gebhart/patrepeval huggingface dataset:
Interactions between scatter factors and their receptors: hints for therapeutic applications (1998)

The scatter factors, which include hepatocyte growth factor and macrophage stimulating protein, stand out from other cytokines because of their uncommon biological properties. In addition to promoting cell growth and protection from apoptosis, they are involved in the control of cell dissociation, migration into extracellular matrices, and a unique process of differentiation called 'branching morphogenesis'. Through the concerted regulation of these complex phenomena, scatter factors promote development, regeneration, and reconstruction of normal organ architecture. In transformed epithelia, scatter factors can mediate tumor invasive growth, a harmful feature of neoplastic progression in which cancer cells invade surrounding tissues, penetrate across the vascular walls, and eventually disseminate throughout the body, giving rise to systemic metastases. A much-debated issue in basic biology, which has strong implications for experimental medicine, is how to dissociate the favorable effects of growth factors from their adverse ones. Accordingly, to find agonists or antagonists with potential therapeutic applications is a crucial undertaking for current research. Domain-mapping analyses of growth factor molecules can help to isolate specific structural requirements for the induction of selective biological effects. Based on the observation that certain growth factors must undergo posttranslational modifications to exert a full response, it is possible to interfere with their activation mechanisms to modulate their functions. Finally, the identification of cell type-specific coreceptors able to potentiate their activity allows drawing of a functional body map, where some organs or tissues may be more responsive than others to growth factors. This review is focused on how, and to what extent, scatter factors can behave 'well' or 'badly' according to their molecular structure, the way they are activated, and the way they interact with cell surface receptors and coreceptors.
Evolution of Peroxisome Proliferator-Activated Receptor Agonists (2007)

Influencing the various PPARs results in improved glucose, lipid, and weight management, with effects dependent on full or partial agonist activity at single or multiple receptors. Although the dual PPAR compounds have been associated with unacceptable toxicities, new PPAR agonist medications continue to be developed and investigated to discover a safe drug with benefits in multiple disease states.
Massive targeting of liposomes, surface-modified with anionized albumins, to hepatic endothelial cells (1997)

Human serum albumin (HSA) derivatized with cis-aconitic anhydride was covalently coupled to liposomes with a size of approximately 100 nm [polyaconitylated HSA (Aco-HSA) liposomes]. Within 30 min after injection into a rat, Aco-HSA liposomes were completely cleared from the blood and almost exclusively taken up by the liver, whereas in control liposomes 80% was still present in the blood at that time. Endothelial cells were shown to account for almost two-thirds of the hepatic uptake of the Aco-HSA liposomes, the remainder being recovered mainly in the liver macrophages (Kupffer cells). With fluorescently labeled liposomes it was shown that the Aco-HSA liposomes target a vast majority (>85%) of the cells in the endothelial cell population. Control liposomes were not taken up to a significant extent by the endothelial cells. Uptake of Aco-HSA liposomes by both endothelial and Kupffer cells was inhibited by preinjection with polyinosinic acid, indicating the involvement of scavenger receptors in the uptake process. The uptake of Aco-HSA liposomes by liver endothelial cells was dependent on liposome size; with increasing liposome diameter endothelial cell uptake decreased in favor of Kupffer cell uptake. We have demonstrated that massive in vivo targeting of liposomes to a defined cell population other than macrophages is possible. Aco-HSA liposomes thus may represent an attractive drug carrier system for treatment of various liver or liver endothelium-associated disorders.
Hg2+-Selective OFF−ON and Cu2+-Selective ON−OFF Type Fluoroionophore Based upon Cyclam (2006)

[structure: see text]. A new cyclam derivative having two different fluorophores of pyrene and NBD subunits was prepared, and its Hg2+- and Cu2+-selective signaling behaviors were investigated. The detection limits for the analysis of Hg2+ and Cu2+ ions were found to be 7.9 x 10(-6) and 2.6 x 10(-7) M in aqueous acetonitrile solution (H2O-CH3CN = 10:90, v/v), respectively. The compound also exhibited a selective Hg2+/Cu2+-induced OFF-ON-OFF type of signaling pattern that can be utilized for the construction of functional supramolecular switching systems.
Stable yttrium oxyfluoride used in plasma process chamber (2017)

