gebhart/patrepeval huggingface dataset:
Code compression techniques using operand field remapping (2002)

Dictionary-based code compression stores the most frequently used instruction sequences in a dictionary, and replaces the occurrences of these sequences in the program with codewords. The large dictionary size is due mainly to many instruction sequences which are different only in operands, but are otherwise the same. The operand factorisation technique divides the expression tree into tree-pattern (opcode sequence) and operand-pattern (operand sequence) to reduce this redundancy; instruction sequences with the same opcodes but different operands may thus share the same tree-pattern dictionary entry. The paper proposes an operand field remapping method to further reduce dictionary size. The key idea is to explore the relations between the current operand to be compressed with those already compressed. The operand-pattern dictionary is therefore divided into an operand remapping dictionary and an operand list dictionary. Each entry in the operand remapping dictionary indicates whether the operand (register or immediate value) to be compressed is the most used operand, the same as the destination register of the previous instructions, or otherwise. With this remapping technique, the operand dictionary size is greatly reduced. An average 46% compression ratio can be achieved where compression ratio=(dictionary size+compressed code size)/(original program size).
Prompt gamma-ray emission from biological tissues during proton irradiation: a preliminary study (2009)

In this paper, we present the results of a preliminary study of secondary 'prompt' gamma-ray emission produced by proton-nuclear interactions within tissue during proton radiotherapy. Monte Carlo simulations were performed for mono-energetic proton beams, ranging from 2.5 MeV to 250 MeV, irradiating elemental and tissue targets. Calculations of the emission spectra from different biological tissues and their elemental components were made. Also, prompt gamma rays emitted during delivery of a clinical proton spread-out Bragg peak (SOBP) in a homogeneous water phantom and a water phantom containing heterogeneous tissue inserts were calculated to study the correlation between prompt gamma-ray production and proton dose delivery. The results show that the prompt gamma-ray spectra differ significantly for each type of tissue studied. The relative intensity of the characteristic gamma rays emitted from a given tissue was shown to be proportional to the concentration of each element in that tissue. A strong correlation was found between the delivered SOBP dose distribution and the characteristic prompt gamma-ray production. Based on these results, we discuss the potential use of prompt gamma-ray emission as a method to verify the accuracy and efficacy of doses delivered with proton radiotherapy.
Electrospray sample deposition for matrix‐assisted laser desorption/ionization (MALDI) and atmospheric pressure MALDI mass spectrometry with attomole detection limits (2004)

Electrospray sample deposition was explored for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). In this method, nanoliter volumes of matrix/analyte mixture were electrosprayed from a high voltage biased (1-2 kV) fused-silica capillary onto a grounded MALDI plate mounted 100-500 microm from the capillary outlet. Electrospray deposition with these conditions produced sample spots 200-300 microm in diameter thus matching the laser spot size. Varying spray voltage and distance resulted in different crystal sizes and volatilization rates for alpha-cyano-4-hydroxycinnamic acid matrix. Best results were obtained when the sample was deposited as wet droplets as opposed to deposition as dried solid. Under 'wet-spray' conditions, 2-4 microm diameter crystals were formed and detection limits for several neuropeptides were 0.7-25 amol. Samples could be pre-concentrated on the plate by spraying continuously and allowing sample to evaporate in a small spot. Sample volumes as large as 580 nL were deposited yielding a detection limit of 35 pM for neurotensin 1-11. Electrospray sample deposition yielded similar results when using atmospheric pressure-MALDI coupled with a quadrupole ion trap mass spectrometer, except that the sensitivity was approximately seven-fold worse.
Information dependencies (2000)

