gebhart/patrepeval huggingface dataset:
A Promoter Region Polymorphism inPDCD-1Gene Is Associated with Risk of Rheumatoid Arthritis in the Han Chinese Population of Southeastern China (2014)

Objective. Programmed cell death 1 (PD-1) induces negative signals to T cells during interaction with its ligands and is therefore a candidate gene in the development of autoimmune diseases such as rheumatoid arthritis (RA). Herein, we investigate the association of PDCD-1 polymorphisms with the risk of RA among Chinese patients and healthy controls. Methods. Using the PCR-direct sequencing analysis, 4 PDCD-1 SNPs (rs36084323, rs11568821, rs2227982, and rs2227981) were genotyped in 320 RA patients and 309 matched healthy controls. Expression of PD-1 was determined in peripheral blood lymphocytes by flow cytometry and quantitative real-time reverse transcriptase polymerase chain reaction. Results. We observed that the GG genotype of rs36084323 was associated with a increased risk for developing RA (OR 1.70, 95% 1.11-2.61, P = 0.049). Patients carrying G/G genotype displayed an increased mRNA level of PD-1 (P = 0.04) compared with A/A genotype and healthy controls. Meanwhile, patients homozygous for rs36084323 had induced basal PD-1 expression on activated CD4+ T cells. Conclusion. The PDCD-1 polymorphism rs36084323 was significantly associated with RA risk in Han Chinese population. This SNP, which effectively influenced the expression of PD-1, may be a biomarker of early diagnosis of RA and a suitable indicator of utilizing PD-1 inhibitor for treatment of RA.
Toxin Entry: Retrograde Transport through the Secretory Pathway (1998)

The synthesis, segregation, intracellular transport, and exocytic export of secretory proteins in eukaryotic cells is now well understood. Synthesis begins on free cytosolic ribosomes that subsequently attach to the ER, resulting in the cotranslational discharge of the nascent proteins into the ER lumen. The targeting signals and the cytosolic and ER membrane components that mediate the translocation step have been extensively characterized and reviewed (for example, see 29). The ER lumen contains a range of resident proteins responsible for modifying newly synthesized polypeptides, and for ensuring correct folding into the biologically active conformation (9). Secretion entails transport of the proteins from the ER, via the Golgi stack and the TGN, to secretory vesicles that ultimately fuse with the plasma membrane to complete protein export. The secretory pathway was elucidated by Palade and his colleagues (24). Protein transport between the various compartments of the secretory pathway is mediated by carrier vesicles that bud from one compartment and fuse with the next. Once again, many of the cellular components that are required for, and that regulate, vesicular transport have been identified, and the mechanisms by which cytoplasmic protein coats drive the individual transport steps are now emerging (31). It has been recognized for some time that the secretory pathway is at least partially reversible. For example, retrograde vesicular transport from the Golgi to the ER is needed to retrieve resident ER proteins that have escaped from this compartment (25), and endocytosis can transport proteins from the cell surface to the TGN (2), which is the cellular location where the secretory and endocytic pathways converge (31). ER resident proteins contain a retrieval signal, the COOH-terminal tetrapeptide Lys-Asp-Glu-Leu (KDEL),1 which binds to a membrane receptor in the cis-Golgi region and returns them to the ER. Indeed the KDEL receptor is capable of retrieving escaped ER resident proteins from as far along the secretory pathway as the TGN; an exogenous synthetic peptide with a COOH-terminal KDEL sequence, which was introduced into the TGN from the cell surface was subsequently transported to the ER lumen (20). Recently, it has become apparent that certain protein toxins follow this same route from the surface to the ER lumen. To reach their targets in the cytosol of mammalian cells the toxins apparently go one step further and cross the ER membrane. The emerging experimental evidence in support of this is reviewed here.
Secretion and Function ofSalmonellaSPI-2 Effector SseF Require Its Chaperone, SscB (2004)

