gebhart/patrepeval huggingface dataset:
Homologous Recombination-Independent Large Gene Cassette Knock-in in CHO Cells Using TALEN and MMEJ-Directed Donor Plasmids (2015)

Gene knock-in techniques have rapidly evolved in recent years, along with the development and maturation of genome editing technology using programmable nucleases. We recently reported a novel strategy for microhomology-mediated end-joining-dependent integration of donor DNA by using TALEN or CRISPR/Cas9 and optimized targeting vectors, named PITCh (Precise Integration into Target Chromosome) vectors. Here we describe TALEN and PITCh vector-mediated integration of long gene cassettes, including a single-chain Fv-Fc (scFv-Fc) gene, in Chinese hamster ovary (CHO) cells, with comparison of targeting and cloning efficiency among several donor design and culture conditions. We achieved 9.6-kb whole plasmid integration and 7.6-kb backbone-free integration into a defined genomic locus in CHO cells. Furthermore, we confirmed the reasonable productivity of recombinant scFv-Fc protein of the knock-in cells. Using our protocol, the knock-in cell clones could be obtained by a single transfection and a single limiting dilution using a 96-well plate, without constructing targeting vectors containing long homology arms. Thus, the study described herein provides a highly practical strategy for gene knock-in of large DNA in CHO cells, which accelerates high-throughput generation of cell lines stably producing any desired biopharmaceuticals, including huge antibody proteins.
Netscape Enterprise Server (1996)

From the Publisher:
In this comprehensive reference, you'll find mechanical details for setting up and running a powerful Netscape Enterprise Server. The book also shows you practical ways to use this system to expand your opportunities; global market reach, employee communication, customer interaction.
Characteristics of Vasospastic Angina With Exercised-Induced Ischemia (1996)

To characterize the vasospastic angina patients with exercise-induced ischemia, we measured hemostasis (platelet factor 4; PF4, fibrinopeptide A; FPA) and fibrinolytic parameters (tissue plasminogen activator antigen; t-PA, free plasminogen activator inhibitor-1 antigen; free PAI-1) in 15 normal subjects and 33 vasospastic angina patients without significant coronary artery stenosis (less than 50% stenosis). All of the vasospastic angina patients began to feel chest pain within 3 months before diagnostic coronary angiography. Blood samples were obtained from all of the study patients at 8:30-9:30 am before exercise 201Tl emission computed tomography. Vasospastic angina patients were divided into 2 groups; 15 patients with exercise-induced ischemia (group 1) and 18 patients without exercise-induced ischemia (group 2). On coronary angiography, the severity of coronary artery stenosis at the site of spasm in group 1 (34 +/- 5%) was greater than that in group 2 (18 +/- 3%). Plasma FPA and PF 4 levels in group 1 were also significantly higher than those in normal subjects and group 2. Plasma t-PA and free PAI-1 levels in group 1 were significantly higher than those in normal subjects and group 2. Plasma levels of free PAI-1 group 2 were also significantly higher than those in normal subjects. The present study demonstrated that all of the patients with vasospastic angina had impaired fibrinolysis, and these patients with exercise-induced ischemia showed enhanced platelet activation, an enhanced coagulation system, and advanced atherosclerotic lesions. These results suggest that vasospastic angina with exercise-induced ischemia puts patients at increased risk for thrombus formation.
A spatial data cube concept to support data analysis in environmental epidemiology (2002)

The project CARLOS (Cancer Registry Lower-Saxony) developed the Epidemiological and Statistical Data Exploration System (CARESS) to support multidimensional analysis of health data. The system is based on an architecture that focuses on extensive interoperability between a database management system and several analysis and visualisation tools. As spatial and statistical aspects of the data play an important role, CARESS provides special support for the integration of both.
Effects of an anti-inflammatory VAP-1/SSAO inhibitor, PXS-4728A, on pulmonary neutrophil migration (2015)

This study demonstrates that the endothelial cell ligand VAP-1/SSAO contributes to the migration of neutrophils during acute lung inflammation, pulmonary infection and airway hyperractivity. These results highlight the potential of inhibiting of VAP-1/SSAO enzymatic function, by PXS-4728A, as a novel therapeutic approach in lung diseases that are characterized by neutrophilic pattern of inflammation.
Ubiquitination of Protein Kinase C-α and Degradation by the Proteasome (1996)

