gebhart/patrepeval huggingface dataset:
Regulation of gene expression by tumor promoters. II. Control of cell shape and developmental programs for macrophages and granulocytes in human myeloid leukemic cells (1981)

Abstract Regulation of the developmental programs for macrophages and granulocytes has been analysed, using two‐dimensional gel electrophorels of the cytoplasmic protein changes, in a human myeloid leukemic cell line (HL60) that can be induced to differentiate to macrophages by the macrophage and granulocyte‐inducing (MGI) protein and the tumor promoter 12‐ O ‐tetradecanoyl‐phorbol‐13‐acetate (TPA), and to granulocytes by dimethylsulfoxide (DMSO). Studies on the protein changes induced by the different inducers showed a similar developmental program for macrophage differentiation induced by MGI or TPA, which differed from the beginning from the granulocyte program induced by DMSO. Comparison with normal cells from human peripheral blood has shown that the developmental programs induced in the HL60 cells are relevant to the normal programs of differentiation for these two cell types. Unlike MGI and DMSO, TPA induces rapid attachment of the HL60 cells to the surface of the Petri dish. Combined treatment with TPA and DMSO showed cell attachment, extensive spreading of the cells, the regulation of specific proteins and expression of the macrophage program. The addition of TPA to cells induced for the granulocyte program by DMSO resulted in cell attachment and spreading and a switchover from the granulocyte to the macrophage program. The results indicate that cells in suspension can express either the macrophage or granulocyte program depending on the inducer, and that changes in cell shape associated with cell attachment induced by TPA can regulate specific proteins and restrict the developmental program to macrophages. It is suggested that the in vivo environment of cells in relation to the possibilities for cell adhesion, which can be regulated by tumor promotors, may play a major role in determining the developmental program of myeloid and other cell types.
Cachectin/tumor necrosis factor induces cachexia, anemia, and inflammation. (1988)

Cachexia is a potentially lethal syndrome of unknown etiology characterized by anorexia, weight loss, and protein wasting that frequently complicates the treatment of chronic inflammation and cancer. Cachectin/TNF was isolated during the search for a humoral mediator of cachexia and found to stimulate the breakdown of energy stores from adipocytes and myocytes in vitro, but the chronic effects of the monokine in vivo are not known. Sublethal doses of recombinant human cachectin administered twice daily for 7-10 d caused cachexia in rats, as evidenced by reduced food intake, weight loss, and depletion of whole-body lipid and protein stores. Significant anemia is also observed and found to be the result of decreased red blood cell mass, not expanded plasma volume. Leukocytosis and histopathological evidence of tissue injury and inflammation are observed in several organs, including omentum, liver, spleen, and heart. These data suggests that the exposure of the normal host to cachectin is capable of inducing a pathophysiological syndrome of cachexia, anemia, and inflammation similar to that observed during inflammatory states or malignancy.
New centrifugation blood culture device (1978)

A single-tube blood culture device designed for centrifugation in a tabletop centrifuge is described. Reconstruction experiments using 21 different organisms and human donor blood indicate that excellent recovery can be obtained by centrifugation for 30 min at 3,000 X g.
Immunocytochemical localization of the major polypeptides of the nuclear pore complex-lamina fraction. Interphase and mitotic distribution. (1978)

This laboratory has previously isolated a fraction from rat liver nuclei consisting of nuclear pore complexes associated with the proteinaceous lamina which underlies the inner nuclear membrane. Using protein eluted from sodium dodecyl sulfate (SDS) gels, we have prepared antibodies in chickens to each of the three predominant pore complex-lamina bands. Ouchterlony double diffusion analysis shows that each of these individual bands cross-reacts strongly with all three antisera. In immunofluorescence localization performed on tissue culture cells with these antibodies, we obtain a pattern of intense staining at the periphery of the interphase nucleus, with little or no cytoplasmic reaction. Electron microscope immunoperoxidase staining of rat liver nuclei with these antibodies labels exclusively the nuclear periphery. Furthermore, reaction occurs in areas which contain the lamina, but not at the pore complexes. While our isolation procedure extracts the internal contents of nuclei completely, semiquantitative Ouchterlony analysis shows that it releases negligible amounts of these lamina antigens. Considered together, our results indicate that these three bands represent major components of a peripheral nuclear lamina, and are not structural elements of an internal "nuclear protein matrix." Fluorescence microscopy shows that the perinuclear interphase localization of these lamina proteins undergoes dramatic changes during mitosis. Concomitant with nuclear envelope disassembly in prophase, these antigens assume a diffuse localization throughout the cell. This distribution persists until telophase, when the antigens become progressively and completely localized at the surface of the daughter chromosome masses. We propose that the lamina is a biological polymer which can undergo reversible disassembly during mitosis.
Gammahydroxybutyrate and Narcolepsy: A Double-Blind Placebo-Controlled Study (1993)

