gebhart/patrepeval huggingface dataset:
Detection of Chlamydia pneumoniae and Helicobacter pylori DNA in Human Atherosclerotic Plaques by PCR (2000)

Chlamydia pneumoniae and Helicobacter pylori can cause persistent infections of the respiratory and gastrointestinal tract, respectively. It has been suggested that persistent infection of arteries with these bacteria can contribute to the development of atherosclerosis. The aims of this study were to determine the presence of C. pneumoniae and H. pylori DNA in atherosclerotic plaque samples by PCR and to evaluate the correlation between clinical status and DNA positivity of these bacteria. Eighty-five consecutive patients (mean age, 59 +/- 10; 75 male, 10 female) undergoing coronary artery bypass grafting, carotid endarterectomy, and surgery of the abdominal aorta for atherosclerotic obstructive lesions were included in the study. Forty-six endarterectomy specimens from the atherosclerotic lesions and 39 specimens from healthy regions of the ascending aorta, which were accepted as the control group, were excised. The presence of microorganism DNA in endarterectomy specimens was assessed by PCR. C. pneumoniae DNA was found in 12 (26%) of 46 endarterectomy specimens and none of the healthy vascular-wall specimens (P < 0.001), while H. pylori DNA was found in 17 (37%) of 46 endarterectomy specimens and none of the controls (P < 0.001). Either C. pneumoniae or H. pylori DNA was positive in 23 (50%) of 46 patients and none of the controls (P < 0. 001). Six of the atherosclerotic lesions showed coexistence of both of the microorganism DNAs. The presence of C. pneumoniae and H. pylori DNA in a considerable number of atherosclerotic plaques but their absence in healthy vascular wall supports the idea that they may have a role in the development of atherosclerosis, especially in countries where infection is prevalent and where conventional risk factors fail to explain the high prevalence of atherosclerotic vascular disease.
Temperature compensation electronics for ISFET readout applications (2005)

This paper presents temperature compensation electronics for ion sensitive field effect transistor (ISFET) sensors. It consists of a bridge-type floating-source ion sensing circuit and a VT extractor centigrade temperature sensor accompanied with a temperature coefficient (TCF) cancellation method. Using LabVlEW packages has developed an extended measurement system including compensation algorithms programming. Experimental results show that the temperature dependence of the Si/sub 3/N/sub 4/-gate ISFET sensor improved from 8mV//spl deg/C to near 0mV//spl deg/C with the proposed temperature compensation circuitry. This system allows a wide range of high accurate pH-level measurements. The method of temperature compensation may also be valid for other biosensors or bioFETs.
High-efficiency robust perovskite solar cells on ultrathin flexible substrates (2016)

Wide applications of personal consumer electronics have triggered tremendous need for portable power sources featuring light-weight and mechanical flexibility. Perovskite solar cells offer a compelling combination of low-cost and high device performance. Here we demonstrate high-performance planar heterojunction perovskite solar cells constructed on highly flexible and ultrathin silver-mesh/conducting polymer substrates. The device performance is comparable to that of their counterparts on rigid glass/indium tin oxide substrates, reaching a power conversion efficiency of 14.0%, while the specific power (the ratio of power to device weight) reaches 1.96 kW kg(-1), given the fact that the device is constructed on a 57-μm-thick polyethylene terephthalate based substrate. The flexible device also demonstrates excellent robustness against mechanical deformation, retaining >95% of its original efficiency after 5,000 times fully bending. Our results confirmed that perovskite thin films are fully compatible with our flexible substrates, and are thus promising for future applications in flexible and bendable solar cells.
Blocking of passive sensitization of human mast cells and basophil granulocytes with IgE antibodies by a recombinant human epsilon-chain fragment of 76 amino acids. (1989)

