gebhart/patrepeval huggingface dataset:
Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues. (1985)

A method is proposed for computing the rates of nucleotide substitution for an oncogene of a retrovirus (v-onc), its cellular homologue (c-onc), and the retrovirus genome simultaneously. The method has been applied to DNA sequences of the v-mos gene of Moloney murine sarcoma virus (Mo-MuSV) and the c-mos and gag genes of Mo-MuSV and Moloney murine leukemia virus (Mo-MuLV). The rates of nucleotide substitution for c-mos, the gag gene, and v-mos are estimated to be 1.71 X 10(-9), 6.3 X 10(-4), and 1.31 X 10(-3) per site per year, respectively. The rate of evolution of c-mos is comparable to that of many functional genes in DNA genomes, suggesting some important biological function played by cellular oncogenes. The rates of nucleotide substitution in the v-mos and gag genes are very high and are similar to those of RNA viral genes such as the hemagglutinin and neuraminidase genes in the influenza A virus. Thus, oncogenes seem to exemplify a general feature of genome evolution: the rate of evolution of RNA genomes can be more than a million times greater than that of DNA genomes because of a high mutation rate in the RNA genome.
Instance Segmentation based Semantic Matting for Compositing Applications (2019)

Image compositing is a key step in film making and image editing that aims to segment a foreground object and combine it with a new background. Automatic image compositing can be done easily in a studio using chroma-keying when the background is pure blue or green. However, image compositing in natural scenes with complex backgrounds remains a tedious task, requiring experienced artists to hand-segment. In order to achieve automatic compositing in natural scenes, we propose a fully automated method that integrates instance segmentation and image matting processes to generate high-quality semantic mattes that can be used for image editing task. Our approach can be seen both as a refinement of existing instance segmentation algorithms and as a fully automated semantic image matting method. It extends automatic image compositing techniques such as chroma-keying to scenes with complex natural backgrounds without the need for any kind of user interaction. The output of our approach can be considered as both refined instance segmentations and alpha mattes with semantic meanings. We provide experimental results which show improved performance results as compared to existing approaches.
Impact of Added Tetraethylthiuram Disulfide Deactivator on the Kinetics of Growth and Reinitiation of Poly(methyl methacrylate) Brushes Made by Surface-Initiated Photoiniferter-Mediated Photopolymerization (2006)

Without intervention, it has been found that surface-initiated photoiniferter-mediated photopolymerization (SI-PMP) of methyl methacrylate suffers from irreversible termination, which leads to cessation of polymerization. These irreversible termination reactions were successfully reduced by preaddition of tetraethylthiuram disulfide (TED). The poly(methyl methacrylate) layers were also reinitiated using styrene as a monomer to investigate the effect of TED concentration on the extent of irreversible termination. The reinitiation efficiency increased as [TED] was increased, indicating that extent of irreversible termination reactions can be reduced by increasing [TED]. It was also observed that dithiocarbamyl radicals generated from TED can initiate polymerization in solution, resulting in significant monomer consumption.
Induced Expression of Trimerized Intracellular Domains of the Human Tumor Necrosis Factor (TNF) p55 Receptor Elicits TNF Effects (1997)

The various biological activities of tumor necrosis factor (TNF) are mediated by two receptors, one of 55 kD (TNF-R55) and one of 75 kD (TNF-R75). Although the phenotypic and molecular responses elicited by TNF in different cell types are fairly well characterized, the signaling pathways leading to them are so far only partly understood. To further unravel these processes, we focused on TNF-R55, which is responsible for mediating most of the known TNF effects. Since several studies have demonstrated the importance of receptor clustering and consequently of close association of the intracellular domains for signaling, we addressed the question of whether clustering of the intracellular domains of TNF-R55 (TNF-R55i) needs to occur in structural association with the inner side of the cell membrane, where many signaling mediators are known to reside. Therefore, we investigated whether induced intracellular clustering of only TNF-R55i would be sufficient to initiate and generate a full TNF response, without the need for a full-length receptor molecule or a transmembrane region. Our results provide clear evidence that inducible forced trimerization of either TNF-R55i or only the death domain elicits an efficient TNF response, comprising activation of the nuclear factor kappaB, induction of interleukin-6, and cell killing.
A rapid crosslinking injectable hydrogel for stem cell delivery, from multifunctional hyperbranched polymers via RAFT homopolymerization of PEGDA (2015)

