gebhart/patrepeval huggingface dataset:
High performance capillary electrophoresis of casein phosphopeptides containing 2‐5 phosphoseryl residues: Relationship between absolute electrophoretic mobility and peptide charge and size (1995)

Abstract Multiple phosphoseryl‐containing peptides from casein containing the cluster sequence ‐Ser( P )‐Ser( P )‐Ser( P )‐Glu‐Glu‐ stabilize amorphous calcium phosphate at neutral and alkaline pH and have been shown to be anticariogenic in various in vitro , animal and human experiments. In an approach to obtain insight into the structure and function of these peptides, we previously developed a method for their analysis using high‐performance capillary electrophoresis (HPCE). A linear relationship was obtained between absolute electrophoretic mobility and q/M 2/3 where q is the net negative charge of the peptide calculated using relevant p K a values and M is the molecular mass. M 2/3 is a measure of the surface area of a sphere that has a volume proportional to the M of the peptide and relates to the frictional drag exerted on the peptide during electrophoretic migration. To examine this relationship further, we have analyzed a range of high‐performance liquid chromatography (HPLC)‐purified cluster, di‐ and triphosphorylated peptides from casein enzymic (trypsin, alcalase and pancreatin) digests using HPCE and attempted to relate their absolute electrophoretic mobility to various models incorporating peptide size and charge. Absolute electrophoretic mobility of casein phosphopeptides containing the cluster sequence‐Ser( P )‐Ser( P )‐Ser( P )‐Glu‐Glu‐ was most closely correlated with q/M 2/3 . Di‐ and triphosphorylated peptide absolute electrophoretic mobility correlated with both q/M 2/3 and In( q +1)/ n 0.43 . However, for both the q/M 2/3 and In( q +1)/ n 0.43 relationships with absolute electrophoretic mobility, the di‐ and triphosphorylated peptides formed a separate linear relationship to that of the cluster peptides. From these relationships, a di‐ or triphosphorylated peptide exhibited a greater absolute electrophoretic mobility than a corresponding cluster peptide with the same q/M 2/3 or In( q +1)/ n 0.43 value. This implies that the cluster peptides have a reduced effective net negative charge due to an electrical double layer effect and/or a larger hydrodynamic volume or a more extended structure relative to the di‐ and triphosphorylated peptides which is associated with a greater frictional drag during electrophoretic migration.
Real-Time Infrared Overtone Laser Control of Temperature in Picoliter H2O Samples: “Nanobathtubs” for Single Molecule Microscopy (2010)

An approach for high spatiotemporal control of aqueous sample temperatures in confocal microscopy is reported. This technique exploits near-IR diode-laser illumination to locally heat picoliter volumes of water via first-overtone excitation in the OH-stretch manifold. A thin water cell after the objective resonantly removes any residual IR light from the detection system, allowing for continuous observation of single-molecule fluorescence throughout the heating event. This technique is tested quantitatively by reproducing single-molecule RNA folding results obtained from "bulk" stage heating measurements. Calibration of sample temperatures is obtained from time-correlated single-photon counting studies of Rhodamine B fluorescence decay. We obtain an upper limit to the heating response time (τ(heat) < 20 ms) consistent with even faster estimates (τ(heat) ≈ 0.25 ms) based on laser spot size, H(2)O heat capacit,y and absorption cross section. This combination of fast, noncontact heating of picoliter volumes provides new opportunities for real-time thermodynamic/kinetic studies at the single-molecule level.
First principle prediction of half metallic ferromagnetism in Heusler NiMnZ (Z = P,Ge) compounds (2011)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Mukhtiyar Singh, Hardev Singh, Manish K. Kashyap; First principle prediction of half metallic ferromagnetism in Heusler NiMnZ (Z = P,Ge) compounds. AIP Conf. Proc. 12 December 2011; 1393 (1): 165–166. https://doi.org/10.1063/1.3653661 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Clinical diagnosis for discogenic low back pain (2009)

