gebhart/patrepeval huggingface dataset:
Protecting Fibrinogen with Rutin during UVC Irradiation for Viral Inactivation (1996)

Fibrinogen solutions were irradiated with UVC (254 nm) to inactivate contaminating viruses. In order to protect fibrinogen during UVC irradiation, 0.5 mM rutin was added prior to UVC exposure and subsequently removed during processing. Viral kill by 0.1 J/cm2 UVC resulted in the following inactivation values (log 10): non-lipid-enveloped viruses: Parvo > or = 5.5; encephalomyocarditis virus > or = 6.5; hepatitis A virus > or = 6.5: lipid-enveloped viruses: human immunodeficiency virus > or = 5.7; vesicular stomatitis virus > or = 5.7. Fibrinogen irradiated with 0.5 mM rutin did not significantly differ from unirradiated material in terms of clot time and breaking strength. In the absence of rutin, UVC irradiation of fibrinogen at similar fluence led to loss of solubility, increased clot time and the cleavage of fibrino-peptides that reacted with dinitrophenyl hydrazine as a test for ketonic carbonyl groups. High-performance liquid chromatography and mass spectrometry data showed that rutin exposed to UVC formed numerous breakdown, oxidation and combinational products. Experiments with 3H-rutin showed that after UVC irradiation, subsequent processing by a C18 resin and alcohol precipitation removed > 99% rutin, representing < 10 ppm rutin in the final fibrinogen preparations. Residual 3H-rutin was not covalently bonded to the fibrinogen. Immunochemical studies with rabbit antisera to UVC irradiated (with rutin) fibrinogen showed the absence of neoimmungens. By all measures, rutin prevents fibrinogen degradation during virucidal UVC irradiation.
Corpus-based predictive text input (2005)

We introduce a new predictive text input system that uses visited documents for predicting the user's next input word. With our method, users can efficiently compose new texts using other documents as dictionaries for the input prediction. We have developed a document storage system Kukura that stores all the texts visited by users and cooperate with our predictive input system PRIME. In this paper, we describe the design, implementation, and evaluation of our approach.
Lymphatic microvessel density as a novel prognostic factor in early-stage invasive cervical cancer (2001)

Few data on the influence of lymphatic microvessel density (MVD) on survival in cancer are available since until recently there was no reliable immunohistological marker for lymphatic endothelium. Using an antibody staining podoplanin, a novel marker for lymphatic endothelium, lymphatic MVD in tissue samples of 85 patients with cervical cancer classification pT1b treated by radical hysterectomy was investigated. Survival was determined using univariate and multivariate analyses. Lymphatic MVD was also compared to MVD assessed by immunostaining against factor VIII-related antigen, which is considered a marker for blood vessels. Patients with >5 lymphatic microvessels/0.25 mm(2) field had significantly better overall survival (mean 91.8 months) than those with < or =5 lymphatic microvessels/field in univariate analysis (mean 113 months) (p = 0.0105, log-rank test). In multivariate analysis, lymphatic node involvement (p =0.0183), vessel infiltration (p =0.0158) and lymphatic MVD (p =0.0269) remained independent prognostic factors. No correlation between lymphatic MVD and various clinical and histopathological parameters was observed. Correlation between lymphatic MVD and MVD assessed by immunostaining against factor VIII was only weak (p = 0.004, r = 0.312, Spearman's coefficient of correlation). Our results suggest that increased lymphatic MVD is associated with favorable prognosis in early-stage cervical cancer.
Identification and cloning of a novel cellular protein Naf1, Nef‐associated factor 1, that increases cell surface CD4 expression1 (1999)

The nef gene of human and simian immunodeficiency virus is a key factor in acquired immunodeficiency syndrome pathogenesis and virus replication. Several Nef-induced phenomena, including the down-regulation of CD4 molecule, have been previously reported. In this study, we have identified and cloned a novel cellular protein Naf1 (Nef-associated factor 1), which associated with Nef in the yeast two-hybrid system and pull-down assay. The Naf1 gene generates two isoforms (Naf1alpha and beta) containing four coiled-coil structures. The Naf1 mRNA is ubiquitously expressed in human tissues with strong expression in peripheral blood lymphocytes and spleen. Naf1 overexpression increased cell surface CD4 expression. Nef suppressed this Naf1-induced augmentation of CD4 expression, providing a novel mode of Nef action in CD4 down-regulation.
Pulmonary hemorrhage syndrome associated with dengue fever, High-resolution computed tomography findings: a case report (2009)

