gebhart/patrepeval huggingface dataset:
Genomic Heterogeneity of AIDS Retroviral Isolates from North America and Zaire (1985)

In an analysis of the genomic variation of AIDS retroviral isolates from patients living in New York, Alabama, and Zaire, restriction maps were constructed by using seven enzymes, each known to cleave the proviral DNA more than once, in conjunction with Southern blot analysis. The maps of LAV, HTLV-III, and ARV-2 as deduced from their published nucleotide sequences were included in this analysis. The results demonstrated that (i) several "signature" restriction sites were common to all isolates; (ii) with the exception of LAV and HTLV-III, the North American and European isolates were all different from one another and showed no geographical specificity; (iii) the African isolates as a group were more diverse than those from North America and Europe; and (iv) the genomic variability was concentrated within the env gene.
Adhesion and Friction Mechanisms of Polymer-on-Polymer Surfaces (2002)

The adhesion and friction of smooth polymer surfaces were studied below the glass transition temperature by use of a surface forces apparatus. The friction force of a crosslinked polymer was orders of magnitude less than that of an uncrosslinked polymer. In contrast, after chain scission of the outermost layers, the adhesion hysteresis and friction forces increase substantially. These results show that polymer-polymer adhesion hysteresis and friction depend on the dynamic rearrangement of the outermost polymer segments at shearing interfaces, and that both increase as a transition is made from crosslinked surfaces to surfaces with long chains to surfaces with quasi-free ends. The results suggest new ways for manipulating the adhesion and friction of polymer surfaces by adjusting the state of the surface chains.
L'armée américaine après l'Irak (2006)

The American counterinsurgency in Iraq represents a watershed for the United States military. Quite unlike the operations for which it had prepared itself since Vietnam, and in some ways counter to the ways in which it had understood war in those years, it has put tremendous pressure on the institutions of the Army, in particular. Its initial missteps reflected the disjunction between how the Army saw itself, and what its tasks really were. But to a remarkable degree the Army has adapted to its mission in Iraq, aided by the vast store of experience accumulated during the 1990&#8217;s, and by certain innate qualities of professionalism and pragmatism. As of this writing, at any rate, it remains a formidable, and on the whole healthy, institution.
Genomic Prospecting for Microbial Biodiesel Production (2014)

This chapter focuses on the structure and regulation of the pathways utilized by various microbes (bacteria, algae, and yeasts) for the production of fatty acids and triacylglycerols (TAGs). An important observation with regard to the possibility of microbial biodiesel production was made when fatty acyl-ACP thioesterase (FAT) enzymes were overproduced in Escherichia coli. Thus far it represents the most efficient way to uncouple fatty acid formation from phospholipid and membrane biosynthesis in E. coli. Phosphatidic acid (PtdOH) is a key branching point in de novo lipid metabolism, and it is converted either to CDP-diacylglycerol (DAG) or DAG depending on the organism. CDP-DAG and DAG serve as intermediates in membrane phospholipid biosynthesis and, in addition, DAG is converted to TAG. Phosphatidate phosphatases (PAPs) in coordination with phospholipid-producing enzymes are key regulators of the flux of carbon towards TAGs. PAPs catalyze the conversion of PtdOH to DAG; the primary destination of DAG is the synthesis of membrane phospholipids, whereas excess DAG is directed towards TAG. The emerging theme from genome comparisons underlines the evolution of distinct regulatory mechanisms in various phylogenetic groups. All free-living organisms have the machinery to synthesize fatty acids, and conceptually, they could be exploited for biodiesel production. However, the photosynthetic organisms provide the unique opportunity to couple CO2 sequestration to lipid accumulation and subsequent biodiesel production.
Fetal skin: a site of dendritic epidermal T cell development (1992)

