gebhart/patrepeval huggingface dataset:
Comparative genomics of rumen methanogens : a thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biochemistry at Massey University, Palmerston North, New Zealand (2016)

Methane (CH4) emissions from agriculture represent around 9% of global anthropogenic greenhouse gas emissions. The single largest source of this CH4 is animal enteric fermentation, predominantly from ruminant livestock, where it is produced mainly in their fermentative forestomach (or reticulo-rumen) by a group of archaea known as methanogens.&#13;\nIn order to reduce CH4 emissions from ruminants, it is necessary to understand the role of methanogenic archaea in the rumen, and to identify their distinguishing characteristics that can be used to develop CH4 mitigation technologies. To gain insights into the role of methanogens in the rumen environment, two methanogens have been isolated from ovine rumen and their genomes were sequenced: methanogenic archaeon ISO4-H5 of the order Methanomassiliicoccales and Methanobrevibacter sp. D5 of Methanobrevibacter gottschalkii clade.&#13;\nGenomic analysis suggests ISO4-H5 is an obligate hydrogen-dependent methylotrophic methanogen, able to use methanol and methylamines as substrates for methanogenesis. Like other organisms within this order, ISO4-H5 does not possess genes required for the first six steps of hydrogenotrophic methanogenesis. Comparison between the genomes of different members of the order Methanomassiliicoccales revealed strong conservation in energy metabolism, particularly in genes of the methylotrophic methanogenesis pathway, as well as in the biosynthesis and use of pyrrolysine. Unlike members of Methanomassiliicoccales from human sources, ISO4-H5 does not contain the genes required for production of coenzyme M (CoM), and requires external supply of CoM to survive.&#13;\nMethanobrevibacter sp. D5 is a hydrogenotrophic methanogen predicted to utilise CO2 + H2 and formate as substrates. Comparisons between the available Methanobrevibacter genomes has revealed a high conservation in energy metabolism and characteristics specific to each clade. The coexistence of different Methanobrevibacter species in the rumen may be partly due to the physical association Methanobrevibacter species with different microorganisms and host surface, which allow unique niches to be established.
Trigger Point Injections for Chronic Non-Malignant Musculoskeletal Pain: A Systematic Review (2008)

The efficacy of TPI is no more certain than it was a decade ago as, overall, there is no clear evidence of either benefit or ineffectiveness. The only advantage of injecting anesthetic into trigger points may be to reduce the pain of the needling process, which may not be an insignificant benefit.
Differential regulation of bile acid homeostasis by the farnesoid X receptor in liver and intestine (2007)

Bile acid concentrations are controlled by a feedback regulatory pathway whereby activation of the farnesoid X receptor (FXR) represses transcription of both the CYP7A1 gene, encoding the rate-limiting enzyme in the classic bile acid synthesis pathway, and the CYP8B1 gene, required for synthesis of cholic acid. The tissue-specific roles of FXR were examined using liver- and intestine-specific FXR-null models. FXR deficiency in either liver (Fxr DeltaL) or intestine (Fxr DeltaIE) increased bile acid pool size. Treatment with the FXR-selective agonist GW4064 significantly repressed CYP7A1 in Fxr DeltaL mice but not Fxr DeltaIE mice, demonstrating that activation of FXR in intestine but not liver is required for short-term repression of CYP7A1 in liver. This intestinal-specific effect of FXR is likely mediated through induction of the hormone FGF15, which suppresses CYP7A1. In comparison to CYP7A1, FXR-mediated repression of CYP8B1 was more dependent on the presence of FXR in liver and less dependent on its presence in intestine. Consistent with these findings, recombinant FGF15 repressed CYP7A1 mRNA levels without affecting CYP8B1 expression. These data provide evidence that FXR-mediated repression of bile acid synthesis requires the complementary actions of FXR in both liver and intestine and reveal mechanistic differences in feedback repression of CYP7A1 and CYP8B1.
Immunological Mapping of the Human Leucocyte Adhesion Glycoprotein gp90 (CD 18) by Monoclonal Antibodies (1988)

