gebhart/patrepeval huggingface dataset:
In vivo muscle gene transfer of full-length dystrophin with an adenoviral vector that lacks all viral genes. (1996)

Duchenne muscular dystrophy (DMD) is an important target for gene transfer because of the disease's high frequency and devastating course. To date, adenoviral vector-mediated gene transfer for DMD has been unavailable because (1) adenoviral vectors were unable to accommodate the full-length dystrophin cDNA (14 kb); and (2) adenoviral vectors induced inflammatory reactions in the gene transfer recipient. We addressed both problems with a novel adenoviral vector that contains no viral genes and encodes 28.2 kb of foreign DNA including both the full-length dystrophin cDNA with the muscle creatine kinase promoter for transcriptional control and a lacZ marker gene. This report presents the in vivo expression of dystrophin and beta-galactosidase from this vector in skeletal muscle of the mdx mouse, a mutant mouse that lacks dystrophin. Somatic delivery of the vector by intramuscular injection in 6-day-old mice resulted in the expression of full-length, recombinant dystrophin at the muscle membrane. Dystrophin-associated proteins were restored in muscle fibers expressing recombinant dystrophin. Mdx muscle injected with our vector showed a decrease in the proportion of fibers with nuclei located centrally; centrally placed nuclei in muscle fibers are characteristic of cycles of degeneration and regeneration suffered by dystrophin-deficient muscle tissue. These results are strong evidence that adenoviral vector-mediated full-length dystrophin delivery provides substantial somatic function.
CNTs as electron emitters for field emission displays (2005)

This paper reviews the work that has been carried out in Cambridge and elsewhere on the optimisation of carbon nanotubes for use as the cold cathode emitters suitable for use in field emission displays (FEDs). This study also discusses the relative merits of such displays compared to state-of the-art alternatives.
The peroxisome proliferator-activated receptor mediates the induction of CYP4A6, a cytochrome P450 fatty acid omega-hydroxylase, by clofibric acid. (1992)

Gene transfer experiments indicate that induction by the peroxisome proliferators, clofibric acid and WY-14,643, of luciferase expression driven by the promoter and 5'-flanking sequences of the rabbit cytochrome P450 4A6 gene (CYP4A6) is dependent on cotransfection of expression plasmids for the peroxisome proliferator-activated receptor, PPAR. Activation by PPAR is observed in the absence of the inducers. However, a mutant, PPAR-G (Glu282----Gly) activated luciferase expression only in the presence of peroxisome proliferators. Deletion analysis has localized a response element to a 34-base pair segment located 677 base pairs upstream of the CYP4A6 transcription start site that is similar to an element that regulates the response of the rat fatty acyl-CoA oxidase gene to peroxisome proliferators and that binds PPAR.
The molecular signature of mediastinal large B-cell lymphoma differs from that of other diffuse large B-cell lymphomas and shares features with classical Hodgkin lymphoma (2003)

Mediastinal large B-cell lymphoma (MLBCL) is a recently identified subtype of diffuse large B-cell lymphoma (DLBCL) that characteristically presents as localized tumors in young female patients. Although MLBCL has distinctive pathologic features, it clinically resembles the nodular sclerosis subtype of classical Hodgkin lymphoma (cHL). To elucidate the molecular features of MLBCL, we compared the gene expression profiles of newly diagnosed MLBCL and DLBCL and developed a classifier of these diseases. MLBCLs had low levels of expression of multiple components of the B-cell receptor signaling cascade, a profile resembling that of Reed-Sternberg cells of cHL. Like cHLs, MLBCLs also had high levels of expression of the interleukin-13 (IL-13) receptor and downstream effectors of IL-13 signaling (Janus kinase-2 [JAK2] and signal transducer and activator of transcription-1 [STAT1]), tumor necrosis factor (TNF) family members, and TNF receptor-associated factor-1 (TRAF1). Increased expression of STAT1 and TRAF1 in MLBCL was confirmed by immunohistochemistry. Given the TRAF1 expression and known link to nuclear factor-kappa B (NF- kappa B), MLBCLs were also evaluated for nuclear translocation of c-REL protein. In almost all cases, c-REL was localized to the nucleus, consistent with activation of the NF-kappa B pathway. These studies identify a molecular link between MLBCL and cHL and a shared survival pathway.
Determination of spin-exchange parameters between optically pumped rubidium andKr83 (1990)

