gebhart/patrepeval huggingface dataset:
A Novel Fast Mode Decision Scheme for Spatial Scalable Video Coding (2009)

In the scalable video coding extension of H.264 standard, the concept of inter-layer prediction is adopted to reduce the redundancy between the base layers and the enhancement layers. Thus, additional coding modes should be calculated during the macroblock mode decision procedure at the enhancement layers. It increases the computational complexity and may obstruct its practical applications. A fast mode decision scheme is developed in this paper to speed up the encoding of the enhancement layers. It makes use of reducing the number of the candidate modes and early termination the mode decision procedure adaptively. The experimental results show the proposed algorithm can achieve a reduction of encoding time by 30% to 70% with negligible bit-rate increases.
Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations (1997)

Gene expression from plasmids containing the araBAD promoter can be regulated by the concentration of arabinose in the growth medium. Guzman et al. [Guzman, L.-M., Belin, D., Carson, M. J. & Beckwith, J. (1995) J. Bacteriol. 177, 4121-4130] showed that expression of a cloned gene could be modulated over several orders of magnitude in cultures grown in the presence of subsaturating concentrations of arabinose. We constructed plasmids expressing a fast-folding mutant Aequorea victoria green fluorescent protein from the araBAD promoter to examine the distribution of expressed gene products in individual cells at intermediate induction levels. Microscopic examination of cells grown at low arabinose concentrations shows mixtures of brightly fluorescent and dark cells, suggesting that intermediate expression levels in cultures reflect a population average of induced and uninduced cells. The kinetics of green fluorescent protein induction suggest that this reflects an "autocatalytic" induction mechanism due to accumulation of the inducer by active transport. This mechanism, which is analogous to the induction of the lac operon at subsaturating inducer concentrations in lacY+ cells, was described 40 years ago by Novick and Weiner [Novick, A. & Weiner, M. (1957) Proc. Natl. Acad. Sci. USA 43, 553-566].
<title>High-resolution measurement of phase-shift amplitude and numeric object phase calculation</title> (2000)

A new method for measuring the object independent irradiance function for combined Gray-code and phase-shift 3-D measurement systems is presented. The irradiance functions of the projected sinusoidal patterns are measured with high resolution in the phase space without leaving the signal chain of the measurement system. This preserves the system specific distortions of the projected intensity functions. The system specific irradiance functions can be used to compute the object phase numerically. It can be shown that the systematic error of phase shift measurement caused by non sinusoidal phase-shift patterns and phase shifter mis-calibration can be reduced significantly.
CC-chemokine receptor 6 is expressed on diverse memory subsets of T cells and determines responsiveness to macrophage inflammatory protein 3 alpha. (1999)

CC-chemokine receptor (CCR) 6 is the only known receptor for macrophage inflammatory protein (MIP)-3alpha, a CC chemokine chemotactic for lymphocytes and dendritic cells. Using anti-serum that we raised against the N-terminal residues of CCR6, we have characterized the surface expression of CCR6 on peripheral blood leukocytes and we have correlated CCR6 expression with responses to MIP-3alpha. We found that CCR6 was expressed only on memory T cells, including most alpha4beta7 memory cells and cutaneous lymphocyte-associated Ag-expressing cells, and on B cells. Accordingly, chemotaxis of T cells to MIP-3alpha was limited to memory cells. Moreover, calcium signals on T cells in response to MIP-3a were confined to CCR6-expressing cells, consistent with CCR6 being the only MIP-3alpha receptor on peripheral blood T cells. Unlike many CC chemokines, MIP-3alpha produced a calcium signal on freshly isolated T cells, and CCR6 expression was not increased by up to 5 days of treatment with IL-2 or by cross-linking CD3. Despite their surface expression of CCR6, freshly isolated B cells did not respond to MIP-3alpha. In addition to staining peripheral blood leukocytes, our anti-serum detected CCR6 on CD34+ bone marrow cell-derived dendritic cells. Our data are the first to analyze surface expression of CCR6, demonstrating receptor expression on differentiated, resting memory T cells, indicating differences in receptor signaling on T cells and B cells and suggesting that CCR6 and MIP-3alpha may play a role in the physiology of resting memory T cells and in the interactions of memory T cells, B cells, and dendritic cells.
The Evolution of Therapeutic Research in Cancer (1978)

