gebhart/patrepeval huggingface dataset:
Danazol distribution in plasma and cell membranes as related to altered cell properties: Implications for mechanism (1995)

Concentrations of danazol in patient plasma and red blood cells (RBC) were assayed over a 6-month period in 75 patients on danazol therapy using a high-pressure liquid chromatography (HPLC) method more reliable than previous radioimmunoassay (RIA) methods. It was found that plasma danazol rose regularly for 15 days after the beginning of treatment, reaching a steady state plateau of 175 +/- 76 ng/ml in 20 patients on normal dose, and less for lower dose schedules. After stopping danazol, concentrations declined to near zero in a similar time frame. RBC concentrations on a packed volume basis were similar to plasma levels. However, the membrane ghosts of RBC contained about 50% of the total RBC danazol, implying about 100-fold higher concentration in membranes than in plasma. Similar distributions were obtained in vitro with both RBC and platelets, and were confirmed by 14-C-labeled danazol. These findings tend to support the hypothesis that the benefits of danazol in immune disorders may be attributable in part to its intercalation in the lipid bilayer of the plasma membrane, altering antigen/receptor expression to modulate immune reactions. This hypothesis was first suggested when it was observed that the RBC of patients on danazol therapy showed morphological changes and increased resistance to osmotic lysis. It was later shown that danazol in vitro reduces binding of autoantibodies, and protects against complement-mediated lysis, suggesting direct action of danazol on the membranes. This hypothesis is discussed, and danazol's effect in protecting against complement-mediated lysis is described.
The effects of low oxygen on self-renewal and differentiation of embryonic stem cells (2009)

Low oxygen influences aspects of ESC pluripotency and differentiation. A better understanding of its effects and mechanism along with better estimation and control of pO2cell is important for applying low oxygen culture to regenerative medicine applications.
Review of Visual Saliency Detection With Comprehensive Information (2018)

The visual saliency detection model simulates the human visual system to perceive the scene and has been widely used in many vision tasks. With the development of acquisition technology, more comprehensive information, such as depth cue, inter-image correspondence, or temporal relationship, is available to extend image saliency detection to RGBD saliency detection, co-saliency detection, or video saliency detection. The RGBD saliency detection model focuses on extracting the salient regions from RGBD images by combining the depth information. The co-saliency detection model introduces the inter-image correspondence constraint to discover the common salient object in an image group. The goal of the video saliency detection model is to locate the motion-related salient object in video sequences, which considers the motion cue and spatiotemporal constraint jointly. In this paper, we review different types of saliency detection algorithms, summarize the important issues of the existing methods, and discuss the existent problems and future works. Moreover, the evaluation datasets and quantitative measurements are briefly introduced, and the experimental analysis and discussion are conducted to provide a holistic overview of different saliency detection methods.
Effect of DOTA Position on Melanoma Targeting and Pharmacokinetic Properties of 111In-Labeled Lactam Bridge-Cyclized α-Melanocyte Stimulating Hormone Peptide (2009)

DOTA position exhibited profound effect on melanoma targeting and pharmacokinetic properties of Ac-GluGlu-CycMSH[DOTA]-111In, providing a new insight into the design of lactam bridge-cyclized peptide for melanoma imaging and therapy.
Recruitment of Sprouty1 to Immune Synapse Regulates T Cell Receptor Signaling (2009)

TCR stimulation not only initiates positive signals for T cell activation, but also induces negative signals that down-regulate T cells. We previously reported that Sprouty1, a negative regulator of Ras-MAPK pathway of receptor tyrosine kinases, was induced by TCR signal and inhibited TCR signaling in CD4+ T cell clones. In this study, we addressed the mechanism underlying Sprouty1 inhibition of T cells. When overexpressed in Jurkat T cells, Sprouty1 inhibited TCR signal-induced IL-2 transcription, and also AP-1, NFAT, and NF-kappaB activation, which suggests that Sprouty1 acts at proximal TCR signalosome. Accordingly, we found that Sprouty1 translocated to immune synapse upon TCR engagement in both Jurkat cells and activated primary T cells and interacted with various signaling molecules in the TCR signalosome, such as linker for activation of T cells (LAT), phospholipase C-gamma1 (PLC-gamma1), c-Cbl/Cbl-b, and HPK1. Sprouty1 inhibited LAT phosphorylation, leading to decreased MAPK activation and IL-2 production. Deletion of C-terminal 54 amino acids in Sprouty1 abolished its inhibitory effect and this deletion mutant was unable to translocate to immune synapse and interact with LAT. Overall, our data suggest that Sprouty1 induced by TCR signal negatively regulates further TCR signaling by interacting with proximal signaling molecules in immune synapse, providing a novel regulatory mechanism of T cells.
twist is required in head mesenchyme for cranial neural tube morphogenesis. (1995)

