gebhart/patrepeval huggingface dataset:
Glycosylation and secretion of human tissue plasminogen activator in recombinant baculovirus-infected insect cells. (1989)

Cell lines established from the lepidopteran insect Spodoptera frugiperda (fall armyworm; Sf9) are used routinely as hosts for the expression of foreign proteins by recombinant baculovirus vectors. We have examined the pathway of protein glycosylation and secretion in these cells, using human tissue plasminogen activator (t-PA) as a model. t-PA expressed in Sf9 cells was both N glycosylated and secreted. At least a subset of the N-linked oligosaccharides in extracellular t-PA was resistant to endo-beta-N-acetyl-D-glucosaminidase H, which removes immature, high-mannose-type oligosaccharides. This refutes the general conclusion from previous studies that Sf9 cells cannot process immature N-linked oligosaccharides to an endo-beta-N-acetyl-D-glucosaminidase H-resistant form. A nonglycosylated t-PA precursor was not detected in Sf9 cells, even with very short pulse-labeling times. This suggests that the mammalian signal sequence of t-PA is efficiently recognized in Sf9 cells and that it can mediate rapid translocation across the membrane of the rough endoplasmic reticulum, where cotranslational N glycosylation takes place. However, t-PA was secreted rather slowly, with a half-time of about 1.6 h. Thus, a rate-limiting step(s) in secretion occurs subsequent to translocation and N glycosylation of the t-PA polypeptide. Treatment of Sf9 cells with tunicamycin, but not with inhibitors of oligosaccharide processing, prevented the appearance of t-PA in the extracellular medium. This suggests that N glycosylation per se, but not processing of the N-linked oligosaccharides, is required directly or indirectly in baculovirus-infected Sf9 cells for the secretion of t-PA. Finally, the relative efficiency of secretion decreased dramatically with time of infection, suggesting that the Sf9 host cell secretory pathway is compromised during the later stages of baculovirus infection.
Synthesis of L-Tryptophan from Pyruvate, Ammonia and Indole (1972)

The tryptophanase activity which synthesizes l-tryptophan from pyruvate, ammonia and indole, was found to be widely distributed in cells of bacteria belonging to Enterobacteriaceae, such genera as Escherichia, Kluyvera, Enterobacter, Erwinia and Proteus. With the cells of Proteus rettgeri, equilibrium of the elimination reaction of l-tryptophan in the presence of high concentration of ammonia was studied. It was found that the equilibrium inclines toward the synthetic state. When 5-hydroxy- and 5-methyl-indole were substituted for indole, 5-hydroxy- and 5-methyl-l-tryptophan, respectively, were synthesized. The synthesis of l-tryptophan was also observed with indole and various amino acids, S-methyl-l-cysteine, S-ethyl-l-cysteine, l-cysteine, 5-fluoro-dl-tryptophan, or oxalacetic acid.
A Machine Learning Approach to Musical Style Recognition (2018)

Much of the work on perception and understanding of music by computers has focused on low-level perceptual features such as pitch and tempo. Our work demonstrates that machine learning can be used to build effective style classifiers for interactive performance systems. We also present an analysis explaining why these techniques work so well when hand-coded approaches have consistently failed. We also describe a reliable real-time performance style classifier.
Identification and characterization of a novel anthocyanin malonyltransferase from scarlet sage (Salvia splendens) flowers: an enzyme that is phylogenetically separated from other anthocyanin acyltransferases (2004)

Anthocyanin acyltransferases (AATs) catalyze a regiospecific acyl transfer from acyl-CoA to the glycosyl moiety of anthocyanins, thus playing an important role in flower coloration. The known AATs are subfamily members of an acyltransferase family, the BAHD family, which play important roles in secondary metabolism in plants. Here, we describe the purification, characterization, and cDNA cloning of a novel anthocyanin malonyltransferase from scarlet sage (Salvia splendens) flowers. The purified enzyme (hereafter referred to as Ss5MaT2) is a monomeric 46-kDa protein that catalyzes the transfer of the malonyl group from malonyl-CoA to the 4"'-hydroxyl group of the 5-glucosyl moiety of anthocyanins. Thus, it is a malonyl-CoA:anthocyanin 5-glucoside 4"'-O-malonyltransferase. On the basis of the partial amino acid sequences of the purified enzyme, we isolated a cDNA that encodes an acyltransferase protein. The steady-state transcript level of the gene was the highest in recently opened, fully pigmented flowers and was also correlated with the trend observed for an AAT gene responsible for the first malonylation step during salvianin biosynthesis. Immunoprecipitation studies using antibodies against the recombinant acyltransferase protein corroborated the identity of this cDNA as that encoding Ss5MaT2. The deduced amino acid sequence of Ss5MaT2 showed a low similarity (22-24% identity) to those of AATs and lacked the AAT-specific signature sequence. A phylogenetic analysis suggested that Ss5MaT2 is more related to acetyl-CoA:benzylalcohol acetyltransferase (BEAT) rather than to AAT. This is another example in which enzymes with similar, although not identical, substrate evolved from different branches of the BAHD family.
Modeling the process of ageing in face images (1999)

