gebhart/patrepeval huggingface dataset:
Partial cloning of rat CD34 cDNA and expression during stem cell- dependent liver regeneration in the adult rat (1997)

The sialomucin CD34 is expressed on human and mouse hematopoietic stem cells and is used as an important marker for isolating the hematopoietic stem/progenitor cells. The involvement of hepatic stem cells in liver regeneration under certain conditions in adult rats is now well supported. The objective of the present research was to explore the idea that CD34 might also be expressed on hepatic stem cell progeny. Polymerase chain reaction (PCR)-based cloning of rat CD34 was partially accomplished. During the hepatic stem cell activation (2-acetylaminofluorene/partial hepatectomy [AAF/PH] model), the CD34 transcripts were increased and reached the peak level between 9 and 12 days after partial hepatectomy when the progenitor cells (e.g., oval cells, early hepatocytes in basophilic foci, and intestinal type of cells) are most abundant. Both in situ hybridization and immunohistochemistry, using anti-mouse CD34 antibody, which recognizes the cytoplasmic domain, clearly showed the expression of CD34 on oval cells as well as on endothelial cells of large hepatic vessels. In addition, bile ductular epithelial (BDE) cells both in the AAF/PH model and in normal liver expressed CD34, suggesting a close relationship between BDE cells and the hepatic stem-cell compartment. Taken together, the data indicate that CD34 would, similar to its role in the hematopoietic system, be an important probe for characterizing the cellular biology of the hepatic stem-cell compartment.
Homogeneous sample preparation for automated high throughput analysis with matrix‐assisted laser desorption/ionisation time‐of‐flight mass spectrometry (1999)

This work presents a simple method for obtaining homogeneous sample surfaces in matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS) for the automated analysis of peptides and proteins. The sample preparation method is based on applying the sample/matrix mixture onto a pre-deposited highly diluted matrix spot. The pre-deposited crystals act as seeds for the new sample containing crystals which become much smaller in size and more evenly distributed than with conventional methods. This ‘seed-layer’ method was developed, optimised and compared with the dried-droplet method using peptides and proteins in the 1000–20 000 Da range. The seed-layer method increases the surface homogeneity, spot to spot reproducibility and sample washability as compared with the commonly used dried-droplet method. This methodology is applicable to α-cyanohydroxycinnamic acid, sinapinic acid and ferulic acid, which all form homogeneous crystal surfaces. Within-spot variation and between-spot variation was investigated using statistics at a 95% confidence level (n = 36). The statistical values were generated from more than 5000 data points collected from 500 spectra. More than 90% of the sample locations results in high intensity spectra with relatively low standard deviations (RSDs). Typically obtained data showed an RSD of 19–35% within a sample spot as well as in-between spots for proteins, and an RSD of ≤50% for peptides. Linear calibration curves were obtained within one order of magnitude using internal calibration with a point-RSD of 3% (n = 10). The sample homogeneity allows mass spectra (average of 16 laser shots) to be obtained on each individual sample within 15 sec, whereby a 100 spot target plate can be run in 25 min. High density target plates using the seed-layer method were prepared by spotting ≈100 picoliter droplets onto the target, resulting in sample spots ≤500 µm in diameter using a flow-through piezo-electric micro-dispenser. By using this automated sample preparation step lower standard deviations are obtained in comparison to manually prepared samples. Copyright © 1999 John Wiley & Sons, Ltd.
Limitation of absorption-based fiber optic gas sensors by coherent reflections (1997)

We report the noise limitation of fiber optic gas sensors with highly coherent laser sources. Interference between signal and reflected waves causes signal fluctuation in the output; this limits the performance of the sensing system. Sensor resolutions limited by coherent reflections are calculated and compared with experimental results.
Inside the Slammer worm (2003)

The Slammer worm spread so quickly that human response was ineffective. In January 2003, it packed a benign payload, but its disruptive capacity was surprising. Why was it so effective and what new challenges do this new breed of worm pose?.
Determination of 16S rRNA Sequences of Enterococci and Application to Species Identification of Nonmotile Enterococcus gallinarum Isolates (1998)

