antigens (ALVAC-4). The DNA vaccine plasmids expressed the corresponding antigens in vitro and induced antiparasite antibodies in mice. Groups of four rhesus monkeys received three doses of a mixture of the four DNA vaccine plasmids and a plasmid encoding rhesus granulocyte-monocyte colony-stimulating factor, followed by boosting with a single dose of ALVAC-4. Three groups received the priming DNA doses by different routes, either by intramuscular needle injection, by intramuscular injection with a needleless injection device, the Biojector, or by a combination of intramuscular and intradermal routes by Biojector. Animals immunized by any route developed antibody responses against sporozoites and infected erythrocytes and against a recombinant PkCSP protein, as well as gamma interferon-secreting T-cell responses against peptides from PkCSP. Following challenge with 100 P. knowlesi sporozoites, 1 of 12 experimental monkeys was completely protected and the mean parasitemia in the remaining monkeys was significantly lower than that in 4 control monkeys. This model will be important in preclinical vaccine development.
Recognition of the Codon-Anticodon Helix by Ribosomal RNA (1999)

Translational fidelity is established by ribosomal recognition of the codon-anticodon interaction within the aminoacyl-transfer RNA (tRNA) site (A site) of the ribosome. Experiments are presented that reveal possible contacts between 16S ribosomal RNA and the codon-anticodon complex. N1 methylation of adenine at position 1492 (A1492) and A1493 interfered with A-site tRNA binding. Mutation of A1492 and A1493 to guanine or cytosine also impaired A-site tRNA binding. The deleterious effects of A1492G or A1493G (or both) mutations were compensated by 2'fluorine substitutions in the mRNA codon. The results suggest that the ribosome recognizes the codon-anticodon complex by adenine contacts to the messenger RNA backbone and provide a mechanism for molecular discrimination of correct versus incorrect codon-anticodon pairs.
ADVANCES IN PARAMETRIC CODING FOR HIGH-QUALITY AUDIO (2003)

Compared to traditional waveform coding standards that employ subband or transform coding, parametric coding is regarded as a technique that allows even further reduction of bit rates. In response to a call for proposals by MPEG-4 in January 2001, Philips submitted a parametric coder targetting at a high quality level. Currently, this coder is improved in the course of the “MPEG-4 Extension 2” standardisation process. Recently, two enhancements have been made increasing the overall performance of the coder. These consist of an improved model for the noise object and a parametric stereo extension.
Visual acuity and erythrocyte docosahexaenoic acid status in breast‐fed and formula‐fed term infants during the first four months of life (1996)

It has been recognized that preterm infants have a more rapid development of visual acuity if fed human milk or a formula enriched with the long-chain polyunsaturated fatty acid (LCPUFA) docosahexaenoic acid (DHA) compared to a standard formula devoid of LCPUFA. Few studies have addressed whether the same is also true in term infants. The aim of the present study was to follow visual acuity and fatty acid composition in red blood cells (RBC) for the first 4 mon of life in 17 breast-fed and 16 formula-fed term infants. The formula used did not contain LCPUFA, but contained 1.7 wt% alpha-linolenic acid, and the linoleic/alpha-linolenic acid ratio was 8.5. The increase in visual acuity measured by Teller acuity cards developed more rapidly in breast-fed infants compared to formula-fed infants (P < 0.001). This was parallelled by a decrease in DHA of RBC in formula-fed infants, and with a significantly lower level at two and four months as compared to breast-fed infants. The content of DHA in milk from the breast-feeding mothers was high compared to other Western countries. The difference in visual acuity between the two feeding groups could be due to differences in DHA status as reflected by the RBC levels, but other explanations are possible. Intervention studies are required to verify if development of visual acuity in term formula-fed infants is dependent on the DHA level of formula.
Chronic Low-Back Pain, Psychologic Distress, and Illness Behavior (1984)

The authors have calculated the mathematic relationship between measured elements of illness behavior in chronic low-back pain. Objective physical impairment accounts for about one-half the total disability that also is affected by psychologic reactions. The most important psychologic disturbance in low-back pain is emotional distress, measured on questionnaires as increased bodily awareness and depression and presenting clinically as inappropriate descriptions of symptoms and inappropriate responses to physical examination. Simple methods for the assessment of distress and illness behavior in chronic low-back pain are developed and described.
Hepatitis C Virus Non-structural Proteins in the Probable Membranous Compartment Function in Viral Genome Replication (2003)

The molecular mechanism of hepatitis C virus(HCV) RNA replication is still unknown. Recently, a cell culture system in which the HCV subgenomic replicon is efficiently replicated and maintained for a long period in Huh-7 cells has been established. Taking advantage of this replicon system, we detected the activity to synthesize the subgenomic RNA in the digitonin-permeabilized replicon cells. To elucidate how and where this viral RNA replicates in the cells, we monitored the activity for HCV RNA synthesis in the permeabilized replicon cells under several conditions. We obtained results suggesting that HCV replication complexes functioning to synthesize the replicon RNA are protected from access of nuclease and proteinase by possible cellular lipid membranes. We also found that a large part of the replicon RNA, including newly synthesized RNA, was present in such a membranous structure but a large part of each NS protein was not. A small part of each NS protein that was resistant to the proteinase action was shown to contribute sufficiently to the synthesis of HCV subgenomic RNA in the permeabilized replicon cells. These results suggested that a major subcellular site of HCV genome replication is probably compartmentalized by lipid membranes and that only a part of each NS protein forms the active replication complex in the replicon cells.
Applications of Phospholipid Bilayer Nanodiscs in the Study of Membranes and Membrane Proteins (2007)