Dengue hemorrhagic fever is an acute infectious disease caused by dengue virus. We described the high-resolution CT findings in a 70-year-old male with the disease, which was diagnosed by clinical examination and confirmed by serological methods. High-resolution CT demonstrated bilateral areas of consolidation with air bronchogram and ground glass opacities, as well as small bilateral pleural effusions. Dengue hemorrhagic fever should be considered in the differential diagnosis of diffuse pulmonary hemorrhage.
On-line post-column Diels-Alder derivatization for the determination of vitamin D3 and its metabolites by liquid chromatography/thermospray mass spectrometry (1993)

Liquid chromatography/thermospray mass spectrometry (LC/TSP MS) has been used for the determination of vitamin D3 and some of its metabolites, i.e. 1 alpha(OH) vitamin D3, 25(OH) vitamin D3, 1 alpha,25(OH)2 vitamin D3 and 24,25(OH)2 vitamin D3, using positive and negative ion detection. Using these two modes positional isomers can be identified. Detection in the negative ion mode was preferred because of the slightly higher sensitivity. The limits of detection, using multiple ion detection, are 50-100 nM (6-12 pmol injected). On-line post-column derivatization based on [4 + 2] cyclo-addition (Diels-Alder reaction) proceeds within 1 min at room temperature. If this step is included in LC/TSP MS, the detection limits of the analytes can be improved 7-70-fold depending on the analyte tested. The best results (detection limits down to 1 nM, i.e. 0.12 pmol injected) are obtained with discharge ionization in the negative ion mode.
A common air interface for a cellular auxiliary personal communications service (2002)

There are several standards for cellular systems that are in use around the world. In the United States, the most prolific is that described in EIA/TIA 553 or as it is more commonly known AMPS. In designing an in-building microcellular PCS, using an existing cellular system standard provides some advantages. Since the two kinds of systems have different requirements, it is not possible to use a cellular system standard for an in-building microcellular PCS design without some changes. In the United States, this has been done by taking the EIA/TIA-553 standard and adapting it for in-building microcellular PCS. The development and the main points of this new standard for a cellular auxiliary personal communications service (CAPCS) are described in this paper. Also, some preliminary results of a field trial of an in-building microcellular PCS based on the CAPCS standard are presented.
Optimized survival of hippocampal neurons in B27‐supplemented neurobasal™, a new serum‐free medium combination (1993)

We have systematically optimized the concentrations of 20 components of a previously published serum-free medium (Brewer and Cotman, Brain Res 494: 65-74, 1989) for survival of rat embryonic hippocampal neurons after 4 days in culture. This serum-free medium supplement, B27, produced neuron survival above 60%, independent of plating density above 160 plated cells/mm2. For isolated cells (< 100 cells/mm2), survival at 4 days was still above 45%, but could be rescued to the 60% level at 40 cells/mm2 by simply applying a coverslip on top of the cells. This suggests a need for additional trophic factors. High survival was achieved with osmolarity lower than found in Dulbecco's Modified Eagle's Medium (DMEM), and by reducing cysteine and glutamine concentrations and by the elimination of toxic ferrous sulphate found in DME/F12. Neurobasal is a new medium that incorporates these modifications to DMEM. In B27/Neurobasal, glial growth is reduced to less than 0.5% of the nearly pure neuronal population, as judged by immunocytochemistry for glial fibrillary acidic protein and neuron-specific enolase. Excellent long-term viability is achieved after 4 weeks in culture with greater than 90% viability for cells plated at 640/mm2 and greater than 50% viability for cells plated at 160/mm2. Since the medium also supports the growth of neurons from embryonic rat striatum, substantia nigra, septum, and cortex, and neonatal dentate gyrus and cerebellum (Brewer, in preparation), support for other neuron types is likely. B27/Neurobasal should be useful for in vitro studies of neuronal toxicology, pharmacology, electrophysiology, gene expression, development, and effects of growth factors and hormones.
The Synthetic Peptide Trp-Lys-Tyr-Met-Val-Met-NH2 Specifically Activates Neutrophils through FPRL1/Lipoxin A4 Receptors and Is an Agonist for the Orphan Monocyte-expressed Chemoattractant Receptor FPRL2 (2001)

