gebhart/patrepeval huggingface dataset:
Design and experimental evaluation of network-assisted strategies for HTTP adaptive streaming (2016)

In this paper we investigate several network-assisted streaming approaches which rely on active cooperation between video streaming applications and the network. We build a Video Control Plane which enforces Video Quality Fairness among concurrent video flows generated by heterogeneous client devices. To the purpose, a max-min fairness optimization problem is solved at run-time. We compare two approaches to actuate the optimal solution in an SDN network: the first one allocating network bandwidth slices to video flows, the second one guiding video players in the video bitrate selection. Performance is assessed through several QoE-related metrics, such as Video Quality Fairness, video quality, and switching frequency. The impact of client-side adaptation algorithms is also investigated.
Interactions among vertebrate helix-loop-helix proteins in yeast using the two-hybrid system. (1993)

The helix-loop-helix (HLH) motif is contained in a rapidly growing family of transcription factors and has been shown to mediate dimerization among heterologous HLH-containing proteins. E12 is a widely expressed HLH protein that preferentially forms heterodimers with cell type-specific HLH proteins such as MyoD, myogenin, and the achaete-scute gene products. As a first step toward screening for novel cell type-specific partners of E12, we used a modification of the two-hybrid assay for detection of protein-protein interactions in vivo to determine whether dimerization of HLH proteins with E12 can occur in yeast. Using the GAL4 DNA-binding domain fused to the E12 HLH motif and the GAL4 transcription activation domain fused to MyoD, we show that E12 and MyoD can efficiently dimerize in yeast and reconstruct a hybrid transcription factor that activates reporter genes linked to the GAL4 DNA-binding site. The GAL4 DNA-binding domain fused to E12 was used to screen a mouse T-cell cDNA library in which the cDNA was fused to the GAL4 activation domain. Several cDNA clones encoding proteins that interact with E12 were isolated, one of which corresponded to the HLH protein Id-2. Given the ability of E12 to dimerize preferentially with cell type-specific HLH proteins, this strategy should be useful for cloning novel partners for E12 from a variety of cell types.
Session guarantees for weakly consistent replicated data (2002)

Four per-session guarantees are proposed to aid users and applications of weakly consistent replicated data: "read your writes", "monotonic reads", "writes follow reads", and "monotonic writes". The intent is to present individual applications with a view of the database that is consistent with their own actions, even if they read and write from various, potentially inconsistent servers. The guarantees can be layered on existing systems that employ a read-any/write-any replication scheme while retaining the principal benefits of such a scheme, namely high availability, simplicity, scalability, and support for disconnected operation. These session guarantees were developed in the context of the Bayou project at Xerox PARC in which we are designing and building a replicated storage system to support the needs of mobile computing users who may be only intermittently connected.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Advances in coeliac disease (2011)

Purpose of review This article critically summarizes the recent scientific and clinical advances in coeliac disease. Recent findings Epidemiological studies have shown that coeliac disease is as common in parts of Asia, Africa and Eastern Europe as in the western world. Genome-wide association studies continue to identify genetic susceptibilities that are both unique to coeliac disease and overlap with other autoimmune diseases. Human leukocyte antigen genotyping offers additional sensitivity in detecting coeliac disease in individuals who have self-prescribed gluten-free diets (GFD) or have atypical presentations. Immunological advances have highlighted the potential proinflammatory pitfalls of vitamin A supplementation in active coeliac disease and have enabled identification of oat and barley subsets that may be safely incorporated into coeliac diets. Large population-based studies have expanded our knowledge of the long-term risks of coeliac disease, in addition to excluding infertility as a cause for concern once a GFD has been established. Summary The long-term implications of active coeliac disease emphasize the need for early detection and strict adherence to GFD, which remains the cornerstone of management. Technological advances in food modulation and immuno-therapies offer promise, but remain in the translational phases of clinical trials at present.
Small molecule inhibitors of RORγt: Targeting Th17 cells and other applications (2012)