The spin-exchange rates due to binary collisions and due to the formation of van der Waals molecules between $^{83}\mathrm{Kr}$ nuclei and optically pumped rubidium-metal vapor have been determined using a technique that relies on the simultaneous observation of frequency shifts of nuclear magnetic resonance lines of noble-gas atoms and corresponding frequency shifts of electron paramagnetic resonance lines of alkali-metal atoms. In contrast, earlier studies have relied on the observation of the spin-relaxation rate of either the alkali-metal atoms or the noble-gas atoms.
HAEM SYNTHASE AND COBALT PORPHYRIN SYNTHASE IN VARIOUS MICRO-ORGANISMS (1965)

1. The preparation of a crude extract of Clostridium tetanomorphum containing cobalt porphyrin synthase but little haem-synthase activity is described. 2. The properties of cobalt porphyrin synthase in the clostridial extracts is compared with the properties of a haem synthase present in crude extracts of the yeast Torulopsis utilis. 3. Cobalt porphyrin synthase in extracts of C. tetanomorphum inserts Co(2+) ions into the following dicarboxylic porphyrins in descending order of rate of insertion: meso-, deutero- and proto-porphyrins. Esterification renders meso- and deutero-porphyrins inactive as substrates. Neither the tetracarboxylic (coproporphyrin III) nor the octacarboxylic (uroporphyrin III) compounds are converted into cobalt porphyrins by the extract, but the non-enzymic incorporation of Co(2+) ions into these two porphyrins is rapid. These extracts are unable to insert Mn(2+), Zn(2+), Mg(2+) or Cu(2+) ions into mesoporphyrin. 4. Crude extracts of T. utilis readily insert both Co(2+) and Fe(2+) ions into deutero-, meso, and proto-porphyrins. Unlike the extracts of C. tetanomorphum, these preparations catalyse the insertion of Co(2+) ions into deuteroporphyrin more rapidly than into mesoporphyrin. This parallels the formation of haems by the T. utilis extract. 5. Cobalt porphyrin synthase is present in the particulate fraction of the extracts of C. tetanomorphum but requires a heat-stable factor present in the soluble fraction. This soluble factor can be replaced by GSH. 6. Cobalt porphyrin synthase in the clostridial extract is inhibited by iodoacetamide and to a smaller extent by p-chloromercuribenzoate and N-ethylmaleimide. The haem synthases of T. utilis and Micrococcus denitrificans are also inhibited by various thiol reagents.
Frequent enrichment for CD8 T cells reactive against common herpes viruses in chronic inflammatory lesions: towards a reassessment of the physiopathological significance of T cell clonal expansions found in autoimmune inflammatory processes (1999)

We recently evidenced a dramatic enrichment for T cells reactive against Epstein-Barr virus (EBV) within inflamed joints of two rheumatoid arthritis patients. To assess the generality of this phenomenon and its relevance to autoimmunity, we studied the responses of CD8 T cells from patients with either acute or chronic inflammatory diseases (rheumatoid arthritis: n = 18, ankylosing spondylitis: n = 5, psoriatic arthritis: n = 4, Reiter's syndrome: n = 3, arthrosis: n = 2, uveitis: n = 2, multiple sclerosis: n = 2, encephalitis: n = 1) against viral proteins derived from EBV and another common herpes virus, human cytomegalovirus (CMV). T cell responses against EBV and/or CMV epitopes were frequently observed within CD8 T cells derived from chronic inflammatory lesions, irrespective of their location (knee, eye, brain) and autoimmune features. In most cases, CD8 T cells derived from affected organs yielded stronger anti-viral T cell responses than CD8 T cells derived from patients' PBL, even in chronic inflammatory diseases devoid of autoimmune features or induced by defined bacterial agents. Taken together, these results suggest that the presence of virus-specific T cells within inflamed lesions of patients suffering from autoimmune diseases is a general phenomenon associated with chronic inflammation rather than the initiating cause of the autoimmune process. Since this phenomenon was sometimes associated with long-term T repertoire biases within inflamed lesions, the physiopathological significance of T cell clonal expansions found in a recurrent fashion within chronically inflamed autoimmune lesions should be interpreted with caution.
Getting a Competitive Edge Through Economics (1996)