Salmonella strains utilize a type III secretion system for their successful survival and replications inside host cells. SseF is one of the several effector proteins that are required for conferring this survival ability by altering the trafficking of the Salmonella-containing vacuoles. These effector proteins often require appropriate chaperones to maintain their stabilities inside the bacteria. These chaperones are also known to assist the subsequent secretion and translocation of their substrates. We report here that SscB acts as the chaperone for SseF, an effector for the Salmonella pathogenicity island 2 (SPI-2). We found that the sscB gene is required for the formation of Salmonella sp.-induced continuous filaments in epithelial cells. Efficient Salmonella replication in macrophages requires SscB function. Intracellular and secretion levels of SseF are greatly reduced in an sscB mutant strain compared to the wild-type strain. A protein stability assay demonstrated that the half-life of SseF is significantly shortened in the absence of SscB. Transcriptional analysis of the sseF gene showed that the effect of SscB on the SseF level is not at the transcriptional level. A coprecipitation experiment indicated that SscB interacts with SseF. In summary, our results indicate that SscB is a chaperone for SPI-2 effector SseF to facilitate its secretion and function inside the host cells.
Epidemic algorithms for reliable content-based publish-subscribe: an evaluation (2004)

Distributed content-based publish-subscribe middleware is emerging as a promising answer to the demands of modern distributed computing. Nevertheless, currently available systems usually do not provide reliability guarantees. This hampers their use in dynamic and unreliable scenarios, notably including mobile ones. We evaluate the effectiveness of an approach based on epidemic algorithms. Three algorithms we originally proposed in [P. Costa et al., (2003)] are thoroughly compared and evaluated through simulation in challenging unreliable settings. The results show that our use of epidemic algorithms improves significantly event delivery, is scalable, and introduces only limited overhead.
A Self-Assembled Nano Optical Switch and Transistor Based on a Rigid Conjugated Polymer, Thioacetyl-End-Functionalized Poly(para-phenylene ethynylene) (2005)

A nanometer-scale optical switch and transistor were fabricated with thioacetyl-end-functionalized poly(para-phenylene ethynylene)s and Au nanogap electrodes by self-assembly. With photoirradiation, the switch can be switched on/off quickly with a switching ratio as high as 1000. Moreover, the device works well as a p-type transistor. With an increase in gate bias, strong conductance oscillation was observed in this self-assembled transistor (under low temperature 147 K), which is very likely due to single-electron charging oscillations arising from electron tunneling through the nanometer-scale transistor.
Effects of a K + Channel Opener to Reduce Transmural Dispersion of Repolarization and Prevent Torsade de Pointes in LQT1, LQT2, and LQT3 Models of the Long-QT Syndrome (2000)

Our data suggest that K(+) channel openers may be capable of abbreviating the long QT interval, reducing TDR, and preventing spontaneous and stimulation-induced TdP when congenital or acquired LQTS is secondary to reduced I(Kr) or I(Ks) but less so when it is due to augmented late I(Na).
Deletions of chromosome 4 at multiple sites are frequent in malignant mesothelioma and small cell lung carcinoma. (1999)

Recent allelotyping studies suggest that allelic losses at one or both arms of chromosome 4 are frequent in several tumor types. Cytogenetic studies of malignant mesothelioma (MM) and comparative genomic hybridization analyses of small cell lung carcinoma (SCLC) suggest that chromosome 4 deletions may also play a role in these tumor types, although these results have not been confirmed by allelotyping. In an effort to more precisely identify and map the locations of putative tumor suppressor gene(s) on chromosome 4 involved in the pathogenesis of these tumors, we performed loss of heterozygosity studies using 16 polymorphic microsatellite markers. After precise microdissection of archival surgical cases, we studied DNA obtained from 20 MMs, 21 SCLCs, and 20 non-SCLCs (NSCLCs). In addition, DNA from 14 SCLC and 17 NSCLC cell lines and corresponding B lymphoblastoid lines were studied. In MM and SCLC, we observed frequent losses at three nonoverlapping regions: (a) 4q33-34 (region R1; >80%); (b) 4q25-26 (region R2; >60%); and (c) 4p15.1-15.3 (region R3; >50%). Losses at these sites occurred at lower frequencies in NSCLC (>20-30%). Data from tumors and cell lines were similar. In MM and SCLC, the most frequently observed pattern was loss at all three regions. However, in NSCLC, the most frequent pattern was loss at R3 alone. Our study has delineated three nonoverlapping regions of frequent deletions on chromosome 4 in MM and SCLC, suggesting that there may be three putative suppressor genes on chromosome 4, the inactivation of which may be important in the pathogenesis of these tumor types.
Survey of methicillin-resistant clinical strains of coagulase-negative staphylococci for mecA gene distribution (1992)

