gebhart/patrepeval huggingface dataset:
Increased expression of beta-amyloid precursor protein during neuronal differentiation is not accompanied by secretory cleavage. (1992)

Despite increasing evidence for a pathogenetic role for the beta-amyloid precursor protein (beta APP) in Alzheimer disease, the physiological function of the protein remains unclear. The expression of the neural-specific isoform containing 695 amino acids, beta APP695, is consistent with a role for the protein in neuronal development. In this study, we analyzed the expression of beta APP during the retinoic acid-induced neuronal differentiation of P19 murine embryonal carcinoma cells. Northern blot and RNase protection analyses show a selective increase in beta APP695 expression, concomitant with the morphologic differentiation of P19-derived neurons. Moreover, the time course of increase observed for the beta APP695 mRNA is paralleled by other neuronal-specific transcripts. A similar increase in beta APP695 is observed at the protein level. Furthermore, we show that levels of beta APP695 protein progressively increase during the in vitro differentiation of primary hippocampal neurons. The finding that beta APP695 increases selectively and progressively during neuronal differentiation in two different cell culture systems suggests that this isoform has an important cellular function during this process in the brain. Unlike beta APP in most peripheral cell types, the increased levels of beta APP found in terminally differentiated neuronal cells are not processed in significant amounts by secretory cleavage. Thus, differentiation of neurons is accompanied by increased beta APP695 expression and membrane retention of the protein as intact, full-length molecules that could serve as potential substrates for amyloidogenesis.
Identification of a GranulocyticEhrlichiaStrain Isolated from a Horse in Switzerland and Comparison with Other Rickettsiae of theEhrlichia phagocytophilaGenogroup (1998)

This case report describes a 12-year-old Arabian mare with granulocytic ehrlichiosis. Clinical signs included fever, apathy, anorexia, icterus, limb edema, and reluctance to move. Examination of buffy coat smears revealed Ehrlichia organisms in neutrophils and eosinophils. A band of 1,428 bp was amplified from DNA of leukocytes via nested PCR and was identified as part of the Ehrlichia 16S rRNA gene. It differed from the gene sequences of Ehrlichia phagocytophila and E. equi at two and three positions, respectively. Interestingly, the nucleotide sequence of the 16S rRNA was 100% identical to that of the agent of human granulocytic ehrlichiosis.
Binary phase modulation using electrically addressed transmissive and silicon backplane spatial light modulators (2000)

The operation and performance of a 128-by-128 matrix elec- trically addressed ferroelectric liquid crystal (FLC) multiplexed transmis- sive spatial light modulator (SLM) and a 320-by-240 reflective silicon- backplane SLM are described. The two-dimensional multiplexed FLC SLM is probably the only device that exists to date optimized for l 51.55-mm operation. The spatial and temporal measurements of the binary phase modulation of the two devices are discussed. For the spa- tial measurements, a novel idea regarding the effects of the LC modula- tion characteristics in the interpixel deadspace of the silicon backplane on the quality of the binary phase modulation is described. For the tem- poral measurements, two addressing schemes for holographic beam- steering applications are described and compared experimentally with the silicon-backplane SLM. The limitation in performance for these two devices is briefly stated, and an indication given of future devices that will be possible using this rapidly advancing technology. © 2000 Society of Photo-Optical Instrumentation Engineers. (S0091-3286(00)01609-3)
Purification (2006)

The enzymatic activity could be readily assayed in the homogenate from a rat liver but disappeared as the purification proceeded. The strategy for the purification of a protein is tailored to the particular problems faced in each instance. The goal of the purification of a protein from the clear solution produced by centrifugation of a homogenate is to isolate that protein, whose presence and relative molar concentration can be followed by a specific assay, from all of the other proteins present. Improvements in the size, uniformity, and rigidity of the particles of the stationary phase have permitted similar increases in the rate at which chromatography of proteins can be performed. A molecule of protein is a macromolecular poly-electrolyte, the effective charge of which is a function of pH and varies over a wide range. Homogenization of a biological specimen produces a complex mixture of proteins.
The Amino Terminus of the Fourth Cytoplasmic Loop of Rhodopsin Modulates Rhodopsin-Transducin Interaction (2000)