The process of ageing causes significant alterations in the facial appearance of individuals. When compared with other sources of variation in face images (e.g. variation due to changes in pose and expression), appearance variation due to ageing displays some unique characteristics. For example ageing variation is specific to a given individual, it occurs slowly and it is affected significantly by other factors, such as the health, gender and the lifestyle of the individual. In this paper we describe how the effects of ageing on facial appearance can be explained using a parameterized statistical model. We present experimental results to show that reasonably accurate estimates of age can be made for unseen images. We also show that we can improve our results significantly by taking into account the fact that different individuals age in different ways and by considering the effect of lifestyle. We also demonstrate how the proposed framework can be used for simulating ageing effects on new face images, in order to predict how an individual might look like in the future, or how he/she used to look in the past. Experimental and visual results on simulation of age effects are presented.
Serologic Evidence for the Presence in Pteropus Bats of a Paramyxovirus Related to Equine Morbillivirus (1996)

Two outbreaks of a previously unknown disease in horses and humans occurred in Queensland in 1994. The outbreaks occurred within 1 month of each other in Brisbane and Mackay, which are approximately 1000 km apart. In the Brisbane incident, 21 horses were infected of which 14 died or were euthanized after severe clinical signs of an acute
respiratory disease. Two human cases were in patients with less well defined clinical signs; one patient died (1,2). In the Mackay incident two horses became seriously ill and died, and one person also died (3). Although it is now known that the two outbreaks occurred in August and September 1994, knowledge of the Mackay outbreak did not occur until late 1995 when the infected person died of a relapsing encephalitis. The name equine morbillivirus (EMV) has been proposed for a paramyxovirus isolated from four of the Brisbane horses and the first patient who died (2).
A mutation in the 530 loop ofEscherichia coli16S ribosomal RNA causes resistance to streptomycin (1988)

Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells were not stimulated by streptomycin to misread the message in a poly(U)-directed assay. They were also restrictive to the stimulation of misreading by other error-promoting related aminoglycoside antibiotics such as neomycin, kanamycin or gentamicin, which do not compete for the streptomycin binding site. The 530 loop where the mutation in the 16S rRNA is located has been mapped at the external surface of the 30S subunit, and is therefore distal from the streptomycin binding site at the subunit interface. Our results support the conclusion that the mutation at position 523 in the 16S rRNA does not interfere with the binding of streptomycin, but prevents the drug from inducing conformational changes in the 530 loop which account for its miscoding effect. Since this effect primarily results from a perturbation of the translational proofreading control, our results also provide evidence that the 530 loop of the 16S rRNA is involved in this accuracy control.
The human ATP binding cassette gene ABCA13, located on chromosome 7p12.3, encodes a 5058 amino acid protein with an extracellular domain encoded in part by a 4.8-kb conserved exon (2002)

