gebhart/patrepeval huggingface dataset:
Characterization of a Shiga Toxin-Encoding Temperate Bacteriophage of Shigella sonnei (2001)

A Shiga toxin (Stx)-encoding temperate bacteriophage of Shigella sonnei strain CB7888 was investigated for its morphology, DNA similarity, host range, and lysogenization in Shigella and Escherichia coli strains. Phage 7888 formed plaques on a broad spectrum of Shigella strains belonging to different species and serotypes, including Stx-producing Shigella dysenteriae type 1. With E. coli, only strains with rough lipopolysaccharide were sensitive to this phage. The phage integrated into the genome of nontoxigenic S. sonnei and laboratory E. coli K-12 strains, which became Stx positive upon lysogenization. Moreover, phage 7888 is capable of transducing chromosomal genes in E. coli K-12. The relationships of phage 7888 with the E. coli Stx1-producing phage H-19B and the E. coli Stx2-producing phage 933W were investigated by DNA cross-hybridization of phage genomes and by nucleotide sequencing of an 8,053-bp DNA region of the phage 7888 genome flanking the stx genes. By these methods, a high similarity was found between phages 7888 and 933W. Much less similarity was found between phages H-19B and 7888. As in the other Stx phages, a regulatory region involved in Q-dependent expression is found upstream of stxA and stxB (stx gene) in phage 7888. The morphology of phage 7888 was similar to that of phage 933W, which shows a hexagonal head and a short tail. Our findings demonstrate that stx genes are naturally transferable and are expressed in strains of S. sonnei, which points to the continuous evolution of human-pathogenic Shigella by horizontal gene transfer.
Inhibitors of C1q biosynthesis suppress activation of murine macrophages for both antibody-independent and antibody-dependent tumor cytotoxicity. (1990)

The inhibitors of C1q biosynthesis and secretion, 3,4-dehydro-DL-proline (DHP) and 2,2'-dipyridyl, were previously shown to suppress murine macrophage FcR-dependent phagocytosis and cytolysis of IgG-opsonized RBC targets. Inasmuch as non-antibody macrophage activators also bind C1q to initiate C1 activation, we determined the effects of these same inhibitors of C1q biosynthesis on activation of macrophages for antibody-independent, nonspecific tumor cytotoxicity by lipid A and a variety of other non-antibody activators. Preexposure of mouse inflammatory peritoneal macrophages to either DHP (0.5 to 2.5 mM) or 2,2'-dipyridyl (0.1 to 0.3 mM) for 24 h produced a dose-related suppression of their response to activation by lipid A to mediate tumor cytotoxicity of L1210 mouse leukemia targets. Inhibition of C1q secretion by DHP-treated macrophages was confirmed both by a complement hemolytic assay and by autoradiographic analysis of [35S]methionine-labeled culture supernatants. DHP-treated macrophages were inhibited in their response to direct activation and triggering of IFN-gamma-primed macrophages by lipid A, Poly I:C, and cobra venom factor for tumor cytotoxicity. DHP inhibited macrophage activation for antibody-dependent cellular cytotoxicity of L1210 tumor targets mediated by antitumor target IgG. The addition of exogenous purified C1q (2 micrograms/ml) to macrophages after DHP treatment, reconstituted their response to activation for both antibody-independent and antibody-dependent tumor cytotoxicity. Our results indicate that C1q synthesis and secretion by effector macrophages is a prerequisite for the initiation of their activation by both immune complex and by non-antibody agents that also bind C1q. It now appears that macrophage-derived C1q may act as an auxiliary amplification signal for autocrine-like modulation of the initiation of macrophage activation by both the antibody-dependent and independent pathways.
Expression of the epidermal growth factor receptor gene in human brain metastases (1992)

