gebhart/patrepeval huggingface dataset:
Optimization of AAV expression cassettes to improve packaging capacity and transgene expression in neurons (2014)

Adeno-associated virus (AAV) vectors can deliver transgenes to diverse cell types and are therefore useful for basic research and gene therapy. Although AAV has many advantages over other viral vectors, its relatively small packaging capacity limits its use for delivering large genes. The available transgene size is further limited by the existence of additional elements in the expression cassette without which the gene expression level becomes much lower. By using alternative combinations of shorter elements, we generated a series of AAV expression cassettes and systematically evaluated their expression efficiency in neurons to maximize the transgene size available within the AAV packaging capacity while not compromising the transgene expression. We found that the newly developed smaller expression cassette shows comparable expression efficiency with an efficient vector generally used for strong gene expression. This new expression cassette will allow us to package larger transgenes without compromising expression efficiency.
The eIF4E RNA regulon promotes the Akt signaling pathway (2008)

Eukaryotic initiation factor 4E (eIF4E) promotes cellular proliferation and can rescue cells from apoptotic stimuli such as serum starvation. However, the mechanisms underlying apoptotic rescue are not well understood. In this study, we demonstrate that eIF4E overexpression leads to enhanced survival signaling through Akt and that eIF4E requires Akt1 to rescue serum-deprived fibroblasts. Furthermore, a mutant form of eIF4E (W73A), which is messenger RNA (mRNA) export competent but does not promote translation, rescues cells as readily as wild-type eIF4E. We show that eIF4E mediates Akt activation via up-regulation of Nijmegen breakage syndrome 1 (NBS1), a phosphoinositide-3 kinase-Akt pathway upstream activator. Additionally, eIF4E coordinately up-regulates the expression of downstream effectors of the Akt pathway, thereby amplifying Akt signaling effects. A negative regulator of eIF4E, the promyelocytic leukemia protein (PML), suppresses Akt activation and apoptotic rescue. These PML activities likely arise, at least in part, through its inhibition of eIF4E-mediated NBS1 mRNA export. In summary, eIF4E coordinately regulates gene expression to potentiate Akt activation, an activity required for apoptotic rescue.
Mutations in Influenza Virus M1 CCHH, the Putative Zinc Finger Motif, Cause Attenuation in Mice and Protect Mice against Lethal Influenza Virus Infection (2006)

Mutations in CCHH, the putative zinc finger motif, apparently do not play an important role in virus replication in MDCK cells in culture (E. K.-W. Hui, K. Ralston, A. K. Judd, and D. P. Nayak, J. Gen. Virol. 84:3105-3113, 2003). In this report, however, we demonstrate that the CCHH motif plays a critical role in virulence in mice and that some CCHH mutants are highly attenuated in BALB/c mice. Some of the mutant viruses replicated the least in mice lungs, induced little or no lung lesions, and caused highly reduced morbidity and mortality. Furthermore, growth patterns of mutant viruses in different cell lines (MDCK, MLE12, 3LL, A549, and 293T) varied. Mutant viruses that were attenuated in mice also grew poorly in mouse and human cells in culture. However, wild-type (WT) and all mutant viruses replicated to the same titer in MDCK (canine) cells or embryonated chicken eggs. Attenuation in mice correlated with reduced growth in mouse cells in culture, suggesting that potential attenuation in a given host can be predicted from the growth characteristics of the virus in cultured cells (preferably lung cells) from the same species. In challenge experiments, mice immunized by infection with attenuated mutant viruses were fully protected from lethal challenge with WT virus. In summary, the replication and attenuating properties of these mutants suggest that the CCHH motif provides a critical determinant for virulence in mouse and that mutations in the CCHH motif yield potential vaccine candidates for the development of live species-specific attenuated influenza virus vaccines.
15-Hydroxyeicosatetraenoic acid is a potent inflammatory mediator and agonist of canine tracheal mucus secretion. (1985)