The ABCA subfamily of ATP-binding cassette (ABC) transporters includes eleven members to date. In this study, we describe a new, unusually large gene on chromosome 7p12.3, ABCA13. This gene spans over 450 kb and is split into 62 exons. The predicted ABCA13 protein consists of 5,058 ami- no acid residues making it the largest ABC protein described to date. Like the other ABCA subfamily members, ABCA13 contains a hydrophobic, predicted transmembrane segment at the N-terminus, followed by a large hydrophilic region. In the case of ABCA13, the hydrophilic region is unexpectedly large, more than 3,500 amino acids, encoded by 30 exons, two of which are 4.8 and 1.7 kb in length. These two large exons are adjacent to each other and are conserved in the mouse Abca13 gene. Tissue profiling of the major transcript reveals the highest expression in human trachea, testis, and bone marrow. The expression of the gene was also determined in 60 tumor cell lines and the highest expression was detected in the SR leukemia, SNB-19 CNS tumor and DU-145 prostate tumor cell lines. ABCA13 has high similarity with other ABCA subfamily genes which are associated with human inherited diseases: ABCA1 with the cholesterol transport disorders Tangier disease and familial hypoalphalipoproteinemia, and ABCA4 with several retinal degeneration disorders. The ABCA13 gene maps to chromosome 7p12.3, a region that contains an inherited disorder affecting the pancreas (Shwachman-Diamond syndrome) as well as a locus involved in T-cell tumor invasion and metastasis (INM7), and therefore is a positional candidate for these pathologies.
Extracellular signal regulated kinase (ERK)/mitogen activated protein kinase (MAPK)-independent functions of Raf kinases (2002)

Raf comprises a family of three kinases, A-Raf, B-Raf and Raf-1, which are best known as key regulators of the MEK-MAPK/ERK cascade. This module is often perceived as a linear pathway in which ERK is the effector. However, recent advances have unveiled a role for Raf outside this established signalling unit. Current evidence, including gene-knockout studies in mice, suggests that there are ERK-independent functions of Raf kinases. Regulation of apoptosis is one area in which Raf may function independently of ERK, although its substrates remain to be identified. Other studies have suggested that Raf has kinase-independent functions and may act as a scaffold protein.
ImageJ for Microscopy (2007)

ImageJ is an essential tool for us that fulfills most of our routine image processing and analysis requirements. The near-comprehensive range of import filters that allow easy access to image and meta-data, a broad suite processing and analysis routine, and enthusiastic support from a friendly mailing list are invaluable for all microscopy labs and facilities-not just those on a budget.
Hyperglycaemia is associated with poor outcomes in patients admitted to hospital with acute exacerbations of chronic obstructive pulmonary disease (2006)

Increasing blood glucose concentrations are associated with adverse clinical outcomes in patients with AECOPD. Tight control of blood glucose reduces mortality in patients in intensive care or following myocardial infarction. A prospective study is now required to determine whether control of blood glucose can also improve outcomes from AECOPD.
Sweet taste receptors in rat small intestine stimulate glucose absorption through apical GLUT2 (2007)

Natural sugars and artificial sweeteners are sensed by receptors in taste buds. T2R bitter and T1R sweet taste receptors are coupled through G-proteins, alpha-gustducin and transducin, to activate phospholipase C beta2 and increase intracellular calcium concentration. Intestinal brush cells or solitary chemosensory cells (SCCs) have a structure similar to lingual taste cells and strongly express alpha-gustducin. It has therefore been suggested over the last decade that brush cells may participate in sugar sensing by a mechanism analogous to that in taste buds. We provide here functional evidence for an intestinal sensing system based on lingual taste receptors. Western blotting and immunocytochemistry revealed that all T1R members are expressed in rat jejunum at strategic locations including Paneth cells, SCCs or the apical membrane of enterocytes; T1Rs are colocalized with each other and with alpha-gustducin, transducin or phospholipase C beta2 to different extents. Intestinal glucose absorption consists of two components: one is classical active Na+-glucose cotransport, the other is the diffusive apical GLUT2 pathway. Artificial sweeteners increase glucose absorption in the order acesulfame potassium approximately sucralose > saccharin, in parallel with their ability to increase intracellular calcium concentration. Stimulation occurs within minutes by an increase in apical GLUT2, which correlates with reciprocal regulation of T1R2, T1R3 and alpha-gustducin versus T1R1, transducin and phospholipase C beta2. Our observation that artificial sweeteners are nutritionally active, because they can signal to a functional taste reception system to increase sugar absorption during a meal, has wide implications for nutrient sensing and nutrition in the treatment of obesity and diabetes.
Noninvasive Mapping of Human Atrial Fibrillation (2008)

Using electrocardiographic body surface mapping during AF, interindividual differences of atrial fibrillatory activation can be observed. The surface activation pattern during AF shows an excellent short-term reproducibility.
The 10,400- and 14,500-dalton proteins encoded by region E3 of adenovirus form a complex and function together to down-regulate the epidermal growth factor receptor (1991)

