gebhart/patrepeval huggingface dataset:
Mutagenesis Studies of the Human Erythropoietin Receptor (1997)

Mutagenesis of the erythropoietin receptor (EPOR) permits analysis of the contribution that individual amino acid residues make to erythropoietin (EPO) binding. We employed both random and site-specific mutagenesis to determine the function of amino acid residues in the extracellular domain (referred to as EPO binding protein, EBP) of the EPOR. Residues were chosen for site-specific alanine substitution based on the results of the random mutagenesis or on their homology to residues that are conserved or have been reported to be involved in ligand binding in other receptors of the cytokine receptor family. Site-specific mutants were expressed in Escherichia coli as soluble EBP and analyzed for EPO binding in several different assay formats. In addition, selected mutant proteins were expressed as full-length EPOR on the surface of COS cells and analyzed for 125I-EPO binding in receptor binding assays. Using these methods, we have identified residues that appear to be involved in EPO binding as well as other residues, most of which are conserved in receptors of the cytokine receptor family, that appear to be necessary for the proper folding and/or stability of the EPOR. We present correlations between these mutagenesis data and the recently solved crystal structure of the EBP with a peptide ligand.
Effects of Prenatal Androgenization and Implantation on the Performance and Carcass Composition of Lactating Heifers in the Single-Calf Heifer System (1999)

Two experiments were conducted to evaluate feedlot performance of heifers and calves and the lactational characteristics and carcass composition and quality of heifers while in the single-calf heifer (SCH) system. In Exp. 1, 24 lactating Angus × Holstein heifers were slowly adapted to an 85% concentrate diet, and one-half of the heifers were implanted with Finaplix-H®, both at 11 wk postpartum. Heifer-calf pairs were then placed in feedlot pens, equipped with pinpointer feeding devices, and fed an 85% concentrate diet for 102 d. The control (C) and implanted (I) heifers had similar (P=0.27) daily gains and similar (P=0.30) DMI; however, I heifers consumed 8.9% less (P<0.05) DM as a percentage of BW. Pair efficiency of feed conversion tended to be higher (P<0.09) for I heifers than for C heifers. Hot carcass weight tended to be higher (P<0.10) for the I heifers. Ribeye area was 13% greater (P<0.05) and marbling score was 8.7% lower (P<0.01) for the I heifers than for the C heifers. In Exp. 2, 26 lactating Angus × Simmental heifers were used in the SCH system. Heifer adaptation to a high concentrate diet began 3 to 4 wk prepartum. Two to 3 d postpartum, 16 control (C) and 10 prenatally androgenized (PA) heifer-calf pairs were weighed, and eight C and five PA heifers were implanted with Synovex-H®. They were then placed in feedlot pens equipped with pinpointer feeding devices. By 1 wk postpartum, all heifers were adapted to an 85% concentrate diet and fed until they possessed approximately 1.1 cm s.c. fat cover over the 12th and 13th ribs. Heifers were slaughtered 12 h postweaning. The PA heifers tended to consume more (P<0.11) DM than C heifers. Gain:feed (G:F) was similar (P=0.35) for the C and PA heifers; however, the C heifers tended to have an improved (P<0.08) pair G:F. Heifer G:F and pair G:F were both similar (P=0.53) for the I and nonimplanted heifers. Most carcass measurements were unaffected by treatment; however, the I heifers tended to have higher marbling scores (P<0.07).
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation (2010)

Enrichment Map is a significant advance in the interpretation of enrichment analysis. Any research project that generates a list of genes can take advantage of this visualization framework. Enrichment Map is implemented as a freely available and user friendly plug-in for the Cytoscape network visualization software (http://baderlab.org/Software/EnrichmentMap/).
The p14 FAST Protein of Reptilian Reovirus Increases Vesicular Stomatitis Virus Neuropathogenesis (2008)

