gebhart/patrepeval huggingface dataset:
Insulin‐like growth factor II mRNA‐binding protein 3 expression predicts unfavorable prognosis in patients with neuroblastoma (2011)

Insulin-like growth factor II mRNA-binding protein 3 (IMP3) has been reported to enhance proliferation and invasion in various cancers. The role of IMP3 on neuroblastoma (NB) is unknown. We aimed to clarify the prognostic significance of IMP3 expression in patients with NB. By microarray analysis, high IMP3 expression was found in patients with poor outcome. IMP3 expression in 90 NB samples was analyzed by immunohistochemical staining to correlate with clinical stages, histology, and patient outcome. Positive IMP3 expression was detected in 52 of 90 patients, and was significantly correlated with undifferentiated histology, advanced stages, MYCN amplification, and poor outcome. In subgroups, positive IMP3 expression could predict an even worse prognosis in patients with advanced disease, with normal MYCN status, or with MYCN amplification (P = 0.005, P = 0.001, and P = 0.033, respectively). The IMP3 expression decreased by induction of differentiation with retinoid acid treatment in SK-N-DZ and SK-N-SH cells in vitro. The invasion ability of NB cells also decreased as IMP3 knockdown by using RNA interference in vitro. In summary, high expression of IMP3 in NB might contribute to the undifferentiated phenotype and invasive behaviors, leading to a poor prognosis. Determining IMP3 expression in NB could help to improve a personalized therapy.
Effect of electrical stimulation on chronic wound healing: a meta‐analysis (1999)

The purpose of this meta-analysis was to quantify the effect of electrical stimulation on chronic wound healing. Fifteen studies, which included 24 electrical stimulation samples and 15 control samples, were analyzed. The average rate of healing per week was calculated for the electrical stimulation and control samples. Ninety-five percentage confidence intervals were also calculated. The samples were then grouped by type of electrical stimulation device and chronic wound and reanalyzed. Rate of healing per week was 22% for electrical stimulation samples and 9% for control samples. The net effect of electrical stimulation was 13% per week, an increase of 144% over the control rate. The 95% confidence intervals of the electrical stimulation (18-26%) and control samples (3.8-14%) did not overlap. Electrical stimulation was most effective on pressure ulcers (net effect = 13%). Findings regarding the relative effectiveness of different types of electrical stimulation device were inconclusive. Although electrical stimulation produces a substantial improvement in the healing of chronic wounds, further research is needed to identify which electrical stimulation devices are most effective and which wounds respond best to this treatment.
Matrix construction using cyclic shifts of a column (2005)

This paper describes the synthesis of matrices with good correlation, from cyclic shifts of pseudonoise columns. Optimum matrices result whenever the shift sequence satisfies the constant difference property. Known shift sequences with the constant (or almost constant) difference property are: quadratic (polynomial) and reciprocal shift modulo prime, exponential shift, Legendre shift, Zech logarithm shift, and the shift sequences of some m-arrays. We use these shift sequences to produce arrays for watermarking of digital images. Matrices can also be unfolded into long sequences by diagonal unfolding (with no deterioration in correlation) or row-by-row unfolding, with some degradation in correlation
Medium- and Large-Vessel Vasculitis (2003)

Giant-cell arteritis typically involves extracranial branches of the aorta, such as the temporal and vertebral arteries. Temporal arteritis and polymyalgia rheumatica often coexist, and systemic manifestations of inflammation occur in virtually all forms of giant-cell arteritis. This article reviews the mechanisms that contribute to the causes of giant-cell arteritis, with an emphasis on immune-mediated injury to arteries.
Specific binding of poly(I) · poly(C) to the membrane of murine B lymphocyte subsets (1978)

