gebhart/patrepeval huggingface dataset:
Biocalcite and Carbonic Acid Activators (2017)

Based on evolution of biomineralizing systems and energetic considerations, there is now compelling evidence that enzymes play a driving role in the formation of the inorganic skeletons from the simplest animals, the sponges, up to humans. Focusing on skeletons based on calcium minerals, the principle enzymes involved are the carbonic anhydrase (formation of the calcium carbonate-based skeletons of many invertebrates like the calcareous sponges, as well as deposition of the calcium carbonate bioseeds during human bone formation) and the alkaline phosphatase (providing the phosphate for bone calcium phosphate-hydroxyapatite formation). These two enzymes, both being involved in human bone formation, open novel not yet exploited targets for pharmacological intervention of human bone diseases like osteoporosis, using compounds that act as activators of these enzymes. This chapter focuses on carbonic anhydrases of biomedical interest and the search for potential activators of these enzymes, was well as the interplay between carbonic anhydrase-mediated calcium carbonate bioseed synthesis and metabolism of energy-rich inorganic polyphosphates. Beyond that, the combination of the two metabolic products, calcium carbonate and calcium-polyphosphate, if applied in an amorphous form, turned out to provide the basis for a new generation of scaffold materials for bone tissue engineering and repair that are, for the first time, morphogenetically active.
Compact surface plasma sources for heavy negative ion production (2004)

Features of a compact surface plasma source designed for heavy negative ion beam production are considered. Discharges in crossed E×B fields with hollow cathodes were used for efficient plasma generation. Production of heavy negative ion beams by plasma interaction with the surface of spherical focusing emitters made of different materials, such as copper and lanthanum hexaboride, with cesium catalysis are presented. The dynamics of emitter activation is discussed. dc ion beams with current up 0.9 mA have been extracted from the compact surface plasma sources with a 12-mm-diam LaB6 emitter and a emission aperture of 3 mm diam. Minimizing plasma and gas thickness between emitter and emission aperture is essential for minimizing negative ion destruction and maximizing high intensity beam production. A small mass analyzer and secondary ion mass spectroscopy were used to quantify boron ion yield. Presence of atomic and molecular boron negative ions is confirmed. The estimated emittance of the 0.5 mA heavy negative ion beam is ε=13 π mm mrad(MeV)1/2.
Bridge sciences (1973)

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<i>Erwinia chrysanthemi</i> <scp>l</scp>-asparaginase: epitope mapping and production of antigenically modified enzymes (1994)

This study shows that the antigenicity of Erwinia chrysanthemi L-asparaginase can be reduced by site-directed mutagenesis. Ten B-cell epitopes of the enzyme were identified using synthetic hexapeptides and polyclonal antisera from rabbits and mice. The region 282GIVPPDEELP292 near the C-terminus was an immunodominant epitope. Binding of two hexapeptides (283IVPPDE288 and 287DEELPG292) to the antibodies was dependent on Pro285, and Pro286, since their replacement by almost any other amino acid resulted in reduced binding. The other residues were less important for binding the antibodies, as binding was relatively unaffected by amino acid substitutions. Three site-directed mutant enzymes, P285T (proline-285-->threonine etc.), P286Q and E288A, were expressed in Escherichia coli. The purified enzymes had subunit M(r) values of 35,000. The pI values of P285T, P286Q and the wild-type enzymes were 8.6, and that for the mutant E288A was 9.2. The kcat. and Km values for the mutants P286Q and E288A with L-asparagine and L-glutamine were comparable with those of the wild-type enzyme. The Km values for the mutant P285T with both substrates was similar to that of the wild-type enzyme, whereas the kcat. was reduced by 2-fold with L-asparagine and by 4-fold with L-glutamine. The change proline-->threonine reduced the antigenicity of the enzyme by 8-fold, as shown in sandwich e.l.i.s.a.s. using monoclonal antibodies raised against the wild-type enzyme.
A Data Definition Facility Based on A Value-Oriented Storage Model (1980)