Bryostatins and phorbol esters acutely activate and subsequently down-regulate protein kinase C (PKC) by inducing its proteolysis via an unknown pathway. Here we show that treatment of renal epithelial cells with bryostatin 1 (Bryo) produced novel PKC-alpha species, which were larger than the native protein (80 kDa). The >80 kDa PKC-alpha species contained Ubi as indicated by immunostaining and accumulated in the presence of lactacystin, a selective inhibitor of proteolysis by the proteasome. In vitro experiments with 125I-ubiquitin and membranes from Bryo-treated cells showed that PKC-alpha became ubiquitinated by a reaction that depended on ATP and a cytosolic fraction. Lactacystin or a peptidyl aldehyde, Bz-Gly-Leu-Ala-leucinal, which inhibits certain proteinase activities of the proteasome, inhibited Bryo-evoked disappearance of PKC-alpha protein from the cells. Lacta preserved Bryo-induced 32P-labeled PKC-alpha indicating that the proteasome inhibitor spared activated enzyme from down-regulation in vivo. These findings show that Bryo induces the degradation of PKC-alpha by the ubiquitin-proteasome complex.
Ca2+/calmodulin-dependent protein kinase II is associated with pelvic pain of neurogenic cystitis (2012)

Interstitial cystitis/painful bladder syndrome is a chronic bladder inflammatory disease of unknown etiology that is often regarded as a neurogenic cystitis. Interstitial cystitis is associated with urothelial lesions, voiding dysfunction, and pain in the pelvic/perineal area. In this study, we used a murine neurogenic cystitis model to identify genes participating in the development of pelvic pain. Neurogenic cystitis was induced by the injection of Bartha's strain of pseudorabies virus (PRV) into the abductor caudalis dorsalis (tail base) muscle of female C57BL/6J mice. Mice infected with PRV developed progressive pelvic pain. The sacral spinal cord was harvested on postinfection days (PID) 2 and 4, and gene expression was analyzed by microarrays and confirmed by quantitative RT-PCR. On PID 2, the overall expression profile was similar to that of uninfected sacral spinal cord; by PID 4, there were substantial differences in expression of multiple functional classes of genes, especially inflammation. Analysis of pain-signaling pathways at the dorsal horn suggested that Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) contributes to neurogenic cystitis pelvic pain. Consistent with this, CaMKIIδ expression exhibited a mast cell-dependent increase in the sacral spinal cord at the mRNA level, and phospho-CaMKII immunoreactivity in the dorsal horn was increased on postinfection day (PID) 4 during PRV infection. Finally, intrathecal injection of the CaMKII inhibitor KN-93 attenuated the PRV pain response. These data suggest that CaMKII plays a functional role in pelvic pain due to neurogenic cystitis.
Opportunities for the Use of Business Data Analysis Technologies (2016)

Abstract The paper analyses the business data analysis technologies, provides their classification and considers relevant terminology. The feasibility of business data analysis technologies handling big data sources is overviewed. The paper shows the results of examination of the online big data source analytics technologies, data mining and predictive modelling technologies and their trends.
Presence of immunoglobulin (Ig) M and IgG double isotype-bearing cells and defect of switch recombination in hyper IgM immunodeficiency. (1990)

We established a transformed B cell line expressing both IgM and IgG on the cell surface from a patient with hyper IgM immunodeficiency using Epstein-Barr viruses. DNA and RNA of the cells were analyzed. DNA rearrangements of Ig JH gene loci were observed on both chromosomes. Cloning and DNA sequence analyses showed that one has a VHDHJH structure while the other has a DHJH structure. Southern hybridization with 5'-S mu and S gamma region-containing probes indicated germline configuration in the switch regions of mu and gamma genes on both chromosomes. To test expression of mu and gamma chains in the transformed cells at the mRNA-level, we used the polymerase chain reaction with three kinds of synthetic oligonucleotides as primers, one of which was part of the VH gene, while the other two were complementary to parts of C mu and C gamma genes. Sequence analysis of the amplified products showed that the same VHDHJH sequence is directly connected with either the C mu or the C gamma sequence in the mRNAs. This is direct evidence showing that in double isotype-bearing cells one VHDHJH exon in the transcript is alternatively spliced to C mu or C gamma without DNA rearrangement. The defect in this disease could be at the S-S recombination stage.
A Learned Representation For Artistic Style (2016)

