gebhart/patrepeval huggingface dataset:
Phase Behavior of Lithium Perchlorate-Doped Poly(styrene-<i>b</i>-isoprene-<i>b</i>-ethylene oxide) Triblock Copolymers (2002)

We report on the phase behavior of a system of lithium perchlorate-doped poly(styrene-b-isoprene-b-ethylene oxide) (SIO) triblock copolymers. Two complete phase diagrams are described along the isopleth formed by equal volume fractions of polystyrene and polyisoprene and varying poly(ethylene oxide) contents at ether oxygen-to-lithium ratios of 48:1 and 24:1 between 70 and 200 °C. Our results, based primarily on small-angle X-ray scattering (SAXS) data, reveal four phases as a function of PEO and salt content: two-domain lamellae (LAM2), a pillared lamellar structure (PLS), core−shell cylinders (CSC), and three-domain lamellae (LAM3). Two microstructures present in the neat material, core−shell gyroid (CSG), and semiperforated lamellae (SPL), are replaced by the CSC phase in the doped systems. In addition, the order−disorder transition temperatures at low PEO content increase dramatically with the addition of salt. Within the CSC phase, LiClO4 can be dispersed up to a loading of 3:1 without inducing macroscopic phase separation. These findings are rationalized on the basis of the associated modifications to the three segment−segment interaction parameters and PEO chain statistics that accompany the selective mixing of LiClO4 in the PEO domains, thereby driving microphase separation toward the strong-segregation limit.
Role for interleukin‐4 in foreign‐body giant cell formation on a poly(etherurethane urea) <i>in vivo</i> (1995)

Interleukin-4 (IL-4) was previously shown to induce extensive macrophage fusion to form foreign-body giant cells (FBGCs) in vitro. In the present study, our goal was to extend these findings to an in vivo test environment on biomaterials. The subcutaneous cage-implant system was modified for mice to elucidate IL-4 participation in mediating FBGC formation in vivo. Exudate leukocyte concentrations from cages containing poly(etherurethane urea) (PEUU A') and empty cage controls indicated a similar inflammatory response that turned toward resolution by 14 days postimplantation, thus confirming the applicability of the cage-implant system in mice. FBGC kinetic analysis showed that the formation of mouse FBGCs occurs through the fusion of adherent macrophages at a constant rate up to 14 days of implantation. Purified goat anti-mouse IL-4 neutralizing antibody (IL4Ab) or normal goat nonspecific control IgG (gtIgG) at various concentrations, or recombinant murine IL-4 (muIL4) was injected into the implanted cages containing PEUU A' every 2 days for 7 days. The injection of IL4Ab significantly decreased the FBGC density on PEUU A' cage-implanted in mice, when compared with the nonspecific IgG or PBS injection controls. Conversely, the FBGC density was significantly increased by the injection of muIL4 when compared with nonspecific IgG and PBS injection controls. Adherent macrophage density, FBGC morphology, FBGC average size, and size distribution were not significantly different among IL4Ab, nonspecific control gtIgG, muIL4, and PBS control groups. Our data suggest that IL-4 participates in FBGC formation on biomaterials in vivo.
Detection of T cells in paraffin wax embedded tissue using antibodies against a peptide sequence from the CD3 antigen. (1989)

Rabbit polyclonal antibodies were raised against a proline rich, peptide sequence, comprising 13 amino acids, in the cytoplasmic domain of the CD3 epsilon chain. Immunoprecipitation experiments showed that this antibody preparation recognised the CD3 antigen on human T lymphoblasts. The antibody stained normal T cells strongly in tissue sections which had been fixed in formalin or Bouin's solution and embedded in paraffin wax. Its reactivity with T cell lymphoma, when evaluated on a series of 96 previously phenotyped cases, closely agreed with the results obtained on cryostat sections. These results indicate that the specific detection of T cells in routinely processed tissue biopsy specimens is now technically feasible on a wide scale in diagnostic laboratories using CD3 peptide antibodies, and they also suggest that in future the use of anti-peptide antibodies may detect other lineage specific antigenic markers in paraffin wax sections.
An HVS-based no-reference perceptual quality assessment of JPEG coded images using neural networks (2005)

