gebhart/patrepeval huggingface dataset:
Receiver-driven bandwidth adaptation for light-weight sessions (1997)

Current Internet multicast conferencing tools treat all sources with equal importance in that they either statically allocate a fixed bandwidth to each source in a session, or they automatically adapt each source's transmission rate independently of all other sources. But not all sources are of equal interest to all receivers. We believe that to effectively support human to human communication, this disparity in receiver interest should be reflected in the rate-adaptation process. To this end, we propose a protocol called "SCUBA" that enables media sources to intelligently account for receiver interest in their rate-adjustment algorithms. SCUBA is orthogonal to and complements existing rate-adaptation schemes and can interoperate with either sender-or receiverdirected control systems. To scale the SCUBA protocol with multicast session size, we decouple the receiver-feedback process from the session size through sampling. This approach introduces a "tunable" tradeoff between convergence time and sampling accuracy that for large sessions is solely dependent on the control traffic bandwidth. In addition to its applicability in video conferencing, our control scheme can be combined with media transcoders to intelligently manage a bottleneck link at a well-known and fixed location in the network. We implemented SCUBA within our video conferencing tool vie and our media gateway rtpgw and feedback from their preliminary deployment indicates that the efficacy of the overall multimedia communication system has been greatly enhanced.
Trans-kingdom Transposition of the Drosophila Element mariner Within the Protozoan Leishmania (1997)

Transposable elements of the mariner/Tc1 family are postulated to have spread by horizontal transfer and be relatively independent of host-specific factors. This was tested by introducing the Drosophila mauritiana element mariner into the human parasite Leishmania major, a trypanosomatid protozoan belonging to one of the most ancient eukaryotic lineages. Transposition in Leishmania was efficient, occurring in more than 20 percent of random transfectants, and proceeded by the same mechanism as in Drosophila. Insertional inactivation of a specific gene was obtained, and a modified mariner element was used to select for gene fusions, establishing mariner as a powerful genetic tool for Leishmania and other organisms. These experiments demonstrate the evolutionary range of mariner transposition in vivo and underscore the ability of this ubiquitous DNA to parasitize the eukaryotic genome.
Palliative nutritional intervention in addition to cyclooxygenase and erythropoietin treatment for patients with malignant disease: Effects on survival, metabolism, and function (2004)

The results of the current study strongly support that nutrition is a limiting factor influencing survival and that nutritional support protects integrated metabolism and metabolic function in patients with progressive cachexia secondary to malignant disease.
Peroxisome Proliferator-Activated Receptor (PPAR) α and PPARβ/δ, but not PPARγ, Modulate the Expression of Genes Involved in Cardiac Lipid Metabolism (2003)

Long-chain fatty acids (FA) coordinately induce the expression of a panel of genes involved in cellular FA metabolism in cardiac muscle cells, thereby promoting their own metabolism. These effects are likely to be mediated by peroxisome proliferator-activated receptors (PPARs). Whereas the significance of PPARalpha in FA-mediated expression has been demonstrated, the role of the PPARbeta/delta and PPARgamma isoforms in cardiac lipid metabolism is unknown. To explore the involvement of each of the PPAR isoforms, neonatal rat cardiomyocytes were exposed to FA or to ligands specific for either PPARalpha (Wy-14,643), PPARbeta/delta (L-165041, GW501516), or PPARgamma (ciglitazone and rosiglitazone). Their effect on FA oxidation rate, expression of metabolic genes, and muscle-type carnitine palmitoyltransferase-1 (MCPT-1) promoter activity was determined. Consistent with the PPAR isoform expression pattern, the FA oxidation rate increased in cardiomyocytes exposed to PPARalpha and PPARbeta/delta ligands, but not to PPARgamma ligands. Likewise, the FA-mediated expression of FA-handling proteins was mimicked by PPARalpha and PPARbeta/delta, but not by PPARgamma ligands. As expected, in embryonic rat heart-derived H9c2 cells, which only express PPARbeta/delta, the FA-induced expression of genes was mimicked by the PPARbeta/delta ligand only, indicating that FA also act as ligands for the PPARbeta/delta isoform. In cardiomyocytes, MCPT-1 promoter activity was unresponsive to PPARgamma ligands. However, addition of PPARalpha and PPARbeta/delta ligands dose-dependently induced promoter activity. Collectively, the present findings demonstrate that, next to PPARalpha, PPARbeta/delta, but not PPARgamma, plays a prominent role in the regulation of cardiac lipid metabolism, thereby warranting further research into the role of PPARbeta/delta in cardiac disease.
A widely expressed transmembrane serine/threonine kinase that does not bind activin, inhibin, transforming growth factor beta, or bone morphogenic factor (1993)