The recombinant peptide corresponding to residues 301-376 at the junction of constant regions 2 and 3 of the human IgE epsilon chain blocked the in vivo passive sensitization of human skin mast cells and in vitro sensitization of human basophil granulocytes with human IgE antibodies. An injection of the recombinant peptide or E myeloma protein into normal skin sites 1 hr before sensitization with an allergic serum blocked passive sensitization. In this system, approximately 10-fold higher molar concentration of the recombinant peptide than E myeloma protein was required for 50% inhibition of Prausnitz-Küstner reactions. When the mononuclear cells of two normal individuals were preincubated with the recombinant peptide or E myeloma protein for 15 min before passive sensitization with the same allergic serum and the cells were challenged with an optimal concentration of an antigen, approximately 11- to 13-fold higher concentration of the recombinant peptide than E myeloma protein was required for 50% inhibition of antigen-induced histamine release. Further studies with several recombinant peptides indicated that amino acid resides 363-376 in the Fc epsilon-chain fragment are not essential for binding of the peptide to Fc epsilon-chain receptor I.
Virtual fixtures: Perceptual tools for telerobotic manipulation (1993)

In order to enhance operator performance and understanding within remote environments, most research and development of telepresence systems has been directed towards improving the fidelity of the link between operator and environment. Although higher fidelity interfaces are important to the advancement of a telepresence system, the beneficial effects of corrupting the link between operator and remote environment by introducing abstract perceptual information into the interface called virtual fixtures are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Escherichia coli molecular phylogeny using the incongruence length difference test (1998)

Molecular phylogeny of the species Escherichia coli using the E. coli reference (ECOR) collection strains has been hampered by (1) the absence of rooting in the commonly used phenogram obtained from multilocus enzyme electrophoresis (MLEE) data and (2) the existence of recombination events between strains that scramble phylogenetic trees reconstructed from the nucleotide sequences of genes. We attempted to determine the phylogeny for E. coli based on the ECOR strain data by extracting from GenBank the nucleotide sequences of 11 chromosomal structural and 2 plasmid genes for which the Salmonella enterica homologous gene sequences were available. For each of the 13 DNA data sets studied, incongruence with a nonnucleotide whole-genome data set including MLEE, random amplified polymorphic DNA, and rrn restriction fragment length polymorphism data was measured using the incongruence length difference (ILD) test of Farris et al. As previously reported, the incongruence observed between the gnd and plasmid gene data and the whole-genome data was multiple, indicating numerous horizontal transfer and/or recombination events. In five cases, the incongruence detected by the ILD test was punctual, and the donor group was identified. Congruence was not rejected for the remaining data sets. The strains responsible for incongruences with the whole-genome data set were removed, leading to a "prior-agreement" approach, i.e., the determination of a phylogeny for E. coli based on several genes, excluding (1) the genes with multiple incongruences with the whole genome data, (2) the strains responsible for punctual incongruences, and (3) the genes incongruent with each other. The obtained phylogeny shows that the most basal group of E. coli strains is the B2 group rather than the A group, as generally thought. The D group then emerges as the sister group of the rest. Finally, the A and B1 groups are sister groups. Interestingly, the most primitive taxon within E. coli in terms of branching pattern, i.e., the B2 group, includes highly virulent extraintestinal strains with derived characters (extraintestinal virulence determinants) occurring on its own branch.
Monte Carlo study of diffuse reflectance at source–detector separations close to one transport mean free path (1999)

The spatially resolved reflectance of turbid media is studied at short source–detector separations (approximately one transport mean free path) with Monte Carlo simulations. For such distances we found that the first and second moments of the phase function play a significant role in the reflectance curve, whereas the effect of higher-order moments is weak. Second-order similarity relations are tested and are found efficient at reducing the number of relevant parameters necessary to predict the reflectance. Indeed, only the four following parameters are necessary: the refractive index, the absorption coefficient, the reduced scattering coefficient, and a phase function parameter γ that depends on the first and second moments of the phase function. For media of known γ, the absorption and reduced scattering coefficients can be determined from the intensity and the slope of the log of the reflectance, measured at a single distance. Other empirical properties of the reflectance are derived from the simulations, using short-distance measurements, which provide clues for determining the scattering and absorption properties. In particular, the slope of the square root of the reflectance does not depend on the absorption coefficient but depends on both the reduced scattering coefficient and the phase function parameter γ.
Hepatitis C virus dynamics in vivo : Effect of ribavirin and interferon alfa on viral turnover (1998)

