gebhart/patrepeval huggingface dataset:
Involvement of high mobility group box‐1 in imiquimod‐induced psoriasis‐like mice model (2016)

Abstract In the previous work, we have indicated that HMGB 1, a pro‐inflammatory cytokine, is closely associated with the pathogenesis of psoriasis. To further clarify the role of HMGB 1 in the pathogenesis of psoriasis, we investigated the direct function of HMGB 1 application and HMGB 1 blockade in imiquimod ( IMQ )‐induced psoriatic mouse model in this study. Mice were treated with imiquimod ( IMQ ) to induce psoriasis‐like inflammation, and consecutively injected with recombinant HMGB 1 or phosphate‐buffered saline ( PBS ) i.d. Abundant cytoplasmic expression of HMGB 1 was observed in lesional skin from IMQ ‐treated skin. The injection of HMGB 1 into the IMQ ‐treated skin further aggravated the psoriasis‐like disease, enhanced the infiltration of CD 3 + T cells, myeloperoxidase + neutrophils and CD 11c + dendritic cells, increased the number of γδ T cells, and upregulated the mRNA expression of interleukin ( IL )‐6, tumor necrosis factor ( TNF )‐α, interferon ( IFN )‐γ and IL ‐17 compared with the PBS injection. Finally, by using anti‐ HMGB 1 monoclonal antibody or HMGB 1 inhibitor glycyrrhizin, we indicated that HMGB 1 blockade reduced the number of γδ T cells, suppressed the mRNA expression of IL ‐6, TNF ‐α, IFN ‐γ and IL ‐17, and moderated clinical and histological evolvement in the IMQ ‐treated skin. Our data suggest that HMGB 1 may act as a pro‐inflammatory cytokine, and contribute to the development of IMQ ‐induced psoriasis‐like inflammation. HMGB 1 blockade may represent a new direction in the suppression of psoriasis.
Differential binding of neutralizing and non-neutralizing antibodies to native-like soluble HIV-1 Env trimers, uncleaved Env proteins, and monomeric subunits (2014)

The antigenicity and structural integrity of cleaved BG505 SOSIP.664 trimers render these proteins good mimics of functional Env spikes on virions. In contrast, uncleaved gp140s antigenically resemble individual gp120-gp41ECTO protomers and gp120 monomers, but not native trimers. Although NAb binding to functional trimers may thus be both necessary and sufficient for neutralization, the kinetics and stoichiometry of the interaction influence the neutralizing efficacy of individual NAbs.
The Oracle Problem in Software Testing: A Survey (2014)

Testing involves examining the behaviour of a system in order to discover potential faults. Given an input for a system, the challenge of distinguishing the corresponding desired, correct behaviour from potentially incorrect behavior is called the “test oracle problem”. Test oracle automation is important to remove a current bottleneck that inhibits greater overall test automation. Without test oracle automation, the human has to determine whether observed behaviour is correct. The literature on test oracles has introduced techniques for oracle automation, including modelling, specifications, contract-driven development and metamorphic testing. When none of these is completely adequate, the final source of test oracle information remains the human, who may be aware of informal specifications, expectations, norms and domain specific information that provide informal oracle guidance. All forms of test oracles, even the humble human, involve challenges of reducing cost and increasing benefit. This paper provides a comprehensive survey of current approaches to the test oracle problem and an analysis of trends in this important area of software testing research and practice.
Pancreatic gastrin stimulates islet differentiation of transforming growth factor alpha-induced ductular precursor cells. (1993)

Gastrin is transiently expressed in fetal islets during a critical period of their development from protodifferentiated islet precursors in fetal pancreatic ducts. To examine the possible role of gastrin as an islet cell growth factor, postnatal islet growth was studied in transgenic mice which overexpress gastrin and TGF alpha in their pancreas. Overexpression of a TGF alpha transgene causes metaplastic ductules containing numerous insulin expressing cells that resemble protodifferentiated precursors of the fetal pancreas. However, islet mass of the TGF alpha transgenic mice was not increased. Pancreatic overexpression of gastrin from a chimeric insulin/gastrin transgene transcribed from the insulin promoter markedly decreased the TGF alpha-stimulated increase in pancreatic duct mass. Furthermore, pancreatic coexpression of both gastrin and TGF alpha significantly increased islet mass in mice expressing both transgenes. These findings indicate that TGF alpha and gastrin can act synergistically to stimulate islet growth, although neither peptide alone is sufficient. Islet growth may possibly be stimulated through gastrin promoting the differentiation of insulin-positive cells in the TGF alpha-induced metaplastic ducts. This transgenic study suggests that islet neogenesis can be reactivated in the ductular epithelium of the adult pancreas by local expression of two growth factors, gastrin and TGF alpha.
Tagging of NS5A expressed from a functional hepatitis C virus replicon (2006)