Nuclear hormone receptors (NHRs) form a family of transcription factors that are composed of modular protein structures with DNA- and ligand-binding domains (DBDs and LBDs). The DBDs confer gene target site specificity, whereas LBDs serve as control switches for NHR function. For many NHRs, both endogenous and synthetic small molecule ligands bind to small pockets within the LBDs, resulting in conformational changes that regulate transcriptional activity. This property of NHRs has been exploited by the pharmaceutical industry for therapeutic targeting of a wide variety of diseases, ranging from inflammatory diseases and cancer to endocrine and metabolic diseases. Th17 cells are CD4(+) T helper effector cells that express several pro-inflammatory cytokines, including IL-17A, and the actions of these cells have been linked to multiple human autoimmune diseases. Our laboratory previously identified the NHR RORγt, an immune cell-specific isoform of RORγ (retinoic acid receptor-related orphan nuclear receptor gamma), as a key transcription factor for the development of Th17 cells both in human and mouse. Although endogenous ligands for RORγt have not yet been reported, it is thought that RORγt activity and Th17-cell development can be modulated with highly specific small molecules that bind to the RORγt LBD and displace its endogenous ligands. Recent studies from multiple groups have reported the activities of such inhibitors. In this mini review, we describe how RORγt inhibitors were identified and how they may contribute to our understanding about RORγt and its biology.
Characterization of threading dislocations in GaN epitaxial layers (2000)

We investigated Si-doped GaN epitaxial layers on a (0001)-sapphire substrate using a HCl vapor-phase etching technique, scanning electron microscopy, atomic force microscopy, and transmission electron microscopy. Three kinds of distinctive etch pits correspond to three different types of threading dislocations, edge, mixed, and screw types. Photoluminescence intensity increases with the decrease in the number of etch pits corresponding to mixed and screw dislocations. The number of etch pits corresponding to edge dislocations, however, did not change. We concluded, therefore, that threading dislocations having a screw-component burgers vector act as strong nonradiative centers in GaN epitaxial layers, whereas edge dislocations, which are the majority, do not act as nonradiative centers.
Fast Temporal Response Fiber-Optic Chemical Sensors Based on the Photodeposition of Micrometer-Scale Polymer Arrays (1997)

Fiber-optic chemical sensor microarrays for the detection of pH and O2 have been developed with subsecond response times. Sensor microarrays are fabricated by the covalent immobilization (pH sensor arrays) or the physical entrapment (O2 sensor arrays) of fluorescent indicators in photodeposited polymer matrices on optical imaging fibers. Polymer microarrays are comprised of thousands of individual elements photodeposited as hemispheres such that each element of the sensor array is coupled directly to a discrete optical element of the imaging fiber and is not in contact with other neighboring elements. Because of the hemispherical shape and the individuality of the array elements, diffusion of analyte to the sensor elements is dominated by radial diffusion, resulting in a rapid response time. pH-sensitive arrays based on fluorescein respond to a 1.5-unit pH change within 300 ms, while the O2-sensitive arrays respond to O2 changes within 200 ms (90% of steady state response).
Complementary DNA Cloning and Sequencing of the Chicken Muscle Ecto-ATPase (1997)

The ecto-ATPase from chicken gizzard (smooth muscle) was solubilized, and the 66-kDa cell membrane ecto-ATPase protein was purified. The protein was then subjected to both enzymatic and chemical cleavage, and the resultant peptides were purified by reverse phase high pressure liquid chromatography and sequenced. Several of these internal peptide sequences were used to design oligonucleotides to screen a chicken muscle library to identify the cDNA encoding the ecto-ATPase. Two overlapping partial clones were sequenced, yielding the complete coding region and a long 3'-untranslated sequence. The deduced amino acid sequence is in agreement with the N-terminal and peptide sequences obtained from the purified protein. The chicken muscle ecto-ATPase is a slightly basic (predicted pI = 7.93) 494-amino acid protein (54.4 kDa), containing a single transmembrane domain at each end of the protein. The majority of the protein is predicted to be extracellular, making it a Type Ia plasma membrane protein. There are four putative N-glycosylation sites, a single potential cAMP/cGMP-dependent protein kinase phosphorylation site, as well as a single putative tyrosine kinase phosphorylation site. Analysis of the sequence using the BLAST programs demonstrated homology with other ecto-ATPases and ecto-apyrases, including those from the parasitic protozoan Toxoplasma gondii, potato tubers, and garden pea, as well as a guanosine diphosphohydrolase from yeast. However, the most striking homology observed was to the human and mouse lymphoid cell activation antigen 39 (CD39), a molecule now known to have apyrase activity. The chicken ecto-ATPase showed considerable amino acid sequence homology with CD39 over the entire length of the sequence, excluding about 30-40 amino acids at the extreme ends of the protein (which include the two membrane-spanning helices). The sequence homology between the gizzard ecto-ATPase and CD39 was confirmed by Western blots demonstrating immunocross-reactivity between mono- and polyclonal antibodies raised against the chicken ecto-ATPase and two commercially available monoclonal antibodies against the human CD39 protein. The results suggest that the muscle ecto-ATPase may be involved in cell adhesion, since the highly homologous CD39 protein is involved in homotypic adhesion of activated B lymphocytes.
Signtiming scheme based on aggregate signature (2008)

