gebhart/patrepeval huggingface dataset:
Overexpression of B7-H1 correlates with malignant cell proliferation in pancreatic cancer (2013)

B7-H1, a member of the B7 family of proteins, is hypothesised to play an important role in the immune escape of tumours through its binding to the PD-1 receptor on activated T and B cells. By inducing T lymphocyte apoptosis, tumour cells can suppress an effective antitumour immune response. Although the immunosuppressive effect of B7-H1 has been studied in many tumours, its other biological functions remain unclear. We previously demonstrated a high expression level of this molecule in pancreatic cancer patient samples and its antiapoptotic effect in pancreatic ductal adenocarcinoma (PDA) cells. The aim of the present study was to investigate the possible role of B7-H1 in the proliferation of PDA cells. Functional studies were performed using pancreatic cell lines that were genetically engineered to express high or low levels of B7-H1, and we found that the overexpression of B7-H1 through plasmid transfection in PDA cells promoted cell proliferation. Conversely, the short-hairpin RNA (shRNA) knockdown of B7-H1 inhibited PDA cell proliferation. Further analyses of the cell cycle and cell cycle-related molecules confirmed this result. Taken together, our results indicate that the upregulation of B7-H1 in pancreatic cancer cells promotes proliferation and accelerates carcinogenesis; these data, therefore, provide insights into the effects of B7-H1 overexpression on pancreatic tumour cells.
Virus-specific CD8+T cell numbers are maintained during γ-herpesvirus reactivation in CD4-deficient mice (1998)

The murine gamma-herpesvirus 68 replicates in epithelial sites after intranasal challenge, then persists in various cell types, including B lymphocytes. Mice that lack CD4(+) T cells (I-Ab-/-) control the acute infection, but suffer an ultimately lethal recrudescence of lytic viral replication in the respiratory tract. The consequences of CD4(+) T cell deficiency for the generation and maintenance of murine gamma-herpesvirus 68-specific CD8(+) set now have been analyzed by direct staining with viral peptides bound to major histocompatibility complex class I tetramers and by a spectrum of functional assays. Both acutely and during viral reactivation, the CD8(+) T cell responses in the I-Ab-/- group were no less substantial than in the I-Ab+/+ controls. Indeed, virus-specific CD8(+) T cell numbers were increased in the lymphoid tissue of clinically compromised I-Ab-/- mice, although relatively few of the potential cytotoxic T lymphocyte effectors were recruited back to the site of pathology in the lung. Thus the viral reactivation that occurs in the absence of CD4(+) T cells was not associated with any exhaustion of the virus-specific cytotoxic T lymphocyte response. It seems that CD8(+) T cells alone are insufficient to maintain long-term control of this persistent gamma-herpesvirus.
Angiogenesis can be stimulated or repressed in vivo by a change in GM3:GD3 ganglioside ratio. (1992)

Formation of new vessels induced by two different angiogenic factors could be stimulated or repressed in the cornea by reduction or enhancement of the GM3:GD3 ratio of tissue gangliosides. Changes in the relative proportion of molecules normally present in adult tissues, like prostaglandin E1, basic fibroblast growth factor, GM3, GD3, were sufficient to modulate or even block angiogenesis.
Liquid biopsy monitoring uncovers acquired RAS-mediated resistance to cetuximab in a substantial proportion of patients with head and neck squamous cell carcinoma (2016)

Resistance to epidermal growth factor receptor (EGFR)-targeted therapy is insufficiently understood in head and neck squamous cell carcinoma (HNSCC), entailing the lack of predictive biomarkers.Here, we studied resistance-mediating EGFR ectodomain and activating RAS mutations by next-generation sequencing (NGS) of cell lines and tumor tissue of cetuximab-naïve patients (46 cases, 12 cell lines), as well as liquid biopsies taken during and after cetuximab/platinum/5-fluorouracil treatment (20 cases). Tumors of cetuximab-naïve patients were unmutated, except for HRAS mutations in 4.3% of patients. Liquid biopsies revealed acquired KRAS, NRAS or HRAS mutations in more than one third of patients after cetuximab exposure. 46% of patients with on-treatment disease progression showed acquired RAS mutations, while no RAS mutations were found in the non-progressive subset of patients, indicating that acquisition of RAS mutant clones correlated significantly with clinical resistance (Chi square p=0.032). The emergence of mutations preceded clinical progression in half of the patients, with a maximum time from mutation detection to clinical progression of 16 weeks.RAS mutations account for acquired resistance to EGFR-targeting in a substantial proportion of HNSCC patients, even though these tumors are rarely mutated at baseline. Liquid biopsies may be used for mutational monitoring to guide treatment decisions.
Reduction of Early Graft Loss After Intraportal Porcine Islet Transplantation in Monkeys (2007)