Rhodopsin is a seven-transmembrane helix receptor that binds and catalytically activates the heterotrimeric G protein transducin (G(t)). This interaction involves the cytoplasmic surface of rhodopsin, which comprises four putative loops and the carboxyl-terminal tail. The fourth loop connects the carboxyl end of transmembrane helix 7 with Cys(322) and Cys(323), which are both modified by membrane-inserted palmitoyl groups. Published data on the roles of the fourth loop in the binding and activation of G(t) are contradictory. Here, we attempt to reconcile these conflicts and define a role for the fourth loop in rhodopsin-G(t) interactions. Fluorescence experiments demonstrated that a synthetic peptide corresponding to the fourth loop of rhodopsin inhibited the activation of G(t) by rhodopsin and interacted directly with the alpha subunit of G(t). A series of rhodopsin mutants was prepared in which portions of the fourth loop were replaced with analogous sequences from the beta(2)-adrenergic receptor or the m1 muscarinic receptor. Chimeric receptors in which residues 310-312 were replaced could not efficiently activate G(t). The defect in G(t) interaction in the fourth loop mutants was not affected by preventing palmitoylation of Cys(322) and Cys(323). We suggest that the amino terminus of the fourth loop interacts directly with G(t), particularly with Galpha(t), and with other regions of the intracellular surface of rhodopsin to support G(t) binding.
Effects of Amino Acids and Peptides on Rumen Microbial Growth Yields (1989)

Experiments were conducted using mixed rumen bacterial cultures to determine which amino acids limited growth. Complete amino acid mixtures stimulated microbial growth alone and when added to casein. Amino acid subgroups did not stimulate growth alone or when added to casein or casein hydrolysates. Results were similar whether growth was limited by periodic addition of low amounts of carbohydrate or when higher amounts were added to batch cultures. Little growth occurred with ammonia as sole N source. Addition of 100 mg/L of amino acids and peptides quadrupled growth, peptides at 10 mg/L resulted in higher growth than the corresponding amount of free amino acids. Apparent saturation of growth occurred when 10 mg/L of a complete amino acid mixture or trypticase was added to cultures. The Michaelis constant values for amino acids and trypticase were determined to be .5 and 1.0 mg/L, respectively. Growth was a linear function of amount of carbohydrate fermented with the coefficient of slope increasing with increasing amino acid concentrations. These experiments demonstrate that growth stimulation from amino acids and proteins is due to the number of amino acids provided in a given mixture rather than specific growth limiting amino acids. Rumen bacterial growth is greatly stimulated by amino acids and peptides, with low affinity constant values, allowing good growth in the concentrations of amino acids and peptides found in vivo
Functional coupling with Gαq and Gαi1 protein subunits promotes high‐affinity agonist binding to the neurotensin receptor NTS‐1 expressed in Escherichia coli (2001)

To analyze the coupling of Galpha subunits to the rat neurotensin receptor NTS-1 (NTR), fusion proteins were expressed in Escherichia coli with various Galpha subunits covalently linked to the receptor C-terminus. The presence of Galpha(q) or Galpha(i/q), in which the six C-terminal residues of Galpha(i1) were replaced with those from Galpha(q), increased the percentage of receptors in the agonist high-affinity state. This effect was less pronounced for wild-type Galpha(i1) and not observed for Galpha(i/s). Functional coupling of neurotensin receptor to Galpha was demonstrated by neurotensin-induced [(35)S]GTPgammaS binding for the Galpha(q), Galpha(i/q) and Galpha(i1) subunits, but not for Galpha(i/s). Our results extend previous findings of the dual coupling of NTR to pertussis toxin-sensitive and -insensitive G-proteins in Chinese hamster ovary cells with preference for the latter.
Cellular localization of interleukin-8 and its inducer, tumor necrosis factor-alpha in psoriasis. (1991)

The importance of immunologic mechanisms in psoriasis has been deduced from the ability of immunosuppressive therapies to ameliorate this common and chronic skin disease. Certainly the histology of psoriatic lesions suggests a dialogue between the hyperplastic keratinocytes and infiltrating T lymphocytes and macrophages. To begin dissecting the cytokine network involved in the pathophysiology of psoriasis, the location, in both epidermal and dermal compartments, of tumor necrosis factor-alpha, interleukin-8, intercellular adhesion molecule-1, and transforming growth factor-alpha at the protein and/or mRNA levels were identified. Tumor necrosis factor-alpha was selected as a potentially key regulatory cytokine, first because it induces cultured keratinocyte interleukin-8, intercellular adhesion molecule-1, and transforming growth factor-alpha production, and second because intercellular adhesion molecule-1 expression by keratinocytes in psoriatic epidermis had been identified previously. Using immunohistochemical localization, tumor necrosis factor-alpha was identified in 12 psoriatic lesions as intense and diffuse expression by dermal dendrocytes (macrophages) in the papillary dermis (without significant staining of endothelial cells, mast cells, or dermal Langerhans cells), and focally by keratinocytes and intraepidermal Langerhans cells. Functional interaction between the dermal dendrocytes and keratinocytes was suggested by the presence of interleukin-8 expression of suprabasal keratinocytes immediately above the tumor necrosis factor-alpha-positive dermal dendrocytes. Interleukin-8 mRNA and transforming growth factor-alpha mRNA were detectable in the epidermal roof of psoriatic lesions, but neither was detectable at the protein or mRNA levels in any normal skin specimens. Treatment of cultured human keratinocytes with phorbol ester (which experimentally produces psoriasiform changes on mouse skin) or tumor necrosis factor-alpha also increased interleukin-8 and transforming growth factor-alpha mRNAs. Further elucidation of the cellular and molecular basis for the genesis and evolution of psoriasis will provide the framework for a better evaluation of the cause and treatment of this skin disease.
On the rendering of surfaces (1979)

