gebhart/patrepeval huggingface dataset:
Resolution of a missense mutant in human genomic DNA by denaturing gradient gel electrophoresis and direct sequencing using in vitro DNA amplification: HPRT Munich. (1988)

The combination of denaturing gradient gel electrophoresis (DGGE) and in vitro DNA amplification has allowed us to (1) localize a DNA mutation to a given 100-bp region of the human genome and (2) rapidly sequence the DNA without cloning. DGGE showed that a mutation had occurred, but the technique revealed little about the nature or position of that mutation. The region of the genome containing the mutation was amplified by the polymerase chain-reaction technique, providing DNA of sufficient quality and quantity for direct sequencing. Amplification was performed with a 32P end-labeled primer that allowed direct Maxam-Gilbert sequencing of the amplified product without cloning. HPRTMunich was found to contain a single-base-pair substitution, a C-to-A transversion at base-pair position 397. We report the generation of a 169-bp, wild-type DNA probe that encompasses most of exon 3 of the human hypoxanthine guanine phosphoribosyltransferase (HPRT) gene and contains a low-temperature melting domain of approximately 100 bp. HPRTMunich, an HPRT mutant isolated from a patient with gout, has a single amino acid substitution; the corresponding DNA sequence alteration must lie within the low-temperature melting domain of exon 3. We report the separation of HPRTMunich from the wild-type sequence using DGGE. In addition to base-pair substitutions, DGGE is also sensitive to the methylation state of the molecule. The cDNA for HPRT was cloned into a vector and propagated in Escherichia coli dam+ and dam- strains; thus, methylated and unmethylated HPRT cDNA was obtained.(ABSTRACT TRUNCATED AT 250 WORDS)
ESDN, a Novel Neuropilin-like Membrane Protein Cloned from Vascular Cells with the Longest Secretory Signal Sequence among Eukaryotes, Is Up-regulated after Vascular Injury (2001)

A novel cDNA has been isolated from primary culture of human coronary arterial cells by a signal sequence trap method, and designated ESDN (endothelial and smooth muscle cell-derived neuropilin-like molecule). ESDN is a type-I transmembrane protein with the longest cleavable secretory signal sequence among eukaryotes. ESDN contains a CUB domain and a coagulation factor V/VIII homology domain, which reminds us of the structure of neuropilins. ESDN also harbors an LCCL domain, which is shared by Limulus factor C and Coch. Mouse and rat counterparts were also identified revealing >84% amino acid identity with human ESDN. The human ESDN gene was mapped between D3S1552 and D3S1271. Northern blot analysis showed that ESDN mRNA was expressed in various tissues; particularly highly expressed in cultured vascular smooth muscle cells. The ESDN expression was up-regulated in platelet-derived growth factor-BB-stimulated vascular smooth muscle cells in vitro and neointima of the balloon-injured carotid artery in vivo. Overexpression of ESDN in 293T cells suppressed their bromodeoxyuridine uptake. In addition, ESDN protein was strongly expressed in nerve bundles in rodents. Thus, ESDN is considered to play a role in regulation of vascular cell growth and may have a wide variety of functions in other tissues including the nervous system, like neuropilins.
Electrostatic Deflections and Electromechanical Resonances of Carbon Nanotubes (1999)

Static and dynamic mechanical deflections were electrically induced in cantilevered, multiwalled carbon nanotubes in a transmission electron microscope. The nanotubes were resonantly excited at the fundamental frequency and higher harmonics as revealed by their deflected contours, which correspond closely to those determined for cantilevered elastic beams. The elastic bending modulus as a function of diameter was found to decrease sharply (from about 1 to 0.1 terapascals) with increasing diameter (from 8 to 40 nanometers), which indicates a crossover from a uniform elastic mode to an elastic mode that involves wavelike distortions in the nanotube. The quality factors of the resonances are on the order of 500. The methods developed here have been applied to a nanobalance for nanoscopic particles and also to a Kelvin probe based on nanotubes.
Forecasting Transformed Series (1976)