It was shown that 15-hydroxyeicosatetraenoic acid (15-HETE) but not 15-H(P)ETE or 5-HETE is a potent agonist for secretion of glycoprotein-containing mucus from the in vivo canine trachea. Given by aerosol into the lungs or by intra-arterial injection into the trachea, 15 HETE also caused the chemotaxis of inflammatory cells into the lumen of the airways. Accompanying this inflammatory cell infiltrate was an increase (183%, p less than 0.05) of expiration of fluid in the partially saturated air coming from the lung. The levels of 15-HETE extracted from tracheal mucus correlated well with hillocks and weight of secreted mucus found in the mucus after hypoxia or after arachidonic acid loading. Indomethacin and atropine blocked the mucus secretagogue effect of 15-HETE in the trachea. Indomethacin and U-52, 412 (a 15-lipoxygenase inhibitor) pretreatment abolished a portion of the 15-HETE-induced enhancement of mucus weight and 15-HETE level in the secretion.
Appearance of immunoglobulin G Fc receptor in cultured human cells infected with varicella-zoster virus (1979)

After infection with varicella-zoster virus, HeLa and human embryo lung cells developed a receptor for the Fc portion of human and rabbit immunoglobulin G. The receptor was detected by both hemadsorption and immunofluorescence, using antibody-coated erythrocytes and heat-aggregated immunoglobulin G. However, sheep erythrocytes sensitized with F(ab')2 of anti-sheep erythrocyte antibody did not adsorb to the receptor. When cell-free varicella-zoster virus was inoculated into the HeLa cell monolayer, the Fc receptor appeared at first 6 h after infection; varicella-zoster virus antigen in the cytoplasm and detectable cytopathic effects appeared later.
On‐Line Monitoring of Adhesion and Proliferation of Cultured Hepatoma Cells Using Optical Waveguide Lightmode Spectroscopy (OWLS) (2002)

Monitoring of cell adhesion, cell spreading, and cell proliferation opens attractive perspectives in the on-line control of monolayer cell cultures in toxicity tests, in bioreactors as used for the serial production of skin grafts, or in extracorporeal liver devices. In this study the hepatoma Hep G2 cell adhesion and proliferation was monitored using an integrated optical method, optical waveguide lightmode spectroscopy (OWLS). This method is based upon refractive index measurements within a 100-nm thin layer above a Si(Ti)O(2) surface on which the cells were cultured and exposed to cytotoxic and cytostatic agents. The OWLS signal was proportional to cell density during the spreading period (4 h), and in long-term experiments (46 h) the OWLS signal correlated on a logarithmic scale with cell density. After administration of the protein synthesis inhibitor cycloheximide (4 microg/mL) to fully spread hepatoma cells, cell growth was arrested and change of the OWLS signal became noticeable within 6 h after drug administration. For exposure to increasing concentrations of the anticancer drug cyclophosphamide (2.5-20 mM) a concentration-dependent reduction of the OWLS signal was found. For cycloheximide and cyclophospamide the OWLS signal was also confirmed by cell viability measurements using the neutral red assay, the thiazolylblue tetrazoliumbromide assay, total protein measurements, and cell morphology. It was demonstrated that the OWLS signal detects minor changes in cell adhesion, which serve as indicators of metabolic state and growth behavior. OWLS is thus a quantitative tool to characterize impaired cell growth mediated by culture medium, by extracellular matrix, or after exposure to a toxin.
Influence of Thermal Processing Conditions on Acrylamide Generation and Browning in a Potato Model System (2006)

Fried potato products such as French fries and chips may contain substantial amounts of acrylamide. Numerous efforts are undertaken to minimize the acrylamide content of these products while sensory properties such as color and flavor have to be respected as well. An optimization of the frying process can be achieved if the basic kinetic data of the browning and acrylamide formation are known. Therefore, heating experiments with potato powder were performed under controlled conditions (moisture, temperature, and time). Browning and acrylamide content both increased with heating time at all temperatures and moisture contents tested. The moisture content had a strong influence on the activation energy of browning and acrylamide formation. The activation energy strongly increased at moisture contents below 20%. At higher moisture contents, it was very similar for both parameters. At low moisture contents, the activation energy of acrylamide formation was larger as compared to the one for browning. This explains why the end of the frying process is very critical. Therefore, a lower temperature toward the end of frying reduces the acrylamide content of the product while color development is still good.
Carbon Dioxide Transport and Carbonic Anhydrase in Blood and Muscle (2000)

