gebhart/patrepeval huggingface dataset:
The Properties of DNA Transferred to Minicells during Conjugation (1968)

We have isolated a mutant of Escherichia coli K12 with an unusual cell division lesion. This mutant divides to produce normal sized cells and produces, in addition, small anucleate spheres about one-tenth the volume of a normal cell. These ‘minicells’ are produced under a variety of growth conditions that support normal cell division. The yield of minicells in a fully grown culture is 1 to 3 times the number of normal sized cells. Because of their small size, minicells can be separated easily from normal cells by differential centrifugation, sucrose gradient centrifugation, or a combination of both techniques. Phase contrast and electron microscopy show that minicells do not have a nuclear structure, and chemical analyses indicate that these cells contain RNA and protein in a ratio similar to that of normal cells but contain little or no DNA (Adler et al., 1967). The absence of DNA...
Wound healing: the role of the macrophage and other immune cells. (1995)

The tissue macrophage has been shown to play a critical role in the wound healing process. Through the generation of bioactive substances, macrophages orchestrate the complex processes of cellular proliferation and functional tissue regeneration within wounds. Recent investigations have enumerated many of the specific proteins that are produced by wound macrophages at the site of injury. These include the following: 1) chemoattractants that recruit and activate additional macrophages at the site of injury, 2) growth factors that promote cellular proliferation and protein synthesis, 3) proteases and extra-cellular matrix molecules, and 4) factors that may restrain tissue growth once repair is completed. The development of therapeutic strategies to modulate wound repair continues to utilize key macrophage secretory products.
mRNA Profiling Reveals Determinants of Trastuzumab Efficiency in HER2-Positive Breast Cancer (2015)

Intrinsic and acquired resistance to the monoclonal antibody drug trastuzumab is a major problem in the treatment of HER2-positive breast cancer. A deeper understanding of the underlying mechanisms could help to develop new agents. Our intention was to detect genes and single nucleotide polymorphisms (SNPs) affecting trastuzumab efficiency in cell culture. Three HER2-positive breast cancer cell lines with different resistance phenotypes were analyzed. We chose BT474 as model of trastuzumab sensitivity, HCC1954 as model of intrinsic resistance, and BTR50, derived from BT474, as model of acquired resistance. Based on RNA-Seq data, we performed differential expression analyses on these cell lines with and without trastuzumab treatment. Differentially expressed genes between the resistant cell lines and BT474 are expected to contribute to resistance. Differentially expressed genes between untreated and trastuzumab treated BT474 are expected to contribute to drug efficacy. To exclude false positives from the candidate gene set, we removed genes that were also differentially expressed between untreated and trastuzumab treated BTR50. We further searched for SNPs in the untreated cell lines which could contribute to trastuzumab resistance. The analysis resulted in 54 differentially expressed candidate genes that might be connected to trastuzumab efficiency. 90% of 40 selected candidates were validated by RT-qPCR. ALPP, CALCOCO1, CAV1, CYP1A2 and IGFBP3 were significantly higher expressed in the trastuzumab treated than in the untreated BT474 cell line. GDF15, IL8, LCN2, PTGS2 and 20 other genes were significantly higher expressed in HCC1954 than in BT474, while NCAM2, COLEC12, AFF3, TFF3, NRCAM, GREB1 and TFF1 were significantly lower expressed. Additionally, we inferred SNPs in HCC1954 for CAV1, PTGS2, IL8 and IGFBP3. The latter also had a variation in BTR50. 20% of the validated subset have already been mentioned in literature. For half of them we called and analyzed SNPs. These results contribute to a better understanding of trastuzumab action and resistance mechanisms.
Arachidonic acid causes cyclooxygenase-dependent and -independent pulmonary vasodilation (1990)