We treated 24 patients with narcolepsy for 4 weeks with gammahydroxybutyrate (GHB), 60 mg/kg/night, in a randomized double-blind placebo-controlled cross-over trial. Both clinical and polysomnographic criteria were used to assess the results. Compared to placebo, GHB reduced the daily number of hypnagogic hallucinations (from 0.87 to 0.28; p = 0.008), daytime sleep attacks (from 2.27 to 1.40; p = 0.001) and the severity of subjective daytime sleepiness (from 1.57 to 1.24 on a 0-4 scale; p = 0.028). The number of daily cataplexy attacks was reduced from 1.26 at baseline to 0.56 after 4 weeks of GHB intake. This reduction, however, was not statistically significantly different from the difference between baseline and placebo. GHB stabilized nocturnal rapid eye movement (REM) sleep, i.e. it reduced the percentage of wakefulness during REM sleep (p = 0.007) and the number of awakenings out of REM sleep (p = 0.016), and tended to increase slow wave sleep (p = 0.053). Adverse events were few and mild. We conclude that GHB is an effective and well-tolerated treatment for narcolepsy.
Sirt2 is a novel in vivo downstream target of Nkx2.2 and enhances oligodendroglial cell differentiation (2011)

Although Sirt2 is primarily expressed in oligodendrocytes of the central nervous system, its role in oligodendroglial lineage differentiation is not fully understood. Our findings demonstrate that the transcription factor Nkx2.2 binds to the Sirt2 promoter via histone deacetylase 1 (HDAC-1), the binding site for Nkx2.2 maps close to the start codon of the Sirt2 gene, and Nkx2.2 negatively regulates Sirt2 expression in CG4 cells, an oligodendroglial precursor cell line. HDAC-1 knock-down not only significantly attenuates the binding capacity of Nkx2.2 to the Sirt2 promoter but also releases repression of Sirt2 expression by Nkx2.2. Nkx2.2 over-expression down-regulates Sirt2 expression and delays differentiation of CG4 cells; in contrast, up-regulation of Sirt2 does not impact Nkx2.2 expression level. Sirt2 knock-down via RNAi or inhibition of Sirt2 by sirtinol, a Sirt2 activity inhibitor, blocks CG4 cell differentiation. Over-expression of Sirt2 facilitates CG4 cell differentiation at both molecular and cellular levels, enhancing expression of myelin basic protein and facilitating the growth of cell processes. We have conclusively demonstrated that Sirt2 enhances CG4 oligodendroglial differentiation and report a novel mechanism through which Nkx2.2 represses CG4 oligodendroglial differentiation via Sirt2.
Tr1 cell–dependent active tolerance blunts the pathogenic effects of determinant spreading (2002)

Experimental autoimmune encephalomyelitis (EAE) is a T cell-mediated autoimmune disease of the CNS. The current study shows that even in an acute episode of disease the autoimmune response spreads from one determinant on myelin basic protein (MBP) to the other linked determinant and that this spread plays a functional role in the pathogenesis of disease. The soluble form of each determinant could be used to induce Ag-specific T cell tolerance and reverse an ongoing disease. We show that the rapid effect of soluble peptide therapy is due to repolarization of autoimmune T cells undergoing activation. We suggest that at least two different types of regulatory T cells participate in the induction of active tolerance. The first, yet to be fully characterized, functions in an IL-4-dependent manner. The second produces high levels of IL-10 and low levels of IL-4 (Tr1). We bring about completing evidence showing that these Tr1 cells play a pivotal role in the regulation of T cell tolerance during determinant spread and that soluble peptide therapy with the determinant to which the autoimmune response spreads amplifies a de novo regulatory mechanism aimed to reduce the pathological consequences of determinant spreading.
Copper-Free “Click” Modification of DNA via Nitrile Oxide−Norbornene 1,3-Dipolar Cycloaddition (2009)