The 16S rRNA sequences of enterococcal species E. faecium, E. faecalis, E. gallinarum, E. casseliflavus/flavescens, E. dispar, E. pseudoavium, E. sulfureus, E. malodoratus, E. raffinosus, E. cecorum, E. hirae, E. saccharolyticus, E. seriolicida, E. mundtii, E. avium, E. durans, E. columbae, and E. solitarius are presented herein. These data were utilized to confirm the species identification of two nonmotile E. gallinarum isolates which had been previously phenotypically identified as E. faecium. The implications of this finding are discussed.
MuIti‐frequency bioelectrical impedance augments the diagnosis and management of lymphoedema in post‐mastectomy patients (1992)

The value of multiple frequency bioelectric impedence analysis (MFBIA) in the monitoring and management of post-mastectomy lymphoedema of the arm was evaluated in 15 patients and controls. The technique was found to produce quantitative agreement with a clinical diagnosis of lymphoedema and with the currently-used measure (limb volume calculated from circumferential measurements) of limb size. The significance of this finding lies in MFBIA being diagnostically informative: it indicates when an observed change in limb volume is directly, albeit theoretically, attributable to accumulation of extracellular fluid. MFBIA potentially offers the means for earlier definitive diagnosis and more-accurate monitoring of extracellular fluid changes during and after treatment.
Intracellular turnover of cystic fibrosis transmembrane conductance regulator. Inefficient processing and rapid degradation of wild-type and mutant proteins. (1994)

Mutant (delta F508) and wild-type cystic fibrosis transmembrane conductance regulator (CFTR) were synthesized initially as an approximately 140-kDa core-glycosylated precursor, which, in the case of wild-type CFTR, was chased to an approximately 160 kDa form bearing complex oligosaccharides. Mutant CFTR disappeared from the detergent-soluble cell extract with rapid (t1/2 = 27 min) kinetics. Only approximately 25% of the initially synthesized wild-type 140-kDa CFTR precursor was detected as mature protein; the remaining approximately 75% decayed with kinetics (t1/2 = 33 min) indistinguishable from those of the mutant. Rapid degradation kinetics and inefficient processing of wild-type CFTR were also observed in the colonic carcinoma lines HT29 and T84 and in stably transfected C127 cells, which express 5-50 times lower levels of CFTR. These results suggest that inefficient processing and rapid degradation of wild-type CFTR precursor are an intrinsic property of CFTR in these diverse cell types and are not an artifact of overexpression. Degradation of wild-type and mutant 140-kDa CFTR began without significant lag following synthesis. These data suggest that wild-type and delta F508 CFTR differ in the efficiency of folding of the core-glycosylated primary translation product.
A novel class of phosphorescent gold(iii) alkynyl-based organic light-emitting devices with tunable colour (2005)

A novel class of luminescent cyclometalated gold(III) alkynyl complexes has been demonstrated to possess EL properties and has been employed in the roles of electrophosphorescent emitters or dopants of organic light-emitting diodes (OLEDs) with high brightness and efficiency.
Airway inflammation: chemokine‐induced neutrophilia and the class I phosphoinositide 3‐kinases (2005)

Class I phosphoinositide 3-kinases (PI3K) are known to play a significant role in neutrophil chemotaxis. However, the relative contributions of different PI3K isoforms, and how these impact on lung inflammation, have not been addressed. In vitro studies using wild-type and PI3Kgamma knockout neutrophils demonstrated the major role of the gamma isoform in chemotactic but not chemokinetic events. This was confirmed by a model of direct chemokine instillation into the airways in vivo. Within all studies, a low yet significant degree of neutrophil movement in the absence of PI3Kgamma could be observed. No role for the delta isoform was demonstrated both in vitro and in vivo using PI3Kdelta kinase-dead knock-in mice. Moreover, further studies using the broad-spectrum PI3K inhibitors wortmannin or LY294002 showed no other class I PI3K isoforms to be involved in these chemotactic processes. Here, we identify a contributory PI3K-independent mechanism of neutrophil movement, yet demonstrate PI3Kgamma as the pivotal mediator through which the majority of neutrophils migrate into the lung in response to chemokines. These data resolve the complexities of chemokine-induced neutrophilia and PI3K signaling and define the gamma isoform as a promising target for new therapeutics to treat airway inflammatory diseases.
Delta-1 Activation of Notch-1 Signaling Results in HES-1 Transactivation (1998)

