gebhart/patrepeval huggingface dataset:
Multidetector computed tomographic angiography of the cardiovascular system (2007)

The introduction of multidetector computed tomography (MDCT) is considered a dramatic development in CT imaging that has direct implication in the imaging of various systems, in particular the cardiovascular system. The advantages of MDCT are an enormous increase in imaging acquisition speed, more coverage of the patient, and high spatial resolution. This article reviews the recent developments in CT angiography and discusses the clinical application relevant to diagnosis and endovascular treatment of cardiovascular diseases.
Comparative Genomics in the Grass Family: Molecular Characterization of Grass Genome Structure and Evolution (2002)

The genomes of grasses are very different in terms of size, ploidy level and chromosome number. Despite these significant differences, it was found by comparative mapping that the linear order (colinearity) of genetic markers and genes is very well conserved between different grass genomes. The potential of such conservation has been exploited in several directions, e.g. in defining rice as a model genome for grasses and in designing better strategies for positional cloning in large genomes. Recently, the development of large insert libraries in species such as maize, rice, barley and diploid wheat has allowed the study of large stretches of DNA sequence and has provided insight into gene organization in grasses. It was found that genes are not distributed randomly along the chromosomes and that there are clusters of high gene density in species with large genomes. Comparative analysis performed at the DNA sequence level has demonstrated that colinearity between the grass genomes is retained at the molecular level (microcolinearity) in most cases. However, detailed analysis has also revealed a number of exceptions to microcolinearity, which have given insight into mechanisms that are involved in grass-genome evolution. In some cases, the use of rice as a model to support gene isolation from other grass genomes will be complicated by local rearrangements. In this Botanical Briefing, we present recent progress and future prospects of comparative genomics in grasses.
Dynamic Delegation Discovery System (DDDS) Part One: The Comprehensive DDDS (2002)

This document specifies the exact documents that make up the complete Dynamic Delegation Discovery System (DDDS).DDDS is an abstract algorithm for applying dynamically retrieved string transformation rules to an application-unique string.This document along with RFC 3402, RFC 3403 and RFC 3404 obsolete RFC 2168 and RFC 2915, as well as updates RFC 2276. Intended AudienceThis document and the documents that it references are intended for anyone attempting to implement or understand the generic DDDS algorithm, URI Resolution, ENUM telephone number to URI resolution, and the NAPTR DNS resource record.The reader is warned that reading one of the documents in this series without reading the others will probably lead to misunderstandings and interoperability problems.
The Eight Stereoisomers of LNA (Locked Nucleic Acid): A Remarkable Family of Strong RNA Binding Molecules (2000)

Hybridization properties are reported for all of the eight possible conformationally restricted stereoisomers of LNA (Locked Nucleic Acid, see picture). Remarkably, six of these, namely LNA, L-LNA, xylo-LNA, L-xylo-LNA, α-LNA, and α-L-LNA, display very high binding affinities towards complementary RNA and can be seen as unique nucleic acid mimics.
Mutations in the zinc fingers of ADR1 that change the specificity of DNA binding and transactivation. (1992)

ADR1 is a yeast transcription factor that contains two zinc fingers of the Cys-2-His-2 (C2H2) class. Mutations that change the specificity of DNA binding of ADR1 to its target site, upstream activation sequence 1 (UAS1), have been identified at three positions in the first zinc finger. Mutations Arg-115 to Gln, His-118 to Thr, and Arg-121 to Asn led to new specificities of DNA binding at adjacent positions 10, 9, and 8 (3'-GAG-5') in UAS1. Arg-115 is at the finger tip, and His-118 and Arg-121 are at positions 3 and 6, respectively, in the alpha helix of finger 1. One double mutant displayed the binding specificity expected from the properties of its constituent new-specificity mutations. Mutations in the second finger that allowed its binding site to be identified through loss-of-contact phenotypes were made. These mutations imply a tail-to-tail orientation of the two ADR1 monomers on their adjacent binding sites. Finger 1 is aligned on UAS1 in an amino-to-carboxyl-terminal orientation along the guanine-rich strand in a 3'-to-5' direction. One of the ADR1 mutants was functional in vivo with both its cognate binding site and wild-type UAS1, but the other two mutants were defective in transactivation despite their ability to bind with high affinity to their cognate binding sites.
EpCAM/CD3-Bispecific T-cell Engaging Antibody MT110 Eliminates Primary Human Pancreatic Cancer Stem Cells (2011)