Indirect immunofluorescence revealed that 13% of BALB/c and 33% of CBA spleen cells of B type carry specific binding sites at their surface for double-stranded poly(I).poly(C). Pretreatment of BALB/c spleen cells with anti-mouse immunoglobulin serum increased the number of B cells capable of binding poly(I).poly(C) indicating the existence of a second B lymphocyte subpopulation carrying masked poly(I).poly(C)-binding sites. Pretreatment of the cells with mitogenic doses of either lipopolysaccharide (LPS) or single-stranded polynucleotides, e.g. poly(I) or double-stranded poly(A).poly(U), failed to affect binding of poly(I).poly(C) to the cells. Poly(I).poly(C) converts small poly(I).poly(C)-binding lymphocytes into lymphoblasts carrying poly(I).poly(C)-binding sites. Lymphoblasts derived from LPS-stimulated cells do not carry poly(I).poly(C)-binding sites. Thymocytes or splenic T cells failed to bind poly(I).poly(C). As measured by thymidine uptake, CBA mice containing a higher percentage of poly(I).poly(C)-binding cells, are high responder mice to poly(I).poly(C), compared with low responder BALB/c mice.
Time-varying, frequency-domain modeling and analysis of phase-locked loops with sampling phase-frequency detectors (2003)

This paper presents a new, frequency-domain based method for modeling and analysis of phase-locked loop (PLL) small-signal behavior, including time-varying aspects. Focus is given to PLLs with sampling phase-frequency detectors (PFDs) which compute the phase error only once per period of the reference signal. Using the harmonic transfer matrix (HTM) formalism, the well known continuous-time, linear time-invariant (LTI) approximations are extended to take the impact of time-varying behavior arising from the sampling nature of the PFD, into account. Especially for PLLs with a fast feedback loop, this time-varying behavior has severe impact on, for example, loop stability and cannot be neglected. Contrary to LTI analysis, our method is able to predict and quantify these difficulties. The method is verified for a typical loop design.
Characterization of monoclonal antibodies specific for adhesion: isolation of an adhesin of Streptococcus sanguis FW213 (1986)

Monoclonal antibodies reactive to an adhesive strain of Streptococcus sanguis (FW213) and nonreactive to a nonadhesive mutant (JL7) were derived from the fusion of myeloma line X63Ag8.653 and spleen cells from BALB/c mice immunized with live S. sanguis cells. Five cell lines, belonging to subclasses of immunoglobulin G, produced monoclonal antibodies specifically directed against the adhesive strain. All five antibodies also failed to react with five additional, independently isolated, nonadhesive mutants. A spontaneous mutant of FW213 (VT508) that no longer reacted with monoclonal antibody F51 (MAbF51) was isolated by serial agglutination with the antibody. Langmuir adsorption isotherms of VT508 indicated that this mutant also had altered ability to adhere to saliva-coated hydroxyapatite further confirming the specificity of MAbF51 for adhesion. Electron microscopy revealed that VT508 had lost the peritrichous fimbriae associated with the adhesion of FW213. MAbF51 was used to purify the adhesin from lysozyme cell extracts by using an affinity column of MAbF51 linked to Sephacryl S1000. Purity was suggested by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and crossed immunoelectrophoresis (CIEP). The adhesin had a molecular weight greater than 150,000 and was not denatured in sodium dodecyl sulfate reducing gels. Two peaks of near electrophoretic mobility were detected in CIEP when the purified material was run against polyclonal antibody to the whole cell. Tandem CIEP analysis and immunoprecipitation provided evidence that the two peaks represented the same antigen in two different forms.
Specificity of guinea pig liver transglutaminase for amine substrates (1979)

The amine specificity of guinea pig liver transglutaminase, a model enzyme for endo-gamma-glutamine:epsilon-lysin transferases, was explored with the aid of synthetic substrates of high apparent affinities. As exemplified by dansyl- (5-dimethylamino-1-naphthalenesulfonyl), (2,4-dinitrobenzenesulfonyl)-, and (2,4,6-triisopropylbenzenesulfonyl)-cadaverines--each of which showed affinities of approximately 4 x 10(7) M-1--the best amine substrates carried a large hydrophobic substituent attached to an alkylamine side chain of about 7.2 A in length. Altogether, our results point to the importance of a hydrophobic binding region in the enzyme from where the alkyl side chain reaches into a narrow crevice toward the active center and positions the primary amine of the substrate for attacking the carbonyl group of the acyl enzyme intermediate.
Binding of Transition Metal Ions [Cobalt, Copper, Nickel and Zinc] with Furanyl-, Thiophenyl-, Pyrrolyl-, Salicylyl-and Pyridyl-Derived Cephalexins as Potent Antibacterial Agents (2004)