Thy-1 Ag and CD3-associated TCR-gamma (V gamma 3)/delta (V delta 1) are coexpressed on virtually all dendritic epidermal T cells (DETC) in the adult mouse. In contrast, day 16 fetal mouse skin contains small numbers of CD45+/Thy-1+/CD3- but no CD3+ cells. To see whether the CD45+/Thy-1+/CD3- fetal skin cells can qualify as DETC precursors, we transplanted day 16 fetal skin of C57BL/6 (Thy-1.2) mice onto adult B6Pl-Thy-1a (Thy-1.1) animals. At certain time points after transplantation, grafts were analyzed for the presence of Thy-1 and CD3/TCR Ag. Examination of the grafts, 4 days after transplantation, revealed the presence of few donor-type Thy-1.2+/CD3- and some Thy-1.2+/CD3+ epidermal cells of either round or dendritic configuration. At 10 weeks after transplantation, essentially all CD45+/Thy-1.2+ epidermal cells were anti-TCR V gamma 3 and anti-CD3-reactive, displayed a uniformly dendritic configuration, and, thus, represent DETC. Our assumption that CD45+/Thy-1+/CD3- cells are the only lymphocytes within day 16 fetal skin gained additional support by the observations: 1) that unfractionated as well as anti-CD45 gated single cell suspensions prepared from day 16 fetal skin were consistently devoid of anti-CD3 epsilon and anti-TCR V gamma 3-reactive cells; and 2) that stimulation of these cell suspensions with either Con A plus IL-2 or IL-2 alone regularly resulted in the outgrowth of CD45+/Thy-1+/CD3-/TCR V gamma 3- cells, but never in the appearance of CD45+/Thy-1+/CD3+/TCR V gamma 3+ cells. Our additional finding that Con A plus IL-2- or IL-2-stimulated day 16 fetal skin cells and cell lines derived therefrom contain transcripts of some (CD3 gamma, TCR C beta, TCR C gamma 1, TCR C gamma 4) but not of other (CD3 delta, CD3 epsilon, TCR C alpha, TCR C delta) genes encoding the CD3/TCR complex suggests that Thy-1+/CD3- fetal murine skin cells are of T cell lineage. We therefore propose that the fetal skin microenvironment can provide the stimuli promoting growth and maturation of CD3/TCR V gamma 3/V delta 1-expressing DETC from their CD3- precursors.
Cloning of the Arabidopsis WIGGUM gene identifies a role for farnesylation in meristem development (2000)

Control of cellular proliferation in plant meristems is important for maintaining the correct number and position of developing organs. One of the genes identified in the control of floral and apical meristem size and floral organ number in Arabidopsis thaliana is WIGGUM. In wiggum mutants, one of the most striking phenotypes is an increase in floral organ number, particularly in the sepals and petals, correlating with an increase in the width of young floral meristems. Additional phenotypes include reduced and delayed germination, delayed flowering, maturation, and senescence, decreased internode elongation, shortened roots, aberrant phyllotaxy of flowers, aberrant sepal development, floral buds that open precociously, and occasional apical meristem fasciation. As a first step in determining a molecular function for WIGGUM, we used positional cloning to identify the gene. DNA sequencing revealed that WIGGUM is identical to ERA1 (enhanced response to abscisic acid), a previously identified farnesyltransferase beta-subunit gene of Arabidopsis. This finding provides a link between protein modification by farnesylation and the control of meristem size. Using in situ hybridization, we examined the expression of ERA1 throughout development and found it to be nearly ubiquitous. This extensive expression domain is consistent with the pleiotropic nature of wiggum mutants and highlights a broad utility for farnesylation in plant growth and development.
Nucleic acid binding proteins affect the subcellular distribution of phosphorothioate antisense oligonucleotides (2017)

Antisense oligonucleotides (ASOs) are versatile tools that can regulate multiple steps of RNA biogenesis in cells and living organisms. Significant improvements in delivery, potency, and stability have been achieved through modifications within the oligonucleotide backbone, sugar and heterocycles. However, these modifications can profoundly affect interactions between ASOs and intracellular proteins in ways that are only beginning to be understood. Here, we report that ASOs with specific backbone and sugar modifications can become localized to cytoplasmic ribonucleoprotein granules such as stress granules and those seeded by the aggregation of specific ASO-binding proteins such as FUS/TLS (FUS) and PSF/SFPQ (PSF). Further investigation into the basis for ASO-FUS binding illustrated the importance of ASO backbone and hydrophobic 2' sugar modifications and revealed that the C-terminal region of FUS is sufficient to retain ASOs in cellular foci. Taken together, the results of this study demonstrate that affinities of various nucleic acid binding domains for ASO depend on chemical modifications and further demonstrate how ASO-protein interactions influence the localization of ASOs.
Fast digital image stabilizer based on Gray-coded bit-plane matching (1999)