The leucocyte surface glycoproteins CD11a (gp160, LFA-1 antigen, TA-1 antigen), CD11b (gp155, Mac-1 antigen, OKM1 antigen, Mo-1 antigen), CD11c (gp130, Leu-M5 antigen), and CD18 (gp90) constitute three heterodimers with different alpha chains and a common beta chain. Monoclonal antibodies to CD11a, b, or c block adhesion of certain types of leucocytes only, while several antibodies to CD18 inhibit adhesion in all of them. The functionally important site or sites on CD18 are not known. We have now isolated the CD11a,b,c-CD18 leucocyte antigen complex in large amounts from human leucocytes, and produced several new monoclonal antibodies reacting with CD18. One of these antibodies, like those described earlier, inhibits leucocyte adhesion, whereas the others do not. By means of competition experiments, at least four epitope regions were found. These antibodies should be valuable in elucidating the regions essential in CD18-mediated leucocyte functions.
Detection of KIT mutations in core binding factor acute myeloid leukemia (2018)

We have investigated the frequency and the effect of <i>KIT</i> mutations on the outcome of patients with CBF-AML. 69 patients (34 pediatrics and 35 adults) with CBF-AML were enrolled in the study. The frequency of <i>KIT</i> mutations was higher in adults compared to pediatrics (22.9% and 14.7%, <i>p</i> = 0.38) respectively. Leukocytosis ≥ 20 × 10<sup>9</sup> /L was significantly associated with pediatrics compared to adults. t(8;21)(q22;22) was significantly associated with thrombocytopenia in adults. We conclude that no significant difference is found between <i>KIT</i> mutated and unmutated CBF-AML in adults and pediatrics. Children with CBF-AML present with leukocytosis. t(8;21) is associated with thrombocytopenia.
Study of spatial–temporal characteristics of optical fiber based on ultrashort-pulse interferometry (2001)

We demonstrate a method for reconstruction of the modal intensity distribution of light at the output of an optical fiber. Spatial modes of the optical fiber are separated in time as a result of differences in group velocity and are detected experimentally by observation of the interference of the modal field distribution with the time-gating reference field. The detected interference patterns of the modal fields are analyzed, providing the spatial impulse response of the fiber. We also use interferometric correlation to determine the spatiotemporal characteristics of the fiber modes, such as pulse width, linear chirp, and group velocity, for each mode.
Low-Molecular-Weight Heparin Therapy and Mortality (1997)

There is ample evidence from clinical trials to justify giving certain low-molecular-weight heparins (LMWHs) subcutaneously rather than administering continuous intravenous unfractionated heparin for the initial treatment of venous thromboembolic disease. The LMWHs given by subcutaneous injection have a predictable anticoagulant response and prolonged duration of action. They can, therefore, be administered once or twice daily to treat venous thrombosis. Furthermore, treatment with these agents does not require laboratory monitoring. Eliminating the need for intravenous therapy and for laboratory monitoring should allow patients to be discharged earlier, and eventually lead to the outpatient treatment of venous thromboembolism. Studies to date indicate that LMWH is safer and as effective as continuous intravenous heparin in the treatment of venous thrombosis. The decreased mortality rates seen in two clinical trials, particularly in patients with metastatic cancer, were an unexpected but intriguing finding. This requires further confirmation, in larger prospective randomized trials.
Energy-efficient spatial-domain-based hybrid multidimensional coded-modulations enabling multi-Tb/s optical transport (2011)

In addition to capacity, the future high-speed optical transport networks will also be constrained by energy consumption. In order to solve the capacity and energy constraints simultaneously, in this paper we propose the use of energy-efficient hybrid D-dimensional signaling (D>4) by employing all available degrees of freedom for conveyance of the information over a single carrier including amplitude, phase, polarization and orbital angular momentum (OAM). Given the fact that the OAM eigenstates, associated with the azimuthal phase dependence of the complex electric field, are orthogonal, they can be used as basis functions for multidimensional signaling. Since the information capacity is a linear function of number of dimensions, through D-dimensional signal constellations we can significantly improve the overall optical channel capacity. The energy-efficiency problem is solved, in this paper, by properly designing the D-dimensional signal constellation such that the mutual information is maximized, while taking the energy constraint into account. We demonstrate high-potential of proposed energy-efficient hybrid D-dimensional coded-modulation scheme by Monte Carlo simulations.
tcRNA as a naturally occurring antisense RNA in eukaryotes (1986)

