gebhart/patrepeval huggingface dataset:
Evolutionary ensembles with negative correlation learning (2000)

Based on negative correlation learning and evolutionary learning, this paper presents evolutionary ensembles with negative correlation learning (EENCL) to address the issues of automatic determination of the number of individual neural networks (NNs) in an ensemble and the exploitation of the interaction between individual NN design and combination. The idea of EENCL is to encourage different individual NNs in the ensemble to learn different parts or aspects of the training data so that the ensemble can learn better the entire training data. The cooperation and specialization among different individual NNs are considered during the individual NN design. This provides an opportunity for different NNs to interact with each other and to specialize. Experiments on two real-world problems demonstrate that EENCL can produce NN ensembles with good generalization ability.
Nonlinear influence on PM-AM conversion measurementof group velocity dispersion in optical fibres (1994)

The authors propose a method for measuring the group velocity dispersion, including the polarity, of optical fibre by using a single wavelength light source. The method is based on the interplay between phase modulation-amplitude modulation (PM-AM) conversion and self-phase modulation (SPM).
Regulated cleavage of intracellular glycosylphosphatidylinositol in a trypanosome (2006)

Cell exposure to hypo-osmolarity and alkalinity triggers a spectrum of responses including activation of phospholipases. Glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC) is expressed in Trypanosoma brucei, a protozoan parasite that causes human African trypanosomiasis. We examined possible contributions of GPI-PLC to the response of T. brucei to hypo-osmotic or mildly alkaline conditions. GPIs were detected at the endoplasmic reticulum (ER). They were cleaved after exposure of T. brucei to hypo-osmolarity or mild alkalinity, which also, strikingly, caused translocation of GPI-PLC from glycosomes (peroxisomes) to the ER. A catalytically inactive Gln81Leu mutant of GPI-PLC failed to cleave GPIs despite being transported from glycosomes to the ER after hypo-osmotic or mild alkaline treatment of the parasites. In contrast, a Cys347Ser mutant of the enzyme could not exit glycosomes after treatment of cells expressing the protein with mild base or hypo-osmotic buffer. We conclude that: (a) GPI-PLC contributes to loss of GPIs in T. brucei treated with hypo-osmotic or mildly alkaline buffer; (b) access of GPI-PLC to its substrate in vivo can be regulated post-translationally; (c) translocation of GPI-PLC from glycosomes to the ER is important for in vivo cleavage of GPIs; (d) Cys347 is part of a peptide motif required for post-translational targeting of GPI-PLC to the ER. Glycosome-to-ER movement of GPI-PLC reveals a novel pathway for intracellular protein traffic. The physiological significance of GPI digestion in cells exposed to mildly alkalinity or hypo-osmolarity is discussed.
A high-brightness duoplasmatron ion source for microprobe secondary-ion mass spectrometry (1995)

A cold-cathode duoplasmatron ion source for producing beams of Ar+ or O− has been designed for the Cambridge P7-Concept microprobe secondary-ion mass spectrometer. An experimental investigation of the performance of the ion source as a function of arc current, extraction potential, magnetic field, anode to extraction-electrode spacing and, in the case of O−, intermediate electrode bore diameter and lateral offset, is presented. The conditions giving maximum source brightness have been determined. Brightness measurements give 1700 and 96 A cm−2 sr−1 for Ar+ and O−, respectively. Focused probes 4.2 μm in diameter have been produced carrying current densities of 0.1 and 0.007 A cm−2 for Ar+ and O−, respectively.
Establishment and characterization of monoclonal antibodies against an octahedral gallium chelate suitable for immunoscintigraphy with PET. (1992)