An yttrium oxyfluoride (YOF) protective material was developed for the inner wall of plasma process equipment. Using microwave-excited surface-wave high-density plasma equipment, the chemical stability of the obtained YOF films was evaluated by exposure to H2/Ar, N2/Ar, NH3/Ar, O2/Ar, and NF3/Ar plasmas. The YOF film surface was stable against these plasmas containing hydrogen, nitrogen, oxygen, and fluorine. Especially, the stability of YOF against fluoridation was better than that of Y2O3, which is currently widely used as the protective material in plasma process chambers.
Plant cell culture : a practical approach (1985)

1: Isolation and maintenance of callus and cell suspension cultures. 2: Isolation, culture, and regeneration of protoplasts. 3: Applications of protoplast technology. 3.A: Fusion and selection of somatic hybrids. 3.B: Transient gene expression and stable transformation. 3.C: Studies with viruses. 4: Selection of plant cells for desirable characteristics. 4.A: Inhibitor resistance. 4.B: Cold tolerance. 4.C: In vitro selection for salt tolerance. 4.D: In vitro selection for disease/toxin resistance. 5: Plant regeneration via embryonic suspension cultures. 6: Applied aspects of plant regeneration. 6.A: Micropropagation. 6.B: Virus-free plants. 6.C: Artificial seeds. 7: Cryopreservation. 8: Secondary products from cultured cells and organs I: molecular and cellular approaches. 9: Secondary products from cultured cells and organs II: large scale culture
Mining Online Deal Forums for Hot Deals (2004)

Online deal forums are public places where participants share with each other news and information regarding such as sales promotion events by online stores. The large number of messages in the forums and their inherent uncertainty make it difficult for even seasoned users to identify useful deal information from the forums. We develop an intelligent deal alert service which assists ordinary Web surfers to find useful deals by mining online deal forums. It periodically crawls relevant deal forums to collect fresh message posts and responses, and evaluate them using a form of probabilistic text classification. Users may be notified of new, potentially useful deal messages via emails or they may browse them using their favorite Web browser. We train and evaluate the service using deal posts and responses collected from actual deal forums in the Web. The preliminary evaluation results show that the service is quite effective in reducing the time to find useful deals.
Cardiac Sodium Channel Gene Variants and Sudden Cardiac Death in Women (2007)

Functionally significant mutations and rare variants in SCN5A may contribute to SCD risk among women.
Clinical and microbiological effects of controlled-release local delivery of minocycline on periodontitis in dogs (1998)

When used as an adjunct to tooth scaling and root planing, minocycline periodontal formulation stimulated favorable clinical and antimicrobial responses.
Continuous glucose monitors (2013)

In a widening set of circumstances, use of CGM has been shown to promote safer and more effective glycemic control than self-monitoring of blood glucose. Imperfections remain in certain scenarios such as hypoglycemia and in certain populations such as young children. Ongoing research on sensors and calibration software should translate to better systems.
A Two-Stage Iterative Decoding of LDPC Codes for Lowering Error Floors (2008)

In iterative decoding of LDPC codes, trapping sets often lead to high error floors. In this work, we propose a two-stage iterative decoding to break trapping sets. Simulation results show that the error floor performance can be significantly improved with this decoding scheme.
Genetic Diversity of Viable, Injured, and Dead Fecal Bacteria Assessed by Fluorescence-Activated Cell Sorting and 16S rRNA Gene Analysis (2005)

A novel approach combining a flow cytometric in situ viability assay with 16S rRNA gene analysis was used to study the relationship between diversity and activity of the fecal microbiota. Simultaneous staining with propidium iodide (PI) and SYTO BC provided clear discrimination between intact cells (49%), injured or damaged cells (19%), and dead cells (32%). The three subpopulations were sorted and characterized by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene amplicons obtained from the total and bifidobacterial communities. This analysis revealed that not only the total community but also the distinct subpopulations are characteristic for each individual. Cloning and sequencing of the dominant bands of the DGGE patterns showed that most of clones retrieved from the live, injured, and dead fractions belonged to Clostridium coccoides, Clostridium leptum, and Bacteroides. We found that some of the butyrate-producing related bacteria, such as Eubacterium rectale and Eubacterium hallii, were obviously viable at the time of sampling. However, amplicons affiliated with Bacteroides and Ruminococcus obeum- and Eubacterium biforme-like bacteria, as well as Butyrivibrio crossotus, were obtained especially from the dead population. Furthermore, some bacterial clones were recovered from all sorted fractions, and this was especially noticeable for the Clostridium leptum cluster. The bifidobacterial phylotypes identified in total samples and sorted fractions were assigned to Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium infantis, Bifidobacterium pseudocatenulatum, and Bifidobacterium bifidum. Phylogenetic analysis of the live, dead, and injured cells revealed a remarkable physiological heterogeneity within these bacterial populations; B. longum and B. infantis were retrieved from all sorted fractions, while B. adolescentis was recovered mostly from the sorted dead fraction.
Vaccinia Virus–Encoded Ribonucleotide Reductase Subunits Are Differentially Required for Replication and Pathogenesis (2010)