The Notch receptor is involved in many cell fate determination events in vertebrates and invertebrates. It has been shown in Drosophila melanogaster that Delta-dependent Notch signaling activates the transcription factor Suppressor of Hairless, leading to an increased expression of the Enhancer of Split genes. Genetic evidence has also implicated the kuzbanian gene, which encodes a disintegrin metalloprotease, in the Notch signaling pathway. By using a two-cell coculture assay, we show here that vertebrate Dl-1 activates the Notch-1 cascade. Consistent with previous data obtained with active forms of Notch-1 a HES-1-derived promoter construct is transactivated in cells expressing Notch-1 in response to Dl-1 stimulation. Impairing the proteolytic maturation of the full-length receptor leads to a decrease in HES-1 transactivation, further supporting the hypothesis that only mature processed Notch is expressed at the cell surface and activated by its ligand. Furthermore, we observed that Dl-1-induced HES-1 transactivation was dependent both on Kuzbanian and RBP-J activities, consistent with the involvement of these two proteins in Notch signaling in Drosophila. We also observed that exposure of Notch-1-expressing cells to Dl-1 results in an increased level of endogenous HES-1 mRNA. Finally, coculture of Dl-1-expressing cells with myogenic C2 cells suppresses differentiation of C2 cells into myotubes, as previously demonstrated for Jagged-1 and Jagged-2, and also leads to an increased level of endogenous HES-1 mRNA. Thus, Dl-1 behaves as a functional ligand for Notch-1 and has the same ability to suppress cell differentiation as the Jagged proteins do.
Multi-Dimensional Hash Chains and Application to Micropayment Schemes (2005)

One-way hash chains have been used in many micropayment schemes due to their simplicity and efficiency. In this paper we introduce the notion of multi-dimensional hash chains, which is a new generalization of traditional one-way hash chains. We show that this construction has storage-computational complexity of O(logN) per chain element, which is comparable with the best result reported in recent literature. Based on multi-dimensional hash chains, we then propose two cash-like micropayment schemes, which have a number of advantages in terms of efficiency and security. We also point out some possible improvements to PayWord and similar schemes by using multi-dimensional hash chains
The labelling of proteins to high specific radioactivities by conjugation to a 125I-containing acylating agent. Application to the radioimmunoassay (1973)

1. A new method is described for labelling proteins to high specific radioactivities with (125)I. The protein is treated with a (125)I-labelled acylating agent, iodinated 3-(4-hydroxyphenyl)propionic acid N-hydroxysuccinimide ester, which reacts with free amino groups in the protein molecule to attach the (125)I-labelled groups by amide bonds. 2. Three protein hormones have been labelled by this method, human growth hormone, human thyroid-stimulating hormone and human luteinizing hormone. Specific radioactivities of up to 170, 120 and 55muCi/mug respectively have been obtained for these hormones. 3. The immunoreactivity of these labelled hormones has been investigated by using a radioimmunoassay system specific for each hormone. These preparations have also been compared with and found to be equal or superior to labelled hormones prepared by chemical substitution of (125)I into tyrosine residues of the proteins by using the chloramine-t-oxidation procedure. 4. With some antisera the immunoreactivity of the antigen was diminished by the introduction of a single I atom into the tyrosyl groups, whereas antigen containing a single (125)I-labelled 3-(4-hydroxyphenyl)propionamide group showed the same immunoreactivity as the unmodified antigen.
The Ubiquitin-Proteasome Pathway in Huntington's Disease (2008)

