gebhart/patrepeval huggingface dataset:
Phase I Trial of the Antivascular Agent Combretastatin A4 Phosphate on a 5-Day Schedule to Patients With Cancer: Magnetic Resonance Imaging Evidence for Altered Tumor Blood Flow (2003)

Doses of CA4P on a daily times five schedule of 52 to 65 mg/m2 were reasonably well-tolerated. The 52 mg/m2 dose is recommended for further study based on cumulative phase I experience with CA4P. Antitumor efficacy was observed, and the use of DCE-MRI provided a valuable noninvasive measure of the vascular effects of CA4P treatment.
Influence of encapsulation on staphylococcal opsonization and phagocytosis by human polymorphonuclear leukocytes (1978)

In previous studies, encapsulated Staphylococcus aureus strains have been shown to resist phagocytosis. In this investigation, the nature of the interference with phagocytosis by human polymorphonuclear leukocytes was examined by studying the opsonization of two pairs of unencapsulated (Smith compact and M variant) and encapsulated (Smith diffuse and M) S. aureus strains. The uptake of [3H]glycine-labeled bacteria by normal leukocytes was quantitatively measured after incubation of bacteria in pooled serum, C2-deficient serum, immunoglobulin-deficient serum, and serum from a rabbit immunized with S. aureus M. The presence of a capsule was found to interfere with opsonization by both the classical and alternative pathways of complement as well as by heat-stable opsonic factors in nonimmune human serum. This interference was significantly greater in the case of the S. aureus M strain than in the case of the Smith diffuse strain. The only effective opsonic source for S. aureus M was immune rabbit serum. It is proposed that encapsulation of S. aureus strains interferes with phagocytosis by preventing effective bacterial opsonization.
Production and characterization of mouse monoclonal antibodies against human monocyte chemoattractant protein-1 (1991)

We developed five different hybridoma cell lines that produced mAb against human monocyte chemoattractant protein-1 (MCP-1). The subclass of all five antibodies was IgG1. All five mAb formed complexes with metabolically labeled MCP-1 that could be demonstrated by immunoprecipitation. The antibodies were specific for MCP-1. They did not cross-react by immunoprecipitation with structurally related host defense cytokines present in metabolically labeled PHA- or LPS-stimulated mononuclear cell culture fluids, nor did they cross-react in a direct ELISA with neutrophil attractant/activation protein-1, with crude platelet lysate proteins, or with pure platelet proteins that have amino acids sequences similar to that of MCP-1. The mAb also reacted with rMCP-1 expressed in Escherichia coli, suggesting that they recognize protein structure rather than the glycosylated portion of human MCP-1. When the mAb were mixed with MCP-1, the monocyte chemotactic response to MCP-1 was inhibited. A sandwich ELISA was developed to detect MCP-1 in biologic fluids containing relatively high concentrations of other proteins. The sensitivity was 300 pg/ml, or 30 pg/ELISA well. An anti-MCP-1 mAb column was used in an improved method of MCP-1 purification. Approximately 240 micrograms of MCP-1 were purified from 5 liters of FCS-containing U-105MG cell culture supernatant. The yield was at least 60%. In addition to two forms of MCP-1 reported previously by us, two more forms of MCP-1 were found in a mixture of culture supernatants of PHA- and LPS-stimulated human PBMC.
Recording and Analyzing High-Density Event-Related Potentials With Infants Using the Geodesic Sensor Net (2001)

This article provides an overview of the use of the Geodesic sensor net system for high-density event-related potential (ERP) recording in infants. Some advantages and disadvantages of the system, as applied to infants, are discussed. First, we illustrate that high-density data can be recorded from infants at comparable quality to that observed with conventional (low density) ERP methods. Second, we discuss ways to utilize the greater spatial information available by applying source separation and localization procedures. In particular, we focus on the application of one recent source separation method, Independent Component Analysis (ICA). Finally, we show that source localization can be applied to infant high-density data, although this entails adopting a number of assumptions that remain to be verified. In the future, with improved source separation algorithms, we suggest that single-trial or single-subject analyses may become feasible.
STK-1, the human homolog of Flk-2/Flt-3, is selectively expressed in CD34+ human bone marrow cells and is involved in the proliferation of early progenitor/stem cells. (1994)