A total number of 125 methicillin-resistant (MIC, greater than or equal to 16) coagulase-negative Staphylococcus strains isolated in Japan were surveyed for the distribution of the mecA gene, the structural gene for penicillin-binding protein 2', which is the causative genetic element for the intrinsic resistance of methicillin-resistant Staphylococcus aureus. Screening with colony hybridization by using a cloned mecA gene probe revealed that 121 strains (96.8%) belonging to the nine coagulase-negative Staphylococcus species (S. epidermidis, S. haemolyticus, S. saprophyticus, S. sciuri, S. simulans, S. hominis, S. capitis, S. warneri, and S. caprae) carried mecA in their genome, indicating wide distribution of the gene among coagulase-negative Staphylococcus species. Most (93.4%) of the mecA-carrying strains were producers of penicillinase. Four strains, including two S. haemolyticus and two S. saprophyticus strains, did not carry mecA in spite of their resistance to methicillin. One of them was of low-level resistance (MIC, 16), but three of them had moderate- to high-level resistance to methicillin (MIC, 64). Analysis of gel electrophoretic banding patterns of penicillin-binding proteins of these strains showed absence of penicillin-binding protein 2' but some alterations in signal intensities of the other penicillin-binding proteins. The result indicated that about 3% of methicillin-resistant coagulase-negative staphylococci in these hospitals had a resistance mechanism different from that associated with the production of penicillin-binding protein 2', as has been reported in the case of a borderline methicillin-resistant strain of S. aureus.
Intracellular Activation of Interferon Regulatory Factor-1 by Nanobodies to the Multifunctional (Mf1) Domain (2010)

IRF-1 is a tumor suppressor protein that activates gene expression from a range of promoters in response to stimuli spanning viral infection to DNA damage. Studies on the post-translational regulation of IRF-1 have been hampered by a lack of suitable biochemical tools capable of targeting the endogenous protein. In this study, phage display technology was used to develop a monoclonal nanobody targeting the C-terminal Mf1 domain (residues 301-325) of IRF-1. Intracellular expression of the nanobody demonstrated that the transcriptional activity of IRF-1 is constrained by the Mf1 domain as nanobody binding gave an increase in expression from IRF-1-responsive promoters of up to 8-fold. Furthermore, Mf1-directed nanobodies have revealed an unexpected function for this domain in limiting the rate at which the IRF-1 protein is degraded. Thus, the increase in IRF-1 transcriptional activity observed on nanobody binding is accompanied by a significant reduction in the half-life of the protein. In support of the data obtained using nanobodies, a single point mutation (P325A) involving the C-terminal residue of IRF-1 has been identified, which results in greater transcriptional activity and a significant increase in the rate of degradation. The results presented here support a role for the Mf1 domain in limiting both IRF-1-dependent transcription and the rate of IRF-1 turnover. In addition, the data highlight a route for activation of downstream genes in the IRF-1 tumor suppressor pathway using biologics.
Monoclonal antibody 2D10 recognizes a novel T cell costimulatory molecule on activated murine B lymphocytes. (1994)