Biopsy specimens of human brain metastases were examined for amplification and expression of the proto-oncogene c-erbB1 (located on chromosome 7) encoding the epidermal growth factor receptor (EGFR). Moreover, the tumour DNA was also examined for amplification of other cancer-related genes on this chromosome: the proto-oncogene c-met, the gene for platelet-derived growth factor A-chain, and the gene for plasminogen activator inhibitory type 1. All 18 brain metastases demonstrated positive binding of biotinylated EGF on cryosections. Three out of 18 metastases had amplification of the EGFR gene; the other chromosome-7 genes tested were not amplified. Thus, an increased EGFR gene expression seems to be a general finding in a wide range of carcinomas metastatic to the brain, whereas we found only occasional selective EGFR gene amplifications in single cases.
Structural Insights into the Interactions between Platelet Receptors and Fibrillar Collagen (2009)

Collagen peptides have been used to identify binding sites for several important collagen receptors, including integrin alpha(2)beta(1), glycoprotein VI, and von Willebrand factor. In parallel, the structures of these collagen receptors have been reported, and their interactions with collagen peptides have been studied. Recently, the three-dimensional structure of the intact type I collagen fiber from rat tail tendon has been resolved by fiber diffraction. It is now possible to map the binding sites of platelet collagen receptors onto the intact collagen fiber in three dimensions. This minireview will discuss these recent findings and their implications for platelet activation by collagen.
Advances in quantification and characterization of telomerase activity by the telomeric repeat amplification protocol (TRAP) (1997)

The telomeric repeat amplification protocol (TRAP) assay has been used to test telomerase activity in numerous cancer specimens. We describe primers, controls and quantification methods for the TRAP assay to accurately measure the level of telomerase activity in clinical samples. The assay is reliable and reproducible in routine analyses and can be used to estimate the processivity of telomerase activity.
Long-Term Treatment with Potassium Citrate and Renal Stones in Medullary Sponge Kidney (2010)

Treatment with KC is effective in preventing renal stones in the typical patient with MSK. It seems that two clinical phenotypes among patients showing typical MSK features during radiologic study exist.
Neuritic Transport of Herpes Simplex Virus in Rat Sensory Neurons in vitro. Effects of Substances Interacting with Microtubular Function and Axonal Flow [Nocodazole, Taxol and Erythro-9-3-(2-hydroxynonyl)adenine] (1986)

Herpes simplex virus type 1 and a fluorescein-labelled lectin (wheat germ agglutinin) were selectively transported to nerve cell bodies located in the inner compartment of a two-chamber tissue culture system after the application of virus or lectin to the neuritic processes in the outer culture compartment. Taxol, which stabilizes and alters intracellular arrangements of microtubules, and nocodazole, which disrupts microtubules, both inhibited this retrograde axonal transport of viral particles and lectin. The transport was also inhibited by erythro-9-3-(2-hydroxynonyl)adenine (EHNA), which blocks ATPases. However, EHNA was also an effective inhibitor of infection with the virus in non-neuronal cells (GMK AH-1). The nature of the action(s) of EHNA on neuritic transport of the virus is therefore less clear.
Towards a Better Gold Standard (2018)

Emotions are often perceived by humans through a series of multimodal cues, such as verbal expressions, facial expressions and gestures. In order to recognise emotions automatically, reliable emotional labels are required to learn a mapping from human expressions to corresponding emotions. Dimensional emotion models have become popular and have been widely applied for annotating emotions continuously in the time domain. However, the statistical relationship between emotional dimensions is rarely studied. This paper provides a solution to automatic emotion recognition for the Audio/Visual Emotion Challenge (AVEC) 2018. The objective is to find a robust way to detect emotions using more reliable emotion annotations in the valence and arousal dimensions. The two main contributions of this paper are: 1) the proposal of a new approach capable of generating more dependable emotional ratings for both arousal and valence from multiple annotators by extracting consistent annotation features; 2) the exploration of the valence and arousal distribution using outlier detection methods, which shows a specific oblique elliptic shape. With the learned distribution, we are able to detect the prediction outliers based on their local density deviations and correct them towards the learned distribution. The proposed method performance is evaluated on the RECOLA database containing audio, video and physiological recordings. Our results show that a moving average filter is sufficient to remove the incidental errors in annotations. The unsupervised dimensionality reduction approaches could be used to determine a gold standard annotations from multiple annotations. Compared with the baseline model of AVEC 2018, our approach improved the arousal and valence prediction of concordance correlation coefficient significantly to respectively 0.821 and 0.589.
Identification of human cancers deficient in antigen processing. (1993)

