gebhart/patrepeval huggingface dataset:
Polymers from renewable sources, 1. Diamines and diisocyanates containing difurylalkane moieties (1984)

Abstract Furan‐based diisocyanates and diamines were prepared unambiguously as potential monomers for polyurethane and polyamide production, starting from methyl furoate and furfurylamine, respectively. The syntheses were optimized and the product identity was confirmed by elemental analysis, IR and NMR spectroscopy, and also by preparation of derivatives which were similarly characterized.
Abstract simulators for the DSDE formalism (1998)

We present the DSDE (Dynamic Structure of Discrete Events) formalism, a methodology for representing discrete event systems that change structure dynamically. We prove that the DSDE formalism is closed under coupling and that it can be used to construct hierarchical and modular models. The abstract simulators which are necessary to execute dynamic structure models are also presented. These simulators allow a description of models independent of the actual simulation procedure, and thus encourage model reuse.
Genome-wide methylation analysis shows similar patterns in Barrett’s esophagus and esophageal adenocarcinoma (2013)

Barrett's esophagus (BE) is a precursor of esophageal adenocarcinoma (EAC). To identify novel tumor suppressors involved in esophageal carcinogenesis and potential biomarkers for the malignant progression of BE, we performed a genome-wide methylation profiling of BE and EAC tissues. Using Illumina's Infinium HumanMethylation27 BeadChip microarray, we examined the methylation status of 27 578 CpG sites in 94 normal esophageal (NE), 77 BE and 117 EAC tissue samples. The overall methylation of CpG sites within the CpG islands was higher, but outside of the CpG islands was lower in BE and EAC tissues than in NE tissues. Hierarchical clustering analysis showed an excellent separation of NE tissues from BE and EAC tissues; however, the clustering of BE and EAC tissues was less clear, suggesting that methylation occurs early during the progression of EAC. We confirmed many previously reported hypermethylated genes and identified a large number of novel hypermethylated genes in BE and EAC tissues, particularly genes encoding ADAM (A Disintegrin And Metalloproteinase) peptidase proteins, cadherins and protocadherins, and potassium voltage-gated channels. Pathway analysis showed that a number of channel and transporter activities were enriched for hypermethylated genes. We used pyrosequencing to validate selected candidate genes and found high correlations between the array and pyrosequencing data (rho > 0.8 for each validated gene). The differentially methylated genes and pathways may provide biological insights into the development and progression of BE and become potential biomarkers for the prediction and early detection of EAC.
Magnetic Bacteria (1992)

Magnetic bacteria synthesize intracellular particles of magnetite, which are aligned in chains and enveloped by a membrane. A new species of magnetic bacterium was recently isolated from aerobic sediment from a pond in Tokyo, and is capable of growing aerobically to high cell densities. This strain may therefore be grown easily in mass culture. In such large-scale cultures a stationary phase is reached after four to five days, with a final cell concentration of 2×109 cells/ml. The small size of the bacterial magnetic particles and the inhibition of aggregation by intact magnetosome membranes result in a large surface/volume ratio. When bacterial magnetic particles were prepared by ultrasonication, they were well dispersed in water. Phospholipids comprised 58% of the total lipid content, and phosphatidyl ethanolamine accounted for 50% of the total phos-pholipid content. A gene relating to bacterial magnetic particles was cloned in Escherichia coli and analyzed. A system for magnetic bacteria gene cloning was also developed.
Reuse and reprocessing of disposable medical devices. Legal liability issues. (1986)

Reuse and reprocessing of disposable medical devices raises issues of legal liability, especially among physicians, hospitals, and device manufacturers. The practice of reuse has been, at least informally, reported to be fairly widespread. However, the medical risks associated with reuse are unresolved in most cases, which may lead to circumstances conducive to litigation. In this paper, the characteristics of reuse pertaining to legal liability, the parties potentially subject to civil liability suits as a result of reuse, the legal theories underlying claims of injury, and the legal implications of possible policy actions will be examined.
Thermographic imaging of the subcutaneous vascular network of the back of the hand for biometric identification (2002)

