gebhart/patrepeval huggingface dataset:
es of Ribonuclease A in H20 (2016)

A resonance (designated a) due to an exchangeable proton titrates (pKa = 6.1) between 11.5 and 13 ppm in the nuclear magnetic resonance spectrum of RNase A-0.2 M NaCl in H20 at 20?. Comparison with models has permitted assignment to a ring-nitrogen proton of histidine in slow exchange with solvent H20. The pH and temperature-dependent line-width changes of resonance a are analyzed in terms of an exchange between histidine and protonated histidine, without the necessity to invoke any exchange processes associated with protein conformational changes. Several other resonances due to exchangeable protons are observed between 10 and 15 ppm in the nuclear magnetic resonance spectrum of RNase A in H20.
Partial characterization of natural and recombinant human soluble CD23 (1992)

The purification to homogeneity of an active soluble 25 kDa fragment of CD23, produced in insect cells using the baculovirus expression system, is described. Peptide mapping and analysis by Edman degradation and mass spectrometry permitted partial characterization of the protein. A total of 165 out of 172 residues, including N-terminal and C-terminal regions, were mapped. The positions of the two disulphide bonds in the IgE-binding region were also determined: residue 110 is joined to residue 124, and residue 42 to residue 133. Natural CD23 25 kDa fragment was also analysed and found to possess the same disulphide bond arrangement. These results extend the previously noted sequence similarity with lectins to elements of secondary structure.
Theory of polymer ablation (1988)

A new formula is presented for the etch depth l per pulse of an excimer laser of fluence F. Incremental ablation is defined as the etch depth per pulse after many pulses. We show that l is proportional to F, rather than ln(F).
[Ca2+]i oscillations regulate type II cell exocytosis in the pulmonary alveolus (2000)

Pulmonary surfactant, a critical determinant of alveolar stability, is secreted by alveolar type II cells by exocytosis of lamellar bodies (LBs). To determine exocytosis mechanisms in situ, we imaged single alveolar cells from the isolated blood-perfused rat lung. We quantified cytosolic Ca(2+) concentration ([Ca(2+)](i)) by the fura 2 method and LB exocytosis as the loss of cell fluorescence of LysoTracker Green. We identified alveolar cell type by immunofluorescence in situ. A 15-s lung expansion induced synchronous [Ca(2+)](i) oscillations in all alveolar cells and LB exocytosis in type II cells. The exocytosis rate correlated with the frequency of [Ca(2+)](i) oscillations. Fluorescence of the lipidophilic dye FM1-43 indicated multiple exocytosis sites per cell. Intracellular Ca(2+) chelation and gap junctional inhibition each blocked [Ca(2+)](i) oscillations and exocytosis in type II cells. We demonstrated the feasibility of real-time quantifications in alveolar cells in situ. We conclude that in lung expansion, type II cell exocytosis is modulated by the frequency of intercellularly communicated [Ca(2+)](i) oscillations that are likely to be initiated in type I cells. Thus during lung inflation, type I cells may act as alveolar mechanotransducers that regulate type II cell secretion.
Factors Affecting Adherence to Antiretroviral Therapy in People Living with HIV/AIDS (2003)

Antiretroviral treatments have given hope to people living with HIV/AIDS and play a role in improving their quality of life. However, the effectiveness of these treatments is directly related to the level of adherence and commitment to them. Researchers have demonstrated that there are many factors that play an important role in adopting and maintaining adherence behavior. In this article, the authors present an indepth review of the literature and from this, enumerate the factors that link adherence behavior to the individual, the treatment, the illness, and the relationship with the health professional. An understanding of these factors is essential to develop interventions that will improve adherence to therapeutic regimens among people with HIV/AIDS.
Pentavalent Arsenate Transport by Zebrafish Phosphate Transporter NaPi-IIb1 (2011)