Students who choose to major or minor in economics do not always do so because they are interested in becoming economists. Unlike degrees in accounting or nursing, the practical applications of an economics degree are not often obvious. Some of us choose economics simply because we enjoy it, and do not realize until later all of the avenues open to graduates with an economics background. This article is available in The Park Place Economist: http://digitalcommons.iwu.edu/parkplace/vol4/iss1/5 From the Economics Department Getting a Competitive Edge Through Economics
Systematic Unraveling of the Unsolved Pathway of Nicotine Degradation in Pseudomonas (2013)

Microorganisms such as Pseudomonas putida play important roles in the mineralization of organic wastes and toxic compounds. To comprehensively and accurately elucidate key processes of nicotine degradation in Pseudomonas putida, we measured differential protein abundance levels with MS-based spectral counting in P. putida S16 grown on nicotine or glycerol, a non-repressive carbon source. In silico analyses highlighted significant clustering of proteins involved in a functional pathway in nicotine degradation. The transcriptional regulation of differentially expressed genes was analyzed by using quantitative reverse transcription-PCR. We observed the following key results: (i) The proteomes, containing 1,292 observed proteins, provide a detailed view of enzymes involved in nicotine metabolism. These proteins could be assigned to the functional groups of transport, detoxification, and amino acid metabolism. There were significant differences in the cytosolic protein patterns of cells growing in a nicotine medium and those in a glycerol medium. (ii) The key step in the conversion of 3-succinoylpyridine to 6-hydroxy-3-succinoylpyridine was catalyzed by a multi-enzyme reaction consisting of a molybdopeterin binding oxidase (spmA), molybdopterin dehydrogenase (spmB), and a (2Fe-2S)-binding ferredoxin (spmC) with molybdenum molybdopterin cytosine dinucleotide as a cofactor. (iii) The gene of a novel nicotine oxidoreductase (nicA2) was cloned, and the recombinant protein was characterized. The proteins and functional pathway identified in the current study represent attractive targets for degradation of environmental toxic compounds.
Common role for each of the cGATA-4/5/6 genes in the regulation of cardiac morphogenesis (1998)

The GATA-4/5/6 genes encode transcription factors implicated previously in the regulation of cardiac-specific differentiation programs. However, recent analyses of mouse GATA-4 null mutations found evidence for function in endoderm development (in vitro) and embryonic morphogenesis (in vivo). Whether each of the three cardiac-associated GATA factors function within distinct or common developmental programs was previously untested; past studies defined specific and distinct roles for each of the GATA-1/2/3 genes in embryonic hematopoiesis. In this study, we compare the transcript patterns of cGATA-4/5/6 during chick embryogenesis. Each of the three GATA factors is expressed in a similar pattern within gastrulating cells of the primitive streak, prior to determination of the cardiomyocyte progenitors, and later within the lateral plate mesoderm and associated endoderm layer. The patterns overlap but extend beyond the presumptive cardiomyocyte population expressing cNkx-2.5. Later in development, cGATA-4/5/6 are all transcribed throughout the differentiating heart, in similar but not identical patterns, within the endocardium, myocardium, and great vessels. In order to test the function of GATA factors during chick cardiogenesis, embryos were cultured in vitro in the presence of antisense oligomers designed to deplete specifically transcripts encoding cGATA-4/5/6, beginning around stage 7. When oligomers are used to target transcripts for all three genes, a high percentage of the embryos develop abnormal hearts related to the failure to form a normal primitive heart tube. In the most severe phenotype, cardiac bifida results in two bilateral beating hearts. In some embryos, the paired heart primordia undergo partial fusion but fail to form a single looping heart tube. In all cases, cellular differentiation is not obviously affected, as the abnormal hearts form beating tissue. Depletion of transcripts encoding any single GATA factor, or any combination of two GATA factors, does not affect development. The partial depletion of all three genes in chick results in a remarkably similar phenotype compared to the null GATA-4 mutation in mouse. Therefore, in the chick, each of the GATA-4/5/6 genes functions in a common pathway, at the time of cardiac crescent formation, for regulating early embryonic cardiac morphogenesis, apparently associated with embryonic folding or the migration of primordia to form a primitive tube.
Three‐dimensional phase contrast angiography (1989)