A novel injectable hydrogel for stem cell delivery was prepared from multifunctional hyperbranched polyPEGDA and thiolated hyaluronic acid.
Evolutionary Implications of Bacterial Polyketide Synthases (2005)

Polyketide synthases (PKS) perform a stepwise biosynthesis of diverse carbon skeletons from simple activated carboxylic acid units. The products of the complex pathways possess a wide range of pharmaceutical properties, including antibiotic, antitumor, antifungal, and immunosuppressive activities. We have performed a comprehensive phylogenetic analysis of multimodular and iterative PKS of bacteria and fungi and of the distinct types of fatty acid synthases (FAS) from different groups of organisms based on the highly conserved ketoacyl synthase (KS) domains. Apart from enzymes that meet the classification standards we have included enzymes involved in the biosynthesis of mycolic acids, polyunsaturated fatty acids (PUFA), and glycolipids in bacteria. This study has revealed that PKS and FAS have passed through a long joint evolution process, in which modular PKS have a central position. They appear to have derived from bacterial FAS and primary iterative PKS and, in addition, share a common ancestor with animal FAS and secondary iterative PKS. Furthermore, we have carried out a phylogenomic analysis of all modular PKS that are encoded by the complete eubacterial genomes currently available in the database. The phylogenetic distribution of acyltransferase and KS domain sequences revealed that multiple gene duplications, gene losses, as well as horizontal gene transfer (HGT) have contributed to the evolution of PKS I in bacteria. The impact of these factors seems to vary considerably between the bacterial groups. Whereas in actinobacteria and cyanobacteria the majority of PKS I genes may have evolved from a common ancestor, several lines of evidence indicate that HGT has strongly contributed to the evolution of PKS I in proteobacteria. Discovery of new evolutionary links between PKS and FAS and between the different PKS pathways in bacteria may help us in understanding the selective advantage that has led to the evolution of multiple secondary metabolite biosyntheses within individual bacteria.
Correlation between articular cartilage collagenase activity and osteoarthritis (1978)

Articular cartilage collagenase activity was determined for 28 sections obtained from twelve femoral heads. For each one square centimeter area, a section was graded by a histologic-histochemical grading system for the severity of the arthritis. Collagenase activity was found primarily in those areas of moderately severe disease, but not in mild or end stage arthritis.
GeneSplicer: a new computational method for splice site prediction (2001)

GeneSplicer is a new, flexible system for detecting splice sites in the genomic DNA of various eukaryotes. The system has been tested successfully using DNA from two reference organisms: the model plant Arabidopsis thaliana and human. It was compared to six programs representing the leading splice site detectors for each of these species: NetPlantGene, NetGene2, HSPL, NNSplice, GENIO and SpliceView. In each case GeneSplicer performed comparably to the best alternative, in terms of both accuracy and computational efficiency.
Magnetic micro-actuators and systems (MAGMAS) (2003)

Magnetic interactions provide outstanding performances for powerful integrated micro-actuators. This paper explains how magnetic interactions involving permanent magnets, currents, and various magnetic materials remain very effective and even improve as dimensions are reduced. The technological problems that have slowed the development of magnetic micro-actuators and systems (MAGMAS) are progressively being solved. As long as materials scientists continue to develop better thick-film patterned permanent magnets compatible with microsystem technologies, MAGMAS will have a promising future.
Identification of CpG oligonucleotide sequences with high induction of IFN-α/β in plasmacytoid dendritic cells (2001)

