gebhart/patrepeval huggingface dataset:
Hypomethylation of DNA from Benign and Malignant Human Colon Neoplasms (1985)

The methylation state of DNA from human colon tissue displaying neoplastic growth was determined by means of restriction endonuclease analysis. When compared to DNA from adjacent normal tissue, DNA from both benign colon polyps and malignant carcinomas was substantially hypomethylated. With the use of probes for growth hormone, gamma-globin, alpha-chorionic gonadotropin, and gamma-crystallin, methylation changes were detected in all 23 neoplastic growths examined. Benign polyps were hypomethylated to a degree similar to that in malignant tissue. These results indicate that hypomethylation is a consistent biochemical characteristic of human colonic tumors and is an alteration in the DNA that precedes malignancy.
Structural and Functional Characterization of the Mouse Sox9 Promoter: Implications for Campomelic Dysplasia (1999)

Mutations in SOX9 cause campomelic dysplasia (CD), a dominant skeletal dysmorphology and XY sex reversal syndrome. The CD phenotype is sensitive to dosage and expression levels of SOX9. Sox9 is expressed during chondrocyte differentiation and is up-regulated in male and down-regulated in female genital ridges during sex differentiation. In order to study the sex- and tissue-specific regulation of Sox9, we have defined the transcription start site and characterized the mouse Sox9 promoter region. The Sox9 proximal promoter shows moderately high nucleotide similarity between mouse and human. Transient transfection experiments using various deletion constructs of the 6.8 kb upstream region of mouse Sox9 fused to a luciferase reporter showed that the interval between 193 and 73 bp from the transcription start site is essential for maximal promoter activity in cell lines and in primary male and female gonadal somatic cells and liver cells isolated from 13.5 d.p.c. mouse embryos. This minimal promoter region was shown by DNase I hypersensitive site assay to be in an 'open' state of chromatin structure in gonads of both sexes, but not in the liver. Promoter activity was higher in testis than in ovary and liver, but deletion of the region from -193 to -73 bp abolished this difference. We conclude that the proximal promoter region is in part responsible for the sex- and tissue-specific expression of the Sox9 gene and that more distal positive and negative elements contribute to its regulation in vivo, consistent with the observation that translocations upstream from SOX9 can result in campomelic dysplasia.
Cardiac motion tracking using CINE harmonic phase (HARP) magnetic resonance imaging (1999)

This article introduces a new image processing technique for rapid analysis of tagged cardiac magnetic resonance image sequences. The method uses isolated spectral peaks in SPAMM-tagged magnetic resonance images, which contain information about cardiac motion. The inverse Fourier transform of a spectral peak is a complex image whose calculated angle is called a harmonic phase (HARP) image. It is shown how two HARP image sequences can be used to automatically and accurately track material points through time. A rapid, semiautomated procedure to calculate circumferential and radial Lagrangian strain from tracked points is described. This new computational approach permits rapid analysis and visualization of myocardial strain within 5–10 min after the scan is complete. Its performance is demonstrated on MR image sequences reflecting both normal and abnormal cardiac motion. Results from the new method are shown to compare very well with a previously validated tracking algorithm. Magn Reson Med 42:1048–1060, 1999. © 1999 Wiley-Liss, Inc.
Monoclonal antibody to a human brain‐granulocyte‐T lymphocyte antigen probably homologous to the W 3/13 antigen of the rat (1980)

The monoclonal antibody (F 10-44-2) described in this report recognizes an antigen which by quantitative absorption analysis is found predominantly on spleen, lymph node, bone marrow, thymus, granulocytes and brain, the amount of antigen on these tissues being approximately the same within a factor of 2 or 3. Analysis with the fluorescence-activated cell sorter showed that 29% of thymus cells, 61% of bone marrow cells, 95% of blood mononuclear cells, 98% of lymph node lymphocytes and 100% of granulocytes carried the antigen. With blood mononuclear cells and lymph node lymphocytes, there were two distinct peaks, with one peak labeling very weakly. Double labeling experiments established that the weakly labeled peak contained the B lymphocytes. Studies on frozen sections of thymus established that positive thymocytes were found only in the medulla indicating that the antigen appears late in T lymphocyte maturation. The lymphatic nodules (B lymphocyte areas) of spleen and lymph node appeared virtually negative on frozen sections showing that there was too little antigen on the B lymphocyte surface for confident detection by fluorescence microscopy. Sodium dodecyl sulfate polyacrylamide gel eletrophoresis of NaB3H4-labeled blood mononuclear cells established that the antigen was a major glycoprotein of the leukocyte membrane and that its mol. wt. was 105000. This antigen shows a striking similarity in biochemistry and tissue distribution to the W 3/13 antigen of the rat and is likely to be the human homologue of this antigen.
Extracellular superoxide dismutase and other superoxide dismutase isoenzymes in tissues from nine mammalian species (1984)

