gebhart/patrepeval huggingface dataset:
The ruxolitinib effect: understanding how molecular pathogenesis and epigenetic dysregulation impact therapeutic efficacy in myeloproliferative neoplasms (2018)

The myeloproliferative neoplasms (MPN), polycythaemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF) are linked by a propensity to thrombosis formation and a risk of leukaemic transformation. Activation of cytokine independent signalling through the JAK/STAT cascade is a feature of these disorders. A point mutation in exon 14 of the JAK2 gene resulting in the formation of the JAK2 V617F transcript occurs in 95% of PV patients and around 50% of ET and PMF patients driving constitutive activation of the JAK/STAT pathway. Mutations in CALR or MPL are present as driving mutations in the majority of remaining ET and PMF patients. Ruxolitinib is a tyrosine kinase inhibitor which inhibits JAK1 and JAK2. It is approved for use in intermediate and high risk PMF, and in PV patients who are resistant or intolerant to hydroxycarbamide. In randomised controlled trials it has demonstrated efficacy in spleen volume reduction and symptom burden reduction with a moderate improvement in overall survival in PMF. In PV, there is demonstrated benefit in haematocrit control and spleen volume. Despite these benefits, there is limited impact to induce complete haematological remission with normalisation of blood counts, reduce the mutant allele burden or reverse bone marrow fibrosis. Clonal evolution has been observed on ruxolitinib therapy and transformation to acute leukaemia can still occur. This review will concentrate on understanding the clinical and molecular effects of ruxolitinib in MPN. We will focus on understanding the limitations of JAK inhibition and the challenges to improving therapeutic efficacy in these disorders. We will explore the demonstrated benefits and disadvantages of ruxolitinib in the clinic, the role of genomic and clonal variability in pathogenesis and response to JAK inhibition, epigenetic changes which impact on response to therapy, the role of DNA damage and the role of inflammation in these disorders. Finally, we will summarise the future prospects for improving therapy in MPN in the JAK inhibition era.
Radioimmunoassay of Procollagen in Serum of Patients with Paget's Disease of Bone (1976)

A new radioimmunoassay for human procollagen showed that the sera of 46 of 50 untreated patients with Paget's disease of bone contained increased concentrations of procollagen protein as compared to normal adults. After therapy with disodium etidronate, all the elevated serum procollagen concentrations decreased significantly, falling to normal levels in 33 of 40 patients. The procollagen levels before and after treatment were coordinate with the values for urinary total hydroxyproline and serum alkaline phosphatase activity. The data show that the radioimmunoassay for procollagen is a dependable and useful adjunct to the study of Paget's disease of bone.
The effect of erythropoietin and other factors on DNA synthesis by mouse spleen cells. (1983)

The effects of pure and crude human urinary erythropoietin, crude sheep plasma erythropoietin and other growth factors on the incorporation of labeled thymidine were studied using spleen cells from mice previously treated with phenylhydrazine hydrochloride. Erythropoietin at 400 mU/ml caused a 40-80 fold increase in the incorporation of the labeled nucleoside. The slope of the dose-response curve found for pure erythropoietin was not significantly different from that found for a crude urinary erythropoietin preparation or for crude sheep plasma erythropoietin. Colony-stimulating factor, interleukin 2, interleukin 3 and the lectin, concanavalin A were also stimulatory but at concentrations from one hundred to one million times higher than that found for erythropoietin.
Infrared Analysis of Peptides and Proteins (1999)

