gebhart/patrepeval huggingface dataset:
15,000 Unique Zebrafish EST Clusters and Their Future Use in Microarray for Profiling Gene Expression Patterns During Embryogenesis (2003)

A total of 15590 unique zebrafish EST clusters from two cDNA libraries have been identified. Most significantly, only 22% (3437) of the 15590 unique clusters matched 2805 (of 15200) clusters in the Danio rerio UniGene database, indicating that our EST set is complementary to the existing ESTs in the public database and will be invaluable in assisting the annotation of genes based on the upcoming zebrafish genome sequence. Blast search showed that 7824 of our unique clusters matched 6710 known or predicted proteins in the nonredundant database. A cDNA microarray representing approximately 3100 unique zebrafish cDNA clusters has been generated and used to profile the gene expression patterns across six different embryonic stages (cleavage, blastula, gastrula, segmentation, pharyngula, and hatching). Analysis of expression data using K-means clustering revealed that genes coding for muscle-specific proteins displayed similar expression patterns, confirming that the coordinate gene expression is important for myogenesis. Our results demonstrate that the combination of microarray technology with the zebrafish model system can provide useful information on how genes are coordinated in a genetic network to control zebrafish embryogenesis and can help to identify novel genes that are important for organogenesis.
Direct evidence for ex vivo expansion of human hematopoietic stem cells (2006)

To characterize human hematopoietic stem cells (HSCs), xenotransplantation techniques such as the severe combined immunodeficiency (SCID) mouse repopulating cell (SRC) assay have proven the most reliable methods thus far. While SRC quantification by limiting dilution analysis (LDA) is the gold standard for measuring in vitro expansion of human HSCs, LDA is a statistical method and does not directly establish that a single HSC has self-renewed in vitro. This would require a direct clonal method and has not been done. By using lentiviral gene marking and direct intra-bone marrow injection of cultured CD34+ CB cells, we demonstrate here the first direct evidence for self-renewal of individual SRC clones in vitro. Of 74 clones analyzed, 20 clones (27%) divided and repopulated in more than 2 mice after serum-free and stroma-dependent culture. Some of the clones were secondary transplantable. This indicates symmetric self-renewal divisions in vitro. On the other hand, 54 clones (73%) present in only 1 mouse may result from asymmetric divisions in vitro. Our data demonstrate that current ex vivo expansion conditions result in reliable stem cell expansion and the clonal tracking we have employed is the only reliable method that can be used in the development of clinically appropriate expansion methods.
γδ T Cells Provide an Early Source of Interferon γ in Tumor Immunity (2003)

Interferon (IFN)-gamma is necessary for tumor immunity, however, its initial cellular source is unknown. Because gammadelta T cells primarily produce this cytokine upon activation, we hypothesized that they would provide an important early source of IFN-gamma in tumor immunosurveillance. To address this hypothesis, we first demonstrated that gammadelta T cell-deficient mice had a significantly higher incidence of tumor development after challenge with a chemical carcinogen methylcholanthrene (MCA) or inoculation with the melanoma cell line B16. In wild-type mice, gammadelta T cells were recruited to the site of tumor as early as day 3 after inoculation, followed by alphabeta T cells at day 5. We then used bone marrow chimeras and fetal liver reconstitutions to create mice with an intact gammadelta T cell repertoire but one that was specifically deficient in the capacity to produce IFN-gamma. Such mice had a higher incidence of tumor development, induced either with MCA or by inoculation of B16 melanoma cells, compared with mice with IFN-gamma-competent gammadelta T cells. Moreover, genetic deficiency of gammadelta T cells resulted in impaired IFN-gamma production by tumor antigen-triggered alphabeta T cell upon immunization with tumor lysate. These results demonstrate that gammadelta T cells can play a necessary role in tumor immunity through provision of an early source of IFN-gamma that in turn may regulate the function of tumor-triggered alphabeta T cells.
Stoichiometric Relation for Extraction of Uranium from UO2Powder using TBP Complex with HNO3and H2O in Supercritical CO2 (2005)