As a prerequisite for preparing bispecific antibody conjugates containing anti-tumor and anti-metal chelate binding sites that can be used for pretargeted immunoscintigraphy, monoclonal antibodies (Mabs) have been raised against an octahedral metal chelate synthetized from gallium (Ga) and the hexadentate ligand N,N'bis[2-hydroxy 5-(ethylene beta carboxy) benzyl] ethylenediamine N,N' diacetic acid (Ga-HBED-CC). With use of the Farr assay, binding studies with the 67Ga-labeled chelate and three clones of anti-chelate Mabs showed that none of the Mabs were able to precipitate more than 50% of the Ga-chelate, suggesting an enatiomerism of the Ga-chelate and a sensitivity of the Mabs to either one or the other chelate enantiomer. This could be confirmed by comparing the circular dichroism spectra of the Ga-chelate fractions that passed affinity columns containing the Mabs immobilized on sepharose without retention. With use of a Ga-HBED-CC enantiomer, whole-body retention in mice, preinjected with the corresponding anti-metal chelate Mab of ca. 70% ID, was measured compared to 2.1% retention in mice not preinjected with the Mab. Due to the high affinity of chelate-to-Mab binding in vivo, bispecific antibody conjugates prepared from the fragments of the anti-Ga-chelate Mab might be suitable for pretargeted immunoscintigraphy with the short-lived positron-emitter 68Ga.
CD4~+CD25~+ regulatory T cells modulate antigen-presenting function of human umbilical vein endothelial cells (2011)

Objective:To investigate whether and how Treg affect the antigen-presenting function of HUVECs,and the mechanism of Treg in the development of atherosclerosis.Methods:Treg were isolated from human peripheral blood mononuclear cells(PBMCs) which obtained from normal volunteers by magnetic cell sorting-column and analyzed by Flow Cytometry.HUVECs were incubated alone(control) or with anti-CD3 mAbs activated Treg(CD25+) and ox-LDL.After 24 h,HUVECs were collected and the expression of HLA DR,CD80 and CD86 were measured by flow cytometry.ox-LDL treated HUVECs which were pre-cultured with different concentrations of human anti-CD3 mAbs activated Treg were used to stimulate CD4+CD25-T cells,and then the effect of HUVECs on the proliferation of CD4+CD25-T cells were detected by Cell Counting Kit-8(CCK-8).Transwell experiment was used to identify how Treg affect the antigen-presenting function of HUVECs.Results:Treg can significantly inhibit the expression of antigen presenting molecular in HUVECs as well as the effect of HUVECs on the proliferation of CD4+CD25-T cells when compared with that in control system;Mechanistic studies reveal that the expression of antigen presenting molecular in HUVECs and the effect of HUVCs on the proliferation of CD4+CD25-T cells in TW system have no difference when compared with that in no T system.Conclusion:Treg are able to modulate the antigen-presenting function of HUVECs,which is largely attributed to a down-regulated expression in CD86 in Treg-treated HUVECs and depended on cell contact.
Alcune considerazioni sulla storia del paesaggio agrario emiliano (1995)

Lipid membranes in prokaryotes and eukaryotes have a wide array of lipids that are necessary for proper membrane structure and function. In this paper, an introduction to lipid diversity in biology and a mini-review on how molecular simulations have been used to model biological membranes (primarily limited to one to three lipid types in most simulation-based models) is provided, which motivates the use of all-atom molecular dynamics (MD) simulations to study the effect of lipid diversity on properties of realistic membrane models of prokaryotes and eukaryotes. As an example, cytoplasmic membrane models of Escherichia coli were developed at different stages of the colony growth cycle (early-log, mid-log, stationary and overnight). The main difference between lipid compositions at each stage was the concentration of a cyclopropane-containing moiety on the sn-2 lipid acyl chain (cyC17:0). Triplicate MD simulations for each stage were run for 300 ns to study the influence of lipid diversity on the surface area per lipid, area compressibility modulus, deuterium order parameters, and electron density profiles. The overnight stage (also known as the death stage) had the highest average surface area per lipid, highest rigidity, and lowest bilayer thickness compare to other stages of E. coli cytoplasmic membrane. Although bilayer thickness did depend on the growth stage, the changes between these were small suggesting that the hydrophobic core of transmembrane proteins fit well with the membrane in all growth stages. Although it is still common practise in MD simulations of membrane proteins to use simple one- or two-component membranes, it can be important to use diverse lipid model membranes when membrane protein structure and function are influenced by changes in lipid membrane composition.
Identification of an essential acidic residue in Cdc25 protein phosphatase and a general three‐dimensional model for a core region in protein phosphatases (1996)