Treatment of patients with chronic hepatitis C with recombinant interferon alfa (rIFN-alpha) can cause a decrease of serum transaminases and hepatitis C virus (HCV) RNA. Recent trials evaluating combination therapy of IFN-alpha and ribavirin suggested a potential synergistic effect. From serial measurements of serum HCV RNA concentrations following treatment-induced perturbation of the balance between virus production and clearance, we compared the antiviral efficacy of both IFN-alpha alone and IFN-alpha in combination with ribavirin. Chronically HCV-infected patients were treated with either 3 x 3 MU or 3 x 6 MU rIFN-alpha per week or 3 x 6 MU rIFN-alpha plus 14 mg/kg of body weight ribavirin per day. The time-dependent HCV RNA concentrations during antiviral treatment were analyzed by iterative least-squares regression. After initiation of antiviral therapy, HCV RNA declined exponentially below the detection limit of the reverse-transcription polymerase chain reaction assay (1,000 HCV RNA molecules per milliliter) in 10 of 26 (39%), 10 of 19 (53%), and 10 of 18 patients (56%) treated with 3 x 3 MU, 3 x 6 MU rIFN-alpha without and with ribavirin, respectively. Viral clearance from serum was faster in patients treated with 3 x 6 MU rIFN-alpha (t1/2 = 0.23 +/- 0.15) compared with patients treated with 3 x 3 MU rIFN-alpha per week (0.67 +/- 0.36 days) (P < .004). However, half-lives of viral clearance were similar in patients treated with rIFN-alpha or rIFN-alpha plus ribavirin. For virus release from infected hepatocytes, absence and presence of ribavirin yielded half-lives of t1/2 = 2.54 +/- 2.10 and t1/2 = 1.99 +/- 1.70, respectively, indicating that ribavirin does not significantly inhibit HCV production. In conclusion, the data of the present study indicate that higher rIFN-alpha doses accelerate viral clearance from serum. Ribavirin (14 mg/kg/d), however, lacks synergistic antiviral effects in the treatment of chronic hepatitis C with 3 x 6 MU rIFN-alpha per week.
Bispecific antibodies (2015)

Bispecific antibodies (bsAbs) combine specificities of two antibodies and simultaneously address different antigens or epitopes. BsAbs with 'two-target' functionality can interfere with multiple surface receptors or ligands associated, for example with cancer, proliferation or inflammatory processes. BsAbs can also place targets into close proximity, either to support protein complex formation on one cell, or to trigger contacts between cells. Examples of 'forced-connection' functionalities are bsAbs that support protein complexation in the clotting cascade, or tumor-targeted immune cell recruiters and/or activators. Following years of research and development (R&D), the first bsAb was approved in 2009. Another bsAb entered the market in December 2014 and several more are in clinical trials. Here, we describe the potentials of bsAbs to become the next wave of antibody-based therapies, focusing on molecules in clinical development.
Quantitative RT-PCR Detection of Tumor Cells in Sentinel Lymph Nodes Isolated From Colon Cancer Patients with an Ex Vivo Approach (2009)

In Brief Objective: To investigate quantitative RT-PCR–based detection of tumor cells in lymph nodes (LNs) isolated from colon cancer patients by ex vivo sentinel lymph node (SLN) mapping. Summary Background Data: Although lymph node status is among the strongest prognostic factors in colon cancer patients, 20% to 30% of node negative patients experience disease recurrence. These patients may have LN metastases that are not detected by routine examination. Methods: Ex vivo SLN mapping was applied to 131 prospectively recruited patients undergoing curative surgery for primary colon cancer. The SLNs were analyzed for the presence of tumor cells by routine histology and real-time RT-PCR quantitation of cytokeratin 20 (CK20) and mucin 2 (MUC2) mRNA. Results: SLNs were identified in 125 (95%) of the 131 patients included. Routine histologic analysis of SLNs and other regional lymph nodes revealed LN metastases in 42 patients (N+), of which 29 (69%) had metastases detected in 1 or more SLNs (sensitivity, 69%; false negative rate, 31%). When analyzing the SLNs by quantitative RT-PCR, the sensitivity, compared with routine LN examination, was 37/42 (88%) for both the CK20 and the MUC2 mRNA markers. In addition, 46% and 27% of the patients’ node-negative by routine LN examination (N0) were positive for the CK20 and MUC2 mRNA markers, respectively, possibly reflecting the presence of occult tumor cells in their SLNs. Conclusions: Quantitative RT-PCR analysis of SLNs identified N+ patients with high sensitivity and revealed a subgroup of N0 patients with potential occult LN disease. Quantitative RT-PCR was applied to detect tumor cells in sentinel lymph nodes isolated in the resection specimens from 131 colon cancer patients by ex vivo mapping. High sensitivity for patients with lymph node metastases was achieved and a subgroup of patients with potential occult lymph node disease was identified.
Measuring Branch Profitability in Banking: A Case Study of a Large Midwestern Bank (1993)