Although pretransplantation complement depletion or anticoagulation reduces porcine islet xenograft loss significantly, neither alone is sufficient to prevent IBMIR.
The Promyelocytic Leukemia Gene Product (PML) Forms Stable Complexes with the Retinoblastoma Protein (1998)

PML is a nuclear protein with growth-suppressive properties originally identified in the context of the PML-retinoic acid receptor alpha (RAR alpha) fusion protein of acute promyelocytic leukemia. PML localizes within distinct nuclear structures, called nuclear bodies, which are disrupted by the expression of PML-RAR alpha. We report that PML colocalizes with the nonphosphorylated fraction of the retinoblastoma protein (pRB) within nuclear bodies and that pRB is delocalized by PML-RAR alpha expression. Both PML and PML-RAR alpha form complexes with the nonphosphorylated form of pRB in vivo, and they interact with the pocket region of pRB. The regions of PML and PML-RAR alpha involved in pRB binding differ; in fact, the B boxes and the C-terminal region of PML, the latter of which is not present in PML-RAR alpha, are essential for the formation of stable complexes with pRB. Functionally, PML abolishes activation of glucocorticoid receptor-regulated transcription by pRB, whereas PML-RAR alpha further increases it. Our results suggest that PML may be part of transcription-regulatory complexes and that the oncogenic potential of the PML-RAR alpha protein may derive from the alteration of PML-regulated transcription.
Rapid recovery from spinal cord injury after subcutaneously administered polyethylene glycol (2001)

Arguably a seminal event in most trauma and disease is the breakdown of the cell membrane. In most cells, this is first observed as a collapse of the axolemmas barrier properties allowing a derangement of ions to occur, leading to a progressive dissolution of the cell or its process. We have shown that an artificial sealing of mechanically damaged membranes by topical application of hydrophilic polymers such as polyethylene glycol (PEG) immediately restores variable levels of nerve impulse conduction through the lesion. This was documented by a rapid recovery of somatosensory evoked potential (SSEP) conduction, and by recovery of the cutaneous trunchi muscle (CTM) reflex in PEG-treated animals. The CTM reflex is a sensorimotor behavior dependent on an intact (and identified) white matter tract within the ventrolateral funiculus of the spinal cord, and is thus an excellent index of white matter integrity. We show that PEG can be safely introduced into the bloodstream by several routes of administration. Using a fluorescein decorated PEG, we demonstrate that the polymer specifically targets the hemorrhagic contusion of the adult guinea pig spinal cord when administered through the vasculature, but not intact regions of the spinal cord. A single subcutaneous injection (30% weight by weight in sterile saline) made 6 hr after a standardized spinal cord contusion in adult guinea pigs was sufficient to produce a rapid recovery of SSEP propagation through the lesion in only PEG-treated animals, accompanied by a statistically significant recovery of the CTM reflex. These data suggest that parenterally administered PEG may be a novel treatment for not only spinal injury, but head injury and stroke as well.
Noise reduction in muon tomography for detecting high density objects (2013)

The muon tomography technique, based on multiple Coulomb scattering of cosmic ray muons, has been proposed as a tool to detect the presence of high density objects inside closed volumes. In this paper a new and innovative method is presented to handle the density fluctuations (noise) of reconstructed images, a well known problem of this technique. The effectiveness of our method is evaluated using experimental data obtained with a muon tomography prototype located at the Legnaro National Laboratories (LNL) of the Istituto Nazionale di Fisica Nucleare (INFN). The results reported in this paper, obtained with real cosmic ray data, show that with appropriate image filtering and muon momentum classification, the muon tomography technique can detect high density materials, such as lead, albeit surrounded by light or medium density material, in short times. A comparison with algorithms published in literature is also presented
Helix-stabilized cyclic peptides as selective inhibitors of steroid receptor–coactivator interactions (2003)