Despite the relative sophistication of modern surface design systems, many graphical renderings of surfaces are rather crude. The paper discusses several possible renderings, including various line drawings methods, realistic and functional shading, and combinations of line drawings and smooth shading. It concludes that a good choice is the superposition of contours or sections on either realistic or Gaussian curvature shading.
Small antibody-like proteins with prescribed ligand specificities derived from the lipocalin fold (1999)

We demonstrate that the ligand pocket of a lipocalin from Pieris brassicae, the bilin-binding protein (BBP), can be reshaped by combinatorial protein design such that it recognizes fluorescein, an established immunological hapten. For this purpose 16 residues at the center of the binding site, which is formed by four loops on top of an eight-stranded beta-barrel, were subjected to random mutagenesis. Fluorescein-binding BBP variants were then selected from the mutant library by bacterial phage display. Three variants were identified that complex fluorescein with high affinity, exhibiting dissociation constants as low as 35.2 nM. Notably, one of these variants effects almost complete quenching of the ligand fluorescence, similarly as an anti-fluorescein antibody. Detailed ligand-binding studies and site-directed mutagenesis experiments indicated (i) that the molecular recognition of fluorescein is specific and (ii) that charged residues at the center of the pocket are responsible for tight complex formation. Sequence comparison of the BBP variants directed against fluorescein with the wild-type protein and with further variants that were selected against several other ligands revealed that all of the randomized amino acid positions are variable. Hence, a lipocalin can be used for generating molecular pockets with a diversity of shapes. We term this class of engineered proteins "anticalins." Their one-domain scaffold makes them a promising alternative to antibodies to create a stable receptor protein for a ligand of choice.
Total synthesis of 3-O-demethylsporaricin A. (1985)

The novel, semisynthetic pseudodisaccharide antibiotic, 3-O-demethylsporaricin A, was synthesized via 3-O-demethylsporaricin B obtained by glycosidation of its aminocyclitol part. The aminocyclitol part was synthesized as D,L-form from D,L-(1,2,3/4,5,6)-1,4-bis(benzyloxy-carbonylamino)-5,6-O-isopropyl idene-2,3,5,6-cyclohexanetetraol via three key steps, namely, deoxygenation, inversion of a hydroxyl group, and N-methylation. The physical and biological properties of synthetic 3-O-demethylsporaricin A and an authentic sample derived from sporaricin B were identical.
Cisplatin-Digoxigenin mRNA Labeling for Nonradioactive Detection of mRNA Hybridized onto Nucleic Acid cDNA Arrays (1999)

We optimized a novel nonradioactive hybridization technique using a cis-platin coupled digoxigenin derivative for direct labeling of mRNA. This new mRNA reporter molecule was applied to cDNA membrane arrays to simultaneously identify expression of hundreds of genes. The sensitivity of this nonradioactive mRNA hybridization technique was comparable to radioactive cDNA labeling on house-keeping gene expression but even superior on the detection limit of the expression of low abundant genes using mRNA isolated from human diploid fibroblasts. Additional advantages are faster readout and decreased total working times because of luminescence technology and avoidance of radioactivity. Finally, no potential artifactual reverse transcription step is necessary because of direct labeling of mRNA used for hybridization on nucleic acid arrays.
Neuroprotective effects of vascular endothelial growth factor (VEGF) upon dopaminergic neurons in a rat model of Parkinson's disease (2004)

