gebhart/patrepeval huggingface dataset:
Osteopontin influences the invasiveness of pancreatic cancer cells and is increased in neoplastic and inflammatory conditions (2005)

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive malignancies, with an overall 5-year survival rate of less than 5%. Invasive tumor growth and early metastasis are two important reasons for this dismal prognosis. Osteopontin (OPN) is a secretory protein with a variety of functions, for example in cell adhesion and migration, inflammatory reaction and apoptosis. In this study the functional role of OPN in human pancreatic cancer and its potential use as a disease marker were analyzed. By real time quantitative PCR, there was a 2.2-fold and 1.6-fold increase of OPN mRNA in pancreatic cancers (n = 23) and chronic pancreatitis samples (n = 22), respectively, compared to normal pancreatic tissues (n = 20). Immunohistochemical analysis demonstrated OPN staining in 60% of the primary pancreatic tumors and in 72% of the lymph node and liver metastases. ELISA analysis of serum samples obtained from pancreatic cancer patients (n = 70), chronic pancreatitis patients (n = 12), and healthy donors (n = 20) showed a 1.6-fold increase in OPN serum levels in patients with tumors and a 1.9-fold increase in patients with chronic pancreatitis. Recombinant human OPN significantly increased the invasiveness of pancreatic cancer cells, without having any impact on cell proliferation. In addition, down regulation of OPN by specific siRNA molecules decreased pancreatic cancer cell invasion. In conclusion, OPN serum levels in pancreatic cancer and chronic pancreatitis patients are not significantly different, thereby restricting its role as a prognostic or follow-up marker. Our results do suggest, however, that blockade of OPN might be useful as a therapeutic approach to inhibit invasion and metastasis of pancreatic cancer cells.
Haemodynamic and pulse wave responses to intravenous infusions of angiotensin II during chronic telmisartan therapy in normal volunteers (2003)

Telmisartan effectively blocked the effects of intravenous Ang II on CI, BP, RI and SI in healthy volunteers. Changes in CI make a major contribution to increase in BP response to intravenous Ang II in normal volunteers.
Phase I and pharmacologic study of intermittent twice-daily oral therapy with capecitabine in patients with advanced and/or metastatic cancer. (1998)

Capecitabine is a tolerable oral outpatient therapy that shows promising clinical activity in a variety of cancers. The recommended phase II dose is 2,510 mg/m2 daily administered by this intermittent schedule.
A Viscous Flow Model to Explain the Appearance of High Density Thermal SiO2 at Low Oxidation Temperatures (1982)

Higher density results from the thermal oxidation of Si in dry at lower oxidation temperatures. More than 3% higher density is observed for grown at 600°C as compared with 1150°C. A consistent model for the formation of this material is deduced based on the following: the temperature dependence of the density, the annealing behavior of the higher density , and on the literature and new measurements of the intrinsic stress in films. The model considers viscous flow of a Maxwell solid and hinges on the attainment of the necessary free volume for oxidation at lower oxidation temperatures.
Cytoplasmic Accumulation of p53 Protein: an Independent Prognostic Indicator in Colorectal Adenocarcinomas (1994)

Cytoplasmic p53CM1 accumulation may be a useful indicator of patients at high risk for disease recurrence who may benefit from aggressive adjuvant therapy.
The geometric and spatial constraints of the microenvironment induce oligodendrocyte differentiation (2008)

The oligodendrocyte precursor cell (OPC) arises from the subventricular zone (SVZ) during early vertebrate development to migrate and proliferate along axon tracts before differentiating into the myelin-forming oligodendrocyte. We demonstrate that the spatial and temporal regulation of oligodendrocyte differentiation depends intimately on the axonal microenvironment and the density of precursor cells along a specified axonal area. Differentiation does not require dynamic axonal signaling, but instead is induced by packing constraints resulting from intercellular interactions. Schwann cells and even artificial beads bound to the axonal surface can mimic these constraints and promote differentiation. Together, these results describe the coordinately controlled biophysical interaction of oligodendrocyte precursors within an axonal niche leading to self-renewal and differentiation.
Integrated src kinase and costimulatory activity enhances signal transduction through single-chain chimeric receptors in T lymphocytes (2001)