The accumulation of mutant protein is a common feature of neurodegenerative disease. In Huntington's disease, a polyglutamine expansion in the huntingtin protein triggers neuronal toxicity. Accompanying neuronal death, mutant huntingtin aggregates in large macromolecular structures called inclusion bodies. The function of the machinery for intracellular protein degradation is linked to huntingtin toxicity and components of this machinery colocalize with inclusion bodies. An increasing body of evidence implicates the ubiquitin-proteasome pathway in the failure of cells to degrade mutant huntingtin. A number of potential mechanisms that link compromised ubiquitin-proteasome pathway function and neurodegeneration have been proposed and may offer opportunities for therapeutic intervention.
Procrustes Methods in the Statistical Analysis of Shape (1991)

SUMMARY Two geometrical figures, X and Y, in RK, each consisting of N landmark points, have the same shape if they differ by at most a rotation, a translation and isotropic scaling. This paper presents a model-based Procrustes approach to analysing sets of shapes. With few exceptions, the metric geometry of shape spaces is quite complicated. We develop a basic understanding through the familiar QR and singular value decompositions of multivariate analysis. The strategy underlying the use of Procrustes methods is to work directly with the N x K co-ordinate matrix, while allowing for an arbitrary similarity transformation at all stages of model formulation, estimation and inference. A Gaussian model for landmark data is defined for a single population and generalized to two-sample, analysis-of-variance and regression models. Maximum likelihood estimation is by least squares superimposition of the figures; we describe generalizations of Procrustes techniques to allow non-isotropic errors at and between landmarks. Inference is based on an N x K linear multivariate Procrustes statistic that, in a double-rotated co-ordinate system, is a simple but singular linear transformation of the errors at landmarks. However, the superimposition metric used for fitting, and the model metric, or covariance, used for testing, may not coincide. Estimates of means are consistent for many reasonable choices of superimposition metric. The estimates are efficient (maximum likelihood estimates) when the metrics coincide. F-ratio and Hotelling's R 2-tests for shape differences in one- and two-sample data are derived from the distribution of the Procrustes statistic. The techniques are applied to the shapes associated with hydrocephaly and nutritional differences in young rats.
Investigation of plaque biomechanics from intravascular ultrasound images using finite element modeling (2002)

Biomechanical properties of atherosclerotic plaque are not well known due to the difficulties involved in experimental testing. In this study an iterative finite element program was developed that estimates the elastic material properties of diseased arteries and plaque based on deformations from intravascular ultrasound images. The program successfully determined the elastic modulus of latex tubes with artificial plaque and of the ex vivo human coronary arteries. The authors conclude that this finite element method provides a way to estimate the material properties of the plaque an wall in stenosed arteries from clinically available data, i.e., ultrasound images and blood pressure measurements.
Chemorepulsion of axons in the developing mammalian central nervous system (1993)

During development of the nervous system, distinct populations of nerve cells extend specialized processes, axons and dendrites, over considerable distances to locate their targets. There is strong evidence for two general mechanisms by which these connections are made. The first involves attractive and repulsive interactions, both between cells and between them and their extracellular matrix. The second depends on the release of diffusible chemoattractants by target structures. Evidence is now provided for a mechanism of axon guidance in which diffusible chemorepulsive factors create exclusion zones for developing axons, causing them to turn away from inappropriate territory.
Atomic Structure Imaging Beyond Conventional Resolution Limits in the Transmission Electron Microscope (2009)

Transmission electron microscopy is an extremely powerful technique for direct characterization of local structure at the atomic scale. However, the resolution of this technique is fundamentally limited by the partial coherence of the electron beam. In this Letter we demonstrate a method that extends the ultimate resolution of the latest generation of aberration corrected transmission electron microscopes by 41% relative to that achievable using conventional axial imaging. Experimental results verify that a real space resolution of 78 pm has been achieved at 200 kV.
Domain exchanges between KNAT3 and KNAT1 suggest specificity of the kn1‐like homeodomains requires sequences outside of the third helix and N‐terminal arm of the homeodomain (1997)