Summary Suppose that a forecasting model is available for the process Xt but that interest centres on the instantaneous transformation Yt = T(Xt). On the assumption that Xt is Gaussian and stationary, or can be reduced to stationarity by differencing, this paper examines the autocovariance structure of and methods for forecasting the transformed series. The development employs the Hermite polynomial expansion, thus allowing results to be derived for a very general class of instantaneous transformations.
Improving the accuracy of protein secondary structure prediction using structural alignment (2006)

By using both sequence and structure databases and by exploiting the latest techniques in machine learning it is possible to routinely predict protein secondary structure with an accuracy well above 80%. A program and web server, called PROTEUS, that performs these secondary structure predictions is accessible at http://wishart.biology.ualberta.ca/proteus. For high throughput or batch sequence analyses, the PROTEUS programs, databases (and server) can be downloaded and run locally.
Pulmonary Embolism in Adolescents (1986)

To clarify the epidemiology of pulmonary embolism in adolescents, a retrospective analysis of adolescent admissions to a general hospital over a 15-year period was performed. Eighteen patients had 19 episodes of pulmonary embolism, an incidence of 78 per 100,000 hospitalized adolescents. There were twice as many female as male patients. Common complaints were chest pain, dyspnea, cough, and hemoptysis. Common findings were hypoxemia and deepvein thrombosis. Major risk factors were oral contraceptive use and elective abortion in 75% of female patients and trauma in 67% of male patients. Unlike its effect in adults, pulmonary embolism is rarely fatal in adolescents. Although clinical features in adolescents are similar to those in adults, there is a high incidence of both overdiagnosis and underdiagnosis. The early use of pulmonary arteriography in difficult diagnostic situations is suggested.
Mechanisms of bone loss in rheumatoid arthritis (2005)

Rheumatoid arthritis (RA) is an autoimmune inflammatory disease in which destruction of bone in the joints causes major morbidity. Recent research has shed light on the cell and molecular mechanisms that lead to this osteolysis, all due directly or indirectly to the chronic inflammation. The aspects of this research covered in this review include the alteration of cell proliferation and survival that results in growth of the RA synovium. This process depends upon an increase in angiogenesis and local blood flow, which is also a feature of increased bone turnover. In addition, the inflammatory environment increases expression of chemokines, which are involved in the recruitment of monocytic osteoclast precursors. Chronic inflammation also promotes an overall catabolic state, with increased osteoclast differentiation and resorptive activity, driven by disregulation of receptor activator of NF-kappaB ligand (RANKL) and the synergistic activity of inflammatory cytokines such as tumor necrosis factor-alpha and interleukin-1. Osteoclast survival is increased in this environment, but osteoblast differentiation and survival are decreased, with a consequent reduction in bone formation and a net loss of bone. Recognition of these processes and the factors involved will enable more effective and targeted treatments for RA.
Effect of Cyclophosphamide on Suppressor Cell Activity in Mice Unresponsive to EAE (1979)

Protection against experimental allergic encephalomyelitis (EAE) was induced in susceptible mice of (SJL/J X BALB/c)F1 hybrid, by injection of either mouse spinal cord homogenate, the small mouse basic protein, or Cop 1 in incomplete Freund's adjuvant, before EAE induction. It was demonstrated that the unresponsiveness induced by the three antigens is mediated by suppressor T cells residing in the spleen cell population and can be adoptively transferred to normal syngeneic recipients. Low dose of cyclophosphamide (20 mg/kg) administered 2 days before the encephalitogenic challenge abrogated the unresponsiveness to EAE and reverted the protected mice sensitive to disease induction. Cyclophosphamide was also active on adoptively transferred unresponsiveness, thus donors that had been treated with cyclophosphamide were unable to further transfer unresponsiveness to EAE. These results indicate the elimination by cyclophosphamide of suppressor cells that interfere with the effector mechanisms leading to EAE.
Pteroic Acid Derivatives. V. Pteroyl-α-glutamyl-α-glutamylglutamic Acid, Pteroyl-γ-glutamyl-α-glutamylglutamic Acid, Pteroyl-α-glutamyl-γ-glutamylglutamic Acid (1949)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPteroic Acid Derivatives. V. Pteroyl-α-glutamyl-α-glutamylglutamic Acid, Pteroyl-γ-glutamyl-α-glutamylglutamic Acid, Pteroyl-α-glutamyl-γ-glutamylglutamic AcidJ. Semb, J. H. Boothe, R. B. Angier, C. W. Waller, J. H. Mowat, B. L. Hutchings, and Y. SubbaRowCite this: J. Am. Chem. Soc. 1949, 71, 7, 2310–2315Publication Date (Print):July 1, 1949Publication History Published online1 May 2002Published inissue 1 July 1949https://pubs.acs.org/doi/10.1021/ja01175a012https://doi.org/10.1021/ja01175a012research-articleACS PublicationsRequest reuse permissionsArticle Views82Altmetric-Citations21LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Sequencing mitochondrial DNA polymorphisms by hybridization (1994)