The interaction between nuclear receptors and coactivators provides an arena for testing whether protein-protein interactions may be inhibited by small molecule drug candidates. We provide evidence that a short cyclic peptide, containing a copy of the LXXLL nuclear receptor box pentapeptide, binds tightly and selectively to estrogen receptor alpha. Furthermore, as shown by x-ray analysis, the disulfide-bridged nonapeptide, nonhelical in aqueous solutions, is able to adopt a quasihelical conformer while binding to the groove created by ligand attachment to estrogen receptor alpha. An i, i+3 linked analog, H-Lys-cyclo(d-Cys-Ile-Leu-Cys)-Arg-Leu-Leu-Gln-NH2 (peptidomimetic estrogen receptor modulator 1), binds with a Ki of 25 nM, significantly better than an i, i+4 bridged cyclic amide, as predicted by molecular modeling design criteria. The induction of helical character, effective binding, and receptor selectivity exhibited by this peptide analog provide strong support for this strategy. The stabilization of minimalist surface motifs may prove useful for the control of other macromolecular assemblies, especially when an amphiphilic helix is crucial for the strong binding interaction between two proteins.
Prediction and Observation of Isostructurality Induced by Solvent Incorporation in Multicomponent Crystals (2006)

The crystal structures of two pharmaceutical molecules-carbamazepine and its 10,11-dihydro derivative-with acetic acid have been successfully predicted by computational methods. While the crystalline structure of the former was known a priori, no structural information was available for the latter. Possible crystal structures were generated in silico before any experimental work was performed. Although the crystal structures of the pure drug molecules are very different, incorporation of acetic acid in their crystal lattices results in isomorphic products.
Memory B cells and CD27. (2000)

Following antigen activation in germinal centers, B cells develop into memory B cells or plasma cells. Triggering via B-cell immunoglobulin receptors by antigens, cytokines and direct cell-to-cell contact by B and T cells plays an important role in the B cell differentiation into memory or plasma cells. Adult human peripheral blood B cells are separated into three subtypes by the expression of IgD and CD27, which belong to the tumor necrosis factor receptor (TNFR) family: IgD+ CD27- naive B cells, IgD+ CD27+ and IgD- CD27+ B cells. CD27+ B cells are larger cells with abundant cytoplasm carrying somatic hypermutation, and have an ability to produce immunoglobulin, indicating that CD27 is a memory marker of B cells. The ligation of CD27 yields crucial signals that positively control the entry of B cells into the pathway to plasma cells. We review observations on subpopulations and differentiation of mature B-cells by T/B cell interaction via CD27/CD70 as compared with CD40/CD154 interaction, and discuss about memory B cells.
On the termination of ingestive behaviour by the medicinal leech (1987)

Hungry leeches, Hirudo medicinalis, ingest blood meals averaging 890% of their mass in 29 min. Ingestion is terminated as a result of distension of the body: experimentally distending leeches as they feed causes an immediate cessation of ingestion and inhibits any subsequent biting behaviour; if distension is circumvented by various experimental procedures, leech ingestive periods are prolonged significantly. Ingestion is not terminated as a result of fatigue, chemical cues or mass change. Distension also underlies satiation, for removing blood from the crops of recently fed leeches qualitatively alters their satiated behaviour to biting. Biting is not a defensive reaction to injury. In rostral ganglia, impulses of the serotonergic Retzius (RZ) and LL neurones evoke the physiological components of ingestion. Localized warming of the prostomial lip induces impulses in these large effector neurones. Distending the body wall tonically hyperpolarizes the RZ and LL cells. This inhibitory response to distension is conducted from the mid-body to the anterior neurones via the ventral nerve cord. Distensive inhibition antagonizes the synaptic excitation evoked in RZ and LL neurones by thermal stimulation. Thus, a stimulus which evokes feeding synaptically excites 5-HT neurones and a stimulus which terminates ingestion inhibits them. The integration of these inputs controls the expression of leech feeding behaviour and these connections match precisely a model proposed to regulate the ingestive behaviour of blowflies.
Intranasal monoclonal immunoglobulin A against respiratory syncytial virus protects against upper and lower respiratory tract infections in mice (1994)