A data definition facility is presented that provides a consistent description of both primitive and user data. It is based on a value-oriented storage model which carefully distinguishes between values and objects. It is values that are typed in this model, and operations of the type work explicitly on the values. Objects are accessible only via reference values. Objects are described via descriptors called templates, which ultimately yield reference type values. Operations, both primitive and user-defined, are part of a “machine interface,” and all executable language constructs can ultimately be defined as explicit operations of the interface. Importantly, these operations must respect the typing constraints imposed by both the primitive types and the user extensions. The interactions of definition facility, storage model, and execution model are illustrated via a series of examples in which commonly user data constructs are defined.
Reconfigurable instruction interface architecture for private-key cryptography on the Altera Nios-II processor (2005)

This paper documents the development of a generic interface between the Altera Nios-II FPGA based soft-processor and a private key encryption core implementation. An existing AES encryption core was used for evaluation purposes. It was found that there was an overhead, relative to the time taken for the test encryption core, of between 40.0% and 72.7% dependent on the level of setup already taken, and the key length for the specific encryption operation. To the author's knowledge there has been no published non-algorithm specific interface to private-key encryption algorithms for use with 32-bit processors prior to the publication of this paper.
Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol (2013)

Assessing the distribution of 16S rRNA gene sequences within a biological sample represents the current state-of-the-art for determination of human gut microbiota composition. Advances in dissecting the microbial biodiversity of this ecosystem have very much been dependent on the development of novel high-throughput DNA sequencing technologies, like the Ion Torrent. However, the precise representation of this bacterial community may be affected by the protocols used for DNA extraction as well as by the PCR primers employed in the amplification reaction. Here, we describe an optimized protocol for 16S rRNA gene-based profiling of the fecal microbiota.
Constructing a Fuzzy Rule System from Examples (1999)

A general framework to construct fuzzy rule systems automatically from given examples is proposed in this paper. The objective is to generate fuzzy systems with good mapping ability and generalization ability as well. The procedure consists of five s
Stabilization of an Intermediate Activation State for Transducin by a Fluorescent GTP Analogue (2004)

The GTP-binding protein (G protein), transducin, serves as a key molecular switch in vertebrate vision through the tight regulation of its GTP-binding (activation)/GTP hydrolytic (deactivation) cycle by the photoreceptor rhodopsin. To better understand the structure-function characteristics of transducin activation, we have set out to identify spectroscopic probes that bind to the guanine nucleotide-binding site of this G protein and maintain its ability to interact with its specific cellular target/effector, the cyclic GMP phosphodiesterase (PDE). In this study, we describe the characterization of a fluorescently labeled GTP analogue, BODIPY-FL GTPgammaS (BOD-GTPgammaS), that binds to the alpha subunit of transducin (alpha(T)) in a rhodopsin- and Gbetagamma-dependent manner, similar to the binding of GTP or GTPgammaS, with an apparent dissociation constant of 100 nM. The rhodopsin-dependent binding of BOD-GTPgammaS to alpha(T) is slow, relative to the rate of binding of GTPgammaS, particularly under conditions where rhodopsin must act catalytically to stimulate the exchange of BOD-GTPgammaS for GDP on multiple alpha(T) subunits. This reflects a slower rate of dissociation of rhodopsin and Gbetagamma from alpha(T)-BOD-GTPgammaS complexes, relative to their rates of dissociation from alpha(T)-GTPgammaS. The binding of BOD-GTPgammaS occurs without a change in the intrinsic tryptophan fluorescence of alpha(T), indicating that only a subtle movement of the Switch 2 domain on alpha(T) accompanies the binding of this GTPgammaS analogue. Nevertheless, the BOD-GTPgammaS-bound alpha(T) subunit is able to bind with high affinity to the recombinant, purified gamma subunit of PDE (gamma(PDE)) labeled with 5-((((2-iodoacetyl)amino)ethyl)amino)naphthalene-1-sulfonic acid (IAEDANS (K(d) approximately 13 nM)), as well as bind to and stimulate the activity of PDE, albeit less efficiently compared to alpha(T)-GTPgammaS. Taken together, these findings suggest that the binding of BOD-GTPgammaS to transducin causes it to adopt a distinct conformation that appears to be intermediate between the inactive and fully active states of alpha(T), and this fluorescent nucleotide analogue can be used as a reporter group to characterize the interactions of alpha(T) in this conformational state with its biological target/effector.
The heterogeneous structure of polyurethane networks (1981)

