gebhart/patrepeval huggingface dataset:
Three-dimensional Borehole Radar Imaging (2005)

Before embarking on any mining operation, it is advantageous to locate the subsurface orebody in three-dimensions with a high resolution (~1m) ahead of actual mining, because this will increase productivity and efficiency. Borehole radar is such an emerging mapping tool in the mining industry, that can be used to image the subsurface orebody with high resolution. 3-D subsurface imaging using two-dimensional aperture synthesis requires many boreholes and is thus not economically feasible in underground orebody imaging. Therefore, the main objective of this thesis is to develop 3-D imaging techniques, using a limited number of boreholes. An interferometric synthetic aperture radar (InSAR) is a well established space-borne/airborne technique for mapping the Earth’s surface. A borehole InSAR simulation study was thus carried out, using a sidelooking antenna configuration to image the subsurface orebodies, such as potholes and cylindrical Kimberlite structures, in 3-D. A performance analysis of an interferometric experiment is presented. In general, borehole radars are a wide-band system, often having bandwidths of 75% of the centre frequency. A 3-D image reconstruction technique was developed by means of correlation-type processing, using magnitude images of multiple boreholes coming from different view angles, which is more suitable for wide-band/ultra wide-band borehole radar signals. The technique was tested by using simulated multiple borehole radar magnitude images, as well as real acoustic images that had been captured in air and water media. The 3-D reconstructed grid spacing derivations are presented for a borehole trajectory fanning outward from the borehole centre. In this thesis, a 40kHz air-based sonar system was used in the laboratory environment to emulate inverse synthetic aperture radar (ISAR) data in the context of a real borehole experiment. A deconvolution processing approach was adopted to range-compress the 40kHz sonar data captured in air. A time domain focusing technique was used to focus the simulated borehole radar as well as the real acoustic data. In the case of homogeneous, isotropic and non-dispersive media, a straight-line wave propagation is considered to process the data in range and azimuth. In a real bore-
Synthesis, structures and biological activity of some 4-amino-3-cinnolinecarboxylic acid derivatives, Part 1. (1994)

6,7,8-Substituted 4-amino-3-cinnolinecarboxylic acids 1 were condensed with amines to the corresponding 4-amino-3-cinnolinecarboxamides 7, 8. A variety of pharmacological tests showed a significant CNS activity of some new amides. Decarboxylation of 4-amino-3-cinnolinecarboxylic acids 1 yielded the corresponding 4-aminocinnolines 4 and alkaline hydrolysis of 1 gave 4-oxo-3-cinnolinecarboxylic acids 2. The acids 1 were converted into pyrimido[5,4-c]cinnolines 6 on two ways of synthesis.
SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling (2013)

Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call variants from human sequencing data disagree on many of their predictions, and current methods to evaluate accuracy and computational performance are ad-hoc and incomplete. Agreement on benchmarking variant calling methods would stimulate development of genomic processing tools and facilitate communication among researchers. Results: We propose SMaSH, a benchmarking methodology for evaluating human genome variant calling algorithms. We generate synthetic datasets, organize and interpret a wide range of existing benchmarking data for real genomes, and propose a set of accuracy and computational performance metrics for evaluating variant calling methods on this benchmarking data. Moreover, we illustrate the utility of SMaSH to evaluate the performance of some leading single nucleotide polymorphism (SNP), indel, and structural variant calling algorithms. Availability: We provide free and open access online to the SMaSH toolkit, along with detailed documentation, at smash.cs.berkeley.edu.
Covalently immobilized biosignal molecule materials for tissue engineering (2007)

Immobilization of biosignal molecules including growth factors and cytokines is important for developing biologically active materials which can contribute to tissue engineering as a component. The immobilization has more meanings than only immobilization of the enzyme in a bioreactor or ligand-receptor interactions, because the immobilized biosignal molecules work on cells which have very complex structures and functions. This review discusses recent progress in immobilization of biosignal molecules, including the mechanisms and design concepts.
High Sensitivity Photodetector for Photon-Counting Applications (2018)