The stoichiometry of UO2 dissolution with a tri-n-butylphosphate (TBP) complex with HNO3 and H2O was experimentally determined in supercritical carbon dioxide (SF-CO2) at 25 MPa, 323 K to estimate the required amount of the complex for a process design calculation. The molecular ratio of TBP:HNO3:H2O was determined as 1.0:1.8:0.6 when prepared as an organic phase after vigorous mixing of concentrated HNO3 and TBP. The HNO3 consumption was approximately 4 times the amount of extracted uranium. In designing a supercritical fluid extraction process, the following equation can be used to describe the overall dissolution of UO2 using the TBP complex with HNO3 and H2O in SF-CO2:
Warning: fatal reaction to the use of fibrin glue in deep hepatic wounds. Case reports. (1991)

Two cases of severe hypotension following the use of fibrin glue for hemostasis in hepatic injuries are reported. A systemic reaction to bovine thrombin via large venous lacerations is suspected. A preliminary animal study supports this hypothesis. Caution is advised in the use of fibrin glue for hemostasis in deep hepatic wounds.
Peptidoglycan-associated lipoprotein (Pal) of Gram-negative bacteria: function, structure, role in pathogenesis and potential application in immunoprophylaxis (2009)

The protein Pal (peptidoglycan-associated lipoprotein) is anchored in the outer membrane (OM) of Gram-negative bacteria and interacts with Tol proteins. Tol-Pal proteins form two complexes: the first is composed of three inner membrane Tol proteins (TolA, TolQ and TolR); the second consists of the TolB and Pal proteins linked to the cell's OM. These complexes interact with one another forming a multiprotein membrane-spanning system. It has recently been demonstrated that Pal is essential for bacterial survival and pathogenesis, although its role in virulence has not been clearly defined. This review summarizes the available data concerning the structure and function of Pal and its role in pathogenesis.
Containment of Simian Immunodeficiency Virus Infection: Cellular Immune Responses and Protection from Rechallenge following Transient Postinoculation Antiretroviral Treatment (2000)

To better understand the viral and host factors involved in the establishment of persistent productive infection by primate lentiviruses, we varied the time of initiation and duration of postinoculation antiretroviral treatment with tenofovir (9-[2-(R)-(phosphonomethoxy)propyl]adenine) while performing intensive virologic and immunologic monitoring in rhesus macaques, inoculated intravenously with simian immunodeficiency virus SIVsmE660. Postinoculation treatment did not block the initial infection, but we identified treatment regimens that prevented the establishment of persistent productive infection, as judged by the absence of measurable plasma viremia following drug discontinuation. While immune responses were heterogeneous, animals in which treatment resulted in prevention of persistent productive infection showed a higher frequency and higher levels of SIV-specific lymphocyte proliferative responses during the treatment period compared to control animals, despite the absence of either detectable plasma viremia or seroconversion. Animals protected from the initial establishment of persistent productive infection were also relatively or completely protected from subsequent homologous rechallenge. Even postinoculation treatment regimens that did not prevent establishment of persistent infection resulted in downmodulation of the level of plasma viremia following treatment cessation, compared to the viremia seen in untreated control animals, animals treated with regimens known to be ineffective, or the cumulative experience with the natural history of plasma viremia following infection with SIVsmE660. The results suggest that the host may be able to effectively control SIV infection if the initial exposure occurs under favorable conditions of low viral burden and in the absence of ongoing high level cytopathic infection of responding cells. These findings may be particularly important in relation to prospects for control of primate lentiviruses in the settings of both prophylactic and therapeutic vaccination for prevention of AIDS.
Wood Flour/Polypropylene Composites: Influence of Maleated Polypropylene and Process and Composition Variables on Mechanical Properties (1991)