Abstract Using small‐angle X‐ray scattering the microheterogeneous structure of amorphous polyurethane networks was investigated. It was found to be determined by the corresponding structural characteristics of the initial oligomeric diols. The structure of the oligomers is preserved more or less depending on their chain length in polymeric networks (poly(oxypropyleneglycol) with molecular weights of 2000 and 500 g/mol, resp.). In the latter case a great influence on the structure is exerted by rigid fragments around crosslinks which are characterized by great concentrations of H‐bonds. This is leading to a decrease in the heterogeneity. The heterogeneous structure of the polyurethane networks becomes more distinct with an increase in the oligomer chain length and degree of conversion. The observed effects are explained by the change in the degree of aggregation of parts of the network structure.
Serendipitous Formation of a Dinuclear Vanadium(III) Amide Complex Containing a Vanadaazacyclobutane Ring. Potassium−Hydrogen Agostic Interactions Holding Together a V<sub>2</sub>K<sub>2</sub>Tetrametallic Framework (1997)

Reaction of [(Me3Si)2N]2V(THF)Cl with KH led to the formation of the dinuclear {[(Me3Si)2N]2V[N(SiMe3)SiMe2CH2]}{K(THF)2}2 (1), whose structure was determined by X-ray analysis. The dinuclear framework is held together via K−H agostic interactions.
[Intravenous enoximone versus conventional treatment in acute lung edema. Preliminary results of a randomized study]. (1990)

The aim of this open study was to compare the efficacy of Enoximone and conventional treatment in 44 patients with acute pulmonary edema. At the time of this interim analysis, 22 patients had received Enoximone (1 mg/kg by rapid intravenous injection every 8 hours for 48 hours) and 22 were given conventional treatment (furosemide, nitrates, dopamine-dobutamine). The treatment schedules were randomised. Clinical data was obtained at 0, 1, 2, 24 and 48 hours and evaluated using the Killip-Kimball score, dyspnoea, pulmonary rales, the need for additional therapy and patient mortality. The patients in the two groups were comparable in all clinical features except the sex ratio. The improvement of all clinical criteria of evaluation seemed to be greater in the Enoximone group, except during the first hour of treatment (due to the action of diuretics). The overall outcome was better in the Enoximone group (17 favourable responses compared to 11 in the group receiving conventional treatment). Normalisation of haemodynamic parameters was observed only with Enoximone. In addition, it became necessary to administer Enoximone to 9 patients in the conventional treatment group. At these doses, Enoximone was at least as effective as conventional treatment of acute pulmonary edema. What is more, no secondary effects or tachyphylaxis were observed during the period of hospital treatment.
Modelling and performance analysis of DOA estimation in adaptive signal processing arrays (2004)

This paper presents a simulation tool for direction-of-arrival (DOA) estimation in adaptive signal processing arrays. The tool implements the multiple signal classification (MUSIC) DOA algorithm. A user-friendly graphical user interface (GUI) is also developed. In addition to its usefulness in the design and analysis of adaptive signal processing arrays, the tool can also be used for computer-aided learning of modem communication systems utilizing smart antennas. To demonstrate the versatility and accuracy of the developed tool, it is used to carry out a detailed performance analysis of DOA estimation using MUSIC. This includes investigating the effect of the number of mobile users and their spatial distribution, the number of array elements and their spacing, and the number of signal snapshots.
Gene Expression Profiling and FLT3 Status Correlate with Outcome in De Novo Acute Myeloid Leukemia (AML) with Normal Karyotype: Results of Children’s Oncology Group (COG) Study POG #9421. (2005)