A method is described for the preparation of novel cephalexin-derived furanyl-, thiophenyl-, pyrrolyl-, salicylyl- and pyridyl-containing compounds showing potent antibacterial activity. The binding of these newly synthesized antibacterial agents with metal ions such as cobalt(II), copper(II), nickel(II) and zinc(II) has been studied and their inhibitory properties against various bacterial species such as Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae are also reported. These results suggest that metal ions to possess an important role in the designing of metal-based antibacterials and that such complexes are more effective against infectious diseases compared to the uncomplexed drugs.
An Integrated Amperometry Waveform for the Direct, Sensitive Detection of Amino Acids and Amino Sugars Following Anion-Exchange Chromatography (1999)

This paper describes a new detection method that uses a six-potential waveform to detect all amino acids without derivatization. The detection limits are less than 1 pmol for most of the analytes. The anion-exchange separation uses a ternary gradient with water, 0.25 M sodium hydroxide, and 1.0 M sodium acetate. We present results of waveform optimization experiments designed to minimize gradient artifacts and to achieve optimum conditions for the quantitative analysis of common amino acids. Analytical results for protein hydrolysates are discussed and compared with those obtained by cation exchange followed by ninhydrin derivatization and spectrophotometric detection.
RXR antagonism induces G0/G1 cell cycle arrest and ameliorates obesity by up‐regulating the p53–p21$^{\rm{Cip1}}$ pathway in adipocytes (2011)

The peroxisome proliferator activated receptor-γ (PPARγ) agonist, pioglitazone (PIO), exerts anti-diabetic properties associated with increased fat mass, whereas the retinoid X receptor (RXR) antagonist HX531 demonstrates anti-obesity and anti-diabetic effects with reduced body weight and fat pad mass. The cell cycle abnormality in adipocytes has not been well-investigated in obesity or during treatment with modulators of nuclear receptors. We therefore investigated cell size and cell cycle distributions of adipocytes in vivo and examined the expression of cell cycle regulators in cultured human visceral preadipocytes. The cell size distribution and cell cycle analyses of in vivo adipocytes derived from OLETF rats demonstrated that HX531 brought about G0/G1 cell cycle arrest associated with the inhibition of cellular hypertrophy, which resulted in the reduction of fat pad mass. In contrast, PIO promoted proliferation activities associated with the increase in M + late M:G0 + G1 ratio and the appearance of both small and hypertrophied adipocytes. In cultured human visceral preadipocytes HX531 up-regulated cell cycle regulators, p53, p21(Cip1), cyclin D1, Fbxw7 and Skp2, which are known contributors towards G0 /G1 cell cycle arrest. The knockdown of p53 with a shRNA lentivirus reversed the HX531-induced up-regulation of p21(Cip1), which is one of the major p53-effector molecules. We conclude that HX531 exerts anti-obesity and anti-diabetes properties by up-regulating the p53-p21(Cip1) pathway, resulting in G0/G1 cell cycle arrest and the inhibition of cellular hypertrophy of adipocytes.
Embryo-Specific Reduction of ADP-Glc Pyrophosphorylase Leads to an Inhibition of Starch Synthesis and a Delay in Oil Accumulation in Developing Seeds of Oilseed Rape (2004)

In oil-storing Brassica napus (rape) seeds, starch deposition occurs only transiently in the early stages of development, and starch is absent from mature seeds. This work investigates the influence of a reduction of ADP-Glc pyrophosphorylase (AGPase) on storage metabolism in these seeds. To manipulate the activity of AGPase in a seed-specific manner, a cDNA encoding the small subunit of AGPase was expressed in the sense or antisense orientation under the control of an embryo-specific thioesterase promoter. Lines were selected showing an embryo-specific decrease in AGPase due to antisense and cosuppression at different stages of development. At early developmental stages (25 days after flowering), a 50% decrease in AGPase activity was accompanied by similar decreases in starch content and the rate of starch synthesis measured by injecting (14)C-Suc into seeds in planta. In parallel to inhibition of starch synthesis, the level of ADP-Glc decreased, whereas Glc 1-phosphate levels increased, providing biochemical evidence that inhibition of starch synthesis was due to repression of AGPase. At 25 days after flowering, repression of starch synthesis also led to a decrease in the rate of (14)C-Suc degradation and its further metabolism via other metabolic pathways. This was not accompanied by an increase in the levels of soluble sugars, indicating that Suc import was inhibited in parallel. Flux through glycolysis, the activities of hexokinase, and inorganic pyrophosphate-dependent phosphofructokinase, and the adenylate energy state (ATP to ADP ratio) of the transgenic seeds decreased, indicating inhibition of glycolysis and respiration compared to wild type. This was accompanied by a marked decrease in the rate of storage lipid (triacylglycerol) synthesis and in the fatty acid content of seeds. In mature seeds, glycolytic enzyme activities, metabolite levels, and ATP levels remained unchanged, and the fatty acid content was only marginally lower compared to wild type, indicating that the influence of AGPase on carbon metabolism and oil accumulation was largely compensated for in the later stages of seed development. Results indicate that AGPase exerts high control over starch synthesis at early stages of seed development where it is involved in establishing the sink activity of the embryo and the onset of oil accumulation.
Neutralizing anti‐vascular endothelial growth factor antibody completely inhibits angiogenesis and growth of human prostate carcinoma micro tumors in vivo (1998)