We have investigated the use of DNA chips for genetic analysis, using human mitochondrial DNA (mtDNA) as a model. The DNA chips are made up of ordered arrays of DNA oligonucleotide probes, synthesized on a glass substrate using photolithographic techniques. The synthesis site for each different probe is specifically addressed by illumination of the substrate through a photolithographic mask, achieving selective deprotection Nucleoside phosphoramidites bearing photolabile protecting groups are coupled only to exposed sites. Repeated cycles of deprotection and coupling generate all the probes in parallel. The set of 4{sup N} N-mer probes can be synthesized in only 4N steps. Any subset can be synthesized in 4N steps. Any subset can be synthesized in 4N or fewer steps. Sequences amplified from the D-loop region of human mitochondrial DNA (mtDNA) were fluorescently labelled and hybridized to DNA chips containing probes specific for mtDNA. Each nucleotide of a 1.3 kb region spanning the D loop is represented by four probes on the chip. Each probe has a different base at the position of interest: together they comprise a set of A, C, G and T probes which are otherwise identical. In principle, only one probe-target hybrid will be a perfect match. Themore » other three will be single base mismatches. Fluorescence imaging of the hybridized chip allows quantification of hybridization signals. Heterozygous mixtures of sequences can also be characterized. We have developed software to quantitate and interpret the hybridization signals, and to call the sequence automatically. Results of sequence analysis of human mtDNAs will be presented.« less
Probiotics for the skin: a new area of potential application? (2003)

Methods for selecting probiotics for potential application on the skin are presented.
Herpesvirus saimiri–transformed macaque T cells are tolerated and do not cause lymphoma after autologous reinfusion (2000)

Human T cells are transformed in vitro to stable growth after infection with herpesvirus saimiri subgroup C strain C488, and they retain their antigen-specific reactivity and other important functional features of mature activated T lymphocytes. The virus persists as nonintegrating episomes in human T cells under restricted viral gene expression and without production of virus particles. This study analyzes the behavior of herpesvirus-transformed autologous T cells after reinfusion into the donor under close-to-human experimental conditions. T cells of 5 macaque monkeys were transformed to stable interleukin-2 dependent growth and were intravenously infused into the respective donor. The animals remained healthy, without occurrence of lymphoma or leukemia for an observation period of more than 1 year. Over several months virus genomes were detectable in peripheral blood cells and in cultured T cells by polymerase chain reaction. In naive control animals, a high-dose intravenous infection rapidly induced pleomorphic peripheral T-cell lymphoma. In contrast, monkeys were protected from lymphoma after challenge infection if they had previously received autologous T-cell transfusions. High levels of antibodies against virus antigens were detectable after challenge infection only. Taken together, herpesvirus-transformed T cells are well tolerated after autologous reinfusion. This may allow us to develop a novel concept for adoptive T-cell mediated immunotherapy.
Isolation and Characterization of a Human Amnion Epithelial Cell Line That Expresses the Pregnancy-Specific β1-Glycoprotein Gene* (1991)