Discogenic lower back pain (DLBP) is the most common type of chronic lower back pain (LBP), accounting for 39% of cases, compared to 30% of cases due to disc herniation, and even lower prevalence rates for other causes, such as zygapophysial joint pain. Only a small proportion (approximately 20%) of LBP cases can be attributed with reasonable certainty to a pathologic or anatomical entity. Thus, diagnosing the cause of LBP represents the biggest challenge for doctors in this field. In this review, we summarize the process of obtaining a clinical diagnosis of DLBP and discuss the potential for serum-based diagnosis in the near future. The use of serum biomarkers to diagnose DLBP is likely to increase the ease of diagnosis as well as produce more accurate and reproducible results.
Performance of alternate routing methods in all-optical switching networks (2002)

We study routing methods in all-optical switching networks. In all-optical switching networks, the connection with more hops encounters more call blocking, and it is especially true in optical networks with no wavelength conversions. We therefore consider an alternate routing method with limited trunk reservation in which connections with more hops are prepared more alternate routes. Through developing an approximate analytic approach, we show that our method keeps good performance when compared with the existing alternate routing methods, and also that the fairness among connections can be improved. Further performance improvement is investigated by introducing a wavelength assignment policy and a dynamic routing method. An effectiveness of the proposed method is investigated through simulation.
A newly discovered gene, tfuA, involved in the production of the ribosomally synthesized peptide antibiotic trifolitoxin (1996)

Trifolitoxin (TFX) is a gene-encoded, posttranslationally modified peptide antibiotic. Previously, we have shown that tfxABCDEFG from Rhizobium leguminosarum bv. trifolii T24 is sufficient to confer TFX production and resistance to nonproducing strains within a distinct taxonomic group of the alpha-proteobacteria (E. W. Triplett, B. T. Breil, and G. A. Splitter, Appl. Environ. Microbiol. 60:4163-4166, 1994). Here we describe strain Tn5-2, a Tn5 mutant of T24 defective in the production of TFX, whose insertion maps outside of the tfx cluster. It is not altered in growth compared with T24, nor does it inactivate TFX in its proximity. The wild-type analog of the mutated region of Tn5-2 was cloned. Sequencing, transcriptional fusion mutagenesis, and subcloning were used to identify tfuA, a gene involved in TFX production. On the basis of computer analysis, the putative TfuA protein has a mass of 72.9 kDa and includes a peroxidase motif but no transmembrane domains. TFX production studies show that extra copies of the tfxABCDEFG fragment increase TFX production in a T24 background while additional copies of tfuA do not. Lysate ribonuclease protection assays suggest that tfuA does not regulate transcription of tfxA. Upstream of tfuA are two open reading frames (ORFs). The putative product of ORF1 shows high similarity to the LysR family of transcriptional regulators. The putative product of ORF2 shows high similarity to the cytosine deaminase (CodA) of Escherichia coli.
Rapid identification of Salmonella serovars in feces by specific detection of virulence genes, invA and spvC, by an enrichment broth culture-multiplex PCR combination assay (1996)

In order to make a rapid and definite diagnosis of Salmonella enteritis in children, an enrichment broth culture-multiplex PCR combination assay was devised to identify Salmonella serovars directly from fecal samples. Two pairs of oligonucleotide primers were prepared according to the sequences of the chromosomal invA and plasmid spvC genes. PCR with these two primers would produce either one amplicon (from the invA gene) or two amplicons (from the invA and spvC genes), depending on whether or not the Salmonella bacteria contained a virulence plasmid. The fecal sample was diluted 10- to 20-fold into gram-negative enrichment broth and incubated to eliminate inhibitory compounds and also to allow selective enrichment of the bacteria. One or two amplicons were obtained, the expected result if Salmonella bacteria were present. The detection limit of this PCR was about 200 bacteria per reaction mixture. The primers were specific, as no amplification products were obtained with 18 species and 22 isolates of non-Salmonella bacteria tested which could be present in the feces or cause contamination. In contrast, when 23 commonly seen Salmonella serovars (38 isolates) were tested, all were shown to carry the invA gene and seven concomitantly harbored the spvC gene of the virulence plasmid. This assay was applied to the diagnosis of Salmonella enteritis in 57 children who were suffering from mucoid and/or bloody diarrhea. Of the 57 children, 38 were PCR positive and 22 were culture positive. There were two culture-positive samples that were not detected by PCR. Thus, this PCR assay showed an efficiency of 95% (38 of 40), which is much higher than the 60% (24 of 40) by culture alone. Not only is this method more sensitive, rapid, and efficient but it will cause only an incremental increase in the cost of stool processing, since enrichment cultivation of fecal samples from diarrheal patients using gram-negative enrichment broth is a routine practice for identification in many diagnostic microbiology laboratories. This PCR method, therefore, has clinical application.
Loss of the Oncogene From Human H-ras-1-Transfected NIH/3T3 Cells Grown in the Presence of Excess Methionine2 (1986)

