gebhart/patrepeval huggingface dataset:
First report of safety and efficacy of daratumumab in 2 cases of advanced immunoglobulin light chain amyloidosis (2016)

To the editor:

Immunoglobulin light chain amyloidosis (AL) with advanced cardiac involvement is characterized by short survival. Outcomes are especially poor for patients who have multiorgan involvement and coexisting multiple myeloma and do not achieve normalization of the serum free light chains
Accounting for Second Life (2008)

RNA interference (RNAi) is a conserved mechanism that catalyzes sequence-specific gene silencing and has been used for loss-of-function genetic screens in many organisms. Here, we demonstrated that the expression of Caenorhabditis elegans SID-1 (CeSID-1) could trigger effective gene silencing in the cultured silkworm cell line, BmN4 (BmN4-SID1). Soaking the BmN4-SID1 in dsRNA corresponding to endogenous target genes induced a significant decrease of the amount of mRNA or protein. A small amount of dsRNA was enough to silence the target gene in a few days. Overexpression of CeSID-1 did not affect the cell viability. Our results suggest that BmN4-SID1 can be used in many applications in silkworm cells and will become a valuable resource for gene analysis.
Circulating Cytokines in Primary Sjögren's Syndrome Determined by a Multiplex Cytokine Array System (2004)

Plasma cytokines play an important role in the pathogenesis of Sjögren's syndrome (SS) by initiating and perpetuating various cellular and humoural autoimmune processes. The aim of the present study was to describe a broad spectrum of T-cell and B-cell cytokines, growth factors, chemokines and molecules that could contribute to cell death in SS. A novel protein array system was utilized to measure simultaneously the levels of 25 plasma cytokines of patients with primary SS and healthy individuals. Furthermore, we correlated these plasma cytokine levels with potential laboratory and clinical parameters related to disease activity in SS. A subset of plasma cytokines [e.g. interleukin-1beta (IL-1beta), IL-6, CXCL8 (IL-8), IL-12 p40, IL-15, tumour necrosis factor-alpha (TNF-alpha), epidermal growth factor, CCL4 (MIP-1beta), CCL2 (MCP-1), CCL11 (Eotaxin), CCL5 (RANTES), TNF-RI and TNF-RII] was found to significantly differ between patients and controls. Also, distinct populations of cytokines were found to differentiate between patients with normal versus elevated ESR or IgG levels and patients with the presence or absence of extra-glandular manifestations (EGMs). Our results support the assumption that the multiplex cytokine array system can be successfully utilized in the diagnosis and disease management of SS. Furthermore, it may provide a powerful tool in the design of individualized anticytokine therapies.
Mitochondrial protein kinase Cϵ (PKCϵ): emerging role in cardiac protection from ischaemic damage (2007)

Mitochondria mediate diverse cellular functions including energy generation and ROS (reactive oxygen species) production and contribute to signal transduction. Mitochondria are also key regulators of cell viability and play a central role in necrotic and apoptotic cell death pathways induced by cardiac ischaemia/reperfusion injury. PKC (protein kinase C) epsilon plays a critical role in cardioprotective signalling pathways that protect the heart from ischaemia/reperfusion. Emerging evidence suggests that the cardioprotective target of PKCepsilon resides at the mitochondria. Proposed mitochondrial targets of PKCepsilon include mitoK(ATP) (mitochondrial ATP-sensitive K(+) channel), components of the MPTP (mitochondrial permeability transition pore) and components of the electron transport chain. This review highlights mitochondrial targets of PKCepsilon and their possible role in cardioprotective signalling in the setting of ischaemia/reperfusion injury.
Novel Chimeric Gene Therapy Vectors Based on Adeno-Associated Virus and Four Different Mammalian Bocaviruses (2019)

