gebhart/patrepeval huggingface dataset:
Adeno-associated Virus (AAV) Capsid Chimeras with Enhanced Infectivity Reveal a Core Element in the AAV Genome Critical for both Cell Transduction and Capsid Assembly (2021)

Adeno-associated viruses (AAV) have attracted significant attention in the field of gene and cell therapy due to highly effective delivery of therapeutic genes into human cells. The ability to generate recombinant AAV vectors compromised of unique or substituted protein sequences has led to the development of capsid variants with improved therapeutic properties. Seeking novel AAV vectors capable of enhanced transduction for therapeutic applications, we have developed a series of unique capsid variants termed AAV <i>X-Vivo</i> (AAV-XV) derived from chimeras of AAV12 VP1/2 sequences and the VP3 sequence of AAV6. These AAV variants showed enhanced infection of human primary T cells, hematopoietic stem cells, and neuronal cell lines over wildtype parental viruses, and superiority over AAV6 for genomic integration of DNA sequences by AAV alone or in combination with CRISPR gene editing. AAV-XV variants demonstrate transduction efficiency equivalent to AAV6 at multiplicities of infection 2 logs lower, enabling T cell engineering at low AAV doses. The protein coding sequence of these novel AAV chimeras revealed disruptions within the assembly-activating protein (AAP) which likely accounted for observed lower virus yield. A series of genome alterations, reverting the AAP sequence back to wildtype AAV6, had a negative impact on the enhanced transduction seen with AAV-VX, indicating overlapping functions within this sequence for both viral assembly and effective T cell transduction. Our findings show these AAV-XV variants are highly efficient at cell transduction at low dose and demonstrates the importance of the AAP coding region in both viral particle assembly and cell infection.<b>IMPORTANCE</b> A major hurdle to the therapeutic potential of AAV in gene therapy lies in achieving clinically meaningful AAV doses, and secondarily, ability to manufacture commercially viable titers of AAV to support this. By virtue of neutralizing antibodies against AAV that impede patient repeat-dosing, the dose of AAV for <i>in vivo</i> gene delivery has been high, which has resulted in unfortunate recent safety concerns and deaths in patients given higher-dose AAV gene therapy. We have generated new AAV variants possessing unique combinations of capsid proteins for gene and cell therapy applications termed AAV-XV, which have high levels of cell transduction and gene delivery at lower MOI. Furthermore, we demonstrate a novel finding, and an important consideration for recombinant AAV design, that a region of the AAV genome encoding the capsid viral protein and AAP is critical for both virus yield and the enhancement of infection/transduction.
Inhibition of IL-12 production by thalidomide (1997)

The immunomodulatory properties of thalidomide are currently being exploited therapeutically in conditions as diverse as erythema nodosum leprosum, chronic graft-vs-host disease, rheumatoid arthritis, and sarcoidosis. The relevant mechanism of action of thalidomide in these diseases remains unclear. The important role recently ascribed to IL-12, a cytokine critical to the development of cellular immune responses, in the pathogenesis of several of these conditions led us to examine whether thalidomide affects the production of IL-12. Thalidomide potently suppressed the production of IL-12 from human PBMC and primary human monocytes in a concentration-dependent manner. Thalidomide-induced inhibition of IL-12 production was additive to that induced by suboptimal inhibiting doses of dexamethasone, and occurred by a mechanism independent of known endogenous inhibitors of IL-12 production. These results suggest that thalidomide may have therapeutic utility in a wide range of immunologic disorders that are characterized by inappropriate cellular immune responses.
The Spider Center Wide File System; From Concept to Reality (2009)

The Leadership Computing Facility (LCF) at Oak Ridge National Laboratory (ORNL) has a diverse portfolio of computational resources ranging from a petascale XT4/XT5 simulation system (Jaguar) to numerous other systems supporting development, visualization, and data analytics. In order to support vastly different I/O needs of these systems Spider, a Lustre-based center wide file system was designed and deployed to provide over 240 GB/s of aggregate throughput with over 10 Petabytes of formatted capacity. A multi-stage InfiniBand network, dubbed as Scalable I/O Network (SION), with over 889 GB/s of bisectional bandwidth was deployed as part of Spider to provide connectivity to our simulation, development, visualization, and other platforms. To our knowledge, while writing this paper, Spider is the largest and fastest POSIX-compliant parallel file system in production. This paper will detail the overall architecture of the Spider system, challenges in deploying and initial testings of a file system of this scale, and novel solutions to these challenges which offer key insights into file system design in the future. LocalWords: TN gshipman dillowda oralhs fwang ornl gov twocolumn maketitle LocalWords: twocolumnfalse petascale SION
Influence of Antioxidants on theQuality of Stored Blood (1997)