Adoptive immunotherapy using receptor-modified T lymphocytes has shown promise in preclinical studies for the treatment of infectious and malignant diseases. These modified T cells express chimeric receptors that link ligand recognition and signal transduction domains in a single gene product. Typically, a single chain Fv fragment is genetically attached to the cytoplasmic domain of the T-cell receptor (TCR) zeta chain. Modulating the signaling characteristics of chimeric receptors will be important for their application to human immunotherapy. It was hypothesized that linking coreceptor and costimulatory signaling motifs together with the zeta signaling domain will enhance receptor function. The present study compares signaling characteristics of 9 single-chain receptors consisting of the H-2K(b) extracellular and transmembrane domains and various combinations of T cell signal transduction domains. Signal transduction regions studied include the TCR zeta chain, the CD4 coreceptor, the lck protein tyrosine kinase, and the CD28 costimulatory receptor. Biochemical characteristics of the receptors, analyzed using calcium flux, receptor, and ZAP-70 phosphorylation, and lck association may be predicted from the known functions of receptor constituents. The combination of zeta together with coreceptor and costimulatory function in a single receptor maximizes chimeric receptor sensitivity and potency. Combining zeta with either the costimulatory or coreceptor function independently also enhances receptor function, though to a lesser extent. It is therefore possible to link TCR, coreceptor, and costimulatory activities in a single functional entity using modular domains. Such receptors demonstrate distinct signaling properties and should prove useful in the development of chimeric receptors for therapeutic purposes.
Activation of an imprinted allele of the insulin-like growth factor II gene implicated in rhabdomyosarcoma. (1994)

The insulin-like growth factor II (IGF2) gene is exclusively silent at the maternal allele in the mouse as well as in normal human tissues and is expressed at a high level in rhabdomyosarcoma (RMS). We report here that the normally imprinted allele of the IGF2 gene is activated in RMS tumors as well as in one RMS cell line. Since overexpression of IGF2 has been shown to be important in the pathogenesis of RMS, our data suggest that loss of imprinting (LOI) may lead to overexpression of IGF2 and play an important role in the onset of RMS. Furthermore, embryonal RMS usually has loss of heterozygosity (LOH) with paternal disomy of the IGF2 locus. One informative embryonal RMS tumor evaluated in this study was heterozygous at the IGF2 allele and had LOI, raising the possibility that LOI may be the functional equivalent of LOH in this tumor with both events leading to overexpression of IGF2.
Clinical Experience with Famciclovir against Hepatitis B Virus (1997)

Famciclovir (FCV, the oral form of penciclovir, PCV) is a potent antiviral agent of hepatitis B virus (HBV) and is currently in phase III clinical trials. In this review, we examine the outcome of FCV treatment in preventing recurrent HBV in patients post transplantation. Resistance to FCV has now been documented in this setting, in which reduced sensitivity to FCV was associated with mutations upstream from the conserved 'YMDD' motif in the HBV polymerase gene. These mutations are in a region which has been designated as the B domain in RNA-dependent polymerases. To understand these mutations we have developed a model of the catalytic regions of the HBV polymerase and located mutations selected during antiviral treatment on this model.
Angoisse et processus de somatisation (2011)

Résumé À partir d’une réflexion confrontant les travaux de Winnicott à ceux des psychosomaticiens de l’Ecole de Paris, l’auteur défend l’hypothèse que les modalités de fonctionnement fréquemment rencontrées chez les patients somatisants sont en relation avec des modalités de défense radicales contre des angoisses de nature psychotique.
Study of the Relationship Between Glucose and Insulin Responses to an Oral Glucose Load in Man (1968)

Oral glucose tolerance tests have been performed on 125 patients, and the ensuing changes in plasma glucose and insulin concentrations have been measured. The possible effects of factors which could modify the nature of these responses (obesity, age, sex, family history of diabetes, and indications for performing the tolerance test) have been extensively evaluated. None of these variables were found to have a statistically significant effect on the plasma glucose and insulin responses. Two general relationships between glucose and insulin responses have been defined within the population studied. One, based on the quantitative aspects of the glucose and insulin responses, indicated that there was at first an increase, and then, a decrease in the insulin response to progressive degrees of hyperglycemia. The second relationship was independent of the absolute concentrations of either glucose and insulin, and states that the pattern of glucose response during the three hours of the tolerance test determines the pattern of the insulin response during this same time interval.
A Mechanistic Study to Assess Whether Isoproterenol Can Reverse the Negative Chronotropic Effect of Fingolimod (2008)