The purpose of this essay is to focus on some of the difficulties in starting and completing well designed therapeutic experiments in the field of cancer. Failure to appreciate the nature and complexity of therapeutic trials in human beings, I believe, has hindered progress in treatment research and can continue to serve as a roadblock to exploiting current opportunities at a critical time in the history of the effort to control cancer.The backbone of therapeutic experiments is knowledge of the natural history of disease. The effect of the experiment on the natural history of disease is the result observed. . . .
Brilliant violet fluorophores: A new class of ultrabright fluorescent compounds for immunofluorescence experiments (2012)

The Nobel Prize in Chemistry was awarded in 2000 for the discovery of conductive organic polymers, which have subsequently been adapted for applications in ultrasensitive biological detection. Here, we report the first use of this new class of fluorescent probes in a diverse range of cytometric and imaging applications. We demonstrate that these "Brilliant Violet" reporters are dramatically brighter than other UV-violet excitable dyes, and are of similar utility to phycoerythrin (PE) and allophycocyanin (APC). They are thus ideally suited for cytometric assays requiring high sensitivity, such as MHC-multimer staining or detection of intracellular antigens. Furthermore, these reporters are sensitive and spectrally distinct options for fluorescence imaging, two-photon microscopy and imaging cytometry. These ultra-bright materials provide the first new high-sensitivity fluorescence probes in over 25 years and will have a dramatic impact on the design and implementation of multicolor panels for high-sensitivity immunofluorescence assays.
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations. (1999)

http://blocks.fhcrc.org/
Functional Coupling between Neurons and Glia (2000)

Neuronal-glial interactions play an important role in information processing in the CNS. Previous studies have indicated that electrotonic coupling between locus ceruleus (LC) neurons is involved in synchronizing the spontaneous activity. The results of the present study extend the functional electrotonic coupling to interactions between neurons and glia. Spontaneous oscillations in the membrane potential were observed in a subset of glia. These oscillations were synchronous with the firing of neurons, insensitive to transmitter receptor antagonists and disrupted by carbenoxolone, a gap junction blocker. Hyperpolarization of neurons with [Met] (5)enkephalin blocked the oscillations in glia. Selective depolarization of glia with a glutamate transporter substrate (l-alpha-aminoadipic acid) increased the neuronal firing rate, suggesting that changes in the membrane potential of glia can modulate neuronal excitability through heterocellular coupling. Dye-coupling experiments further confirmed that small molecules could be transferred through gap junctions between these distinct cell types. No dye transfer was observed between neurons and oligodendrocytes or between astrocytes and oligodendrocytes, suggesting that the junctional communication was specific for astrocytes and neurons. Finally, immunoelectron microscopy studies established that connexins, the proteins that form gap junctions, were present on portions of the plasmalemma, bridging the cytoplasm of neurons and glia in LC. This heterocellular coupling extends the mechanisms by which glia participate in the network properties of the LC in which the degree of coupling is thought to influence cognitive performance.
A Potential New Pathway for PD-L1 Costimulation of the CD8-T Cell Response to Listeria monocytogenes Infection (2013)

Programmed death ligand-1 (PD-L1) is an important negative regulator of T cell immune responses via interactions with PD-1 and CD80. However, PD-L1 can also act as a positive costimulator, but the relevant counterreceptor is not known. We analyzed the role of PD-L1 in CD8-T cell responses to infection with Listeria monocytogenes (LM) or vesicular stomatitis virus (VSV). PD-L1 blockade impaired antigen-specific CD8 effector T cell expansion in response to LM, but not to VSV infection, particularly limiting short-lived effector cell differentiation. Simultaneous CD4-T cell depletion and anti-PD-L1 blockade revealed that PD-L1 provided costimulation even in the absence of CD4-T cells. Most importantly, specific blockade of PD-L1 binding to CD80 or to PD-1 did not recapitulate PDL-1 blockade. The results suggested that PD-L1 plays an important costimulatory role for antigen-specific CD8 T cells during LM infection perhaps through a distinct receptor or interaction epitope.
Enzymic Cyclization of Linear Peptide Esters Using Subtiligase (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnzymic Cyclization of Linear Peptide Esters Using SubtiligaseDavid Y. Jackson, John P. Burnier, and James A. WellsCite this: J. Am. Chem. Soc. 1995, 117, 2, 819–820Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ja00107a027https://doi.org/10.1021/ja00107a027research-articleACS PublicationsRequest reuse permissionsArticle Views670Altmetric-Citations69LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Primary Structure, Regioselectivity, and Evolution of the Membrane-bound Fatty Acid Desaturases of Claviceps purpurea (2007)