A fast digital image stabilizer based on the Gray-coded bit-plane matching is proposed which is robust to irregular conditions such as moving objects and intentional panning. The proposed digital image stabilization (DIS) system performs motion estimation using the Gray-coded bit-plane of video sequences, greatly reducing the computational load. This motion estimation method can be realized using only binary Boolean functions which have significantly reduced computational complexity, while the accuracy of motion estimation is maintained. In order to further improve the computational efficiency, the Gray-coded bit-plane matching with the three-step search (3SS) is proposed. Experimental results indicate that the proposed digital image stabilizer is a computationally efficient alternative to existing DIS systems.
Relationships between Cargo, Cell Penetrating Peptides and Cell Type for Uptake of Non-Covalent Complexes into Live Cells (2013)

Modulating signaling pathways for research and therapy requires either suppression or expression of selected genes or internalization of proteins such as enzymes, antibodies, nucleotide binding proteins or substrates including nucleoside phosphates and enzyme inhibitors. Peptides, proteins and nucleotides are transported by fusing or conjugating them to cell penetrating peptides or by formation of non-covalent complexes. The latter is often preferred because of easy handling, uptake efficiency and auto-release of cargo into the live cell. In our studies complexes are formed with labeled or readily detectable cargoes for qualitative and quantitative estimation of their internalization. Properties and behavior of adhesion and suspension vertebrate cells as well as the protozoa Leishmania tarentolae are investigated with respect to proteolytic activity, uptake efficiency, intracellular localization and cytotoxicity. Our results show that peptide stability to membrane-bound, secreted or intracellular proteases varies between different CPPs and that the suitability of individual CPPs for a particular cargo in complex formation by non-covalent interactions requires detailed studies. Cells vary in their sensitivity to increasing concentrations of CPPs. Thus, most cells can be efficiently transduced with peptides, proteins and nucleotides with intracellular concentrations in the low micromole range. For each cargo, cell type and CPP the optimal conditions must be determined separately.
Blockade of a Chemokine, CCL2, Reduces Chronic Colitis-Associated Carcinogenesis in Mice (2009)

Accumulating evidence indicates the crucial contribution of chronic inflammation to various types of carcinogenesis, including colon carcinoma associated with ulcerative colitis and asbestosis-induced malignant mesothelioma. Ulcerative colitis-associated colon carcinogenesis can be recapitulated in mice by azoxymethane administration followed by repetitive dextran sulfate sodium ingestion. In the course of this carcinogenesis process, the expression of a macrophage-tropic chemokine, CCL2, was enhanced together with intracolonic massive infiltration of macrophages, which were a major source of cyclooxygenase (COX)-2, a crucial mediator of colon carcinogenesis. Mice deficient in CCL2-specific receptor, CCR2, exhibited less macrophage infiltration and lower tumor numbers with attenuated COX-2 expression. Moreover, CCL2 antagonists decreased intracolonic macrophage infiltration and COX-2 expression, attenuated neovascularization, and eventually reduced the numbers and size of colon tumors, even when given after multiple colon tumors have developed. These observations identify CCL2 as a crucial mediator of the initiation and progression of chronic colitis-associated colon carcinogenesis and suggest that targeting CCL2 may be useful in treating colon cancers, particularly those associated with chronic inflammation.
A self-assessment questionnaire to determine morningness-eveningness in human circadian rhythms. (1976)