In the last years, there has been a large development of low-light applications, and many of them are based on photon counting using single-photon detectors (SPDs). These are very sensitive detectors typically with an internal gain. The first candidate SPD was the photomultiplier tube (PMT), reaching a very high gain (~106), but there have been a large development of many other solutions, like solid-state solutions. Among them, single-photon avalanche diodes (SPADs) have been used in spectroscopy, florescence imaging, etc., particularly for their good detection efficiency and time resolution (tens of picoseconds). SPADs have been developed in silicon and III–V materials, for the NIR wavelength range. SPADs can be used as single high-performance pixels, or in arrays. SPAD arrays have imaging capabilities, with high sensitivity. Another kind of array is the silicon photomultiplier (SiPM), where all the pixels are connected to a common anode and a common cathode. SiPMs are used in nuclear medicine, physics experiments, quantum-physics experiments, light detection and ranging (LIDAR), etc., due to their high detection efficiency combined with large sensitive areas, and high dynamic range. SiPMs with many small cells present several advantages and nowadays the SPAD pitch can be reduced down to 5 μm.
SONET ring applications for survivable fiber loop networks (1991)

Synchronous optical network (SONET) self-healing rings (SHR) are studied in the loop environment. SONET SHR architectures for loop feeder networks are discussed, focusing on three possible dual central office (CO) architectures for fiber loop networks, using SONET SHRs to reduce network costs and provide network service survivability. These architectures reflect an integrated planning concept for SONET networks that eliminates the boundary between the access network and the inter-office network. It is shown that the use of SONET SHRs makes it easy to evolve to a protected dual CO access architecture. Economic and survivability studies are discussed. The economic studies show that using the ring approach yields significant advantages over the traditional diverse protection approach in terms of cost and survivability, especially for the dual CO architectures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Near‐field optical microscopy for DNA studies at the single molecular level (1998)

An aperture-type near-field optical microscope (NSOM) with two polarization detection channels has been used to image fluorescently labelled DNA with high spatial resolution and single molecule fluorescence sensitivity. The sample has been engineered such that there is only one rhodamine dye per DNA strand. Lateral and vertical DNA dimensions in the shear-force image are 14 ± 2 nm and 1.4 ± 0.2 nm, respectively. No sample deformation was observed under our imaging conditions. Near-field fluorescence imaging of individual fluorophores shows an optical resolution of 70 nm at full-width at half-maximum. Large intensity differences between individual rhodamine molecules attached to DNA are observed from the NSOM images. Statistics on rhodamine dyes in different environments (attached to glass, embedded in a polymer layer and attached to DNA) show bleaching rates of 10−5. Total intensity line profiles together with in-plane angle orientation are used to characterize individual dyes. Rhodamine dyes show strong intensity fluctuations independent of the particular environment. These results are in contrast with the more stable photophysical behaviour as observed for carbocyanine molecules embedded in polymer matrices. The mobility of rhodamine—both lateral and rotational—is clearly influenced by its immediate surrounding and attachment to the surface.
Quantitation of Chlamydia trachomatis 16S rRNA Using NASBA Amplification and a Bioluminescent Microtiter Plate Assay (2000)