Mouse NIH/3T3 cells, transfected with T24 genomic DNA (J10 cells), carry the human H-ras-1 (hu-H-ras-1) oncogene stably integrated in the chromosomal DNA and display the transformed phenotype with a "criss-cross" morphology and capacity for anchorage-independent growth. When these cells were cultured in the presence of 25 mM DL-methionine, they lost their transformed phenotype; the characters of the normal phenotype (before transfection) reappeared, even though cell viability, as measured by the cloning potential on a solid support, was fully conserved. Southern blot analysis showed that cells continuously propagated in methionine-supplemented medium (J10met), unlike cells grown in normal medium, progressively segregated the hu-H-ras-1 gene. The progressively fewer cells still retaining the oncogene could be selected by inoculation of J10met cells into nude (nu/nu) mice of Swiss background. After prolonged methionine treatment, however, no such oncogene-positive cells could be detected, even when the excess methionine was withdrawn from the culture medium after 105 days. Conclusive evidence for the loss of the hu-H-ras-1 oncogene sequence was provided by subcloning the J10met cells. The oncogene sequence could no longer be found, and a fraction of subclones was no longer tumorigenic when assayed in nude mice. Other subclones generated late tumors negative for the hu-H-ras-1 transforming sequence, and a small fraction of subclones gave rise to rapidly growing early tumors that were also negative for the transforming sequence. The question of how methionine can induce the phenotypic and genetic change from malignancy to normality is discussed.
Novel PNLIPRP3 and DOCK8 gene expression and prognostic implications of DNA loss on chromosome 10q25.3 in hepatocellular carcinoma. (2009)

Our previous study of gene alterations in 29 hepatocellular carcinoma (HCC) using AP-PCR amplified with 59 different 10-mer arbitrary primers and gene cloning, indicated DNA alterations by DNA fingerprints from 34 primers. Among these, the altered DNA fragment from primer U-8 predominated (62%). The aim of this report is to identify the gene alterations on chromosomal banding and gene expression in these patients, including the association of these alterations with patient demographic data. Seven different sequences, mapped to chromosomes 5q33.3, 7q31.33, 7q34, 9p24.3, 10q25.3, 13q31.3, and 16p11.2, were identified by gene cloning and nucleotide sequencing. Novel PNLIPRP3 gene over-expression and DOCK8 gene under-expression were observed in 41% and 44% of these patients, respectively, which point to an association of these genes and the development of HCC. Likewise, allelic loss on chromosome 10q25.3 was associated with shorter survival among HCC patients (P=0.03); this indicated that allelic loss on chromosome 10q25.3 may serve as a prognostic marker in patients with HCC.
Performance modeling and analysis of the Survivable Signaling Network (2002)

The Survivable Signaling Network (SSN), designed to provide a robust, highly survivable signaling network for national security emergency preparedness needs, is discussed. The network uses an adaptive routing algorithm based on a minimum-hop routing algorithm and a flooding technique to provide the required network robustness and survivability. The performance objectives of this network, specifically the network capacity objective, are addressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Using multiple microphone arrays and reflections for 3D localization of sound sources (2013)