Timestamping is a cryptographic technique providing us with a proof-of-existence of a digital document at a given time. Combining both digital signature and provable time-stamping guarantees authentication, integrity and non-repudiation of electronic documents. In this paper, we introduce such a service, so called signtiming. Our scheme is based on an ID-based aggregate signature and is secure in the random oracle model.
Discrimination of Mumps Virus Small Hydrophobic Gene Deletion Effects from Gene Translation Effects on Virus Virulence (2011)

Deletion of the small hydrophobic (SH) protein of certain paramyxoviruses has been found to result in attenuation, suggesting that the SH protein is a virulence factor. To investigate the role of the mumps virus (MuV) SH protein in virulence, multiple stop codons were introduced into the open reading frame (ORF) of a MuV molecular clone (r88-1961(SHstop)), preserving genome structure but precluding production of the SH protein. No differences in neurovirulence were seen between the wild-type and the SH(stop) viruses. In contrast, upon deletion of the SH gene, significant neuroattenuation was observed. These data indicate that the MuV SH protein is not a neurovirulence factor and highlight the importance of distinguishing gene deletion effects from protein-specific effects.
Production of 1,3-Propanediol from Glycerol by Clostridium acetobutylicum and Other Clostridium Species (1987)

Glycerol was fermented with the production of 1,3-propanediol as the major fermentation product by four strains of Clostridium acetobutylicum, six of C. butylicum, two of C. beijerinckii, one of C. kainantoi, and three of C. butyricum. 1,3-Propanediol was identified by its retention times in gas chromatography and high-pressure liquid chromatography and by its mass spectrum. During growth of C. butylicum B593 in a chemostat culture at pH 6.5, 61% of the glycerol fermented was converted to 1,3-propanediol. When the pH was decreased to 4.9, growth and 1,3-propanediol production were substantially reduced.
A 3‐week, randomized, placebo‐controlled trial of asenapine in the treatment of acute mania in bipolar mania and mixed states (2009)

These results indicate that asenapine is rapidly acting, efficacious, and well tolerated for patients with bipolar I disorder experiencing an acute manic episode.
The Efficacy of Calcifediol in Renal Osteodystrophy (1978)

Bone disease continues to be a problem for patients who are undergoing long-term hemodialysis.<sup>1-4</sup>Although the clinical syndrome of renal osteodystrophy varies from center to center and from patient to patient, it is generally believed that disturbances in vitamin D metabolism are almost always present and play a pivotal role in its pathogenesis. Most patients demonstrate at least some clinical, biochemical, or histological evidence of vitamin D resistance.<sup>1-7</sup> The two principal circulating vitamin D metabolites are 25-hydroxyvitamin D (25OHD) (25OHD refers to 25OHD<sub>2</sub>and 25OHD<sub>3</sub>since the assay does not differentiate between either of these), the liver product, and 1,25-dihydroxyvitamin D (1,25[OH]<sub>2</sub>D), the kidney product.<sup>7</sup>Most investigators have focused attention on the latter since it is the final step in vitamin D synthesis, it is the most potent form of vitamin D, and it is synthesized by the kidney.<sup>7</sup>Indeed, 1,25(OH)<sub>2</sub>
A possible role for complement in the pathogenesis of chronic chagasic cardiomyopathy (2002)