The diversity of painting styles represents a rich visual vocabulary for the construction of an image. The degree to which one may learn and parsimoniously capture this visual vocabulary measures our understanding of the higher level features of paintings, if not images in general. In this work we investigate the construction of a single, scalable deep network that can parsimoniously capture the artistic style of a diversity of paintings. We demonstrate that such a network generalizes across a diversity of artistic styles by reducing a painting to a point in an embedding space. Importantly, this model permits a user to explore new painting styles by arbitrarily combining the styles learned from individual paintings. We hope that this work provides a useful step towards building rich models of paintings and offers a window on to the structure of the learned representation of artistic style.
Laboratory detection of primary and acquired drug resistance in human lymphatic neoplasms. (1986)

We tested the ability of the differential staining cytotoxicity (DiSC) assay to discriminate between sensitive and resistant cell populations in human lymphatic neoplasms. First, the in vitro activity spectra of the most important drugs paralleled the known clinical activity spectra of the same agents. Second, there were highly significant correlations between in vitro chemosensitivity and the results of clinical chemotherapy. Third, specimens from previously untreated patients were significantly more sensitive to the most important drugs than were specimens from patients who had previously received chemotherapy. Finally, metachronous assays performed on specimens from the same patients showed little change in chemosensitivity if there had been no intervening chemotherapy between the times that the first and second assays were performed. However, if the patients had received intervening chemotherapy between the times of the first and second assays, the specimens in the second assays tended to be significantly more resistant than were the specimens in the first assays. These data indicate that the DiSC assay may be of value in the design of strategies to circumvent drug resistance in human lymphatic neoplasms.
The Cholinergic Neuronal Differentiation Factor from Heart Cells Is Identical to Leukemia Inhibitory Factor (1989)

A protein secreted by cultured rat heart cells can direct the choice of neurotransmitter phenotype made by cultured rat sympathetic neurons. Structural analysis and biological assays demonstrated that this protein is identical to a protein that regulates the growth and differentiation of embryonic stem cells and myeloid cells, and that stimulates bone remodeling and acute-phase protein synthesis in hepatocytes. This protein has been termed D factor, DIA, DIF, DRF, HSFIII, and LIF. Thus, this cytokine, like IL-6 and TGF beta, regulates growth and differentiation in the embryo and in the adult in many tissues, now including the nervous system.
Subgenomic replicons of the flavivirus Kunjin: construction and applications (1997)

Several Kunjin virus (KUN) subgenomic replicons containing large deletions in the structural region (C-prM-E) and in the 3' untranslated region (3'UTR) of the genome have been constructed. Replicon RNA deltaME with 1,987 nucleotides deleted (from nucleotide 417 [in codon 108] in the C gene to nucleotide 2403 near the carboxy terminus of the E gene, inclusive) and replicon RNA C20rep with 2,247 nucleotides deleted (from nucleotide 157 [in codon 20] in C to nucleotide 2403) replicated efficiently in electroporated BHK21 cells. A further deletion from C20rep of 53 nucleotides, reducing the coding sequence in core protein to two codons (C2rep RNA), resulted in abolishment of RNA replication. Replicon deltaME/76 with a deletion of 76 nucleotides in the 3'UTR of deltaME RNA (nucleotides 10423 to 10498) replicated efficiently, whereas replicon deltaME/352 with a larger deletion of 352 nucleotides (nucleotides 10423 to 10774), including two conserved sequences RCS3 and CS3, was significantly inhibited in RNA replication. To explore the possibility of using a reporter gene assay to monitor synthesis of the positive strand and the negative strand of KUN RNA, we inserted a chloramphenicol acetyltransferase (CAT) gene into the 3'UTR of deltaME/76 RNA under control of the internal ribosomal entry site (IRES) of encephalomyelocarditis virus RNA in both plus (deltaME/76CAT[+])- and minus (deltaME/76CAT[-])-sense orientations. Although insertion of the IRES-CAT cassette in the plus-sense orientation resulted in a significant (10- to 20-fold) reduction of RNA replication compared to that of the parental deltaME/76 RNA, CAT expression was readily detected in electroporated BHK cells. No CAT expression was detected after electroporation of RNA containing the IRES-CAT cassette inserted in the minus-sense orientation despite its apparently more efficient replication (similar to that of deltaME/76 RNA); this result indicated that KUN negative-strand RNA was probably not released from its template after synthesis. Replacement of the CAT gene in the deltaME/76CAT(+) RNA with the neomycin gene (Neo) enabled selection and recovery of a BHK cell culture in which the majority of cells were continuously expressing the replicon RNA for 41 days (nine passages) without apparent cytopathic effect. The constructed KUN replicons should provide valuable tools to study flavivirus RNA replication as well as providing possible vectors for a long-lasting and noncytopathic RNA virus expression system.
Tissue factor pathway inhibitor (2002)