Cytotoxic T cells can be effectively redirected against primary human pancreatic cancer cells by T-cell-engaging BiTE antibody MT110 including a subpopulation of highly tumorigenic CSCs.
Molecular Characterization of EGFR and EGFRvIII Signaling Networks in Human Glioblastoma Tumor Xenografts (2012)

Glioblastoma multiforme (GBM) is a malignant primary brain tumor with a mean survival of 15 months with the current standard of care. Genetic profiling efforts have identified the amplification, overexpression, and mutation of the wild-type (wt) epidermal growth factor receptor tyrosine kinase (EGFR) in ≈ 50% of GBM patients. The genetic aberration of wtEGFR is frequently accompanied by the overexpression of a mutant EGFR known as EGFR variant III (EGFRvIII, de2-7EGFR, ΔEGFR), which is expressed in 30% of GBM tumors. The molecular mechanisms of tumorigenesis driven by EGFRvIII overexpression in human tumors have not been fully elucidated. To identify specific therapeutic targets for EGFRvIII driven tumors, it is important to gather a broad understanding of EGFRvIII specific signaling. Here, we have characterized signaling through the quantitative analysis of protein expression and tyrosine phosphorylation across a panel of glioblastoma tumor xenografts established from patient surgical specimens expressing wtEGFR or overexpressing wtEGFR (wtEGFR+) or EGFRvIII (EGFRvIII+). S100A10 (p11), major vault protein, guanylate-binding protein 1(GBP1), and carbonic anhydrase III (CAIII) were identified to have significantly increased expression in EGFRvIII expressing xenograft tumors relative to wtEGFR xenograft tumors. Increased expression of these four individual proteins was found to be correlated with poor survival in patients with GBM; the combination of these four proteins represents a prognostic signature for poor survival in gliomas. Integration of protein expression and phosphorylation data has uncovered significant heterogeneity among the various tumors and has highlighted several novel pathways, related to EGFR trafficking, activated in glioblastoma. The pathways and proteins identified in these tumor xenografts represent potential therapeutic targets for this disease.
ApoE-deficient mice are a model of lipoprotein oxidation in atherogenesis. Demonstration of oxidation-specific epitopes in lesions and high titers of autoantibodies to malondialdehyde-lysine in serum. (1994)

Apolipoprotein (apo) E-deficient transgenic mice develop marked hyperlipidemia and progressive atherosclerotic lesions. To explore whether oxidative modification of lipoproteins is involved in atherogenesis in this murine model, we performed extensive immunocytochemical studies. Atherosclerotic lesions ranging from early fatty streaks to very advanced plaques were examined from the aortic valve region and the thoracic and abdominal aorta. Using guinea pig antisera against malondialdehyde (MDA)-lysine and 4-hydroxynonenal-lysine, two epitopes generated during the oxidative modification of low-density lipoprotein (LDL), we demonstrated the presence of these "oxidation-specific epitopes" in atherosclerotic lesions. In early lesions, oxidation-specific epitopes were found predominantly in macrophage-rich areas, whereas diffuse extracellular staining predominated in necrotic areas of advanced lesions. We have previously shown that autoantibodies against MDA-lysine are present in the circulation of humans and rabbits and that the immunoglobulin fraction extracted from their lesions contains autoantibodies against several "oxidation-specific" epitopes. Sera from apoE-deficient mice also contained circulating autoantibodies to MDA-lysine, and both early and advanced lesions were rich in murine immunoglobulins. Titers of serum autoantibodies were significantly higher in apoE-deficient mice than in C57BL/6 mice. Autoantibodies in murine plasma recognized MDA-lysine epitopes in atherosclerotic lesions of rabbits, and the immunostaining was competitively inhibited by excess human MDA-LDL. Similar findings were obtained by competitive radioimmunoassay. Finally, a morphometric technique was developed and tested in these mice that allows a quantitative assessment of aortic atherosclerosis. These findings suggest that in apoE-deficient mice, lipoprotein oxidation is involved in atherogenesis and that these transgenic mice constitute an appropriate model with which to study the antiatherogenic effect of antioxidant intervention.
Pertussis toxin-catalyzed ADP-ribosylation of transducin. Cysteine 347 is the ADP-ribose acceptor site. (1985)