To understand the role of twist during mammalian development, we generated twist-null mice. twist-null embryos died at embryonic day 11.5. Their most prominent phenotype was a failure of the cranial neural folds to fuse. Mutant embryos also had defects in head mesenchyme, somites, and limb buds. Chimera analysis suggested that head mesenchyme was required for cranial neural tube closure and that twist acted in a cell-autonomous manner in this tissue. In addition, in the head mesenchyme region of chimeras, twist-null cells were segregated from wild-type cells, and in the forebrain they lacked mesenchymal characteristics. These results suggest that twist regulates the cellular phenotype and behavior of head mesenchyme cells that are essential for the subsequent formation of the cranial neural tube.
Non-manifold Mesh Extraction from Time-varying Segmented Volumes used for Modeling a Human Heart (2005)

We present a new algorithm extracting and fairing surfaces from segmented volumes composed of multiple materials. In a first pass, the material boundaries in the volume are smoothed considering signed distance functions for the individual materials. Second, we apply a marching-cubes-like contouring method providing initial meshes defining material boundaries. Non-manifold features emerge along lines where more than two materials encounter. Finally, the mesh geometry is relaxed in a constrained fairing process. We use our algorithm to construct a heart model from segmented time-varying magnetic resonance images. Information concerning the heart ontology is used to merge certain structures to functional units.
Functions of F Pili in Mating-Pair Formation and Male Bacteriophage Infection Studied by Blending Spectra and Reappearance Kinetics (1969)

The extent of removal at various blending speeds (blending spectrum) and the kinetics of reappearance after blending of the ability of male Escherichia coli bacteria to form mating pairs, to adsorb and be infected by ribonucleic acid male phage, and to adsorb and be infected by deoxyribonucleic male phage were identical to the blending spectrum and reappearance kinetics of microscopically visible F pili. The same results were obtained with an Hfr (high-frequency recombinant), F', or resistance transfer factor (RTF) fi(+) mating system. Blending did not affect the viability, growth rate, ability to adsorb T4 phage, or ability to produce new F pili at any of the speeds used. It can be concluded that microscopically visible F pili are an absolute requirement for all three functions. Three classes of F pili have been found in bacterial cultures: attached, adsorbed, and free. Bacteria with adsorbed F pili in addition to attached ones were proportionately more susceptible to male phage infection, suggesting that adsorbed F pili may be at least partially functional. Free F pili did not compete with bacteria for phage. Some implications of the virus-like nature of F-pilus outgrowth for the mechanisms of mating and male phage infection are discussed.
Differential effects of combined trk receptor mutations on dorsal root ganglion and inner ear sensory neurons (1995)

We have generated double mutant mice deficient in pairs of two different Trk receptors and have analysed the effects on survival and differentiation of dorsal root ganglion (DRG), inner ear cochlear and vestibular sensory neurons. In most combinations of mutant trk alleles, the defects observed in double compared to single mutant mice were additive. However, double homozygous trkA-/-;trkB-/- DRG and trkB-/-;trkC-/- vestibular neurons showed the same degree of survival as single trkA-/- and trkB-/- mice, respectively, suggesting that those neurons required both Trk signaling pathways for survival. In situ hybridisation analysis of DRG neurons of double mutant mice revealed differential expression of excitatory neuropeptides. Whereas calcitonin-gene-related peptide expression correlated with the trkA phenotype, substance P expression was detected in all combinations of double mutant mice. In the inner ear, TrkB- and TrkC-dependent neurons were shown to at least partially depend on each other for survival, most likely indirectly due to abnormal development of their common targets. This effect was not observed in DRGs, where neurons depending on different Trk receptors generally innervate different targets.
SDNHAS: An SDN-Enabled Architecture to Optimize QoE in HTTP Adaptive Streaming (2017)