The membrane attack complex (MAC) of complement participates in several inflammatory and proliferative processes by releasing pro-inflammatory cytokines and growth factors from target cells. Chronic Chagasic cardiomyopathy (CCH) is a parasitic dilated cardiopathy, characterized by severe fibrosis and inflammation, which differs from idiopathic dilated cardiomyopathy (DCM). Trypanosoma cruzi, the pathogenic organism of CCH, is a strong complement activator and can also induce alternative pathway activation by mammalian cells. This study explored whether the myocardium in CCH patients has increased MAC deposition, an expression of complement activation, compared to DCM patients. MAC was semi-quantified in endomyocardial human samples (29 CCH subjects, 18 DCM subjects, and four controls) by immunohistochemistry. MAC was present in the sarcolemma of 38% of CCH, 5.5% of DCM (p<0.02), and 0% of controls, and in interstitial inflammatory cells of CCH. No difference was observed in the expression of the complement regulatory protein CD59, indicating that increased MAC deposition is likely to be the result of complement activation rather than decreased protection. It is proposed that the increased MAC deposition found in CCH, but not in DCM or controls, may help to explain the diffuse myocardial fibrosis and inflammation characteristic of the disease.
HLA-linked nonresponsiveness to Cryptomeria japonica pollen antigen. I. Nonresponsiveness is mediated by antigen-specific suppressor T cell. (1987)

The objective of this study was to elucidate the cellular mechanism of IgE nonresponse to the Cryptomeria japonica (Japanese cedar) pollen antigen (CPAg), which was shown in our previous study to be HLA-linked (1). We established an assay system for the measurement of small amounts of anti-CPAg IgE antibody, both in an antigen-specific and isotype-specific manner, and a culture system to induce antigen-driven IgE antibody synthesis in vitro. By using these methods, we clarified that the function of the HLA-DR molecule in the CPAg-driven IgE response is similar to that of I-A or I-E molecule in mice, namely the product of immune response genes (Ir-genes), because anti-HLA-DR monoclonal antibody blocked the response, and the interaction between monocyte and monocyte-depleted peripheral blood lymphocytes (PBL) to respond to CPAg was restricted by HLA-DR. Furthermore, PBL from nonresponders revealed a specific IgE response to CPAg when the Leu-2+3- T cell fraction was depleted, thereby suggesting that even nonresponders have Leu-2-3+ T cell and B cell clones specific for CPAg, and they apparently show no response due to the presence of CPAg-specific Leu-2+3- suppressor T cells. This suppressor T cell fraction abolished the IgE response of the autologous B + monocyte + Leu-2-3+ T cell in a CPAg-specific manner. The current cellular analysis together with our previous genetic analysis strongly suggest that the HLA-linked IgE nonresponse to CPAg is mediated by CPAg-specific suppressor T cells. The HLA-linked gene controlling the nonresponsiveness to CPAg is thus designated as the immune suppression gene for CPAg (Is-CPAg). Mapping of Is-CPAg within HLA-DQ subregion is discussed.
Retinoic acid is a negative regulator of AP-1-responsive genes. (1991)

We present evidence that retinoic acid can down-regulate transcriptional activation by the nuclear protooncogene c-jun. All three members of the retinoic acid receptor (RAR) subfamily (RAR alpha, RAR beta, and RAR gamma) can repress transcriptional induction of the human collagenase gene or a heterologous promoter that contains the collagenase promoter AP-1-binding site. In contrast, the retinoid X receptor fails to repress Jun/AP-1 activity, demonstrating a significant difference between the two regulatory systems through which retinoids exert their transcriptional control. Analysis of RAR alpha mutants in transfection studies reveals that the DNA-binding domain is important for the inhibition of Jun/AP-1 activity, even though the RAR does not bind the collagenase AP-1 site. Rather, gel-retardation assays reveal that bacterially expressed full-length RAR alpha inhibits binding of Jun protein to target DNA. These data suggest that the RAR alpha may form a nonproductive complex with c-Jun and provides a simple mechanisms by which retinoic acid may limit cell growth and possibly malignant progression.
Clinical aspects of intratumoral gene therapy. (1999)