Intracellular antigens must be processed before presentation to CD8+ T cells by major histocompatibility complex (MHC) class I molecules. Using a recombinant vaccinia virus (Vac) to transiently express the Kd molecule, we studied the antigen processing efficiency of 26 different human tumor lines. Three cell lines, all human small cell lung carcinoma, consistently failed to process endogenously synthesized proteins for presentation to Kd-restricted, Vac-specific T cells. Pulse-chase experiments showed that MHC class I molecules were not transported by these cell lines from the endoplasmic reticulum to the cell surface. This finding suggested that peptides were not available for binding to nascent MHC molecules in the endoplasmic reticulum. Northern blot analysis of these cells revealed low to nondetectable levels of mRNAs for MHC-encoded proteasome components LMP-7 and LMP-2, as well as the putative peptide transporters TAP-1 and TAP-2. Treatment of cells with interferon gamma enhanced expression of these mRNAs and reversed the observed functional and biochemical deficits. Our findings suggest that downregulation of antigen processing may be one of the strategies used by tumors to escape immune surveillance. Potential therapeutic applications of these findings include enhancing antigen processing at the level of the transcription of MHC-encoded proteasome and transporter genes.
A promoter activity is present in the DNA sequence corresponding to the hepatitis C virus 5' UTR (2003)

The hepatitis C virus (HCV) 5' untranslated region (UTR) has been extensively studied with regard to its internal ribosomal entry site (IRES) activity. In this work we present results suggesting the existence of a strong promoter activity carried by the DNA sequence corresponding to the HCV 5' UTR. This activity was not detected when the HCV 5' UTR sequence was replaced by HCV 3' UTR or poliovirus 5' UTR sequences. These results were further confirmed by using bicistronic constructions. We demonstrated the presence of an mRNA initiated in this 5' UTR sequence and located the initiation site by the 5' RACE method at nucleotide 67. Furthermore, northern experiments and flow cytometry analysis showed the unambiguous activity of such a promoter sequence in stably transfected cells. Our results strongly suggest that the data obtained using bicistronic DNA constructs carrying the HCV 5' UTR should be analyzed not only at the translational but also at the transcriptional level.
Concise Review: Apoptotic Cell-Based Therapies–Rationale, Preclinical Results and Future Clinical Developments (2016)

The objectives of this review are to summarize the experimental data obtained using apoptotic cell-based therapies, and then to discuss future clinical developments. Indeed, apoptotic cells exhibit immunomodulatory properties that are reviewed here by focusing on more recent mechanisms. These immunomodulatory mechanisms are in particular linked to the clearance of apoptotic cells (called also efferocytosis) by phagocytes, such as macrophages, and the induction of regulatory T cells. Thus, apoptotic cell-based therapies have been used to prevent or treat experimental inflammatory diseases. Based on these studies, we have identified critical steps to design future clinical trials. This includes: the administration route, the number and schedule of administration, the appropriate apoptotic cell type to be used, as well as the apoptotic signal. We also have analyzed the clinical relevancy of apoptotic-cell-based therapies in experimental models. Additional experimental data are required concerning the treatment of inflammatory diseases (excepted for sepsis) before considering future clinical trials. In contrast, apoptotic cells have been shown to favor engraftment and to reduce acute graft-versus-host disease (GvHD) in different relevant models of transplantation. This has led to the conduct of a phase 1/2a clinical trial to alleviate GvHD. The absence of toxic effects obtained in this trial may support the development of other clinical studies based on this new cell therapy. Stem Cells 2016;34:1464-1473.
Herpes Simplex Virus gE/gI Expressed in Epithelial Cells Interferes with Cell-to-Cell Spread (2003)