Molecular cloning of complementary DNAs (cDNA) whose expression products bind activin and transforming growth factor beta (TGF-beta 1 and -beta 2) suggests that transmembrane serine/threonine kinases constitute a new class of signaling molecules. A human liver cell cDNA which codes for a new serine/threonine kinase receptor (SKR1) was identified using degenerate oligonucleotide primers complementary to coding sequence for mouse activin and Caenorhabditis elegans daf-1 serine/threonine receptor kinase subdomains VI and VIII in the polymerase chain reaction. The deduced 509-amino acid product consisted of a cysteine-rich extracellular domain and a cytoplasmic serine/threonine kinase domain which are 10-20 and 40% homologous to the respective domains in the activin and transforming growth factor beta receptor kinases. Cells overexpressing SKR1 exhibited no increase in binding of activin, inhibin, TGF-beta 1, TGF-beta 2, or bone morphogenic factor type 2B. Except for its absence in bone and spleen, SKR1 exhibits a tissue expression pattern similar to the TGF-beta receptor II gene. Similarly, SKR1 is expressed in normal parenchymal cells, endothelial cells, fibroblasts, and tumor-derived epithelial cells. The expression pattern and lack of binding to prototypic members of the TGF-beta 1-5 branch of the TGF-beta superfamily suggests that SKR1 is potentially a receptor for a new member of the TGF-beta branch of the ligand superfamily.
ISCOMATRIX vaccines mediate CD8+ T‐cell cross‐priming by a MyD88‐dependent signaling pathway (2011)

Generating a cytotoxic CD8(+) T-cell response that can eradicate malignant cells is the primary objective of cancer vaccine strategies. In this study we have characterized the innate and adaptive immune response to the ISCOMATRIX adjuvant, and the ability of vaccine antigens formulated with this adjuvant to promote antitumor immunity. ISCOMATRIX adjuvant led to a rapid innate immune cell response at the injection site, followed by the activation of natural killer and dendritic cells (DC) in regional draining lymph nodes. Strikingly, major histocompatibility complex (MHC) class I cross-presentation by CD8α(+) and CD8α(-) DCs was enhanced by up to 100-fold when antigen was formulated with ISCOMATRIX adjuvant. These coordinated features enabled efficient CD8(+) T-cell cross-priming, which exhibited prophylactic and therapeutic tumoricidal activity. The therapeutic efficacy of an ISCOMATRIX vaccine was further improved when co-administered with an anti-CD40 agonist antibody, suggesting that ISCOMATRIX-based vaccines may combine favorably with other immune modifiers in clinical development to treat cancer. Finally, we identified a requirement for the myeloid differentiation primary response gene 88 (MyD88) adapter protein for both innate and adaptive immune responses to ISCOMATRIX vaccines in vivo. Taken together, our findings support the utility of the ISCOMATRIX adjuvant for use in the development of novel vaccines, particularly those requiring strong CD8(+) T-cell immune responses, such as therapeutic cancer vaccines.
cDNA sequence, predicted primary structure, and evolving amphiphilic helix of human aspartyl-tRNA synthetase (1989)

Eight of the mammalian aminoacyl-tRNA synthetases associate as a multienzyme complex, whereas prokaryotic and low eukaryotic synthetases occur only as free soluble enzymes. Association of the synthetases may result in effective compartmentalization of synthetases and suggests the association of the entire protein biosynthetic machinery. To elucidate the structural elements and the nature of the molecular interactions involved in the association of the synthetases, we have cloned and sequenced the complementary DNA coding human aspartyl-tRNA synthetase. The full length cDNA encodes an open reading frame of 500 amino acids with 56% identity with yeast aspartyl-tRNA synthetase. The similarity with yeast aspartyl-tRNA synthetase is unevenly distributed with a high percent of identity at the C-terminus and relatively low identity at the N-terminus. The N-terminal sequence strongly prefers an alpha-helical secondary structure and shows amphiphilic characteristics. Further comparison with the yeast synthetases showed that the basic positively charged helixes in yeast synthetases are evolved to a neutral amphiphilic helix in this mammalian synthetase. The mammalian neutral amphiphilic helix is so far unique among all known sequences of bacterial, yeast, and mammalian synthetases and may account for the association of synthetases in the synthetase complex.
A dielectrophoretic continuous flow sorter using integrated microelectrodes coupled to a channel constriction (2011)