Human pregnancy-specific beta 1-glycoprotein (PSG) is a family of closely related glycoproteins of 72K, 64K, 62K, and 54K. Together with the carcinoembryonic antigen, they form new members of the immunoglobulin superfamily. To study the molecular mechanisms that regulate expression of the PSG gene, we established a human amnion cell line, HAA58OD-8C, immortalized with an origin-defective simian virus-40 (SV40) temperature-sensitive A58 mutant virus. HAA58OD-8C cells were temperature sensitive for maintenance of transformation and expressed genes encoding PSG and the alpha- and beta-subunits of hCG. At the permissive temperature (33 C; transformed phenotype), they expressed low levels of PSG, hCG alpha, and hCG beta mRNAs and synthesized low levels of a 48K PSG polypeptide. At the nonpermissive temperature (39.5 C), HAA58OD-8C cells exhibited a differentiated phenotype, expressed increased levels of PSG, hCG alpha, and hCG beta mRNAs, and produced high levels of PSG polypeptides of 72K and 48K. Sodium butyrate induced PSG mRNA expression, and in the presence of butyrate, HAA58OD-8C cells produced high amounts of PSG polypeptides of 72K, 62K, and 48K. Ribonuclease protection analysis indicated that similar PSG transcripts were expressed by HAA58OD-8C cells and human term placenta. However, these amnion cells expressed selectively a certain population of PSG transcripts. Our results show that this amnion cell line provides a suitable model for studies of PSG gene expression and regulation.
Decoding the Fingerprint of Ferroelectric Loops: Comprehension of the Material Properties and Structures (2013)

Due to the nature of domains, ferroics, including ferromagnetic, ferroelectric, and ferroelastic materials, exhibit hysteresis phenomena with respect to external driving fields (magnetic field, electric field, or stress). In principle, every ferroic material has its own hysteresis loop, like a fingerprint, which contains information related to its properties and structures. For ferroelectrics, many characteristic parameters, such as coercive field, spontaneous, and remnant polarizations can be directly extracted from the hysteresis loops. Furthermore, many impact factors, including the effect of materials (grain size and grain boundary, phase and phase boundary, doping, anisotropy, thickness), aging (with and without poling), and measurement conditions (applied field amplitude, fatigue, frequency, temperature, stress), can affect the hysteretic behaviors of the ferroelectrics. In this feature article, we will first give the background of the ferroic materials and multiferroics, with an emphasis on ferroelectrics. Then it is followed by an introduction of the characterizing techniques for the loops, including the polarization–electric field loops and strain–electric field curves. A caution is made to avoid misinterpretation of the loops due to the existence of conductivity. Based on their morphologic features, the hysteresis loops are categorized to four groups and the corresponding material usages are introduced. The impact factors on the hysteresis loops are discussed based on recent developments in ferroelectric and related materials. It is suggested that decoding the fingerprint of loops in ferroelectrics is feasible and the comprehension of the material properties and structures through the hysteresis loops is established.
Tumor vaccine for ovarian carcinoma targeting sperm protein 17 (2002)

The results of the current study suggest the potential of Sp17 as a target for immunotherapy in patients with ovarian carcinoma.
osteoprotegerin-deficient mice develop early onset osteoporosis and arterial calcification (1998)

Osteoprotegerin (OPG) is a secreted protein that inhibits osteoclast formation. In this study the physiological role of OPG is investigated by generating OPG-deficient mice. Adolescent and adult OPG-/- mice exhibit a decrease in total bone density characterized by severe trabecular and cortical bone porosity, marked thinning of the parietal bones of the skull, and a high incidence of fractures. These findings demonstrate that OPG is a critical regulator of postnatal bone mass. Unexpectedly, OPG-deficient mice also exhibit medial calcification of the aorta and renal arteries, suggesting that regulation of OPG, its signaling pathway, or its ligand(s) may play a role in the long observed association between osteoporosis and vascular calcification.
Asian Citrus Psyllid (2006)

Much has changed since the 2006 release of this publication. Research and treatment methods are changing. For the latest information on Asian Citrus Psyllid visit UC ANR&#39;s interactive website on &lt;A HREF=&quot;https://ucanr.edu/sites/ACP&quot; TARGET=&quot;_blank&quot;&gt; &lt;STRONG&gt;ACP/HLB management.&lt;/STRONG&gt;&lt;/a&gt; for growers, home owners, and master gardeners.
Morphological and functional reversal of phenotypes in a mouse model of Rett syndrome (2012)