Journal Article tcRNA as a naturally occurring antisense RNA in eukaryotes Get access Stuart M. Heywood Stuart M. Heywood Department of Molecular and Cell Biology, University of ConnecticutStorrs, CT 06268, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 14, Issue 16, 26 August 1986, Pages 6771–6772, https://doi.org/10.1093/nar/14.16.6771 Published: 26 August 1986 Article history Received: 14 July 1986 Published: 26 August 1986
LENS CRYSTALLINS: THE EVOLUTION AND EXPRESSION OF PROTEINS FOR A HIGHLY SPECIALIZED TISSUE (1988)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Appropriate in vivo expression of a muscle-specific promoter by using avian retroviral vectors for gene transfer [corrected] (1992)

The promoter regions of the chicken skeletal muscle alpha-actin (alpha sk-actin) and the cytoplasmic beta-actin genes were linked to the bacterial chloramphenicol acetyltransferase (CAT) gene. Replication-competent retroviral vectors were used to introduce these two actin/CAT cassettes into the chicken genome. Chickens infected with retroviruses containing the alpha sk-actin promoter expressed high levels of CAT activity in striated muscle (skeletal muscle and heart); much lower levels of CAT activity were produced in the other nonmuscle tissues. In contrast, chickens infected with retroviruses containing the beta-actin promoter linked to the CAT gene expressed low levels of CAT activity in many different tissue types and with no discernible tissue specificity. Data are presented to demonstrate that the high levels of CAT activity that were detected in the skeletal muscle of chickens infected with the retrovirus containing the alpha sk-actin promoter/CAT cassette were not due to preferential infectivity, integration, or replication of the retrovirus vector in the striated muscles of these animals.
Painterly rendering for animation (1996)

We present a technique for rendering animations in a painterly style. The difficulty in using existing still frame methods for animation is getting the paint to "stick" to surfaces rather than randomly change with each frame, while still retaining a hand-crafted look. We extend the still frame method to animation by solving two major specific problems of previous techniques. First our method eliminates the "shower door" effect in which an animation appears as if it were being viewed through textured glass because brush strokes stick to the viewplane not to the animating surfaces. Second, our technique provides for frame-to-frame coherence in animations so that the resulting frames do not randomly change every frame. To maintain coherence, we model surfaces as 3d particle sets which are rendered as 2d paint brush strokes in screen space much like an artist lays down brush strokes on a canvas. We use geometric and lighting properties of the surfaces to control the appearance of brush strokes. This powerful combination of using 3d particles, surface lighting information, and rendering 2d brush strokes in screen space gives us the painterly style we desire and forces the brush strokes to stick to animating surfaces. By varying lighting and choosing brush stroke parameters we can create many varied painterly styles. We illustrate the method with images and animated sequences and present specific technical and creative suggestions for achieving different looks.
Thermoreversible hydrogels XIV. Synthesis and swelling behavior of the (n-isopropylacrylamide-co-2-hydroxyethyl methacrylate) copolymeric hydrogels (2000)