In this paper, we present a novel no-reference (NR) metric to assess the quality of JPEG-coded images. The features for predicting the perceived image quality are extracted by considering the key human visual sensitivity factors such as, edge amplitude, edge length, background activity and background luminance. The extracted features with the subjective test results are used to train a multi-layer perceptron (MLP) neural network. Experimental results show that the prediction of the trained neural network is very close to the mean opinion score (MOS). The subjective test results of the proposed metric are compared with the Wang-Bovik's NR blockiness metric. Further, this metric can be extended to assess the quality of the MPLG/H.26x compressed videos.
Crystallographic Structures of <i>Discosoma</i> Red Fluorescent Protein with Immature and Mature Chromophores:  Linking Peptide Bond <i>Trans−Cis</i> Isomerization and Acylimine Formation in Chromophore Maturation<sup>,</sup> (2005)

The mature self-synthesizing p-hydroxybenzylideneimidazolinone-like fluorophores of Discosoma red fluorescent protein (DsRed) and Aequorea victoria green fluorescent protein (GFP) are extensively studied as powerful biological markers. Yet, the spontaneous formation of these fluorophores by cyclization, oxidation, and dehydration reactions of tripeptides within their protein environment remains incompletely understood. The mature DsRed fluorophore (Gln 66, Tyr 67, and Gly 68) differs from the GFP fluorophore by an acylimine that results in Gln 66 Calpha planar geometry and by a Phe 65-Gln 66 cis peptide bond. DsRed green-to-red maturation includes a green-fluorescing immature chromophore and requires a chromophore peptide bond trans-cis isomerization that is slow and incomplete. To clarify the unique structural chemistry for the individual immature "green" and mature "red" chromophores of DsRed, we report here the determination and analysis of crystal structures for the wild-type protein (1.4 A resolution), the entirely green DsRed K70M mutant protein (1.9 A resolution), and the DsRed designed mutant Q66M (1.9 A resolution), which shows increased red chromophore relative to the wild-type DsRed. Whereas the mature, red-fluorescing chromophore has the expected cis peptide bond and a sp(2)-hybridized Gln 66 Calpha with planar geometry, the crystal structure of the immature green-fluorescing chromophore of DsRed, presented here for the first time, reveals a trans peptide bond and a sp(3)-hybridized Gln 66 Calpha with tetrahedral geometry. These results characterize a GFP-like immature green DsRed chromophore structure, reveal distinct mature and immature chromophore environments, and furthermore provide evidence for the coupling of acylimine formation with trans-cis isomerization.
Consolidated strategy for the analysis of microarray spike-in data (2008)

As the number of users of microarray technology continues to grow, so does the importance of platform assessments and comparisons. Spike-in experiments have been successfully used for internal technology assessments by microarray manufacturers and for comparisons of competing data analysis approaches. The microarray literature is saturated with statistical assessments based on spike-in experiment data. Unfortunately, the statistical assessments vary widely and are applicable only in specific cases. This has introduced confusion into the debate over best practices with regards to which platform, protocols and data analysis tools are best. Furthermore, cross-platform comparisons have proven difficult because reported concentrations are not comparable. In this article, we introduce two new spike-in experiments, present a novel statistical solution that enables cross-platform comparisons, and propose a comprehensive procedure for assessments based on spike-in experiments. The ideas are implemented in a user friendly Bioconductor package: spkTools. We demonstrated the utility of our tools by presenting the first spike-in-based comparison of the three major platforms--Affymetrix, Agilent and Illumina.
Hydrophobicity and structural classes in proteins (1992)

The bulk hydrophobic character for the 20 natural amino acid residues, has been obtained from a database of 60 protein structures, grouped in the four structural classes alpha alpha, beta beta, alpha + beta and alpha/beta. The hydrophobicity coefficients thus obtained are compared with Ponnuswamy's original values using scales normalized to average = 0.0 and standard deviation = 1.0. Even though most of the amino acid residues do not change their hydropathic character in the different structural classes, their behaviour suggests the convenience that averaging methods should only consider proteins of the same structural class and that this information should be included in the secondary structure methods.
pH 值调节剂对 CO2 吸收富液解吸能耗的影响 (2010)