The fusogenic orthoreoviruses express nonstructural fusion-associated small transmembrane (FAST) proteins that induce cell-cell fusion and syncytium formation. It has been speculated that the FAST proteins may serve as virulence factors by promoting virus dissemination and increased or altered cytopathology. To directly test this hypothesis, the gene encoding the p14 FAST protein of reptilian reovirus was inserted into the genome of a heterologous virus that does not naturally form syncytia, vesicular stomatitis virus (VSV). Expression of the p14 FAST protein by the VSV/FAST recombinant gave the virus a highly fusogenic phenotype in cell culture. The growth of this recombinant fusogenic VSV strain was unaltered in vitro but was significantly enhanced in vivo. The VSV/FAST recombinant consistently generated higher titers of virus in the brains of BALB/c mice after intranasal or intravenous infection compared to the parental VSV/green fluorescent protein (GFP) strain that expresses GFP in place of p14. The VSV/FAST recombinant also resulted in an increased incidence of hind-limb paralysis, it infected a larger volume of brain tissue, and it induced more extensive neuropathology, thus leading to a lower maximum tolerable dose than that for the VSV/GFP parental virus. In contrast, an interferon-inducing mutant of VSV expressing p14 was still attenuated, indicating that this interferon-inducing phenotype is dominant to the fusogenic properties conveyed by the FAST protein. Based on this evidence, we conclude that the reovirus p14 FAST protein can function as a bona fide virulence factor.
Linkage Disequilibrium Mapping of Arabidopsis CRY2 Flowering Time AllelesSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AY576055, AY576271. (2004)

The selfing plant Arabidopsis thaliana has been proposed to be well suited for linkage disequilibrium (LD) mapping as a means of identifying genes underlying natural trait variation. Here we apply LD mapping to examine haplotype variation in the genomic region of the photoperiod receptor CRYPTOCHROME2 and associated flowering time variation. CRY2 DNA sequences reveal strong LD and the existence of two highly differentiated haplogroups (A and B) across the gene; in addition, a haplotype possessing a radical glutamine-to-serine replacement (AS) occurs within the more common haplogroup. Growth chamber and field experiments using an unstratified population of 95 ecotypes indicate that under short-day photoperiod, the AS and B haplogroups are both highly significantly associated with early flowering. Data from six genes flanking CRY2 indicate that these haplogroups are limited to an approximately 65-kb genomic region around CRY2. Whereas the B haplogroup cannot be delimited to <16 kb around CRY2, the AS haplogroup is characterized almost exclusively by the nucleotide polymorphisms directly associated with the serine replacement in CRY2; this finding strongly suggests that the serine substitution is directly responsible for the AS early flowering phenotype. This study demonstrates the utility of LD mapping for elucidating the genetic basis of natural, ecologically relevant variation in Arabidopsis.
Data mining The Cancer Genome Atlas in the era of precision cancer medicine (2015)

The Cancer Genome Atlas (TCGA) has given researchers and clinicians unprecedented access to many different cancers through multiple platforms that include exome sequencing, comparative genomic hybridisation (CGH) arrays, DNA methylation arrays, RNA sequencing, reverse protein phase arrays (RPPA), and clinical features. Most data are available to the public in their raw and processed forms; however, analysis and interpretation of these data require specialised training and software. To address this problem, online tools such as cBioportal, canEvolve, GDAC firehose, PROGgeneV2, and UCSC Cancer browser have been developed by various groups to explore and perform analyses on the datasets that are easily understandable by basic researchers and clinicians. In this mini-review, we give an overview of the datasets available from TCGA and the public tools available for integrative analysis of survival with the genomic and transcriptomic datasets, and introduce a tool being developed by our group to analyse the datasets within TCGA.
Rapid Quantitative Test for Free Oil (Oiling Off) in Melted Mozzarella Cheese (1990)