Ribonucleotide reductases (RRs) are evolutionarily-conserved enzymes that catalyze the rate-limiting step during dNTP synthesis in mammals. RR consists of both large (R1) and small (R2) subunits, which are both required for catalysis by the R1(2)R2(2) heterotetrameric complex. Poxviruses also encode RR proteins, but while the Orthopoxviruses infecting humans [e.g. vaccinia (VACV), variola, cowpox, and monkeypox viruses] encode both R1 and R2 subunits, the vast majority of Chordopoxviruses encode only R2 subunits. Using plaque morphology, growth curve, and mouse model studies, we investigated the requirement of VACV R1 (I4) and R2 (F4) subunits for replication and pathogenesis using a panel of mutant viruses in which one or more viral RR genes had been inactivated. Surprisingly, VACV F4, but not I4, was required for efficient replication in culture and virulence in mice. The growth defects of VACV strains lacking F4 could be complemented by genes encoding other Chordopoxvirus R2 subunits, suggesting conservation of function between poxvirus R2 proteins. Expression of F4 proteins encoding a point mutation predicted to inactivate RR activity but still allow for interaction with R1 subunits, caused a dominant negative phenotype in growth experiments in the presence or absence of I4. Co-immunoprecipitation studies showed that F4 (as well as other Chordopoxvirus R2 subunits) form hybrid complexes with cellular R1 subunits. Mutant F4 proteins that are unable to interact with host R1 subunits failed to rescue the replication defect of strains lacking F4, suggesting that F4-host R1 complex formation is critical for VACV replication. Our results suggest that poxvirus R2 subunits form functional complexes with host R1 subunits to provide sufficient dNTPs for viral replication. Our results also suggest that R2-deficient poxviruses may be selective oncolytic agents and our bioinformatic analyses provide insights into how poxvirus nucleotide metabolism proteins may have influenced the base composition of these pathogens.
In Vivo Cellular Imaging for Translational Medical Research (2009)

Personalized treatment using stem, modified or genetically engineered, cells is becoming a reality in the field of medicine, in which allogenic or autologous cells can be used for treatment and possibly for early diagnosis of diseases. Hematopoietic, stromal and organ specific stem cells are under evaluation for cell-based therapies for cardiac, neurological, autoimmune and other disorders. Cytotoxic or genetically altered T-cells are under clinical trial for the treatment of hematopoietic or other malignant diseases. Before using stem cells in clinical trials, translational research in experimental animal models are essential, with a critical emphasis on developing noninvasive methods for tracking the temporal and spatial homing of these cells to target tissues. Moreover, it is necessary to determine the transplanted cell's engraftment efficiency and functional capability. Various in vivo imaging modalities are in use to track the movement and incorporation of administered cells. Tagging cells with reporter genes, fluorescent dyes or different contrast agents transforms them into cellular probes or imaging agents. Recent reports have shown that magnetically labeled cells can be used as cellular magnetic resonance imaging (MRI) probes, demonstrating the cell trafficking to target tissues. In this review, we will discuss the methods to transform cells into probes for in vivo imaging, along with their advantages and disadvantages as well as the future clinical applicability of cellular imaging method and corresponding imaging modality.
Ion-exchanged waveguide lasers in Er^3+/Yb^3+ codoped silicate glass (1999)