在0.2 mol/LMEA、DEA和MDEA吸收CO2饱和溶液的解吸过程中加入一定量的己二酸和辛二酸,对解吸能耗和CO2析出速率的影响进行了实验.发现加酸后在其它解吸实验条件不变情况下,CO2析出速率加快,且加酸剂量在0~0.6g范围内,CO2解吸速率与加酸量成正比.对加酸前后的CO2解吸能耗进行了计算和比较,发现在解吸过程加酸后解吸CO2的能耗率明显减少,且能耗减少量随加酸量的增加而增大.研究结果表明,采用pH值调节法可降低CO2解吸过程的能耗,加快解吸速率.Solvent absorption is one of the main commercial methods for CO2 capture. However, the process of solvent regeneration is energy intensive and constitutes the main cost in the whole process. The paper investigates the feasibility of a new method, which is, to control the pH value of solvent in reducing the energy consumption in solvent regeneration. Some Selected weak organic acids are added into typical solvents which are MEA, DEA and MDEA. It is found that the energy requirement for the release of CO2 is significantly reduced, which however is sensitive to the type of acid added. Meanwhile, CO2 releases faster as more amount of acids added. PH controlling method is thus potentially applicable in solvent technology.
Vector quantization using tree-structured self-organizing feature maps (1994)

In this paper, we propose a binary-tree structure neural network model suitable for structured clustering. During and after training, the centroids of the clusters in this model always form a binary tree in the input pattern space. This model is used to design tree search vector quantization codebooks for image coding. Simulation results show that the acquired codebook not only produces better-quality images but also achieves a higher compression ratio than conventional tree search vector quantization. When source coding is applied after VQ, the new model performs better than the generalized Lloyd algorithm in terms of distortion, bits per pixel, and encoding complexity for low-detail and medium-detail images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A handheld device for potential point-of-care screening of cancer (2007)

A simple handheld device based on the fluorescence analysis of 3,6-bis(1-methyl-4-vinylpyridinium)carbazole diiodide (BMVC) stained cells was established for routine screening and potentially for early detection of cancer cells at extremely low cost. Flow cytometry assay further supported the utility of this simple device, where a preliminary study of tissue biopsy showed highly encouraging results.
<i>ARP</i>/<i>wARP</i> and molecular replacement (2001)

The aim of ARP/wARP is improved automation of model building and refinement in macromolecular crystallography. Once a molecular-replacement solution has been obtained, it is often tedious to refine and rebuild the initial (search) model. ARP/wARP offers three options to automate that task to varying extents: (i) autobuilding of a completely new model based on phases calculated from the molecular-replacement solution, (ii) updating of the initial model by atom addition and deletion to obtain an improved map and (iii) docking of a structure onto a new (or mutated) sequence, followed by rebuilding and refining the side chains in real space. A few examples are presented where ARP/wARP made a considerable difference in the speed of structure solution and/or made possible refinement of otherwise difficult or uninterpretable maps. The resolution range allowing complete autobuilding of protein structures is currently 2.0 A, but for map improvement considerable advances over more conventional refinement techniques are evident even at 3.2 A spacing.
Tau Aggregation in Alzheimer's Disease (2007)

The crucial role of the neuronal Tau protein in microtubule stabilization and axonal transport suggests that too little or too much Tau might lead to neuronal dysfunction. The presence of a hyper phosphorylated but non aggregated molecule as a toxic species that might sequester normal Tau is discussed. We present recent in vitro results that might allow us to dissect the role of individual phosphorylation sites on its structure and function. We also discuss in this review the role of phosphorylation for the aggregation of the neuronal Tau protein, and compare it to the aggregation induced by external poly anions.
Comparison of various periodograms for single tone detection and frequency estimation (2002)