Infrared spectroscopy is being increasingly utilized for the analysis of peptides and proteins because it probes the universally available amide (peptide) bonds, which display distinct IR signals for differently folded peptides and proteins. Other spectroscopic techniques useful for studying protein structures in solutions are circular dichroism (CD), ultraviolet absorption and fluorescence spectroscopy, Raman and nuclear magnetic resonance (NMR). Among the techniques for secondary structure, NMR and Raman spectroscopy need unusually high concentration of proteins, and NMR analysis is still limited to small proteins of about 200 amino acid residues. CD analysis is limited to clear protein solution (as opposed to membrane proteins) due to the problem with light scattering. Furthermore, for estimation of secondary structure of protein by CD accurate protein concentration is needed. Infrared spectroscopy is an emerging technique for protein analysis. Amide I, II and III are most commonly used IR spectral regions used for protein structure-function analysis. Recent advances in the development of instrumentation (Fourier transformation, sampling), protein IR data bank (band assignments to different components of secondary structure), and techniques (two-dimensional IR methods, time-resolution, and isotopic labeling) have significantly augmented IR spectroscopy as an analytical tool for peptides and proteins. This chapter provides an overview of the basic technique and some of the applications of IR spectroscopy to examine structure, interaction, and conformational changes in peptides and proteins.
Studies on the Formation of Transfer Ribonucleic Acid-Ribosome Complexes (1968)

Abstract Aminoacyl transfer RNA bound to 70 S ribosomes in the presence of a template was resistant to digestion by pancreatic ribonuclease. On the basis of this observation, a convenient sensitive assay for codon recognition and aminoacyl-tRNA binding to ribosomes was described. The protection occurred as a result of the association of aminoacyl-tRNA with the 50 S subribosomal particle; thus, the assay provided a sensitive functional test involving the specific interaction of tRNA with the 50 S subunit of Escherichia coli ribosomes. The kinetics of attachment of 50 S subunits to 30 S ribosome-polyribonucleotide template-aminoacyl-tRNA complexes was studied by the assay. Furthermore, the assay provides an additional parameter for evaluating the site of action of antibiotics and other substances interfering with protein biosynthesis.
Detection and Tracking of Humans by Probabilistic Body Part Assembly (2005)

This paper presents a probabilistic framework of assembling detected human body parts into a full 2D human configuration. The face, torso, legs and hands are detected in cluttered scenes using boosted body part detectors trained by AdaBoost. Body configurations are assembled from the detected parts using RANSAC, and a coarse heuristic is applied to eliminate obvious outliers. An a priori mixture model of upper-body configurations is used to provide a pose likelihood for each configuration. A joint-likelihood model is then determined by combining the pose, part detector and corresponding skin model likelihoods. The assembly with the highest likelihood is selected by RANSAC, and the elbow positions are inferred. This paper also illustrates the combination of skin colour likelihood and detection likelihood to further reduce false hand and face detections.
Pirlindole and dehydropirlindole protect rat cultured neuronal cells against oxidative stress‐induced cell death through a mechanism unrelated to MAO‐A inhibition (2002)

It has been shown that the MAO (monoamine oxidase)-B inhibitor deprenyl (DPR, selegiline) protects some cell types against oxidative stress. By decreasing H(2)O(2) production, MAO-A inhibitors could also reduce oxidative stress. This study reports the effect of the MAO-A inhibitors, pirlindole (PIR), dehydropirlindole (DHP), brofaromine (BRO) and moclobemide (MCL) on primary-cultured brain cells exposed to iron-mediated toxicity. A comparison with trolox (TRO), a hydrosoluble vitamin-E analogue that protects against such an induced stress, was performed. Rat hippocampal or cortical cultured cells were exposed either to 2 microM FeSO(4) alone or in the presence of PIR, DHP, BRO, DPR, MCL or TRO. Cell survival (lactate-dehydrogenase measurements, 16 h incubation), intracellular peroxide production (DCF-fluorescence, 1 h incubation), lipoperoxidation (TBARS-fluorescence, 6 h incubation) and mitochondrial function (MTT-test, 16 h incubation) were assessed. PIR, DHP and TRO significantly protected cultures (P<0.05) against Fe(2+)-induced toxicity in a concentration-dependent manner. The EC(50s) of these compounds were 6, 12 and 19 microM, respectively, in hippocampal cells. For cortical cell cultures incubated in the presence of iron and PIR or DHP, EC(50s) were 5 and 6 microM respectively. All Hill coefficients were close to unity. BRO, MCL and DPR were not protective in any type of culture. The IC(50s) for the inhibition of MAO-A were 2, 2 and 0.2 microM for PIR, DHP and BRO, respectively. PIR, DHP and TRO, but not DPR, induced a significant decrease in both intracellular peroxide production and lipoperoxidation. They also improved mitochondrial function. These experiments show that PIR and DHP can protect hippocampal and cortical neurons against oxidative stress at pharmacologically relevant concentrations. This protective effect seems unrelated to inhibition of MAO-A, but possibly involves free radical scavenging.
Plant Cells CLEave Their Way to Differentiation (2006)