Neutrophils express the G protein-coupled N-formyl peptide receptor (FPR) and its homologue FPRL1, whereas monocytes express FPR, FPRL1, and FPRL2, an orphan receptor sharing 83% amino acid identity with FPRL1. FPRL1 is a promiscuous receptor activated by serum amyloid A and by different synthetic peptides, including the hexapeptide Trp-Lys-Tyr-Met-Val-d-Met-NH(2) (WKYMVm). By measuring calcium flux in HL-60 cells transfected with FPR, FPRL1, or FPRL2, we show that WKYMVm activated all three receptors, whereas the l-conformer WKYMVM activated exclusively FPRL1 and FPRL2. The functionality of FPRL2 was further assessed by the ability of HL-60-FPRL2 cells to migrate toward nanomolar concentrations of hexapeptides. The half-maximal effective concentrations of WKYMVM for calcium mobilization in HL-60-FPRL1 and HL-60-FPRL2 cells were 2 and 80 nm, respectively. Those of WKYMVm were 75 pm and 3 nm. The tritiated peptide WK[3,5-(3)H(2)]YMVM bound to FPRL1 (K(D) approximately 160 nm), but not to FPR. The two conformers similarly inhibited binding of (125)I-labeled WKYMVm to FPRL2-expressing cells (IC(50) approximately 2.5-3 micrometer). Metabolic labeling with orthophosphoric acid revealed that FPRL1 was differentially phosphorylated upon addition of the l- or d-conformer, indicating that it induced different conformational changes. In contrast to FPRL1, FPRL2 was already phosphorylated in the absence of agonist and not evenly distributed in the plasma membrane of unstimulated cells. However, both receptors were internalized upon addition of either of the two conformers. Taken together, the results indicate that neutrophils are activated by WKYMVM through FPRL1 and that FPRL2 is a chemotactic receptor transducing signals in myeloid cells.
Enzyme-Linked Immunosorbent Assay-Based Method to Quantify the Association of Small Molecules with Aggregated Amyloid Peptides (2012)

This paper describes a simple enzyme linked immunosorbent assay (ELISA) protocol for quantifying the binding of small molecules to aggregated β-amyloid (Aβ) peptides. Amyloid-targeting small molecules have attracted wide interest as potential agents for the treatment or diagnosis of neurodegenerative disorders such as Alzheimer's disease. The lack of general methods to evaluate small molecule-amyloid binding interactions, however, has significantly limited the number of amyloid-targeting molecules that have been studied to date. Here, we demonstrate a general method to quantify small molecule-amyloid binding interactions via a modified quantitative ELISA protocol. A key feature of this protocol is the treatment of commercial ELISA plates with an air plasma to help maintain the desired β-sheet content of the aggregated Aβ upon immobilization of these peptides on to the polystyrene surface. We developed an ELISA-based competition assay on these air plasma-treated plates and evaluated the binding of five previously known amyloid-binding small molecules to aggregated Aβ. We show that this general ELISA-based competition assay can be used to quantify small molecule-amyloid binding interactions in the low nanomolar to low micromolar range, which is the typical range of affinities for many amyloid-targeting diagnostic agents under current development. This simple protocol for quantifying the interaction of small molecules with aggregated Aβ peptides overcomes many limitations of previously reported spectroscopic or radioactivity assays and may, therefore, facilitate the screening and evaluation of a more structurally diverse set of amyloid-targeting agents than had previously been possible.
Chemical Modification of Polymers via a Phase-Transfer Catalyst or Organic Strong Base (1997)

It is well-known that phase-transfer catalysis (PTC) is a very convenient and useful method for organic synthesis. This method can also be used for the chemical modification of polymers to synthesize various functional polymers. That is, functional polymers can be synthesized ordinarily by two different methods. One method is synthesis of monomers with functional groups and selective polymerization of the monomers to give the corresponding polymers with pendant functional groups. Although polymers containing mostly 100 mol% of the functional group can usually be obtained, synthesis and isolation of the monomers are not easy, and polymerization of these monomers is strongly affected or inhibited some times by the functional groups in the monomers. The other method is synthesis of functional polymers by the chemical modification of polymers containing reactive groups such as pendant chloromethyl groups. Although synthesis of polymers containing fully 100% of functional groups is very difficult by this method,
Iron deficiency and impaired child development (2001)

Papers p 1389 

Iron deficiency affects 20% to 50% of the world's population, making it the most common nutritional deficiency.1 In developing countries about half of all cases of anaemia in women and children result from iron deficiency, but other important and often coexisting contributors include malaria, hookworm infestation, HIV, and deficiencies in other nutrients such as vitamin A and folates. 2 3 Conversely, anaemia is just one manifestation of iron deficiency, and there are forms of mild to moderate iron deficiency in which anaemia is absent but tissue function is impaired.