We developed a nucleic acid sequence based amplification (NASBA) assay which employs the recombinant photoprotein Aequorin in a microtiter plate format for detection and quantitation of C. trachomatis that may be useful in large scale epidemiological studies aimed at improving our understanding of factors affecting transmission of this sexually transmitted pathogen. The conditions for NASBA amplification of the16S rRNA target were optimized (90 mM KCl, 12 mM MgCl(2), 0.2 microM P1 and P2 primers), amplified RNA was captured by a biotin-labelled capture probe immobilized onto streptavidin coated microtiter plates and detected with an FITC-labelled oligonucleotide probe and Aequorin-anti-FITC antibody conjugate. The analytical sensitivity of NASBA was 1,000 in vitro generated RNA transcripts and 1.6 IFU of C. trachomatis. The sensitivity of NASBA using the bioluminescent assay was 10 fold higher than Northern blotting. Time course amplification experiments performed with 10 fold serial dilutions of target established that amplification was linear at 75 min and extended over a range of five log units of input RNA copy number. Linear regression analysis confirmed a linear fit for the data with r(2) = 0.959 (p < 0.004). A double log plot of RLU signal versus copy number was linear; analysis of residuals from a series of runs tests confirmed a fit with a linear model (number of runs = 3, p = 0.5 where p < 0.05 indicates statistical deviation from a linear model). NASBA amplification coupled with bioluminescent detection in a microtiter plate format should provide a useful tool for quantitation of C. trachomatis in clinical specimens for use in epidemiological studies.
Adenovirus respiratory infection: significant increase in diagnosis using PCR comparing with antigen detection and culture methods (2010)

Adenovirus (AdV) respiratory infections are usually described as being associated with high mortality rates. Laboratory diagnosis is essential for the establishment of the appropriate therapy, and for guiding the implementation of preventive measures in order to prevent the spread of the infection. Aiming to analyze the sensitivity and specificity of the laboratorial diagnosis methods available, we compared antigen detection by indirect immunofluorescence assay (IF), and a specific nested polymerase chain reaction (PCR), to detect AdV in respiratory samples collected from patients admitted to hospital with acute respiratory disease. Positive samples were inoculated into a cell culture to confirm the results. We analyzed 381 samples from the nasopharyngeal aspirates collected during the year 2008; of these, 2.6% tested were positive for adenovirus through IF and 10% through PCR; positive isolation was obtained in 40% and 26% of these cases, respectively. Most infected patients were children under six months of age, and despite of the fact that a significant number of patients required intensive care, the mortality rate was low (5%). In conclusion, molecular methods were found to be useful for rapid diagnosis of adenovirus infections with higher sensitivity than antigen detection; their introduction permitted a significant increase in diagnoses of adenovirus infections.
Differential Management of Ca<sup>2+</sup> Oscillations by Anterior Pituitary Cells: A Comparative Overview (1998)

Most electrical and ionic properties of anterior pituitary cells are common to all pituitary cell types; only gonadotropes exhibit a few cell specific features. Under basal conditions, the majority of pituitary cells in vitro, irrespective of their cell type, display spontaneous action potentials and [Ca2+]i transients that result from rhythmic Ca2+ entry through L-type Ca2+ channels. The main function of these action potentials is to maintain cells in a readily activable responsive state. We propose to call this state a 'pacemaker mode', since it persists in the absence of extrinsic stimulation. When challenged by hypothalamic releasing hormones, cells exhibit two distinct response patterns: amplification of pacemaker activity or shift to internal Ca2+ release mode. In the internal Ca2+ release mode, [Ca2+]i oscillations are not initiated by entry of external Ca2+, but by release of Ca2+ from intracellular stores. In somatotropes and corticotropes, GHRH or CRH triggers the pacemaker mode in silent cells and amplifies it in spontaneously active cells. In contrast, in gonadotropes GnRH activates the internal Ca2+ release mode in silent cells and switches already active cells from the pacemaker to the internal Ca2+ release mode. Interestingly, homologous normal and tumoral cells display the same type of activity in vitro, in the absence or presence of hypothalamic hormones. Pacemaker and internal Ca2+ release modes are likely to serve different purposes. Pacemaker activity allows long-lasting sequences of [Ca2+]i oscillations (and thus sustained periods of secretion) that stop under the influence of hypothalamic inhibitory peptides. In contrast, the time during which cells can maintain internal Ca2+ release mode depends upon the importance of intracellular Ca2+ stores. This mode is thus more adapted to trigger secretory peaks of large amplitude and short duration. On the basis of these observations, theoretical models of pituitary cell activity can be proposed.
Inverse modelling in estimating soil hydraulic functions: a Genetic Algorithm approach (2002)