HTTP adaptive streaming (HAS) is receiving much attention from both industry and academia as it has become the de facto approach to stream media content over the Internet. Recently, we proposed a streaming architecture called SDNDASH [1] to address HAS scalability issues including video instability, quality of experience (QoE) unfairness, and network resource underutilization, while maximizing per player QoE. While SDNDASH was a significant step forward, there were three unresolved limitations: 1) it did not scale well when the number of HAS players increased; 2) it generated communication overhead; and 3) it did not address client heterogeneity. These limitations could result in suboptimal decisions that led to viewer dissatisfaction. To that effect, we propose an enhanced intelligent streaming architecture, called SDNHAS, which leverages software defined networking (SDN) capabilities of assisting HAS players in making better adaptation decisions. This architecture accommodates large-scale deployments through a cluster-based mechanism, reduces communication overhead between the HAS players and SDN core, and allocates the network resources effectively in the presence of short- and long-term changes in the network.
Ionic Liquids:  Ion Mobilities, Glass Temperatures, and Fragilities (2003)

We combine old, unpublished data on ionic liquids containing quaternary ammonium cations with new data on salts of aromatic cations containing a variety of anions, to demonstrate the existence for ionic liquids of an unexpectedly wide range of liquid fragilities. The pattern is one now familiar for other liquids. Here, the pattern is important in determining the relative fluid properties at ambient temperatures. We find that the optimization of ionic liquids for ambient temperature applications requiring low-vapor-pressure fluid phases involves the proper interplay of both cohesive energy and fragility factors. The cohesive energy is discussed in terms of the coulomb and van der Waals contributions to the attractive part of the pair potential. On the basis of the relation between the glass-transition temperature and the molar volume for salts with less-polarizable anions, we find evidence for a broad minimum in the ionic liquid cohesive energy at an internuclear separation of ca. 0.6 nm. This minimum lies between those of the B and TFSI- anions for the small quaternary ammonium cations of this study. The minimum is expected to be narrower and less well-defined for salts with polarizable anions. The relation of fluidity to conductance is considered in terms of a Walden plot that is shown to provide a useful basis for organizing the observations on ionic liquids and solutions. Low vapor pressure and ideal Walden products are intimately related.
Compressed sensing and Bayesian experimental design (2008)

We relate compressed sensing (CS) with Bayesian experimental design and provide a novel efficient approximate method for the latter, based on expectation propagation. In a large comparative study about linearly measuring natural images, we show that the simple standard heuristic of measuring wavelet coefficients top-down systematically outperforms CS methods using random measurements; the sequential projection optimisation approach of (Ji & Carin, 2007) performs even worse. We also show that our own approximate Bayesian method is able to learn measurement filters on full images efficiently which outperform the wavelet heuristic. To our knowledge, ours is the first successful attempt at "learning compressed sensing" for images of realistic size. In contrast to common CS methods, our framework is not restricted to sparse signals, but can readily be applied to other notions of signal complexity or noise models. We give concrete ideas how our method can be scaled up to large signal representations.
Targeting the mTOR Signaling Network for Cancer Therapy (2009)

The serine-threonine kinase mammalian target of rapamycin (mTOR) plays a major role in the regulation of protein translation, cell growth, and metabolism. Alterations of the mTOR signaling pathway are common in cancer, and thus mTOR is being actively pursued as a therapeutic target. Rapamycin and its analogs (rapalogs) have proven effective as anticancer agents in a broad range of preclinical models. Clinical trials using rapalogs have demonstrated important clinical benefits in several cancer types; however, objective response rates achieved with single-agent therapy have been modest. Rapalogs may be more effective in combination with other anticancer agents, including chemotherapy and targeted therapies. It is increasingly apparent that the mTOR signaling network is quite complex, and rapamycin treatment leads to different signaling responses in different cell types. A better understanding of mTOR signaling, the mechanism of action of rapamycin, and the identification of biomarkers of response will lead to more optimal targeting of this pathway for cancer therapy.
DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment (2008)