We investigated an Er(3+)/Yb(3+) codoped silicate glass as a host material for waveguide lasers operating near 1.5 microm. Spectroscopic properties of the glass are reported. Waveguide lasers were fabricated by K(+)-ion exchange from a nitrate melt. The waveguides support a single transverse mode at 1.5 microm. An investigation of the laser performance as a function of the Yb:Er ratio was performed, indicating an optimal ratio of approximately 5:1. Slope efficiencies of as great as 6.5% and output powers as high as 19.6 mW at 1.54 microm were realized. The experimental results are compared with a waveguide laser model that is used to extract the Er(3+) upconversion coefficients and the Yb(3+)-Er(3+) cross-relaxation coefficients. The results indicate the possibility of obtaining high-performance waveguide lasers from a durable silicate host glass.
Semantic video segmentation: Exploring inference efficiency (2015)

We explore the efficiency of the CRF inference beyond image level semantic segmentation and perform joint inference in video frames. The key idea is to combine best of two worlds: semantic co-labeling and more expressive models. Our formulation enables us to perform inference over ten thousand images within seconds and makes the system amenable to perform video semantic segmentation most effectively. On CamVid dataset, with TextonBoost unaries, our proposed method achieves up to 8% improvement in accuracy over individual semantic image segmentation without additional time overhead. The source code is available at https: //github. com/subtri/video inference.
Phenotypically diverse mouse thymic stromal cell lines which induce proliferation and differentiation of hematopoietic cells (1993)

The heterogeneity of the thymic stroma has made careful characterization of particular thymic stromal cell types difficult. To this end, we have derived a panel of cloned thymic stromal cell lines from simian virus 40 T antigen (SV40-T antigen) transgenic mice. Based on their analysis with monoclonal antibodies that distinguish among subsets of thymic stroma cells, and on the morphology and ultrastructural features of the different clones, we suggest that our panel includes representatives of the thymic subcapsular cortex or thymic nurse cells (427.1), the deep cortex or cortical reticular cells (1308.1) and the medulla including medullary interdigitating (IDC)-like cells (6.1.1) and medullary epithelial cells (6.1.7). A fifth cell type of undesignated but apparent medullary origin (6.1.11) was also isolated. All of the cell lines constitutively express the SV40 T antigen transgene and the class I antigens of the major histocompatibility complex (MHC), and they can be induced to express MHC class II antigens upon stimulation with recombinant interferon-gamma (IFN-gamma). These cell lines elaborate a factor(s) that induces the proliferation of cells from the fetal liver and bone marrow, but not from the neonatal thymus. A factor(s) elaborated by the 1308.1 cell line also induces the proliferation of fetal thymocytes in the absence of mitogens, phorbol esters or calcium ionophore which is augmented with the addition of recombinant interleukin-2 (IL-2). Analysis by reverse transcription polymerase chain reaction with primers for some mouse cytokines reveals that each of these cell lines contain granulocyte-macrophage colony-stimulating factor (GM-CSF) transcripts and that 1308.1, 6.1.1 and 6.1.7 produce IL-6 mRNA. Cell lines 1308.1 and 6.1.1 also produce IL-7; 6.1.1 produces IL-1 beta and tumor necrosis factor (TNF)-alpha while the 427.1 cell line produces IL-5 and IFN-gamma mRNA. None of the cell lines tested express the IL-2 receptor, IL-2, IL-3, IL-4, TNF-beta or macrophage inflammatory proteins mRNA. Conditioned medium (CM) from 1308.1 and 6.1.11 induced differentiation of cells purified from the mouse fetal liver into granulocytes; 1308.1 CM also induced differentiation of the mouse hematopoietic stem cell line 32DCl3(G) suggesting that the CM contains granulocyte (G)-CSF activity. Each cell line produces GM-CSF but the greatest activity is associated with 1308.1 and 6.1.11 CM. The availability of these well-characterized, functional, cloned thymic stromal cells will allow a more detailed analysis of the role of each cell type in both myeloid and T cell development.
Pyrido [2, 3-<I>d</I>] pyrimidine Antibacterial Agents. I. 8-Alkyl-5, 8-dihydro-5-oxopyrido [2, 3-<I>d</I>]-pyrimidine-6-carboxylic Acids and Related Compounds (1971)

MeOH-soluble part) was allowed to stand at room temperature and colorless crystals (25) which separated out were collected, 11mg, mp 175 (decomp.)
Novel keto acid formate‐lyase and propionate kinase enzymes are components of an anaerobic pathway in Escherichia coli that degrades L‐threonine to propionate (1998)

