gebhart/patrepeval huggingface dataset:
Pattern Recognition and Image Preprocessing (2002)

Describing non-parametric and parametric theoretic classification and the training of discriminant functions, this second edition includes new and expanded sections on neural networks, Fisher's discriminant, wavelet transform, and the method of principal components. It contains discussions on dimensionality reduction and feature selection; novel computer system architectures; proven algorithms for solutions to common roadblocks in data processing; computing models including the Hamming net, the Kohonen self-organizing map, and the Hopfield net; detailed appendices with data sets illustrating key concepts in the text; and more.
Light-Controlled Molecular Shuttles Made from Motor Proteins Carrying Cargo on Engineered Surfaces (2001)

Molecular shuttles have been built from motor proteins capable of moving cargo along engineered paths. We illustrate alternative methods of controlling the direction of motion of microtubules on engineered kinesin tracks, how to load cargo covalently to microtubules, and how to exploit UV-induced release of caged ATP combined with enzymatic ATP degradation by hexokinase to turn the shuttles on and off sequentially. These are the first steps in the development of a tool kit to utilize molecular motors for the construction of nanoscale assembly lines.
Synthesis and Biophysical Studies of Modified Oligonucleotides Containing Acyclic Amino Alcohol Nucleoside Analogs (1999)

Abstract Novel serine derivative of thymine was prepared and incorporated into oligonucleotides. These modified oligonucleotides were studied for their binding affinity with complementary DNA/RNA.
A thermoacidophilic endoglucanase (CelB) from Alicyclobacillus acidocaldarius displays high sequence similarity to arabinofuranosidases belonging to family 51 of glycoside hydrolases (2003)

A 100-kDa protein with endoglucanase activity was purified from Triton X-100 extract of cells of the thermoacidophilic Gram-positive bacterium Alicyclobacillus acidocaldarius. The enzyme exhibited activity towards carboxy methyl cellulose and oat spelt xylan with pH and temperature optima of 4 and 80 degrees C, respectively. Cloning and nucleotide sequence analysis of the corresponding gene (celB) revealed an ORF encoding a preprotein of 959 amino acids which is consistent with an extracellular localization. Purified recombinant CelB and a variant lacking the C-terminal 203 amino acid residues (CelBtrunc) displayed similar enzymatic properties as the wild-type protein. Analysis of product formation suggested an endo mode of action. Remarkable stability was observed at pH values between 1 and 7 and 60% of activity were retained after incubation for 1 h at 80 degrees C. CelB displayed homology to members of glycoside hydrolase family 51, being only the second entry with activity typical of an endoglucanase but lacking activity on p-nitrophenyl-alpha-l-arabinofuranoside (pNPAraf). Highest sequence similarity was found towards the other endoglucanase F from Fibrobacter succinogenes (EGF), forming a distinct group in the phylogenetic tree of this family. Analysis of the amino acid composition of the catalytic domains demonstrated that CelB contains fewer charged amino acids than its neutrophilic counterparts, which is in line with adaptation to low pH. Wild-type and full-length recombinant CelB were soluble only in Triton X-100. In contrast, CelBtrunc was completely water soluble, suggesting a role of the C-terminal region in cell association. This C-terminal hydrophobic region displayed local sequence similarities to an alpha-amylase from the same organism.
pKa of the Protonated Schiff Base and Aspartic 85 in the Bacteriorhodopsin Binding Site Is Controlled by a Specific Geometry between the Two Residues (1995)