Knowledge of how hepatitis C virus (HCV) proteins associate with components of the host cell to form a functional replication complex is still limited. To address this issue, HCV replicon constructs were generated where either green fluorescent protein (GFP) or the Propionibacterium shermanii transcarboxylase domain (PSTCD) was introduced into the NS5A coding region. Insertion of both GFP and PSTCD was tolerated well, allowing formation of stable replicon-containing cell lines that contained viral protein and transcript levels that were comparable to those of an unmodified parental replicon. Cell lines generated from the GFP-tagged NS5A replicon allowed live-cell visualization of the location of NS5A. Cell lines generated from the PSTCD-tagged replicons allowed rapid and efficient precipitation of the PSTCD-tagged NS5A, as well as other HCV non-structural proteins, using streptavidin-coated magnetic beads. Both replicons represent useful tools that offer different but complementary ways of examining replication-complex formation in cells.
Restoration of β-adrenergic signaling in failing cardiac ventricular myocytes via adenoviral-mediated gene transfer (1997)

Cardiovascular gene therapy is a novel approach to the treatment of diseases such as congestive heart failure (CHF). Gene transfer to the heart would allow for the replacement of defective or missing cellular proteins that may improve cardiac performance. Our laboratory has been focusing on the feasibility of restoring beta-adrenergic signaling deficiencies that are a characteristic of chronic CHF. We have now studied isolated ventricular myocytes from rabbits that have been chronically paced to produce hemodynamic failure. We document molecular beta-adrenergic signaling defects including down-regulation of myocardial beta-adrenergic receptors (beta-ARs), functional beta-AR uncoupling, and an up-regulation of the beta-AR kinase (betaARK1). Adenoviral-mediated gene transfer of the human beta2-AR or an inhibitor of betaARK1 to these failing myocytes led to the restoration of beta-AR signaling. These results demonstrate that defects present in this critical myocardial signaling pathway can be corrected in vitro using genetic modification and raise the possibility of novel inotropic therapies for CHF including the inhibition of betaARK1 activity in the heart.
CO2-laser micromachining and back-end processing for rapid production of PMMA-based microfluidic systems (2002)

In this article, we focus on the enormous potential of a CO(2)-laser system for rapidly producing polymer microfluidic structures. The dependence was assessed of the depth and width of laser-cut channels on the laser beam power and on the number of passes of the beam along the same channel. In the experiments the laser beam power was varied between 0 and 40 W and the passes were varied in the range of 1 to 7 times. Typical channel depths were between 100 and 300 microm, while the channels were typically 250 microm wide. The narrowest produced channel was 85 microm wide. Several bonding methods for microstructured PMMA [poly(methyl methacrylate)] parts were investigated, such as solvent-assisted glueing, melting, laminating and surface activation using a plasma asher. A solvent-assisted thermal bonding method proved to be the most time-efficient one. Using laser micromachining together with bonding, a three-layer polymer microstructure with included optical fibers was fabricated within two days. The use of CO(2)-laser systems to produce microfluidic systems has not been published before. These systems provide a cost effective alternative to UV-laser systems and they are especially useful in microfluidic prototyping due to the very short cycle time of production.
Fc‐fusion proteins: new developments and future perspectives (2012)

Since the first description in 1989 of CD4-Fc-fusion antagonists that inhibit human immune deficiency virus entry into T cells, Fc-fusion proteins have been intensely investigated for their effectiveness to curb a range of pathologies, with several notable recent successes coming to market. These promising outcomes have stimulated the development of novel approaches to improve their efficacy and safety, while also broadening their clinical remit to other uses such as vaccines and intravenous immunoglobulin therapy. This increased attention has also led to non-clinical applications of Fc-fusions, such as affinity reagents in microarray devices. Here we discuss recent results and more generally applicable strategies to improve Fc-fusion proteins for each application, with particular attention to the newer, less charted areas.
Improved and Versatile Transformation System Allowing Multiple Genetic Manipulations of the Hyperthermophilic Archaeon Thermococcus kodakaraensis (2005)