Nitrile oxides react smoothly and rapidly with norbornene-modified DNA in a copper-free click reaction. The reaction allows high density functionalization of oligodeoxyribonucleotides (ODNs) with a large variety of molecules directly on solid supports and even in synthesizers without the need for an additional catalyst.
The Yield-Management Approach to Hotel-Room Pricing (1989)

Yield management can dramatically increase revenues for a hotel operator. But it's not a substitute for poor marketing or poor sales. Here is how yield management can work for you
The underlying neurobiology of bipolar disorder. (2003)

Clinical studies over the past decades have attempted to uncover the biological factors mediating the pathophysiology of bipolar disorder (BD) utilizing a variety of biochemical and neuroendocrine strategies. Indeed, assessments of cerebrospinal fluid chemistry, neuroendocrine responses to pharmacological challenge, and neuroreceptor and transporter binding have demonstrated a number of abnormalities in the amine neurotransmitter systems in this disorder. However, recent studies have also implicated critical signal transduction pathways as being integral to the pathophysiology and treatment of BD, in addition to a growing body of data suggesting that impairments of neuroplasticity and cellular resilience may also underlie the pathophysiology of the disorder. It is thus noteworthy that mood stabilizers and antidepressants indirectly regulate a number of factors involved in cell survival pathways - including MAP kinases, CREB, BDNF and bcl-2 protein - and may thus bring about some of their delayed long-term beneficial effects via underappreciated neurotrophic effects.
Embedding a seal into a picture under orthogonal wavelet transform (2002)

Proposes a method to embed a signature seal in a picture under an orthogonal wavelet transform. Three parts of a multi-resolution representation are expressed in a vector and are related to each other. The maximum and minimum values among the entries in the vector are obtained, and the absolute value of the difference between them is used for controlling the embedding of the seal. When the seal is needed, one can extract it from the picture. It is clear from the presented experimental results that the seal does not prevent one from seeing the picture comfortably. Therefore, it seems that this method could be used for signing one's name in multimedia.
Cell cycle arrest in Metformin treated breast cancer cells involves activation of AMPK, downregulation of cyclin D1, and requires p27<sup>Kip1</sup> or p21<sup>Cip1</sup> (2008)

Cell cycle arrest in response to metformin requires CDK inhibitors in addition to AMPK activation and cyclin D1 downregulation. This is of interest because many cancers are associated with loss or downregulation of CDK inhibitors and the results may be relevant to the development of anti-tumor reagents that target the AMPK pathway.
Expression of a Prokaiyotic Gene in Cultured Lung Endothelial Cells After Lipofection with a Plasmid Vector (1989)

Transfection of cultured cells with functioning foreign genes can be a powerful tool for delineating mechanisms controlling gene expression and for manipulating cellular synthetic machinery. We transfected cultured bovine pulmonary artery endothelial cells with a plasmid (pRSVCAT) containing the prokaryotic gene, chloramphenicol acetyltransferase (CAT), driven by a Rous sarcoma virus (RSV) promoter. Transfection was accomplished by binding the plasmid DNA to specially synthesized cationic liposomes and incubating cell monolayers with the liposome-DNA complex (a process called lipofection). We found marked CAT expression in endothelial cells by 24 h after lipofection (complete chloramphenicol acetylation in a 4-h assay incubation with less than 0.1 mg cell protein). Marked CAT expression persisted after splitting the cells 1:2 at 6 days after lipofection. Detectable CAT activity was present 14 days after lipofection following two 1:2 splits of the cells. CAT expression was related to the quantity of plasmid DNA used for lipofection; 1.0 micrograms DNA per 60-mm dish of cells resulted in less CAT activity at 48 h than did 5 or 10 micrograms DNA per dish. Ten micrograms of DNA-liposome complex per dish caused substantial numbers of endothelial cells to detach from the dish, but little cytotoxic effect was seen with 5 or 1 micrograms DNA-liposome complex per dish. This simple, highly efficient method for introducing functioning foreign genes into cultured endothelial cells will permit a broad range of studies of molecular mechanisms of endothelial cell function and studies of the consequences of highly specific modifications in protein synthesis on endothelial responses.
Circulating Tumor Nucleic Acids: Perspective in Breast Cancer (2010)