An English language self-assessment Morningness-Eveningness questionnaire is presented and evaluated against individual differences in the circadian vatiation of oral temperature. 48 subjects falling into Morning, Evening and Intermediate type categories regularly took their temperature. Circadian peak time were identified from the smoothed temperature curves of each subject. Results showed that Morning types and a significantly earlier peak time than Evening types and tended to have a higher daytime temperature and lower post peak temperature. The Intermediate type had temperatures between those of the other groups. Although no significant differences in sleep lengths were found between the three types, Morning types retired and arose significantly earlier than Evening types. Whilst these time significatly correlated with peak time, the questionnaire showed a higher peak time correlation. Although sleep habits are an important déterminant of peak time there are other contibutory factors, and these appear to be partly covered by the questionnaire. Although the questionnaire appears to be valid, further evaluation using a wider subject population is required.
Score Following in Practice (1992)

Score following was first presented at the 1984 ICMC, independently, by Barry Vercoe and Roger Dannenburg. By 1987, IRCAM was incorporating score following in concert productions. To date, ten IRCAM pieces have relied on score following to synchronize live electronics with flute, clarinet, percussion, and piano. We noticed quickly that algorithms which work well in theory, or even in the laboratory, often cease working when confronted with real examples of instrumental writing. In the case of the clarinet and the flute it has been necessary to use acoustic-only pitch detection, which has further complicated the score following problem. The solutions we have found to date seem far from definitive, but it now seems a good moment to describe carefully and in detail what we are doing, before launching another foray into the unknown. This paper describes, in detail, the algorithm we now use, as well as the compromises that composers are still having to make in order to avoid certain of the algorithm&amp;apos;s pitfalls. The work reported here is part of a long-term research program at IRCAM that aims to extend the possibilities of live electronic music performance. As part of this program, several generations of digital synthesis hardware have been developed. The machine in current use for music production is the IRCAM Signal Processing Workstation (ISPW) (Lindemann 1991), which recently replaced the 4X machine as the predominant real-time signal processor at IRCAM.
The repeated sequence CATT(A/T) is required for granulocyte-macrophage colony-stimulating factor promoter activity. (1990)

The hematopoietic growth factor GM-CSF (granulocyte-macrophage colony-stimulating factor) is expressed by activated but not resting T lymphocytes. Previously, we localized GM-CSF-inducible promoter activity to a 90-bp region of GM-CSF 5'-flanking sequences extending from bp -53 to +37. To more precisely identify the GM-CSF DNA sequences required for inducible promoter activity in T lymphocytes, we have performed mutagenesis within a region of GM-CSF 5'-flanking sequences (bp -57 to -24) that contains the repeated sequence CATT(A/T). Mutations that do not alter the repeated CATT(A/T) sequence do not eliminate inducible promoter activity, whereas mutation or deletion of either of the CATT(A/T) repeats eliminates all inducible promoter activity in T-cell lines and in primary human T lymphocytes. Thus, both copies of the direct repeat CATT(A/T) are required for mitogen-inducible expression of GM-CSF in T cells.
Expression of tie-2, a member of a novel family of receptor tyrosine kinases, in the endothelial cell lineage (1993)

We are interested in the molecular mechanisms that are involved in the development of the vascular system. In order to respond to morphogenetic and mitogenic signals, endothelial cells must express appropriate receptors. To characterize endothelial cell-specific receptors, we have concentrated on receptor tyrosine kinases, because several lines of evidence suggested the importance of controlled phosphotyrosine levels in endothelial cells. A strategy based on PCR amplification using degenerate oligonucleotides and mouse brain capillaries as mRNA source, led to the identification of a novel receptor tyrosine kinase, which we designated tie-2. In situ hybridization using a tie-2-specific probe revealed an interesting spatial and temporal expression pattern. The gene was expressed specifically in the endothelial lineage. tie-2 transcripts were present in endothelial cell precursors (angioblasts) and also in endothelial cells of sprouting blood vessels throughout development and in all organs and tissues so far examined. tie-2 was down-regulated in the adult. Because of the unusual combination of immunoglobulin, EGF-like and fibronectin type III domains in the extracellular portion of tie-2 which is shared by TEK and tie, these molecules may be considered members of a new family of receptor tyrosine kinases. Signal transduction via this new class of tyrosine kinases could lead to a better understanding of the molecular mechanisms of blood vessel formation.
Tritium labeling of proteins to high specific radioactivity by reduction methylation. (1980)