In adenovirus-infected cells, the epidermal growth factor receptor (EGF-R) is internalized from the cell surface via endosomes and is degraded, and the E3 10,400-dalton protein (10.4K protein) is required for this effect (C. R. Carlin, A. E. Tollefson, H. A. Brady, B. L. Hoffman, and W. S. M. Wold, Cell 57:135-144, 1989). We now report that both the E3 10.4K and E3 14.5K proteins are required for this down-regulation of EGF-R in adenovirus-infected cells. Down-regulation of cell surface EGF-R was demonstrated by results from several methods, namely the absence of EGF-R autophosphorylation in an immune complex kinase assay, the inability to iodinate EGF-R on the cell surface, the formation of endosomes containing EGF-R as detected by immunofluorescence, and the degradation of the metabolically [35S]Met-labeled fully processed 170K species of EGF-R. No effect on the initial synthesis of EGF-R was observed. This down-regulation was ascribed to the 10.4K and 14.5K proteins through the analysis of cells infected with rec700 (wild-type), dl748 (10.4K-, 14.5K+), or dl764 (10.4K+, 14.5K-) or coinfected with dl748 plus dl764. Further evidence that the 10.4K and 14.5K proteins function in concert was obtained by demonstrating that the 10.4K protein was coimmunoprecipitated with the 14.5K protein by using three different antisera to the 14.5K protein, strongly implying that the 10.4K and 14.5K proteins exist as a complex. Together, these results indicate that the 10.4K and 14.5K proteins function as a complex to stimulate endosome-mediated internalization and degradation of EGF-R in adenovirus-infected cells.
Heterologous recombination in the double-stranded RNA bacteriophage phi 6 (1992)

Bacteriophage phi 6 contains three double-stranded RNA genomic segments. We have constructed a virus with an insertion of a kanamycin resistance gene in genomic RNA segment M. The virus forms small, turbid plaques, and its genome is unstable. Virus from a single plaque contained from about 0.1 to 10% large clear-plaque forms of the virus; these were usually missing the kanamycin resistance gene, and in many cases, the resulting segment M was larger or smaller than its normal size. Sequence analysis of the genomic RNA of the apparent deletions showed that they were formed by recombination events between segment M and either segment S or L. These heterologous recombination events resulted in the loss of the kanamycin resistance gene from segment M and the replacement of the 3' end of segment M with the 3' end of segment S or L. Although the 3' ends of the single-stranded RNA transcripts of the genomic segments appear to have extensive secondary structure, the sequences at the 3' ends are not involved in the specificity of genomic packaging.
Nuclear hormone receptors : molecular mechanisms, cellular functions, clinical abnormalities (1991)

Overview of the nuclear receptor family, E.V.Jensen the oestrogen receptor - from perception to mechanism, S.Green and P.Chambom the gluticocorticoid receptor, M.Danielson nuclear thyroid hormone receptors, W.W.Chin the steroid receptor superfamily transactivators of gene expression, S.Y.Tsai et al hormone response elements, E.Martinez and W. Wahli co-operative trans-activation of steroid receptors, M.Nukker et al repression of gene expression by steroid and thyroid hormones, I.E. Akerbolm characterization of DNA receptor interactions, M. Beato et al the interaction of steroid receptors with chromatin, G.L.Hager et al ontogeny of sex steroids in mammals, G.R.Cunha et al retinoic acid receptors and vertebrate limb morphogenesis, C.W.Ragsdale and J.P. Brockes the role of steroid hormones and growth factors in the control of normal and malignant growth, R.Clarke et al genetic defects of receptors involved in disease, M.R.Hughes and B.W.O'Malley.
Suppression of Dualtropic Human Immunodeficiency Virus Type 1 by the CXCR4 Antagonist AMD3100 Is Associated with Efficiency of CXCR4 Use and Baseline Virus Composition (2008)