Vascular endothelial growth factor (VEGF) has previously been shown to display neuroprotective effects following ischemia, suggesting that VEGF may potentially be applied as a neuroprotective agent for the treatment of other neurological diseases. In this study, we investigated the neuroprotective capacity of VEGF in a model of Parkinson's disease. VEGF was found to be neuroprotective against cell death of primary E14 murine ventral mesencephalic neurons induced by 6-hydroxydopamine (6-OHDA) treatment in vitro. Further, rats receiving a continuous infusion of VEGF into the striatum via encapsulated hVEGF-secreting cells (baby hamster kidney-VEGF) displayed a significant decrease in amphetamine-induced rotational behavior and a significant preservation of tyrosine hydroxylase-positive neurons and fibers compared with control animals. VEGF likely functions via direct mechanisms by signaling through the neuropilin receptor expressed upon dopaminergic neurons in response to 6-OHDA treatment. Further, VEGF is likely to promote neuroprotection indirectly by activating the proliferation of glia and by promoting angiogenesis. Our results support a potential neuroprotective role for VEGF in the treatment of Parkinson's disease.
Anti-Tumor Effect of Adenoviral Vector-Mediated p53 Gene Transfer on the Growth of Canine Osteosarcoma Xenografts in Nude Mice (2011)

We evaluated the anti-tumor effect of adenoviral vector-mediated p53 gene therapy on the growth of canine osteosarcoma xenografts formed in nude mice. Nude mice were subcutaneously transplanted with cells of 2 P53 mutant canine osteosarcoma cell lines, POS and CHOS. The osteosarcoma xenografts were injected with either an adenoviral vector that expresses canine wild-type P53 (AxCA-cp53) or LacZ (AxCA-LacZ). Tumor growth was significantly inhibited in the xenografts injected with AxCA-cp53 in comparison to those injected with AxCA-LacZ or PBS during the observation period of 27 days. An increase of the amount of p21(WAF1/CDKN1A) mRNA, and the number of apoptotic cells was shown in the tumors injected with AxCA-cp53 in comparison to those injected with AxCA-LacZ or PBS. The present study revealed that the adenoviral vector-mediated p53 gene transfer had an anti-tumor effect in canine osteosarcoma xenografts formed in nude mice.
Sacral neuromodulation: new applications in the treatment of female pelvic floor dysfunction (2002)

While the data are encouraging in these new arenas of pelvic floor disorders, investigators acknowledge the need for multicenter, statistically powered studies to evaluate the validity of these findings.
A new route to incompletely condensed silsesquioxanes: acid-mediated cleavage and rearrangement of (c-C6H11)6Si6O9 to C2-[(c-C6H11)6Si6O8X2] (1999)

Acid-mediated cleavage and rearrangement of (c-C6H11)6Si6O9 1 by triflic acid (TfOH) and methanesulfonic acid (MsOH) produces good yields of C2-[(c-C6H11)6Si6O8X2] (4a, X = OTf; 4b, X = MsO), which reacts with water, LiNMe2 and LiCCPh to afford C2-[(c-C6H11)6Si6O8(OH)2] 5, C2-[(c-C6H11)6Si6O8(NMe2)2] 8 and C2-[(c-C6H11)6Si6O8(CCPh)2] 9; silylation of 5 with ClSiMe2H–Et3N produces C2-[(c-C6H11)6Si6O8(OSiMe2H)2] 6, while reaction of 5 with HBF4·OMe2–BF3·OEt2 produces C2-[(c-C6H11)6Si6O8F2] 7, which also reacts with LiNMe2 and LiCCPh to afford 8 and 9.
Technical Note: Design of a Flow Perfusion Bioreactor System for Bone Tissue-Engineering Applications (2003)

Several different bioreactors have been investigated for tissue-engineering applications. Among these bioreactors are the spinner flask and the rotating wall vessel reactor. In addition, a new type of culture system has been developed and investigated, the flow perfusion culture bioreactor. Flow perfusion culture offers several advantages, notably the ability to mitigate both external and internal diffusional limitations as well as to apply mechanical stress to the cultured cells. For such investigation, a flow perfusion culture system was designed and built. This design is the outgrowth of important design requirements and incorporates features crucial to successful experimentation with such a system.
Tumor-Infiltrating and Peripheral Blood T-cell Immunophenotypes Predict Early Relapse in Localized Clear Cell Renal Cell Carcinoma (2017)