This paper uses the tools of information theory to examine and reason about the information content of the attributes within a relation instance. For two sets of attributes X and Y, an information dependency measure (InD measure) characterizes the uncertainty remaining about the values for the set Y when the values for the set X are known. A variety of arithmetic inequalities (InD inequalities) are shown to hold among InD measures; InD inequalities hold in any relation instance. Numeric constraints (InD constraints) on InD measures, consistent with the InD inequalities, can be applied to relation instances. Remarkably, functional and multivalued dependencies correspond to setting certain constraints to zero, with Armstrong's axioms shown to be consequences of the arithmetic inequalities applied to constraints. As an analog of completeness, for any set of constraints consistent with the inequalities, we may construct a relation instance that approximates these constraints within any positive ε. InD measures suggest many valuable applications in areas such as data mining.
Three-dimensional optical tomographic imaging of breast in a human subject (2001)

We present for the first time a full three-dimensional (3-D) reconstruction of absorption images of breast from continuous-wave (cw) measurements performed on a premenopausal woman. Our 3-D optical images clearly reveal a large primary tumor as well as a small secondary tumor in a separate location of the breast. The multiple tumors identified by our 3-D optical imaging have been confirmed by the subsequent biopsy examination of the breast. Quantitative information of the optical images obtained is provided in terms of the location, size, and absorption coefficient of the tumors.
Why Charged Molecules Move Across a Temperature Gradient: The Role of Electric Fields (2014)

Methods to move solvated molecules are rare. Apart from electric fields, only thermal gradients are effective enough to move molecules inside a fluid. This effect is termed thermophoresis, and the underlying mechanisms are still poorly understood. Nevertheless, it is successfully used to quantify biomolecule binding in complex liquids. Here we show experiments that reveal that thermophoresis in water is dominated by two electric fields, both established by the salt ions of the solution. A local field around the molecule drives molecules along an energy gradient, whereas a global field moves the molecules by a combined thermoelectrophoresis mechanism known as the Seebeck effect. Both mechanisms combined predict the thermophoresis of DNA and RNA polymers for a wide range of experimental parameters. For example, we correctly predict a complex, nonlinear size transition, a salt-species-dependent offset, a maximum of thermophoresis over temperature, and the dependence of thermophoresis on the molecule concentration.
Spectral Analysis of Nanomaterials using a Transition-Edge Sensor Microcalorimeter Mounted on a Field-Emission Scanning Electron Microscope (2008)

A prototype transition-edge sensor (TES) microcalorimeter is successfully integrated into a commercial field-emission scanning electron microscope (FE-SEM). The microcalorimeter is composed of a gold (Au) absorber, a Au/Ti bilayer thermometer and a thermal isolation structure with a SiNx membrane. Operating temperatures of 100–150 mK are obtained with a dilution refrigerator. The measured energy resolution was between 19–22 eV for Al Kα at an acceleration voltage of 5 keV. The newly developed system was applied to the analysis of nanosheets for the first time at a low acceleration voltage (≤ 5 kV). The energy dispersive spectrometer (EDS) spectra of Nb3O8 nanosheets of different thicknesses (less than 20 nm) were successfully detected. Moreover, Au particles on carbon nanotubes with a thickness less than 1 nm are detected clearly. With further improvement of both energy resolution and count rate, this system holds the promise for practical X-ray compositional characterization of nanomaterials with high image spatial resolution in the low-acceleration-voltage regime.
Studies on 13C-Phenacetin Metabolism. II. A Combination of Breath Test and Urine Test of in vivo Metabolites in the Diagnosis of Liver Disease. (1996)

We determined the optimum 13C-labeling position in phenacetin for use in a breath test to diagnose liver disease based on infrared spectroscopy detection of 13CO2 in exhaled air. ([1-13C]Ethoxy)phenacetin gave the best result. This compound was also employed in a urine test using 13C-NMR spectroscopy. In the urine test, healthy subjects gave a higher signal of phenacetin than of its metabolite, phenetidine, whereas in patients with liver disease the situation was the reverse. The combination of the breath and urine tests may be a valuable new tool for the diagnosis of liver disease.
Time‐lapse imaging assay using the BioStation <scp>CT</scp>: A sensitive drug‐screening method for three‐dimensional cell culture (2015)