On BALIBASE3, our new program performs significantly better than the previous program DIALIGN-T and outperforms the popular global aligner CLUSTAL W, though it is still outperformed by programs that focus on global alignment like MAFFT, MUSCLE and T-COFFEE. On the locally related test sets in IRMBASE 2 and DIRM-BASE 1, our method outperforms all other programs while MAFFT E-INSi is the only method that comes close to the performance of DIALIGN-TX.
(-)-Epiafzelechin: Cyclooxygenase-1 Inhibitor and Anti-Inflammatory Agent from Aerial Parts ofCelastrus orbiculatus (1999)

An inhibitor of cyclooxygenase (COX)-1 activity of prostaglandin H2 synthase was isolated from aerial parts of Celastrus orbiculatus Thunb. (Celastraceae), an oriental folk medicine for rheumatoid arthritis by activity-guided column chromatographic methods. The COX inhibitor was identified as (-)-epiafzelechin, a member of flavan-3-ols by the structural analysis with HR-EI-mass, 1H-NMR and 13C-NMR spectral data. The compound exhibited a dose-dependent inhibition on the COX activity with an IC50 value of 15 microM. (-)-Epiafzelechin exhibited about 3-fold weaker inhibitory potency on the enzyme activity than indomethacin as a positive control. (-)-Epiafzelechin exhibited significant anti-inflammatory activity on carrageenin-induced mouse paw edema when the compound (100 mg/kg) was orally administrated at 1 h before carrageenin treatment.
The Role of Maternal Syphilis, Gonorrhoea and HIV-1 Infections in Spontaneous Abortion (1992)

The role of the human immunodeficiency virus (HIV) and other sexually transmitted diseases (STDs) as risk factor for spontaneous abortion was investigated in a case-control study in Nairobi, Kenya. Cases (n = 195) were women admitted with clinical signs and symptoms of spontaneous abortion, before 20 weeks of gestation. Patients with induced or clinically septic abortion were excluded. Controls were unselected pregnant women in their second or third trimester (n = 195). Spontaneous abortion was independently associated with maternal HIV-1 antibody (14.4% versus 6.2%; adjusted odds ratio, 2.3; 95% confidence interval, 1.1-4.8), with maternal syphilis seroreactivity (6.8% vs 2.1%, adjusted odds ratio, 4.3; 95% confidence interval 1.2-15.6), and with vaginal colonization with group B streptococci (15.6% vs 5.2%; adjusted odds ratio, 3.2; 95% confidence interval, 1.5-6.7). No significant association was found between maternal infections with gonococci and genital mycoplasmas, and spontaneous abortion.
Horizontal Transfer of Diatomaceous Earth and Botanical Insecticides in the Common Bed Bug, Cimex lectularius L.; Hemiptera: Cimicidae (2013)

Our data clearly demonstrate horizontal transfer of diatomaceous earth and botanical insecticides in the common bed bug, C. lectularius. Use of a fluorescent dust provided visual confirmation that contaminated bed bugs transfer dust to untreated bed bugs in harborage. This result is important because bedbugs live in hard-to-reach places and interaction between conspecifics can be exploited for delivery and dissemination of management products directed at this public health pest.
Inhibition of NF-κB activation and chemokine expression by the leukocyte glycoprotein, CD43, in colon cancer cells (2006)

CD43 is a heavily O-glycosylated type I trans-membrane protein, expressed at high levels on the surface of leukocytes. It is frequently overexpressed in early colon adenomas, but not in normal colon epithelial cells. To identify CD43 target genes, gene array analysis was performed using a tetracycline-inducible CD43 expression system in human colon adenocarcinoma SW480 cells. CD43 was demonstrated to down-regulate a variety of chemokine genes. Overexpression of CD43 suppressed constitutive as well as PMA-induced NF-kappaB activation and reduced the DNA binding of transcription factor p65 but not p50. Furthermore, a reduced NF-kappaB responsive promoter activity was observed and a decreased expression of proinflammatory chemokines MCP-1, IL-8 and GRO-alpha. These results suggest that overexpression of CD43 suppresses a subset of NF-kappaB target genes, partly via the inhibition of p65 transcriptional activity.
3D curve sketch: Flexible curve-based stereo reconstruction and calibration (2010)