Parvoviruses are highly attractive templates for the engineering of safe, efficient, and specific gene therapy vectors, as best exemplified by adeno-associated virus (AAV). Another candidate that currently garners increasing attention is human bocavirus 1 (HBoV1). Notably, HBoV1 capsids can cross-package recombinant (r)AAV2 genomes, yielding rAAV2/HBoV1 chimeras that specifically transduce polarized human airway epithelia (pHAEs). Here, we largely expanded the repertoire of rAAV/BoV chimeras, by assembling packaging plasmids encoding the capsid genes of four additional primate bocaviruses, HBoV2-4 and GBoV (Gorilla BoV). Capsid protein expression and efficient rAAV cross-packaging were validated by immunoblotting and qPCR, respectively. Interestingly, not only HBoV1 but also HBoV4 and GBoV transduced pHAEs as well as primary human lung organoids. Flow cytometry analysis of pHAEs revealed distinct cellular specificities between the BoV isolates, with HBoV1 targeting ciliated, club, and KRT5+ basal cells, whereas HBoV4 showed a preference for KRT5+ basal cells. Surprisingly, primary human hepatocytes, skeletal muscle cells, and T cells were also highly amenable to rAAV/BoV transduction. Finally, we adapted our pipeline for AAV capsid gene shuffling to all five BoV isolates. Collectively, our chimeric rAAV/BoV vectors and bocaviral capsid library represent valuable new resources to dissect BoV biology and to breed unique gene therapy vectors.
The Replicator of the Epstein-Barr Virus Latent Cycle Origin of DNA Replication, oriP , Is Composed of Multiple Functional Elements (2001)

Replication of the Epstein-Barr virus genome initiates at one of several sites in latently infected, dividing cells. One of these replication origins is close to the viral DNA maintenance element, and, together, this replication origin and the maintenance element are referred to as oriP. The replicator of oriP contains four binding sites for Epstein-Barr virus nuclear antigen 1 (EBNA-1), the sole viral protein required for the replication and maintenance of oriP plasmids. We showed previously that these EBNA-1 sites function in pairs and that mutational inactivation of one pair does not eliminate replicator function. In this study we characterized the contribution of each EBNA-1 site within the replicator and flanking sequences through the use of an internally controlled replication assay. We present evidence that shows that all four EBNA-1 sites are required for an oriP plasmid to be replicated in every cell cycle. Results from these experiments also show that the paired EBNA-1 binding sites are not functionally equivalent and that the low affinity of sites 2 and 3 compared to that of sites 1 and 4 is not essential for replicator function. Our results suggest that a host cell protein(s) binds sequences flanking the EBNA-1 sites and that interactions between EBNA-1 and this protein(s) are critical for replicator function. Finally, we present evidence that shows that the minimal replicator of oriP consists of EBNA-1 sites 3 and 4 and two copies of a 14-bp repeat that is present in inverse orientation flanking these EBNA-1 sites. EBNA-1 sites 1 and 2, together with an element(s) within nucleotides 9138 to 9516, are ancillary elements required for full replicator activity.
Targeting carcinogenesis: A role for the prolyl isomerase Pin1? (2006)

Abstract Phosphorylation of proteins on serine or threonine residues that immediately precede proline (pSer/Thr‐Pro) is a central signaling mechanism in cell proliferation and transformation. Recent studies indicate that certain pSer/Thr‐Pro motifs in native proteins exist in two completely distinct conformations, cis and trans , whose conversion is markedly slowed down upon phosphorylation, but specifically catalyzed by the peptidyl‐prolyl cis / trans isomerase Pin1. Importantly, such Pin1‐catalyzed conformational changes can have profound effects on the function of many phosphorylation signaling pathways, thereby playing an important role in various cellular processes. Moreover, increasing evidence indicates that aberrant Pin1 function plays an important role in the pathogenesis of some human diseases. Notably, Pin1 is not only overexpressed in a large number of human cancers, but also is an excellent prognostic marker in some cancers. Furthermore, Pin1 overexpression can function as a critical catalyst that amplifies multiple oncogenic signaling pathways during oncogenesis. Moreover, Pin1 overexpression causes cell transformation, centrosome amplification, genomic instability, and tumor development. In contrast, Pin1 knockout in mice prevents certain oncogenes from inducing tumors and Pin1 inhibition in cancer cells suppresses their cell proliferation, transformed phenotype and tumorigenicity in nude mice as well as increases the response to other anticancer agents. These results suggest that Pin1‐mediated postphosphorylation regulation may provide a unique opportunity for disrupting oncogenic pathways, and thereby represent an appealing target for novel anticancer therapies. © 2006 Wiley‐Liss, Inc.
Die andere Dimension des Spiels: streetfootballworld festival 06 – zur Rekonstruktion der Verknüpfung von Gewalt, Verwundbarkeit und Identität über Erinnerung, Gedächtnis, Kommunikation und Raum (2009)