Arsenate is a pentavalent form of arsenic that shares similar chemical properties to phosphate. It has been shown to be taken up by phosphate transporters in both eukaryotic and prokaryotic microbes such as yeast and Escherichia coli. Recently, the arsenate uptake in vertebrate cells was reported to be facilitated by mammalian type II sodium/phosphate transporter with different affinities. As arsenate is the most common form of arsenic exposure in aquatic system, identifying the uptake pathway of arsenate into aquatic animals is a crucial step in the elucidation of the entire metabolic pathway of arsenic. In this study, the ability of a zebrafish phosphate transporter, NaPi-IIb1 (SLC34a2a), to transport arsenate was examined. Our results demonstrate that a type II phosphate transporter in zebrafish, NaPi-IIb1, can transport arsenate in vitro when expressed in Xenopus laevis oocytes. NaPi-IIb1 mediates a high-affinity arsenate transport, with a K(m) of 0.22 mM. The natural substrate of NaPi-IIb1, dibasic phosphate, inhibits arsenate transport. Arsenate transport via NaPi-IIb1 is coupled with Na(+) and exhibits sigmoidal kinetics with a Hill coefficient of 3.24 ± 0.19. Consistent with these in vitro studies, significant arsenate accumulation is observed in all examined zebrafish tissues where NaPi-IIb1 is expressed, particularly intestine, kidney, and eye, indicating that zebrafish NaPi-IIb1 is likely the transport protein that is responsible for arsenic accumulation in vivo.
Multivariate sensory characteristics of low and ultra‐low linolenic soybean oils displayed as faces (2003)

Abstract The effects of linolenic acid (18∶3) concentration, combined with IBHQ addition, temperature, and storage time, on the flavor stability of soybean oils (SBO) were evaluated. A descriptive panel was trained to evaluate the overall oil quality and the intensity of individual flavors of SBO during 12 mon of storage under fluorescent light at both 21 and 32°C. Chernoff faces were used to achieve a simplified and integrated interpretation of the multivariate sensory data and to facilitate the interpretation of the vast amount of the data. In early storage, SBO with low 18∶3 (2.2% 18∶3, LLSBO) showed better flavor stability than did SBO with ultra‐low 18∶3 (1.0% 18∶3, ULSBO). This trend disappeared during storage. During 10‐ to 12‐mon storage, a painty flavor became predominant in all oils, which may have made it difficult for panelists to detect differences in treatment effect on flavor characteristics of SBO. During early storage, oils with TBHQ addition had poorer overall oil quality and stronger beany, painty, and fishy flavors than did oils without TBHQ addition. This trend disappeared as storage time progressed to 10 mon. Oils storedat 32°C had poorer overall oil quality and stronger painty, fishy, and beany flavors than did oils stored at 21°C starting from 2‐mon storage.
Skimmilk Solids as Substrate for the Preparation of Casein Enzymatic Hydrolysates (1995)

ABSTRACT The time‐course hydrolysis curves of low‐heat (LH) and high‐heat (HH) skimmilk powders (SMP) by trypsin or chymotrypsin were compared to that of sodium caseinate (SC). Rates of hydrolysis, shown to be different (P &lt; 0.05), were SC &gt; LH‐SMP &gt; HH‐SMP. A two‐step ultrafiltration process was applied to hydrolyzed LH‐SMP and to hydrolyzed SC, and results were compared. Protein and lactose composition differences between LH‐SMP and SC were accentuated by ultrafiltration. The hydrolysis profile (molecular weight distribution of peptides, amino acid content) of LH‐SMP tryptic hydrolysate showed a greater proportion of short peptides (&lt;2000 Daltons) and a lower content in GLU, PRO, VAL and TYR, compared to that of SC.
DWDM data receiver based on monolithic integration of an echelle grating demultiplexer and waveguide photodiodes (2005)

A practical approach for the design and manufacture of a monolithically integrated, multiple wavelength data receiver is presented. It utilises an InP-based, birefringence compensated echelle grating demultiplexer and high speed, singlemode, vertically integrated waveguide photodiodes. As an example of this approach, a 32-channel, C-band, polarisation independent data receiver chip operating at OC-3 (155 Mbit/s) bit rate is demonstrated with a compact footprint of 5×16 mm.
Input Data Representation for Self-Organizing Map in Software Classification (2009)

A self-organizing map (SOM) is used to classify software documents and the associated software components with the aim to facilitate software reuse. SOM learns from input stimuli rather than training data, therefore the quality of input data representation is crucial to the success of SOM. In this paper, we use automatic indexing method to represent a document collection as the input data to train a SOM. The automatic indexing uses a phrase formation method to promote precision and a domain dependent relational thesaurus to enhance recall. A retrieval experiment based on a document collection containing 97 Unix manual pages was conducted to evaluate the effectiveness of this input data representation scheme. Promising retrieval results were observed.
1,2,5,6-Tetramethylenecyclo-octane (1970)