The immature plasmacytoid dendritic cell (PDC) is identical with the principal type I IFN-producing cell upon viral infection. Oligodeoxynucleotides which contain unmethylated CpG motifs (CpG ODN) are recognized by the vertebrate immune system. Previously, we described CpG ODN that strongly activate human B cells and human blood dendritic cells. Here we describe distinct CpG-containing oligonucleotide sequences which, in contrast to previously described CpG ODN, induced high amounts of IFN-alpha and IFN-beta in peripheral blood mononuclear cells (PBMC). Intracellular staining for IFN-alpha revealed that within PBMC CpG ODN-induced IFN-alpha is produced exclusively by PDC. Unlike IFN-alpha, TNF-alpha is up-regulated in PDC by all CpG ODN tested. Purified PDC responded to CpG ODN, demonstrating direct activation of PDC by CpG ODN. The most active sequence induced the production of up to 5 pg IFN-alpha per single PDC, resulting in more than 400 ng/ml IFN-alpha in the supernatant of PBMC enriched for PDC. The potency of CpG ODN to stimulate IFN-alpha correlated with their ability to stimulate NK cell lytic activity, while purified NK cells did not respond to CpG ODN. IFNgamma production in PBMC was dependent on CpG ODN-induced IFN-alpha/beta as demonstrated by IFN-alpha/beta blocking antibodies. IFN-alpha-inducing CpG ODN strongly supported IFN-gamma production of TCR-triggered CD4 T cells but were less active than other CpG ODN in stimulating B cells. In conclusion our results demonstrate that particular CpG ODN sequences exist which, due to high IFN-alpha/beta induction in PDC, induce a set of immune responses typical for viral infection.
Use of 1,2,4-Dithiazolidine-3,5-Dione (DtsNH) and 3-Ethoxy-1,2,4-Dithiazoline-5-One (EDITH) for Synthesis of Phosphorothioate-Containing Oligodeoxyribonucleotides (1996)

Previous methods for the preparation of phosphorothioate-containing oligodeoxyribonucleotides rely on the reaction of phosphite triesters with sulfurizing reagents such as tetraethylthiuram disulfide (TETD) and 3H-1,2-benzodithiol-3-one 1,1-dioxide (Beaucage reagent). However, these and other sulfurizing reagents suffer from several disadvantages, and there is great impetus for the development of improved methods for sulfur transfer that are fully compatible with standard automated DNA synthesis. The present report describes the use of 1,2,4-dithiazolidine-3,5-dione (DtsNH) and 3-ethoxy-1,2,4-dithiazoline-5-one (EDITH) as effective sulfurizing reagents that meet these needs. Both reagents are easily prepared, and are stable upon prolonged room temperature storage in acetonitrile solution. The reagents are used at low concentrations (0.05 M) and for short reaction times (30 s). The methodology has been proven for the automated synthesis on 0.2-1.0 micromol scales of oligodeoxyribonucleotides, of length 6-20 bases, containing the phosphorothioate substitution at either a single site or at all positions.
Just‐in‐Time to Save Lives: A Pilot Study of Layperson Tourniquet Application (2015)

Just-in-time instructions increase laypeople's successful application of C-A-T. This pilot study provides evidence that JiT instructions may assist the lay public in providing effective point-of-injury hemorrhage control.
Extended depth of field and aberration control for inexpensive digital microscope systems (1999)

We present a new application and current results for extending depth of field using wave front coding. A cubic phase plate is used to code wave fronts in microscopy resulting in extended depths of field and inexpensive chromatic aberration control. A review of the theory behind cubic phase plate extended depth of field systems is given along with the challenges that are face when applying the theory to microscopy. Current results from the new extended depth of field microscope systems are shown.
Primary structure of and studies on Acanthamoeba actophorin (1993)