One of the major obstacles to the development of gene therapy for cancer is our inability to deliver genes to all targets within the body. Thus, effective methodology does not exist to deliver a gene intravenously with the expectation that it will selectively localize within the target tumor, will not localize in other tissues and will be expressed efficiently. While one can take advantage of tissue-specific promoters to activate the gene only in a given target tissue, only a small fraction of the vector will be taken up in the target tissue and expressed. Consequently, since accessible local or regional tumor masses are a major problem in many cancers, there has been a strong emphasis on clinical trials in intratumoral and peritumoral gene delivery.
Roles of different hydrophobic constituents in the adsorption of pulmonary surfactant (1996)

Surface tension-time adsorption isotherms were measured at 37 degrees C for calf lung surfactant extract (CLSE) and subfractions of its constituents: the complete mix of surfactant phospholipids (PPL), phospholipids depleted in anionic phospholipids (mPPL), hydrophobic surfactant proteins plus phospholipids (SP&PL, SP&mPL), and neutral lipids plus phospholipids (N&PL). Adsorption experiments were done using a static bubble surfactometer where diffusion resistance was present, and in a Teflon dish where diffusion was minimized by subphase stirring. The contribution of diffusion to bubble adsorption measurements decreased as phospholipid concentration increased, and was small at 0.25 mM phospholipid. At this phospholipid concentration, PPL, mPPL, and N&PL all adsorbed more rapidly and to lower final surface tensions than dipalmitoyl phosphatidylcholine (DPPC) on the bubble. However, none of these phospholipid mixtures adsorbed to surface tensions below 46 mN/m after 20 min, behavior that was significantly worse than CLSE, SP&PL, and SP&mPL which additionally contained hydrophobic SP. Both CLSE and SP&PL rapidly adsorbed to surface tensions below 25 mN/m at 0.25 mM phospholipid concentration on the bubble, as did SP&mPL at a somewhat reduced rate. Further experiments defining the influence of hydrophobic protein content showed that addition of even 0.13% SP (by wt) to PPL improved adsorption substantially, and that mixtures of PPL combined with 1% SP had adsorption very similar to CLSE. Mixtures of SP combined with mPPL had faster adsorption than corresponding mixtures of SP:DPPC, and neither fully matched the adsorption rates of CLSE and SP&PL even at high SP levels (4% in SP:mPPL and 5.2% in SP:DPPC). These results demonstrate that although the secondary zwitterionic and anionic phospholipids and neutral lipids in lung surfactant enhance adsorption relative to DPPC, the hydrophobic SP have a much more pronounced effect in promoting the rapid entry of pulmonary surfactant into the air-water interface.
IFN-γ-Inducible Chemokines Enhance Adaptive Immunity and Colitis (2003)

T helper type 1 (Th1) cells secreting interferon-gamma (IFN-gamma) have been closely associated with Crohn's disease (CD). Monokine-induced by IFN-gamma (MIG), IFN-gamma-inducible T cell alpha chemoattractant (I-TAC), and IFN-gamma-inducible protein-10 (IP-10), are chemokines that bind CXCR3 and mediate the chemotaxis of leukocytes. IP-10, MIG, and CXCR3 have been shown to be expressed at sites of CD. The current study stems from our recent findings that IP-10, MIG, and I-TAC significantly contribute to the development of Th1-mediated inflammatory responses. To better understand the role of CXCR3 interactions during CD, we characterized the effects of IP-10, MIG, I-TAC, and CXCR3+ T cells on mucosal immune responses. IP-10, MIG, and I-TAC significantly enhanced antigen-specific serum and mucosal antibodies through Th1-mediated events and CD28 modulation. Additionally, the adoptive transfer of naive CXCR3+ T cells and CD4+CD45RB(HI) to T cell receptor beta (TCRbeta) x delta(-/-) mice resulted in the onset of murine colitis. Taken together, these studies suggest that IP-10, MIG, I-TAC, and CXCR3 interactions are involved in mucosal immune responses required for the induction of CD.