Periodograms are a simple and efficient way to detect and estimate parameters of sinusoidal signals. In this paper, we attempt to determine the optimum periodogram implementation for a single real tone detection in the presence of white Gaussian noise, among its variants such as the Bartlett's procedure and Welch method. The possibility of delaying threshold effect using different realizations for frequency estimation is also investigated. Simulation results show that the standard periodogram generally gives the best detection performance and it provides the minimum mean square frequency estimation error for all signal-to-noise ratio conditions.
Regenerative braking for aircraft landing roll phase using an electric machine (2012)

High speed air transportation became the most common way of transportation, especially on the long distances. Though very fast and convenient, air transportation is a significant source of pollution: noise pollution and air pollution. The alternative to reduce emissions and noise pollution is to improve the operational performance of the aircraft. In this paper the new ground traction system for the aircraft LTO cycle based on an electric machine is proposed to reduce the pollution.
The regulation and function of micrornas in kidney diseases (2013)

MicroRNAs (miRNA) are endogenous short noncoding RNAs, which regulate virtually all major cellular processes by inhibiting target gene expression. In kidneys, miRNAs have been implicated in renal development, homeostasis, and physiological functions. In addition, miRNAs play important roles in the pathogenesis of various renal diseases, including renal carcinoma, diabetic nephropathy, acute kidney injury, hypertensive nephropathy, polycystic kidney disease, and others. Furthermore, miRNAs may have great values as biomarkers in different kidney diseases.
Security embedding codes (2010)

This paper considers the problem of simultaneously communicating high-security and low-security messages, referred to as the security embedding problem. An information-theoretic model is presented. A coding scheme that combines superposition coding and random binning is proposed and is shown to achieve the capacity region in several communication scenarios. As an application, it is shown that a simple scheme that combines security embedding codes and secure network coding can achieve the secrecy capacity of a parallel multi-eavesdropper wiretap channel with two reversely degraded components.
Induction and Transcription Studies of the Dextransucrase Gene in <i>Leuconostoc mesenteroides</i> NRRL B-512F (1999)

Dextransucrase production by Leuconostoc mesenteroides NRRL B-512F in media containing carbon sources other than sucrose is reported for the first time. Dextransucrases were analyzed by gel electrophoresis and by an in situ activity assay. Their polymers and acceptor reaction products were also compared by (13)C nuclear magnetic resonance and high-performance liquid chromatography techniques, respectively. From these analyses, it was found that, independently of the carbon source, L. mesenteroides NRRL B-512F produced dextransucrases of the same size and product specificity. The 5' ends of dextransucrase mRNAs isolated from cells grown under different culture conditions were identical. Based on this evidence, we conclude that dextransucrases obtained from cells grown on the various carbon sources result from the transcription of the same gene. The control of expression occurs at this level. The low dextransucrase yields from cultures in D-glucose or D-fructose and the enhancement of dextransucrase gene transcription in the presence of sucrose suggest that an activating phenomenon may be involved in the expression mechanism. Dextransucrase mRNA has a size of approximately 4.8 kb, indicating that the gene is located in a monocistronic operon. The transcription start point was localized 34 bp upstream from the ATG start codon. The -10 and -35 sequences found, TATAAT and TTTACA, were highly homologous to the only glycosyltransferase promoter sequence reported for lactic acid bacteria.
Fail-Safe PVM: A Portable Package for Distributed Programming with Transparent Recovery (1993)

Many scientific problems benefit from computations that are parallel at a coarse grain. Collections loosely-coupled, heterogeneous computers are increasingly being applied to these problems. While individual computers are designed to be relatively reliable, a collection of several autonomous machines necessarily has a greater rate of failure. As data networks improve, and larger multicomputers are being used, rates of failure will increase. PVM (Parallel Virtual Machine) is a popular software framework that facilitates message-passing network programming. We present enhancements to PVM to mask fail-stop, single-node failures from the application. Fail-safe PVM uses checkpoint and rollback to recover from such failures. Both checkpoints and rollbacks are transparent to the application if the application does not depend on real-time events. Recovery occurs without wait for repair of the failed computer. The system does not rely on shared stable storage and does not require modifications to the operating system. We describe the design and implementation of fail-safe PVM, present measurements of checkpoint costs, and briefly discuss shortcomings and potential avenues for improvement.
Anaerobic <scp>l</scp> -α-Glycerophosphate Dehydrogenase of <i>Escherichia coli:</i> Its Genetic Locus and Its Physiological Role (1971)