We cloned the cDNA for stem cell tyrosine kinase 1 (STK-1), the human homolog of murine Flk-2/Flt-3, from a CD34+ hematopoietic stem cell-enriched library and investigated its expression in subsets of normal human bone marrow. The cDNA encodes a protein of 993 aa with 85% identity and 92% similarity to Flk-2/Flt-3. STK-1 is a member of the type III receptor tyrosine kinase family that includes KIT (steel factor receptor), FMS (colony-stimulating factor 1R), and platelet-derived growth factor receptor. STK-1 expression in human blood and marrow is restricted to CD34+ cells, a population greatly enriched for stem/progenitor cells. Anti-STK-1 antiserum recognizes polypeptides of 160 and 130 kDa in several STK-1-expressing cell lines and in 3T3 cells transfected with a STK-1 expression vector. Antisense oligonucleotides directed against STK-1 sequences inhibited hematopoietic colony formation, most strongly in long-term bone marrow cultures. These data suggest that STK-1 may function as a growth factor receptor on hematopoietic stem and/or progenitor cells.
Effective and efficient Semantic Table Interpretation using TableMiner+ (2016)

This article introduces TableMiner+, a Semantic Table Interpretation method that annotates Web tables in a both effective and efficient way. Built on our previous work TableMiner, the extended version advances state-of-the-art in several ways. First, it improves annotation accuracy by making innova tive use of various types of contextual information both inside and outside tables as features for inference. Second, it reduces computational overheads by adopting an incremental, bootstrapping approach that starts by creating preliminary and partial annotations of a table using ‘sample’ data in the table, then using the outcome as ‘seed’ to guide interpretation of remaining contents. This is then followed by a message passing process that iteratively refines results on the entire table to create the final optimal annotations. Third, it is able to handle all annotation tasks of Semantic Table Interpretation (e.g., annotating a column, or entity cells) while state-of-the-art methods are limited in different ways. We also compile the largest dataset known to date and extensively evaluate TableMiner+ against four baselines and two re-implemented (near-identical, as adaptations are needed due to the use of different knowledge bases) state-of-the-art methods. TableMiner+ consistently outperforms all models under all experimental settings. On the two most diverse datasets covering multiple domains and various table schemata, it achieves improvement in F1 by between 1 and 42 percentage points depending on specific annotation tasks. It also significantly reduces computational overheads in terms of wall-clock time when compared against classic methods that ‘exhaustively’ process the entire table content to build features for inference. As a concrete example, compared against a method based on joint inference implemented with parallel computation, the non-parallel implementation of TableMiner+ achieves significant improvement in learning accuracy and almost orders of magnitude of savings in wall-clock time.
On the Readability of Graphs Using Node-Link and Matrix-Based Representations: A Controlled Experiment and Statistical Analysis (2005)

In this article, we describe a taxonomy of generic graph related tasks along with a computer-based evaluation designed to assess the readability of two representations of graphs: matrix-based representations and node-link diagrams. This evaluation encompasses seven generic tasks and leads to insightful recommendations for the representation of graphs according to their size and density. Typically, we show that when graphs are bigger than twenty vertices, the matrix-based visualization outperforms node-link diagrams on most tasks. Only path finding is consistently in favor of node-link diagrams throughout the evaluation.
Effects of a standardized mistletoe preparation on metastatic B16 melanoma colonization in murine lungs. (1998)

The immune response-modifying drug Lektinol is a mistletoe preparation which is standardized with respect to bioactive viscum album agglutinin, the most active component of mistletoe. The present study was designed to evaluate the antimetastatic effects of this preparation following intravenous injection of B16 melanoma cells into mice. The standardized mistletoe extract was administered intravenously in doses of 100, 1000 or 5000 microliters/kg (equivalent to 3, 30 or 150 ng/kg of viscum album agglutinin) once daily for three weeks. An inhibition of mean pulmonary metastatic colonization of 58 to 95%, as measured by the number of melanoma cells on lung tissue slides, and a significant decrease of percentage of bronchoalveolar lavage pigmented cells were observed. In addition, a correlation of this antimetastatic activity with cellular immune parameters was investigated. In lavage fluids from the tumor-bearing mice, there was a 5 to 6-fold significant increase in the percentage of MAC-1+ (CD11b/CD18) immunocompetent macrophages in comparison with cells from vehicle-treated animals. The percentages of double-positive immature CD4+8+ thymocytes were significantly increased in animals treated with the standardized mistletoe extract. There were no signs of treatment-related toxicity. The results of this study indicate that the standardized mistletoe extract shows antimetastatic activity against B16 melanoma lung colonization.
Cost-effectiveness analysis of ferric carboxymaltose in pre-operative haemoglobin optimisation in patients undergoing primary knee arthroplasty. (2018)