A series of thermoreversible hydrogels were prepared from various molar ratios of N-isopropylacrylamide (NIPAAm), and 2-hydroxyethyl methacrylate (HEMA) with N,N-methylene-bis-acrylamide (NMBA) as a crosslinker in various polymerization media. The appearance of the gel membrane formed in various polymerization media, and the influences of various swelling media on the swelling behavior for the copolymeric gels, were investigated in this article. The results indicated that the gel would change from opaque to transparent, and the swelling diffusion mechanism of the gel in water was changed from non-Fickian diffusion to Fickian diffusion when the content of HEMA in the copolymeric compositions increased. The effect of the swelling media on the swelling ratio for poly(NIPAAm-co-HEMA) indicated that the more the HEMA content, the lower the swelling ratio of the gel in water and solvent, but the contrary result for the gel was obtained in the 50% solvent aqueous solution. The result for the influence of the polymerization media on the swelling ratio for poly(NIPAAm-co-HEMA) indicated that the larger the solvent molecular size of polymerization media, the higher the swelling ratio. On the other hand, the gel transition temperature and the thermoreversibility of the copolymeric gels gradually disappeared as the content of the HEMA in the gel was increased. The larger the solvent molecular sizes of polymerization media, the better the thermoreversiblity of the gel, but the gel transition temperature was not significantly affected. Finally, the drug release and drug diffusion in these copolymeric gels was also investigated. © 2000 John Wiley & Sons, Inc. J Appl Polym Sci 77: 1769–1781, 2000
Niobium nitride Josephson tunnel junctions with oxidized amorphous silicon barriers (1981)

High-quality NbN/NbN Josephson tunnel junctions have been fabricated by rf sputtering. Tunneling barriers are formed by oxidizing amorphous silicon films produced with rf glow discharge deposition. For patterning the base and counter electrode, sputtered ZnO films are employed as a resist mask. The juncitons are found to have large gaps (2ΔNbN) =4.4 mV), to have low leakage current, and to be quite stable for storage and thermal cyclings.
Limits of resolution of genetic linkage studies: implications for the positional cloning of human disease genes. (1994)

Positional cloning studies to identify disease genes are being carried out for many human genetic diseases. Such studies often include a genome-scan linkage analysis to identify the rough chromosomal location of a disease gene, fine structure genetic mapping to define and narrow the chromosomal interval in which the disease gene may be located, and physical mapping and gene identification in the genetically defined interval to clone the disease gene. During the planning of a positional cloning study, it is important to know that, if linkage is found, the genetic interval identified is likely to be sufficiently narrow to be dissected efficiently by methods of physical mapping and gene identification. Thus, we wish to know the limits of resolution of a genetic linkage study. In this paper, I determine for Mendelian diseases the distributions and moments of three measures of linkage resolution: (1) in a set of N chromosomes, the distance between the nearest crossovers that flank a disease locus, (2) the distance between the nearest genetic markers that flank the pair of flanking crossovers after a genome scan, and (3) the distance between the nearest flanking markers after additional randomly placed markers are generated and typed in an identified interval. These results provide explicit sample-size guidelines for future positional cloning studies of Mendelian diseases and make possible a more objective evaluation of whether a proposed positional cloning study is likely to be successful. I also briefly discuss the more difficult problem of linkage resolution for complex genetic diseases.
Epidemiology of Diabetes and Diabetes-Related Complications (2008)

from randomized controlled trials provide evidence that intensive lifestyle interventions can prevent or delay the onset of diabetes in high-risk individuals. In addition, adequate and sustained control of blood sugar levels, blood pressure, and blood lipid levels can prevent or delay the onset of diabetes-related complications in people with diabetes. Effective interventions, at both the individual and population levels, are desperately needed to slow the diabetes epidemic and reduce diabetes-related complications in the United States. This report describes the current diabetes epidemic and the health and economic impact of diabetes complications on individuals and on the health care system. The report also provides suggestions by which the epidemic can be curbed.
The intramuscular nerve supply of the posterior cricoarytenoid muscle of the dog (1992)

The paired posterior cricoarytenoid (PCA) muscle has three separate muscle bellies that differ in muscle fiber type (percentage of fast vs. slow twitch) and electromyelographic activity, and, in addition, produce different movements of the arytenoids when stimulated. An investigation of the innervation of the muscle was undertaken to demonstrate the existence of separate functional units. The intramuscular nerve supply of the PCA from five sacrificed dogs were microdissected. The intramuscular nerves of three additional dogs were removed and stained for acetylcholinesterase, which differentiates axons bound for fast- and slow-twitch muscle, and sensory end organs. Three separate fascicles are described entering the PCA muscle from a single branch of the recurrent laryngeal nerve. The three fascicles differ in axon type composition and in sensory, autonomic, and motor percentages, with the ratio of fast twitch to slow twitch varying from 0.78 to 1.5 to 1.7 (P less than .05). This variation supports separate functional capabilities for the three muscle bellies of the PCA.
Assaying the Circulating Factor VIII Activity in Hemophilia A Patients Treated with Recombinant Factor VIII Products (2002)