Three-dimensional (3D) cell culture is beneficial for physiological studies of tumor cells, due to its potential to deliver a high quantity of cell culture information that is representative of the cancer microenvironment and predictive of drug responses in vivo. Currently, gel-associated or matrix-associated 3D cell culture is comprised of intricate procedures that often result in experimental complexity. Therefore, we developed an innovative anti-cancer drug sensitivity screening technique for 3D cell culture on NanoCulture Plates (NCP) by employing the imaging device BioStation CT. Here, we showed that the human breast cancer cell lines BT474 and T47D form multicellular spheroids on NCP plates and compared their sensitivity to the anti-cancer drugs trastuzumab and paclitaxel using the BioStation CT. The anticancer drugs reduced spheroid migration velocity and suppressed spheroid fusion. In addition, primary cells derived from the human breast cancer tissues B58 and B61 grown on NCP plates also exhibited similar drug sensitivity. These results were in good agreement with the conventional assay method using ATP quantification. We confirmed the antitumor effects of the drugs on cells seeded in 96-well plates using the BioStation CT imaging technique. We expect this method to be useful in research for new antitumor agents and for drug sensitivity tests in individually-tailored cancer treatments.
Molecular determinants of inactivation in voltage‐gated Ca<sup>2+</sup> channels (2000)

Evolution has created a large family of different classes of voltage-gated Ca2+ channels and a variety of additional splice variants with different inactivation properties. Inactivation controls the amount of Ca2+ entry during an action potential and is, therefore, believed to play an important role in tissue-specific Ca2+ signalling. Furthermore, mutations in a neuronal Ca2+ channel (Ca(v)2.1) that are associated with the aetiology of neurological disorders such as familial hemiplegic migraine and ataxia cause significant changes in the process of channel inactivation. Ca2+ channels of a given subtype may inactivate by three different conformational changes: a fast and a slow voltage-dependent inactivation process and in some channel types by an additional Ca2+-dependent inactivation mechanism. Inactivation kinetics of Ca2+ channels are determined by the intrinsic properties of their pore-forming alpha1-subunits and by interactions with other channel subunits. This review focuses on structural determinants of Ca2+ channel inactivation in different parts of Ca2+ channel alpha1-subunits, including pore-forming transmembrane segments and loops, intracellular domain linkers and the carboxyl terminus. Inactivation is also affected by the interaction of the alpha1-subunits with auxiliary beta-subunits and intracellular regulator proteins. The evidence shows that pore-forming S6 segments and conformational changes in extra- (pore loop) and intracellular linkers connected to pore-forming segments may play a principal role in the modulation of Ca2+ channel inactivation. Structural concepts of Ca2+ channel inactivation are discussed.
ChemInform Abstract: Solution‐Phase Combinatorial Chemistry in Lead Discovery (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Jubilat w oczach przyjaciół z Chin (2015)

The Celebrant in the eyes of friends from China The Author describes and analyzes the achievements and experiences of Edward Kajdanski against changing political situation, first in Harbin, and then generally in China. The Author emphasizes the outstanding role that E. Kajdanski played in bringing closer to the Poles the Chinese culture, history and medicine, as well as in mutual acquaintance and recognition of both nations.
Next-generation sequencing technologies: breaking the sound barrier of human genetics (2014)