We have recently developed a gene disruption system for the hyperthermophilic archaeon Thermococcus kodakaraensis by utilizing a pyrF-deficient mutant, KU25, as a host strain and the pyrF gene as a selectable marker. To achieve multiple genetic manipulations for more advanced functional analyses of genes in vivo, it is necessary to establish multiple host-marker systems or to develop a system in which repeated utilization of one marker gene is possible. In this study, we first constructed a new host strain, KU216 (DeltapyrF), by specific and almost complete deletion of endogenous pyrF through homologous recombination. In this refined host, there is no need to consider unknown mutations caused by random mutagenesis, and unlike in the previous host, KU25, there is little, if any, possibility that unintended recombination between the marker gene and the chromosomal allele occurs. Furthermore, a new host-marker combination of a trpE deletant, KW128 (DeltapyrF DeltatrpE::pyrF), and the trpE gene was developed. This system made it possible to isolate transformants through a more simple selection procedure as well as to deduce the transformation efficiency, overcoming practical disadvantages of the first system. The effects of the transformation conditions were also investigated using this system. Finally, we have also established a system in which repeated utilization of the counterselectable pyrF marker is possible through its excision by pop-out recombination. Both endogenous and exogenous sequences could be applied as tandem repeats flanking the marker pyrF for pop-out recombination. A double deletion mutant, KUW1 (DeltapyrF DeltatrpE), constructed with the pop-out strategy, was demonstrated to be a useful host for the dual markers pyrF and trpE. Likewise, a triple deletion mutant, KUWH1 (DeltapyrF DeltatrpE DeltahisD), could also be constructed. The transformation systems developed here now provide the means for extensive genetic studies in this hyperthermophilic archaeon.
FollowMe: Efficient Online Min-Cost Flow Tracking with Bounded Memory and Computation (2015)

One of the most popular approaches to multi-target tracking is tracking-by-detection. Current min-cost flow algorithms which solve the data association problem optimally have three main drawbacks: they are computationally expensive, they assume that the whole video is given as a batch, and they scale badly in memory and computation with the length of the video sequence. In this paper, we address each of these issues, resulting in a computationally and memory-bounded solution. First, we introduce a dynamic version of the successive shortest-path algorithm which solves the data association problem optimally while reusing computation, resulting in faster inference than standard solvers. Second, we address the optimal solution to the data association problem when dealing with an incoming stream of data (i.e., online setting). Finally, we present our main contribution which is an approximate online solution with bounded memory and computation which is capable of handling videos of arbitrary length while performing tracking in real time. We demonstrate the effectiveness of our algorithms on the KITTI and PETS2009 benchmarks and show state-of-the-art performance, while being significantly faster than existing solvers.
Induction of high mobility group box-1 in dorsal root ganglion contributes to pain hypersensitivity after peripheral nerve injury (2010)

Pro-inflammatory cytokine high mobility group box-1 (HMGB-1) is involved in inflammation in the central nervous system, but less is known about its biological effects in the peripheral nervous system. In the present study, the role of HMGB-1 in the primary afferent nerve was investigated in the context of the pathophysiology of peripheral nerve injury-induced pain hypersensitivity. Real-time PCR confirmed an increase in HMGB-1 mRNA expression in the dorsal root ganglion (DRG) and spinal nerve at 1 day after spinal nerve ligation (SNL). Induction of HMGB-1 mRNA was observed in both injured L5 and uninjured L4. Immunohistochemistry for HMGB-1 revealed that SNL-induced HMGB-1 expression in the primary afferent neurons and satellite glial cells (SGCs) in the DRG, and in Schwann cells in the spinal nerve. Up-regulation of HMGB-1 was associated with translocation of its signal from the nucleus to the cytoplasm. Injection of HMGB-1 into the sciatic nerve produces transient behavioural hyperalgesia. Neutralizing antibody against HMGB-1 successfully alleviated the mechanical allodynia observed after SNL treatment. Receptor for advanced glycation end products (RAGE), one of the major receptors for HMGB-1, was expressed in the primary afferent neurons and SGCs in the DRG, as well as in Schwann cells in the spinal nerve. These results indicate that HMGB-1 is synthesized and secreted into the DRG and spinal nerve, and contributes to the development of neuropathic pain after nerve injury. Blocking HMGB-1/RAGE signalling might thus be a promising therapeutic strategy for the management of neuropathic pain.
Double replacement: strategy for efficient introduction of subtle mutations into the murine Col1a-1 gene by homologous recombination in embryonic stem cells. (1994)