Deutschland feierte Premiere – mit dem streetfootballworld festival 06 in Berlin wurde zum ersten Mal eine Straßenfußballweltmeisterschaft während einer Fußball- Weltmeisterschaft veranstaltet. Für die international agierende social-profitorganisation streetfootballworld war das festival 06 ein Höhepunkt ihrer Arbeit, mit der die Mitgliedsorganisationen des von streetfootballworld koordinierten globalen Netzwerks die andere Dimension des Spiels ins Zentrum rücken. Kernanliegen der Arbeit von streetfootballworld ist es, benachteiligten und bedrohten Kindern und Jugendlichen weltweit die Möglichkeit gewaltfreier Konfliktlösung, Chancen zur Integration und einer selbstbestimmten Zukunft zu schaffen. Zusammen mit den Organisationen aus dem streetfootballworld Netzwerk schöpft streetfootballworld aus dem Pool erfolgreicher Ansätze im Bereich Entwicklung durch Fußball und entwickelt neue, innovative Lösungen für soziale Herausforderungen. Am Beispiel von „Fútbol por la Paz“ - „Fußball für den Frieden“ in Medellín (Kolumbien), wo eine dieser lokalen Erfolgsgeschichten ihren Anfang nahm, wird die Verknüpfung zwischen Gewalt, Verwundbarkeit und Identität über Erinnerung, Gedächtnis, Kommunikation und Raum rekonstruiert. Seit seiner Gründung 2002 ermöglicht streetfootballworld seinen Mitgliedern Wissen zu teilen, neue Partnerschaften aufzubauen und Inspiration für ihre Arbeit im Austausch mit den anderen zu finden. Diese werden dann in Investitionsmöglichkeiten übersetzt oder fließen in regionale und globale Entwicklungsstrategien ein.
Role of microRNAs in stem/progenitor cells and cardiovascular repair (2011)

MicroRNAs (miRNAs), small non-coding RNAs, play a critical role in differentiation and self-renewal of pluripotent stem cells, as well as in differentiation of cardiovascular lineage cells. Several miRNAs have been demonstrated to repress stemness factors such as Oct4, Nanog, Sox2 and Klf4 in embryonic stem cells, thereby promoting embryonic stem cell differentiation. Furthermore, targeting of different miRNAs promotes reprogramming towards induced pluripotent stem cells. MicroRNAs are critical for vascular smooth muscle cell differentiation and phenotype regulation, and miR-143 and miR-145 play a particularly important role in this respect. Notably, these miRNAs are down-regulated in several cardiovascular disease states, such as in atherosclerotic lesions and vascular neointima formation. MicroRNAs are critical regulators of endothelial cell differentiation and ischaemia-induced neovascularization. miR-126 is important for vascular integrity, endothelial cell proliferation and neovascularization. miR-1 and miR-133 are highly expressed in cardiomyocytes and their precursors and regulate cardiomyogenesis. In addition, miR-499 promotes differentiation of cardiomyocyte progenitor cells. Notably, miRNA expression is altered in cardiovascular disease states, and recent studies suggest that dysregulated miRNAs may limit cardiovascular repair responses. Dysregulation of miRNAs may lead to an altered function and differentiation of cardiovascular progenitor cells, which is also likely to represent a limitation of autologous cell-based treatment approaches in these patients. These findings suggest that targeting of specific miRNAs may represent an interesting novel opportunity to impact on endogenous cardiovascular repair responses, including effects on stem/progenitor cell differentiation and functions. This approach may also serve to optimize cell-based treatment approaches in patients with cardiovascular disease.
Chronic exercise enhances endothelium-mediated dilation of epicardial coronary artery in conscious dogs. (1993)

Whether endothelium-derived relaxing factor (EDRF)/nitric oxide (NO) plays a role in the dilation of the left circumflex coronary artery during acute exercise and whether endothelium-mediated dilation of this artery is altered after chronic exercise training have not been determined previously. Nine dogs were chronically instrumented for measurements of systemic hemodynamics, left circumflex coronary artery diameter, and blood flow. Acute treadmill exercise (10.9 km/h) caused dilation of the circumflex coronary artery by 4.33 +/- 0.84% and an increase in coronary blood flow by 32 +/- 5.2 mL/min. After the administration of intravenous nitro-L-arginine, the dilation of the circumflex coronary artery was converted to vasoconstriction (-4.13 +/- 1.58%), whereas the increase in coronary blood flow was not altered (24 +/- 3.6 mL/min). Chronic exercise training (2 hours each day at a speed of 10.9 km/h for 7 days) enhanced acetylcholine-induced dilation and reactive dilation (following release of a brief coronary artery occlusion) of the large coronary artery (P < .05), whereas the coronary blood flow responses were not changed. These enhanced acetylcholine-induced and reactive dilations of the circumflex coronary artery were due to a greater release of EDRF/NO since they were eliminated by nitro-L-arginine. Thus, in the circumflex coronary artery, EDRF/NO-dependent dilation was enhanced after 7 days of exercise training. This may represent the mechanism responsible for the perception that chronic exercise induces cardiovascular "well being."
Hypersensitive PCR, Ancient Human mtDNA, and Contamination (2003)