Access control systems require positive identification of authorised persons for entry to restricted facilities. Possession of a card by an authorised person has been the traditional approach to high security access control. These cards range from simple magnetic swipe cards through to proximity smart cards for identification. More recently, serious attempts have been made to identify appropriate biometric characteristics of individuals to provide positive identification. The more popular biometric access control techniques have included facial images, hand geometry, fingerprints and retina patterns. Also, the dynamics of keyboard input, handwritten signature and voice patterns have been reasonably successful in identifying authorised persons. This paper describes research that has been undertaken by the authors to use the subcutaneous vascular network (vein pattern) of the back of the hand as a unique personal biometric for identification. An outline will be given of a prototype low cost automatic thermographic imaging system which has been developed by the authors to obtain vein patterns for positive identification. The paper includes consideration of the image acquisition, image processing and vein pattern matching strategies. A summary of experimental results concerning the acceptance and rejection rates for the system is also provided.
Strain sensing of modern composite materials with a spatial/wavelength-division multiplexed fiber grating network (1996)

A spatial/wavelength-division multiplexing topology with combination of a tunable-wavelength filter and an interferometric wavelength scanner is used to interrogate a range of fiber Bragg grating (FBG) strain sensors embedded in modern composite materials. A nine-element FBG sensor system based on this topology is demonstrated for quasi-static strain sensing of a carbon fiber reinforced plastic plate for aerospace applications. Preliminary experimental results show that a strain resolution of ~1.8micro rms with an ~30-Hz bandwidth (~0.32micro/ radicalHz) for quasi-static strain measurement has been achieved.
Molecular dynamics simulations of the structure and transport properties of tetra-butylphosphonium amino acid ionic liquids (2011)

Systematic molecular dynamics simulations are used to study the structure, dynamics and transport properties of the ionic liquids composed of the tetra-butylphosphonium ([TBP](+), or [P(C(4)H(9))(4)](+)) cation with six amino acid ([AA](-)) anions. The structural features of these ionic liquids were characterized by calculating the partial site-site radial distribution functions, g(r), and computing the dihedral angle distribution of n-butyl side chains in the [TBP](+) cations. The dynamics of the ionic liquids are described by studying the velocity autocorrelation function (VACF) and the mean-square displacement (MSD) for the centers of mass of the ions at different temperatures. The ionic diffusion coefficients and the electrical conductivities were evaluated from both the Einstein and Green-Kubo methods. The cross-correlation terms in the electric-current autocorrelation functions, which are an indication of the ion pair correlations, are investigated. The cationic transference numbers were also estimated to study the contributions of the anions and cations to the transport of charge in these ionic liquids. We determined the role of the amino acid anion structures on the dynamical behavior and the transport coefficients of this family of ionic liquids. In general, the MSD and self-diffusion coefficients of the relatively heavier non-planar [TBP](+) cations are smaller than those of the lighter amino acid anions. Introducing polar functional groups (acid or amide) in the side chain of [AA](-) decreases the diffusion coefficient and electrical conductivity of AAILs. The major factors for determining the magnitude of the transport coefficients are the chemical functionality and the length of the alkyl side chain of the [AA](-) anion of these [TBP][AA] ionic liquids.
Extracellular deposition of beta-amyloid upon p53-dependent neuronal cell death in transgenic mice. (1996)

The finding that intracellular expression of the beta-amyloid protein (Abeta) under a neuron-specific promoter led progressively to degeneration and death of neurons in the brains of transgenic mice provides a unique opportunity to utilize this animal model to both understand the mechanism that underlies neuronal cell death and define the complexity of events which may ensue. We observed a correlation between Abeta accumulation in selective neurons and activation of p53, a protein that has been implicated in the induction of apoptosis. Histological and immunohistochemical evaluations of adjacent brain sections suggest that expression of p53 is accompanied by nuclear DNA fragmentation. In certain regions with marked neuronal cell death, extracellular deposition of A(beta) became evident, together with the local activation of astrocytes. Interestingly, the neuritic structures underlying the Abeta deposits showed altered synaptophysin immunoreactivity and morphologic evidence for damage. This transgenic mouse model suggests that intracellular generation of the Abeta protein not only leads to the death of the neuron but may also functionally impair neighboring neurons as well. It further offers a mechanism whereby neuritic plaques may be derived.
New CPU benchmark suites from SPEC (2003)