We have analyzed several mathematical models that describe inhibition of the factor VIIa-tissue factor complex (VIIa-TF) by tissue factor pathway inhibitor (TFPI). At the core of these models is a common mechanism of TFPI action suggesting that only the Xa-TFPI complex is the inhibitor of the extrinsic tenase activity. However, the model based on this hypothesis could not explain well all the available experimental data. Here, we show that a good quantitative description of all experimental data could be achieved in a model that contains two more assumptions. The first assumption is based on the hypothesis originally proposed by Baugh et al. [Baugh, R.J., Broze, G.J. Jr & Krishnaswamy, S. (1998) J. Biol. Chem. 273, 4378-4386], which suggests that TFPI could inhibit the enzyme-product complex Xa-VIIa-TF. The second assumption proposes an interaction between the X-VIIa-TF complex and the factor Xa-TFPI complex. Experiments to test these hypotheses are suggested.
A shunted ring fiber optic network topology providing fault detection, isolation and circumvention (2002)

This paper describes an electro-optic and all optical implementation of a novel "shunted ring" network topology which uses optical waveguide shunts to bypass faults in ring networks. This technique eliminates the need for costly bypass switches and their related deficiencies. "One-by-N" tree couplers are used as the fanout mechanism from an LED or laser to send optical signals to a primary fiber and "N" shunt fibers. These shunt fiber waveguides can be "switched" into the active network when the optical signal in the primary fiber drops below a prescribed level. This permits rapid reconfiguration around a failed node or primary fiber path and minimizes or eliminates the loss of data. In a near term implementation of the concept, the signals from the input primary and shunt fibers are converted to electrical form with standard PIN photodiodes and the signal level is analyzed. If the signal falls below the preset threshold, the output from the shunt fiber(s) is electronically switched into the network node to restore robust network operation. The power budget to determine the number of successive nodes which can be bypassed is identically that of a "1*N" tree network permitting any number of bypasses within the link margin.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Role of glycogen synthase kinase-3β and PPAR-γ on epithelial-to-mesenchymal transition in DSS-induced colorectal fibrosis (2017)

The DSS-induced intestinal fibrosis was improved by the new PPAR-γ modulator GED-0507-34 Levo through the modulation of EMT mediators and pro-fibrotic molecules and through GSK-3β induction.
Development of the pancreas inXenopus laevis (2000)

Xenopus embryos have several experimental advantages for studying development. Although these advantages have traditionally been used to elucidate mechanisms of early development, they can also be exploited to investigate issues later in development such as organogenesis. We have begun to study pancreatic organogenesis in Xenopus. Using histological and molecular marker analysis, we characterized the anatomy of the developing pancreas in Xenopus embryos from the time of initial pancreatic rudiment formation to the time when the tadpole starts to feed. We examined the expression of various endocrine hormones, exocrine gene products, and pancreatic transcription factors. Interestingly, the endocrine hormone insulin has restricted expression in the dorsal pancreas. Investigation of pancreatic specification during gastrulation demonstrates that insulin expression is regionalized along the dorsoventral axis early in development.
Unified model of brain tissue microstructure dynamically binds diffusion and osmosis with extracellular space geometry (2016)