The herpes simplex virus (HSV) glycoprotein heterodimer gE/gI plays an important role in virus cell-to-cell spread in epithelial and neuronal tissues. In an analogous fashion, gE/gI promotes virus spread between certain cell types in culture, e.g., keratinocytes and epithelial cells, cells that are polarized or that form extensive cell junctions. One mechanism by which gE/gI facilitates cell-to-cell spread involves selective sorting of nascent virions to cell junctions, a process that requires the cytoplasmic domain of gE. However, the large extracellular domains of gE/gI also appear to be involved in cell-to-cell spread. Here, we show that coexpression of a truncated form of gE and gI in a human keratinocyte line, HaCaT cells, decreased the spread of HSV between cells. This truncated gE/gI was found extensively at cell junctions. Expression of wild-type gE/gI that accumulates at intracellular sites, in the trans-Golgi network, did not reduce cell-to-cell spread. There was no obvious reduction in production of infectious HSV in cells expressing gE/gI, and virus particles accumulated at cell junctions, not at intracellular sites. Expression of HSV gD, which is known to bind virus receptors, also blocked cell-to-cell spread. Therefore, like gD, gE/gI appears to be able to interact with cellular components of cell junctions, gE/gI receptors which can promote HSV cell-to-cell spread.
Combination of adenoviral virotherapy and temozolomide chemotherapy eradicates malignant glioma through autophagic and apoptotic cell death in vivo (2009)

Conditionally replicative adenoviruses (CRAds) represent a novel treatment strategy for malignant glioma. Recent studies suggest that the cytopathic effect elicited by these vectors is mediated through autophagy, a form of programmed cell death. Likewise, temozolomide (TMZ), a chemotherapeutic agent used for the treatment of malignant gliomas, also triggers autophagic cell death. In this study, we examined the potential to combine the two treatments in the setting of experimental glioma. In vitro, pretreatment with TMZ followed by CRAd-Surivin-pk7 enhanced cytotoxicity against a panel of glioma cell lines. Western blot analysis showed increased expression of BAX and p53, decreased expression of BCL2 and elevated level of APG5. Treatment with TMZ followed by CRAd-Survivin-pk7 (CRAd-S-pk7) led to a significant over-expression of autophagy markers, acidic vesicular organelles and light-chain 3 (LC3). These results were further evaluated in vivo, in which 90% of the mice with intracranial tumours were long-term survivors (>100 days) after treatment with TMZ and CRAd-S-pk7 (P<0.01). Analysis of tumours ex vivo showed expression of both LC3 and cleaved Caspase-3, proving that both autophagy and apoptosis are responsible for cell death in vivo. These results suggest that combination of chemovirotherapy offers a powerful tool against malignant glioma and should be further explored in the clinical setting.
Solid-Phase Unnatural Peptide Synthesis (UPS) (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSolid-Phase Unnatural Peptide Synthesis (UPS)Martin J. O'Donnell, Changyou Zhou, and William L. ScottView Author Information Department of Chemistry, Indiana University−Purdue University at Indianapolis, Indianapolis, Indiana 46202 Technology Core Research, Lilly Research Laboratories Lilly Corporate Center, Eli Lilly and Company Indianapolis, Indiana 46285 Cite this: J. Am. Chem. Soc. 1996, 118, 25, 6070–6071Publication Date (Web):June 26, 1996Publication History Received16 January 1996Published online26 June 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja9601245https://doi.org/10.1021/ja9601245rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views2127Altmetric-Citations125LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (2)»Supporting Information Supporting Information SUBJECTS:Alcohols,Monomers,Organic polymers,Peptides and proteins,Solid phase synthesis Get e-Alerts
IQCB1Mutations in Patients with Leber Congenital Amaurosis (2010)

Results show that the onset of renal failure in patients with IQCB1 mutations is highly variable, and that mutations are also found in LCA patients without nephronophthisis, rendering IQCB1 a new gene for LCA. However, these patients are at high risk for developing renal failure, which in early stages is often not recognized and can cause sudden death from fluid and electrolyte imbalance. It is therefore recommended that all LCA patients be screened for IQCB1 mutations, to follow them more closely for kidney disease.
Evaluierung der Reproduzierbarkeit dopplersonographischer Messungen in der Geburtshilfe (2004)