The author describes the new CPU benchmark suites from the Standard Performance Evaluation Corporation (SPEC). The author describes the reasons for the release, and analyzes and compares new suites with the SPEC Release 1 benchmark suite. The new benchmark CPU suites are CINT2.0 (integer) and CFP2.0 (floating-point). CINT2.0 and CFP2.0 replace the SPEC Release 1 benchmark suite. The new suites provide a wider 'SPECtrum' of performance characterization by adding new application benchmarks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Laser tumor thermotherapy: Is there a clinically relevant effect on the immune system? (2006)

Laser thermotherapy is interesting from an immunological point of view since it can reduce tumor volume without causing immunosuppression at the same time as it may induce and/or enhance tumor immunity. In a rat liver tumor model, we have demonstrated that laser thermotherapy 1) is superior to surgical resection, 2) gives a strong rejection immunity associated with an immune cellular response of tumor-infiltrating macrophages and CD8 lymphocytes, 3) results in pronounced suppression of the growth of a simultaneous untreated tumor (distant bystander effect), 4) produces an increased anti-tumor lymphocyte proliferative response in tumor-draining and systemic lymph nodes and spleen, and 5) results in increased HSP70 immunoreactivity in tumors and tumor-infiltrating macrophages. Thus, the evidence for a laser-induced immunologic effect in tumor-bearing rats is strong. Some observations suggest that laser thermotherapy may be used for inducing favorable immunologic effects also in patients. Thus, we have shown a laser-induced bystander effect in a patient with malignant melanoma. In patients with breast cancer we have shown that laser thermotherapy induces intratumoral infiltration of immunocompetent cells like CD68 macrophages and CD8 lymphocytes. Laser thermotherapy is likely to be beneficial mainly when tumor burden is small, that is, when treatment is performed with curative intent, either with laser alone or together with surgical resection. For optimal effect, it appears likely that thermotherapy should be combined with other therapies. Most likely, a clinically meaningful effect can only be proven in prospective randomized studies comparing thermotherapy with other methods, particularly surgical resection.
Trees, shrubs, and lianas of West African dry zones (2004)

This field handbook is the result of over fifteen years' experience of forestry operations under projects conducted by CIRAD. It sets out to fill a gap in the literature available on the flora of the dry zones of West Africa. Its 1 300 colour photographs of flowers, fruits, leaves and bark will facilitate identification of each of the 360 species presented. As trees are an integral part of the landscape and have many functions and uses, an up-to-date inventory is also given of the traditional uses of the different parts of plants for pharmaceutical and human and animal food purposes and in daily life. The determination keys and descriptive sheets are accessible to non-specialists in botany, be they technicians working in forestry, agriculture or animal production, teachers or students. This book is a reference for anyone in need of information on the trees and shrubs of the region.
First Efficacy and Safety Results with the Antibody Containing Leukocyte Inhibition Module in Cardiac Surgery Patients with Neutrophil Hyperactivity (2005)