W. T. Borden, L. Sharpe and I. L. Reich, J. Chem. Soc. D, 1970, 461 DOI: 10.1039/C29700000461
A mild and efficient synthesis of chloroesters by the cleavage of cyclic and acyclic ethers using Bi(NO3)3·5H2O as a catalyst under solvent-free conditions (2007)

A facile, efficient synthesis of chloroesters is described. The reaction of cyclic and acyclic ethers with acid chlorides in the presence of catalytic amounts of Bi(NO 3 ) 3 ·5H 2 O under solvent-free conditions yielded the corresponding chloroesters. Also, the catalyst can be recovered conveniently and reused efficiently for at least six times.Key words: Bismuth(III) nitrate pentahydrate, cyclic and acyclic ethers, chloroesters.
Accelerated Mission Tests and Reliability Improvement of F3-30 Engine (1990)

F3-30 is the low-bypass-ratio turbofan engine which has been developed to power the T-4 intermediate trainer for the Japan Air Self Defence Force (JASDF). The qualification tests of the engine were successfully completed in March, 1986, and the actual field service was started in September, 1988. Before the start of the actual use, accelerated mission tests (AMT) were conducted for the purpose of finding deficiencies which would occur in the actual mission usage, and verifying the time between overhaul (TBO) of the initial service. This paper describes the test method, the results, and the evaluation for them. Also it presents current status and basic ideas for the future reliability improvement of the F3-30 engine.
Subunit structure of external invertase from Saccharomyces cerevisiae. (1977)

Because 50% of the mass of the external invertase of Saccharomyces cerevisiae consists of carbohydrate, it has been extremely difficult to obtain an accurate molecular weight of this enzyme by centrifugal or electrophoretic techniques. However, on removing almost all of the oligosaccharide chains of this enzyme with the endo-beta-N-acetyl-glucosaminidase H from Streptomyces plicatus, it has been possible to show that carbohydrate-free invertase is composed of two 60,000-dalton subunits. Terminal sequence analysis with carboxypeptidases A, B, and Y provided strong evidence that the subunits are identical.
Effect of Yttrium Aluminum Garnet Additions on Alumina‐Fiber‐Reinforced Porous‐Alumina‐Matrix Composites (2004)

The effects of incorporating yttrium aluminum garnet (YAG) into a porous alumina matrix reinforced with Nextel 610 alumina fibers were investigated. Composites with various amounts of YAG added to the matrix were prepared to determine its effect on retained tensile strengths after heating to 1100° and 1200°C. Strengths of YAG‐containing composites were slightly lower than those of an all‐alumina‐matrix composite after heating for 5 h to 1100°C. However, after heating for 5 or 100 h at 1200°C, all the YAG‐containing composites displayed greater strengths and greater strains to failure than the all‐alumina composite. At the higher temperature, the presence of YAG is believed to inhibit the densification of the matrix, which helps to maintain higher levels of porosity and weaker interparticle bonding that allows for crack‐energy dissipation within the matrix. A reduction in grain growth of the fibers by the presence of segregated Y was also observed, which may also contribute to higher fiber strength, thereby increasing the retained strengths of the YAG‐containing composites.
Dense Tactile Force Estimation using GelSlim and inverse FEM (2019)

In this paper, we present a new version of tactile sensor GelSlim 2.0 with the capability to estimate the contact force distribution in real time. The sensor is vision-based and uses an array of markers to track deformations on a gel pad due to contact. A new hardware design makes the sensor more rugged, parametrically adjusTable AND Improves illumination. leveraging the sensor's increased functionality, we propose to use inverse finite element method (ifem), a numerical method to reconstruct the contact force distribution based on marker displacements. the sensor is able to provide force distribution of contact with high spatial density. experiments and comparison with ground truth show that the reconstructed force distribution is physically reasonable with good accuracy.A sequence of Kendama manipulations with corresponding displacement field (yellow) and force field (red). Video can be found on Youtube: https://youtu.be/hWw9A0ZBZuU.
Molecular cloning of rat sperm galactosyl receptor, a C-type lectin with in vitro egg binding activity (2000)