Demand for new technologies that deliver fast, inexpensive and accurate genome information has never been greater. This challenge has catalysed the rapid development of advances in next-generation sequencing (NGS). The generation of large volumes of sequence data and the speed of data acquisition are the primary advantages over previous, more standard methods. In 2013, the Food and Drug Administration granted marketing authorisation for the first high-throughput NG sequencer, Illumina's MiSeqDx, which allowed the development and use of a large number of new genome-based tests. Here, we present a review of template preparation, nucleic acid sequencing and imaging, genome assembly and alignment approaches as well as recent advances in current and near-term commercially available NGS instruments. We also outline the broad range of applications for NGS technologies and provide guidelines for platform selection to best address biological questions of interest. DNA sequencing has revolutionised biological and medical research, and is poised to have a similar impact on the practice of medicine. This tool is but one of an increasing arsenal of developing tools that enhance our capabilities to identify, quantify and functionally characterise the components of biological networks that keep us healthy or make us sick. Despite advances in other 'omic' technologies, DNA sequencing and analysis, in many respects, have played the leading role to date. The new technologies provide a bridge between genotype and phenotype, both in man and model organisms, and have revolutionised how risk of developing a complex human disease may be assessed. The generation of large DNA sequence data sets is producing a wealth of medically relevant information on a large number of individuals and populations that will potentially form the basis of truly individualised medical care in the future.
Laser‐Induced Acoustic Desorption Mass Spectrometry of Single Bioparticles (2006)

Single charged bioparticles such as viruses, bacteria, and mammalian whole cells have been successfully desorbed by laser-induced acoustic waves and analyzed with a quadrupole ion-trap mass spectrometer (see picture). This approach offers a high sensitivity of detection and good accuracy of the mass measurement. The capability to measure the mass of an entire cell has broad potential in biomedical applications.
Amino Acid Residues in Ribonuclease MC1 from Bitter Gourd Seeds Which Are Essential for Uridine Specificity (2000)

The ribonuclease MC1 (RNase MC1), isolated from seeds of bitter gourd (Momordica charantia), consists of 190 amino acids and is characterized by specific cleavage at the 5'-side of uridine. Site-directed mutagenesis was used to evaluate the contribution of four amino acids, Asn71, Val72, Leu73, and Arg74, at the alpha4-alpha5 loop between alpha4 and alpha5 helices for recognition of uracil base by RNase MC1. Four mutants, N71T, V72L, L73A, and R74S, in which Asn71, Val72, Leu73, and Arg74 in RNase MC1 were substituted for the corresponding amino acids, Thr, Leu, Ala, and Ser, respectively, in a guanylic acid preferential RNase NW from Nicotiana glutinosa, were prepared and characterized with respect to enzymatic activity. Kinetic analysis with a dinucleoside monophosphate, CpU, showed that the mutant N71T exhibited 7.0-fold increased K(m) and 2.3-fold decreased k(cat), while the mutant L73A had 14.4-fold increased K(m), although it did retain the k(cat) value comparable to that of the wild-type. In contrast, replacements of Val72 and Arg74 by the corresponding amino acids Leu and Ser, respectively, had little effect on the enzymatic activity. This observation is consistent with findings in the crystal structure analysis that Asn71 and Leu73 are responsible for a uridine specificity for RNase MC1. The role of Asn71 in enzymatic reaction of RNase MC1 was further investigated by substituting amino acids Ala, Ser, Gln, and Asp. Our observations suggest that Asn71 has at least two roles: one is base recognition by hydrogen bonding, and the other is to stabilize the conformation of the alpha4-alpha5 loop by hydrogen bonding to the peptide backbone, events which possibly result in an appropriate orientation of the alpha-helix (alpha5) containing active site residues. Mutants N71T and N71S showed a remarkable shift from uracil to guanine specificity, as evaluated by cleavage of CpG, although they did exhibit uridine specificity against yeast RNA and homopolynucleotides.
Evolution of Memory Architecture (2015)