Pertussis toxin catalyzes the transfer of ADP-ribose from NAD to the guanine nucleotide-binding regulatory proteins Gi, Go, and transducin. Based on a partial amino acid sequence for a tryptic peptide of ADP-ribosylated transducin, asparagine had been characterized as the site of pertussis toxin-catalyzed ADP-ribosylation. Subsequently, cDNA data for the alpha subunit of transducin indicated that the putative asparagine residue was, in fact, not present in the protein. To determine the amino acid that served as the ADP-ribose acceptor, radiolabel from [adenine-U-14C]NAD was incorporated, in the presence of pertussis toxin, into the alpha subunit of transducin (0.3 mol/mol). An ADP-ribosylated, tryptic peptide was purified and fully sequenced by automated Edman degradation. The amino acid sequence, Glu-Asn 343-Leu-Lys-Asp 346-X-Gly 348-Leu-Phe, corresponds to the cDNA sequence coding the carboxyl-terminal nonapeptide, Glu 342-Phe 350, which includes by cDNA sequence cysteine at position 347. Neither Asn 343 nor Asp 346 appeared to be modified; residue 347 adhered to the sequencing resin. Cysteine, the missing residue, was eluted from the sequencing resin with acetic acid along with 76% of the peptide-associated radioactivity, half of which, presumably ADP-ribosylcysteine, eluted from an anion exchange column between NAD and ADP-ribose; the other half had a retention time corresponding to 5'-AMP. We conclude that Cys 347 and not Asn 343 or Asp 346 is the site of pertusis toxin-catalyzed ADP-ribosylation in transducin.
Immune Recovery in Adult Patients after Myeloablative Dual Umbilical Cord Blood, Matched Sibling, and Matched Unrelated Donor Hematopoietic Cell Transplantation (2012)

Immunologic reconstitution after allogeneic hematopoietic cell transplantation is a critical component of successful outcome. Umbilical cord blood (UCB) transplantation in adult recipients is associated with slow and often inadequate immune recovery. We characterized the kinetics and extent of immune recovery in 95 adult recipients after a dual UCB (n = 29) and matched sibling donor (n = 33) or matched unrelated donor (n = 33) transplantation. All patients were treated with myeloablative conditioning. There were no differences in the immune recovery profile of matched sibling donor and matched unrelated donor recipients. Significantly lower levels of CD3+, CD4+, and CD8+ T cells were observed in UCB recipients until 6 months after transplantation. Lower levels of regulatory T cells persisted until 1 year after transplantation. Thymopoiesis as measured by TCR rearrangement excision circle was comparable among all recipients by 6 months after transplantation. In a subset of patients 1 year after transplantation with similar levels of circulating T cells and TCR rearrangement excision circle, there was no difference in TCR diversity. Compared to HLA-identical matched sibling donor and matched unrelated donor adult hematopoietic cell transplantation recipients, quantitative lymphoid recovery in UCB transplantation recipients is slower in the first 3 months, but these differences disappeared by 6 to 12 months after transplantation.
Leukemia inhibitory factor (LIF) binding protein attenuates the phlogistic and abolishes the chondral effects of LIF in goat joints. (1997)

Murine LBP has the ability to attenuate the phlogistic effects of rhLIF in radiocarpal joints of goats and also abolishes the stimulatory effect of rhLIF on cartilage proteoglycan catabolism and depression of ex vivo proteoglycan synthesis. These antiinflammatory and chondral effects suggest that a humanized derivative of mLBP could be a clinically useful antagonist for LIF in inflammatory diseases.
A 10/100 Mb/s CMOS Ethernet transceiver for 10BaseT, 100BaseTX, and 100BaseFX (2002)