We present a universal model of brain tissue microstructure that dynamically links osmosis and diffusion with geometrical parameters of brain extracellular space (ECS). Our model robustly describes and predicts the nonlinear time dependency of tortuosity (λ=sqrt[D/D^{*}]) changes with very high precision in various media with uniform and nonuniform osmolarity distribution, as demonstrated by previously published experimental data (D = free diffusion coefficient, D^{*} = effective diffusion coefficient). To construct this model, we first developed a multiscale technique for computationally effective modeling of osmolarity in the brain tissue. Osmolarity differences across cell membranes lead to changes in the ECS dynamics. The evolution of the underlying dynamics is then captured by a level set method. Subsequently, using a homogenization technique, we derived a coarse-grained model with parameters that are explicitly related to the geometry of cells and their associated ECS. Our modeling results in very accurate analytical approximation of tortuosity based on time, space, osmolarity differences across cell membranes, and water permeability of cell membranes. Our model provides a unique platform for studying ECS dynamics not only in physiologic conditions such as sleep-wake cycles and aging but also in pathologic conditions such as stroke, seizure, and neoplasia, as well as in predictive pharmacokinetic modeling such as predicting medication biodistribution and efficacy and novel biomolecule development and testing.
Characterisation of human CD5 B cells (1992)

The human 67kDa glycoprotein termed CD5, is equivalent to Ly1 (B-1) in the mouse. This molecule was, originally, described as a pan-T cell marker. Evidence has been accumulating, suggesting that the B cells carrying this marker, would play a key role as producers of antibodies to self-constituents. These studies were initiated, to clarify the repertoires of human CD5 B cells. CD5 molecules were found to be barely detectable on a minority of circulating B lymphocytes. A number of techniques improved the sensitivity of their detection and it was established that the blood of some patients with autoimmune disease, may, in fact, have a higher number of this subpopulation of B cells. Furthermore, chronic lymphocytic leukemia B cells, expressing CD5, were shown to produce auto and polyreactive antibodies. Since it was found that a high proportion of B cells, early in development, express CD5, clones were established by Epstein-Barr virus transformation of CD5+ and CD5- cord blood B lymphocytes, separated by flow cytometry. IgM from many of both CD5+ and CD5- clones reacted with a variety of autoantigens. Examination for expression of cross-reactive idiotypes, associated with defined VH and VK subgroups, revealed that auto and polyreactivity does not appear to be the property of any particular V gene family. Indeed, IgM produced by both subsets of cord blood B cells, were found with equal frequencies of expression of VhI and VhIH associated idiotopes. In contrast, a higher frequency of a VKllIb subgroup associated idiotope, the phenotypic marker for the VK32S germline gene, was found in the CD5+ clones and of particular interest was the restricted association of the CD5 B cells with a VHIV subfamily. In conclusion, differences may exist in the expression of certain germline genes between CD5+ and CD5- cord blood B cells and may indicate an expansion of CD5 B cells within the fetal environment.
Inhibition of Monocyte Adhesion to Brain-Derived Endothelial Cells by Dual Functional RNA Chimeras (2014)

Because adhesion of leukocytes to endothelial cells is the first step of vascular-neuronal inflammation, inhibition of adhesion and recruitment of leukocytes to vascular endothelial cells will have a beneficial effect on neuroinflammatory diseases. In this study, we used the pRNA of bacteriophage phi29 DNA packaging motor to construct a novel RNA nanoparticle for specific targeting to transferrin receptor (TfR) on the murine brain-derived endothelial cells (bEND5) to deliver ICAM-1 siRNA. This RNA nanoparticle (FRS-NPs) contained a FB4 aptamer targeting to TfR and a siRNA moiety for silencing the intercellular adhesion molecule-1 (ICAM-1). Our data indicated that this RNA nanoparticle was delivered into murine brain-derived endothelial cells. Furthermore, the siRNA was released from the FRS-NPs in the cells and knocked down ICAM-1 expression in the TNF-α-stimulated cells and in the cells under oxygen-glucose deprivation/reoxygenation (OGD/R) condition. The functional end points of the study indicated that FRS-NPs significantly inhibited monocyte adhesion to the bEND5 cells induced by TNF-α and OGD/R. In conclusion, our approach using RNA nanotechnology for siRNA delivery could be potentially applied for inhibition of inflammation in ischemic stroke and other neuroinflammatory diseases, or diseases affecting endothelium of vasculature.