Fragestellung: In wie weit lassen sich dopplersonographische Messungen der fetalen und maternalen Flow-Parameter in der Geburtshilfe reproduzieren?
Temperature Dependence of Spin-Transfer-Induced Switching of Nanomagnets (2004)

We measure the temperature, magnetic-field, and current dependence for the switching of nanomagnets by a spin-polarized current. Depending on current bias, switching can occur between either two static magnetic states or a static state and a current-driven precessional mode. In both cases, the switching is thermally activated and governed by the sample temperature, not a higher effective magnetic temperature. The activation barriers for switching between static states depend linearly on current, with a weaker dependence for dynamic to static switching.
A gene region in Dichelobacter nodosus encoding a lipopolysaccharide epitope (1995)

Dichelobacter nodosus is a Gram-negative anaerobic bacterium that is the causative organism of footrot in sheep. A D. nodosus locus responsible for a modification of the host lipopolysaccharide (LPS) in Escherichia coli was cloned and sequenced. Genetic studies showed that the modification occurred within the inner-core region of the host LPS, most likely to one or more of the heptose molecules. Antibodies eluted from the modified LPS reacted preferentially with the lipid-A-core region of D. nodosus LPS, suggesting that the cloned epitope was present in this region of the D. nodosus LPS. The gene responsible for the modification, IpsA, potentially encoded a polypeptide of approximately 37 kDa which was highly basic, a characteristic of enzymes which interact with the acidic inner LPS core. The IpsA gene appeared to be arranged in a complex operon with a downstream gene, prfC, which encoded a protein with similarity to E. coli peptide-chain release factor 3.
Inhalation Studies With Drugs of Abuse (1997)

In recent years, smoking or inhalation of drugs has become a popular route of administration among drug users. Various drugs of different classes have been abused by inhalation or smoking, including phencyclidine (PCP), cocaine, heroin, methamphetamine, and marijuana. This increased popu-larity of smoking drugs has resulted from the fast onset of drug action and fears related to contracting acquired immunodeficiency syndrome (AIDS) or other infectious diseases from intravenous (IV) injections. In particular, heroin smoking has increased dramatically; approximately 74 percent of the heroin addicts in India use this method of administration, and it is also popular in the United States (Griffiths et al. 1994). The shift toward smoking heroin has also been associated with an increased availability of illicit heroin on the streets, which has declined in price and increased in purity (Huizer 1987). Consequently, there is an increased risk of overdose.
Multiple T cell specificities for Bet v I, the major birch pollen allergen, within single individuals. Studies using specific T cell clones and overlapping peptides (1993)

Twenty-five T cell clones specific for Bet v I were established from the peripheral blood of two birch pollen-allergic patients. The T cell epitopes of these clones were mapped using dodecapeptides overlapping for 2 amino acids (neighbors share 10 residues) spanning the whole amino acid sequence of the protein (159 amino acids). In total, 7 epitopes could be detected. One donor displayed 6 distinct T cell specificities for the Bet v I molecule in 14 T cell clones; for the other donor, 4 stimulating peptides for 11 clones could be identified. Two T cell epitopes were recognized by both subjects. One of these might represent an immunodominant epitope located at amino acid position 77-92 of the Bet v I molecule, as in 13/25 T cell clones activation could be induced by this amino acid sequence. One T cell clone reacted with purified pollen-derived Bet v I, but neither with any peptide synthesized according to a Bet v I-encoding cDNA nor with the respective recombinant protein. Upon stimulation with allergen, the majority of the clones (21/24) revealed the TH0 or TH2 type of cytokine production (interleukin-4 production), indicating their importance in the pathogenesis of the allergic disease.
Disjoint paths in a network (1974)

Abstract Routes between two given nodes of a network are called diversified if they are node‐disjoint, except at the terminals. Diversified routes are required for reliability in communication, and an additional criterion is that their total cost, assumed to be the sum of individual arc lengths or costs, is minimum. An algorithm and related theory is described for a general number K of node‐disjoint paths with minimum total length. The algorithm applies shortest path labeling algorithms familiar in the literature. K node‐disjoint paths are found in K iterations of a single shortest path algorithm.