We have developed a panel of rat mAbs against dibutyryl cAMP-activated 5C2 cells. In this panel, one mAb, 1G10, recognized murine B7. Another mAb designated 2D10 did not bind to murine B7 but could recognize a surface molecule expressed only on dibutyryl cAMP-activated 5C2 mouse B lymphoma cells or on LPS-stimulated splenic B cells. This new molecule is referred to as early T cell costimulatory molecule-1 (ETC-1). From both activated 5C2 cells and splenic B cells, mAb 2D10 immunoprecipitated a 59- to 60-kDa protein, which was different from the 47- to 55-kDa murine B7 protein precipitated from the same cell populations. FACS analysis showed that, in contrast to B7, the expression of ETC-1 on 5C2 cells was induced by lower concentrations of dibutyryl cAMP and displayed a faster kinetics. LPS-stimulated splenic B cells expressed relatively low levels of B7 and much higher levels of ETC-1. Importantly, in an Ag presentation assay using activated 5C2 cells as APC, the secretion of IL-2 by C8A3 T hybrids was partially inhibited by mAb 2D10 alone and completely blocked by combination use of mAbs 2D10 and 1G10 in a dose-dependent and synergistic fashion. In a one-way primary MLR, mAb 2D10 alone at 0.1 to 1 microgram/ml inhibited T cell proliferation by 19 to 56%. However, an additive blocking effect (up to 76%) was observed when two mAbs were added in combination. Thus, our data have demonstrated that a novel T cell costimulatory molecule is present on activated murine B cells, which, in cooperation with B7, may play a critical role in optimal T cell activation.
Arabidopsis Ethylene-Response Gene ETR1 : Similarity of Product to Two-Component Regulators (1993)

Ethylene behaves as a hormone in plants, regulating such aspects of growth and development as fruit ripening, flower senescence, and abscission. Ethylene insensitivity is conferred by dominant mutations in the ETR1 gene early in the ethylene signal transduction pathway of Arabidopsis thaliana. The ETR1 gene was cloned by the method of chromosome walking. Each of the four known etr1 mutant alleles contains a missense mutation near the amino terminus of the predicted protein. Although the sequence of the amino-terminal half of the deduced ETR1 protein appears to be novel, the carboxyl-terminal half is similar in sequence to both components of the prokaryotic family of signal transducers known as the two-component systems. Thus, an early step in ethylene signal transduction in plants may involve transfer of phosphate as in prokaryotic two-component systems. The dominant etr1-1 mutant gene conferred ethylene insensitivity to wild-type Arabidopsis plants when introduced by transformation.
[Synthesis and platelet aggregation inhibitory activity of 6-(4-substituted phenyl)-4,5-dihydro-3(2H)-pyridazinones]. (1990)

To search for more ideal antithrombotic drugs sixteen 6-(4-substituted phenyl)-4,5-dihydro-3(2H)-pyridazinones were designed and synthesized. Some improvement of the synthetic method involved in constructing the piperazinyl group by cyclization of bisbromoethyl amine with 4-pyridazinonyl anilines. Preliminary pharmacological tests showed that all of the target compounds inhibited ADP induced platelet aggregation. Compounds II2, II3 and II4 were more potent than CCI-17810. The 5-methyl derivative of CCI-17810 (II4) was the most potent compound.
Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome (2013)

A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome.
Nano‐engineered optical fibers and applications 1 (2013)

Abstract The paper reviews optical fibers with nano‐engineered features and methods to fabricate them. These optical fibers have nano‐engineered regions comprising of randomly distributed voids which provide unique properties for designing next generation of fibers. Discussion of impact of void morphology on fiber optical properties is presented, along with the methods to control the void characteristics. Use of nano‐engineered fibers for different applications (ultra‐low bend loss single mode fiber, quasi‐single mode bend loss fiber, endless single‐mode fiber, light diffusing fibers) is discussed and the unique optical attributes of the fibers in these applications is highlighted.
Akt Signaling and Cancer: Surviving but not Moving On (2006)