In 1940, it was demonstrated that free DNA could be identified in the bloodstream. It was later shown that circulating nucleic acids (CNA), both DNA and RNA, are present in several neoplastic and non-neoplastic diseases, and that in cancer they originate mostly from the tumor. In this review, we discuss the potential application of CNA as a breast cancer biomarker for early diagnosis and patient evaluation. Most of the initial studies on CNA compared the levels of CNA in cancer patients and healthy individuals. To increase sensitivity and specificity, cancer-specific molecular alterations were then utilized. In this respect, epigenetic alterations and microRNA offer considerable advantages over mutations because of their easiness of detection. Epigenetic signatures, being early events of carcinogenesis, may also be valuable markers for screening purposes. Monitoring the follow-up of the patients is one of the most interesting applications of CNA-based assays, and it is reasonable to hypothesize that CNA may become a surrogate marker for circulating cancer cells in the prediction of patient outcome. Transferring these findings to the clinical practice is the next effort, and this will be possible when a 'common language' is defined to allow proper validation of these new markers.
Cinacalcet for Secondary Hyperparathyroidism in Patients Receiving Hemodialysis (2004)

Cinacalcet lowers parathyroid hormone levels and improves calcium-phosphorus homeostasis in patients receiving hemodialysis who have uncontrolled secondary hyperparathyroidism.
C−H···F Interactions in the Crystal Structures of Some Fluorobenzenes (1998)

The existence and nature of C−H···F−C interactions in crystalline fluorobenzenes 1−3 and 7−10 are discussed. These compounds were chosen because they contain only C, H, and F atoms; this is necessary in the evaluation of the weak acceptor capabilities of the C−F group. All of these compounds are liquids at room temperature, and single crystals for X-ray diffraction were grown in situ. The analysis of the C−H···F interactions that are found in all of these crystal structures takes the form of comparisons with related C−H···O/C−H···N analogues. Fluorobenzene, 1, bears a close relationship to pyridinium fluoride, pyridine 1-oxide, and benzonitrile at the level of individual interactions, showing that the character of the structure-determining intermolecular interactions in these four crystal structures are the same. Similarly, 1,4-difluorobenzene, 3, and 1,4-benzoquinone are related, the C−H···F interactions in the former playing the same structural role as the C−H···O interactions in the latter. A comparison of 3 with the unsymmetrical 1,4-dihalogenated benzenes, 4−6 indicates the importance of C−H···F interactions in these structures. With an increase in the F content of the molecules, the C−H acidity also increases and the C−H···F interactions in 1,3,5-trifluorobenzene, 7, and 1,2,4,5-tetrafluorobenzene, 8, become stronger and more important. Compounds 7 and 8 are structurally very similar to 1,3,5-triazine and 1,2,4,5-tetrazine, and this similarity further strengthens the argument that C−H···F interactions resemble C−H···N interactions and provides evidence for their description as weak hydrogen bonds. 1,2,3,4-Tetrafluorobenzene, 9, is polymorphic but the role of the C−H···F interactions in the two forms is similar. A comparison of the C−H···F geometries in compounds 1−10 with other C-, H-, and F-containing compounds in the Cambridge Structural Database reveals that the hydrogen bond properties are more pronounced in 1−10. It is concluded that only when the carbon acidity is enhanced to the levels of the compounds in the present study, is the hydrogen-bond nature of the C−H···F interaction even revealed. This study also demonstrates that the C−F group prefers to form C−H···F interactions rather than F···F contacts. The behavior of organic fluorine in crystal packing is therefore quite different from the heavier halogens.
The ASTRAL compendium for protein structure and sequence analysis (2000)

The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. The SPACI scores included in the system summarize the overall characteristics of a protein structure. A structural alignments database indicates residue equivalencies in superimposed protein domain structures. The PDB sequence-map files provide a linkage between the amino acid sequence of the molecule studied (SEQRES records in a database entry) and the sequence of the atoms experimentally observed in the structure (ATOM records). These maps are combined with information in the SCOPdatabase to provide sequences of protein domains. Selected subsets of the domain database, with varying degrees of similarity measured in several different ways, are also available. ASTRALmay be accessed at http://astral.stanford.edu/
ADVANCED AND REFINED TECHNIQUE IN THE PETROGRAPHIC STUDY OF CRYSTALLINE REFRACTORIES* (1936)