We determined the amino acid sequence of the actin monomer binding/actin filament severing protein actophorin from Acanthamoeba castellanii by automated Edman degradation of peptide fragments and by sequencing of full-length cDNA. Actophorin consists of 138 amino acids (calculated molecular weight of 15,543) and shares a high degree of sequence similarity to other low molecular weight actin monomer sequestering proteins, especially vertebrate cofilin, vertebrate actin depolymerizing factor/destrin, and echinoderm depactin. Actophorin is smaller and does not contain a nuclear localization sequence like the related vertebrate proteins. Southern blot analysis indicates that actophorin is a single-copy gene; however, Northern blots show two distinct mRNA species of 1 and 0.9 kb in size. Homogeneous recombinant actophorin purified from Escherichia coli is indistinguishable from the native protein in its physical properties and in biochemical assays of its interaction with actin, but is less reactive with three monoclonal antibodies raised against the native protein. The NH2 terminus of native actophrin is blocked, while the initiating methionine residue is removed from recombinant actophorin. This difference has no measurable effect on activity. By fluorescent antibody staining of Acanthamoeba, actophorin colocalizes with actin filaments in the cortical cytoplasm, especially at the leading edge of the cell. Additionally, actophorin binds phosphatidylinositol 4',5'-bisphosphate. The recombinant actophorin forms X-ray diffraction quality crystals of superior quality in poly(ethylene glycol)/2-propanol and, like the native crystal form, belongs to space group P2(1)2(1)2(1).
Cloning and expression of a cDNA encoding a hepatic microsomal lipase that mobilizes stored triacylglycerol (1999)

A microsomal triacylglycerol hydrolase (TGH) was recently purified from porcine liver [Lehner and Verger (1997) Biochemistry 36, 1861-1868]. To gain further insight into the function of TGH, we have cloned a cDNA encoding TGH from a rat liver cDNA library and generated McArdle RH7777 rat hepatoma cell lines that stably express the rat TGH. The putative protein derived from the cDNA sequence contains a cleavable signal sequence and a catalytic site serine residue present within a pentapeptide motif (GXSXG) that is conserved in all known lipases. TGH-transfected cells showed a 2-fold increase, compared with control cells, in the rate of depletion of prelabelled triacylglycerol stores. Thus, TGH is capable of hydrolysis of stored triacylglycerol. In contrast, the rate of turnover of labelled phosphatidylcholine was similar in both the vector- and TGH-transfected cells. Studies in TGH-transfected cells demonstrated that utilization of intracellular triacylglycerol pools for secretion was approx. 30% higher than in vector-transfected cells. Whereas phosphatidylcholine secretion was essentially the same in control and TGH-transfected cells, TGH-transfected cells also secreted an approx. 25% greater mass of triacylglycerol into the medium and had increased levels of apolipoprotein B100 in the very-low-density lipoprotein density range compared with control cells. The results suggest that the microsomal TGH actively participates in the mobilization of cytoplasmic triacylglycerol stores, some of which can be used for lipoprotein assembly.
Localization of human variable and constant region immunoglobulin heavy chain genes on subtelomeric band q32 of chromosome 14 (1982)

Analysis of a group of human/rodent somatic cell hybrids with nucleic acid probes prepared from cloned human variable region (VH), junctional (JH), and constant region (C epsilon) heavy chain immunoglobulin genes indicates that all of these IgH genes are localized on the subtelomeric (q32) band of chromosome 14. Somatic cell hybrids were isolated in selective medium after fusing human fibroblasts with hprt- Chinese hamster cells. The human parental cells contained two translocation chromosomes representing a reciprocal translocation between chromosomes X and 14. Only those hybrid cell lines retaining a complete human autosome 14 or the X/14 translocation chromosome (i.e. containing band 14q32) retained the human IgH genes. Retention of these genes did not correlate with the presence of the other translocation chromosome, 14/X. These results indicate that all human IgH genes (VH, JH, and CH) map to the same chromosomal band (14q32) which is commonly involved in reciprocal translocations with human chromosome 8 (8q24) in B-cell neoplasms.
Dietary supplementation with apple juice concentrate alleviates the compensatory increase in glutathione synthase transcription and activity that accompanies dietary- and genetically-induced oxidative stress. (2004)