Computer memories continue to serve the role that they first served in the electronic discrete variable automatic computer (EDVAC) machine documented by John von Neumann, namely that of supplying instructions and operands for calculations in a timely manner. As technology has made possible significantly larger and faster machines with multiple processors, the relative distance in processor cycles of this memory has increased considerably. Microarchitectural techniques have evolved to share this memory across ever-larger systems of processors with deep cache hierarchies and have managed to hide this latency for many applications, but are proving to be expensive and energy-inefficient for newer types of problems working on massive amounts of data. New paradigms include scale-out systems distributed across hundreds and even thousands of nodes, in-memory databases that keep data in memory much longer than the duration of a single task, and near-data computation, where some of the computation is off-loaded to the location of the data to avoid wasting energy in the movement of data. This paper provides a historical perspective on the evolution of memory architecture, and suggests that the requirements of new problems and new applications are likely to fundamentally change processor and system architecture away from the currently established von Neumann model.
Comprehending new words beyond their original contexts (2006)

When one encounters a novel word, it may be in a context that does not specify its complete meaning and possible uses in other contexts. One source of information speakers can use is how similar, familiar words are used. I describe preliminary results from an experiment in which people read novel words in one context and then had to understand them in a new use. In some cases, these uses followed patterns of familiar words. The question is whether such patterns aid in comprehension even when the word has never been encountered in that use before. Key words: novel word, familiar word, interpretation, experiment 1.
Robust Correlation based True-Speed-over-Ground Measurement System employing a FMCW Radar (2018)

This paper presents a novel approach for the determination of True-Speed-Over-Ground for trains. Speed determination is accomplished by correlating the received signals of two side-looking radar sensors. The theoretically achievable precision is derived. Test measurements are done to give a prove of concept. The measurements are done in two different scenarios. The test measurements are carried out using a bi-static 24 GHz frequency modulated continuous wave (FMCW) radar.
A Framework for Constructing Fast MPC over Arithmetic Circuits with Malicious Adversaries and an Honest-Majority. (2017)

Protocols for secure multiparty computation enable a set of parties to compute a function of their inputs without revealing anything but the output. The security properties of the protocol must be preserved in the presence of adversarial behavior. The two classic adversary models considered are semi-honest (where the adversary follows the protocol specification but tries to learn more than allowed by examining the protocol transcript) and malicious (where the adversary may follow any arbitrary attack strategy). Protocols for semi-honest adversaries are often far more efficient, but in many cases the security guarantees are not strong enough. In this paper, we present a new efficient method for compiling a large class of protocols that are secure in the presence of semi-honest adversaries into protocols that are secure in the presence of malicious adversaries. Our method assumes an honest majority (i.e., that tn/2 where t is the number of corrupted parties and n is the number of parties overall), and is applicable to many semi-honest protocols based on secret-sharing. In order to achieve high efficiency, our protocol is secure with abort and does not achieve fairness, meaning that the adversary may receive output while the honest parties do not. We present a number of instantiations of our compiler, and obtain protocol variants that are very efficient for both a small and large number of parties. We implemented our protocol variants and ran extensive experiments to compare them with each other. Our results show that secure computation with an honest majority can be practical, even with security in the presence of malicious adversaries. For example, we securely compute a large arithmetic circuit of depth 20 with 1,000,000 multiplication gates, in approximately 0.5 seconds with three parties, and approximately 29 seconds with 50 parties, and just under 1 minute with 90 parties.
Sensorless drive of surface-mounted permanent-magnet motor by high-frequency signal injection based on magnetic saliency (2003)

This paper presents a new sensorless control scheme of a surface-mounted permanent-magnet (SMPM) motor using high-frequency voltage signal injection method based on the high-frequency impedance difference. In the SMPM motor, due to the flux of the permanent magnet, the stator core around the q-axis winding is saturated. This makes the magnetic saliency in the motor. This magnetic saliency has the information about the rotor position. The high-frequency voltage signal is injected into the motor in order to detect the magnetic saliency and estimate the rotor position. In this paper, the relationship between the high-frequency voltages and high-frequency currents is developed using the voltage equations at the high frequency, and the high-frequency impedance characteristics are analyzed experimentally under various conditions. The proposed sensorless control scheme makes it possible to drive the SMPM motor in the low-speed region including zero speed, even under heavy load conditions. The experimental results verify the performance of the proposed sensorless algorithm.