An immunological analysis of an Escherichia coli strain unable to synthesize the main pyruvate formate-lyase enzyme Pfl revealed the existence of a weak, cross-reacting 85 kDa polypeptide that exhibited the characteristic oxygen-dependent fragmentation typical of a glycyl radical enzyme. Polypeptide fragmentation of this cross-reacting species was shown to be dependent on Pfl activase. Cloning and sequence analysis of the gene encoding this protein revealed that it coded for a new enzyme, termed TdcE, which has 82% identity with Pfl. On the basis of RNA analyses, the tdcE gene was shown to be part of a large operon that included the tdcABC genes, encoding an anaerobic threonine dehydratase, tdcD, coding for a propionate kinase, tdcF, the function of which is unknown, and the tdcG gene, which encodes a L-serine dehydratase. Expression of the tdcABCDEFG operon was strongly catabolite repressed. Enzyme studies showed that TdcE has both pyruvate formate-lyase and 2-ketobutyrate formate-lyase activity, whereas the TdcD protein is a new propionate/acetate kinase. By monitoring culture supernatants from various mutants using 1H nuclear magnetic resonance (NMR), we followed the anaerobic conversion of L-threonine to propionate. These studies confirmed that 2-ketobutyrate, the product of threonine deamination, is converted in vivo by TdcE to propionyl-CoA. These studies also revealed that Pfl and an as yet unidentified thiamine pyrophosphate-dependent enzyme(s) can perform this reaction. Double null mutants deficient in phosphotransacetylase (Pta) and acetate kinase (AckA) or AckA and TdcD were unable to metabolize threonine to propionate, indicating that propionyl-CoA and propionyl-phosphate are intermediates in the pathway and that ATP is generated during the conversion of propionyl-P to propionate by AckA or TdcD.
Effects of mask bias on the mask error enhancement factor (MEEF) of contact holes (2001)

The effects of mask bias on the Mask Error Enhancement Factor (MEEF) of 180 nm contact holes is studied through lithographic simulation using commercial software and a DUV (248 nm) ESCAP photoresist model. Dense contacts show higher MEEF than isolated or semi-dense contacts. However, dense features exhibit a minimum in MEEF at a single negative mask bias (CD on reticle &gt; 180 nm). Aerial image simulations indicated that low MEEF correlates approximately with high normalized aerial image log-slope (NILS). Hence, factors that affect NILS, such as numerical aperture, partial coherence, and wavelength, also influence MEEF, although without altering the optimum mask bias for minimum dense MEEF. Numerical aperture and wavelength of exposure have the greatest influence on MEEF. For 180 nm contact holes worst case MEEF values below 2 can be achieved by increasing NA to 0.8 at 248 nm or by decreasing (lambda) to 193 nm at 0.6 NA. Resist identity has little influence on the magnitude of MEEF but was the only factor affecting the mask bias setting for minimum dense MEEF.
Reactions between half- and full-FLP recombination target sites. A model system for analyzing early steps in FLP protein-mediated site-specific recombination. (1992)

The FLP recombination target (FRT) can be cut in half so that only one FLP protein binding site is present (a "half site"). FLP protein binds the half sites and joins them into dimeric, asymmetric head-to-head complexes held together chiefly by strong noncovalent interactions. These complexes react with full (normal) FRT sites to generate a variety of products. Analysis of these DNA species reveals that the reaction follows a well-defined reaction pathway that generally parallels the normal reaction pathway. The system is useful in analyzing early steps in recombination, since the identity of the products in a given recombination event unambiguously pinpoints the order in which the cleavage and strand exchange reactions occur. Two conclusions are derived from the present study: (i) Formation of the dimeric head-to-head complex of half sites is a prerequisite to further steps in recombination. (ii) The identity of the base pairs at positions 6 and -6 within the FRT site has a subtle effect in directing the first strand exchange event in the reaction to predominantly one of two possible cleavage sites. In addition, results are presented that suggest that a DNA-DNA pairing intermediate involving only two base pairs of the core sequence is formed prior to the first cleavage and strand exchange. DNA-DNA interactions may therefore not be limited to the isomerization step that follows the first strand exchange.