In primary knee arthroplasty, pre-operative haemoglobin optimisation with intravenous ferric carboxymaltose is less expensive than other reported patient blood management modalities and must be considered in patients with iron deficiency anaemia.
Structural Basis for Cyclic Terpene Biosynthesis by Tobacco 5-Epi-Aristolochene Synthase (1997)

Terpene cyclases catalyze the synthesis of cyclic terpenes with 10-, 15-, and 20-carbon acyclic isoprenoid diphosphates as substrates. Plants have been a source of these natural products by providing a homologous set of terpene synthases. The crystal structures of 5-epi-aristolochene synthase, a sesquiterpene cyclase from tobacco, alone and complexed separately with two farnesyl diphosphate analogs were analyzed. These structures reveal an unexpected enzymatic mechanism for the synthesis of the bicyclic product, 5-epi-aristolochene, and provide a basis for understanding the stereochemical selectivity displayed by other cyclases in the biosynthesis of pharmacologically important cyclic terpenes. As such, these structures provide templates for the engineering of novel terpene cyclases.
Effects on virulence of mutations in a locus essential for hyaluronic acid capsule expression in group A streptococci (1994)

Mucoid or highly encapsulated strains of group A streptococci have been associated both with unusually severe infections and with acute rheumatic fever. Previously, we described an acapsular mutant, TX4, derived from a mucoid M-type 18 strain of a group A streptococcus by transposon mutagenesis (M. R. Wessels, A. E. Moses, J. B. Goldberg, and T. J. DiCesare, Proc. Natl. Acad. Sci. USA 88:8317-8321, 1991). We now report studies further characterizing strain TX4 as well as an additional acapsular mutant, TX72. Strain TX4 was found to contain a 9.5-kb deletion of chromosomal DNA adjacent to the site of transposon Tn916 insertion. Cloned chromosomal DNA from TX4 flanking the transposon insertion site was used as a probe to demonstrate the presence of homologous regions in 11 of 11 wild-type group A streptococcal strains of various M protein types. A second acapsular mutant, TX72, had a single transposon insertion and had no apparent deletion of chromosomal DNA. The Tn916 insertion in TX72 was mapped to the hasA locus (encoding hyaluronate synthase), which lies within the chromosomal region deleted in TX4. Strain TX72 was avirulent in mice and sensitive to phagocytic killing in vitro. Transduction of either the insertion-deletion mutation from TX4 or the simple insertion mutation from TX72 to a type 24 group A streptococcus strain also resulted in loss of capsule expression, demonstrating that a homologous region of the chromosome controls capsule expression in another serotype of group A streptococci. We conclude that the hyaluronic acid capsule plays an important role in virulence and that a region of the chromosome essential for capsular polysaccharide expression is conserved among diverse group A streptococcal strains.
Caspase-8 promotes NLRP1/NLRP3 inflammasome activation and IL-1β production in acute glaucoma (2014)