The reaction mechanism of protein tyrosine phosphatases (PTPases) and dual-specificity protein phosphatases is thought to involve a catalytic aspartic acid residue. This residue was recently identified by site-directed mutagenesis in Yersinia PTPase, VHR protein phosphatase, and bovine low molecular weight protein phosphatase. Herein we identify aspartic acid 383 as a potential candidate for the catalytic acid in human Cdc25A protein phosphatase, using sequence alignment, structural information, and site-directed mutagenesis. The D383N mutant enzyme exhibits a 150-fold reduction in kcat, with Kw only slightly changed. Analysis of sequence homologies between several members of the Cdc25 family and deletion mutagenesis substantiate the concept of a two-domain structure for Cdc25, with a regulatory N-terminal and a catalytic C-terminal domain. Based on the alignment of catalytic residues and secondary structure elements, we present a three-dimensional model for the core region of Cdc25. By comparing this three-dimensional model to the crystal structures of PTP1b, Yersinia PTPase, and bovine low molecular weight PTPase, which share only very limited amino acid sequence similarities, we identify a general architecture of the protein phosphatase core region, encompassing the active site loop motif HCXXXXXR and the catalytic aspartic acid residue.
Statistical parametric maps in functional imaging: A general linear approach (1994)

Abstract Statistical parametric maps are spatially extended statistical processes that are used to test hypotheses about regionally specific effects in neuroimaging data. The most established sorts of statistical parametric maps (e.g., Friston et al. [1991]: J Cereb Blood Flow Metab 11:690–699; Worsley et al. [1992]: J Cereb Blood Flow Metab 12:900–918) are based on linear models, for example ANCOVA, correlation coefficients and t tests. In the sense that these examples are all special cases of the general linear model it should be possible to implement them (and many others) within a unified framework. We present here a general approach that accomodates most forms of experimental layout and ensuing analysis (designed experiments with fixed effects for factors, covariates and interaction of factors). This approach brings together two well established bodies of theory (the general linear model and the theory of Gaussian fields) to provide a complete and simple framework for the analysis of imaging data. The importance of this framework is twofold: (i) Conceptual and mathematical simplicity, in that the same small number of operational equations is used irrespective of the complexity of the experiment or nature of the statistical model and (ii) the generality of the framework provides for great latitude in experimental design and analysis. © 1995 Wiley‐Liss, Inc.
Self-Assembly of Block Copolymer Micelles in an Ionic Liquid (2006)

Four amphiphilic poly((1,2-butadiene)-block-ethylene oxide) (PB-PEO) diblock copolymers were shown to aggregate strongly and form micelles in an ionic liquid, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF(6)]). The universal micellar structures (spherical micelle, wormlike micelle, and bilayered vesicle) were all accessed by varying the length of the corona block while holding the core block constant. The nanostructures of the PB-PEO micelles formed in an ionic liquid were directly visualized by cryogenic transmission electron microscopy (cryo-TEM). Detailed micelle structural information was extracted from both cryo-TEM and dynamic light scattering measurements, with excellent agreement between the two techniques. Compared to aqueous solutions of the same copolymers, [BMIM][PF(6)] solutions exhibit some distinct features, such as temperature-independent micellar morphologies between 25 and 100 degrees C. As in aqueous solutions, significant nonergodicity effects were also observed. This work demonstrates the flexibility of amphiphilic block copolymers for controlling nanostructure in an ionic liquid, with potential applications in many arenas.
Dual-frequency aperture-coupled square patch antenna with double notches (2000)

A novel design method for an aperture-coupled microstrip patch antenna with a single feeding structure is proposed for dual resonance frequencies with mutually perpendicular polarizations. A new type of square patch with double notches is used as a radiator, and the crossed slot and bended microstrip feeder are adopted for the dual polarizations in the aperture-coupled structure. The characteristics of this antenna were experimentally investigated for generalizing the dual-frequency behavior. A Ku-band Tx/Rx 2×2 subarray antenna was designed and manufactured to examine the applicability as a ground terminal antenna for satellite communications. © 2000 John Wiley & Sons, Inc. Microwave Opt Technol Lett 24: 370–374, 2000.
Robust meshes from multiple range maps (2002)

This paper presents a method for modeling the surface of an object from a sequence of range maps. Our method is based on a volumetric approach that produces a compact surface without boundary. It provides robustness through the use of interval analysis techniques and computational efficiency through hierarchical processing using octrees.
Stimulating Very Long Gross Intervals (1985)