CO(2) produced within skeletal muscle has to leave the body finally via ventilation by the lung. To get there, CO(2) diffuses from the intracellular space into the convective transport medium blood with the two compartments, plasma and erythrocytes. Within the body, CO(2) is transported in three different forms: physically dissolved, as HCO(3)(-), or as carbamate. The relative contribution of these three forms to overall transport is changing along this elimination pathway. Thus the kinetics of the interchange have to be considered. Carbonic anhydrase accelerates the hydration/dehydration reaction between CO(2), HCO(3)(-), and H(+). In skeletal muscle, various isozymes of carbonic anhydrase are localized within erythrocytes but are also bound to the capillary wall, thus accessible to plasma; bound to the sarcolemma, thus producing catalytic activity within the interstitial space; and associated with the sarcoplasmic reticulum. In some fiber types, carbonic anhydrase is also present in the sarcoplasm. In exercising skeletal muscle, lactic acid contributes huge amounts of H(+) and by these affects the relative contribution of the three forms of CO(2). With a theoretical model, the complex interdependence of reactions and transport processes involved in CO(2) exchange was analyzed.
Promyelocytic Leukemia Activates Chk2 by Mediating Chk2 Autophosphorylation (2006)

Chk2 is a kinase critical for DNA damage-induced apoptosis and is considered a tumor suppressor. Chk2 is essential for p53 transcriptional and apoptotic activities. Although mutations of p53 are present in more than half of all tumors, mutations of Chk2 in cancers are rare, suggesting that Chk2 may be inactivated by unknown alternative mechanisms. Here we elucidate one such alternative mechanism regulated by PML (promyelocytic leukemia) that is involved in acute promyelocytic leukemia (APL). Although p53-inactivating mutations are extremely rare in APL, t(15;17) chromosomal translocation which fuses retinoic acid receptor (RARalpha) to PML is almost always present in APL, while the other PML allele is intact. We demonstrate that PML interacts with Chk2 and activates Chk2 by mediating its autophosphorylation step, an essential step for Chk2 activity that occurs after phosphorylation by the upstream kinase ATM (ataxia telangiectasia-mutated). PML/RARalpha in APL suppresses Chk2 by dominantly inhibiting the auto-phosphorylation step, but inactivation of PML/RARalpha with alltrans retinoic acid (ATRA) restores Chk2 autophosphorylation and activity. Thus, by fusing PML with RARalpha, the APL cells appear to have achieved functional suppression of Chk2 compromising the Chk2-p53 apoptotic pathway.
In vivo evidence of cerebellar atrophy and cerebral white matter loss in Huntington disease (2004)

The cerebellum and the integrity of cerebral white matter may play a more significant role in the symptomatology of HD than previously thought. Furthermore, changes in cortical gray and cerebral white matter were related to caudate atrophy, supporting a similar mechanism of degeneration.
Immunoprotective Leishmania major synthetic T cell epitopes. (1990)

Using the predictive algorithm of Rothbard and Taylor (1988. EMBO J. 7:93) and the primary structure of gp63 (Button, L., and M.R. McMaster. 1988. J. Exp. Med. 167:724; Miller, R.A., S.G. Reed, and M. Parsons. 1990. Mol. Biochem. Parasitol. 39:267) we have been able to delineate the structures of a number of gp63 T-cell epitopes which stimulate the proliferation of CD4+ cells. One of these synthetic antigens, inoculated subcutaneously with adjuvant, was shown to specifically induce proliferation of the Th1 subset and provided immunoprotection against two species of Leishmania parasites.
Stabilization of RNA hairpins using non-nucleotide linkers and circularization (2017)