Abstract The mechanical properties of wood flour/polypropylene composites may be improved by using coupling agents to enhance the bonding between filler and matrix. We used a two-level, full-factorial experiment to examine the effectiveness of a commercially available additive, Epolene E-43, on strength (tensile, flexural, and cantilever-beam), modulus, impact energy, density, and melt viscosity of composites. The effect of Epolene E-43 was studied alone and in combination with three other variables: the weight ratio of wood flour to total polymer in the composites (45/55 or 55/45), size of wood flour particles (nominal 20 or 40 mesh), and extruder residence time (one or three extrusions). Of all the variables, Epolene E-43 had the greatest effect on strength. This effect was somewhat enhanced by using the 40-mesh wood flour and three extrusions; for this combination of variables, Epolene E-43 caused a 30 percent increase in strength. The combination of Epolene E-43 with a 55/45 wood flour/polymer ratio and 40-mesh wood flour resulted in the largest values of flexural and cantilever-beam modulus. Addition of Epolene E-43 slightly decreased notched impact energy but possibly increased unnotched impact energy. None of the variables had a significant effect on melt viscosity. Average wood flour particle size was decreased by processing, particularly in the presence of Epolene E-43. Overall, these findings indicate that Epolene E-43 exerts some degree of coupling action, which results in improvements in mechanical properties that have practical value. The higher cost of Epolene E-43 can be compensated by increasing the ratio of wood flour to polypropylene.
Automatic Estimation and Removal of Noise from a Single Image (2007)

Image denoising algorithms often assume an additive white Gaussian noise (AWGN) process that is independent of the actual RGB values. Such approaches are not fully automatic and cannot effectively remove color noise produced by todays CCD digital camera. In this paper, we propose a unified framework for two tasks: automatic estimation and removal of color noise from a single image using piecewise smooth image models. We introduce the noise level function (NLF), which is a continuous function describing the noise level as a function of image brightness. We then estimate an upper bound of the real noise level function by fitting a lower envelope to the standard deviations of per-segment image variances. For denoising, the chrominance of color noise is significantly removed by projecting pixel values onto a line fit to the RGB values in each segment. Then, a Gaussian conditional random field (GCRF) is constructed to obtain the underlying clean image from the noisy input. Extensive experiments are conducted to test the proposed algorithm, which is shown to outperform state-of-the-art denoising algorithms.
Early induction of apoptosis in B‐chronic lymphocytic leukaemia cells by hydroxychloroquine: activation of caspase‐3 and no protection by survival factors (2001)

We have investigated the effect of hydroxychloroquine (HCQ), an anti-rheumatic drug, on malignant B cells from 20 patients with B-chronic lymphocytic leukaemia (B-CLL). HCQ induced a decrease in cell viability in a dose- and time-dependent manner. The mean IC50 was 32 +/- 7 microg/ml (range, 10-75 microg/ml) for 24 h of exposure. This cytotoxic effect was owing to apoptosis, as demonstrated by morphological changes, annexin V binding capacity and DNA fragmentation (28 +/- 4% of apoptotic cells as early as 5 h post incubation, increasing to 82 +/- 4% at 18 h post treatment). The apoptosis was associated with caspase-3 activation because the cleavage and activity of caspase-3 were increased by HCQ. The amount of bcl-2 protein was reduced during apoptosis, evidenced using quantitative flow cytometry. As early as 1 h post-HCQ treatment, a reduction of the mitochondrial transmembrane potential was measured by 3,3'-dihexyloxacarbocyanine iodide. Interestingly, the HCQ effect was not affected by exposure to interleukin-4 or co-culture with bone marrow stromal cells. Our observations suggest that HCQ may offer a new therapeutic tool in the treatment of B-CLL patients.
Human Cytomegalovirus Tropism for Endothelial Cells: Not All Endothelial Cells Are Created Equal (2007)

Human cytomegalovirus (HCMV) is a ubiquitous herpesvirus that persists for the life of the host following initial infection.Genome analysis indicates that mammalian CMVs have cospeciated with their respective host over the last 80 million years (39).This prolonged period of coevolution has resulted in a high level of coadaptation between virus and host.The study of CMV, a virus that is exquisitely adapted for persistence within the host, is beginning to reveal strategies critical for virus survival.Although all herpesviruses persist for the life span of the host, recent findings suggest that HCMV has a unique replication strategy for maintenance within the host, wherein the virus establishes sites of persistent active replication even in the presence of high levels of preexisting HCMVspecific immunity.A number of cell types, including myeloid lineage cells, smooth muscle cells, and endothelial cells (ECs), appear to be critical as sites of HCMV persistent replication and latency.HCMV infections of myeloid lineage and of smooth muscle cells have been the focuses of previous reviews (see references 32 and 66).This review will focus on HCMV infection of ECs and the role of this cell type in virus persistence and latency.We will describe a "genomic island" of three genes that are essential for HCMV EC tropism and discuss mechanisms by which the products of these genes mediate HCMV infection in ECs.
Natural Killer T Cells in Cancer Immunotherapy (2017)