Rett syndrome is a neurological disorder caused by mutation of the X-linked MECP2 gene. Mice lacking functional Mecp2 display a spectrum of Rett syndrome-like signs, including disturbances in motor function and abnormal patterns of breathing, accompanied by structural defects in central motor areas and the brainstem. Although routinely classified as a neurodevelopmental disorder, many aspects of the mouse phenotype can be effectively reversed by activation of a quiescent Mecp2 gene in adults. This suggests that absence of Mecp2 during brain development does not irreversibly compromise brain function. It is conceivable, however, that deep-seated neurological defects persist in mice rescued by late activation of Mecp2. To test this possibility, we have quantitatively analysed structural and functional plasticity of the rescued adult male mouse brain. Activation of Mecp2 in ∼70% of neurons reversed many morphological defects in the motor cortex, including neuronal size and dendritic complexity. Restoration of Mecp2 expression was also accompanied by a significant improvement in respiratory and sensory-motor functions, including breathing pattern, grip strength, balance beam and rotarod performance. Our findings sustain the view that MeCP2 does not play a pivotal role in brain development, but may instead be required to maintain full neurological function once development is complete.
Cross-Linking of 4-1BB Activates TCR-Signaling Pathways in CD8+ T Lymphocytes (2005)

Cross-linking of 4-1BB, a member of the TNFR family, increased tyrosine phosphorylation of TCR-signaling molecules such as CD3epsilon, CD3zeta, Lck, the linker for activation of T cells, and SH2 domain-containing leukocyte phosphoprotein of 76 kDa (SLP-76). In addition, incubation of activated CD8+ T cells with p815 cells expressing 4-1BBL led to redistribution of the lipid raft domains and Lck, protein kinase C-theta;, SLP-76, and phospholipase C-gamma1 (PLC-gamma1) on the T cell membranes to the areas of contact with the p815 cells and recruitment of 4-1BB, TNFR-associated factor 2, and phospho-tyrosine proteins to the raft domains. 4-1BB ligation also caused translocation of TNFR-associated factor 2, protein kinase C-theta;, PLC-gamma1, and SLP-76 to detergent-insoluble compartments in the CD8+ T cells, and cross-linking of 4-1BB increased intracellular Ca2+ levels apparently by activating PLC-gamma1. The redistribution of lipid rafts and Lck, as well as translocation of PLC-gamma1, and degradation of IkappaB-alpha in response to 4-1BB were inhibited by disrupting the formation of lipid rafts with methyl-beta-cyclodextrin. These findings demonstrate that 4-1BB is a T cell costimulatory receptor that activates TCR-signaling pathways in CD8+ T cells.
A comparison of the properties of different retroviral vectors containing the murine tyrosinase promoter to achieve transcriptionally targeted expression of the HSVtk or IL-2 genes. (1994)

To target therapeutic genes specifically to melanoma cells, we have constructed recombinant retroviruses where transcriptional control of the murine interleukin-2 (mIL-2) or herpes simplex virus thymidine kinase (HSVtk) genes is provided by the 5' promoter region of the murine tyrosinase gene. Tissue-specific expression of these genes is observed both at the mRNA and protein levels in the B16 melanoma line compared with NIH3T3 fibroblasts. Thus, B16 cells infected with one such retrovirus containing the HSVtk gene exhibited a > 90% reduction in colony-forming efficiency after exposure to 1 microgram/ml ganciclovir, relative to controls, whereas similarly infected NIH3T3 cells showed < 10% reduction in colony-forming efficiency under comparable conditions. The degree of preservation of tissue-specific expression from the internal tyrosinase promoter depended upon the exact molecular design of the vector, possibly as a consequence of the interference between closely juxtaposed promoters within the provirus. Our results show that retroviral vectors can be prepared with the capacity to regulate expression of inserted genes specifically in a particular cell type and may be useful for developing efficient, targeted vectors for the in vivo delivery of genetic therapies for malignant melanoma.