The structure and function of the light-driven proton pump bacteriorhodopsin appear to be determined by the exact geometrical conformation of specific groups in the retinal binding site, including bound water molecules. This applies to the pKa values of the protonated Schiff base, which links the retinal chromophore to Lys216, and to Asp85. In the present work we show that the geometrical constraints imposed by the ring structures of several synthetic retinals can induce substantial changes in the pKa values of the Schiff base and of Asp85. Thus, the artificial pigments derived from 13-demethyl-11,14-epoxyretinal (2) and 13-demethyl-9,12-epoxyretinal (3) show protonated Schiff base pKa values of 8.2 +/- 0.1 and 9.1 +/- 0.1, respectively, as compared with 13.3 in the native (all-trans-retinal) pigment. We also suggest that in both systems the pKa of Asp85 increases from 3.2 in the native bR to above 9. Analogous, though smaller, effects are obtained for artificial bR pigments derived from 12,14-ethanoretinal (4), 11,13-propanoretinal (5), 11,13-ethanoretinal (6), and p-(CH3)2N-C6H4-HC = CH-C(CH3) = CH-CHO 7. The effects of geometry on the pKa values (those on Asp85 being more pronounced) are attributed to the disruption of the original, well-defined, structure in which the Schiff base and its Asp85 counterion are bridged by bound water molecules. These results are the first to show that it is possible to modify the pKa values of the Schiff base and Asp85 in appropriate artificial pigments, without inducing intrinsic pKa changes in the chromophore or introducing a mutation in the protein.(ABSTRACT TRUNCATED AT 250 WORDS)
Predicting proteasomal cleavage sites: a comparison of available methods (2003)

The proteasome plays an essential role in the immune responses of vertebrates. By degrading intercellular proteins from self and non-self, the proteasome produces the majority of the peptides that are presented to cytotoxic T cells (CTL). There is accumulating evidence that the C-terminal, in particular, of CTL epitopes is cleaved precisely by the proteasome, whereas the N-terminal is produced with an extension, and later trimmed by peptidases in the cytoplasm and in the endoplasmic reticulum. Recently, three publicly available methods have been developed for prediction of the specificity of the proteasome. Here, we compare the performance of these methods on a large set of CTL epitopes. The best method, NetChop at www.cbs.dtu.dk/Services/NetChop, can capture approximately 70% of the C-termini correctly. This result suggests that the predictions can still be improved, particularly if more quantitative degradation data become available.
Synthetic estrogen 17alpha-ethinyl estradiol induces pattern of uterine gene expression similar to endogenous estrogen 17beta-estradiol. (1999)

17alpha-Ethinyl estradiol is one of most widely prescribed estrogens. We compared the effects of this synthetic estrogen to those of the endogenous ovarian hormone 17beta-estradiol on the expression of four estrogen-inducible genes in the rat uterus. The genes examined include c-fos, c-jun, vascular endothelial growth factor, and creatine kinase B, which are all known to be primary responses to estrogen administration. Both estrogens induced the four target genes with similar time courses and produced the same pattern of cell-specific expression of c-fos and vascular endothelial growth factor in the uterine epithelium and stroma, respectively. Dose-response studies established that the potency and efficacy of both estrogens in the uterus were the same for all four hormone-regulated genes. These studies suggest that 17alpha-ethinyl and 17beta-estradiol produce similar if not identical patterns of gene expression in the uterus.
Receptor protein tyrosine kinase DDR is up‐regulated by p53 protein (1996)

We have previously reported on radiation-induction of ptk-3 in rat astrocyte culture [Sakuma et al. (1995) Radiat. Res. 143, 1-7]. Ptk-3 was considered to be a rat version of human DDR (discoidin domain receptor). We cloned and analyzed genomic DNA of the DDR and its promoter region. We discovered that the promoter region contained a consensus sequence of the p53 tumor suppressor binding site. Adenovirus-mediated p53 transfection induced a high level of DDR mRNA in SAOS2 human osteosarcoma cells. These results indicate that DDR is up-regulated by the p53 protein.
Genetic basis of the neurovirulence of pseudorabies virus (1984)