Natural killer T (NKT) cells are specialized CD1d-restricted T cells that recognize lipid antigens. Following stimulation, NKT cells lead to downstream activation of both innate and adaptive immune cells in the tumor microenvironment. This has impelled the development of NKT cell-targeted immunotherapies for treating cancer. In this review, we provide a brief overview of the stimulatory and regulatory functions of NKT cells in tumor immunity as well as highlight preclinical and clinical studies based on NKT cells. Finally, we discuss future perspectives to better harness the potential of NKT cells for cancer therapy.
The Hepatitis C Virus Internal Ribosome Entry Site Adopts an Ion-dependent Tertiary Fold (1999)

Hepatitis C virus (HCV) contains an internal ribosome entry site (IRES) located in the 5' untranslated region of the genomic RNA that drives cap-independent initiation of translation of the viral message. The approximate secondary structure and minimum functional length of the HCV IRES are known, and extensive mutagenesis has established that nearly all secondary structural domains are critical for activity. However, the presence of an IRES RNA tertiary fold and its functional relevance have not been established. Using chemical and enzymatic probes of the HCV IRES RNA in solution, we show that the IRES adopts a unique three-dimensional structure at physiological salt concentrations in the absence of additional cofactors or the translation apparatus. Folding of the IRES involves cooperative uptake of magnesium and is driven primarily by charge neutralization. This tertiary structure contains at least two independently folded regions which closely correspond to putative binding sites for the 40 S ribosomal subunit and initiation factor 3 (eIF3). Point mutations that inhibit IRES folding also inhibit its function, suggesting that the IRES tertiary structure is essential for translation initiation activity. Chemical and enzymatic probing data and small-angle X-ray scattering (SAXS) experiments in solution show that upon folding, the IRES forms an extended structure in which functionally important loops are exposed. These results suggest that the 40 S ribosomal subunit and eIF3 bind an HCV IRES that is prefolded to spatially organize recognition domains.
Macromol. Rapid Commun. 6/2013 (2013)

Front Cover: A polymer microsphere, crosslinked and functionalized by amine, can be used as a solid-state template for the synthesis of gold (Au) crystals in the form of either nanoparticles (NPs) or plates. The polymer microsphere acts as an internal template to cultivate Au NPs inside the microsphere or an external template to generate the singlecrystal plates depending on the critical concentration of gold ions. Further details can be found in the article by J. S. Oh, L. N. Dang, S. W. Yoon, P. C. Lee, D. O. Kim, K. J. Kim, and J. D. Nam* on page 504.
Nanosphere formation in copolymerization of methyl methacrylate with poly(ethylene glycol) macromonomers (2000)

Polymeric nanospheres consisting of poly(methyl methacrylate) (PMMA) cores and poly(ethylene glycol) (PEG) branches on their surfaces were prepared by free radical copolymerization of methyl methacrylate (MMA) with PEG macromonomers in ethanol/water mixed solvents. PEG macromonomers having a methacryloyl (MMA-PEG) and p-vinylbenzyl (St-PEG) end group were used. It has become clear that the obtained polymer dispersions form three kinds of states, particle dispersion (milky solution), clear solution, and gel/precipitation. It was found that the reaction parameters such as MMA concentration, molecular weight, and concentration of PEG macromonomers, and water content can affect nanosphere formation in a copolymerization system. The water volume fraction of mixed ethanol/water solvents affected the particle size of the nanospheres. These differences in the formation of nanospheres were due to the solvophilic/solvophobic balance between the copolymers and solvents during the self-assembling process of the copolymers. The sizes of nanospheres can be controlled by varying concentration of PEG macromonomer and water content in solvents. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 1811–1817, 2000
Control of Paralysed Axial Muscles by Electrical Stimulation (1977)