We proposed a method for estimating sound source locations in a 3D space by integrating sound directions estimated by multiple microphone arrays and taking advantage of reflection information. Two types of sources with different directivity properties (human speech and loudspeaker speech) were evaluated for different positions and orientations. Experimental results showed the effectiveness of using reflection information, depending on the position and orientation of the sound sources relative to the array, walls, and the source type. The use of reflection information increased the source position detection rates by 10% on average and up to 60% for the best case.
Novel highly sensitive Cu‐based SERS platforms for biosensing applications (2015)

Novel surface enhanced Raman spectroscopy (SERS) platforms have been prepared and used for the bacteria detection. Unlike typical, expensive SERS platforms prepared from gold or silver, the presented platforms are prepared using copper. A new, simple, cost‐efficient and fast high pressure method is used for platform fabrication, through the decomposition of copper hydride. The platform enhancement factors are verified using the malachite green isothiocyanate as a standard. The platforms exhibit extremely high SERS enhancement factors depending on pressure used for their preparation. The calculated enhancement factors have been found in the range between 1.5 × 10 6 and 4.6 × 10 7 . The SERS spectra reproducibility is established both across a single platform and among different platforms. The average spectral correlation coefficient (Γ) has been calculated to be 0.82. Fully characterized SERS platforms have then been used for detecting Staphylococcus aureus bacteria. These novel platforms have great potential to become excellent tools for biological or medical diagnostics as an alternative to more common silver or gold SERS platforms. Copyright © 2015 John Wiley &amp; Sons, Ltd.
Efficient, Stable Infrared Photovoltaics Based on Solution-Cast Colloidal Quantum Dots (2008)

Half of the sun's power lies in the infrared. As a result, the optimal bandgaps for solar cells in both the single-junction and even the tandem architectures lie beyond 850 nm. However, progress in low-cost, large-area, physically flexible solar cells has instead been made in organic and polymer materials possessing absorption onsets in the visible. Recent advances have been achieved in solution-cast infrared photovoltaics through the use of colloidal quantum dots. Here we report stable solution-processed photovoltaic devices having 3.6% power conversion efficiency in the infrared. The use of a strongly bound bidentate linker, benzenedithiol, ensures device stability over weeks. The devices reach external quantum efficiencies of 46% in the infrared and 70% across the visible. We investigate in detail the physical mechanisms underlying the operation of this class of device. In contrast with drift-dominated behavior in recent reports of PbS quantum dot photovoltaics, we find that diffusion of electrons and holes over hundreds of nanometers through our PbSe colloidal quantum dot solid is chiefly responsible for the high external quantum efficiencies obtained in this new class of devices.
Synthesis and study of the anti-leukaemic activity of N,N'-substituted amidines and bis-amidines. (1985)

SCOPUS: ar.j
Structural and energetic determinants of the S1‐site specificity in serine proteases (1999)

In recent years the number of determined three-dimensional structures of serine proteases that are accompanied by detailed mutational studies has grown rapidly. In particular, spatial structures have been described for enzymes involved in processes of critical medical significance, often related to severe pathophysiological diseases. There has also been significant progress in the understanding of the structural grounds for the substrate specificity of serine proteases. This review is concerned mainly with primary structural determinants of the S1 specificity, the crucial component of substrate selectivity, often in relation to more distant specificity elements, which cooperatively influence the S1 site.
Reducing audible spectral discontinuities (2001)

A common problem in diphone synthesis is discussed, viz., the occurrence of audible discontinuities at diphone boundaries. Informal observations show that spectral mismatch is the most likely the clause of this phenomenon. We first set out to find an objective spectral measure for discontinuity. To this end, several spectral distance measures are related to the results of a listening experiment. Then, we studied the feasibility of extending the diphone database with context-sensitive diphones to reduce the occurrence of audible discontinuities. The number of additional diphones is limited by clustering consonant contexts that have a similar effect on the surrounding vowels on the basis of the best performing distance measure. A listening experiment has shown that the addition of these context-sensitive diphones significantly reduces the amount of audible discontinuities.
Guided bone regeneration in implant dentistry (1994)