In this study we examined the action of arachidonic acid in the isolated rat lung perfused with a cell- and protein-free physiological salt solution. When pulmonary vascular tone was elevated by hypoxia, bolus injection of a large dose of arachidonic acid (75 micrograms) caused transient vasoconstriction followed by vasodilation. When arachidonic acid (100 micrograms) was injected during normoxia and at base-line perfusion pressure (low vascular tone) or when vascular tone was elevated by KCl, arachidonic acid (50 micrograms) caused only vasoconstriction. Doses less than 7.5 micrograms caused vasodilation only when injected during hypoxic vasoconstriction and subsequent blunting of either angiotensin II- or hypoxia-induced pulmonary vasoconstriction. The higher doses of arachidonic acid (7.5 and 75 micrograms), but not the lower doses (7.5-750 ng), caused increases in effluent 6-ketoprostaglandin F1 alpha, thromboxane B2, and prostaglandin E2 and F2 alpha. 6-Ketoprostaglandin F1 alpha was the major cyclooxygenase product. Meclofenamate (10(-5) M) blocked the increased metabolite synthesis over the entire dose range of arachidonic acid tested (7.5 ng-75 micrograms). Because vasodilation immediately after arachidonic acid was cyclooxygenase-independent, we investigated whether this effect was due to the unsaturated fatty acid properties of arachidonic acid and compared its action with that of oleic acid and docosahexaenoic acid. Because neither compound mimicked the vasodilation observed with arachidonic acid, we concluded that the cyclooxygenase-independent action of arachidonic acid could not be explained by unsaturated fatty acid properties per se. Because 1-aminobenzotriazole, a cytochrome P-450 inhibitor, partially inhibited the immediate arachidonic acid-induced pulmonary vasodilation, we concluded that cytochrome P-450-dependent metabolites can account for some of the cyclooxygenase-independent vasodilation of arachidonic acid.
Diabetes Studies Conflict on Power of Spleen Cells (2006)

Three separate attempts have failed to replicate promising results that electrified the diabetes community 2 years ago. The outcome severely weakens the theory that the spleen cradles stem cells with curative powers against mouse diabetes. But some researchers, including the leader of the original studies, haven't given up on the idea.
ABCG1 is deficient in alveolar macrophages of GM-CSF knockout mice and patients with pulmonary alveolar proteinosis (2007)

Patients with pulmonary alveolar proteinosis (PAP) display impaired surfactant clearance, foamy, lipid-filled alveolar macrophages, and increased cholesterol metabolites within the lung. Neutralizing autoantibodies to granulocyte-macrophage colony-stimulating factor (GM-CSF) are also present, resulting in virtual GM-CSF deficiency. We investigated ABCG1 and ABCA1 expression in alveolar macrophages of PAP patients and GM-CSF knockout (KO) mice, which exhibit PAP-like pulmonary pathology and increased pulmonary cholesterol. Alveolar macrophages from both sources displayed a striking similarity in transporter gene dysregulation, consisting of deficient ABCG1 accompanied by highly increased ABCA1. Peroxisome proliferator-activated receptor gamma (PPARgamma), a known regulator of both transporters, was deficient, as reported previously. In contrast, the liver X receptor alpha, which also upregulates both transporters, was highly increased. GM-CSF treatment increased ABCG1 expression in macrophages in vitro and in PAP patients in vivo. Overexpression of PPARgamma by lentivirus-PPARgamma transduction of primary alveolar macrophages, or activation by rosiglitazone, also increased ABCG1 expression. These results suggest that ABCG1 deficiency in PAP and GM-CSF KO alveolar macrophages is attributable to the absence of a GM-CSF-mediated PPARgamma pathway. These findings document the existence of ABCG1 deficiency in human lung disease and highlight a critical role for ABCG1 in surfactant homeostasis.
Autologous preparations rich in growth factors promote proliferation and induce VEGF and HGF production by human tendon cells in culture (2004)

Blood platelets become activated and aggregate at the site of vessel injury. Upon activation by thrombin, platelets release storage pools of proteins and growth factors (GFs), including those involved in tissue repair. Our goal was to evaluate the potential beneficial effect of proteins released from platelet-rich clots on tendon healing. PDGF, TGF-beta-1, IGF-I, HGF, VEGF and EGF were measured in human platelet-poor plasma (PPP) and in the releasates collected from either platelet-poor or platelet-rich clots prepared in vitro. We then studied the effects of the releasates on human tendon cells in culture. Releasates from both platelet-rich and platelet-poor clots stimulated tendon cell proliferation, in contrast to un-clotted PPP. The mitogenic activity of the supernatants was not decreased by the thrombin inhibitor, hirudin. Cultured tendon cells synthesise VEGF and HGF in the presence of PPP-clots and PRP-clot releasates, thus the synthesised amount was significantly higher with supernatants from platelet-rich clots than supernatants from a platelet-poor clot (p < 0.05). These results suggest that administering autologous platelet-rich clots may be beneficial to the treatment of tendon injuries by inducing cell proliferation and promoting the synthesis of angiogenic factors during the healing process.
A periplasmic protein disulfide oxidoreductase is required for transformation of Haemophilus influenzae Rd. (1992)