Abstract The event-free survival (EFS) estimate for patients with normal karyotype (NK) on COG study POG #9421 (n=144) was 36%. We previously reported a subgroup of patients (n=68) with AML and NK that could be divided into 2 groups whose clinical outcomes correlated with abnormalities of FLT3 [internal tandem duplications (ITD) or activating loop mutations]. EFS estimates were 13% for patients with mutant FLT3 and 61% for children with wild-type FLT3 (P=0.01). We hypothesized that gene expression profiling would identify signatures that are linked to clinical outcome and can be used for risk determination. Cytogenetic testing was carried out in clinical laboratories at the institutions in which AML was diagnosed and then centrally reviewed. We analyzed bone marrow from 45 patients with NK on 43,760-element spotted arrays containing 41,751 unique genes and expressed sequence tags; arrays were obtained from the Stanford University Microarray Core Facility. FLT3 status (mutant or wild type) was determined by RT-PCR analysis of RNA from these 45 samples (exon 11 for ITDs, exon 17 for point mutations): 18 expressed mutant FLT3, 27 expressed wild-type FLT3. Using prediction analysis for microarrays (PAM) to find the minimum number of genes that identified samples associated with and unassociated with events (relapse or death), we identified a 128 gene cluster that differentiated patients with NK on the basis of clinical outcome (classification error rates were 15% for samples associated with events and 12.5% for event-unassociated samples). Significance analysis of microarrays (SAM) identified, with a false-discovery rate of 1.25%, 82 genes in the cluster whose expression differed significantly between the event-associated samples and the event-unassociated samples. Hierarchical clustering based on these 82 genes yielded 2 signatures: one event-associated and one event-unassociated. FLT3 Status Event-Associated Signature Event-Unassociated Signature Wild-type EFS=44% (n=15) EFS=90% (n=12) Mutant EFS=7% (n=13) EFS=60% (n=5) The median WBC counts at the time of diagnosis were 68 x 109/L in the event-associated group and 61 x 109/L in the event-unassociated group (P=0.27). The gene list and d-scores from SAM analysis were analyzed using Ingenuity Pathway Analysis software (Ingenuity™ Systems, Mountain View, CA). Canonical pathways associated with poor outcome included apoptosis signaling (↑BCL2A1, ↓BAK1), ERK/MAP signaling (↑RAC2), cell cycle (↓ABL1), SAPK/JNK signaling (↑RAC2, ↓CDC42), integrin signaling (↑RAC2, ↓BCAR3, ↓ABL1, ↓CDC42), and IL6 signaling (↑IL6R). We conclude that risk assignment for patients with NK can be more precisely determined by combining FLT3 analysis and gene expression profiling. Such an approach identified 4 distinct groups with different outcomes. We will validate these findings by analyzing additional diagnostic samples with normal karyotype. Prospective validation of this strategy in clinical trials may be warranted.
Preparation, isolation, and characterization of permethylated galactosides and fucosides (1999)

Sugar analysis involving permethylation followed by methanolysis can lead to significant results, given that permethylated monosaccharide standards are available for comparison of spectral and chromatographic data. Such standards are not readily commercially available, especially the furanoside forms. This note describes the isolation and characterization of permethylated pyranoside and furanoside species of D(+)-galactose and L(-)-fucose. Separation of the isomers was optimized using a combination of column chromatography and continuous elution thin-layer chromatography (TLC). TLC, gas chromatography - mass spectrometry, and 1 H nuclear magnetic resonance (NMR) spectroscopy were used as the characterization methods. The isolation of furanosides is emphasized, since no specific NMR data have been reported on those to date, while several reports have already discussed the structural aspects of pyranosides.Key words: permethylation, monosaccharide, GC-MS, TLC, NMR.
Stick-Slip Vibrations in Violin Strings (2018)

The vibrations of a bowed violin string have been studied since the 19th century. The string was found to oscillate in a simple triangular pattern described by Helmholtz. Today these vibrations are known as stick and slip vibrations caused by friction and have been studied by many researchers. Stick-slip vibrations are self-sustained oscillations induced by dry friction. The theoretical analysis of stick-slip vibrations was solved by Cellular Automaton Method during prior research. However, it is not solved by Modal Analysis Method. In this research, stick-slip vibration is solved by Modal Analysis Method. At the time of slip, as a result of the simulation, it was possible to obtain results by Modal Analysis Method which is reasonable compared with Cellular Automaton Method.
In vivo model of intracranial stent implantation: a pilot study to examine the histological response of cerebral vessels after randomized implantation of heparin-coated and uncoated endoluminal stents in a blinded fashion (2003)