In this article, we propose a novel dielectrophoretic continuous flow sorter using planar micro electrodes coupled to a channel constriction. This design enables a high particle sorting efficiency at low voltages while relying on a simple fabrication and integration process. We have numerically simulated the AC electrokinetic effects and the fluid behavior to predict particle trajectories. Simulation results are in accordance with experimental data: 10 and 5 μm polystyrene beads were continuously sorted with <2% errors at flow speeds of 100 μm/s. We were also able to change the particle buffer while sorting beads. Finally, to demonstrate the interest of our device for cell sorting, we also sorted dead and living yeast cells according to their different dielectric properties. Living cell concentration was enriched by a factor of 4 versus dead cell concentration after passing the sorting device.
Contribution of Hepatic Cytochrome P450 3A4 Metabolic Activity to the Phenomenon of Clopidogrel Resistance (2004)

Clopidogrel administration results in interindividual variability in platelet inhibition, which correlates with CYP3A4 metabolic activity. Measurement of antiplatelet drug efficacy with a point-of-care device and alternative antithrombotic strategies for aspirin or clopidogrel nonresponders and low responders could reduce the incidence of thrombotic events that continue to occur despite oral antiplatelet therapy.
Functional domains of Epstein-Barr virus nuclear antigen EBNA-1 (1991)

The Epstein-Barr virus (EBV)-encoded latency product EBNA-1 is functionally pleiotropic, being required for replication of the episomal form of the EBV genome and having a role in the regulation of latency transcription. EBNA-1 is a direct DNA-binding protein, and both replication and transactivation are dependent on the interaction of EBNA-1 with its cognate DNA recognition sequences. To better understand EBNA-1 function, we have further characterized the DNA-binding domain of EBNA-1 and have examined the contributions of other domains of the protein to EBNA-1 transactivation activity. A Bal31 deletional analysis of the carboxy-terminal region of EBNA-1 identified a core DNA-binding domain located between amino acids 493 and 584. Column chromatographic, sedimentation, and cross-linking studies indicated that EBNA-1 exists in solution as a dimer. Mobility retardation assays using in vitro-translated variants of EBNA-1 showed that the active DNA-binding form of EBNA-1 is also a dimer. In short-term cotransfections, a pFRTK-CAT target containing EBNA-1-binding sites from the EBV origin of plasmid replication, ori-P, was transactivated by a carboxy-terminal EBNA-1 construction (amino acids 450 to 641) that also carried a c-myc nuclear localization signal. These reconstruction experiments demonstrated that a transactivation domain exists within the carboxy-terminal region of EBNA-1, that transactivation is more efficient when a nuclear localization signal is present, and that the natural karyophilic signal lies outside of the carboxy-terminal 191 amino acids. To identify the EBNA-1 nuclear localization signal, small oligonucleotides representing EBNA-1 sequences that encode clusters of basic peptides were transferred into two different vectors expressing cytoplasmic proteins (pyruvate kinase and herpes simplex virus delta IE175 protein) and the cellular locations of the fusion constructions were determined by immunofluorescence staining of transfected cells. In this way we identified a functional nuclear localization signal, Leu-Lys-Arg-Pro-Arg-Ser-Pro-Ser-Ser, encompassing amino acids 379 to 386 of the EBNA-1 protein.
Increased neuronal damage in apolipoprotein E-deficient mice following global ischaemia (1999)