Abstract. The practical application of simulation models in the field is sometimes hindered by the difficulty of deriving the soil hydraulic properties of the study area. The procedure so-called inverse modelling has been investigated in many studies to address the problem where most of the studies were limited to hypothetical soil profile and soil core samples in the laboratory. Often, the numerical approach called forward-backward simulation is employed to generate synthetic data then added with random errors to mimic the real-world condition. Inverse modelling is used to backtrack the expected values of the parameters. This study explored the potential of a Genetic Algorithm (GA) to estimate inversely the soil hydraulic functions in the unsaturated zone. Lysimeter data from a wheat experiment in India were used in the analysis. Two cases were considered: (1) a numerical case where the forward-backward approach was employed and (2) the experimental case where the real data from the lysimeter experiment were used. Concurrently, the use of soil water, evapotranspiration (ET) and the combination of both were investigated as criteria in the inverse modelling. Results showed that using soil water as a criterion provides more accurate parameter estimates than using ET. However, from a practical point of view, ET is more attractive as it can be obtained with reasonable accuracy on a regional scale from remote sensing observations. The experimental study proved that the forward-backward approach does not take into account the effects of model errors. The formulation of the problem is found to be critical for a successful parameter estimation. The sensitivity of parameters to the objective function and their zone of influence in the soil column are major determinants in the solution. Generally, their effects sometimes lead to non-uniqueness in the solution but to some extent are partly handled by GA. Overall, it was concluded that the GA approach is promising to the inverse problem in the unsaturated zone. Keywords. Genetic Algorithm, inverse modelling, Mualem-Van Genuchten parameters, unsaturated zone, evapotranspiration, soil water
The hBracelet: A Wearable Haptic Device for the Distributed Mechanotactile Stimulation of the Upper Limb (2018)

Haptic interfaces are mechatronic devices designed to render tactile sensations; although they are typically based on robotic manipulators external to the human body, recently, interesting wearable solutions have been presented. Toward a more realistic feeling of virtual and remote environment interactions, we propose a novel wearable skin stretch device for the upper limb called “hBracelet.” It consists of two main parts coupled with a linear actuator. Each part contains two servo actuators that move a belt. The device is capable of providing distributed mechanotactile stimulation on the arm by controlling the tension and the distance of the two belts in contact with the skin. When the motors spin in opposite directions, the belt presses into the user's arm, while when they spin in the same direction, the belt applies a shear force to the skin. Moreover, the linear actuator exerts longitudinal cues on the arm by moving the two parts of the device. In this letter, we illustrate the mechanical structure, working principle, and control strategies of the proposed wearable haptic display. We also present a qualitative experiment in a teleoperation scenario as a case study to demonstrate the effectiveness of the proposed haptic interface and to show how a human can take advantage of multiple haptic stimuli provided at the same time and on the same body area. The results show that the device is capable of successfully providing information about forces acting at the remote site, thus, improving telepresence.
Activation of human epidermal Langerhans cells by engagement of the high affinity receptor for IgE, Fc ε RI (1995)

Human epidermal Langerhans cells (LCs) bind IgE via the high affinity receptor (Fc epsilon RI), and therefore are suspected to be involved in the genesis of atopic diseases. In this study, we report that surface expression of Fc epsilon RI is increased dramatically on LCs from patients with atopic dermatitis (AD) when compared with nonatopic individuals. Cross-linking of Fc epsilon RI on LCs from nonatopic individuals and patients with AD leads to a rapid tyrosine phosphorylation of several proteins, including p72, p77, and p95. However, upon receptor ligation, calcium mobilization is only detected in LCs freshly isolated from patients with AD (responder LCs), but not in those from normal skin of healthy individuals (nonresponder LCs). The beta-chain of Fc epsilon RI is not detected in normal LCs and only in a minority of LCs from atopic individuals, indicating that it is not related to the capacity of LCs to respond to Fc epsilon RI-mediated activation. In contrast, LCs from both nonatopic and atopic individuals internalize Fc epsilon RI by receptor-mediated endocytosis as a prerequisite for Ag focusing. Therefore, LCs from normal individuals and individuals with AD differ functionally by their Fc epsilon RI expression and by a distinct ability to respond to Fc epsilon RI-mediated activation.
Solid recovered fuel as coal substitute in the electricity generation sector (2005)