In children iron deficiency develops slowly and produces few acute symptoms. As the deficiency worsens children become pale and weak, eat less, and tire easily. They gain weight poorly, have frequent respiratory and intestinal infections, and may develop pica. The most worrying association is that between iron deficiency and impaired development in behaviour, cognition, and psychomotor skills. Over the past three decades many studies have confirmed this relation, but whether iron deficiency is the sole …
On modeling impact of sub-wavelength lithography on transistors (2007)

As the VLSI technology marches beyond 65 and 45 nm process technologies, variation in gate length has a direct impact on leakage and performance of CMOS transistors. Due to sub-wavelength lithography, the shape of the transistor often differs from idealized rectangles. In silicon, the effective channel length of a transistor varies across its width. This is a modeling problem. The average effective channel length is different for ON current and OFF currents, making it difficult, if not impossible for a single Leff to accurately represent both. In this paper, we report an accurate post-litho non-rectangular transistor modeling methodology. We further studied the impact of focus and dose variations in lithographic process on transistor parameters. The resulting transistor models were applied for standard cell characterization in successive steps of lithographic simulation of layout and device characterization. Results show that the new models can improve the accuracy of estimation of leakage current by 40% or more over a nominal model that is primarily tuned for ON current.
Prognostic Relevance of Integrated Genetic Profiling in Acute Myeloid Leukemia (2012)

We found that DNMT3A and NPM1 mutations and MLL translocations predicted an improved outcome with high-dose induction chemotherapy in patients with AML. These findings suggest that mutational profiling could potentially be used for risk stratification and to inform prognostic and therapeutic decisions regarding patients with AML. (Funded by the National Cancer Institute and others.).
Dual-color fluorescence imaging distinguishes tumor cells from induced host angiogenic vessels and stromal cells (2003)

We have developed a simple yet powerful technique for delineating the morphological events of tumor-induced angiogenesis and other tumor-induced host processes with dual-color fluorescence. The method clearly images implanted tumors and adjacent stroma, distinguishing unambiguously the host and tumor-specific components of the malignancy. The dual-color fluorescence imaging is effected by using red fluorescent protein (RFP)-expressing tumors growing in GFP-expressing transgenic mice. This model shows with great clarity the details of the tumor-stroma interaction, especially tumor-induced angiogenesis and tumor-infiltrating lymphocytes. The GFP-expressing tumor vasculature, both nascent and mature, could be readily distinguished interacting with the RFP-expressing tumor cells. GFP-expressing dendritic cells were observed contacting RFP-expressing tumor cells with their dendrites. GFP-expressing macrophages were observed engulfing RFP-expressing cancer cells. GFP lymphocytes were seen surrounding cells of the RFP tumor, which eventually regressed. Dual-color fluorescence imaging visualizes the tumor-host interaction by whole-body imaging and at the cellular level in fresh tissues, dramatically expanding previous studies in fixed and stained preparations.
Antiangiogenic and Antimetastatic Activity of JAK Inhibitor AZD1480 (2011)

STAT3 has important functions in both tumor cells and the tumor microenvironment to facilitate cancer progression. The STAT regulatory kinase Janus-activated kinase (JAK) has been strongly implicated in promoting oncogenesis of various solid tumors, including the use of JAK kinase inhibitors such as AZD1480. However, direct evidence that JAK drives STAT3 function and cancer pathogenesis at the level of the tumor microenvironment is yet to be established clearly. In this study, we show that AZD1480 inhibits STAT3 in tumor-associated myeloid cells, reducing their number and inhibiting tumor metastasis. Myeloid cell-mediated angiogenesis was also diminished by AZD1480, with additional direct inhibition of endothelial cell function in vitro and in vivo. AZD1480 blocked lung infiltration of myeloid cells and formation of pulmonary metastases in both mouse syngeneic experimental and spontaneous metastatic models. Furthermore, AZD1480 reduced angiogenesis and metastasis in a human xenograft tumor model. Although the effects of AZD1480 on the tumor microenvironment were important for the observed antiangiogenic activity, constitutive activation of STAT3 in tumor cells themselves could block these antiangiogenic effects, showing the complexity of the JAK/STAT signaling network in tumor progression. Together, our results indicated that AZD1480 can effectively inhibit tumor angiogenesis and metastasis mediated by STAT3 in stromal cells as well as tumor cells.
A counterselection for the tryptophan pathway in yeast: 5-fluoroanthranilic acid resistance (2000)