The contents of extracellular superoxide dismutase, CuZn superoxide dismutase and Mn superoxide dismutase were determined in tissues from nine mammalian species. The pattern of CuZn superoxide dismutase distribution was similar in all species, with high activity in metabolically active organs such as liver and kidney and low activity in, for example, skeletal muscle. Mn superoxide dismutase activity was high in organs with high respiration, such as liver, kidney, and myocardium. Overall the Mn superoxide dismutase activity in organs was almost as high as the CuZn superoxide dismutase activity. The content of extracellular superoxide dismutase was, almost without exception, lower than the content of the other isoenzymes. The pattern of tissue distribution was distinctly different from those of CuZn superoxide dismutase and Mn superoxide dismutase. The tissue distribution of extracellular superoxide dismutase differed among species, but in general there was much in lungs and kidneys and little in skeletal muscle. In man, pig, sheep, cow, rabbit and mouse the overall tissue extracellular superoxide dismutase activities were similar to each other, whereas dog, cat and rat tissues contained distinctly less. There was no general correlation between the tissue extracellular superoxide dismutase activity of any of the various species and the variable plasma activity. The ratio between the plasma and the overall tissue activities was high, for some species over unity, providing further evidence for the notion that one role of extracellular superoxide dismutase is as a plasma protein.
Recombinant Vaccine Displaying the Loop-Neutralizing Determinant from Protective Antigen Completely Protects Rabbits from Experimental Inhalation Anthrax (2013)

We previously showed that a multiple antigenic peptide (MAP) vaccine displaying amino acids (aa) 304 to 319 from the 2β2-2β3 loop of protective antigen was capable of protecting rabbits from an aerosolized spore challenge with Bacillus anthracis Ames strain. Antibodies to this sequence, referred to as the loop-neutralizing determinant (LND), are highly potent at neutralizing lethal toxin yet are virtually absent in rabbit and human protective antigen (PA) antiserum. While the MAP vaccine was protective against anthrax, it contains a single heterologous helper T cell epitope which may be suboptimal for stimulating an outbred human population. We therefore engineered a recombinant vaccine (Rec-LND) containing two tandemly repeated copies of the LND fused to maltose binding protein, with enhanced immunogenicity resulting from the p38/P4 helper T cell epitope from Schistosoma mansoni. Rec-LND was found to be highly immunogenic in four major histocompatibility complex (MHC)-diverse strains of mice. All (7/7) rabbits immunized with Rec-LND developed high-titer antibody, 6 out of 7 developed neutralizing antibody, and all rabbits were protected from an aerosolized spore challenge of 193 50% lethal doses (LD(50)) of the B. anthracis Ames strain. Survivor serum from Rec-LND-immunized rabbits revealed significantly increased neutralization titers and specific activity compared to prechallenge levels yet lacked PA or lethal factor (LF) antigenemia. Control rabbits immunized with PA, which were also completely protected, appeared sterilely immune, exhibiting significant declines in neutralization titer and specific activity compared to prechallenge levels. We conclude that Rec-LND may represent a prototype anthrax vaccine for use alone or potentially combined with PA-containing vaccines.
A Bivalent Immunoadhesin of the Human Interferon-γ Receptor Is an Effective Inhibitor of IFN-γ Activity (1995)

We describe here the bioengineering of a bivalent IFN-gamma-RFc immunoadhesin consisting of the extracellular domain of the human IFN-gamma receptor alpha chain (IFN-gamma-R) fused to a human IgG1 Fc region (encoding hinge, CH2 and CH3 domain) that was efficiently expressed as a covalently linked homodimer in insect cells and purified in a one-step purification procedure. The IFN-gamma-RFc fusion protein exerted a 3-fold higher ligand binding affinity in binding competition studies in vitro compared with the monovalent extracellular IFN-gamma-R domain. In addition, the in vitro antagonistic activity of IFN-gamma-RFc, as determined by inhibition of IFN-gamma-induced virus protection and HLA-DR expression, was more than 30-fold higher in comparison with the monovalent soluble receptor. The described IFN-gamma-R immunoadhesin is a potential therapeutic reagent to interfere with the disease-promoting activities of IFN-gamma in several autoimmune diseases.
Etiology of obstructive sleep apnoea syndrome (2017)