The mutated gene in JG16, a Haemophilus influenzae strain deficient in competence-induced DNA binding and uptake, was cloned and the wild-type allele was sequenced. The gene was shown by Northern analysis to be constitutively expressed on a 1.7-kilobase transcript. The gene product was identified as a 20.6-kDa protein targeted to the periplasm. The protein contains the sequence Cys-Pro-His-Cys (CPHC) and is highly similar to two other periplasmic CPHC motif-containing proteins: DsbA, an Escherichia coli protein (45% identity, 87% homology) and TcpG, a Vibrio cholerae protein (32% identity, 74% homology). Both DsbA and TcpG promote disulfide bond formation in periplasmic proteins, are required for pilus biogenesis, and, like thioredoxin, are capable of reducing insulin in vitro. The Haemophilus protein was shown to complement an E. coli mutation in DsbA and was named Por (periplasmic oxidoreductase). In JG16 the competence-dependent redistribution of inner membrane proteins did not occur. These findings suggest that Por is required for the correct assembly and/or folding of one or more disulfide-containing cell envelope protein involved either in competence development or in the DNA-binding and -uptake machinery.
Thieno[3,2-b]pyrrole-5-carboxamides as New Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1. Part 2: Structure-Based Drug Design and Structure–Activity Relationship (2017)

The balance of methylation levels at histone H3 lysine 4 (H3K4) is regulated by KDM1A (LSD1). KDM1A is overexpressed in several tumor types, thus representing an emerging target for the development of novel cancer therapeutics. We have previously described ( Part 1, DOI 10.1021.acs.jmedchem.6b01018 ) the identification of thieno[3,2-b]pyrrole-5-carboxamides as novel reversible inhibitors of KDM1A, whose preliminary exploration resulted in compound 2 with biochemical IC<sub>50</sub> = 160 nM. We now report the structure-guided optimization of this chemical series based on multiple ligand/KDM1A-CoRest cocrystal structures, which led to several extremely potent inhibitors. In particular, compounds 46, 49, and 50 showed single-digit nanomolar IC<sub>50</sub> values for in vitro inhibition of KDM1A, with high selectivity in secondary assays. In THP-1 cells, these compounds transcriptionally affected the expression of genes regulated by KDM1A such as CD14, CD11b, and CD86. Moreover, 49 and 50 showed a remarkable anticlonogenic cell growth effect on MLL-AF9 human leukemia cells.
Evi-1 expression in leukemic patients with rearrangements of the 3q25-q28 chromosomal region. (1992)

The Evi-1 zinc-finger protein gene is normally not expressed in hematopoietic cells. However, high Evi-1 mRNA expression has been reported in mouse myeloblastic leukemias, due to transcriptional activation by proviral integration in either the Fim-3 or Evi-1 loci. The human Evi-1 gene is located on chromosome 3q24-q28. In this paper three examples are presented of human acute myelogenous leukemias presenting common characteristics: (i) high Evi-1 mRNA expression; (ii) chromosomal abnormalities t(3;3)(q21;q26) or inv(3;3)(q21-22;q26); and (iii) high platelet counts and dystrophic megakaryocytes. Thirty-four other patients with hematological malignancies, among which 11 had chromosomal rearrangements in the 3q24-q28 region did not exhibit such abnormalities. Of the 13 permanent hemopoietic cell lines tested, Evi-1 RNA expression was found in HEL and K-562 cell lines. Weak Evi-1 expression was also seen in fibroblasts and lung cells. This expression was affected neither in skin cells from a patient with a 3q27 constitutional translocation nor in a lung epithelioma cell line containing an excess of chromosome 3 long arm. Ectopic strong expression of Evi-1 in human leukemias could define an uncommon subclass of acute myelogenous leukemias with translocations involving the 3q25-28 chromosomal domain and abnormal megakaryopoiesis.
Surveillance of patients at high risk for cutaneous malignant melanoma using digital dermoscopy (2005)

Follow-up examinations using digital dermoscopy revealed unchanged morphology in the large majority of melanocytic naevi. Excisions were only performed in cases of asymmetrical growth, asymmetrical changes of pigmentation, or development of dermoscopic features indicative of melanoma. The ratio of 33 lesions excised in order to identify two melanomas in situ seems reasonable and may be further reduced in future.
Understanding interactions of gastric inhibitory polypeptide (GIP) with its G‐protein coupled receptor through NMR and molecular modeling (2007)