A subtle mutation that rendered type I collagen resistant to mammalian collagenase has been introduced into the murine Col1a-1 (recently redesignated Cola-1) gene by homologous recombination in embryonic stem (ES) cells. Initially, a "hit and run" procedure was used. Since two steps were required for introducing each mutation and more than one mutation was to be introduced in the same genomic region independently, we have developed a streamlined procedure that involves two sequential replacement-type homologous recombination events. In the first step, an internal deletion was introduced into the Col1a-1 locus along with the positive and negative selectable markers, neo and tk, to mark the region of interest. G418-resistant homologous recombinants were isolated and used in the second step in which the deleted Col1a-1 allele was replaced with a construct containing the desired mutation. Homologous recombinants containing the mutation were identified among the Tk- ES clones after selection with FIAU [1-(2-deoxy-2-fluoro-beta-D-arabinofuranosyl)-5-iodouracil (called fialuridine)]. Approximately 10% of such clones contained the desired mutation. The double replacement procedure greatly reduces the time and amount of work required to introduce mutations independently into the same or closely linked regions. Once the homologous recombinants derived from the first step are established, the introduction of other mutations into the deleted region becomes a one-step procedure. For X number of introduced mutations, 2X selections are required with the "hit and run" approach, but only X + 1 are required with the double-replacement method. This innovative procedure could be very useful in studies of gene structure and function as well as gene expression and regulation.
Immunohistochemical localization of capsular polysaccharide antigen in the central nervous system cells in cryptococcal meningoencephalitis. (1996)

Cryptococcal meningoencephalitis (CME) is caused by the encapsulated fungus Cryptococcus neoformans (CN) and is a major cause of mortality and morbidity in patients with AIDS. The polysaccharide capsule of CN is important for virulence, and soluble polysaccharide has the potential to cause immune modulation. To better understand the interactions of central nervous system cells and cryptococcal capsular polysaccharide (CNPS) in the pathogenesis of human CME, postmortem brain tissue from 21 patients with CME (13 AIDS and 8 non-AIDS patients) was analyzed. Histopathology and distribution of tissue CNPS antigen were analyzed using monoclonal antibodies against CNPS in combination with cell type-specific markers (glial fibrillary acidic protein for astrocytes, Ricinus communis agglutinin (RCA)-l for macrophage/microglia and endothelial cells; UCHL-1 for T cells, L26 for B cells). The CN cells showed discrete capsular immunoreactivity as expected; however, diffuse and particulate cellular and tissue staining for CNPS was detected in the brain parenchyma and the meninges in all cases. By quantitative analysis, the CNPS immunoreactive area ranged from 0.1 to 88 percent of tissue cross sectional area, and tended to be higher in brains of AIDS (median values from two sections ranged from 1 to 57 percent; mean, 26 percent) than in non-AIDS (0.1 to 40 percent; mean, 9.6 percent) patients. The proportion of CNPS immunoreactive area was positively correlated with the estimated number of CN. None (0/13) of the AIDS patients displayed significant inflammatory responses to CN, whereas most (7/8) non-AIDS patients showed granulomatous inflammatory responses. The phenotype of infiltrating lymphocytes was UCHL-1+/L26-/RC4-, thus consistent with activated T cells, both in AIDS and non-AIDS patients. Double immunolabeling studies revealed that tissue CNPS immunoreactivity was most often localized in macrophages and microglia, less frequently in reactive astrocytes and endothelial cells, but not in lymphocytes. This study demonstrates that CNPS can be detected not only in the serum and cerebrospinal fluid (CSF) of patients, but also in the affected tissue, most often localized in cells of mononuclear phagocyte system. Potential implications of these findings for the pathogenesis of CME are discussed.
Morphologische Untersuchungen an heterologen Herzklappentransplantaten unter verschiedenen Sterilisationsbedingungen (1969)