Lomniczi et al. (J. Virol. 49:970-979, 1984) have shown previously that two attenuated vaccine strains of pseudorabies virus have a similar deletion in the short unique (US) region of the genome. The region which is deleted normally codes for several translationally competent mRNAs. As expected, these mRNAs are not formed in the cells infected with the vaccine strains. The function specified by these mRNAs is thus not necessary for growth in cell culture. Using intracerebral inoculation of 1-day-old chicks as a test system, we have attempted to determine whether a gene within the region that is missing from the attenuated strains specifies functions that are required for the expression of virulence. An analysis of recombinants between the Bartha vaccine strain and a virulent pseudorabies virus strain (having or lacking a thymidine kinase gene [TK+ or TK-]) revealed the following. None of the recombinant plaque isolates that were either TK- or which had a deletion in the US was virulent. Not all recombinant plaque isolates which were both TK+ and had an intact US were virulent. These results indicate that both thymidine kinase activity and an intact US were necessary but not sufficient for the expression of virulence. Marker rescue experiments involving cotransfection of the Bartha strain DNA and a restriction fragment spanning the region of the genome that was missing from the Bartha strain resulted in the isolation of virions to which an intact US had been restored. These virions were not virulent but had an improved ability to replicate in the brains of chicks compared with that of the parental nonrescued Bartha strain. Our results show that genes in the US region, which are missing from the Bartha strain, were necessary for virulence but that this strain was also defective in other genes required for the expression of virulence. Thus, the virulence of pseudorabies virus, as measured by intracerebral inoculation into chicks, appears to be controlled multigenically.
Poly(vinyl alcohol) synthetic polymer foams as scaffolds for cell encapsulation (1998)

Poly(vinyl alcohol) (PVA) foams were used as scaffolds in hollow fiber membrane-based cell encapsulation devices. The surrounding permselective membrane serves as an immunoisolation barrier while allowing metabolites and other small molecules to be freely transported. The internal matrix defines the microenvironment for the encapsulated cells. PC12 cell-containing devices represent one possible strategy for safe transplantation of dopamine-secreting cells for the treatment of dopamine-deficient diseases such as Parkinson's disease. PC12 cells--a dopamine-secreting cell line--were encapsulated with PVA foam as a matrix material in the lumen of these hollow fibers. In this work, we demonstrate the presence of the PVA matrix increased the catecholamine secretion efficiency of the cells as compared to devices containing a chitosan matrix. Devices were implanted in vivo into rodent striatum and device output of catecholamines was measured preimplant and post-explant. Evoked stores of dopamine remained constant (preimplant vs explant) for devices encapsulated with the foam matrix and increased with devices encapsulated with chitosan matrix. Cell proliferation within devices was inhibited in the presence of the foam matrix. Cell viability and distribution was significantly improved with the inclusion of the foam matrix in both in vitro and in vivo studies. In comparison to chitosan--a typical matrix material for PC12 cells--addition of a foam-type matrix altered the encapsulated cell microenvironment and resulted in more efficient secretion of catecholamines and improved distribution within the device resulting in smaller necrotic regions and a lower rate of cell proliferation.
Feline Immunodeficiency Virus Infection Phenotypically and Functionally Activates Immunosuppressive CD4+CD25+ T Regulatory Cells (2004)

Disease progression of feline immunodeficiency virus (FIV) infection is characterized by up-regulation of B7.1 and B7.2 costimulatory molecules and their ligand CTLA4 on CD4(+) and CD8(+) T cells. The CD4(+)CTLA4(+)B7(+) phenotype described in FIV(+) cats is reminiscent of CD4(+)CD25(+)CTLA4(+) cells, a phenotype described for immunosuppressive T regulatory (Treg) cells. In the present study, we describe the phenotypic and functional characteristics of CD4(+)CD25(+) T cells in PBMC and lymph nodes (LN) of FIV(+) and control cats. Similar to Treg cells, feline CD4(+)CD25(+) but not CD4(+)CD25(-) T cells directly isolated from LN of FIV(+) cats do not produce IL-2 and fail to proliferate in response to mitogen stimulation. Unstimulated CD4(+)CD25(+) T cells from FIV(+) cats significantly suppress the proliferative response and the IL-2 production of Con A-stimulated autologous CD4(+)CD25(-) T cells compared with unstimulated CD4(+)CD25(+) T cells from FIV(-) cats. Flow-cytometric analysis confirmed the apparent activation phenotype of the CD4(+)CD25(+) cells in LN of chronically FIV(+) cats, because these cells showed significant up-regulation of expression of costimulatory molecules B7.1, B7.2, and CTLA4. These FIV-activated, anergic, immunosuppressive CD25(+)CTLA4(+)B7(+)CD4(+) Treg-like cells may contribute to the progressive loss of T cell immune function that is characteristic of FIV infection.
Increasing recombinant protein production in Escherichia coli through metabolic and genetic engineering (2011)