According to the 1999/31 EC Directive, municipal solid waste should not be disposed for landfill from 2005. In this way, more environmental friendly waste management options are promoted towards the volume reduction and limitation of negative consequences. In this context, attention is focused on the utilization of solid recovered fuels derived from the waste treatment as coal substitute in large-scale power plants. Such activities are realized within an EU-funded project RECOFUEL, in which the solid recovered fuels co-combustion with brown coal is demonstrated in two commercial-scale PF-boilers at R WE Power's power plant site in Weisweiler, Germany. During testing the thermal share of solid recovered fuels in the overall thermal input was adjusted to some 2%, resulting into a feeding rate of about 2 x 12.5 tons per hour. NTUA-LSB in cooperation with IVD-University of Stuttgart, Germany, is responsible for the boiler measurements and the characterization of boilers operational behavior. Among the main activities are the technology transfer of co-combustion practice in the Balkan countries and the perspectives of its future application in the Greek region, with respect to the special characteristics of the Greek brown coal and municipal solid waste. Co-combustion tests of brown coal and solid recovered fuels, that have been taken place up to now, have been successfully performed and the strict European emission limits are kept. The waste quantities in Greece that can be utilized are estimated in 200,000 Mg/year while their utilization in existing thermal plants is expected to bring savings of 3% lignite use and avoidance of up to 200,000 Mg CO2 per year.
Assessment of Nutritional Correlates of Blood Pressure (1983)

Nutritional factors are thought to contribute to the development of hypertension in susceptible humans. This review categorizes the types of nutrition-related data currently available on the relation between diet and blood pressure and provides guidelines for interpreting and using these data. The nutrition data base and the net effect of specific nutrients on blood pressure are discussed, and examples from the Health and Nutrition Examination Survey are given to compare demographic characteristics of various nutrients with demographic characteristics of hypertension in our society. Criteria for evaluating the strength and relevance of a specific nutrient's influence on blood pressure are presented. A comprehensive, continued assessment of all studies of diet and blood pressure control should assure better understanding of the pathogenesis and treatment of human hypertension.
Mucormycosis as the Elusive Cause of an Aortic Thrombus and Tissue-Obliterating Abscess (2019)

Invasive mucormycosis is an increasingly common cause of morbidity and mortality in hematologic malignancy patients. Early consideration of the diagnosis is essential in at-risk patients, exhibiting suggestive signs and symptoms. A 56-year-old female with acute myeloid leukemia initially presented with neutropenic fever before subsequently developing dense hemiplegia due to septic emboli to the spine and multifocal abscesses. These findings were later determined to be a result of a disseminated mucor infection and represented a rare manifestation of the disease. Despite the disseminated nature of the infection, identification of the causative organism was initially impeded by limitations in obtaining a tissue sample in a severely thrombocytopenic patient, as is common among hematologic malignancy patients. As a result of this limitation, diagnosis was ultimately made via PCR on bronchiolar lavage fluid. Early consideration of the diagnosis with prompt initiation of treatment is of utmost importance in this invasive infection. Further research is needed to identify and validate rapid, minimally invasive strategies for early diagnosis of mucormycosis.
Synthesis mechanism and technology of ultrafine diamond from detonation (2004)

Ultrafine diamond (UFD) is a hybrid product of explosion mechanics and material science. In this paper, we established the synthesis mechanism of UFD, built the direct-simulation Monte Carlo computing method for the generation of liquid drops from free carbon through coagulation during detonation, and constructed the computing programs for explosion thermodynamics conditions and phase-transition dynamics. The synthesis and purification technology were studied systemically.