ABSTRACT Conventional acidizing and fracturing techniques are not applicable when very long gross intervals on the order of 1,000 to 3,000 feet are to be stimulated. Concepts such as fracture length and improved wellbore radius have little meaning in such cases since it is very difficult to predict or control the placement of stimulation fluids. Good diversion of fluids is the controlling factor for successful stimulation of very long gross intervals. The problem is compounded when long net intervals on the order of 500 to 1,000 feet are to be stimulated within these very long gross intervals. In such cases, the surface injection pressure required for conventional limited entry techniques can be prohibitive. These problems often can be solved by stimulating with high injection rates, buoyant ball sealers, and limited perforations. Amoco Sharjah Oil Company has encountered these problems in attempting to stimulate the Thamama in Sajaa Field. A brief history of Amoco's experience in Sajaa Field with mechanical isolation and various diverting agents is presented. To date, 6 wells have been stimulated by using high injection rates, buoyant ball sealers, and limited perforations. Some of these jobs have contained the largest fluid volumes ever injected in the Middle East and at the highest rates attempted. The results of this technique have been encouraging. The job design, equipment requirements, fluid formulations, and results of these stimulations will be presented.
The Role of Polyamines in Supporting Growth of Mammalian Cells Is Mediated through Their Requirement for Translation Initiation and Elongation (2010)

Polyamines are essential cell constituents whose depletion results in growth cessation. Here we have investigated potential mechanisms of action of polyamines in supporting mammalian cell proliferation. We demonstrate that polyamines regulate translation both at the initiation and at the elongation steps. L-alpha-difluoromethylornithine treatment resulting in polyamine depletion reduces protein synthesis via inhibition of translation initiation. N1-guanyl-diaminoheptane (GC7), a spermidine analogue that inhibits eukaryotic initiation factor 5A (eIF5A) hypusination, also caused inhibition of translation initiation. In contrast, depletion of eIF5A by short hairpin RNA inhibits translation elongation as was recently demonstrated in yeast and Drosophila. These results suggest that in addition to competing with spermidine in the hypusination reaction, GC7 also competes with spermidine at yet undefined sites required for translation initiation. Finally, we show that either polyamine depletion or GC7 treatment induced eIF2alpha phosphorylation and reduced phosphorylation of 4E-BP, thus setting the molecular basis for the observed inhibition of translation initiation.
How Viral and Intracellular Bacterial Pathogens Reprogram the Metabolism of Host Cells to Allow Their Intracellular Replication (2019)

Viruses and intracellular bacterial pathogens (IBPs) have in common the need of suitable host cells for efficient replication and proliferation during infection. In human infections, the cell types which both groups of pathogens are using as hosts are indeed quite similar and include phagocytic immune cells, especially monocytes/macrophages (MOs/MPs) and dendritic cells (DCs), as well as nonprofessional phagocytes, like epithelial cells, fibroblasts and endothelial cells. These terminally differentiated cells are normally in a metabolically quiescent state when they are encountered by these pathogens during infection. This metabolic state of the host cells does not meet the extensive need for nutrients required for efficient intracellular replication of viruses and especially IBPs which, in contrast to the viral pathogens, have to perform their own specific intracellular metabolism to survive and efficiently replicate in their host cell niches. For this goal, viruses and IBPs have to reprogram the host cell metabolism in a pathogen-specific manner to increase the supply of nutrients, energy, and metabolites which have to be provided to the pathogen to allow its replication. In viral infections, this appears to be often achieved by the interaction of specific viral factors with central metabolic regulators, including oncogenes and tumor suppressors, or by the introduction of virus-specific oncogenes. Less is so far known on the mechanisms leading to metabolic reprogramming of the host cell by IBPs. However, the still scant data suggest that similar mechanisms may also determine the reprogramming of the host cell metabolism in IBP infections. In this review, we summarize and compare the present knowledge on this important, yet still poorly understood aspect of pathogenesis of human viral and especially IBP infections.
Physical Data Modeling for Multidimensional Access Methods. (1999)