An RNA hairpin is an essential structural element of RNA. Hairpins play crucial roles in gene expression and intermolecular recognition but are also involved in the pathogenesis of some congenital diseases. Structural studies of the hairpin motifs are impeded by their thermodynamic instability, as they tend to unfold to form duplexes, especially at high concentrations required for crystallography or nuclear magnetic resonance spectroscopy. We have elaborated techniques to stabilize the RNA hairpins by linking the free ends of the RNA strand at the base of the hairpin stem. One method involves stilbene diether or hexaethylene glycol linkers and circularization by T4 RNA ligase. Another method uses click chemistry to stitch the RNA ends with a triazole linker. Both techniques are efficient and easy to perform. They should be useful in making stable, biologically relevant RNA constructs for structural studies.
Generation of a Dominant-negative Mutant of Endothelial PAS Domain Protein 1 by Deletion of a Potent C-terminal Transactivation Domain (1999)

Endothelial PAS domain protein 1 (EPAS1) is a basic helix-loop-helix/PAS domain transcription factor that is preferentially expressed in vascular endothelial cells. EPAS1 shares high homology with hypoxia-inducible factor-1alpha (HIF-1alpha) and, like HIF-1alpha, has been shown to bind to the HIF-1-binding site and to activate its downstream genes such as vascular endothelial growth factor (VEGF) and erythropoietin. In this report, we show that EPAS1 increased VEGF gene expression through the HIF-1-binding site. This transactivation was enhanced further by cotransfection of an aryl hydrocarbon receptor nuclear translocator expression plasmid. Deletion analysis of EPAS1 revealed a potent activation domain (amino acids 486-639) essential for EPAS1 to transactivate the VEGF promoter. We confirmed the ability of this domain to activate transcription using a Gal4 fusion protein system. Because a truncated EPAS1 protein lacking the transactivation domain at amino acids 486-639 eliminated induction of the VEGF promoter by wild-type EPAS1, the truncated protein functions as a dominant-negative mutant. Most important, infection of the cells with an adenoviral construct expressing this mutant inhibited the induction of VEGF mRNA under conditions that mimic hypoxia. Our results suggest that EPAS1 is an important regulator of VEGF gene expression. Since VEGF plays a crucial role in angiogenesis, the ability of dominant-negative EPAS1 to inhibit VEGF promoter activity raises the possibility of a novel approach to inhibiting pathological angiogenesis.
β-Trace Protein, Cystatin C, β2-Microglobulin, and Creatinine Compared for Detecting Impaired Glomerular Filtration Rates in Children (2002)

BTP is superior to serum creatinine and an alternative for Cys-C to detect mildly reduced GFR in children, but it is not better than the Schwartz GFR estimate.
A New Class of Branched Aminoglycosides:  Pseudo-Pentasaccharide Derivatives of Neomycin B (2003)

[reaction: see text] The clinically important antibiotic neomycin B was modified at position C5' ' by adding one extra sugar ring in the beta-configuration, and the observed pseudo-pentasaccharides were tested against various bacterial strains, including pathogenic and resistant strains. The designed antibiotics show antibacterial activity superior to that of neomycin B against pathogenic and resistant bacterial strains.
Attenuation of ceramide-induced apoptosis by diglyceride in human myeloid leukemia cells. (1994)

Prior studies demonstrated that increased intracellular availability of ceramide induces apoptotic DNA degradation and cell death in the human leukemia cell lines HL-60 and U937 (Jarvis, W. D., Kolesnick, R. N., Fornari, F. A., Traylor, R. S., Gewirtz, D. A., and Grant, S. (1994) Proc. Natl. Acad. Sci. U. S. A. 91, 73-77). The present findings show that diglyceride opposes ceramide-related apoptosis in HL-60 and U937 cells. Acute (6-12-h) exposure to sphingomyelinase (100 milliunits/ml) or synthetic ceramide (10 microM) promoted apoptotic degradation of genomic DNA as indicated by (a) the appearance of both approximately 50-kilobase pair (kbp) DNA fragments and approximately 0.2-1.2-kbp DNA fragment ladders on agarose gels, (b) formation and release of small double-stranded DNA fragments, and (c) loss of integrity of bulk DNA. DNA damage was associated with reduced clonogenicity and expression of apoptotic morphology. In contrast, exposure to phospholipase C (0.001-100 milliunits/ml) or synthetic diglyceride (10 microM) failed to promote apoptosis and abolished the lethal actions of ceramide as defined by each of the indices outlined above. Ceramide-related apoptosis was also reduced by acute (6-h) exposure to tumor promoters such as phorbol dibutyrate and mezerein and the non-tumor-promoting agent bryostatin 1; conversely, chronic (24-h) pretreatment with these agents failed to modify ceramide-mediated cytotoxicity, but abolished the protective actions of diglyceride. These findings demonstrate that diglyceride and pharmacological protein kinase C activators reduce or abolish ceramide-mediated apoptosis in human leukemia cells and support the concept of a cytoprotective function for protein kinase C in the regulation of leukemic cell survival. In addition, the capacity of diglyceride to prevent very early genomic lesions (e.g. generation of 50-kbp DNA fragments) suggests that acute activation of protein kinase C arrests apoptosis at an initial stage.
Flow Cytometry Detection and Evaluation of Bladder Tumors (1990)