Acute glaucoma is a sight-threatening condition characterized by a sudden and substantial rise in intraocular pressure (IOP) and consequent retinal ganglion cell (RGC) death. Angle closure glaucoma, a common cause of glaucoma in Asia that affects tens of millions of people worldwide, often presents acutely with loss of vision, pain, and high IOP. Even when medical and surgical treatment is available, acute angle closure glaucoma can cause permanent and irreversible loss of vision. Toll-like receptor 4 (TLR4) signaling has been previously implicated in the pathogenesis of IOP-induced RGC death, although the underlying mechanisms are largely unknown. In the present study, we used an acute IOP elevation/glaucoma model to investigate the underlying mechanism of RGC death. We found that TLR4 leads to increased caspase-8 expression; this elevation increases IL-1β expression and RGC death via a caspase-1-dependent pathway involving Nod-like receptor family, pyrin domain containing 1 (NLRP1)/NLRP3 inflammasomes and a caspase-1-independent pathway. We show that inhibition of caspase-8 activation significantly attenuates RGC death by down-regulating the activation of NLRP1 and NLRP3, thus demonstrating the pivotal role of caspase-8 in the TLR4-mediated activation of inflammasomes. These findings demonstrate collectively a critical role of caspase-8 in transducing TLR4-mediated IL-1β production and RGC death and highlight signal transduction in a caspase-1-dependent NLRP1/NLRP3 inflammasome pathway and a caspase-1-independent pathway in acute glaucoma. These results provide new insight into the pathogenesis of glaucoma and point to a treatment strategy.
Protein sequence of endothelial glycoprotein IIIa derived from a cDNA clone. Identity with platelet glycoprotein IIIa and similarity to “integrin”. (1987)

Platelet membrane glycoprotein (GP) IIIa forms a Ca2+-dependent heterodimer complex with GP IIb. The GP IIb-IIIa complex constitutes the fibrinogen and fibronectin receptor on stimulated platelets. A biochemically and immunologically similar membrane glycoprotein complex is present on endothelial cells. A human umbilical vein endothelial cell cDNA library was screened using oligonucleotide probes designed from peptide sequences obtained from platelet GP IIIa. A cDNA clone was sequenced and found to encode a protein of 84.5 kDa. The translated endothelial cDNA contained five sequences that corresponded to peptide sequences in platelet GP IIIa, including the amino-terminal 19 residues. Thus, the endothelial and platelet forms of GP IIIa are apparently identical. Glycoprotein IIIa consists of a long amino-terminal extracellular domain with several potential N-linked glycosylation sites and four cysteine-rich tandem repeats, a 29-residue hydrophobic transmembrane segment, and a short carboxyl-terminal cytoplasmic domain. Glycoprotein IIIa has a 47% amino acid sequence homology to "integrin," a fibronectin receptor from chicken embryo fibroblasts. This homology suggests that GP IIIa is a member of a family of cell-surface adhesion receptors.
Folate analogs. 21. Synthesis and antifolate and antitumor activities of N10-(cyanomethyl)-5,8-dideazafolic acid (1983)

A close analogue of the antileukemic agent 5,8-dideaza-N10 propargylfolic acid (2) was synthesized by replacing the propargyl moiety of 2 with a cyanomethyl group. This compound, N10-(cyanomethyl)-5,8-dideazafolic acid (3), was evaluated for its antifolate and antitumor activities in several biological test systems. Alkylation of diethyl N-(4-aminobenzoyl)-L-glutamate with bromoacetonitrile gave diethyl N-[4-[(cyanomethyl)amino]benzoyl]-L-glutamate (7). Reaction of 7 with 2 amino-6-(bromomethyl)-4-hydroxyquinazoline (9) in dimethylacetamide gave the corresponding diethyl ester 11, which was hydrolyzed to the target compound 3. The known antileukemic agent 2 was also synthesized for comparative studies by employing a modified procedure, which resulted in a better yield of this product. Both compounds 2 and 3 were evaluated for their antifolate activities by using two folate-requiring microorganisms, Streptococcus faecium and Lactobacillus casei. They were further evaluated as inhibitors of thymidylate synthase and dihydrofolate reductase derived from the above organisms, as well as for their antitumor activity by using selected tumor cells in culture. Compound 2 was found to be as equally potent as methotrexate (MTX) against S. faecium, and it was an excellent inhibitor of L. casei thymidylate synthase. The cyanomethyl analogue 3 was less active than 2 in all the test systems, except the inhibition of dihydrofolate reductase.
Demyelination in primate autoimmune encephalomyelitis and acute multiple sclerosis lesions: A case for antigen-specific antibody mediation (1999)