Anatomic, surgical and aesthetic considerations in implant dentistry scientific background of guided bone regeneration bone regeneration - biologic basis membrane design criteria for guided bone regeneration of the alveolar ridge bone promotion around e-PTFE-augmented implants placed in immediate extraction sockets guided bone regeneration in dehiscence defects and delayed extraction sockets localized ridge augmentation using guided bone regeneration guided bone graft augmentation.
Microarray technology displays the complexities of the humoral immune response (2010)

Keywords:: antibodyB-cell repertoirebiomarkerhumoral immune responseimmunosignaturemRNA displaypeptide arrayphage display
Pathway alignment: application to the comparative analysis of glycolytic enzymes (1999)

Comparative analysis of metabolic pathways in different genomes yields important information on their evolution, on pharmacological targets and on biotechnological applications. In this study on glycolysis, three alternative ways of comparing biochemical pathways are combined: (1) analysis and comparison of biochemical data, (2) pathway analysis based on the concept of elementary modes, and (3) a comparative genome analysis of 17 completely sequenced genomes. The analysis reveals a surprising plasticity of the glycolytic pathway. Isoenzymes in different species are identified and compared; deviations from the textbook standard are detailed. Several potential pharmacological targets and by-passes (such as the Entner-Doudoroff pathway) to glycolysis are examined and compared in the different species. Archaean, bacterial and parasite specific adaptations are identified and described.
Control of Dkk‐1 ameliorates chondrocyte apoptosis, cartilage destruction, and subchondral bone deterioration in osteoarthritic knees (2010)

Interference with the cartilage- and bone-deleterious actions of Dkk-1 provides therapeutic potential for alleviating cartilage destruction and subchondral bone damage in OA knee joints.
Shape and size dependence of radiative, non-radiative and photothermal properties of gold nanocrystals (2000)

Driven by the search for new materials with interesting and unique properties and also by the fundamental question of how atomic and molecular physical behaviour develops with increasing size, the field of nanoparticle research has grown immensely in the last two decades. Partially for these reasons, colloidal solutions of metallic (especially silver and gold) nanoparticles have long fascinated scientists because of their very intense colours. The intense red colour of colloidal gold nanoparticles is due to their surface plasmon absorption. This article describes the physical origin of the surface plasmon absorption in gold nanoparticles with emphasis on the Mie and also the Maxwell-Garnett theory and reviews the effects of particle size and shape on the resonance condition. A better understanding of the relationship between the optical absorption spectrum (in particular, the plasmon resonance) and such particle properties as its dimensions or surrounding environment can prove fruitful for the use of the plasmon absorption as an analytical tool. The plasmon resonance has also had a great impact on the Raman spectrum of surface-adsorbed molecules and a large enhancement of the fluorescence quantum yield of gold nanorods is observed. Furthermore, following the changes in the plasmon absorption induced by excitation (heating) with ultrashort laser pulses allows one to monitor the electron dynamics (electron-electron and electron-phonon interactions) in real time, which is important in understanding such fundamental questions regarding the thermal and electrical conductivity of these nanoparticles. Very intense heating with laser pulses leads to structural changes of the nanoparticles (nuclear rearrangements in the form of melting and fragmentation).
Finding similar files in a large file system (1994)

We present a tool, called sif, for finding all similar files in a large file system. Files are considered similar if they have significant number of common pieces, even if they are very different otherwise. For example, one file may be contained, possibly with some changes, in another file, or a file may be a reorganization of another file. The running time for finding all groups of similar files, even for as little as 25% similarity, is on the order of 500MB to 1GB an hour. The amount of similarity and several other customized parameters can be determined by the user at a post-processing stage, which is very fast. Sif can also be used to very quickly identify all similar files to a query file using a preprocessed index. Application of sif can be found in file management, information collecting (to remove duplicates), program reuse, file synchronization, data compression, and maybe even plagiarism detection. 1. Introduction Our goal is to identify files that came from the same source ...