Bipolar flow-encoding gradients can be used in a three-dimensional magnetic resonance imaging procedure to provide a noninvasive measure of in vivo blood flow. The resulting volume angiogram is a three-dimensional data matrix which can be retrospectively analyzed and displayed in a variety of ways. This angiographic technique provides good suppression of signals arising from stationary tissue, thereby permitting the visualization of small vessels having relatively slow flow. This suppression is obtained by modulating the amplitude of the flow-encoding gradient pulse to either cancel the stationary tissue signal or displace it relative to the flow signal in the volume image.
Techniques of DNA hybridization detect small numbers of mycobacteria with no cross-hybridization with non-mycobacterial respiratory organisms. (1985)

The traditional methods used in identifying mycobacteria, such as acid-fast bacillus stains and culture, are often time-consuming, insensitive, and nonspecific. As part of an ongoing program to improve diagnosis and characterization of mycobacteria, we have found that deoxyribonucleic acid (DNA) hybridization techniques using isotopically labeled, single-stranded, total DNA can be used to detect as little as 10(-4) micrograms of Mycobacterium tuberculosis (MTb) DNA. This amount of DNA represents approximately 2 X 10(4) genomes. We have also shown the MTb DNA is sufficiently different from the DNA of non-mycobacterial microorganisms such that cross-hybridization with MTb DNA does not occur under the hybridization conditions we employed. We speculate that DNA hybridization techniques may allow the rapid, sensitive, and specific identification of mycobacteria.
Antibodies specific for N6‐methyladenosine react with intact snRNPs U2 and U4/U6 (1987)

Antibodies specific for N6-methyladenosine (m6A) were elicited in rabbits and used to study the accessibility in intact snRNPs of the m6A residues present in the snRNAs U2, U4 and U6. The antibody quantitatively precipitates snRNPs U2 and U4/U6 from total nucleoplasmic snRNPs U1-U6 isolated from HeLa cells, which demonstrates that the m6A residues of the respective snRNAs are not protected by snRNP proteins in the snRNP particles. While the anti-m6A IgG does not react at all with U5 RNPs lacking m6A, a significant amount of U1 RNPs was co-precipitated despite the fact that U1 RNA does not contain m6A either. Since anti-m6A IgG does not react with purified U1 RNPs and co-precipitation of U1 RNPs is dependent on the presence of U2 RNPs but not of U4/U6 RNPs, these data indicate an interaction between snRNPs U1 and U2 in vitro. The anti-m6A precipitation pattern described above was also observed with snRNPs isolation from mouse Ehrlich ascites tumor cells, indicating similar three-dimensional arrangements of snRNAs in homologous snRNP particles from different organisms.
Progressive band selection (2009)

Progressive band selection (PBS) reduces spectral redundancy without significant loss of information, thereby reducing hyperspectral image data volume and processing time. Used onboard a spacecraft, it can also reduce image downlink time. PBS prioritizes an image's spectral bands according to priority scores that measure their significance to a specific application. Then it uses one of three methods to select an appropriate number of the most useful bands. Key challenges for PBS include selecting an appropriate criterion to generate band priority scores, and determining how many bands should be retained in the reduced image. The image's Virtual Dimensionality (VD), once computed, is a reasonable estimate of the latter. We describe the major design details of PBS and test PBS in a land classification experiment.
Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides (2005)

Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties. In order to study the conformation of cyclohexenyl nucleosides by NMR, the HexRot program was developed to calculate conformations from scalar coupling constants of cyclohexenyl compounds, analogous to the methods applied for (deoxy)ribose nucleosides. The conformational equilibria and the values of the thermodynamic parameters are very similar between a cyclohexenyl nucleoside [energy difference between 2H3 (N-type) and 2H3 (S-type) is 1.8 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 10.9 kJ/mol] and a natural ribose nucleoside (energy difference between N-type and S-type is 2 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 4-20 kJ/mol). The flexibility of the cyclohexenyl nucleoside was demonstrated by the fast equilibrium between two conformational states that was observed in a CeNA-U monomer, combined with the 2H3 conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the 2H3 conformation when incorporated in a d(5'-GCGT*GCG-3')/d(5'-CGCACGC-3') duplex, as determined by the NMR spectroscopy. This represents the first example of a synthetic nucleoside that adopts different conformations when incorporated in different double-stranded DNA sequences.
Botulinum toxin types A, B and D inhibit catecholamine secretion from bovine adrenal medullary cells (1986)