Increased oxidative stress, which can arise from dietary, environmental and/or genetic sources, contributes to the decline in cognitive performance during normal aging and in neurodegenerative conditions such as Alzheimer's disease. Supplementation with fruits and vegetables that are high in antioxidant potential can compensate for dietary and/or genetic deficiencies that promote increased oxidative stress. We have recently demonstrated that apple juice concentrate (AJC) prevents the increase in oxidative damage to brain tissue and decline in cognitive performance observed when transgenic mice lacking apolipoprotein E (ApoE-/-) are maintained on a vitamin-deficient diet and challenged with excess iron (included in the diet as a pro-oxidant). However, the mechanism by which AJC provided neuroprotection was not conclusively determined. Herein, we demonstrate that supplementation with AJC also prevents the compensatory increases in glutathione synthase transcription and activity that otherwise accompany maintenance of ApoE-/- mice on this vitamin-free diet in the presence of iron. Inclusion of the equivalent composition and concentration of sugars of AJC did not prevent these increases. These findings provide further evidence that the antioxidant potential of AJC can compensate for dietary and genetic deficiencies that otherwise promote neurodegeneration.
I/O subsystem configurations for ESA: New roles for processor storage (1993)

I/O subsystem configurations are dictated by the storage and I/O requirements of the specific applications that use the disk hardware. Treating the latter requirement as a given, however, draws a boundary at the channel interface that is not well-suited to the capabilities of the Enterprise Systems Architecture (ESA). This architecture allows hardware expenditures in the I/O subsystem to be managed, while at the same time improving transaction response time and system throughput capability, by a strategy of processor buffering coupled with storage control cache. The key is to control the aggregate time per transaction spent waiting for physical disk motion. This paper investigates how to think about and accomplish such an objective. A case study, based on data collected at a large Multiple Virtual Storage installation, is used to investigate the potential types and amounts of memory use by individual files, both in storage control cache and in processor buffers. The mechanism of interaction between the two memory types is then examined and modeled so as to develop broad guidelines for how best to deploy an overall memory budget. These guidelines tend to contradict the usual metrics of storage control cache effectiveness, underscoring the need for an adjustment in pre-ESA paradigms.
Inter-alpha-inhibitor, hyaluronan and inflammation. (2003)

Inter-alpha-inhibitor is an abundant plasma protein whose physiological function is only now beginning to be revealed. It consists of three polypeptides: two heavy chains and one light chain called bikunin. Bikunin, which has antiproteolytic activity, carries a chondroitin sulphate chain to which the heavy chains are covalently linked. The heavy chains can be transferred from inter-alpha-inhibitor to hyaluronan molecules and become covalently linked. This reaction seems to be mediated by TSG-6, a protein secreted by various cells upon stimulation by inflammatory cytokines. Inter-alpha-inhibitor has been shown to be required for the stabilization of the cumulus cell-oocyte complex during the expansion that occurs prior to ovulation. Hyaluronan-linked heavy chains in the extracellular matrix of this cellular complex have recently been shown to be tightly bound to TSG-6. Since TSG-6 binds to hyaluronan, its complex with heavy chains could stabilize the extracellular matrix by cross-linking hyaluronan molecules. Heavy chains linked to hyaluronan molecules have also been found in inflamed tissues. The physiological role of these complexes is not known but there are indications that they might protect hyaluronan against fragmentation by reactive oxygen species. TSG-6 also binds to bikunin thereby enhancing its antiplasmin activity. Taken together, these results suggest that inter-alpha-inhibitor is an anti-inflammatory agent which is activated by TSG-6.
A short-term comparison of the effects of clomiphene citrate and conjugated equine estrogen in menopausal/castrate women. (1991)

An attempt was made to assess the potential role for an antiestrogen in the hormone replacement therapy of menopausal women who have a contraindication to estrogen use. Two groups of menopausal or castrate women were given either conjugated equine estrogen or clomiphene citrate in a cyclic manner for 25 days each month for 3 months. The effects were measured after 3 months and compared with baseline values. Clomiphene lowered FSH slightly, but had no effect on subjective vasomotor symptoms. With respect to bone metabolism, it produced no change in plasma parathyroid hormone level, whereas estrogen lowered it; both compound lowered serum calcium but clomiphene had less effect. The hydroxyproline/creatinine ratio was decreased more by clomiphene than by the estrogen. These findings are consistent with a beneficial effect on bone. Clomiphene had no adverse effects on clotting parameters and showed effects similar to those of conjugated equine estrogens on certain measures of lipid metabolism.