The role of secretory antibody in protection against respiratory syncytial virus (RSV) infection was examined by using monoclonal immunoglobulin A (IgA) antibody for intranasal passive immunization of mice. Eight anti-RSV IgA hybridomas were produced by fusing myeloma cells with lung lymphocytes from RSV-immunized mice. Five IgA antibodies recognized RSV strains of both the A and the B subgroups, and two of these neutralized virus in a plaque reduction assay. Monoclonal IgA antibody HNK20, which bound to F glycoprotein, was most effective, reducing plaques by 50% at a concentration of 0.1 microgram/ml for both subgroup A and subgroup B strains. HNK20 also neutralized all of eight clinical isolates of RSV tested. When delivered intranasally to mice 24 h prior to RSV challenge, HNK20 reduced virus titers in the lungs by nearly 100-fold. Maximal protection occurred at a dose of 0.5 mg/kg of body weight. Significant protection against lung infection was seen when the interval between antibody treatment and challenge was as long as 72 h. HNK20 also decreased virus titers in the nose approximately 10-fold when given 1 h, but not 24 h, before challenge. When mice were treated with HNK20 intranasally 3 days after challenge, viral titers were reduced in the lungs but not the nose. The results indicate that topical application of relatively small amounts of monoclonal IgA can protect against both upper and lower respiratory tract infections caused by RSV.
Preparation, characterization, and immunogenicity of meningococcal immunotype L2 and L3,7,9 phosphoethanolamine group-containing oligosaccharide-protein conjugates (1991)

A method was developed for the well-defined coupling of phosphoethanolamine group (PEA)- and carboxylic acid group-containing polysaccharides and oligosaccharides to proteins without the need for extensive modification of the carbohydrate antigens. The carboxylic acid group of the terminal 2-keto-3-deoxyoctulosonic acid moiety was utilized to introduce a thiol function in meningococcal immunotype L2 and L3,7,9 lipopolysaccharide-derived oligosaccharides. The thiol group-containing oligosaccharides were subsequently coupled to bromoacetylated proteins. Immunotype L2 and L3,7,9 PEA group-containing oligosaccharide-tetanus toxoid conjugates were prepared, and their immunogenicities were studied in rabbits. Both the immunotype L2 and immunotype L3,7,9 conjugates evoked high immunoglobulin G (IgG) antibody titers after the first booster injection. These conjugates also displayed an ability to induce long-lasting IgG antibody levels which could be detected until 9 months after one booster injection at week 3. The adjuvant Quil A enhanced the immune response to all the conjugates to a minor extent, which is in contrast with reported adjuvant effects of Quil A on these types of antigens in mice. A conjugate prepared from the dephosphorylated L3,7,9 oligosaccharides evoked a significantly lower IgG response than a similar PEA-containing conjugate, and enzyme-linked immunosorbent assay inhibition studies indicated a different epitope specificity. Furthermore, antisera elicited with the complete bacteria contained antibodies directed against PEA-containing epitopes, which stresses the importance of the presence of unmodified PEA groups in meningococcal lipopolysaccharide-derived oligosaccharide-protein conjugates. The procedure developed offers an elegant solution for the specific coupling of meningococcal PEA-containing oligosaccharides to proteins and may therefore be a very useful tool in the development of a vaccine against group B meningococci.
Rapid Prenatal Diagnosis of Trisomy 21 by Real-time Quantitative Polymerase Chain Reaction with Amplification of Small Tandem Repeats and S100B in Chromosome 21 (2005)

Trisomy 21 (Down syndrome) is the most common congenital anomaly, and it occurs in one out of 700-1000 births. Current techniques such as amniocentesis and chorionic villi sampling (CVS) require lengthy laboratory culture procedures and high costs. This study was undertaken to establish a rapid prenatal diagnosis of trisomy 21 using real-time quantitative polymerase chain reaction (PCR) of fetal DNA from amniotic fluid. Real-time quantitative PCR was performed with DNA templates obtained from 14 normal blood samples, 10 normal amniotic fluid samples, 14 Down syndrome blood samples, and 7 Down syndrome amniotic fluid samples. Primers for D21S167 and S100B of chromosome 21 were used. Primers that direct the amplification of the 165-bp fragment of the insulin-like growth factor (IGF)-1 gene on chromosome 12 using a PCR primer were included to generate an internal standard for quantitation. The relative levels of D21S167 and S100B were 2.6 and 2.4 times higher in the blood of Down syndrome patients than those in the control group. The differences between these two groups were statistically significant (p-values were 0.0012 and 0.0016, respectively). The relative levels of D21S167 and S100B were 2.1 and 2.7 times higher in the amniotic fluid of Down syndrome fetuses than those in the control group. The difference between these two groups was statistically significant (p-values were 0.0379 and 0.0379, respectively). Prenatal diagnosis of trisomy 21 by real-time quantitative PCR using STR (small tandem repeats) amplification of D21S167 and S100B is a useful, accurate and rapid diagnostic method. Furthermore, it may also be useful for prenatal diagnosis with fetal DNA from maternal blood, and for preimplantation genetic diagnosis and prenatal counseling.
The emerging distinct role of TNF-receptor 2 (p80) signaling in chronic inflammatory disorders. (2002)