Domain exchange constructs that traded regions surrounding the homeodomain were constructed for two kn1-like genes, KNAT1 and KNAT3, and introduced into Arabidopsis thaliana under the control of the 35S CaMV promoter. The kn1-like homeodomain proteins all have the homeodomain located near the C-terminus of the protein, and also share a second conserved domain (the ELK domain) immediately N-terminal to the homeodomain. Progeny were scored for the appearance of the KNAT1 overexpression phenotype. A construct containing the KNAT3 N-terminus and the KNAT1 ELK- and homeodomain resulted in a KNAT1 overexpression phenotype, indicating that specificity mainly resides within the ELK- and homeodomain region. Further exchanges demonstrated that specificity probably does not arise from a single region within the ELK and/or homeodomain but rather requires sequences both N-terminal and C-terminal to residue 23 of the homeodomain. Further, in contrast to some animal homeodomains, KNAT1 does not utilize the residues of the N-terminal arm of the homeodomain for specificity.
Porcine Reproductive and Respiratory Syndrome (PRRS) Virus-Specific Interferon-γ + T-Cell Responses After PRRS Virus Infection or Vaccination with an Inactivated PRRS Vaccine (2005)

Although field studies have found porcine reproductive and respiratory syndrome (PRRSV) inactivated vaccines to be beneficial in reducing losses linked to PRRSV infection, immune mechanisms induced by these vaccines need better understanding. In the study reported here, we examined the interferon-gamma(+) (IFNgamma(+)) PRRS-specific T cell responses induced after infection and vaccination with an inactivated PRRS vaccine. Autologous monocyte-derived dendritic cells loaded with the PRRSV P120 strain were used to re-stimulate ex vivo T cells that had been primed in vivo by either the virus or the vaccine, or both. Virus-specific IFNgamma(+) T cells were quantified by using a porcine IFNgamma- ELISpot assay. A specific but low live virus-induced response was observed between days 35 and 70 for most of the pigs tested, while a significant inactivated vaccine-induced PRRSV-specific IFNgamma(+) T-cell response was measured soon after vaccination. Moreover, we observed that vaccination of pre-challenged pigs clearly favoured the PRRSV-specific cell-mediated immunity primed by the live virus. To characterize further the nature of the PRRSV-specific T cells, the different T-cell subsets involved in PRRSV immunity were analyzed by flow cytometry. We showed that the inactivated vaccine was able to prime both CD4(+)CD8(int+) and CD8(high) virus-specific T cells and that CD4(+)CD8(int+) were preferentially recalled by the live virus.
Omega‐3 fatty acid supplementation and total homocysteine levels in end‐stage renal disease patients (2008)

Potential reasons for this non-significant result may be found in a dose-response relationship, advancement of disease progression in our sample population, or potentially the lack of a significant relationship between fish oil and tHcy. Future studies should address whether a dose-response relationship between n-3 fatty acid supplementation and tHcy levels exists, and how stage of disease progression affects intervention success or failure.
Post‐transplant upregulation of chemokine messenger RNA in non‐human primate recipients of intraportal pig islet xenografts (2005)

Our data suggest that CXCR3, with ligands IP-10 and Mig, is involved in T cell recruitment in acute islet xenograft rejection in non-human primates. Upregulation of RANTES and MIP-1alpha transcripts in the absence of a significant CCR5 increase suggests a possible involvement of other chemokine receptors. MCP-1 expression is associated with T cell and macrophage infiltration. Elevated cytotoxic effector molecule expression (Fas ligand, perforin, granzyme B) indicates T-cell mediated graft destruction by cytotoxic and cytolytic mechanisms within 48 to 72 h after transplantation. These results identify the CXCR3-mediated chemoattractant pathway as an immunosuppressive target in pig-to-primate islet xenotransplantation.
Energy efficient sensor data logging with amnesic flash storage (2009)

We present FlashLogger, an energy-efficient sensor data logging system that uses lazy amnesic compression in a flash-efficient manner. FlashLogger incorporates a suite of compression algorithms suitable for progressively compressing time series scalar, audio, and image data. It uses a novel data structure for efficiently organizing and querying compressed data on flash memory. All our methods are designed for the limited memory and processing capabilities typical of low power sensor nodes, and are prototyped on Tmote Sky platform running TinyOS. Evaluation of FlashLogger with several real world data sets shows orders of magnitude energy savings for both logging data and retrieving data within a time range.