Evoked catecholamine secretion from cultured bovine adrenal medullary cells is inhibited by commercially available botulinum toxins - types A, B and D (10(4)-10(6) MLD/ml of culture medium). Basal secretion is also inhibited. The catecholamine content of such toxin-treated cells is larger than that of control cells and may in part be a result of the inhibition of basal release. The onset of action of botulinum toxin types A and D can be neutralised by their respective antisera. Concentrations of botulinum toxins A, B or D that inhibit secretion leave unaffected the 45Ca2+ influxes normally associated with secretion. These data provide further evidence to support the idea [(1985) Nature 317, 719-721] that botulinum toxins block secretion by acting downstream of the Ca2+ transient at or near the site of exocytosis.
Stimulation of tumor-cell growth by alpha-fetoprotein (1998)

It has been recognized that alpha-fetoprotein (AFP), as an oncofetal antigen, is re-expressed in large amounts in adult tumor cells and serves clinically useful purposes in tumor-marker assays. However, its biological activities are still undefined. In the present study, the ability of AFP to stimulate tumor-cell growth was observed by an in vitro experimental system. Mouse ascites cancer cells derived from hepatoma-22(H-22) or Ehrlich ascites carcinoma(EAC) were extracted intraperitoneally and cultured in RPMI 1640 medium containing 10% newborn calf serum for 48 hr. Cell growth was quantitated by a colorimetric assay using a MTT microculture tetrazolium dye. The results demonstrated that AFP significantly increased H-22-cell proliferation, with stimulation per cents of 122 to 156%. A similar growth-promoting effect of AFP was observed using EAC cells, with stimulation per cents of 86 to 210%. Moreover, the growth-stimulatory activity of AFP could be abrogated with anti-AFP antibodies. In addition, 5-fluorouracil could obviously inhibit AFP-induced proliferation of H-22 or EAC cells in vitro. These results suggest that AFP is associated with tumor-cell growth and may serve as an important target of tumor therapy.
<title>Digital signature of color images using amplitude modulation</title> (1997)

Watermarking techniques, also referred to as digital signature, sign images by introducing changes that are imperceptible to the human eye but easily recoverable by a computer program. Generally, the signature is a number which identifies the owner of the image. The locations in the image where the signature is embedded are determined by a secret key. Doing so prevents possible pirates from easily removing the signature. Furthermore, it should be possible to retrieve the signature from an altered image. Possible alternations of signed images include blurring, compression and geometrical transformations such as rotation and translation. These alterations are referred to as attacks. A new method based on amplitude modulation is presented. Single signature bits are multiply embedded by modifying pixel values in the blue channel. These modifications are either additive or subtractive, depending on the value of the bit, and proportional to the luminance. This new method has shown to be resistant to both classical attacks, such as filtering, and geometrical attacks. Moreover, the signature can be extracted without the original image.
Surgical Closure of the Patent Ductus Arteriosus with an Intravascular Prosthesis: Clinical Experience (1994)

The authors developed a new prosthesis for patent ductus arteriosus (PDA) closure, using a delivery device inserted through the main pulmonary artery (MPA) avoiding ductal dissection and use of cardiopulmonary bypass. The prosthesis was inserted in 19 consecutive patients between 1985 and 1992. They have been followed for a mean of 4.8 years (minimum 30 days, maximum 7.5 years). There were 14 women (72%) and the average age was 11 years (16 months to 38 years). All patients presented with pulmonary hypertension (4 severe, 5 moderate, and 10 mild). Simultaneous surgical procedures for congenital heart disease were performed in two cases. One patient had a diffuse calcified PDA. The average diameter of the inserted prosthesis was 7.5 mm (3.5 to 12.5 mm). Neither hemorrhage nor prosthesis dislocation/embolization occurred during the implantation or in the postoperative period. In a newborn (30 days) with severe cardiomegaly and thin MPA, we decided to ligate the ductus. Chronic cor pulmonale contributed to death in one patient 3.7 years after operation. The remaining patients recovered well, without clinical evidence of residual shunt. Therefore, we recommend the use of this new prosthesis for PDA closure in cases of large ductus or ductus complicated with calcification, pulmonary hypertension, and when associated open heart surgery is required.