The function of a paralysed axial (laryngeal, facial, extraocular) muscle could conceivably be restored if it were made to contract again like its contralateral partner. A muscle stimulation device was designed and constructed so that the stimulus delivered to a given paralysed muscle was modulated by a signal reflecting the contractile state of its contralateral partner. Studies in dog larygneal muscles indicate that paralysed muscles stimulated by such an open-loop device could mimic their partners. However, their tracking accuracies were limited by the nature of their stimulus-reponse characteristics. On the other hand, significantly greater tracking accuracies were observed if a closed-loop device was employed, that is, if feedback information from the stimulated muscles was also used to control the device stimulus level. Considerations in implanting such a (closed-loop or open-loop) device in paralysed axial muscles for chronic stimulation are discussed.
Cellular basis of ectopic germinal center formation and autoantibody production in the target organ of patients with Sjögren's syndrome (2003)

Lymphoid neogenesis and functional ectopic GC formation take place in salivary glands of a subset of patients with SS. Our data suggest that the ectopic secondary lymphoid follicles contain all elements needed for driving the autoimmune response. Our findings underscore a key role for the target organ in recruitment of inflammatory cells and propagation of the disease process.
A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. (1996)

Detecting and determining the relative abundance of diverse individual sequences in complex DNA samples is a recurring experimental challenge in analyzing genomes. We describe a general experimental approach to this problem, using microscopic arrays of DNA fragments on glass substrates for differential hybridization analysis of fluorescently labeled DNA samples. To test the system, 864 physically mapped lambda clones of yeast genomic DNA, together representing >75% of the yeast genome, were arranged into 1.8-cm x 1.8-cm arrays, each containing a total of 1744 elements. The microarrays were characterized by simultaneous hybridization of two different sets of isolated yeast chromosomes labeled with two different fluorophores. A laser fluorescent scanner was used to detect the hybridization signals from the two fluorophores. The results demonstrate the utility of DNA microarrays in the analysis of complex DNA samples. This system should find numerous applications in genome-wide genetic mapping, physical mapping, and gene expression studies.
Release tags: a new class of analytical reagents. (1982)

Release tags are novel compounds made up of three molecular groups: "signal," "release," and "reactivity." The signal group is the detected part of the tag, the release group provides a site for specific covalent cleavage, and the reactivity group attaches the tag to a substance of interest. The general purpose of release tags is to function as molecular labels, analogous to radioisotopes. Release tags also extend the applicability of gas-phase electrophores as signal groups to the analysis of nonvolatile substances. These electrophores are measured with high sensitivity and specificity by gas chromatography with electron-capture detection (GC-ECD). Because extensive multiplicity is potentially available with GC-ECD electrophores, many analogous but distinctive release tags can be used simultaneously as labels in a given assay. In this paper, we use N-pentafluorobenzoylmethionylglycine-N-hydroxysuccinimide ester, our first GC-ECD release tag, to determine thyroxin in serum by a method called "labeling analysis," which involves the principle of isotope-derivative analysis.
BRL.8988 (Talampicillin), a Well-Absorbed Oral Form of Ampicillin (1974)

The phthalidyl ester (BRL.8988, talampicillin) of ampicillin gave serum levels in man two and a half times those obtained with ampicillin itself.
Chemical genetics suggests a critical role for lysyl oxidase in zebrafish notochord morphogenesis (2006)

As a result of a chemical genetic screen for modulators of metalloprotease activity, we report that 2-mercaptopyridine-N-oxide induces a conspicuous undulating notochord defect in zebrafish embryos, a phenocopy of the leviathan mutant. The location of the chemically-induced wavy notochord correlated with the timing of application, thus defining a narrow chemical sensitivity window during segmentation stages. Microscopic observations revealed that notochord undulations appeared during the phase of notochord cell vacuolation and notochord elongation. Notochord cells become swollen as well as disorganized, while electron microscopy revealed disrupted organization of collagen fibrils in the surrounding sheath. We demonstrate by assay in zebrafish extracts that 2-mercaptopyridine-N-oxide inhibits lysyl oxidase. Thus, we provide insight into notochord morphogenesis and reveal novel compounds for lysyl oxidase inhibition. Taken together, these data underline the utility of small molecules for elucidating the dynamic mechanisms of early morphogenesis and provide a potential explanation for the recently established role of copper in zebrafish notochord formation.