Different hosts have been used for recombinant protein production, ranging from simple bacteria, such as Escherichia coli and Bacillus subtilis, to more advanced eukaryotes as Saccharomyces cerevisiae and Pichia pastoris, to very complex insect and animal cells. All have their advantages and drawbacks and not one seems to be the perfect host for all purposes. In this review we compare the characteristics of all hosts used in commercial applications of recombinant protein production, both in the area of biopharmaceuticals and industrial enzymes. Although the bacterium E. coli remains a very often used organism, several drawbacks limit its possibility to be the first-choice host. Furthermore, we show what E. coli strains are typically used in high cell density cultivations and compare their genetic and physiological differences. In addition, we summarize the research efforts that have been done to improve yields of heterologous protein in E. coli, to reduce acetate formation, to secrete the recombinant protein into the periplasm or extracellular milieu, and to perform post-translational modifications. We conclude that great progress has been made in the incorporation of eukaryotic features into E. coli, which might allow the bacterium to regain its first-choice status, on the condition that these research efforts continue to gain momentum.
Expression of theRenilla reniformis Luciferase Gene in Mammalian Cells (1996)

A cDNA encoding the Renilla reniformis luciferase was expressed in similan and murine cells in a transient and stable manner, respectively. Light emission catalyzed by luciferase was detected from transfected cells both in vitro and in vivo. This work establishes the Renilla luciferase gene as a new efficient marker of gene expression in mammalian cells.
Microstructure and Rheology of Yogurt Made with Cultures Differing Only in Their Ability to Produce Exopolysaccharides (2003)

Yogurt was made using an exopolysaccharide-producing strain of Streptococcus thermophilus and its genetic variant that only differed from the mother strain in its inability to produce exopolysaccharides. The microstructure was investigated using confocal scanning laser microscopy, allowing observation of fully hydrated yogurt and the distribution of exopolysaccharide within the protein network. Yogurt made with the exopolysaccharide-producing culture exhibited increased consistency coefficients, but lower flow behavior index, yield stress, viscoelastic moduli and phase angle values than did yogurt made with the culture unable to produce exopolysaccharide. The exopolysaccharides, when present, were found in pores in the gel network separate from the aggregated protein. These effects could be explained by the incompatibility of the exopolysaccharides with the protein aggregates in the milk. Stirring affected the yogurt made with exopolysaccharide differently from yogurt without exopolysaccharide, as it did not exhibit immediate syneresis, although the structural breakdown was increased. The shear-induced microstructure in a yogurt made with exopolysaccharide-producing culture was shown to consist of compartmentalized protein aggregates between channels containing exopolysaccharide, hindering syneresis as well as the buildup of structure after stirring.
Small but mighty: How the MACS®‐technology based on nanosized superparamagnetic particles has helped to analyze the immune system within the last 20 years (2010)