The sphingosine-1-phosphate receptor modulator fingolimod (FTY720) elicits a negative chronotropic effect at treatment initiation that attenuates thereafter. The authors determined whether isoproterenol can counteract this effect. In this randomized, crossover study, 14 healthy subjects received 5 infusions of isoproterenol (titrated to increase heart rate to 100-120 bpm) or intravenous placebo. The first infusion was 2 hours before and the other 4 infusions were between 3 and 6 hours after a 5-mg oral dose of fingolimod. Telemetry and pharmacokinetic data were collected for 24 hours. During isoproterenol infusion 1 (before fingolimod administration), heart rate was increased 80% from preinfusion 68 +/- 9 bpm to a maximum 122 +/- 15 bpm. Administration of fingolimod decreased heart rate from 73 +/- 11 bpm predose to a nadir of 57 +/- 8 bpm. The subsequent isoproterenol infusion 2 in the presence of fingolimod increased mean heart rate by 85% to a maximum 105 +/- 21 bpm. A 41% higher total isoproterenol dose was needed to increase heart rate to the target range with fingolimod (97 +/- 6 mcg) compared with isoproterenol alone (69 +/- 27 mcg). Isoproterenol infusions 3 to 5 had similar effects on heart rate as infusion 2. Fingolimod had no significant influence on blood pressure responses to isoproterenol. Isoproterenol did not alter the pharmacokinetics of fingolimod. The pure beta-agonist isoproterenol can reverse the heart rate reduction that occurs transiently after initiating fingolimod treatment.
The 69-kDa 2-5A synthetase is composed of two homologous and adjacent functional domains. (1992)

The existence of three distinct forms of 2-5A synthetase, p40-p46, p69, and p100, has been established in interferon-treated human cells. The expression of these enzymes varies according to the cell type studied, and their properties are relatively different. By the use of polyclonal antibodies specific to p69, we have cloned several cDNAs which identify four interferon-induced RNAs of 5.7, 4.5, 3.7, and 3.2 kilobases (kb). Analysis of the nucleotide sequence of three full-length cDNAs (5.6, 3.1, and 2.9 kb) revealed that they have a common open reading frame of 683 amino acids with different 3' termini; cDNAs 5.6 and 3.1 have an extension of 4 amino acids, whereas cDNA 2.9 has an extension of 44 amino acids. In vitro transcription-translation of cDNAs 3.1 and 2.9 kb generated proteins of 69 and 71 kDa, respectively. Both proteins bind a monoclonal antibody specific for p69 and can synthesize 2-5A. The deduced amino acid sequence of p69 revealed that it can be divided into two homologous and adjacent domains, each sharing strong homology to the first 346 amino acids common to the two isoforms of the small 2-5A synthetase (p40, p46). These results suggest that p69 might have two functional catalytic domains required for 2-5A synthetase activity and favor the hypothesis that its gene might have derived from the fusion of two ancestral genes analogous to the small 2-5A synthetase gene.
Induction of iron regulated proteins during normal growth of Neisseria meningitidis in a chemically defined medium (1994)

The expression of iron regulated proteins (IRPs) in vitro has been obtained in the past by adding iron chelators to the culture after bacterial growth, in the presence of an organic iron source. We have investigated aspects concerning full expression of the meningococcal IRPs during normal growth, in defined conditions using Catlin medium, Mueller Hinton and Tryptic Soy Broth (TSB). The expression of IRPs varied between different strains with respect to Ethylenediamine Di-ortho-Hidroxy-phenyl-acetic acid (EDDA) concentrations, and according to culture medium, and also between different lots of TSB. For each strain, a specific set of IRPs were expressed and higher EDDA concentrations, or addition of glucose, or use of different culture media did not resulted in a differential expression of IRPs. We were not able to grow N. meningitidis under normal growth conditions using Desferal. We looked for a good yield of outer membrane vesicles (OMVs) expressing IRPs in iron-deficient Catlin medium containing EDDA and Hemin. Culture for 32 h at 30 degrees C after growing for 16 h at 37 degrees C supported good bacterial growth. Bacterial lysis was noted after additional 24 h at 30 degrees C. Approximately 4 times more OMVs was recoverable from a culture supernatant after 24 h at 30 degrees C than from the cells after 16 h at 37 degrees C. The IRP were as well expressed in OMVs from culture supernatant obtained after 24 h at 30 degrees C as from the cells after 16 h at 37 degrees C.
fur gene expression as a discriminating marker for small cell and nonsmall cell lung carcinomas. (1987)