In a phase I/II evaluation of the CXCR4 antagonist AMD3100, human immunodeficiency virus RNA levels were significantly reduced in a single study subject who harbored CXCR4 (X4)-tropic virus, but not in subjects who harbored either dual/mixed (DM)-tropic or CCR5 (R5)-tropic virus (C. W. Hendrix et al., J. Acquir. Immune Defic. Syndr. 37:1253-1262, 2004). In this study, we analyzed the envelope clones of DM-tropic virus in baseline and treated virus populations from 14 subjects. Ten subjects exhibited significant reductions in CXCR4-mediated infectivity after 10 days of AMD3100 therapy relative to baseline (X4 suppressor group), while four subjects had no reduction of CXCR4-mediated infectivity (X4 nonsuppressor group). The baseline viruses of the X4 suppressor group infected CXCR4-expressing cells less efficiently than those of the X4 nonsuppressor group. Clonal analysis indicated that the baseline viruses from the X4 suppressor group contained a higher proportion of R5-tropic variants mixed with CXCR4-using variants, while the X4 nonsuppressor group was enriched for CXCR4-using variants. AMD3100 suppressed X4-tropic variants in all subjects studied, but not all dualtropic variants. Furthermore, dualtropic variants that used CXCR4 efficiently were suppressed by AMD3100, while dualtropic variants that used CXCR4 poorly were not. This study demonstrated that AMD3100 has the ability to suppress both X4-tropic and certain dualtropic variants in vivo. The suppression of CXCR4-using variants by AMD3100 is dependent on both the tropism composition of the virus population and the efficiency of CXCR4 usage of individual variants.
Successful High Angle Completions, Cementing, and Drilling’s Impact (1988)

ABSTRACT Successful well completions are the key to exploiting the potential benefits of high angle/horizontal drilling. Successful primary cementing is vital to completion success. Cementing success is often jeopardized by the wellbore created during the drilling process. This paper unfolds this dilemma and takes a look at what must be done to overcome it.
INCREASED SUSCEPTIBILITY TO SEPTIC AND ENDOTOXIC SHOCK IN MONOCYTE CHEMOATTRACTANT PROTEIN 1/CC CHEMOKINE LIGAND 2-DEFICIENT MICE CORRELATES WITH REDUCED INTERLEUKIN 10 AND ENHANCED MACROPHAGE MIGRATION INHIBITORY FACTOR PRODUCTION (2006)

The chemokine monocyte chemoattractant protein 1/CC chemokine ligand 2 (MCP-1/CCL2) is a potent chemoattractant of mononuclear cells and a regulatory mediator involved in a variety of inflammatory diseases. In the present study, we demonstrate that mcp-1/ccl2-deficient mice are more susceptible to systemic inflammatory response syndrome induced by lipopolysaccharide and to polymicrobial sepsis induced by cecum ligation and puncture (CLP) when compared with wild-type mice. Interestingly, in the CLP model, mcp-1/ccl2-deficient mice efficiently cleared the bacteria despite an impaired recruitment of leukocytes, especially mononuclear cells. The increased lethality rate in these models correlates with an impaired production of interleukin (IL) 10 in vivo. Furthermore, macrophages from mcp-1/ccl2-deficient mice activated with lipopolysaccharide also produced lower amounts of IL-10 and similar tumor necrosis factor compared with wild-type mice. We observed a drastic increase in the amounts of macrophage migration inhibitory factor at 6 and 24 h after CLP in mcp-1/ccl2-deficient mice. These results indicate that endogenous MCP-1/CCL2 positively regulates IL-10 but negatively controls macrophage migration inhibitory factor during peritoneal sepsis, thus suggesting an important immunomodulatory role for MCP-1/CCL2 in controlling the balance between proinflammatory and anti-inflammatory factors in sepsis.
Rate Acceleration of Light‐Driven Rotary Molecular Motors (2007)

Abstract One of the key challenges in taking light‐driven unidirectional rotary motors from discovery to application is to increase the rate of rotation. Herein, we review our ongoing efforts to address this issue by meticulous improvement to the molecular design. To accelerate the rotary cycle, we have focused primarily on the rate‐limiting thermal isomerization step. This has been a fascinating and formidable objective, given that the first system we reported had a half‐life of over one week at room temperature! Our research has ultimately led to the construction of a unidirectional rotary molecular motor with a cycle 10 8 times faster than the original; that is, it can in principle function at 44 rotations per second.
Programmability and service creation for multimedia networks (1996)

The Binding Architecture is an open architecture for building multimedia networks that must guarantee quality of service (QOS). We explore the notion of a service in the Binding Architecture and propose a conceptual model for building scalable multimedia distribution services based on it. We begin first by examining the relation between resources, their abstractions and the services that can be built from them and use this to derive a general model for binding. Based on this model, we identify a general set of capabilities required for building any multimedia distribution service. We also describe how these capabilities can be incorporated into our view of the service creation process. Finally, we augment our discussion with the description of an example service which we have developed using this paradigm.