There is accumulating evidence that apolipoprotein E (apoE) plays a role in regulating the response to and outcome following brain injury. The present study compared the histological outcome and recovery following an episode of global ischaemia in apoE-deficient mice and wild-type littermates (12-week-old males, n = 8 per group). Transient global ischaemia was induced for a period of 17 min and the animals were allowed to recover for 72 h. Transient global ischaemia induced selective neuronal degeneration in several brain regions in wild-type mice. There was statistically significant increased ischaemic neuronal damage in apoE-deficient mice compared with wild-type mice in six of the seven regions examined (hippocampal regions CA1, CA3/CA4 and dentate gyrus; thalamus; cortex and caudate nucleus; P < 0.05). The data substantiate a role for apoE in modifying the response of the CNS to acute injury.
NLO properties of polymeric Langmuir-Blodgett films of sulfonamide-substituted azobenzenes (1999)

The behaviour at the air/water interface of polymeric materials containing sulfonamide-substituted azobenzene chromophores has been investigated using surface pressure versus area measurements. Langmuir-Blodgett (LB) films of the polymers have been built up and then studied using X-ray diffraction. The polymer which gave the best organised LB film has been used to prepare an alternating Y-type multilayer structure with a polymer inactive in non-linear optics. The obtained film has a well-ordered polymeric LB structure giving three Bragg peaks. A series of films with various numbers of bilayers within the range from 2 to 80 has been prepared and the second harmonic generating properties of the films investigated. The measured intensity of the SH signal produced from incident light of wavelength 1064 nm was proportional to the square of the number of bilayers. The alternating LB films exhibited a non-linear susceptibility of up to 24 pm V –1 corresponding to a chromophore non-linear vector susceptibility of magnitude χ zzz (2) =170 pm V –1 .
A Crowdsourcing framework for Detecting Cross-Browser Issues in Web Application (2015)

With the advent of Web 2.0 application, and the increasing number of browsers and platforms on which the applications can be executed, cross-browser incompatibilities (XBIs) are becoming a serious problem for organizations to develop web-based software with good user experience. Although some techniques and tools have been proposed to identify XBIs, some XBIs are still missed as only partial state space is explored (by the crawler) in the testing environment. To address this limitation, based on record/replay technique, this paper proposed a crowdsourcing framework to detect cross-browser issues for Web application deployed in the field. Our empirical evaluation shows that the proposed technique is effective and efficient, improves on the state of the art.
Chaperonins (1998)

The molecular chaperones are a diverse set of protein families required for the correct folding, transport and degradation of other proteins in vivo. There has been great progress in understanding the structure and mechanism of action of the chaperonin family, exemplified by Escherichia coli GroEL. The chaperonins are large, double-ring oligomeric proteins that act as containers for the folding of other protein subunits. Together with its co-protein GroES, GroEL binds non-native polypeptides and facilitates their refolding in an ATP-dependent manner. The action of the ATPase cycle causes the substrate-binding surface of GroEL to alternate in character between hydrophobic (binding/unfolding) and hydrophilic (release/folding). ATP binding initiates a series of dramatic conformational changes that bury the substrate-binding sites, lowering the affinity for non-native polypeptide. In the presence of ATP, GroES binds to GroEL, forming a large chamber that encapsulates substrate proteins for folding. For proteins whose folding is absolutely dependent on the full GroE system, ATP binding (but not hydrolysis) in the encapsulating ring is needed to initiate protein folding. Similarly, ATP binding, but not hydrolysis, in the opposite GroEL ring is needed to release GroES, thus opening the chamber. If the released substrate protein is still not correctly folded, it will go through another round of interaction with GroEL.
Murine and Bovine Blue Cone Pigment Genes: Cloning and Characterization of Two New Members of the S Family of Visual Pigments (1994)

Two novel visual pigment genes, mouse blue and bovine blue, have been isolated from mouse and bovine genomic libraries, respectively, using a human blue cone pigment cDNA as probe. Corresponding cDNA clones have also been obtained from mouse retinas. The intron-exon boundaries for the mouse gene were determined by comparing the genomic and cDNA sequences. The visual pigments encoded by the mouse and bovine blue pigment genes are highly homologous to each other (89% amino acid identity) and to human blue and chicken violet cone pigments (greater than 80% identity), but are less homologous to chicken or goldfish blue cone pigments (less than 50% identity). These results indicate that phylogenetically both mouse and bovine blue pigments belong to the S branch of visual pigments, rather than to the M branch.
Secular Trends in Incidence of Atrial Fibrillation in Olmsted County, Minnesota, 1980 to 2000, and Implications on the Projections for Future Prevalence (2006)