Phospholipid bilayer Nanodiscs are novel model membranes derived from high-density lipoprotein particles and have proven to be useful in studies of membrane proteins. Membrane protein enzymology has been hampered by the inherent insolubility of membrane proteins in aqueous environments and has necessitated the use of model membranes such as liposomes and detergent-stabilized micelles. Current model membranes display a polydisperse particle size distribution and can suffer from problems of inconsistency and instability. It is also unclear how well they mimic biological lipid bilayers. In contrast, Nanodiscs, the particle size of which is constrained by a coat of scaffold proteins, are relatively monodisperse, stable model membranes with a "nativelike" lipid bilayer. Nanodiscs have already been used to study a variety of membrane proteins, including cytochrome P450s, seven-transmembrane proteins, and bacterial chemoreceptors. These proteins are simultaneously monomerized, solubilized, and incorporated into the well-defined membrane environment provided by Nanodiscs. Nanodiscs may also provide useful insights into the thermodynamics and biophysics of biological membranes and binding of small molecules to membranes.
Dislocation glide and blocking kinetics in compositionally graded SiGe/Si (2001)

The effects of growth temperature, substrate offcut, and dislocation pileup formation on threading dislocation density (TDD) in compositionally graded SiGe buffers are explored. To investigate dislocation glide kinetics in these structures, a series of identical samples graded to 30% Ge were grown at temperatures between 650 and 900 °C on (001)-, (001) offcut 6° towards an in-plane 〈110〉-, and (001) offcut 6° towards an in-plane 〈100〉-oriented Si substrates. The field threading dislocation density (field TDD) in the on-axis samples varied exponentially with temperature, from 3.7×106 cm−2 at 650 °C to 9.3×104 cm−2 at 900 °C. The activation energy for dislocation glide in this series, calculated from the evolution of field TDD with growth temperature, was 1.38 eV, much lower than the expected value for this composition. This deviation indicates that strain accumulating during the grading process at low growth temperatures is forcing further dislocation nucleation, resulting in a deviation from pure glide-limited relaxation. The TDD of samples grown on offcut substrates exhibited a more complicated temperature dependence, likely because films grown on offcut substrates have an increased tendency towards saturation in dislocation reduction reactions at high temperature. Dislocation reduction processes were further explored by initiating compositional grading up to 15% Ge at 650 °C and continuing the grade to 30% Ge at 900 °C. The low temperature portion of this growth provided an excess concentration of threading dislocations which could subsequently be annihilated during the high temperature portion of the growth, enabling a comparison of reduction rates for different substrate offcuts. Combining these results with threading dislocation densities in a variety of other samples, a complete picture of strain relaxation kinetics in compositionally graded SiGe/Si emerges. Generally, strain relaxation in these structures is limited by dislocation glide, and threading dislocation densities are independent of final Ge content. However, we theorize that dislocation pileup formation inhibits the strain relaxation process and is therefore accompanied by a rise in field threading dislocation density. Based on these results, we now have a predictive model for TDD in compositionally graded SiGe/Si over a wide range of growth conditions.
Peptide synthesis with a template-like RNA guide and aminoacyl phosphate adaptors (2003)

The genetic code is thought to have developed from an early system of RNA-dependent peptide synthesis. To investigate one kind of template-like peptide synthesis that might emerge from an RNA world, we constructed highly reactive aminoacyl phosphate oligonucleotides as adaptors that bound to RNA guide sequences. The reactive aminoacyl groups mimic a chemistry found in modern protein biosynthesis. Guide sequence interactions with adaptors were borrowed in part from universal contacts seen between tRNAs and rRNA. With these constructions, di- and tripeptides formed in a single guide sequence-dependent reaction. The order of amino acids was not random but directional in a way consistent with substrate reactivities. No ribosomes or ribozymes were required. Thus, aminoacyl phosphate adaptors and RNA guides could, in principle, have been intermediates in the transition from the RNA world to modern template-dependent protein synthesis.
Novel ENU-induced eye mutations in the mouse: models for human eye disease (2002)

We have carried out a genome-wide screen for novel N-ethyl-N-nitrosourea-induced mutations that give rise to eye and vision abnormalities in the mouse and have identified 25 inherited phenotypes that affect all parts of the eye. A combination of genetic mapping, complementation and molecular analysis revealed that 14 of these are mutations in genes previously identified to play a role in eye pathophysiology, namely Pax6, Mitf, Egfr and Pde6b. Many of the others are located in genomic regions lacking candidate genes and these define new loci. Four of the mutants display a similar phenotype of dilated pupils but do not appear to be allelic, and at least two of these are embryonic lethal when homozygous. This collection of eye mutations will be valuable for understanding gene function, for dissecting protein function and as models of human eye disease.