Tumor necrosis factor alpha (TNF-alpha) is a pleiotropic cytokine with strong proinflammatory and immunomodulatory properties. TNF-alpha plays a critical role in many acute or chronic inflammatory diseases and anti-TNF strategies have proven to be clinically effective. Two TNF-specific cell surface receptors, TNF-R1 (p60) and TNF-R2 (p80), have been identified and the function of these receptors and the downstream intracellular signal-transduction pathways have been extensively studied in vitro. For a long time p60 was considered to be the predominant mediator of TNF signaling, whereas p80 was ascribed only an auxilliary function. However, there is increasing clinical and experimental evidence for an important independent role of p80 signaling in chronic inflammatory conditions. To date, most data exist for Crohn's disease. Upregulation of p80 and increased p80 signaling aggravates experimental colitis and is likely to contribute to the chronicity of inflammation in vivo. Further studies are required to elucidate critically important steps in TNF signaling that might be dysregulated. This will lead to a better understanding of the pathogenesis of these diseases and potentially reveal new, more specific therapeutic targets.
Amélioration de codecs audio standardisés avec maintien de l'interopérabilité (2016)

Résumé : L’audio numérique s’est déployé de façon phénoménale au cours des dernières décennies, notamment grâce à l’établissement de standards internationaux. En revanche, l’imposition de normes introduit forcément une certaine rigidité qui peut constituer un frein à l’amélioration des technologies déjà déployées et pousser vers une multiplication de nouveaux standards.&#13;\n Cette thèse établit que les codecs existants peuvent être davantage valorisés en améliorant leur qualité ou leur débit, même à l’intérieur du cadre rigide posé par les standards établis. Trois volets sont étudiés, soit le rehaussement à l’encodeur, au décodeur et au niveau du train binaire. Dans tous les cas, la compatibilité est préservée avec les éléments existants. Ainsi, il est démontré que le signal audio peut être amélioré au décodeur sans transmettre de nouvelles informations, qu’un encodeur peut produire un signal amélioré sans ajout au décodeur et qu’un train binaire peut être mieux optimisé pour une nouvelle application.&#13;\n En particulier, cette thèse démontre que même un standard déployé depuis plusieurs décennies comme le G.711 a le potentiel d’être significativement amélioré à postériori, servant même de cœur à un nouveau standard de codage par couches qui devait préserver cette compatibilité. Ensuite, les travaux menés mettent en lumière que la qualité subjective et même objective d’un décodeur AAC (Advanced Audio Coding) peut être améliorée sans l’ajout d’information supplémentaire de la part de l’encodeur. Ces résultats ouvrent la voie à davantage de recherches sur les traitements qui exploitent une connaissance des limites des modèles de codage employés. Enfin, cette thèse établit que le train binaire à débit fixe de l’AMR WB+ (Extended Adaptive Multi-Rate Wideband) peut être compressé davantage pour le cas des applications à débit variable. Cela démontre qu’il est profitable d’adapter un codec au contexte dans lequel il est employé.
Studies on the electrical conductivity of carbon black filled polymers (1996)

The conductivity mechanism for a carbon black (CB) filled high-density polyethylene (HDPE) compound was investigated in this work. From the experimental results obtained, it can be seen that the relation between electrical current density (J) and applied voltage across the sample (V) coincides with Simmons's equation (i.e., the electrical resistivity of the compound decreases with the applied voltage, especially at the critical voltage). The minimum electrical resistivity occurs near the glass transition temperature (Tg) of HDPE (198 K). It can be concluded that electron tunneling is an important mechanism and a dominant transport process in the HDPE/CB composite. A new model of carbon black dispersion in the matrix was established, and the resistivity was calculated by using percolation and quantum mechanical theories. © 1996 John Wiley & Sons, Inc.