Background and objectives: Blood is exposed to oxidation stress and therefore has a high antioxidant capacity (AOC). With the many factors increasing the demands on the AOC, there may be damage to erythrocytes by free radicals. This study was to investigate evidence of erythrocyte damage in stored donor blood and to affect this by premedication of blood donors. Materials and methods:Blood samples of 15 healthy donors were collected in CPDA-1 solution and analyzed immediately, and then again after 10 days of incubation at 4°C and 1 day of incubation at 37°C. Prior to incubation, the following parameters were evaluated:Na+, K+, malondialdehyde (MDA), hemoglobin (Hb), AOC in the supernatant,superoxide dismutase (SOD) in erythrocytes, and glutathione peroxidase(GSHPx) in whole blood. Blood donors of group 1 were not given any drugs or vitamins before blood sampling. The same blood donors were then supplemented with the following daily doses of antioxidants for 10 days before the next blood sampling: 36 mg of ß-carotene, 300 mg of vitamin E, 200 mg of vitamin C,and 40 mg of selenium. Results: The blood from donors of group 2 had a significantly smaller increase in MDA, K+, and Hb, and a smaller decrease in Na+ and AOC in the supernatant compared with that of group 1, while the activity of SOD and GSHPx did not change during blood storage. Conclusions: These results suggest that antioxidants given to blood donors can improve red cell storage parameters by reducing cell damage caused by free radicals.
Endocannabinoid Hydrolysis Generates Brain Prostaglandins That Promote Neuroinflammation (2011)

Phospholipase A(2)(PLA(2)) enzymes are considered the primary source of arachidonic acid for cyclooxygenase (COX)-mediated biosynthesis of prostaglandins. Here, we show that a distinct pathway exists in brain, where monoacylglycerol lipase (MAGL) hydrolyzes the endocannabinoid 2-arachidonoylglycerol to generate a major arachidonate precursor pool for neuroinflammatory prostaglandins. MAGL-disrupted animals show neuroprotection in a parkinsonian mouse model. These animals are spared the hemorrhaging caused by COX inhibitors in the gut, where prostaglandins are instead regulated by cytosolic PLA(2). These findings identify MAGL as a distinct metabolic node that couples endocannabinoid to prostaglandin signaling networks in the nervous system and suggest that inhibition of this enzyme may be a new and potentially safer way to suppress the proinflammatory cascades that underlie neurodegenerative disorders.
Augmentation of umbilical cord blood (UCB) transplantation with ex vivo–expanded UCB cells: results of a phase 1 trial using the AastromReplicell System (2003)

Allogeneic stem cell transplantation with umbilical cord blood (UCB) cells is limited by the cell dose a single unit provides recipients. Ex vivo expansion is one strategy to increase the number of cells available for transplantation. Aastrom Biosciences developed an automated continuous perfusion culture device for expansion of hematopoietic stem cells (HSCs). Cells are expanded in media supplemented with fetal bovine serum, horse serum, PIXY321, flt-3 ligand, and erythropoietin. We performed a phase 1 trial augmenting conventional UCB transplants with ex vivo-expanded cells. The 28 patients were enrolled on the trial between October 8, 1997 and September 30, 1998. UCB cells were expanded in the device, then administered as a boost to the conventional graft on posttransplantation day 12. While expansion of total cells and colony-forming units (CFUs) occurred in all cases, the magnitude of expansion varied considerably. The median fold increase was 2.4 (range, 1.0-8.5) in nucleated cells, 82 (range, 4.6-266.4) in CFU granulocyte-macrophages, and 0.5 (range, 0.09-2.45) in CD34+ lineage negative (lin-) cells. CD3+ cells did not expand under these conditions. Clinical-scale ex vivo expansion of UCB is feasible, and the administration of ex vivo-expanded cells is well tolerated. Augmentation of UCB transplants with ex vivo-expanded cells did not alter the time to myeloid, erythroid, or platelet engraftment in 21 evaluable patients. Recipients of ex vivo-expanded cells continue to have durable engraftment with a median follow-up of 47 months (range, 41-51 months). A randomized phase 2 study will determine whether augmenting UCB transplants with ex vivo-expanded UCB cells is beneficial.
Alternative Chelator for 89Zr Radiopharmaceuticals: Radiolabeling and Evaluation of 3,4,3-(LI-1,2-HOPO) (2014)