Gastric inhibitory polypeptide (GIP, or glucose-dependent insulinotropic polypeptide) is a 42-amino acid incretin hormone moderating glucose-induced insulin secretion. Antidiabetic therapy based on GIP holds great promise because of the fact that its insulinotropic action is highly dependent on the level of glucose, overcoming the sideeffects of hypoglycemia associated with the current therapy of Type 2 diabetes. The truncated peptide, GIP(1-30)NH2, has the same activity as the full length native peptide. We have studied the structure of GIP(1-30)NH2 and built a model of its G-protein coupled receptor (GPCR). The structure of GIP(1-30)NH2 in DMSO-d6 and H2O has been studied using 2D NMR (total correlation spectroscopy (TOCSY), nuclear overhauser effect spectroscopy (NOESY), double quantum filtered-COSY (DQF-COSY), 13C-heteronuclear single quantum correlation (HSQC) experiments, and its conformation built by MD simulations with the NMR data as constraints. The peptide in DMSO-d6 exhibits an alpha-helix between residues Ile12 and Lys30 with a discontinuity at residues Gln19 and Gln20. In H2O, the alpha-helix starts at Ile7, breaks off at Gln19, and then continues right through to Lys30. GIP(1-30)NH2 has all the structural features of peptides belonging to family B1 GPCRs, which are characterized by a coil at the N-terminal and a long C-terminal alpha-helix with or without a break. A model of the seven transmembrane (TM) helices of the GIP receptor (GIPR) has been built on the principles of comparative protein modeling, using the crystal structure of bovine rhodopsin as a template. The N-terminal domain of GIPR has been constructed from the NMR structure of the N-terminal of corticoptropin releasing factor receptor (CRFR), a family B1 GCPR. The intra and extra cellular loops and the C-terminal have been modeled from fragments retrieved from the PDB. On the basis of the experimental data available for some members of family B1 GPCRs, four pairs of constraints between GIP(1-30)NH2 and its receptor were used in the FTDOCK program, to build the complete model of the GIP(1-30)NH2:GIPR complex. The model can rationalize the various experimental observations including the potency of the truncated GIP peptide. This work is the first complete model at the atomic level of GIP(1-30)NH2 and of the complex with its GPCR.
Cerebral neurogenesis is induced by intranasal administration of growth factors (2003)

Neurogenesis persists in the adult brain, where it may contribute to repair and recovery after injury, but the lack of methods for noninvasive stimulation of cerebral neurogenesis limits its potential for clinical application. We report that intranasal administration of either fibroblast growth factor-2 or heparin-binding epidermal growth factor-like growth factor increases neurogenesis, measured by the incorporation of bromodeoxyuridine into cells that express the early neuronal marker protein doublecortin in the subventricular zone of mouse brain. These findings indicate that intranasal growth factors may have potential as neurogenesis-promoting therapeutic agents.
Discourse structures for text generation (1984)

Text generation programs need to be designed around a theory of text organization. This paper introduces Rhetorical Structure Theory, a theory of text structure in which each region of text has a central nuclear part and a number of satellites related to it. A natural text is analyzed as an example, the mechanisms of the theory are identified, and their formalization is discussed. In a comparison, Rhetorical Structure Theory is found to be more comprehensive and more informative about text function than the text organization parts of previous text generation systems.
Sulphur passivation of gallium antimonide surfaces (1994)

Improvement in optical and electrical properties were observed after sulphur passivation of gallium antimonide surface. Enhancement of photoluminescence intensity up to 60 times, reduction in surface state density by two orders of magnitude, and reverse leakage currents by a factor of 20–30 were obtained as a result of surface passivation. While the reduction of surface recombination is attained, the surface is not unpinned.
Studies on the relationship of gamma-aminobutyric acid-stimulated diazepam binding and the gamma-aminobutyric acid receptor. (1981)