When highly efficient polymerase was used with high cycle numbers (50-60), strong amplifications were observed, but negative controls were also unexpectedly amplified in a study of ancient human mtDNA from 2000-year-old skeletons. The results of a series of tests revealed that the hypersensitive polymerase chain reaction (PCR) generated by higher cycles and the presence of contaminant DNA (though at extremely low levels) should be responsible for the amplification of negative controls. We suggest that PCR sensitivity be optimized to take advantage of highly efficient polymerase and at the same time prevent "background DNA" from becoming "contaminant DNA" and obscuring the analysis of authentic ancient DNA. We propose the use of multiple positive controls when amplifying ancient human mtDNA samples to indicate the sensitivity of individual PCR amplifications and to monitor the contamination levels of modern human DNA. This study provides some suggestions as to how to amplify and analyze ancient human mtDNA when unavoidable and extremely tiny amounts of modern human DNA exist.
Cloning and Deduced Amino Acid Sequence of a Novel Cartilage Protein (CILP) Identifies a Proform Including a Nucleotide Pyrophosphohydrolase (1998)

The cDNA cloning and expression in vitro and in eukaryotic cells of a novel protein isolated from human articular cartilage, cartilage intermediate layer protein (CILP) is described. A single 4. 2-kilobase mRNA detected in human articular cartilage encodes a polypeptide of 1184 amino acids with a calculated molecular mass of 132.5 kDa. The protein has a putative signal peptide of 21 amino acids, and is a proform of two polypeptides. The amino-terminal half corresponds to CILP (molecular mass of 78.5 kDa, not including post-translational modifications) and the carboxyl-terminal half corresponds to a protein homologous to a porcine nucleotide pyrophosphohydrolase, NTPPHase (molecular mass of 51.8 kDa, not including post-translational modifications). CILP has 30 cysteines and six putative N-glycosylation sites. The human homolog of porcine NTPPHase described here contains 10 cysteine residues and two putative N-glycosylation sites. In the precursor protein the NTPPHase region is immediately preceded by a tetrapeptide conforming to a furin proteinase cleavage consensus sequence. Expression of the full-length cDNA in a cell-free translation system and in COS-7 or EBNA cells indicates that the precursor protein is synthesized as a single polypeptide chain that is processed, possibly by a furin-like protease, into two polypeptides upon or preceding secretion.
Serine-409 phosphorylation and oxidative damage define aggregation of human protein tau in yeast (2010)

Unraveling the biochemical and genetic alterations that control the aggregation of protein tau is crucial to understand the etiology of tau-related neurodegenerative disorders. We expressed wild type and six clinical frontotemporal dementia with parkinsonism (FTDP) mutants of human protein tau in wild-type yeast cells and cells lacking Mds1 or Pho85, the respective orthologues of the tau kinases GSK3β and cdk5. We compared tau phosphorylation with the levels of sarkosyl-insoluble tau (SinT), as a measure for tau aggregation. The deficiency of Pho85 enhanced significantly the phosphorylation of serine-409 (S409) in all tau mutants, which coincided with marked increases in SinT levels. FTDP mutants tau-P301L and tau-R406W were least phosphorylated at S409 and produced the lowest levels of SinT, indicating that S409 phosphorylation is a direct determinant for tau aggregation. This finding was substantiated by the synthetic tau-S409A mutant that failed to produce significant amounts of SinT, while its pseudophosphorylated counterpart tau-S409E yielded SinT levels higher than or comparable to wild-type tau. Furthermore, S409 phosphorylation reduced the binding of protein tau to preformed microtubules. The highest SinT levels were found in yeast cells subjected to oxidative stress and with mitochondrial dysfunction. Under these conditions, the aggregation of tau was enhanced although the protein is less phosphorylated, suggesting that additional mechanisms are involved. Our results validate yeast as a prime model to identify the genetic and biochemical factors that contribute to the pathophysiology of human tau.
Functional characterization of MT3‐MMP in transfected MDCK cells: progelatinase A activation and tubulogenesis in 3‐D collagen lattice (2000)