Two peptides with very similar amino acid sequences mediate short-range cell-cell signaling in plants. One suppresses and the other promotes the differentiation of stem cells.
High efficiency gene transfer into murine T cell clones using a retroviral vector. (1986)

To establish a gene transfer and expression system for murine T cell clones, we have introduced the neomycin phosphotransferase gene encoding resistance to the neomycin analogue, G418, into non-neoplastic inducer T cell clones by using a replication-defective retroviral vector. This method allowed highly efficient gene transfer (20 to 40%) into two inducer T cell clones. The level of viral RNA expression in G418r T cells was 0.1% of poly(A)+ RNA. The infected G418r cells retained physiologic responsiveness to specific antigen as judged by antigen-specific proliferation and production of IL 3.
Sp1 and NF-Y Are Necessary and Sufficient for Growth-dependent Regulation of the Hamster Thymidine Kinase Promoter (1999)

Thymidine kinase (TK) genes from different species are growth- and cell cycle-regulated in a very similar manner; still, the promoter regions of these genes show little homology to each other. It was previously shown that the murine TK gene is growth-regulated by Sp1 and E2F. Here we have characterized cis-regulatory elements in the hamster promoter that are essential and sufficient to confer efficient and serum-responsive expression. The TK promoter was isolated from baby hamster kidney cells. DNase I protection experiments revealed a protected region from positions -24 to -99 relative to the transcription start site. Within this region, binding sites for the transcription factor Sp1 and a CCAAT box, which interacts with the transcription factor NF-Y, were identified. An E2F-like sequence was found not to bind protein, and its removal did not affect promoter activity. This was supported by the observation that cotransfection of a hamster TK reporter gene construct with E2F-1 does not lead to transactivation of the promoter. A 122-base pair region that contains a single Sp1 site, a CCAAT box, and a TATA element was found to be sufficient for serum-responsive expression of a reporter gene. Mutations that inactivate any one of these three elements caused a strong reduction or a loss of promoter activity.
An influenza A virus containing influenza B virus 5' and 3' noncoding regions on the neuraminidase gene is attenuated in mice. (1991)

Influenza A and B viruses have not been shown to form reassortants. It had been assumed that the lack of genotypic mixing between influenza virus types reflected differences in polymerase and packaging specificity. In this study, we show that an influenza A virus polymerase transcribes and replicates a chloramphenicol acetyltransferase (CAT) gene flanked by the nontranslated sequences of an influenza B virus gene. Although the transcription level of this CAT gene was several times lower than that of a CAT gene flanked by the homologous nontranslated sequences of an influenza A virus, we proceeded to construct a chimeric type A/B influenza virus. Using recombinant DNA techniques, a chimeric neuraminidase gene was introduced into the genome of influenza A/WSN/33 virus. The hybrid influenza A/B virus gene contained the coding region of the A/WSN neuraminidase and the 3' and 5' nontranslated sequences of the nonstructural gene of influenza B/Lee virus. The resulting chimeric virus formed plaques in Madin-Darby bovine kidney cells but replicated more slowly and achieved lower titers than wild-type influenza A/WSN/33 virus. The chimeric virus was attenuated for mice as indicated by a 400-fold increase in its LD50. Interestingly, the virus was greatly restricted in replication in the upper respiratory tract and partially restricted in the lungs. Animals infected with the transfectant virus were highly resistant to influenza virus challenge. It appears that this chimeric virus has many of the properties desirable for a live attenuated virus vaccine.
HIV‐1 gp120‐dependent induction of apoptosis in antigen‐specific human T cell clones is characterized by ‘tissue’ transglutaminase expression and prevented by cyclosporin A (1994)