BACKGROUND Neovascularization mediated by growth factors produced by tumors is critical for the growth of tumors. Vascular endothelial growth factor (VEGF) is one such growth factor. A neutralizing anti-VEGF antibody (A4.6.1) was recently shown in vivo to inhibit tumor angiogenesis and growth of the human rhabdomyosarcoma cell line A673. The antibody profoundly changed the growth characteristics of the tumor line from a rapidly growing malignancy to a dormant microcolony. METHODS In the present study, we evaluated the effects of A4.6.1 (100 μg twice weekly, i.p.) on growth and angiogenic activity of spheroids of the human prostatic cell line DU 145 (diameter 700 μm at implantation) implanted in dorsal skinfold chambers in nude mice (n = 11). An antibody of the same isotype (n = 5) or saline (n = 5) was used as control. Tumor cells were prelabeled with a fluorescent vital dye (CMTMR), which allowed measurement of size of the implanted tumor spheroids throughout a two week observation period. FITC-dextran was used for plasma enhancement to visualize angiogenic activity. RESULTS Tumors of control animals induced a neo-vasculature with high vascular density (350 ± 12 cm\-1). In animals treated with the anti-VEGF antibody, there was complete inhibition of neovascularization of the micro tumors and complete inhibition of tumor growth after the initial prevascular angiogenesis independent growth phase. CONCLUSIONS These results demonstrate that inhibition of the key regulatory paracrine growth factor for endothelial cells, VEGF, results in complete suppression of prostate cancer induced angiogenesis and prevents tumor growth beyond the initial prevascular growth phase. Prostate 35:1–10, 1998. © 1998 Wiley-Liss, Inc.
Empirically Estimable Classification Bounds Based on a Nonparametric Divergence Measure (2015)

Information divergence functions play a critical role in statistics and information theory. In this paper we show that a non-parametric <i>f</i>-divergence measure can be used to provide improved bounds on the minimum binary classification probability of error for the case when the training and test data are drawn from the same distribution <i>and</i> for the case where there exists some mismatch between training and test distributions. We confirm the theoretical results by designing feature selection algorithms using the criteria from these bounds and by evaluating the algorithms on a series of pathological speech classification tasks.
Design of phased-array wavelength division multiplexers using multimode interference couplers (1997)

Novel designs for phased-array wavelength-division multiplexers based on self-imaging properties of multimode interference (MMI) couplers are presented. These devices, which operate on N equally spaced wavelength channels, consist of two MMI couplers connected by an array of N monomode waveguides. The MMI couplers function as power splitters/combiners, and the waveguide array is the dispersive element. The excellent characteristics of MMI couplers offer the possibility of designing small-size devices with low loss and with high uniformity among different channels. A general theoretical formulation for an N-channel multiplexer is presented, and a simple procedure for finding an optimum set of lengths for the array guides is given. We show that these multiplexers can function as N x N wavelength-selective interconnecting components. The simulated performance of three variations of a five-channel device, designed in a rib waveguide system, is given. It is demonstrated that sidelobes in the multiplexer spectral response can be suppressed by weighting the power samples in the array waveguides through appropriate design of a nonuniform MMI power splitter.
Intensity dependent spatial quantization with application in HEVC (2013)