MT3-MMP, a membrane-anchored matrix metalloproteinase, has been proposed to participate in the remodeling of extracellular matrix either by direct proteolysis or via activating other enzymes such as progelatinase A. To test this hypothesis, we analyzed the effect of exogenously transfected MT3-MMP in a tissue remodeling system: growth and tubulogenesis of Madin-Darby canine kidney (MDCK) cells in collagen gels. Although the parental cells require MMP activities for both growth and tubulogenesis, over-expression of wild-type MT3-MMP, but not its catalytically inactive mutant, leads to further enhancement of both processes, independent of its downstream substrate, progelatinase A. Mechanistically, MT3-MMP accomplishes such an effect by displaying on cell surfaces as active species, ready to activate progelatinase A or degrade ECM molecules. These data strongly suggest that MT3-MMP possesses the potential to directly enhance the growth and invasiveness of cells in vivo, two critical processes for development and carcinogenesis.
Best-practice patterns and tool support for configuring secure Web services messaging (2004)

This paper presents an emerging tool for security configuration of service-oriented architectures with Web Services. Security is a major concern when implementing mission-critical business transactions and such concern motivated the development of Web Services Security (WS-Security). However, the existing tools for configuring the security properties of Web Services give a technology-oriented view, and only assist in choosing the data to encrypt and selecting an encryption algorithm. The users must construct their own mental models of how the security configurations actually relate to business policies. In contrast, the tool described here gives a simplified, business-policy-oriented view. It models the messaging with customers and business partners, lists various threats, and presents best-practice security patterns against the threats. A user can select among variations on the basic patterns according to the business policies, and then apply them to the messaging model through the GUI. The result of the pattern application is described in the Web Services Security Policy Language (WS-Security Policy).
Mutations of familial hemophagocytic lymphohistiocytosis (FHL) related genes and abnormalities of cytotoxicity function tests in patients with macrophage activation syndrome (MAS) occurring in systemic juvenile idiopathic arthritis (sJIA) (2014)

MAS is a severe complication of rheumatic diseases, mostly sJIA. Clinical and laboratory features are similar to those of FHL resulting from mutations in selected genes involved in the cytotoxicity pathway.
Biodegradation of Silk Biomaterials (2009)

Silk fibroin from the silkworm, Bombyx mori, has excellent properties such as biocompatibility, biodegradation, non-toxicity, adsorption properties, etc. As a kind of ideal biomaterial, silk fibroin has been widely used since it was first utilized for sutures a long time ago. The degradation behavior of silk biomaterials is obviously important for medical applications. This article will focus on silk-based biomaterials and review the degradation behaviors of silk materials.
Identification of Tyrosine Phosphorylated Adhesion Proteins in Human Cancer Cells (1998)

Tyrosine phosphorylation is a form of signal transduction that regulates cell growth, differentiation, migration, and survival. This knowledge has promoted much interest in the role of tyrosine kinases and phosphatases in regulating cell behavior during development and tumorigenesis. However, it is generally less well appreciated that tyrosine phosphorylated proteins are enriched within sites of cell adhesion, particularly in transformed cells. To identify these, we developed a panel of monoclonal antibodies specific for tyrosine phosphorylated proteins in breast cancer cells, using extensive modifications of existing technologies for immunization, somatic fusion, and antibody screening. Mice were immunized with a complex mixture of phosphotyrosine containing proteins using the newly developed RIMMS method. By increasing the sensitivity of antigen recognition, we isolated reagents specific for a wide diversity of tyrosine phosphorylated adhesion proteins in breast cancer cells.
Groupwise serial multiuser detectors for multirate DS-CDMA (2003)

This paper presents the performance of groupwise successive interference cancellation (GSIC) in a DS-CDMA system with multiple data rates (multirate). The performance is evaluated both in AWGN and Rayleigh fading channels. In the GSIC scheme users with the same data rate are grouped and detected, using either a matched filter or a parallel interference cancellation (PIC) receiver, interference between the groups is cancelled in a successive order. The results show that in a multirate system the GSIC yields a better performance than the PIC receiver. Further a delay error of 0.1 T/sub c/ is found to be tolerable.