The frequent deregulation of the phosphoinositide 3-kinase/Akt survival signaling pathway in cancer has prompted significant interest in blocking this pathway to treat cancer. Recently, however, two studies have shown that the Akt isoform Akt1 limits the invasive migration of breast cancer cells. These studies suggest that Akt1 may have a dual role in tumorigenesis, acting not only pro-oncogenically by suppressing apoptosis but also anti-oncogenically by suppressing invasion and metastasis. We discuss the possible implications of these findings for therapeutic development of Akt inhibitors to treat cancer.
Dendritoma vaccination combined with low dose interleukin-2 in metastatic melanoma patients induced immunological and clinical responses (2006)

A pilot clinical trial using dendritomas, purified hybrids from the fusion of dendritic/tumor cells combined with a low dose of IL-2, in metastatic melanoma patients was conducted in order to determine its safety and potential immunological and clinical responses. Ten metastatic melanoma patients were enrolled into this study. Dendritoma vaccines were created by fusing dendritic cells stained with green fluorescent dye with irradiated autologous tumor cells stained with red fluorescent dye and purifying the hybrids using immediate fluorescent-activated cell sorting. Initial vaccine was given subcutaneously and followed by IL-2 in serially elevated doses from 3-9 million units/m2 for 5 days. Repeated vaccinations were administered without IL-2, at 3-month intervals for a maximum of 5 times. Immune reactions were measured by the increase of interferon-gamma (IFN-gamma) expressing T cells. Vaccine doses ranged from 250,000 to 1,000,000 dendritomas. There was no grade 2 or higher toxicity directly attributable to the vaccine. All patients experienced toxicity due to IL-2 administration (9-grade 2, 3-grade 3, 1-grade 4). Eight of nine evaluable patients demonstrated immunologic reactions by increased IFN-gamma expressing T cells. One patient developed partial response at 12 weeks after the first vaccine. Nine months later, this patient achieved a complete response. In addition, two patients had stable disease for 9 and 4 months, respectively; one patient had a mixed response. Our findings demonstrated that dendritoma vaccines with a low dose of IL-2 can be safely administered to patients with metastatic melanoma and induce immunological and clinical responses.
Mitochondria in lung biology and pathology: more than just a powerhouse (2014)

An explosion of new information about mitochondria reveals that their importance extends well beyond their time-honored function as the "powerhouse of the cell." In this Perspectives article, we summarize new evidence showing that mitochondria are at the center of a reactive oxygen species (ROS)-dependent pathway governing the response to hypoxia and to mitochondrial quality control. The potential role of the mitochondrial genome as a sentinel molecule governing cytotoxic responses of lung cells to ROS stress also is highlighted. Additional attention is devoted to the fate of damaged mitochondrial DNA relative to its involvement as a damage-associated molecular pattern driving adverse lung and systemic cell responses in severe illness or trauma. Finally, emerging strategies for replenishing normal populations of mitochondria after damage, either through promotion of mitochondrial biogenesis or via mitochondrial transfer, are discussed.
Recent advances in research on multistage tumorigenesis (2000)

Tumour development is a multi-step process during which genetic and epigenetic events determine the transition from a normal to a malignant cellular state. In the past decade, extensive effort has been made not only to define the molecular mechanisms underlying progression to malignancy but also to predict the development of the disease and to identify possible molecular targets for therapy. Common to most tumours, several regulatory circuits are altered during multistage tumour progression, most importantly, the control of proliferation, the balance between cell survival and programmed cell death (apoptosis), the communication with neighbouring cells and the extracellular matrix, the induction of tumour neovascularization (angiogenesis) and, finally, tumour cell migration, invasion and metastatic dissemination. De-regulation of each of these processes represents a rate-limiting step for tumour development and, hence, has to be achieved by tumour cells in a highly selective manner during tumour progression. In this review we summarize recent advances in cancer research that have provided new insights in the molecular mechanisms underlying the transition between one tumour stage and the next and into their concerted action during tumour progression. Cultured human tumour cell lines as well as transgenic and knock-out mouse models of tumorigenesis have been instrumental in these experimental approaches.