Zirconium-89 is an effective radionuclide for antibody-based positron emission tomography (PET) imaging because its physical half-life (78.41 h) matches the biological half-life of IgG antibodies. Desferrioxamine (DFO) is currently the preferred chelator for (89)Zr(4+); however, accumulation of (89)Zr in the bones of mice suggests that (89)Zr(4+) is released from DFO in vivo. An improved chelator for (89)Zr(4+) could eliminate the release of osteophilic (89)Zr(4+) and lead to a safer PET tracer with reduced background radiation dose. Herein, we present an octadentate chelator 3,4,3-(LI-1,2-HOPO) (or HOPO) as a potentially superior alternative to DFO. The HOPO ligand formed a 1:1 Zr-HOPO complex that was evaluated experimentally and theoretically. The stability of (89)Zr-HOPO matched or surpassed that of (89)Zr-DFO in every experiment. In healthy mice, (89)Zr-HOPO cleared the body rapidly with no signs of demetalation. Ultimately, HOPO has the potential to replace DFO as the chelator of choice for (89)Zr-based PET imaging agents.
Detection and isolation of thermophilic acidophilic bacteria from fuit juices (2006)

Fruit juices were until recently considered to only be susceptible to spoilage by yeasts, mycelial fungi and lactic acid bacteria.Spoilage by these organisms was prevented by the acidic pH of fruit juices and the heat-treatment applied during the hot-fill-hold process.Despite these control measures, an increasing number of spoilage cases of fruit juices, fruit juice products and acidic vegetables due to contamination by thermophilic acidophilic bacteria (TAB) have been reported.The genus Alicyclobacillus, containing TAB were first classified as Bacillus, but were reclassified in 1992.Species of Alicyclobacillus are Gram-positive, rod-shaped, endospore-forming bacteria.The unique characteristic of these organisms is the presence of -alicyclic fatty acids, such as -cyclohexane and -cycloheptane, as the major components of the cellular membrane.This organism has been shown to survive pasteurisation conditions of 95C for 2 min and grows within a pH range of 2.5 to 6.0 and temperatures between 25 and 60C.The genus currently consists of 11 species, with A. acidoterrestris, A. acidocaldarius and A. pomorum being the only species associated with the spoilage of fruit juices and fruit juice products.The aim of this study was to evaluate culture-dependent and cultureindependent approaches for the detection and isolation of Alicyclobacillus spp.from pasteurised South African fruit juices and concentrates.The culture-dependent approach was evaluated by comparing five different growth media, for growth and recovery of A. acidoterrestris, A. acidocaldarius and A. pomorum at different incubation temperatures, from sterile saline solution (SSS) (0.85% (m/v) NaCl), diluted and undiluted fruit juice concentrates.The five media evaluated included potato dextrose agar (PDA), orange serum agar (OSA), K-agar, yeast extract (YSG)agar and Bacillus acidocaldarius medium (BAM).The culture-independent approach was used to identify the micro-organisms present in fruit juices and concentrates from different South African manufacturers before and after pasteurisation, using polymerase chain reaction (PCR)-based denaturing gradient gel electrophoresis (DGGE) and DNA sequencing.Spread plates of PDA at pH 3.7 and incubation temperature of 50C for 3 days was found to be the best isolation media for species of Alicyclobacillus from fruit juice and fruit juice concentrate.With the inclusion of a heat shock treatment at 80C for 10 min the growth media of preference for spores of Alicyclobacillus from fruit juice concentrates was OSA at pH 5.5 and an incubation temperature of 50C for 3 days.
Characterization of a High-Affinity Folate Receptor in Normal and Malignant Human Testicular Tissue (1999)