&lt;p class="abstract"&gt;&lt;strong&gt;Background:&lt;/strong&gt; The aims of the study were to evaluate the various etiological factors of obstructive sleep apnoea syndrome and to make recommendations based on study findings.&lt;/p&gt;&lt;p class="abstract"&gt;&lt;strong&gt;Methods:&lt;/strong&gt; The study group consists of 60 patients who are diagnosed clinically and polysomnographically to have obstructive sleep apnoea syndrome at ENT and Pulmonary Medicine outpatient departments. &lt;/p&gt;&lt;p class="abstract"&gt;&lt;strong&gt;Results:&lt;/strong&gt; Most cases of severe OSA were in age group of 21-40 (47.8%). No significant association was observed between age distribution and severity of OSA (p=0.295). A significant association was observed between obesity and increasing severity of OSA (p&amp;lt;0.05). The mean AHI of patients with mild, moderate and severe OSA was 8.45, 23.31 and 49.07 respectively (p&amp;lt;0.05). Enlarged adenoids, narrow oropharyngeal inlet, bulky tongue, enlarged tonsils and greater neck circumference were significantly associated with OSA (p&amp;lt;0.05). No significant association between DNS, ITH, concha bullosa and enlarged adenoids with OSA (p&amp;gt;0.05).&lt;/p&gt;&lt;p class="western"&gt;&lt;strong&gt;Conclusions:&lt;/strong&gt; Certain naso-oro-pharyngeal parameters were found to be significantly associated with obstructive sleep apnoea syndrome viz. enlarged adenoids, bulky tongue, greater neck circumference and narrow&lt;strong&gt; &lt;/strong&gt;oropharyngeal inlet. Patients with these features should further be investigated with CPAP titration polysomnography and surgical intervention. &lt;/p&gt;
An electroclinical case‐control study of sudden unexpected death in epilepsy (2010)

Prolonged PGES (>50 seconds) appears to identify refractory epilepsy patients who are at risk of SUDEP. Risk of SUDEP may be increased in direct proportion to duration of PGES. Profound postictal cerebral dysfunction, possibly leading to central apnea, may be a pathogenetic mechanism for SUDEP.
Water Stability of Microporous Coordination Polymers and the Adsorption of Pharmaceuticals from Water (2010)

The stability of a variety of microporous coordination polymers (MCPs) to water-containing solutions was studied using powder X-ray diffraction. It was determined that the stability of the MCP is related to the metal cluster present in the structure with trinuclear chromium clusters more stable than copper paddlewheel clusters which are more stable than basic zinc acetate clusters. Zn(2-methylimidizolate)(2) was found to be more water stable than zinc MCPs with carboxylate linkers; however, extended exposure to water led to decomposition of all zinc-based MCPs. Matériaux de l'Institut Lavoisier (MIL)-100 was also found to be completely water stable and was used to adsorb the pharmaceuticals furosemide and sulfasalazine from water with large uptakes achievable at low concentrations, indicating that the adsorption of wastewater contaminants may be a feasible application for these materials.
Localizing sound source by incorporating biological auditory mechanism (1988)

A novel system for multiple sound-source localization has been developed. It consists of three microphones, to resolve the anterior-posterior ambiguity inherent in the binaural time-difference cue. As in the biological auditory system, acoustic signals are decomposed into their frequency components via a set of bandpass filters and the intermicrophone phase differences are obtained around the onsets of the transiently changing signals. The phase differences at various frequencies are utilized to resolve the ambiguity in the correspondence relationship between the onsets derived from pairs of microphones. The scheme has been implemented as a personal-computer-based system and applied successfully to systems of two sound sources as well as a single sound source.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Oligonucleotide-mediated triple helix formation using an N3-protonated deoxycytidine analog exhibiting pH-independent binding within the physiological range. (1992)