The diagnosis and classification of bladder cancer are based primarily on histologic and cytologic light microscopy. The significant cytologic alternations are abnormal (increased) DNA content and structural changes in chromatin. Measurements of DNA content carried out by flow cytometry on suspensions of tumor cells and bladder irrigation specimens correlate well with clinical and biopsy findings. Badalament et al (Badalament RA, Kimmel M, Gay H, et al. Cancer 1987;59:2078-2085) reported that a single bladder wash flow cytometry correctly detected 83% of bladder cancers. The technique is most sensitive in detecting early, in situ, and superficially invasive carcinoma. In 100 urologic patients with non-neoplastic disease of the bladder, Klein et al (Klein FA, Herr HW, Sogani PC, et al. J Urol. 1982;127:946-948) reported only two false-positive examinations. Flow cytometry appears to be at least as valuable as conventional urinary cytology, without the need of an experienced cytopathologist. However, as specimens must be collected by bladder irrigation via catheter or cytoscope, the technique is most suitable not for population screening, but in monitoring high-risk populations: industrial workers or others exposed to carcinogens, persons with a history of urothelial tumors, and adult patients referred for urologic examinations because of hematuria, unexplained, recurrent cystitis, or other urologic symptoms. DNA flow cytometry also has been valuable in monitoring the conservative treatment of bladder cancer and of predictive value in the intravesical bacille Calmette-Guérin treatment of superficial carcinomas of the bladder. Dual parameter measurements of DNA content and antigen expression are now under evaluation, as are measurements of chromatin structure alteration, metabolism, and proliferative rate. These promise to discriminate subsets of bladder cancer that may be predictive of clinical behavior.
Effects of 5-aminolevulinic acid-mediated photodynamic therapy on GVHD and GVL following Allo-BMT in ALL mice (2007)

Objectives To elucidate the effects of 5-aminolevulinic acid-mediated photodynamic therapy(ALA-PDT)on graft-versus-host disease(GVHD)and graft-versus-leukemia(GVL)effect following allogenic bone marrow transplantation(allo-BMT)in mice with acute lymphoblast leukemia(ALL).Methods Allo-BMT was carried out in ALL mice following lethal dose of 60Co radiation;meanwhile,mixed lymphocytes prepared by ALA-PDT were infused into ALL mice.Bone marrow cells-spleen cells transplantation group and radiated mice without any intervention were used as controls.General condition,survival rate on day 30,recovery of haematopoietic function,and pathological changes of the liver were applied to evaluate the beneficial effects of ALA-PDT on GVHD and GVL in ALL mice.Results ALA-PDT pretreatment significantly(P 0.01=improved the survival rate of ALL mice.Recovery of haematopoietic function and GVHD development are more improved than that of the other two control groups.Conclusions ALA-PDT significantly alleviated GVHD in ALL mice following allo-BMT and reserved its GVL effect.
Treatment of glioblastoma with intravenous taurolidine. First clinical experience. (2004)

Both patients achieved a transient, marked improvement in quality of life and partial tumor remission. There was a clear response to the taurolidine treatment.