The recently discovered fur gene encodes a membrane-associated protein with a recognition function. To further characterize the gene, we studied its expression by Northern blot analysis using poly(A)-selected RNA from a variety of organs of African green monkey and rat. The fur gene appeared to be differentially expressed, relatively high levels of fur mRNA being present in specimens of liver and kidney, low levels in brain, spleen, and thymus, and very low levels in heart muscle, lung, and testis. mRNA levels in specimens of human lung tissue without neoplastic lesions were also very low. Similar analyses of primary human lung carcinomas of different histopathological types revealed a highly selective and strong elevation of fur expression in nonsmall cell lung carcinomas, but not in small cell lung carcinomas. These results indicate that fur expression can be used to discriminate between these two types of human lung cancer.
Impaired glucose homeostasis, neutrophil trafficking and function in mice lacking the glucose-6-phosphate transporter (2003)

Glycogen storage disease type Ib (GSD-Ib) is caused by a deficiency in the glucose-6-phosphate transporter (G6PT). In addition to disrupted glucose homeostasis, GSD-Ib patients have unexplained and unexpected defects in neutrophil respiratory burst, chemotaxis and calcium flux, in response to the bacterial peptide f-Met-Leu-Phe, as well as intermittent neutropenia. We generated a G6PT knockout (G6PT-/-) mouse that mimics all known defects of the human disorder and used the model to further our understanding of the pathogenesis of GSD-Ib. We demonstrate that the neutropenia is caused directly by the loss of G6PT activity; that chemotaxis and calcium flux, induced by the chemokines KC and macrophage inflammatory protein-2, are defective in G6PT-/- neutrophils; and that local production of these chemokines and the resultant neutrophil trafficking in vivo are depressed in G6PT-/- ascites during an inflammatory response. The bone and spleen of G6PT-/- mice are developmentally delayed and accompanied by marked hypocellularity of the bone marrow, elevation of myeloid progenitor cell frequencies in both organs and a corresponding dramatic increase in granulocyte colony stimulating factor levels in both GSD-Ib mice and humans. So, in addition to transient neutropenia, a sustained defect in neutrophil trafficking due to both the resistance of neutrophils to chemotactic factors, and reduced local production of neutrophil-specific chemokines at sites of inflammation, may underlie the myeloid deficiency in GSD-Ib. These findings demonstrate that G6PT is not just a G6P transport protein but also an important immunomodulatory protein whose activities need to be addressed in treating the myeloid complications in GSD-Ib patients.
Structural glycobiology: A game of snakes and ladders (2008)

Oligo- and polysaccharides are infamous for being extremely flexible molecules, populating a series of well-defined rotational isomeric states under physiological conditions. Characterization of this heterogeneous conformational ensemble has been a major obstacle impeding high-resolution structure determination of carbohydrates and acting as a bottleneck in the effort to understand the relationship between the carbohydrate structure and function. This challenge has compelled the field to develop and apply theoretical and experimental methods that can explore conformational ensembles by both capturing and deconvoluting the structural and dynamic properties of carbohydrates. This review focuses on computational approaches that have been successfully used in combination with experiment to detail the three-dimensional structure of carbohydrates in a solution and in a complex with proteins. In addition, emerging experimental techniques for three-dimensional structural characterization of carbohydrate-protein complexes and future challenges in the field of structural glycobiology are discussed. The review is divided into five sections: (1) The complexity and plasticity of carbohydrates, (2) Predicting carbohydrate-protein interactions, (3) Calculating relative and absolute binding free energies for carbohydrate-protein complexes, (4) Emerging and evolving techniques for experimental characterization of carbohydrate-protein structures, and (5) Current challenges in structural glycoscience.
The Watson speech recognition engine (2002)