Rat sperm galactosyl receptor is a member of the C-type animal lectin family showing preferential binding to N-acetylgalactosamine compared to galactose. Binding is mediated by a Ca(2+)-dependent carbohydrate-recognition domain (CRD) identical to that of the minor variant of rat hepatic lectin receptor 2/3 (RHL-2/3). The molecular organization of the genomic DNA, cDNA, and derived amino acid sequence of rat testis galactosyl receptor have been determined and in vitro fertilization studies were conducted to ascertain its role. We have determined that the rat testis galactosyl receptor gene generates two mRNA species: one species, designated liver-type, is identical to RHL-2/3; the other, designated testis-type, contains one unspliced intron (86 nt) which alters the reading frame and changes the amino acid sequence of the carboxyl terminus. As a result, the CRD (glutamine-proline-aspartic acid/QPD) and flanked Ca(2+)-binding amino acid sequences were not present in the testis-type protein. Northern and Southern blots demonstrated presence of transcripts with unspliced intron in rat sperm but not liver. Similarly, antibody, raised against a synthetic 12-amino acid peptide (p12) encoded by the unspliced intron, recognized in immunoblots a 54 kDa receptor protein in protein extracts from testis but not from liver. Immunofluorescence and immunogold electron microscopy studies demonstrated that both protein species localized on the plasma membrane surface of the head and tail of rat sperm. Furthermore, capacitated rat sperm preincubated with polyclonal antisera to RHL-2/3 or to the CRD of the liver-type galactosyl receptor showed a statistically significant decrease in the in vitro fertilization rate. We conclude that rat sperm galactosyl receptor may play a role in egg binding and that an undetermined molecular mechanism operates to generate two proteins with identical intracellular amino terminal domain but only one of them displays a CRD and associated Ca(2+)-binding sites at the carboxyl terminal extracellular domain.
Expression of interleukin‐6 in osteoarthritic chondrocytes and effects of fluid‐induced shear on this expression in normal human chondrocytes in vitro (1996)

This study tested the effect of fluid-induced shear on interleukin-6 expression in normal human articular chondrocytes in vitro. As determined by Northern blot analysis, interleukin-6 mRNA expression occurs in chondrocytes from osteoarthritic cartilage but not in normal chondrocytes. Applying fluid-induced shear stress to primary high density cultures of chondrocytes increased interleukin-6 mRNA signal 4-fold at 1 hour and 10 to 15-fold at 48 hours compared with unsheared control cultures. At 48 hours, fluid-induced shear stress increased interleukin-6 protein levels in the culture medium 9 to 10-fold compared with unsheared controls. mRNA signals for interleukin-1alpha, interleukin-1beta, and tumor necrosis factor-alpha in RNA from sheared or control chondrocytes were not detected by Northern blotting. Transforming growth factor-beta mRNA signal was detectable but was not affected by shear. In contrast, human lung fibroblasts (WI-38) responded to fluid-induced shear with increased signal for transforming growth factor-beta, but not interleukin-6, mRNA. Both cell types did respond to interleukin-1alpha with increased interleukin-6 mRNA signal. These data demonstrated that distortional forces, such as fluid-induced shear stress, alter interleukin-6 levels in normal chondrocytes in vitro and suggest that increased interleukin-6 expression in osteoarthritic cartilage may result, in part, from alterations in the mechanical loading of the tissue.
Computational Modeling Aspects of Light Propagation in Biological Tissue for Medical Applications (2013)