In mutant cells of Escherichia coli missing the particulate l-alpha-glycerophosphate (l-alpha-GP) dehydrogenase necessary for aerobic growth on glycerol or l-alphaGP, a soluble, flavine-dependent l-alpha-GP dehydrogenase supports normal anaerobic growth rates on either of the two substrates with fumarate or nitrate as exogenous hydrogen acceptor. In an experiment in which glycerol served as the carbon source and nitrate as the acceptor, the growth of such a mutant was arrested upon the admission of air, whereas the growth of wild-type cells continued smoothly. Mutant cells lacking the soluble l-alpha-GP dehydrogenase, but possessing the particulate enzyme, can grow at normal rates aerobically on glycerol and l-alpha-GP or anaerobically on these compounds with nitrate, but not fumarate, as the hydrogen acceptor. Double mutants lacking both of the dehydrogenases fail to show significant growth on either glycerol or l-alpha-GP under any condition. Mutations affecting the anaerobic dehydrogenase (glpA locus) are situated at about minute 43 of the Taylor map, just clockwise beyond glpT, and show cotransduction with purF (1.5%), glpT (91%), and nalA (50%). The anaerobic dehydrogenase is a member of the glp regulon as judged by its inducibility by l-alpha-GP and by its constitutive formation in strains of glpR(c) genotype. The level of the anaerobic dehydrogenase is about the same in cells grown either aerobically or anaerobically with nitrate serving as a terminal hydrogen acceptor. With fumarate as terminal acceptor, the level is elevated several fold.
An edge-adaptive iterative method for image restoration (1992)

The paper proposes an edge-adaptive iterative method for restoring a blurred image. An original image is represented as a multiple image model composed of four kinds of edge regions and a flat region. The image is restored with the maximum a posteriori (MAP) criterion, which is realized by the steepest descent technique. The parameters of the original image and edge orientation are estimated from the image temporally restored by a deconvolution method. Computer simulations show that this method suppresses ringing artifacts near sharp edges and avoids smoothing edges in the cases of a motion blur and an out-of-focus blur.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
On parallelizing the multiprocessor scheduling problem (1999)

Existing heuristics for scheduling a node and edge weighted directed task graph to multiple processors can produce satisfactory solutions but incur high time complexities, which tend to exacerbate in more realistic environments with relaxed assumptions. Consequently, these heuristics do not scale well and cannot handle problems of moderate sizes. A natural approach to reducing complexity, while aiming for a similar or potentially better solution, is to parallelize the scheduling algorithm. This can be done by partitioning the task graphs and concurrently generating partial schedules for the partitioned parts, which are then concatenated to obtain the final schedule. The problem, however, is nontrivial as there exists dependencies among the nodes of a task graph which must be preserved for generating a valid schedule. Moreover, the time clock for scheduling is global for all the processors (that are executing the parallel scheduling algorithm), making the inherent parallelism invisible. In this paper, we introduce a parallel algorithm that is guided by a systematic partitioning of the task graph to perform scheduling using multiple processors. The algorithm schedules both the tasks and messages, and is suitable for graphs with arbitrary computation and communication costs, and is applicable to systems with arbitrary network topologies using homogeneous or heterogeneous processors. We have implemented the algorithm on the Intel Paragon and compared it with three closely related algorithms. The experimental results indicate that our algorithm yields higher quality solutions while using an order of magnitude smaller scheduling times. The algorithm also exhibits an interesting trade-off between the solution quality and speedup while scaling well with the problem size.
Sterically congested, hexameric tetrakispyridinyl-PdII/CdII-metallomacrocycles: self-assembly and structural characterization (2011)

Hexagonal Pd(II)- or Cd(II)-tetrakispyridinyl-based macrocycles are quantitatively self-assembled from 4'-(3-pyridinyl)-4,4''-di(tert-butyl)-2,2' : 6',2''-terpyridine and structurally confirmed by NMR and TWIM-MS.