The third component of human complement, hemoglobin A2, and IgG have been radiolabeled with tritium to specific activities of 179, 103, and 89 Ci/mmol, respectively, by reductive methylation. The labeling procedure is mild, requiring only brief exposure to formaldehyde (10 to 12 mM) and tritiated sodium borohydride (3 to 5 mM), and specific for the alpha amino groups of NH2-terminal residues and epsilon-amino groups of lysyl residues. The extent of modification for each protein ranged between 5 and 16% at available amino groups based on a stoichiometric reactivity of 2 mol of formaldehyde/mol of primary amine. Although the degree of substitution required to obtain these specific activities was high, no significant loss of antigenic or biological activities was apparent. Each labeled protein was 90 to 95% precipitable with antiserum elicited to the unreacted protein. The hemolytic activity of C3 was reduced by only 16%; the oxygen affinity of HbA2 was minimally decreased, and the phosphorylcholine binding affinity of an IgA myeloma protein (TEPC-15) was not significantly affected. Precise double antibody radioimmunoassays were developed with each tritiated protein capable of detecting less than 10(-8) g of antigen. Labeled protein samples have been stored for time periods up to 1 year without appreciable deterioration.
Effect of Sodium Bromide on the Bactericidal Effectiveness of Hypochlorite Sanitizers of High Alkalinity (1958)

Studies were conducted, in which comparisons were made of a standard hypochlorite sanitizer of high alkalinity (pH 11 at 100 p.p.m.) and the same sanitizer to which was added crystalline NaBr'2H20. Addition of the NaBr. 2tI20 improved the germicidal effectiveness of the hypochlorite sanitizer under laboratory conditions. The rate of increase in effectiveness varied with the concentration of NaBr'2H20 and the test organism. A standard mixture of 1.35% l%Br-2H20 and the sanitizer resulted in a 33 to 1,000% increase in bactericidal effectiveness against a variety of bacteria, in comparison to results obtained by using the sanitizer alone. Mixtures of 4% of NaBr. 2H20 and the alkaline sanitizer compared favorably in germicidal effectiveness against all test organisms to a hypochlorite sanitizer of relatively low alkalinity.
Human [Gly2]GLP-2 reduces the severity of colonic injury in a murine model of experimental colitis (1999)

The pathology of Crohn's disease and ulcerative colitis is characterized by chronic inflammation and destruction of the gastrointestinal epithelium. Although suppression of inflammatory mediators remains the principle component of current disease therapeutics, strategies for enhancing repair and regeneration of the compromised intestinal epithelium have not been widely explored. The demonstration that a peptide hormone secreted by the intestinal epithelium, glucagon-like peptide-2 (GLP-2), is a potent endogenous stimulator of intestinal epithelial proliferation in the small bowel prompted studies of the therapeutic efficacy of GLP-2 in CD1 and BALB/c mice with dextran sulfate (DS)-induced colitis. We report here that a human GLP-2 analog (h[Gly2]GLP-2) significantly reverses weight loss, reduces interleukin-1 expression, and increases colon length, crypt depth, and both mucosal area and integrity in the colon of mice with acute DS colitis. The effects of h[Gly2]GLP-2 in the colon are mediated in part via enhanced stimulation of mucosal epithelial cell proliferation. These observations suggest that exploitation of the normal mechanisms used to regulate intestinal proliferation may be a useful adjunct for healing mucosal epithelium in the presence of active intestinal inflammation.
Selective degeneration of sudomotor fibers in Ross syndrome and successful treatment of compensatory hyperhidrosis with botulinum toxin (1998)

We report a 5-year follow-up of a patient with Ross syndrome. A biopsy of the anhidrotic skin immunostained with protein gene product 9.5 visualized by confocal microscopy revealed selective loss of sudomotor fibers, whereas epidermal innervation remained intact, providing the first morphologic evidence of selective loss of sudomotor fibers in this syndrome. Among the different treatment strategies employed for the patient's disabling segmental hyperhidrosis, intracutaneous injection of botulinum toxin A was the most helpful.