The results indicate that [(131)I]-labeled anti-CEA MoAbs can be effective in RIT on colonic cancers.
Alzheimer-Like Changes in Rat Models of Spontaneous Diabetes (2007)

The data show that beta-amyloid and phospho-tau accumulation occur in experimental diabetes and that this is associated with neurite degeneration and neuronal loss. The changes were more severe in the type 2 diabetic model and appear to be associated with insulin resistance and possibly hypercholesterolemia. The two models will provide useful tools to unravel further mechanistic associations between diabetes and Alzheimer's disease.
Recommended terminology for the description of carbon as a solid (IUPAC Recommendations 1995) (1995)

Abstract
A Methodology for Task placement and Scheduling Based on Virtual Machines (2011)

Task placement and scheduling are traditionally studied in following aspects: resource utilization, application throughput, application execution latency and starvation, and recently, the studies are more on application scalability and application performance. A methodology for task placement and scheduling centered on tasks based on virtual machines is studied in this paper to improve the performances of systems and dynamic adaptability in applications development and deployment oriented parallel computing. For parallel applications with no real-time constraints, we describe a thought of feature model and make a formal description for four layers of task placement and scheduling. To place the tasks to different layers of virtual computing systems, we take the performances of four layers as the goal function in the model of task placement and scheduling. Furthermore, we take the personal preference, the application scalability for a designer in his (her) development and deployment, as the constraint of this model. The workflow of task placement and scheduling based on virtual machines has been discussed. Then, an algorithm TPVM is designed to work out the optimal scheme of the model, and an algorithm TEVM completes the execution of tasks in four layers. The experiments have been performed to validate the effectiveness of time estimated method and the feasibility and rationality of algorithms. It is seen from the experiments that our algorithms are better than other four algorithms in performance. The results show that the methodology presented in this paper has guiding significance to improve the efficiency of virtual computing systems.
Polymers for delivering peptides and proteins (1994)

The use of polymers for delivering peptide and protein drugs is described. Soluble-polymer technology attempts to bind a polymer to all sites on therapeutic protein molecules that cause the body to recognize the molecules as foreign. Goals include a stable linkage, water solubility, low immunogenicity, prolonged half-life, and intact biological activity. Polyethylene glycol (PEG)-adenosine deaminase (ADA), or pegademase bovine, has FDA-approved labeling as replacement therapy for ADA deficiency in patients with severe combined immunodeficiency disease who are not suitable candidates for bone marrow transplantation. Pegademase bovine reverses the toxic accumulation of adenosine and deoxyadenosine in adenosine deaminase-deficient cells, restoring the immune system. PEG-asparaginase (pegaspargase) has shown promise in patients with acute lymphocytic leukemia; allergic reactions have been minimal. Animal studies suggest that superoxide dismutase has potential use in conditions in which the body's ability to remove oxygen free radicals is reduced, such as burns and myocardial infarction; coupling with PEG may greatly increase the protein's half-life. Other PEG-conjugated proteins under investigation include PEG-catalase, PEG-uricase, PEG-honeybee venom, PEG-hemoglobin, and PEG-modified ragweed pollen extract. Dextran, albumin, DL-amino acids, and polyvinyl pyrrolidone have also been studied as protein carriers; most of the products created thus far have not shown much promise. The coupling of polymers to proteins has yielded protein drugs with intact biological activity and reduced immunogenicity, but much remains to be learned about this technology.
Behavior-based Intelligent Robot In Dynamic Indoor Environments (2005)