We have characterized the folate receptor in normal and malignant tissue from male gonads. Radioligand binding displayed characteristics typical of other folate receptors. Those included a high-affinity type of binding (K = 10(10M-1)), apparent positive cooperativity changing into non-cooperativity at low receptor concentrations, a tendency to increased binding affinity with decreasing receptor concentrations, a slow dissociation at pH 7.4 becoming rapid at pH 3.5 and inhibition by folates, in particular oxidized forms. The gel filtration profile of Triton X-100 solubilized tissue contained a 25 and 100 kDa peak of radioligand-receptor. The latter peak could represent receptor equipped with a hydrophobic membrane anchor that inserts into Triton X-100 micelles. The concentration of radiolabelled receptor ranged from 0.41 nmol/g protein to 1.68 nmol/g protein in specimens of normal testicular tissue from patients with prostatic carcinomas and from 1.54 nmol/g protein to 3.82 nmol/g protein in testicular tissue from young individuals. Compared to normal testicular tissue the concentration of receptor in seminoma tissue was low (0.38-1.27 nmol/g protein) but showed a higher degree of immunoreactivity in the presence of antibodies against human milk folate binding protein as evidenced by ELISA and immunohistochemistry data. Hence a folate receptor isoform homologous to human milk folate binding protein is apparently expressed in seminomas where the total expression of receptor, however, seems to be lower than in normal testicles.
Isolation of tobacco DNA segments with plant promoter activity. (1986)

We constructed a promoter probe vector, pGVL120, to isolate plant DNA segments with promoter activity in tobacco. Plant nuclear DNA Sau3A fragments were inserted in front of the npt-II sequence, and a mixture of recombinant plasmids was mobilized to Agrobacterium sp. and used to transform tobacco protoplasts. By kanamycin selection, transformed plant cell lines containing NPT-II T-DNAs were isolated. Eight of these cell lines were regenerated and analyzed for the levels of NPT-II activity in stem, root, midrib, and leaf. These levels demonstrated novel regulation patterns in each isolate. One cell line, T20, was analyzed in detail and found to contain four different T-DNAs. One of the recloned T-DNAs, T20-2, contains an insert of 401 base pairs in front of the NPT-II sequence, and by reintroducing this T-DNA into plant cells we could demonstrate that this insert provides a promoter sequence. The NPT-II enzyme activity under the control of the P20 promoter is especially high in stem and root, but low in leaf and callus, both in the originally isolated T20 plant and in independently isolated transformants with the T20-2 T-DNA.
Quantitative Proteome Analysis of Human Plasma following in Vivo Lipopolysaccharide Administration Using 16O/18O Labeling and the Accurate Mass and Time Tag Approach (2005)

Identification of novel diagnostic or therapeutic biomarkers from human blood plasma would benefit significantly from quantitative measurements of the proteome constituents over a range of physiological conditions. Herein we describe an initial demonstration of proteome-wide quantitative analysis of human plasma. The approach utilizes postdigestion trypsin-catalyzed 16O/18O peptide labeling, two-dimensional LC-FTICR mass spectrometry, and the accurate mass and time (AMT) tag strategy to identify and quantify peptides/proteins from complex samples. A peptide accurate mass and LC elution time AMT tag data base was initially generated using MS/MS following extensive multidimensional LC separations to provide the basis for subsequent peptide identifications. The AMT tag data base contains >8,000 putative identified peptides, providing 938 confident plasma protein identifications. The quantitative approach was applied without depletion of high abundance proteins for comparative analyses of plasma samples from an individual prior to and 9 h after lipopolysaccharide (LPS) administration. Accurate quantification of changes in protein abundance was demonstrated by both 1:1 labeling of control plasma and the comparison between the plasma samples following LPS administration. A total of 429 distinct plasma proteins were quantified from the comparative analyses, and the protein abundances for 25 proteins, including several known inflammatory response mediators, were observed to change significantly following LPS administration.
Identification of adipocyte adhesion molecule (ACAM), a novel CTX gene family, implicated in adipocyte maturation and development of obesity (2005)