Aortenklappengewebe von 6 Monate alten Kälbern wurde mit verschiedenen Sterilisationsverfahren behandelt und danach anhand von histologischen Schnitten mikroskopisch und histometrisch untersucht. Dabei ließ sich je nach Art der Sterilisierung eine unterschiedlich starke zystische Auflockerung der Faserstruktur des Herzklappengewebes nachweisen. Die stärksten Veränderungen verursacht die Behandlung mit Gamma-Strahlen. In abnehmender Wirkungsstärke folgen die Äthylenoxyd-Begasung, die Behandlung mit Beta-propiolactone-Lösung, Cialit-Lösung und schließlich die reine Lyophilisierung, die nur geringe morphologisch nachweisbare Strukturveränderungen bewirkt. Diese morphologischen Veränderungen stehen vermutlich mit Veränderungen der interfibrillären Grundsubstanz in Zusammenhang, die zu Diffusionsstörungen und damit zu Ernährungsstörungen des Gewebes führen können.
Adenovirus-Mediated Expression of a Ribozyme to c- myb mRNA Inhibits Smooth Muscle Cell Proliferation and Neointima Formation In Vivo (1999)

Smooth muscle cell (SMC) proliferation is an important component of restenosis in response to injury after balloon angioplasty. Inhibition of proliferation in vivo can limit neointima hyperplasia in animal models of restenosis. Ribozymes against c-myb mRNA have been shown to be effective inhibitors of SMC proliferation in vitro. The effectiveness of adenovirus as a gene therapy vector in animal models of restenosis is well documented. In order to test the utility of ribozymes to inhibit SMC proliferation by a gene therapy approach, recombinant adenovirus expressing ribozymes against c-myb mRNA was generated and tested both in vitro and in vivo. This adenovirus ribozyme vector is shown to inhibit SMC proliferation in culture and neointima formation in a rat carotid artery balloon injury model of restenosis.
Affinity enhancement of a recombinant antibody: formation of complexes with multiple valency by a single-chain Fv fragment–core streptavidin fusion (1996)

In antigen-antibody interactions, the high avidity of antibodies depends on the affinity and number of the individual binding sites. To develop artificial antibodies with multiple valency, we have fused the single-chain antibody Fv fragments to core streptavidin. The resulting fusion protein, termed scFv::strep, was found after expression in Escherichia coli in periplasmic inclusion bodies. After purification of the recombinant product by immobilized metal affinity chromatography, refolding and size-exclusion FPLC, tetrameric complexes resembling those of mature streptavidin were formed. The purified tetrameric scFv::strep complexes demonstrated both antigen- and biotin-binding activity, were stable over a wide range of pH and did not dissociate at high temperatures (up to 70 degrees C). Surface plasmon resonance measurements in a BIAlite system showed that the pure scFv::strep tetramers bound immobilized antigen very tightly and no dissociation was measurable. The association rate constant for scFv::strep tetramers was higher than those for scFv monomers and dimers. This was also reflected in the apparent constants, which was found to be 35 times higher for pure scFv::strep tetramers than monomeric single-chain antibodies. We could also show that most of biotin binding sites were accessible and not blocked by biotinylated E.coli proteins or free biotin from the medium. These sites should therefore facilitate the construction of bispecific multivalent antibodies by the addition of biotinylated ligands.
Localization of guanylate cyclase-activating protein 2 in mammalian retinas (1997)

Guanylate cyclase-activating proteins (GCAP1 and GCAP2) are thought to mediate the intracellular stimulation of guanylate cyclase (GC) by Ca2+, a key event in recovery of the dark state of rod photoreceptors after exposure to light. GCAP1 has been localized to rod and cone outer segments, the sites of phototransduction, and to photoreceptor synaptic terminals and some cone somata. We used in situ hybridization and immunocytochemistry to localize GCAP2 in human, monkey, and bovine retinas. In human and monkey retinas, the most intense immunolabeling with anti-GCAP2 antibodies was in the cone inner segments, somata, and synaptic terminals and, to a lesser degree, in rod inner segments and inner retinal neurons. In bovine retina, the most intense immunolabeling was in the rod inner segments, with weaker labeling of cone myoids, somata, and synapses. By using a GCAP2-specific antibody in enzymatic assays, we confirmed that GCAP1 but not GCAP2 is the major component that stimulates GC in bovine rod outer segment homogenates. These results suggest that although GCAP1 is involved in the Ca2+-sensitive regulation of GC in rod and cone outer segments, GCAP2 may have non-phototransduction functions in photoreceptors and inner retinal neurons.