We present a navigation system using multiple sensors for unknown and dynamic indoor environments. To achieve the robustness and flexibility of the mobile robot, we propose a new behavior-based architecture with three groups of clustered (reflexive, purposive, and adaptive) agents that realizes both efficiency in attaining the mission of the robot and robustness against the various kinds or failures that may occur in a dynamic environment. Basic behaviors required for navigation, such as, avoiding obstacles, moving towards free space, and following targets, are redundantly developed as agents and combined in the behavior-based system architecture.
TEM8 Interacts with the Cleaved C5 Domain of Collagen α3(VI) (2004)

Tumor endothelial marker (TEM)8 was uncovered as a gene expressed predominantly in tumor endothelium, and its protein product was recently identified as the receptor for anthrax toxin. Here, we demonstrate that TEM8 protein is preferentially expressed in endothelial cells of neoplastic tissue. We used the extracellular domain of TEM8 to search for ligands and identified the alpha 3 subunit of collagen VI as an interacting partner. The TEM8-interacting region on collagen alpha 3(VI) was mapped to its COOH-terminal C5 domain. Remarkably, collagen alpha 3(VI) is also preferentially expressed in tumor endothelium in a pattern concordant with that of TEM8. These results suggest that the TEM8/C5 interaction may play an important biological role in tumor angiogenesis.
Evaluation of the Audio Beat Tracking System BeatRoot (2007)

Abstract BeatRoot is an interactive beat tracking and metrical annotation system which has been used for several years in studies of performance timing. This paper describes improvements to the original system and a large-scale evaluation and analysis of the system's performance. The beat tracking algorithm remains largely unchanged: BeatRoot uses a multiple agent architecture which simultaneously considers several different hypotheses concerning the rate and placement of musical beats, resulting in accurate tracking of the beat, quick recovery from errors, and graceful degradation in cases where the beat is only weakly implied by the data. The original time domain onset detection algorithm, which caused problems for beat tracking music without prominent drums, has been replaced with a more robust onset detector based on spectral flux. Other new features include annotation of multiple metrical levels and phrase boundaries, as well as improvements in the user interface. The software has been rewritten entirely in Java, and it runs on all major operating systems. BeatRoot is evaluated on a new test set of 1360 musical excerpts from a wide range of Western musical styles, and the results are compared with other evaluations such as the MIREX 2006 Audio Beat Tracking Evaluation.
Assembly of the 30S subunit from Escherichia coli ribosomes occurs via two assembly domains which are initiated by S4 and S7 (1988)

A protein which initiates assembly of ribosomes is defined as a protein which binds to the respective rRNA without cooperativity (i.e., without the help of other proteins) during the onset of assembly and is essential for the formation of active ribosomal subunits. The number of proteins binding without cooperativity was determined by monitoring the reconstitution output of active particles at various inputs of 16S rRNA, in the presence of constant amounts of 30S-derived proteins (TP30): This showed that only two of the proteins of the 30S subunit are assembly-initiator proteins. These two proteins are still present on a LiCl core particle comprising 16S rRNA and 12 proteins (including minor proteins). The 12 proteins were isolated, and a series of reconstitution experiments at various levels of rRNA excess demonstrated that S4 and S7 are the initiator proteins. Pulse-chase experiments performed during the early assembly with 14C- and 3H-labeled TP30 and the determination of the 14C/3H ratio of the individual proteins within the assembled particles revealed a bilobal structure of the 30S assembly: A group of six proteins headed by S4 (namely, S4, S20, S16, S15, S6, and S18) resisted the chasing most efficiently (S4 assembly domain). None of the proteins depending on S7 during assembly were found in this group but rather in a second group with intermediate chasing stability [S7 assembly domain; consisting of S7, S9, (S8), S19, and S3]. A number of proteins could be fully chased during the early assembly and therefore represent "late assembly proteins" (S10, S5, S13, S2, S21, S1). These findings fit well with the 30S assembly map.(ABSTRACT TRUNCATED AT 250 WORDS)
DOSING REGIMEN AND THE FREQUENCY OF MACULAR HEMORRHAGES IN NEOVASCULAR AGE-RELATED MACULAR DEGENERATION TREATED WITH RANIBIZUMAB (2010)

Treatment with monthly intravitreal ranibizumab was associated with reduced risk of new macular hemorrhages when compared with photodynamic therapy (ANCHOR) or sham (MARINA and PIER). There was no difference between PIER quarterly ranibizumab-treated and sham patients.