The age-adjusted incidence of AF increased significantly in Olmsted County during 1980 to 2000. Whether or not this rate of increase continues, the projected number of persons with AF for the United States will exceed 10 million by 2050, underscoring the urgent need for primary prevention strategies against AF development.
‘Original antigenic sin’, T cell memory, and malaria sporozoite immunity: an hypothesis for immune evasion (1993)

Prior to any exposure to malaria, most adults have T cells specific for malaria parasites and various malaria proteins. The protein for which this has been shown more than any other is the circumsporozoite protein (CSP) of Plasmodium falciparum. These T cells can be present in high frequency and appear to have arisen through exposure to other (non-malaria) organisms. Although T cells are thought to provide protection against sporozoites, these T cells specific for cross-reactive organisms are clearly unable to protect against malaria, and may be preferentially expanded following exposure to malaria sporozoites. Thus, cross-reactive organisms have the potential to skew the repertoire of sporozoite-induced T cells and affect the induction of protective immunity. This is analogous to the concept of 'original antigenic sin' whereby prior exposure to one strain of influenza virus was shown to be able to divert the antibody response to a second challenging strain to focus on the shared (cross-reactive) epitopes.
Identification of Two Separate Domains in the Influenza Virus PB1 Protein Involved in the Interaction with the PB2 and PA Subunits: A Model for the Viral RNA Polymerase Structure (1996)

The domains of the PB1 subunit of the influenza virus polymerase involved in the interaction with the PB2 and PA subunits have been defined by mutational analysis of PB1 protein. The experimental approach included in vivo competition of the PB1 activity, two-hybrid interaction assays and in vitro binding to PB1-specific matrices. Mutants of the PB1 gene including N-terminal, C-terminal and internal deletions and single amino acid insertions were constructed. They were unable to support polymerase activity in a reconstituted transcription-replication system and were tested for their competition activity when expressed in excess over wild-type PB1 protein. The pattern of competition obtained suggested that the N-terminal 78 amino acids and the sequences between positions 506 and 659 in the PB1 protein are involved in the interaction with the other components of the polymerase. We identified the N-terminal region of PB1 protein as responsible for the interaction with the PA subunit by two-hybrid assays in mammalian cells. N- and C-terminal fragments of the PB1 protein were expressed as His-tagged proteins and purified on Ni2+-NTA resin. Such PB1-specific matrices were used in binding assays in vitro with metabolically labelled PB2 and PA proteins and mutants thereof. The results obtained indicated that the N-terminal and the C-terminal regions of PB1 are responsible for binding to PA and PB2 subunits, respectively. With this information and previously published results we propose a preliminary model for the architecture of the influenza virus RNA polymerase.
Biology of ticks (1991)

Part IV: Ecology, Behavior, and Host-Parasite Interactions. 23: Ecology of Non-Nidicolous Ticks. 24: Ecology of Nidiculous Ticks. 25: Acquired Immunity to Ticks. Part V: Tick-Borne and Tick-Caused Diseases. 26: Tick-Borne Protozoan Diseases. 27: Tick-Borne Arboviral Diseases. 28: Tick-Borne Rickettsioses. 29: Tick-Borne Bacteral Diseases. 30: Tick Paralysis and other Tick-Borne Toxicoses. Part VI: Control of Ticks and Tick-Borne Diseases. 31: Control of Ticks. Appendix. Literature Cited. Index
Collagen-receptor signaling in health and disease. (2001)

Collagens are not only essential for the mechanical resistance and resilience of multicellular organisms, but are also signaling molecules defining cellular shape and behavior. The communication between collagens and cells is achieved by cell surface receptors. Three types of cell surface receptors for collagen are known: integrins, discoidin domain receptors and glycoprotein VI. All three types independently trigger a variety of signaling pathways upon collagen-binding. Besides regulating numerous cellular responses, both integrin and discoidin domain receptors monitor the integrity of the collagenous extracellular matrix by triggering matrix degradation and renewal. Some recently discovered mechanisms of locally controlled expression of collagen, collagen-binding receptors and collagen-degrading proteases in the cellular microenvironment are described.