The three binding parameters [3H]muscimol binding, [3H]diazepam binding, and γ-aminobutyric acid (GABA)-stimulated [3H]diazepam binding are compared in various brain areas and in response to various protein and membrane modifying reagents. Comparison of rat forebrain and cerebellum revealed a much higher ratio of [3H]muscimol- to [3H]diazepam-binding sites in cerebellum and less GABA-stimulated [3H]diazepam binding. Both sulfhydryl reducing and alkylating agents reduced [3H]muscimol binding (decreased binding affinity), and increased GABA-stimulated [3H]diazepam binding. Triton X-100-treated membranes display an increase in both the number and affinity of [3H]muscimol-binding sites, no change in basal [3H]diazepam binding, and a decrease in GABA-stimulated [3H]diazepam binding. The observed relationship between [3H]-muscimol-binding sites and the degree of GABA-stimulated [3H]diazepam binding suggests that the high affinity muscimol-binding site is not mediating the GABA enhancement effect.
Synergy between cyclosporin A and a monoclonal antibody to B7 in blocking alloantigen-induced T-cell activation (1994)

Costimulatory signals are absolutely required for T-cell activation after T-cell receptor/major histocompatibility complex-peptide interaction. So far, the best-known candidate essential costimulatory signal is mediated by interaction of CD28 on T cells with B7 on antigen- presenting cells. Using an allogeneic B7+ Epstein-Barr virus- transformed B-cell line as stimulator, we found that addition of a monoclonal antibody (MoAb) to B7 that efficiently blocks B7-CD28 interaction only partially inhibited proliferation and interleukin-2 (IL-2) production in primary and secondary mixed lymphocyte reactions (MLR), whereas the generation of cytotoxic T lymphocytes (CTL) was not affected. Inhibition of primary or secondary MLR-induced T-cell activation with cyclosporin A (CsA) at nontoxic concentrations also was never complete. However, the combination of CsA and anti-B7 MoAb B7–24 synergistically blocked allogeneic B cell-induced T-cell proliferation, IL-2 production, and CTL generation. These data suggest that the mere blockage of B7-CD28 interaction during allotransplantation will be insufficient to prevent rejection or graft-versus-host disease. However, low CsA concentrations, when combined with an agent blocking B7-CD28 interaction, can potentially achieve complete immunosuppression.
Integrated optical sigma‐delta modulators (1996)

Abstract : Modern avionics equipment, such as super resolution direction-finding systems, now require resolutions on the order of 20 to 22 bits. Oversampled analog-to-digital converter architectures offer a means of exchanging resolution in time for that in amplitude and represent an attractive approach to implementing precision converters without the need for complex precision analog circuits. Using oversampling techniques based on sigma-delta modulation, a convenient tradeoff exists between sampling rate and resolution. One of the major advantages of integrated optics is the capability to efficiently couple wideband signals into the optical domain. Typically, sigma-delta processors require simple and relatively low-precision analog components and thus are well suited to integrated optical implementations. This thesis reviews the current sigma-delta methodology, the advantages of optical integrated circuits and presents the design of a second-order, integrated optical sigma-delta modulator. Simulation results for both a first and second order architecture are presented by evaluating the transfer characteristics numerically. Design parameters such as limit cycles are quantified and explained. Performance issues and future efforts are also considered. (AN)
Dronedarone for Atrial Fibrillation — An Odyssey (2009)

On March 18, 2009, the Cardiovascular and Renal Drugs Advisory Committee of the Food and Drug Administration (FDA) convened to determine whether the antiarrhythmic drug dronedarone should be approved for the reduction of cardiovascular morbidity and mortality among patients with atrial fibrillation or atrial flutter. It has been 10 years since the FDA approved dofetilide, the last antiarrhythmic drug for suppression of atrial fibrillation to reach the U.S. market. Because of an increased risk of torsades de pointes, particularly at the initiation of therapy, dofetilide's label includes a requirement that therapy be initiated in the hospital and monitored by a . . .
Improvements in Phrase-Based Statistical Machine Translation (2004)

Primary biliary cirrhosis (PBC) tends to affect females more than males. PBC selectively damages intrahepatic small bile ducts, particularly interlobular bile ducts. The clinical presentation of PBC has changed according to recent advances in clinicobiological diagnosis and improvements in therapeutic effects and prognosis. In particular, we encounter PBC patients with hepatocellular carcinoma (HCC), and the number of these patients appears to have increased. The precise reason for the increased number of PBC patients with HCC in recent decades remains unknown, but recognizing the current status of carcinogenesis in PBC patients, identifying the associated clinicopathological risk factors and understanding how the pathogenesis of PBC is directly associated with HCC, is important. In this review, we summarize the data from two nationwide surveys undertaken in Japan as well as recent data from Japanese and international studies.