The ability to counterselect, as well as to select for, a genetic marker has numerous applications in microbial genetics. Described here is the use of 5-fluoroanthranilic acid for the counterselection of TRP1, a commonly used genetic marker in the yeast Saccharomyces cerevisiae. Counterselection using 5-fluoroanthranilic acid involves antimetabolism by the enzymes of the tryptophan biosynthetic pathway, such that trp1, trp3, trp4 or trp5 strains, which lack enzymes required for the conversion of anthranilic acid to tryptophan, are resistant to 5-fluoroanthranilic acid. Commonly used genetic procedures, such as selection for loss of a chromosomally integrated plasmid, and a replica-plating method to rapidly assess genetic linkage in self-replicating shuttle vectors, can now be carried out using the TRP1 marker gene. In addition, novel tryptophan auxotrophs can be selected using 5-fluoroanthranilic acid.
Purification and characterization of the human platelet alpha 2-adrenergic receptor. (1986)

Human platelet alpha 2-adrenergic receptors have been purified approximately 80,000-fold to apparent homogeneity by a five-step chromatographic procedure. The overall yield starting from the membranes is approximately 2%. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of radioiodinated protein from purified receptor preparations shows a single major band of Mr 64,000. The specific binding activity of the alpha 2-adrenergic receptor after four chromatographic steps is 14.5 nmol/mg protein. This value is consistent with the expected theoretical specific activity (15.6 nmol/mg) for a protein with a molecular mass of 64,000 daltons if it is assumed that there is one ligand-binding site/receptor molecule. The purified protein can be covalently labeled with the alkylating alpha-adrenergic ligand, [3H]phenoxybenzamine. This labeling is specific, and it shows that the Mr 64,000 protein contains the ligand binding site of the alpha 2-adrenergic receptor. In addition, the competitive binding of ligands to the purified receptor protein shows the proper alpha 2-adrenergic specificity. The alpha 2-adrenergic receptor contains an essential sulfhydryl residue. Thus, exposure of the purified receptor to the sulfhydryl-specific reagent, phenylmercuric chloride, resulted in an 80% loss of binding activity. This loss of binding activity was prevented when exposure to phenylmercuric chloride was done in the presence of alpha 2-adrenergic ligands, and it was reversed by subsequent exposure to dithiothreitol. Partial proteolysis of purified alpha 2-adrenergic receptors was obtained with Staphylococcus aureus V-8 protease, alpha-chymotrypsin, and papain. In a comparison with purified beta 2-adrenergic receptors, no common partial proteolytic products were found.
Disulfide Bonds in the Extracellular Calcium-Polyvalent Cation-sensing Receptor Correlate with Dimer Formation and Its Response to Divalent Cations in Vitro (1998)

Extracellular calcium/polyvalent cation-sensing receptors (CaR) couple to G proteins and contain highly conserved extracellular cysteine residues. Immunoblotting of proteins from rat kidney inner medullary collecting duct endosomes with CaR-specific antibodies reveals alterations in the apparent molecular mass of CaR depending on protein denaturation conditions. When denatured by SDS under nonreducing conditions, CaR migrates as a putative dimeric species of 240-310 kDa. This is twice the predicted molecular mass of the CaR monomer observed after SDS denaturation in the presence of sulfhydryl-reducing agents. In sucrose density gradients, Triton X-100-solubilized CaR sediments as a 220-kDa complex, not explainable by binding of G proteins to CaR monomers. Treatment of Triton-soluble CaR with divalent (Ca2+, Mg2+) and trivalent (Gd3+) metal ion CaR agonists, but not monovalent ions (Na+), partially shifts the electrophoretic mobility of CaR under reducing conditions from a predominantly monomeric to this putative dimeric species on immunoblots in a manner similar to their rank order of functional potency for CaR activation (Gd3+ >> Ca2+ > Mg2+). This Ca2+ effect is blocked by pretreatment with N-ethylmaleimide. We conclude that disulfide bonds present in CaRs mediate formation of dimers that are preserved in Triton X-100 solution. In addition, CaR exposure to Ca2+ induces formation of additional disulfide bonds within the Triton-soluble CaR complex.