Today, magnetic cell sorting and flow cytometric cell sorting both are state-of-the-art technologies, with a plethora of applications in biology and biomedicine. Both technologies have their stand-alone applications, but they also perfectly complement each other, in particular for the analysis and isolation of fragile and rare cells. The technological evolution from simple magnets and steel wool separation columns to sophisticated instrumentation and automated procedures has paved the way for magnetic cell separation in the scientific community. This review will focus on applications of magnetic cell sorting with commercially available paramagnetic MACS(R)-nanoparticles (Miltenyi Biotech, Bergisch-Gladbach, Germany) that have allowed unprecedented approaches to the exploration of the immune system in basal and clinical research of humans and rodents. Thus, during the last 20 years this technology has been continuously developed so that the widest array of leukocyte subsets, stem cells, and connective tissue cells can be addressed by MACS(R)-conjugated antibodies directed against cell-specific surface antigens or secreted cytokines for research and clinical applications.
Conditional Generative Adversarial Nets (2014)

Generative Adversarial Nets [8] were recently introduced as a novel way to train generative models. In this work we introduce the conditional version of generative adversarial nets, which can be constructed by simply feeding the data, y, we wish to condition on to both the generator and discriminator. We show that this model can generate MNIST digits conditioned on class labels. We also illustrate how this model could be used to learn a multi-modal model, and provide preliminary examples of an application to image tagging in which we demonstrate how this approach can generate descriptive tags which are not part of training labels.
Error/failure analysis using event logs from fault tolerant systems (2002)

A methodology for the analysis of automatically generated event logs from fault tolerant systems is presented. The methodology is illustrated using event log data from three Tandem systems. Two are experimental systems, with nonstandard hardware and software components causing accelerated stresses and failures. Errors are identified on the basis of knowledge of the architectural and operational characteristics of the measured systems. The methodology takes a raw event log and reduces the data by event filtering and time-domain clustering. Probability distributions to characterize the error detection and recovery processes are obtained, and the corresponding hazards are calculated. Multivariate statistical techniques (factor analysis and cluster analysis) are used to investigate error and failure dependency among different system components. The dependency analysis is illustrated using processor halt data from one of the measured systems. It is found that the number of errors is small, even though the measurement period is relatively long. This reflects the high dependability of the measured systems.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Topography of the human factor VIII-von Willebrand factor complex. (1990)

Factor VIII circulates in noncovalent complex with von Willebrand factor (vWf). The topography of this complex was evaluated by fluorescence energy transfer using factor VIII subunits modified with N-(1-pyrenyl)maleimide (NPM; fluorescence donor) and vWf-derived fragments modified with 7-diethylamino-3-[4'-maleimidylphenyl]-4-methyl coumarin (CPM; fluorescence acceptor). Results from a previous study indicated an interfactor VIII subunit distance of 20 A separating Cys528 and Cys1858 in the factor VIII heavy and light chains, respectively (Fay, P.J., and Smudzin, T. M. (1989) J. Biol. Chem. 264, 14005-14010). Fluorophore modification of the vWf SPIII homodimer (residues 1-1365) indicated multiple attachment sites at Cys126/135/1360 as determined from sequence analysis of fluorescent tryptic peptides derived from the modified protein. Based upon donor quenching data, an interfluorophore distance of approximately 28 A was calculated separating NPM-factor VIII light chain or factor VIII reconstituted from NPM-light chain plus unmodified heavy chain, from CPM-SPIII. A similar value (29 A) was obtained for NPM-light chain paired with CPM-SPIII-T4 (vWf residues 1-272), suggesting that donor quenching resulted primarily from modified residue(s) Cys126/135 in the acceptor. No energy transfer was observed for the NPM-heavy chain/CPM-SPIII pairing. However, when NPM-heavy chain was reassociated with unmodified light chain prior to reaction with CPM-SPIII or CPM-SPIII-T4, energy transfer was observed with calculated interfluorophore distances of approximately 31 and 34 A, respectively. Levels of acceptor resulting in maximal donor quenching suggested an equimolar stoichiometry of factor VIII (light chain)/vWf fragment in the reconstituted complexes. These results indicate a close spatial arrangement among the A3 domain of factor VIII light chain, the A2 domain of factor VIII heavy chain, and the NH2 terminus region of vWf in the factor VIII-vWf complex.