Triple helix formation with pyrimidine deoxyoligonucleotides for the sequence-specific recognition of DNA duplex targets suffers from a decrease in affinity as the pH of the medium increases to that of physiological fluids. A solution to this problem has been identified and entails the substitution of N6-methyl-8-oxo-2'-deoxyadenosine (M) for the 5-methyl-deoxycytosine base residues. The triple helix forming ability of an oligonucleotide consisting of thymidine and M residues is pH independent in the physiological range. Furthermore, M has been found to be superior to the previously used 5-methyldeoxycytidine and deoxyguanosine in conferring increased affinity for duplex DNA under physiological salt conditions.
Chimeric HIV‐1 and HIV‐2 lentiviral vectors with added safety insurance (2006)

Lentiviruses are unique in their ability to infect both dividing and non-dividing cells. This makes the vectors derived from them particularly useful for gene transfer into non-dividing cells, including stem cells. Lentiviral vectors are becoming the vectors of choice for si/shRNA delivery. The utility of the lentiviral vectors will be enhanced if additional elements of safety are built into their design. One safety concern is the generation of replication competent virus by recombination. We reasoned that HIV-1 and HIV-2 hybrid or chimeric lentiviral vectors will have added safety insurance in this regard. This is based on the premise that HIV-1 and HIV-2 are dissimilar enough in sequence to curtail recombination, yet similar enough to complement functionally. For hybrid vectors, we found that both HIV-1 and HIV-2 transfer vector RNAs could be packaged to equivalent titer by the HIV-1 packaging machinery. However, HIV-2 packaging machinery was unable to package HIV-1 transfer vector as well as it did HIV-2 transfer vector. This non-reciprocacity suggested that the requirement for HIV-2 vectors was more stringent and that for HIV-1 vectors more promiscuous. When the HIV-1 transfer vector was packaged with the chimeric packaging construct where the leader-gag region of HIV-2 was replaced with that of HIV-1 packaging construct, the titer of the vector went up. This suggests that at least some of the determinants of specificity for vector assembly reside in the leader-gag region. Incorporation of central polypurine tract (cPPT) and woodchuck post-transcriptional enhance element (WPRE) into the HIV-2 vectors had only modest effect on vector titer. Thus, chimeric lentiviral vectors with added safety features can be designed without compromising transduction efficiency.
Cell contact, prostaglandin E2 and transforming growth factor beta 1 play non-redundant roles in human mesenchymal stem cell induction of CD4+CD25Highforkhead box P3+ regulatory T cells (2009)

Adult human mesenchymal stromal or stem cells (MSC) can differentiate into a variety of cell types and are candidate cellular therapeutics in regenerative medicine. Surprisingly, these cells also display multiple potent immunomodulatory capabilities, including allosuppression, making allogeneic cell therapy a possibility. The exact mechanisms involved in regulatory T cell induction by allogeneic human MSC was examined, using purified CD4+ populations and well-characterized bone marrow-derived adult human MSC. Allogeneic MSC were shown to induce forkhead box P3 (FoxP3)+ and CD25+ mRNA and protein expression in CD4+ T cells. This phenomenon required direct contact between MSC and purified T cells, although cell contact was not required for MSC induction of FoxP3 expression in an unseparated mononuclear cell population. In addition, through use of antagonists and neutralizing antibodies, MSC-derived prostaglandins and transforming growth factor (TGF)-beta1 were shown to have a non-redundant role in the induction of CD4+CD25+FoxP3+ T cells. Purified CD4+CD25+ T cells induced by MSC co-culture expressed TGF-beta1 and were able to suppress alloantigen-driven proliferative responses in mixed lymphocyte reaction. These data clarify the mechanisms of human MSC-mediated allosuppression, supporting a sequential process of regulatory T cell induction involving direct MSC contact with CD4+ cells followed by both prostaglandin E(2) and TGF-beta1 expression. Overall, this study provides a rational basis for ongoing clinical studies involving allogeneic MSC.
The role of IL-2 in gene therapy. (1994)