With the increase of video resolutions used in multimedia applications, solutions for improved compression are sought. The next generation video compression standard, High Efficiency Video Coding (HEVC) is being developed by ITU-T and ISO/IEC MPEG with the goal to provide significant improvements over H.264/AVC. To further increase compression capabilities of HEVC, this paper proposes an additional bitrate saving mechanism. In this context, an Intensity Dependant Spatial Quantization (IDSQ) perceptual tool is proposed which exploits the intensity masking of the human visual system and perceptually adjusts quantization. The proposed IDSQ allows for adaptation to the video characteristics and its design meets low complexity implementation requirements. The proposed IDSQ has been tested in the HEVC test model and its performance is reported under “just noticeable distortion” or “perceptually lossless” conditions. In this setup, bitrate reductions of up to 25% are reported with an average of 3.4% over an exhaustive test setup.
Synthesis, characterizations, and physical properties of carbon nanotubes coated by conducting polypyrrole (1999)

A new type of carbon nanotube (CNT) (diameter of <100 nm) coated by conducting polypyrrole (PPY) was synthesized by in situ polymerization on CNTs. The structure of the resulting complex nanotubes (CNT-PPY) was characterized by elemental analysis, X-ray photoelectron spectroscopy, Raman spectra, and X-ray diffraction. These indicated no significant chemical interaction between PPY and the CNT. The electrical, magnetic, and thermal properties of the complex nanotubes were measured and showed the physical properties of the CNTs were modified by conducting PPY. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 74: 2605–2610, 1999
A distinct distribution of natural killer cell subgroups in human tissues and blood (1998)

Natural killer (NK) cells have been subdivided according to their CD16/ CD56 expression into at least 2 subgroups. We examined the distribution of these NK subgroups in humans. In the blood of normal individuals, CD16++/ CD56+/ CD3– NK cells predominate, constituting more than 90% of all NK cells. In contrast, decidua is infiltrated almost exclusively by CD16+/–/ CD56+/ CD3– NK cells (>90%), a fact so far seen in context with decidua being an immunoprivileged tissue. However, this NK subgroup can also be detected in the blood, where it comprises about 10% of NK cells. We have found that normal (colon) as well as neoplastic (ovarian and urothelial carcinoma) tissues are also predominantly infiltrated by this CD16+/– NK subgroup. Lymphatic fluid draining solid tissues contains CD16+/– NK cells exclusively, with absolute numbers of NK cells being very low. No predominating NK subgroup was seen in ascites. CD16+/– NK cells, when tested against the target cell lines K562 and JAR, revealed a cytotoxic spectrum different from CD16++ NK cells and from T cells. A change in the CD16/ CD56/ CD3 phenotype was not seen in either subgroup in long-term cultures containing IL-2 (1,000 U/ ml). Our data indicate that the decidua is not the only solid tissue infiltrated by CD16+/– NK cells. Other normal and malignant tissues were also infiltrated predominantly by this NK cell subgroup. We suggest that CD16+/– NK cells represent a functionally distinct NK subgroup involved in the surveillance of solid tissues. Int. J. Cancer 78:533–538, 1998. © 1998 Wiley-Liss, Inc.
Performing statistical analyses on quantitative data in Taverna workflows: An example using R and maxdBrowse to identify differentially-expressed genes from microarray data (2008)

Taverna can be used by data analysis experts as a generic tool for composing ad hoc analyses of quantitative data by combining the use of scripts written in the R programming language with tools exposed as services in workflows. When these workflows are shared with colleagues and the wider scientific community, they provide an approach for other scientists wanting to use tools such as R without having to learn the corresponding programming language to analyse their own data.
Fibrin Glue (TisseelR) Added with Sodium Hyaluronate in Microvascular Anastomosing (1993)

To test the effect on the handling properties of a two component fibrin glue, the viscosity was increased with sodium hyaluronate and the glue was applied to a microvascular anastomosis in rats. The femoral artery of each rat was anastomosed with three conventional sutures and then sealed with fibrin glue. Three glues with different viscosities were tested: original TisseelR fibrin glue (Immuno AG. Vienna); TisseelR with 0.9% sodium chloride added to the fibrinogen component; and TisseelR with a high molecular weight sodium hyaluronate (10 mg/ml, HealonR, Pharmacia, Sweden) added to the fibrinogen component. The increased viscosity of the fibrin glue to which hyaluronate had been added resulted in a significantly higher patency rate 20 minutes after completion of the anastomosis (p<0.01), and reduced the amount of fibrin that entered the vessels.