The IEEE 802.3 standard and the ANSI Fiber Distributed Data Interface (FDDI) standard define a 10 Mb/s twisted-pair standard, 10BaseTX, a 100 Mb/s twisted-pair standard, 100BaseTX, and a 100 Mb/s fiber standard, 100BaseFX. This chip incorporates the 10BaseTX, 100BaseTX, and 100BaseFx Transceivers. In the 100 Mb/s modes, 4 data bits are encoded into 5 bits that are sent at 125 Mb/s. In 100BaseFX mode, transmit data is NRZI encoded and is sent to an external fiber module as a differential quasi-ECL 125 Mb/s signal. Simultaneously, a differential quasi-ECL 125 Mb/s signal is received from the fiber module and decoded. In the twisted-pair mode, the chip negotiates with the far-end transceiver to either the 10BaseT or 100BaseTX mode. In the 10BaseT mode the chip uses Manchester coding. In the 100BaseTX mode, the chip uses MLT3 coding. The paper concentrates on the 100BaseTX mode.
Bifidobacterium mixture (B longum BB536, B infantis M-63, B breve M-16V) treatment in children with seasonal allergic rhinitis and intermittent asthma (2017)

ClinicalTrials.gov ID NCT02807064 .
Glass-Coated, Analyte-Tagged Nanoparticles:  A New Tagging System Based on Detection with Surface-Enhanced Raman Scattering (2003)

Glass-coated, analyte-tagged nanoparticles (GANs) are core−shell particles where a nanometer-scale Au or Ag core is functionalized with Raman active molecules and encapsulated in a glass shell. The glass shell provides the particle with mechanical and chemical stability. Specifically, the glass coating renders the particle amenable to use in many solvents without altering the Raman spectral response and makes agglomeration a nonfactor. The density and thickness of the glass shell are controllable through synthetic conditions; thus, the rate of diffusion through the silica network can be tuned and the metal cores kept sequestered from any exterior reaction. This will allow for the attachment of biomolecules to the glass shell without altering the Raman response. GANs can be identified by the Raman spectrum of the attached Raman tag, and two differently labeled samples are unambiguously identified. The scattering from the Raman tag is amplified through surface-enhanced Raman scattering. The narrow bandwidth (∼20 cm-1) of the Raman peaks and fingerprint-like spectra will allow multiple Raman tags to be simultaneously evaluated with a single excitation source.
cDNAs of cell adhesion molecules of different specificity induce changes in cell shape and border formation in cultured S180 cells. (1990)

The liver cell adhesion molecule (L-CAM) and N-cadherin or adherens junction-specific CAM (A-CAM) are structurally related cell surface glycoproteins that mediate calcium-dependent adhesion in different tissues. We have isolated and characterized a full-length cDNA clone for chicken N-cadherin and used this clone to transfect S180 mouse sarcoma cells that do not normally express N-cadherin. The transfected cells (S180cadN cells) expressed N-cadherin on their surfaces and resembled S180 cells transfected with L-CAM (S180L cells) in that at confluence they formed an epithelioid sheet and displayed a large increase in the number of adherens and gap junctions. In addition, N-cadherin in S180cadN cells, like L-CAM in S180L cells, accumulated at cellular boundaries where it was colocalized with cortical actin. In S180L cells and S180cadN cells, L-CAM and N-cadherin were seen at sites of adherens junctions but were not restricted to these areas. Adhesion mediated by either CAM was inhibited by treatment with cytochalasin D that disrupted the actin network of the transfected cells. Despite their known structural similarities, there was no evidence of interaction between L-CAM and N-cadherin. Doubly transfected cells (S180L/cadN) also formed epithelioid sheets. In these cells, both N-cadherin and L-CAM colocalized at areas of cell contact and the presence of antibodies to both CAMs was required to disrupt the sheets of cells. Studies using divalent antibodies to localize each CAM at the cell surface or to perturb their distributions indicated that in the same cell there were no interactions between L-CAM and N-cadherin molecules. These data suggest that the Ca(++)-dependent CAMs are likely to play a critical role in the maintenance of epithelial structures and support a model for the segregation of CAM mediated binding. They also provide further support for the so-called precedence hypothesis that proposes that expression and homophilic binding of CAMs are necessary for formation of junctional structures in epithelia.
The Natural Product Avrainvillamide Binds to the Oncoprotein Nucleophosmin (2007)