Near-eld scanning optical microscopy (NSOM/SNOM) is a microscopy technique for nanostructure investigation that breaks the far-eld resolution limit by exploiting the properties of evanescent waves with lateral resolution of 20 nm and vertical resolution of 2-5 nm that have been demonstrated. However, the current widely used NSOM probe by metal-coated tapered optical ber has intrinsic disadvantage of conning light in an inefcient manner due to its strong light propagation mode mismatch at the tip aperture. In this book chapter we propose a novel light-conning probe of the combination by the embedded metallic grating coupler and photonic crystal (PhC) slotted waveguide onCONTENTS7.1 Introduction ........................................................................................................................ 261 7.2 Design of Embedded Metal Focus Grating Coupler ..................................................... 2637.2.1 Analysis of the Etched Dielectric Grating Coupler ...........................................264 7.2.2 Ag and Au Dispersion Optical Properties ......................................................... 267 7.2.3 Compact Embedded Metallic Focus Grating Coupler Overview ................... 269 7.2.4 2D FDTD Analysis of the Embedded Grating Coupler .................................... 2707.3 Far-Field Radiation Pattern of the Embedded Metal Focus Grating Coupler ........... 271 7.3.1 Optical Antenna Theory ....................................................................................... 271 7.3.2 3D Directivity Analysis ......................................................................................... 2727.4 Design of Slotted Photonic Crystal Nano-Resonator for Near-Field Light Focusing ........................................................................................2767.5 Biological Applications ..................................................................................................... 279 7.5.1 Grating Coupler ..................................................................................................... 279
Consistency matrices: Quantified structure alignments for sets of related proteins (2003)

Comparing two remotely similar structures is a difficult problem: more often than not, resulting structure alignments will show ambiguities and a unique answer usually does not even exist. In addition, alignments in general have a limited information content because every aligned residue is considered equally important. To solve these issues to a certain extent, one can take the perspective of a whole group of similar structures and then evaluate common structural features. Here, we describe a consistency approach that, although not actually performing a multiple structure alignment, does produce the information that one would conceivably want from such an experiment: the key structural features of the group, e.g., a fold, which in this case are projected onto either a pair of proteins or a single protein. Both representations are useful for a number of applications, ranging from the detection of (partially) wrong structure alignments to protein structure classification and fold recognition. To demonstrate some of these applications, the procedure was applied to 195 SCOP folds containing a total of 1802 domains sharing very low sequence similarity.
A traceability system for beef products based on radio frequency identification technology in China (2007)

Abstract Radio frequency identification (RFID) technology is an automatic identification and data capture (AIDC) technique and it is the representative technology for handling beef traceability. In this paper we offer a complete solution including: frequency, identifier information system, information system, data organisation, tag reclaimation and control technology, from three segments of the beef production process in China. From the farm to the slaughterhouse, electronic identification ear tag technology was used to identify the individual animal. From the slaughterhouse to the processing plant, gambrel identification was used to transfer the carcass information from the “old ear tag” to a “new ear tag”. Last, gambrel RFID was converted to UCC/EAN‐128 barcode labelling with a wireless electronic scale. The whole solution was evaluated successfully in Beijing.
HDAC6 deacetylation of tubulin modulates dynamics of cellular adhesions (2007)

Genetic or pharmacological alteration of the activity of the histone deacetylase 6 (HDAC6) induces a parallel alteration in cell migration. Using tubacin to block deacetylation of alpha-tubulin, and not other HDAC6 substrates, yielded a motility reduction equivalent to agents that block all NAD-independent HDACs. Accordingly, we investigated how the failure to deacetylate tubulin contributes to decreased motility in HDAC6-inhibited cells. Testing the hypothesis that motility is reduced because cellular adhesion is altered, we found that inhibiting HDAC6 activity towards tubulin rapidly increased total adhesion area. Next, we investigated the mechanism of the adhesion area increase. Formation of adhesions proceeded normally and cell spreading was more rapid in the absence of active HDAC6; however, photobleaching assays and adhesion breakdown showed that adhesion turnover was slower. To test the role of hyperacetylated tubulin in altering adhesion turnover, we measured microtubule dynamics in HDAC6-inhibited cells because dynamic microtubules are required to target adhesions for turnover. HDAC6 inhibition yielded a decrease in microtubule dynamics that was sufficient to decrease focal adhesion turnover. Thus, our results suggest a scenario in which the decreased dynamics of hyperacetylated microtubules in HDAC6-inhibited cells compromises their capacity to mediate the focal adhesion dynamics required for rapid cell migration.
Erratum: Control of Raman Lasing in the Nonimpulsive Regime [Phys. Rev. Lett.92, 243003 (2004)] (2005)

Received 20 April 2005DOI:https://doi.org/10.1103/PhysRevLett.94.209901©2005 American Physical Society