Few cell adhesion molecules have been reported to be expressed in mature adipocytes, and the significance of cell adhesion process in adipocyte biology is also unknown. In the present study, we identified ACAM (adipocyte adhesion molecule), a novel homologue of the CTX (cortical thymocyte marker in Xenopus) gene family. ACAM cDNA was isolated during PCR-based cDNA subtraction, and its mRNA was shown to be up-regulated in WATs (white adipose tissues) of OLETF (Otsuka Long-Evans Tokushima fatty) rats, an animal model for Type II diabetes and obesity. ACAM, 372 amino acids in total, has a signal peptide, V-type (variable) and C2-type (constant) Ig domains, a single transmembrane segment and a cytoplasmic tail. The amino acid sequence in rat is highly homologous to mouse (94%) and human (87%). ACAM mRNA was predominantly expressed in WATs in OLETF rats, and increased with the development of obesity until 30 weeks of age, which is when the peak of body mass is reached. Western blot analysis revealed that ACAM protein, approx. 45 kDa, was associated with plasma membrane fractions of mature adipocytes isolated from mesenteric and subdermal adipose deposits of OLETF rats. Up-regulation of ACAM mRNAs in obesity was also shown in WATs of genetically obese db/db mice, diet-induced obese ICR mice and human obese subjects. In primary cultured mouse and human adipocytes, ACAM mRNA expression was progressively up-regulated during differentiation. Several stably transfected Chinese-hamster ovary K1 cell lines were established, and the quantification of ACAM mRNA and cell aggregation assay revealed that the degree of homophilic aggregation correlated well with ACAM mRNA expression. In summary, ACAM may be the critical adhesion molecule in adipocyte differentiation and development of obesity.
Functional Differences between the N-Terminal Domains of Mouse and Human Myosin Binding Protein-C (2010)

The N-terminus of cMyBP-C can activate actomyosin interactions in the absence of Ca2+, but it is unclear which domains are necessary. Prior studies suggested that the Pro-Ala rich region of human cMyBP-C activated force in permeabilized human cardiomyocytes, whereas the C1 and M-domains of mouse cMyBP-C activated force in permeabilized rat cardiac trabeculae. Because the amino acid sequence of the P/A region differs between human and mouse cMyBP-C isoforms (46% identity), we investigated whether species-specific differences in the P/A region could account for differences in activating effects. Using chimeric fusion proteins containing combinations of human and mouse C0, Pro-Ala, and C1 domains, we demonstrate here that the human P/A and C1 domains activate actomyosin interactions, whereas the same regions of mouse cMyBP-C are less effective. These results suggest that species-specific differences between homologous cMyBP-C isoforms confer differential effects that could fine-tune cMyBP-C function in hearts of different species.
ATS materials support (1996)

The technology based portion of the Advanced Turbine System Program (ATS) contains several subelements which address generic technology issues for land-base gas turbine systems. One subelement is the Materials/Manufacturing Technology Program which is coordinated by DOE-Oak Ridge Operations and Oak Ridge National laboratory (ORNL) for the Department of Energy. The work in this subelement is being performed predominantly by industry with assistance from national laboratories and universities. Projects in this subelement are aimed toward hastening the incorporation of new materials and components in gas turbines. The materials manufacturing subelement was developed with input from gas turbine manufacturers, material suppliers, government laboratories and universities. Work is currently ongoing on thermal barrier coatings (TBCs), the scale-up of single-crystal airfoil manufacturing technologies, materials characterization and technology information exchange. Westinghouse Power Generation and Pratt and Whitney each have material programs to develop dependable TBCs that enable increased turbine inlet temperatures while maintaining airfoil substrate temperatures at levels to meet the ATS life goals. Howmet and PCC Airfoils each have projects to extend the capability of single-crystal complex-cored airfoil technology to larger sizes so that higher turbine inlet temperatures can be attained in land-based turbines in a cost-effective manner. Materials characterization tasks are ongoing on TBCs in support of the industrial projects. In addition, a project on long-term testing of ceramics and ceramic-matrix composites for gas turbines is being conducted in support of programs at Solar Turbines, Allison Engines, and Westinghouse Power Generation.