Introduction Despite the fact that the database community has proposed a vast number of indexing methods over the years, no standard physical data model has been established like it has been achieved on the conceptual and logical level. How to optimize a given data model by using various indexing methods is still the &amp;apos;trade secret` of the database administrators. Only recently, some approaches have been tried to make this knowledge available to the normal database user by easy to use optimization tools (e.g., AutoAdmin-Tool of MS SQL Server 7.0). In addition, physical data modeling has concentrated on one-dimensional access methods, since these were the only ones available in commercial database management systems. As multidimensional access methods (MDAMs) are making their way from the research labs into commercial products, a general physical data model should also take MDAMs into account, especially since MDAMs have a high potential to improve processing in important applica
The notch gene product is a glycoprotein expressed on the cell surface of both epidermal and neuronal precursor cells during Drosophila development. (1989)

The Notch locus of Drosophila melanogaster is one of a small number of zygotically acting "neurogenic" genes involved in the correct segregation of neural from epidermal lineages during embryogenesis as well as in other postembryonic developmental events. We have generated antibody probes against three regions of the Notch protein to study the expression of Notch and begin a biochemical characterization of the protein. Consistent with predictions based on DNA sequence data, here we gather evidence showing that Notch encodes a large, glycosylated surface protein with an apparent molecular mass of 300 kD: (a) all three antibodies detect Notch on Western blots as a high molecular mass, primarily full-length product; (b) immunoelectron microscopy localizes the Notch protein to the cell membrane; and (c) lentil lectin column binding demonstrates that the protein is glycosylated, indicative of its surface protein nature. In general, the distribution of the Notch protein coincides with that of the Notch transcript determined previously by in situ hybridizations. Notch is expressed in a much wider range of tissue types than those disrupted in the neurogenic mutant, as determined by antibody localization. Early labeling in the blastoderm appears ubiquitous except for the pole cells, but as development proceeds some distinctive features emerge: stronger staining is seen within the germ band layer where neuroblast delamination occurs, and the developing embryonic nervous system shows pronounced axonal staining. In third instar larvae, Notch is expressed in imaginal disks and in the central nervous system. Based on these results, certain models for how Notch controls the neuroblast cell fate choice are eliminated. We discuss how Notch may function in this choice as well as in other lineage fate determinations.
Catecholamines Abrogate Antimitogenic Effects of 2-Hydroxyestradiol on Human Aortic Vascular Smooth Muscle Cells (2001)

Catechol-O-methyltransferase (COMT)-mediated methylation of 2-hydroxyestradiol (endogenous estradiol metabolite) to 2-methoxyestradiol (angiogenesis inhibitor) may be responsible for the antimitogenic effects of 2-hydroxyestradiol on vascular smooth muscle cells (VSMCs). Catecholamines are also substrates for COMT, and increased levels of catecholamines are associated with vasoocclusive disorders. We hypothesize that catecholamines may abrogate the vasoprotective effects of 2-hydroxyestradiol by competing for COMT and inhibiting 2-methoxyestradiol formation. To test this hypothesis, we investigated the antimitogenic effects of 0.001 to 0.1 micromol/L of 2-hydroxyestradiol on human aortic VSMC proliferation (cell number and DNA synthesis), collagen synthesis, and migration in the presence and absence of catecholamines. Norepinephrine, epinephrine, and isoproterenol concentration-dependently abrogated the inhibitory effects of 2-hydroxyestradiol on cell number, DNA synthesis, collagen synthesis, and cell migration. These modulatory/attenuating effects of catecholamines were not abrogated in the presence of the alpha- and beta-adrenergic receptor antagonists, phentolamine mesylate and propranolol, respectively. In contrast to 2-hydroxyestradiol, the antimitogenic effects of 2-methoxyestradiol (0.1 micromol/L) were not attenuated by isoproterenol (1 micromol/L) or quercetin (competitive inhibitor of COMT, 10 micromol/L). Norepinephrine, epinephrine, and isoproterenol concentration-dependently (10 to 500 micromol/L) inhibited the metabolism of 2-hydroxyestradiol (0.25 to 2 micromol/L) to 2-methoxyestradiol, and the potency of the catecholamines to reverse 2-hydroxyestradiol-induced inhibition of VSMC proliferation, collagen synthesis, and migration was correlated with their ability to inhibit 2-methoxyestradiol formation. Our findings suggest that catecholamines within the vasculature may abrogate the anti-vaso-occlusive effects of estradiol and 2-hydroxyestradiol by blocking 2-methoxyestradiol formation.