In 1995, AT&T Research (then within Bell Labs) began work on a software-only automated speech recognition system named Watson(TM). The goal was ambitious; Watson was to serve as a single code base supporting applications ranging from PC-desktop command and control through to scaleable telephony interactive voice services. Furthermore, the software was to be the new code base for the research group, allowing fast deployment of new algorithmic advances from the lab into the field. A set of C++ objects has been developed which support these objectives. This paper gives an overview of the Watson automatic speech recognizer software architecture, describes the algorithms employed, and provides performance numbers for some sample tasks.
Role of CC Chemokines Subfamily in the Platinum Drugs Resistance Promotion in Cancer (2020)

Cancer is a significant medical issue, being one of the main causes of mortality around the world. The therapies for this pathology depend on the stage in which the cancer is found, but it is usually diagnosed at an advanced stage in which the treatment is chemotherapy. Platinum drugs are among the most commonly used in therapy, unfortunately, one of the main obstacles to this treatment is the development of chemoresistance, which is the ability of cancer cells to evade the effects of drugs. Although some molecular mechanisms involved in resistance to platinum drugs are described, elucidation is still required of others. Secretion of inflammatory mediators such as cytokines and chemokines, by tumor microenvironment components or tumor cells, show direct influence on proliferation, metastasis and progression of cancer and are related to chemoresistance and poor prognosis. In this review, the general mechanisms associated with resistance to platinum drugs, inflammation on cancer development and chemoresistance in various types of cancer will be approached with special emphasis on the current history of CC chemokines subfamily-mediated chemoresistance.
A Conserved Gly436-Trp-Leu-Ala-Gly-Leu-Phe-Tyr Motif in Hepatitis C Virus Glycoprotein E2 Is a Determinant of CD81 Binding and Viral Entry (2006)

The hepatitis C virus (HCV) glycoproteins E1 and E2 form a heterodimer that mediates CD81 receptor binding and viral entry. In this study, we used site-directed mutagenesis to examine the functional role of a conserved G436WLAGLFY motif of E2. The mutants could be placed into two groups based on the ability of mature virion-incorporated E1E2 to bind the large extracellular loop (LEL) of CD81 versus the ability to mediate cellular entry of pseudotyped retroviral particles. Group 1 comprised E2 mutants where LEL binding ability largely correlated with viral entry ability, with conservative and nonconservative substitutions (W437 L/A, L438A, L441V/F, and F442A) inhibiting both functions. These data suggest that Trp-437, Leu-438, Leu-441, and Phe-442 directly interact with the LEL. Group 2 comprised E2 glycoproteins with more conservative substitutions that lacked LEL binding but retained between 20% and 60% of wild-type viral entry competence. The viral entry competence displayed by group 2 mutants was explained by residual binding by the E2 receptor binding domain to cellular full-length CD81. A subset of mutants maintained LEL binding ability in the context of intracellular E1E2 forms, but this function was largely lost in virion-incorporated glycoproteins. These data suggest that the CD81 binding site undergoes a conformational transition during glycoprotein maturation through the secretory pathway. The G436P mutant was an outlier, retaining near-wild-type levels of CD81 binding but lacking significant viral entry ability. These findings indicate that the G436WLAGLFY motif of E2 functions in CD81 binding and in pre- or post-CD81-dependent stages of viral entry.
Inducing All Steps of a Chemical Reaction with the Scanning Tunneling Microscope Tip: Towards Single Molecule Engineering (2000)

All elementary steps of a chemical reaction have been successfully induced on individual molecules with a scanning tunneling microscope (STM) in a controlled step-by-step manner utilizing a variety of manipulation techniques. The reaction steps involve the separation of iodine from iodobenzene by using tunneling electrons, bringing together two resultant phenyls mechanically by lateral manipulation and, finally, their chemical association to form a biphenyl molecule mediated by excitation with tunneling electrons. The procedures presented here constitute an important step towards the assembly of individual molecules out of simple building blocks in situ on the atomic scale.