Interleukin-2 (IL-2) is a growth factor for T-cells which enhances both non-specific immune responses such as natural killer (NK) and lymphokine-activated killer (LAK) cells as well as MHC-restricted cytotoxic T-cell responses. Early studies using IL-2 to treat a number of advanced cancers suggested that it may be active against malignant melanoma and renal cell carcinoma. However, responses were at the expense of considerable morbidity and mortality. Those, and subsequent studies, which aimed at increasing the efficacy and reducing the toxicity of IL-2-based treatments, are briefly reviewed and the current situation in which IL-2 is being used more frequently, in low dose subcutaneously administered regimens (often in combination with other agents such as alpha-interferon) assessed. The ultimate application of IL-2 against human cancer may be when it is secreted either by tumour-infiltrating lymphocytes or the tumour cells themselves. A number of studies using this approach are about to commence or have already started. Tumour cells transduced with IL-2 could effectively act as a therapeutic vaccine against low volume disease.
Purification of Heterotrimeric G Protein α Subunits by GST-Ric-8 Association (2010)

Ric-8A and Ric-8B are nonreceptor G protein guanine nucleotide exchange factors that collectively bind the four subfamilies of G protein α subunits. Co-expression of Gα subunits with Ric-8A or Ric-8B in HEK293 cells or insect cells greatly promoted Gα protein expression. We exploited these characteristics of Ric-8 proteins to develop a simplified method for recombinant G protein α subunit purification that was applicable to all Gα subunit classes. The method allowed production of the olfactory adenylyl cyclase stimulatory protein Gα(olf) for the first time and unprecedented yield of Gα(q) and Gα(13). Gα subunits were co-expressed with GST-tagged Ric-8A or Ric-8B in insect cells. GST-Ric-8·Gα complexes were isolated from whole cell detergent lysates with glutathione-Sepharose. Gα subunits were dissociated from GST-Ric-8 with GDP-AlF(4)(-) (GTP mimicry) and found to be >80% pure, bind guanosine 5'-[γ-thio]triphosphate (GTPγS), and stimulate appropriate G protein effector enzymes. A primary characterization of Gα(olf) showed that it binds GTPγS at a rate marginally slower than Gα(s short) and directly activates adenylyl cyclase isoforms 3, 5, and 6 with less efficacy than Gα(s short).
Hydrocracking of the oils of Botryococcus braunii to transport fuels (1982)

Hydrocarbon oils of the alga Botryococcus braunii, extracted from a natural "bloom" of the plant, have been hydrocracked to produce a distillate comprising 67% gasoline fraction, 15% aviation turbine fuel fraction, 15% diesel fuel fraction, and 3% residual oil. The distillate was examined by a number of standard petroleum industry test methods. This preliminary investigation indicates that the oils of B. braunii are suitable as a feedstock material for hydrocracking to transport fuels.
Thyroid Hormone and the Cardiovascular System (2001)

Thyroid hormone has many effects on the heart and vascular system.1 Many of the clinical manifestations of hyperthyroidism are due to the ability of thyroid hormone to alter cardiovascular hemodynamics.2 The hemodynamic effects of hypothyroidism are opposite to those of hyperthyroidism, although the clinical manifestations are less obvious. This review will integrate what is known about the mechanisms of thyroid hormone action on the heart25 with recent observations from both experimental and clinical studies of hyperthyroidism and hypothyroidism. We will also address the potential role of thyroid hormone treatment in patients with acute or chronic cardiac disease.Effects of . . .
Analysis of chemical modification of RNA from formalin-fixed samples and optimization of molecular biology applications for such samples (1999)

Formalin-fixed archival samples are known to be poor materials for molecular biological applications. We conducted a series of experiments to understand the alterations in RNA in fixed tissue. We found that formalin-fixed tissue was resistant to solubilization by chaotropic agents. However, proteinase K completely solubilized the fixed tissue and enabled the extraction of almost the same amount of RNA as from a fresh sample. The extracted RNA did not show apparent degradation. However, as reported, successful PCR amplification was limited to short targets. The nature of such 'fixed' RNA was analyzed using synthetic homo-oligo RNAs. The heterogeneous increase in molecular weight of the RNAs, measured by MALDI-TOF mass spectrometry, showed that all four bases showed addition of mono-methylol (-CH(2)OH) groups at various rates. The modification rate varied from 40% for adenine to 4% for uracil. In addition, some adenines underwent dimerization through methylene bridging. The majority of the methylol groups, however, could be removed from bases by simply elevating the temperature in formalin-free buffer. This demodification proved effective in restoring the template activity of RNA from fixed tissue. The improvement in PCR results suggested that more than half of the modification was removed by this demodification.