This in vivo intracranial stent model was developed to assess proliferative and inflammatory responses to endoluminal stent implantation in the cerebrovasculature. The results indicate that a lower percentage of occlusion occurs 12 weeks after implantation of heparin-coated compared with uncoated stents.
Comparing similarity calculation methods in conversational CBR (2005)

Conversational case-based-reasoning (CCBR) provides a mixed-initiative dialog for guiding users to construct their problem description incrementally through a question-answering sequence. Similarity calculation in CCBR, as in traditional CBR, plays an important role in the retrieval process since it decides the quality of the retrieved case. In this paper, we analyze the different characteristics of the query (new case) between CCBR and traditional CBR, and argue that the similarity calculation method that only takes the features appearing in the query into account, so called query-biased, is more suitable for CCBR. An experiment is designed and executed on 36 datasets. The results show us that on 31 datasets out of the total 36, the CCBR system using the query-biased similarity calculation method achieves more effective performance than those using case-biased and equally-biased similarity calculation methods.
Safety of a new, single, integrated, closed photopheresis system in patients with cutaneous T-cell lymphoma (2009)

This new ECP system provides lower extracorporeal volumes, faster treatment times, and flexibility to use either single- or dual-needle access, while not being associated in this study with any ADEs, and therefore having a positive benefit-risk ratio for patients with CTCL.
Characterization of Solid-Phase Epitaxially-Grown Silicon Films on SiO<sub>2</sub> (1984)

Lateral solid-phase epitaxial (L-SPE) films of vacuum-deposited Si on SiO 2 have been examined, mainly through TEM observation, and compared with (100) vertical solid-phase epitaxial (V-SPE) films. Typical defects in L-SPE layers with a rough growth front are high-density twins and dislocations, which are generated regardless of whether the films are <100> or <110> laterally-grown films. On the other hand, in V-SPE layers containing low-density short dislocations, {111} and {110} facets are formed at the <110> and <100> directed oxide window edges, respectively. The facets are thought to act as a barrier for the change from V-SPE to L-SPE across the SiO 2 edge. Successive 1050°C high-temperature heat treatment generates interstitial-type faulted and unfaulted dislocation loops in Si + ion implanted V-SPE layers. This is in contrast to the reduced dislocation density resulting in L-SPE layers containing no residual amorphous regions after the first 600°C annealing.
Letter to the Editor Fractional flow reserve — The influence of the collateral circulation (2009)

Fractional flow reserve (FFR) is a widely used invasive index of coronary artery stenosis. FFR is not influenced by haemodynamic parameters (such as blood pressure and pulse rate) or by the vessel studied. However, true FFR value may be influenced by the presence of major collateral vessels. In this article we describe a case demonstrating this observation and discuss a potential physiological mechanism to account for this finding. © 2007 Elsevier Ireland Ltd. All rights reserved. A 77 year old man with a short history of stable exertional angina (CCS 2) underwent cardiac catheterisation. His risk factors for vascular disease included hypertension and type II diabetes mellitus. He had no other past medical history. Diagnostic angiography demonstrated well-preserved left ventricular (LV) systolic function (ejection fraction 65%) and significant three vessel coronary artery disease. The left anterior descending (LAD) and left circumflex (LCx) arteries both had moderate midvessel stenosis and the right coronary (RC) artery had a proximal functional occlusion. The distal RC artery vascular bed was perfused via well-established collaterals from the distal LAD artery. The management strategy adopted was to initially attempt percutaneous des-occlusion of the proximal RC artery. If successful the patient would in turn undergo fractional flow reserve-guided (FFR-guided) percutaneous intervention (PCI) to the LCx and LAD arteries. Coronary artery bypass graft (CABG) surgery would be adopted in the event that PCI to the proximal RC artery was not successful. FFR was measured as partofthediagnosticprocedureandwas0.75inthedistalLAD (Fig.1, Panel A)and 0.72inthe distalLCx artery (FFR ≥0.80