Interest point-based multiview 3D reconstruction and calibration methods have been very successful in select applications but are not applicable when an abundance of feature points are not available. They also lead to an unorganized point cloud reconstruction where the geometry of the scene is not explicit. The multiview stereo methods on the other hand yield dense surface geometry but require a highly controlled or calibrated setting. We propose and develop a novel framework for 3D reconstruction and calibration based on image curve content, whose output is a 3D curve sketch, an unorganized set of 3D curve fragments. This approach, which is meant to augment the previous approaches, results in a reconstruction of geometric curve structure which can serve as a scaffold on which surface patches can be potentially reconstructed. It is intented for the setting where a number of images are available with coarsely calibrated cameras. The approach operates in two stages. A reliable partial 3D curve sketch is first reconstructed and this is used to refine the cameras to yield a more complete 3D curve sketch in a second stage. A key advantage of this approach is the ability to integrate information across a large number of views. The results have been evaluated on a few datasets.
A new DNA nanostructure, the G-wire, imaged by scanning probe microscopy (1995)

G-DNA is a polymorphic family of quadruple helical nucleic acid structures containing guanine tetrad motifs [G-quartets; Williamson, J.R., Raghuraman, M.K. and Cech, T.R. (1989) Cell 59, 871-880; Williamson, J.R. (1993) Proc. Natl. Acad. Sci. USA 90, 3124-3124]. Guanine rich oligonucleotides that are self-complimentary, as found in many telomeric G-strand repeat sequences, form G-DNA in the presence of monovalent and/or divalent metal cations. In this report we use the atomic force microscope (AFM) to explore the structural characteristics of long, linear polymers formed by the telomeric oligonucleotide d(GGGGTTGGGG) in the presence of specific metal cations. In the AFM these polymers, termed G-wires, appear as filaments whose height and length are determined by the metal ions present during the self-assembly process. The highly ordered, controllable self-assembly of G-wires could provide a basis for developing advanced biomaterials.
IL-18 Receptors, Their Role in Ligand Binding and Function: Anti-IL-1RAcPL Antibody, a Potent Antagonist of IL-18 (2000)

IL-18 is critical in eliciting IFN-gamma production from Th1 cells both in vitro and in vivo. Th1 cells have been implicated in the pathogenesis of autoimmune disorders, making antagonists of IL-18 promising therapeutics. However, specificity and binding characteristics of IL-18R components have only been superficially explored. In this study, we show that IL-1R related protein 1 (IL-1Rrp1) and IL-1R accessory protein-like (IL-1RAcPL) confer responsiveness to IL-18 in a highly specific (no response to other IL-1 ligands) and unique manner (no functional pairing with other IL-1Rs and IL-1R-like molecules). Cotransfection with both receptor components resulted in expression of both low and high affinity binding sites for IL-18 (K:(d) of 11 and 0.4 nM, respectively). We prepared anti-IL-1RAcPL mAb TC30-28E3, which, in contrast to soluble R proteins, effectively inhibited the IL-18-induced activation of NF-kappaB. Quantitative PCR showed that Th1 but not Th2 cells are unique in that they coexpress IL-1Rrp1 and IL-1RAcPL. mAb TC30-28E3 inhibited IL-18-induced production of IFN-gamma by Th1 cells, being at least 10-fold more potent than anti-IL-18 ligand mAb. This study shows that IL-1RAcPL is highly specific to IL-18, is required for high affinity binding of IL-18, and that the anti-IL-1RAcPL mAb TC30-28E3 potently antagonizes IL-18 responses in vitro, providing a rationale for the use of anti-IL-1RAcPL Abs to inhibit Th1-mediated inflammatory pathologies.
Synovial distribution of “systemically” administered acetylsalicylic acid in the isolated perfused equine distal limb (2013)

ASA and SA accumulated in the in the synovial fluid of the ex vivo model despite decreasing systemic concentrations. This suggests a prolonged anti-inflammatory effect within the joint that remains to be further elucidated.