We investigated the effect of cyclosporin (CsA) on HIV-gp120-dependent induction of cell death by apoptosis of human T cell clones specific for influenza virus haemagglutinin and restricted by HLA-DR1. Preincubation of the clones with gp120 induced a large inhibition of their proliferation which was paralleled by the induction of apoptosis. Exposure to the specific antigen alone was able to trigger apoptosis in a significant fraction of cells, this effect was potentiated by pretreatment with gp120. Apoptosis was characterized by the typical morphological changes and by the expression of 'tissue' Transglutaminase (tTG), one of the few characterized effector elements of programmed cell death. Interestingly, the tTG protein induction was detectable within the first 24 hours following the gp120 treatment and preceded the appearance of the typical apoptotic phenotype. Noteworthy, CsA treatment prevented the gp120-dependent induction of apoptosis by blocking the activation of the Ca(2+)-dependent effector elements such as tTG.
Blockade of physiologically secreted IFN-gamma inhibits human T lymphocyte and natural killer cell activation (1991)

The role of physiologically secreted human IFN-gamma in T lymphocyte and NK cell activation has been probed with a panel of mouse mAb directed against various epitopes of the human IFN-gamma molecule, or human IFN-gamma R. Addition to the culture medium of those mAb that neutralize the antiviral activity of IFN-gamma or interact with its receptor inhibited proliferative and cytotoxic responses elicited in PBL by HLA alloantigens, anti-CD3 mAb, and IL-2, but not the proliferative response to PHA. The IFN-gamma blockade also inhibited IFN-gamma, IL-2, and TNF-alpha release during MLC. Kinetic experiments showed that reduction of proliferative and cytotoxic responses to HLA alloantigens is maximal when IFN-gamma is blocked within the first 48 h. Exogenous rIFN-gamma restored the proliferative response only when added at the beginning. Moreover, when IFN-gamma was blocked, T lymphocytes recovered from 6-day MLC displayed a profound decrease in their expression of p55 and p75 chains of the IL-2R, as well as in the number of high-affinity IL-2 binding sites. These findings strongly suggest that IFN-gamma is required in the early phases of induction of the oligo- and polyclonal proliferative and cytotoxic responses of lymphocytes.
Direct Observations of the Mechanical Behaviors of the Cytoskeleton in Living Fibroblasts (1999)

Cytoskeletal proteins tagged with green fluorescent protein were used to directly visualize the mechanical role of the cytoskeleton in determining cell shape. Rat embryo (REF 52) fibroblasts were deformed using glass needles either uncoated for purely physical manipulations, or coated with laminin to induce attachment to the cell surface. Cells responded to uncoated probes in accordance with a three-layer model in which a highly elastic nucleus is surrounded by cytoplasmic microtubules that behave as a jelly-like viscoelastic fluid. The third, outermost cortical layer is an elastic shell under sustained tension. Adhesive, laminin-coated needles caused focal recruitment of actin filaments to the contacted surface region and increased the cortical layer stiffness. This direct visualization of actin recruitment confirms a widely postulated model for mechanical connections between extracellular matrix proteins and the actin cytoskeleton. Cells tethered to laminin-treated needles strongly resisted elongation by actively contracting. Whether using uncoated probes to apply simple deformations or laminin-coated probes to induce surface-to-cytoskeleton interaction we observed that experimentally applied forces produced exclusively local responses by both the actin and microtubule cytoskeleton. This local accomodation and dissipation of force is inconsistent with the proposal that cellular tensegrity determines cell shape.
Mouse MHC class I-like Fc receptor encoded outside the MHC. (1993)

In many mammalian species antibodies transmitted from the mother provide humoral immunity to the young. Maternal IgG from milk is transported across the intestinal epithelium of neonatal rats by an Fc receptor (FcRn) that comprises an alpha-chain similar to the class I Ag of the MHC and beta 2-microglobulin. Suckling mice also acquire antibodies by uptake from the gut. We made a neonatal mouse intestinal cDNA library and screened it with a probe encoding rat FcRn alpha-chain. The nucleotide and predicted amino acid sequences of the two positive clones were very similar to those of rat FcRn. Comparison of the FcRn domains to various MHC class I and CD1 molecules suggests a divergence of FcRn from MHC early in the mammalian lineage. We expressed one of these cDNA in mouse 3T3 fibroblasts. Cells that expressed the cDNA product bound the Fc fragment of IgG with the same pH dependence as neonatal rat intestinal epithelium. We detected RNA that hybridize with the mouse cDNA only in neonatal small intestine and fetal yolk sac, two tissues involved in IgG transport. These data show that the mouse cDNA code for FcRn alpha-chain. The mouse FcRn alpha-chain is similar in sequence to the class I MHC Ag, encoded on chromosome 17 in the mouse. However, we find that the mouse FcRn gene lies outside the MHC, on chromosome 7.
Fluorescent Labeling of Proteins (2011)