Systemic administration of immune modulating antibodies may play an important role in reducing neutrophil hyperactivity, for example, in patients undergoing cardiac surgery with extracorporeal circulation or in trauma patients. However, this strategy has extremely high costs and is often associated with severe adverse effects. We developed the Leukocyte-Inhibition-Module (LIM), an extracorporeal circulation (ECC) device housing a polyurethane matrix with covalently bound Fas (CD95; APO-1) stimulating antibodies to rapidly prevent neutrophil hyperactivation. A feasibility study with 14 patients undergoing cardiac surgery with the use of immunogenic ECC without (n = 5) and with (n = 9) LIM (venous line) was performed. Our data show that the usually observed ECC associated perioperative increase in neutrophils (control) was prevented by LIM (p = 0.023). Moreover, the increase of the proinflammatory markers tumor necrosis factor (TNF)-alpha and polymorphonuclear elastase was limited by LIM (p = 0.038 and p = 0.002). In both groups, no significant changes in liver enzymes or in clotting were detected after surgery, and up to 12 months follow up, no unusual complications were reported. This study shows for the first time to our knowledge the feasibility, efficacy, and safety of a new cost effective, immune management strategy in patients with aberrant immune activation by exposing the blood stream to immobilized agonistic anti-Fas antibodies.
Artificial neural network based autopicker for micro‐earthquake data (2011)

Earthquake data collected from the Geysers geothermal field from the period 2006 to 2010 was studied. An artificial neural network (ANN) based autopicker was developed to study and compare the picks with available autopickers in use at Lawrence Berkeley National Lab (LBNL) as well as in house autopicker at USC. The results indicate the following: 1. The ANN autopicker is able to generate good picks in most situations where other autopickers work. 2. The ANN autopicker is able to pick in situations where the other autopickers fail to generate good picks or do not generate any picks at all due to noise. 3. STA/LTA ratio and frequency based attributes show highest weight in the trained ANN. Despite the low misclassification error observed in the final results (3.7%), the ANN autopicker failed in some situations. The next step is to incorporate improved attribute sets and look at a hybrid neuro‐fuzzy approach to tide over the limitations of the present network.
An open-source <i>k</i> -mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes (2018)

Abstract For many disease-causing virus species, global diversity is clustered into a taxonomy of subtypes with clinical significance. In particular, the classification of infections among the subtypes of human immunodeficiency virus type 1 (HIV-1) is a routine component of clinical management, and there are now many classification algorithms available for this purpose. Although several of these algorithms are similar in accuracy and speed, the majority are proprietary and require laboratories to transmit HIV-1 sequence data over the network to remote servers. This potentially exposes sensitive patient data to unauthorized access, and makes it impossible to determine how classifications are made and to maintain the data provenance of clinical bioinformatic workflows. We propose an open-source supervised and alignment-free subtyping method (K AMERIS ) that operates on k -mer frequencies in HIV-1 sequences. We performed a detailed study of the accuracy and performance of subtype classification in comparison to four state-of-the-art programs. Based on our testing data set of manually curated real-world HIV-1 sequences ( n = 2, 784), Kameris obtained an overall accuracy of 97%, which matches or exceeds all other tested software, with a processing rate of over 1,500 sequences per second. Furthermore, our fully standalone general-purpose software provides key advantages in terms of data security and privacy, transparency and reproducibility. Finally, we show that our method is readily adaptable to subtype classification of other viruses including dengue, influenza A, and hepatitis B and C virus.
Statistical data analysis of thin film photovoltaic modules deployed in hot and humid climate of Florida (2008)

Current accelerated tests of photovoltaic (PV) modules mostly prevent infant mortality but cannot duplicate changes occurring in the field nor can predict useful lifetime. Therefore, monitoring of field-deployed PV modules was undertaken at FSEC with goals to assess their performance in hot and humid climate under high voltage operation and to correlate the PV performance with the meteorological parameters. This paper presents performance analysis of U.S. Company manufactured thin film a-Si:H PV modules that are encapsulated using flexible front sheets and framed to be outdoor tested. Statistical data analysis of PV parameters along with meteorological parameters, monitored continuously, is carried out on regular basis with PVUSA type regression analysis. Current-voltage (I-V) characteristic of module arrays that are obtained periodically complement the continuous data monitoring. Moreover, effect of high voltage bias and ambient parameters on leakage current in PV modules on individual modules is studied. Any degradation occurring during initial 18 months could not be assessed due to data acquisition and hurricane problems. No significant degradation was observed in the performance of PV modules during the subsequent 30-months. It is planned to continue this study for a prolonged period so as to serve as basis for their long-term warranties.
Role of hydrogen during rapid vapor-phase doping analyzed by x-ray photoelectron spectroscopy and Fourier-transform infrared-attenuated total reflection (1998)