Here we present evidence that (+)-avrainvillamide, a naturally occurring alkaloid with antiproliferative effects, binds to the nuclear chaperone nucleophosmin, a proposed oncogenic protein that is overexpressed in many different human tumors. Among other effects, nucleophosmin is known to regulate the tumor suppressor protein p53. A synthetic biotin-avrainvillamide conjugate, nearly equipotent to the natural product in inhibiting the growth of cultured T-47D cells, was used for affinity-isolation of a protein identified as nucleophosmin by MS sequencing and Western-blotting. Affinity-isolation of nucleophosmin was inhibited in the presence of iodoacetamide (10 mM), free (+)-avrainvillamide (100 microM), and a series of closely related structural analogues of (+)-avrainvillamide, the latter with inhibitory effects that appear to correlate with measured growth-inhibitory potencies. Using fluorescence microscopy, a synthetic dansyl-avrainvillamide conjugate was observed to localize within the nucleoli and the cytosol of treated cancer cells. Site-directed mutagenesis of each of the three cysteine residues of a truncated nucleophosmin coexpressed with native nucleophosmin in COS-7 cells revealed that the mutation cys275 --> ala275 effectively and uniquely reduced affinity-isolation of the truncated protein, suggesting that avrainvillamide targets cys275 of nucleophosmin. Finally, we show that treatment of adhered LNCaP or T-47D cells with (+)-avrainvillamide leads to an increase in cellular p53 concentrations, and that siRNA-promoted depletion of nucleophosmin in a population of HeLa S3 cells leads to increased sensitivity of that population toward apoptotic death upon treatment with (+)-avrainvillamide. Although potentially desirable as lead compounds for the development of novel anticancer therapies, nonpeptidic, synthetic small molecules that bind to nucleophosmin have not been described, prior to this report.
Influence of molecular weight and degree of crosslinking on the specific volume and glass temperature of polymers (1955)

Abstract On the basis of simple assumptions, equations are derived for predicting the specific volume‐temperature‐molecular weight ( v ‐ T ‐ M ) relationships for a homologous series of polymers from the v ‐ T curves for the monomer and the polymer of infinite molecular weight. Analogous v ‐ T ‐ρ relationships (where ρ is the degree of crosslinking) are similarly obtained. The result, that v decreases linearly with decreasing 1/ M and with increasing ρ, conforms with the picture that either the removal of two chain ends (as M increases) or the introduction of a crosslinkage involves, between two polymer segments, the exchange of a van der Waals bond for a shorter covalent bond. The validity of these equations is illustrated by comparison with the observed data for polymers covering a wide range in M , T , and chemical type. For several polymer series the extrapolated value of v at 0°K ( v 0 ) is the same for all members of the series, indicating that at this temperature the average length of the van der Waals and covalent bonds between polymer segments are the same. Assuming that the form of the linear relationship observed for polystyrene between the specific volume ( v g ) at the glass temperature and the value ( T g ) of the latter is valid for other polymer series, equations are derived which predict T g as a function of M from the limiting value of the glass temperature for a chain of infinite length, and from the v ‐ T curves in the liquid state for the monomer and for the polymer of M = ∞. Analogous T g ‐ρ relationships are similarly obtained. According to these equations, a linear relationship between 1/ T g and 1/ M should be obtained, which reduces at high M to a linear dependence of T g on 1/ M . Similarly, a linear dependence of T g on ρ is predicted at low ρ. These predictions are in satisfactory agreement with data on polystyrene fractions and on crosslinked copolymers of styrene with divinylbenzene. The conclusion that T g for polystyrenes represent a state of iso‐free volume irrespective of M is shown to be an approximation that is valid, within experimental error, only for large values of M .
New Cyanine–Oligonucleotide Conjugates: Relationships between Chemical Structures and Properties (2006)

Abstract Because the influence of the chemical structure of monomethine cyanine–oligo‐2′‐deoxyribonucleotide (ODN) conjugates on their binding and fluorescence properties has remained largely undetermined, we synthesized and studied a wide range of conjugates with various structural patterns. Different cyanine dyes such as thiocyanine, quinocyanine, and thiazole orange isomers were obtained. In the case of unsymmetrical cyanines, the linker was attached to either the quinoline or the benzothiazole nucleus. The influence of the ODN counterpart was evaluated by linking the cyanines to the 5′‐end or to an internucleotidic phosphate. In the first case, the influence of neighboring nucleic bases was studied, whereas in the second, the stereochemical configuration at the phosphorus atom bearing the cyanine was investigated. We report here on relationships between the structures of the dyes and conjugates and some of their properties, such as the stability and fluorescence changes observed on their hybridization with the target sequence. This study provides useful information towards the design of ODN–cyanine conjugates.