A bstract The new technique for the determination of the refractive indices of minerals, as developed by R. C. Emmons of the University of Wisconsin, is described. The paper contains a discussion of immersion media and a description of the double‐variation apparatus, the modified universal stage, and the smithsonite refractometer. Application of the technique to crystalline refractories is considered.
Stomatocyte–discocyte–echinocyte sequence of the human red blood cell: Evidence for the bilayer– couple hypothesis from membrane mechanics (2002)

Red-cell shape is encoded in the mechanical properties of the membrane. The plasma membrane contributes bending rigidity; the protein-based membrane skeleton contributes stretch and shear elasticity. When both effects are included, membrane mechanics can reproduce in detail the full stomatocyte-discocyte-echinocyte sequence by variation of a single parameter related to the bilayer couple originally introduced by Sheetz and Singer [Sheetz, M. P. & Singer, S. J. (1974) Proc. Natl. Acad. Sci. USA 71, 4457-4461].
G-quartets in biology: reprise. (1993)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Screening Cucumber for Resistance to Downy Mildew Caused by Pseudoperonospora cubensis (Berk. and Curt.) Rostov. (2012)

ABSTRACT Downy mildew, a foliar disease caused by the oomycete Pseudoperonospora cubensis (Berk. and Curt.) Rostov. is one of the most destructive diseases of cucumber ( Cucumis sativus L.). Moderately resistant cultivars are available, but yield losses are high without the use of fungicides. Higher levels of resistance are needed to reduce the need for fungicides. The objective of this study was to identify new sources of resistance to downy mildew among Plant Introduction accessions from the U.S. National Plant Germplasm System, elite cultivars, and breeding lines of cucumber. A total of 1300 cultigens were tested in Clinton, NC, and Skierniewice, Poland, in 2005 to 2007 under natural field epidemics. The most resistant and susceptible cultigens were further evaluated in replicated experiments in North Carolina and India in 2007 to 2009. Fungicide experiments were run in 2008 and 2009 to identify tolerance, involving weekly applications to one of two sets of material at a location. Results from the retest study confirmed the results of the initial screening. The most resistant cultigens over all environments were PI 605996, PI 330628, and PI 197088. Cultigens have been found that significantly outperform checks in all resistance traits. High yielding and tolerant cultigens have also been identified that could be used in developing improved cultivars.
Isolation of high-affinity GTP aptamers from partially structured RNA libraries (2002)

Aptamers, RNA sequences that bind to target ligands, are typically isolated by in vitro selection from RNA libraries containing completely random sequences. To see whether higher-affinity aptamers can be isolated from partially structured RNA libraries, we selected for aptamers that bind GTP, starting from a mixture of fully random and partially structured libraries. Because stem-loops are common motifs in previously characterized aptamers, we designed the partially structured library to contain a centrally located stable stem-loop. We used an off-rate selection protocol designed to maximize the enrichment of high-affinity aptamers. The selection produced a surprisingly large number of distinct sequence motifs and secondary structures, including seven different aptamers with K(d)s ranging from 500 to 25 nanomolar. The engineered stem-loop was present in the three highest affinity aptamers, and in 12 of 13 independent isolates with a single consensus sequence, suggesting that its inclusion increased the abundance of high-affinity aptamers in the starting pool.
Mechanism of interleukin‐25 (IL‐17E)‐induced pulmonary inflammation and airways hyper‐reactivity (2006)

IL-25 potently (single dose) induces sustained AHR and acute pulmonary inflammation with eosinophilia. IL-25-induced AHR is dependent on the production of Th type-2 cytokines, and removal of IL-13 and its signal transduction pathway prevents IL-25-induced airways inflammation and AHR. IL-25 potently induces inflammatory cascades that may exacerbate allergic airways inflammation by promoting Th type-2 cytokine responses in conjunction with the up-regulation of factors (eotaxin and arg-I) that can amplify inflammation associated with allergic disorders. Dysregulation in IL-25 production may predispose to features of allergic airways disease.