The surface of boron-doped layers formed by rapid vapor-phase doping was analyzed by x-ray photoelectron spectroscopy (XPS) and Fourier-transform infrared-attenuated total reflection (FTIR-ATR), to determine the role of the hydrogen carrier gas. Boron doping was carried out with a B2H6 source gas and a hydrogen carrier gas at 800 and 900 °C. A nitrogen carrier gas was also used for comparison. Using hydrogen carrier gas, no evidence of boron segregation was observed in the XPS spectra. FTIR-ATR analysis confirmed that the hydrogen termination of the surface was maintained during doping. Using nitrogen carrier gas, layers that included segregated boron and silicon nitride were produced on the surface, which led to poor controllability of the boron concentration. When a hydrogen carrier gas is used, the hydrogen termination should promote the surface migration of adsorbed species. The hydrogen carrier gas plays an important role in terminating the silicon dangling bonds, thus preventing excessive chemisorption of boron.
Acid resistance in enteric bacteria (1993)

Shigella species require a uniquely small inoculum for causing dysentery. One explanation for the low infective dose is that Shigella species are better able to survive the acidic conditions encountered in the stomach than are other enteric pathogens. We have tested Shigella species, Escherichia coli, and Salmonella species for the ability to survive at pH 2.5 for at least 2 h. Most isolates of Shigella and E. coli survived this treatment, whereas none of the Salmonella isolates were able to do so. The ability of Shigella species to survive at low pHs does not require the presence of the large virulence plasmid or growth at 37 degrees C but is strikingly dependent on growth phase. We have also found that Shigella isolates exposed to acid lose the ability to invade epithelial cells.
Sensitive Chemiluminescence Enzyme Immunoassay for Vascular Endothelial Growth Factor/Vascular Permeability Factor in Human Serum (1995)

A sandwich chemiluminescence enzyme immunoassay for measuring the level of VEGF/VPF in serum was constructed. The detectability of the assay is very low (1.0 pg/ml) and the measurable range of the assay was very wide (1-1000 pg/ml). The assay showed that the average level of VEGF/VPF in human sera from healthy blood donors was approximately 19 pg/ml.
The Treatment of Acetaminophen Poisoning (1983)

Acetaminophen has become a very popular over-the-counter analgesic in some countries and as a result it is used increasingly as an agent for self-poisoning. Without treatment only a minority of patients develop severe liver damage and 1 to 2% die in hepatic failure. Until Mitchell and his colleagues discovered the biochemical mechanisms of toxicity in 1973 there was no effective treatment. They showed that the metabolic activation of acetaminophen resulted in the formation of a reactive arylating intermediate, and that hepatic reduced glutathione played an essential protective role by preferential conjugation and inactivation of the metabolite. Early treatment with sulphydryl compounds and glutathione precursors has been dramatically effective in preventing liver damage, renal failure, and death following acetaminophen overdosage. It seems likely that these agents act primarily by stimulating glutathione synthesis. Inhibition of the metabolic activation of acetaminophen is another potential therapeutic approach that has not yet been put to the test clinically. The clinical management of acetaminophen poisoning has been transformed and it is particularly gratifying to have effective treatment based on a well established biochemical mechanism of toxicity. It is likely that effective treatment will be developed for toxicity caused through similar mechanisms by other agents.
Identification of Tubular Vortices in Turbulence (1997)

A new method is proposed to extract the axes of tubular vortices in turbulence. Loci of sectional local minimum of the pressure associated with the advection acceleration are traced numerically. It is applied to a homogeneous isotropic turbulence to demonstrate that swirling motions actually exist around these axes. The present method is shown to be superior to several typical ones commonly used in identifying tubular vortices.