A test for free oil in melted Mozzarella cheese using standard Babcock equipment was developed and evaluated.Eighteen grams of whole milk or part skim Mozzarella were weighed into 50 or 20% Paley-Babcock bottles, respectively.Bottles were immersed in boiling water for 4.0 min to melt cheese.Distilled water (20 ml at 57SC) was then added and the bottles were centrifuged hot (ca.57SC) for 10 min.A portion of 1:1 distilled water:methanol (21°C) was added to a final level in the upper region of the calibrated neck and then centrifuged for 2 min.Bottles were then rocked by hand for 10 s, centrifuged for 2 min, and a second time rocked by hand for 10 s and centrifuged for 2 min.Finally, bottles were tempered in 57.5°C water for 5 min and the fat column then measured with glymol.This procedure gave a clear, defined fat column.Free oil was expressed as percentage in cheese and percentage in cheese fat.A series of recovery trials in which low moisture and low moisture.part skim Mozzarellas were spiked with butter oil gave recoveries ranging from 97.3% to 104.5%.Eighteen replicates of a low moisture and low moisture, part skim Mozzarella gave coefficients of variation of 3.3 and 6.2%, respectively.Free oil was measured in 64 Mozzarella cheese obtained from local supermarkets and two industrial cheese plants.Free oil as a percentage of total cheese fat
Syntheses of Aromatic Substituted6′-Thiothalidomides (2008)

A resurgence of interest in thalidomide has occurred as a consequence of its diverse immunomodulatory and anticancer actions, which has fuelled interest in synthetic analogues with higher potencies or less undesirable side effect profiles. Several novel aromatic substituted 6′-thiothalidomides were synthesized whose synthetic route and strategy were developed on the basis of an analysis of reaction mechanisms. The regioselectivity of mono-thionation of aromatic substituted thalidomides with Lawesson's reagent is described, and the chemoselectivity of hydrogenation between the nitro­ group and 6′-thiocarbonyl group is discussed. Full characterization of eight substituted 6′-thiothalidomides is reported.
Visual Spike Processing based on Cellular Automaton (2011)

Cellular organization in biology has been an inspiration in several research fields, such as the description and definition of Cellular Automaton, Neural Networks, Spiking Systems, etc. Cellular Automaton (CA) is a bio-inspired processing model for problem solving, initially proposed by Von Neumann. This approach modularizes the processing by dividing the solution into synchronous cells that change their states at the same time in order to get the solution. The communication between them and the operations performed by each cell are crucial to achieve the correct solution. On the other hand, Spiking Systems (SS) are composed by spiking neurons that receive the information codified into spikes, also called action potential, from several inputs with different weights, and after an internal processing, they produce new spikes in the output that are sent to other spiking neurons. The number and the connectivity between spiking neurons will determine the Spiking System. Weights are programmable and usually learned in order to make effective the result of the network. These weights usually depend on the spike rate of the inputs. The learning process for these weights is called Spike-Timing-Dependent Plasticity. One example of spiking neuron is the Integrate and Fire neuron This neuron can receive weighted spikes from different inputs. It performs internally an addition operation. When the internal value is greater than a configurable threshold, an output spike is produced and the neuron is reset. Researches and engineers try to integrate into a chip several thousand of these IF neurons, but a connectivity problem arises when they try to extract the output of all cells from the chip. The Address-Event-Representation (AER) is a possible solution. AER is a neuromorphic communication protocol for transferring asynchronous events between VLSI chips that implement a spike-based process typically by using spiking neurons. These neuroinspired implementations have been used to design sensor chips, like retinas Both CA and SS have important similarities and they also complement each other. CA is a processing model for problem solving and SS with AER gives a solution for implementing a grid of neurons in hardware. In this chapter our goal is to join both of them and study the viability of this new field for visual processing. Most of the complex visual processing mechanisms are based on solving a set of convolutions for edge detection, contrast adjustment, blur, noise reduction ... But it may also be possible to detect or recognize simple www.intechopen.com
Robust Controller Design for Active Vibration Control (1993)

A novel frequency-domain technique, having its roots in Quantitative Feedback Theory (QFT), has been developed to design controllers for active vibration control (AVC). The advantages are a plant-based design according to performance specifications, and the ability to include structured uncertainties in the critical plant parameters like passive bearing stiffness or damping. In this paper, we describe the background theory of single-input, single-output (SISO) and multi-input, multi-output (MIMO) QFT design, followed by development of the theory adapted for AVC. Application examples are considered next, outlining the design method for both cases. Simulation results for the systems studied are presented showing the effectiveness of the technique in attenuating vibration.
Integrated Magnetic Bionanocomposites through Nanoparticle-Mediated Assembly of Ferritin (2007)