<b>Purpose:</b> The efficacy of PD-1 checkpoint blockade as adjuvant therapy in localized clear cell renal cell carcinoma (ccRCC) is currently unknown. The identification of tumor microenvironment (TME) prognostic biomarkers in this setting may help define which patients could benefit from checkpoint blockade and uncover new therapeutic targets.<b>Experimental Design:</b> We performed multiparametric flow cytometric immunophenotypic analysis of T cells isolated from tumor tissue [tumor-infiltrating lymphocytes (TIL)], adjacent non-malignant renal tissue [renal-infiltrating lymphocytes (RIL)], and peripheral blood lymphocytes (PBL), in a cohort of patients (<i>n</i> = 40) with localized ccRCC. Immunophenotypic data were integrated with prognostic and histopathologic variables, T-cell receptor (TCR) repertoire analysis of sorted CD8<sup>+</sup>PD-1<sup>+</sup> TILs, tumor mRNA expression, and digital quantitative immunohistochemistry.<b>Results:</b> On the basis of TIL phenotypic characterization, we identified three dominant immune profiles in localized ccRCC: (i) immune-regulated, characterized by polyclonal/poorly cytotoxic CD8<sup>+</sup>PD-1<sup>+</sup>Tim-3<sup>+</sup>Lag-3<sup>+</sup> TILs and CD4<sup>+</sup>ICOS<sup>+</sup> cells with a Treg phenotype (CD25<sup>+</sup>CD127<sup>-</sup>Foxp3<sup>+</sup>/Helios<sup>+</sup>GITR<sup>+</sup>), that developed in inflamed tumors with prominent infiltrations by dysfunctional dendritic cells and high PD-L1 expression; (ii) immune-activated, enriched in oligoclonal/cytotoxic CD8<sup>+</sup>PD-1<sup>+</sup>Tim-3<sup>+</sup> TILs, that represented 22% of the tumors; and (iii) immune-silent, enriched in TILs exhibiting RIL-like phenotype, that represented 56% of patients in the cohort. Only immune-regulated tumors displayed aggressive histologic features, high risk of disease progression in the year following nephrectomy, and a CD8<sup>+</sup>PD-1<sup>+</sup>Tim-3<sup>+</sup> and CD4<sup>+</sup>ICOS<sup>+</sup> PBL phenotypic signature.<b>Conclusions:</b> In localized ccRCC, the infiltration with CD8<sup>+</sup>PD-1<sup>+</sup>Tim-3<sup>+</sup>Lag-3<sup>+</sup> exhausted TILs and ICOS<sup>+</sup> Treg identifies the patients with deleterious prognosis who could benefit from adjuvant therapy with TME-modulating agents and checkpoint blockade. This work also provides PBL phenotypic markers that could allow their identification. <i>Clin Cancer Res; 23(15); 4416-28. ©2017 AACR</i>.
Down-regulation of p27 Promotes Cell Proliferation of Rat Neonatal Cardiomyocytes Induced by Nuclear Expression of Cyclin D1 and CDK4 (2004)

Mammalian cardiomyocytes lose their capacity to proliferate during terminal differentiation. We have previously reported that the expression of nuclear localization signal-tagged cyclin D1 (D1NLS) and its partner cyclin-dependent kinase 4 (CDK4) induces proliferation of rat neonatal cardiomyocytes. Here we show that the D1NLS/CDK4 cells, after their entry into the cell cycle, accumulated cyclin-dependent kinase inhibitor p27 in the nuclei and decreased the cyclin-dependent kinase 2 (CDK2) activity, leading to early cell cycle arrest. Biochemical analysis demonstrated that Skp2-dependent p27 ubiquitylation was remarkably suppressed in cardiomyocytes, whereas Skp2, a component of Skp1-Cullin-F-box protein ubiquitin ligase, was more actively ubiquitylated compared with proliferating rat fibroblasts. Specific degradation of p27 by co-expressing Skp2 or p27 small interfering RNA caused an increase of CDK2 activity and overrode the limited cell cycle. These data altogether indicate that the impaired Skp2-dependent p27 degradation is causally related to the loss of proliferation in cardiomyocytes. This provides a novel insight in understanding the molecular mechanism by which mammalian cardiomyocytes cease to proliferate during terminal differentiation.
Phase I/II studies of docetaxel (Taxotere) combined with estramustine in men with hormone-refractory prostate cancer. (1999)

Evaluation of the combined regimen of estramustine and docetaxel (Taxotere; Rhône-Poulenc Rorer, Collegeville, PA) in men with hormone-refractory prostate cancer is in its early stages. While this combination is promising in terms of efficacy, adverse events associated with estramustine are a concern. Estramustine has been associated with side effects such as nausea, vomiting, edema, and serious vascular events. Reported here are the results of phase I and phase II trials in which 280 mg estramustine was given three times daily on days I to 5 in 21-day treatment cycles with docetaxel at varying doses. Data from patients evaluable thus far support the efficacy of this combination, both in chemotherapeutically naive patients and in those who have had prior therapy. A survival benefit from this combination appears achievable from these early studies. As significant antitumor activity can be achieved with docetaxel alone, future studies need to define the minimal dose of estramustine for this combination.