Neuropathological and ultrastructural features of central nervous system demyelination were compared in marmoset experimental autoimmune encephalomyelitis (EAE) induced with myelin/oligodendrocyte glycoprotein (MOG), and in 3 cases of multiple sclerosis (MS) displaying recent lesions. At the edges of EAE and MS lesions, a zone of myelin vacuolation was common, whereas in the lesion proper, myelin sheaths were consistently transformed into vesiculated membranous networks. These networks became dissociated from axons by cell processes from macrophages. Oligodendrocytes were remarkably spared and evidence of myelin repair was present but not prominent. Axonal pathology was more common in the MS material than in marmoset EAE. Immunocytochemistry, using gold-labeled encephalitogenic peptides of MOG and silver enhancement to detect MOG autoantibodies, revealed the presence of MOG-specific autoantibodies over vesiculated myelin networks. Gold-labeled antibody to IgG also gave a positive reaction. Gold-labeled peptide of myelin basic protein did not react with MOG/EAE tissue, but the same conjugate gave positive staining in MS (and in marmoset EAE induced by whole white matter), perhaps indicating broader spectrum immunoreactivity or sensitization to myelin antigens. Thus, vesicular disruption of myelin was a constant feature in these evolving, highly active lesions in primate EAE and MS and appeared causally related to the deposition of antigen-specific autoantibodies.
Subunit Cell Wall of Sulfolobus acidocaldarius (1974)

The cell wall of Sulfolobus acidocaldarius has been isolated. Cells were mechanically disrupted with a French press, and the cytoplasmic membrane was removed by extracting cell-envelope fragments with Triton X-100. The Triton-insoluble cell wall material retained the characteristic subunit structure when examined in the electron microscope. Isolated cell wall fragments formed in open sheets that were easily separated from cytoplasmic contamination. Chemical studies showed that the Triton-insoluble cell wall fragments consisted of lipoprotein with small amounts of carbohydrate and hexosamine. The amino acid composition indicated a highly charged hydrophobic cell surface. The presence of diaminopimelic acid with only traces of muramic acid indicates that the cell envelope does not have a rigid peptidoglycan layer. The results of chemical analyses and electron microscopy suggest a wall-membrane interaction stabilizing the cell envelope. The chemical and physical properties of this type of cell envelope would appear to form the basis for a new major division of bacteria with the definitive characteristics of a morphologically distinct subunit cell wall devoid of peptidoglycan.
All-fiber multifunction continuous-wave coherent laser radar at 155 µm for range, speed, vibration, and wind measurements (2000)

The design and performance of a simple, multifunction 1.55-µm continuous-wave (cw) and frequency-modulated cw coherent laser radar system with an output power of 1 W is presented. The system is based on a semiconductor laser source plus an erbium-doped fiber amplifier, a polarization-independent fiber-optic circulator used as the transmit–receive switch, and digital signal processing. The system is shown to be able to perform wind-speed measurements even in clear atmospheric conditions when the visibility exceeds 40 km. The aerosol measurements indicate the potential to use single-particle detection for wind measurements with enhanced sensitivity. The system can perform range and line-of-sight velocity measurements of hard targets at ranges of the order of several kilometers with a range accuracy of a few meters and a velocity accuracy of 0.1 m/s by use of triangular-wave frequency modulation with compensation of the frequency-modulation response of the semiconductor laser. The system also demonstrates a capability for vibration sensing.
Monodispersed Colloidal Spheres: Old Materials with New Applications (2000)

This article presents an overview of current research activities that center on monodispersed colloidal spheres whose diameter falls anywhere in the range of 10 nm to 1 μm. It is organized into three parts: The first part briefly discusses several useful methods that have been developed for producing monodispersed colloidal spheres with tightly controlled sizes and well-defined properties (both surface and bulk). The second part surveys some techniques that have been demonstrated for organizing these colloidal spheres into two- and three-dimensionally ordered lattices. The third part highlights a number of unique applications of these crystalline assemblies, such as their uses as photonic bandgap (PBG) crystals; as removable templates to fabricate macroporous materials with highly ordered and three-dimensionally interconnected porous structures; as physical masks in lithographic patterning; and as diffractive elements to fabricate new types of optical sensors. Finally, we conclude with some personal perspectives on the directions towards which future research in this area might be directed.
Effect of Sacral Neuromodulation Rate on Overactive Bladder Symptoms: A Randomized Crossover Feasibility Study (2012)

Rate significantly affected the number of incontinence episodes and pad changes per day. The number of adverse events was similar across the three rate settings with programming-related adverse events lowest in the 14 Hz group.