Magnetic (FePt) and nonmagnetic (Au) nanoparticles were used to assemble ferritin into near-monodisperse bionanocomposites featuring regular interparticle spacing. The FePt/ferritin assemblies are integrated magnetic materials with ferritin providing added magnetic volume fraction to the magnetic nanocomposite. These assemblies differ from either of their constituent particles in terms of blocking temperature (TB), net magnetic moment, coercivity, and remnance.
Program load adaptive voltage generator for flash memories (1997)

This paper describes a program load voltage generator for flash memories. It is based on an adaptive feedback loop which senses the current delivered to the memory cells during programming and adjusts the output voltage accordingly to compensate for the voltage drop caused by the programming current across the bit-line select transistors. The proposed circuit (silicon area=0.065 mm/sup 2/) was integrated in a 0.8-/spl mu/m CMOS 4 Mb flash memory device (0.6 /spl mu/m in the matrix). Experimental evaluations showed that very effective compensation is achieved, with bit-line voltage kept at the desired value during the whole programming operation. A spread as small as 70 mV was measured between the single-bit and 16-b programming cases.
<title>Automated 3D nonlinear deformation procedure for determination of gross morphometric variability in human brain</title> (1994)

We describe an automated method to register MRI volumetric datasets to a digital human brain model. The technique employs 3D non-linear warping based on the estimation of local deformation fields using cross-correlation of invariant intensity features derived from image data. Results of the non-linear registration on a simple phantom, a complex brain phantom and real MRI data are presented. Anatomical variability is expressed with respect to the Talairach-like standardized brain-based coordinate system of the model. We show that the automated non-linear registration reduces the inter-subject variability of homologous points in standardized space by 15% over linear registration methods. A 3D variability map is shown.
Global Analysis of Antibody Repertoires. 1. An Immunoblot Method for the Quantitative Screening of a Large Number of Reactivities (1994)

This paper describes a procedure for analysing multiple antibody reactivities that explores a commercially available immunoblot system, and is based on a double staining of nitrocellulose membranes, revealing both antibody reactivities and the migration position of the blotted proteins in the membrane. Quantification of both stainings by densitometry allowed the accurate superposition of the immunoreactivity and total protein profiles of each lane. Moreover, the protein stainings of the different lanes could be adjusted with a simple-scale transformation algorithm, correcting for possible distortions during electrophoretic migration, and allowing for the precise comparison of the immunoreactivity profiles in different lanes. The procedure is discriminatory enough to identify unique reactivity patterns in random pools of 10(4) activated B cells, and to define strain-specific natural antibody repertoires. The utility of this immunoblot method as an assay for simultaneously scoring multiple reactivities to hundreds of antigens in complex mixtures of antibodies, and thus defining antibody repertoires in a global manner, is discussed.
Adenoviral expression of p53 represses telomerase activity through down-regulation of human telomerase reverse transcriptase transcription. (2000)

Telomerase activation is a critical step in cellular immortality and oncogenesis. The activity of telomerase is known to be correlated with cell proliferation, but its regulation by cell cycle regulators is not well understood. In the present study, we examined the effects of p53 on telomerase activity. Wild-type p53 was introduced into SiHa cells via a recombinant adenoviral vector, Ad5CMV-p53, and change in telomerase activity was examined by quantitative telomerase assay. Telomerase activity in the Ad5CMV-p53-infected cells was significantly repressed 36 h after infection following down-regulation of human telomerase catalytic subunit [human telomerase reverse transcriptase (hTERT)] mRNA expression, whereas no change in telomerase activity was observed in the cells infected with control vector AdSCMV-beta-gal. Interestingly, repression of telomerase activity was an early event that preceded cell growth inhibition or apoptosis induced by p53 overexpression, suggesting that p53 directly regulates telomerase activity. Transient expression assays using hTERT-promoter reporter constructs revealed that overexpression of p53 significantly repressed promoter activity of hTERT. 5'-Truncation of the promoter sequences revealed that the proximal core promoter region containing multiple binding sites for transcription factor Spl was responsible for p53-mediated transcriptional repression. Mutations in these binding sites for Spl led to failure of p53 to repress transcription. These findings suggest that p53 repressed telomerase activity through down-regulation of hTERT transcription and that interaction of p53 with Sp1 or other transcription factors may be involved in this regulation.
Monoclonal anti-mouse macrophage antibodies recognize the globular portions of C1q, a subcomponent of the first component of complement. (1984)