Large discrepancies between factor VIII assay methods have been reported from pharmacokinetic studies of recombinant factor VIII concentrates. In the assay of postinfusion patient plasma samples, traditional activated partial thromboplastin time (aPTT)-based one-stage clotting methods usually give results that are 20 to 50% lower than those obtained by chromogenic substrate assays. Investigations into the cause of these discrepancies have shown that the choice of phospholipid in the one-stage assay is crucial. The use of platelets or liposomes resembling platelet factor 3 instead of traditional aPTT reagents results in an increase in the apparent one-stage activity and a fairly good correlation with the chromogenic results. These and other functional test results, antigen measurements as well as clinical data, support the view that the chromogenic assay most accurately reflects the therapeutic effect. In addition to the differences among assay methods, there is also a discrepancy between the World Health Organization (WHO) standards for concentrates and plasma. The use of product-specific standards, prepared by diluting the factor VIII concentrate into hemophilic plasma, when assaying postinfusion plasma samples seems to be a feasible approach to overcome the problems encountered in pharmacokinetic studies.
Viral load, physical status, and E6/E7 mRNA expression of human papillomavirus in head and neck squamous cell carcinoma (2012)

E6/E7 mRNA expression in patients with HNSCC with low viral load remains low even in cases of integration to the host genome. Tonsillar carcinomas were significantly associated with HPV among various types of HNSCC.
Comparison of N‐Linked Oligosaccharides of Recombinant Human Tissue Kallikrein Produced by Chinese Hamster Ovary Cells on Microcarrier Beads and in Serum‐Free Suspension Culture (1994)

Glycosylation heterogeneity in recombinant human tissue kallikrein (r-HuTK) produced by Chinese hamster ovary (CHO) cells from microcarrier culture and from a serum-free suspension cell recycle process has been compared. Significant differences in the degree of sialylation were observed in glycoform distribution and oligosaccharide heterogeneity. High-performance liquid chromatography with a pellicular anion-exchange column under low pH eluant conditions was used to characterize the number and types of N-linked complex type oligosaccharides present. The oligosaccharides were released by N-glycanase and, after reduction, were resolved into a number of peaks containing one, two, three, and four sialic acids with an additional subfractionation based on the nature of the antennary structure. The microcarrier process resulted in a reduced amount of sialylated oligosaccharide species as compared to the suspension cell process. Removal of sialic acid followed by chromatography of the asialooligosaccharides under high pH anion-exchange conditions indicated that the same antennary structures were present but in slightly different relative amounts. The oligosaccharide profiles are indicative of a highly complex array of microheterogeneity present, encompassing mono-, di-, tri-, and tetrasialylated complex type oligosaccharides.
Signaling mechanisms implicated in cranial sutures pathophysiology: Craniosynostosis (2016)

Normal extension and skull expansion is a synchronized process that prevails along the osteogenic intersections of the cranial sutures. Cranial sutures operate as bone growth sites allowing swift bone generation at the edges of the bone fronts while they remain patent. Premature fusion of one or more cranial sutures can trigger craniosynostosis, a birth defect characterized by dramatic manifestations in appearance and functional impairment. Up until today, surgical correction is the only restorative measure for craniosynostosis associated with considerable mortality. Clinical studies have identified several genes implicated in the pathogenesis of craniosynostosis syndromes with useful insights into the underlying molecular signaling events that determine suture fate. In this review, we exploit the intracellular signal transduction pathways implicated in suture pathobiology, in an attempt to identify key signaling molecules for therapeutic targeting.