Many single-molecule experimental techniques exploit fluorescence as a tool to investigate conformational dynamics, molecular interactions, or track the movement of proteins in order to gain insight into their biological functions. A prerequisite to these experimental approaches is to graft one or more fluorophores on the protein of interest with the desired photophysical properties. Here, we describe procedures for efficient methods used to covalently attach fluorophores to proteins. Alternative direct and indirect labeling strategies are also described.
PspA, a surface protein of Streptococcus pneumoniae, is capable of eliciting protection against pneumococci of more than one capsular type (1991)

Monoclonal antibodies against pneumococcal surface protein A (PspA) have been shown to protect mice from fatal pneumococcal infection. PspA is highly variable serologically, raising the possibility that PspA from one strain might not be able to elicit protective responses against strains which possess serologically different PspA. We have prepared a lambda gt11 library of pneumococcal genomic DNA and identified a clone expressing PspA. The recombinant PspA in this phage lysate elicited protection against pneumococcal infections with three strains of two different capsular serotypes. This finding demonstrated that PspA could elicit a protective response in the absence of other pneumococcal antigens. The observed protection was probably antibody mediated because it could be passively transferred with immune sera. Lambda lysates producing pneumococcal proteins other than PspA failed to elicit protection against fatal pneumococcal infection.
Occludin confers adhesiveness when expressed in fibroblasts (1997)

Occludin is an integral membrane protein specifically associated with tight junctions. Previous studies suggest it is likely to function in forming the intercellular seal. In the present study, we expressed occludin under an inducible promotor in occludin-null fibroblasts to determine whether this protein confers intercellular adhesion. When human occludin is stably expressed in NRK and Rat-1 fibroblasts, which lack endogenous occludin and tight junctions but do have well developed ZO-1-containing adherens-like junctions, occludin colocalizes with ZO-1 to points of cell-cell contact. In contrast, L-cell fibroblasts which lack cadherin-based adherens junctions, target neither ZO-1 nor occludin to sites of cell contact. Occludin-induced adhesion was next quantified using a suspended cell assay. In NRK and Rat-1 cells, occludin expression induces adhesion in the absence of calcium, thus independent of cadherin-cadherin contacts. In contrast, L-cells are nonadhesive in this assay and show no increase in adhesion after induction of occludin expression. Binding of an antibody to the first of the putative extracellular loops of occludin confirmed that this sequence was exposed on the cell surface, and synthetic peptides containing the amino acid sequence of this loop inhibit adhesion induced by occludin expression. These results suggest that the extracellular surface of occludin is directly involved in cell-cell adhesion and the ability to confer adhesiveness correlates with the ability to colocalize with its cytoplasmic binding protein, ZO-1.
Bisucaberin, a new siderophore, sensitizing tumor cells to macrophage-mediated cytolysis. I. Taxonomy of the producing organism, isolation and biological properties. (1987)

Alteromonas haloplanktis strain SB-1123 isolated from deep-sea mud produced a new siderophore, bisucaberin. Bisucaberin rendered tumor cells susceptible to cytolysis mediated by murine peritoneal macrophages which were elicited by Proteose peptone and not yet activated by lymphokine. Bisucaberin exerted its sensitizing activity by both the preincubation with tumor cells and the addition to co-culture of macrophages and tumor cells. The activity of bisucaberin was specifically inhibited by ferric ion. Bisucaberin showed direct cytostasis for tumor cells but did not cause cytolysis in the absence of macrophages. Cytostasis by bisucaberin was attributable to the specific inhibition of DNA synthesis in tumor cells.