One of seven monoclonal antibodies generated against mouse macrophages (M phi) was found to recognize isolated heterologous C1q. This antibody was shown to be cytotoxic and to react in a strain-independent way with mouse M phi derived from bone marrow cells as well as with M phi from the peritoneal cavity; it did not react, however, with mouse granulocytes, thymocytes, or T and B lymphocytes. The hemolytic activity of fluid phase C1q was inhibited to 50% at a 2 X 10(-4) dilution of hybridoma supernatant, whereas a 100-fold higher concentration was required to inhibit C1q bound to immune complexes ( EAC1q ) to the same extent. It was demonstrated that this antibody recognizes the isolated globular, Fc-binding portions of the C1q molecule and reacts with the A and B chains. Because M phi have been shown to synthesize C1q, the Fc-recognizing subcomponent of the first component of complement, evidence was provided that endogeneous C1q can serve as an Fc receptor on M phi during secretion. This fact was demonstrated by a dose-dependent inhibition of Fc-receptor activity for EIgG by the F(ab')2 fragment of this monoclonal antibody. These experiments further support the concept that C1q produced by M phi functions on the surface as an Fc-recognizing molecule before it is released and incorporated into the macromolecular complex of serum C1.
On Magnus' Freiheitssatz and free polynomial algebras (2015)

The Freiheitssatz of Magnus for one-relator groups is one of the cornerstones of combinatorial group theory. In this short note which is mostly expository we discuss the relationship between the Freiheitssatz and corre- sponding results in free power series rings over fields. These are related to results of Schneerson not readily available in English. This relationship uses a faithful representation of free groups due to Magnus. Using this method in free polynomial algebras provides a proof of the Freiheitssatz for one-relation monoids. We show how the classical Freiheitssatz depends on a condition on certain ideals in power series rings in noncommuting variables over fields. A proof of this result over fields would provide a completely dif erent proof of the classical Freiheitssatz.
β-Glycosides of Hydroxyproline via an Umpolung Approach (2006)

Reaction of 1,2-O-dibutylstannylene-3,4-6-tri-O-benzyl-beta-D-mannopyranose with Nalpha-fluorenylmethoxycarbonyl-cis-4-trifluoromethanesulfonyloxyproline allyl ester led to formation of a beta-mannoside of trans-4-hydroxyproline. Subsequent manipulation of the C2 hydroxy group gave rise to beta-D-Glc and beta-D-GlcNAc derivatives.
IQGAP1 modulates activation of B-Raf (2007)

IQGAP1 modulates several cellular functions, including cell-cell adhesion, transcription, cytoskeletal architecture, and selected signaling pathways. We previously documented that IQGAP1 binds ERK and MAPK kinase (MEK) and regulates EGF-stimulated MEK and ERK activity. Here we characterize the interaction between IQGAP1 and B-Raf, the molecule immediately upstream of MEK in the Ras/MAPK signaling cascade. B-Raf binds directly to IQGAP1 in vitro and coimmunoprecipitates with IQGAP1 from cell lysates. Importantly, IQGAP1 modulates B-Raf function. EGF is unable to stimulate B-Raf activity in IQGAP1-null cells and in cells transfected with an IQGAP1 mutant construct that is unable to bind B-Raf. Interestingly, binding to IQGAP1 significantly enhances B-Raf activity in vitro. Our data identify a previously unrecognized interaction between IQGAP1 and B-Raf and suggest that IQGAP1 is a scaffold necessary for activation of B-Raf by EGF.