Two cDNAs with sequence similarity to fatty acid desaturase genes were isolated from the phytopathogenic fungus, Claviceps purpurea. The predicted amino acid sequences of the corresponding genes, named CpDes12 and CpDesX, share 87% identity. Phylogenetic analysis indicates that CpDes12 and CpDesX arose by gene duplication of an ancestral Delta(12)-desaturase gene after the divergence of Nectriaceae and Clavicipitaceae. Functional expression of CpDes12 and CpDesX in yeast (Saccharomyces cerevisiae) indicated that CpDes12 is primarily a "Delta(12)"-desaturase, whereas CpDesX is a novel desaturase catalyzing "Delta(12)," "Delta(15)," and "omega(3)" types of desaturation with omega(3) activity predominating. CpDesX sequentially desaturates both 16:1-9c and 18:1-9c to give 16:3-9c,12c,15c and 18:3-9c,12c,15c, respectively. In addition, it could also act as an omega(3)-desaturase converting omega(6)-polyunsaturates 18:3-6c,9c,12c, 20:3-8c,11c,14c, and 20:4-5c,8c,11c,14c to their omega(3) counterparts 18:4-6c,9c,12c,15c, 20:4-8c,11c,14c,17c, and 20:5-5c,8c,11c,14c,17c, respectively. By using reciprocal site-directed mutagenesis, we demonstrated that two residues (isoleucine at 152 and alanine at 206) are critical in defining the catalytic specificity of these enzymes and the C-terminal amino acid sequence (residues 302-477) was also found to be important. These data provide insights into the nature of regioselectivity in membrane-bound fatty acid desaturases and the relevant structural determinants. The authors suggest that the regios-electivity of such enzymes may be best understood by considering the relative importance of more than one regioselective preference. In this view, CpDesX is designated as anu + 3(omega(3)) desaturase, which primarily references an existing double bond (nu + 3 regioselectivity) and secondarily shows preference for omega(3) desaturation.
Umbilical Cord-Derived Mesenchymal Stem Cell-Derived Exosomal MicroRNAs Suppress Myofibroblast Differentiation by Inhibiting the Transforming Growth Factor-β/SMAD2 Pathway During Wound Healing (2016)

Exosomes have been identified as a new type of major paracrine factor released by umbilical cord-derived mesenchymal stem cells (uMSCs). They have been reported to be an important mediator of cell-to-cell communication. However, it is still unclear precisely which molecule or group of molecules carried within MSC-derived exosomes can mediate myofibroblast functions, especially in the process of wound repair. The present study explored the functional roles of uMSC-exosomal microRNAs in the process of myofibroblast formation, which can cause excessive scarring. This is an unreported function of uMSC exosomes. Also, for the first time, the uMSC-exosomal microRNAs were examined by high-throughput sequencing, with a group of specific microRNAs (miR-21, miR-23a, miR-125b, and miR-145) found to play key roles in suppressing myofibroblast formation by inhibiting excess α-smooth muscle actin and collagen deposition associated with activity of the transforming growth factor-β/SMAD2 signaling pathway.
Genetic predisposition in patients undergoing cardiopulmonary bypass surgery is associated with an increase of inflammatory cytokines (2001)

The presence of the E4 allele is associated with increased release of IL-8 and TNF-alpha after CBP surgery. The preoperative determination of E4 in patients undergoing cardiac surgery may lead to additional perioperative measures for the treatment of an increased systemic inflammatory response.
Human natural anti-alpha-galactosyl IgG. II. The specific recognition of alpha (1----3)-linked galactose residues. (1985)

A natural IgG antibody (anti-Gal) with alpha-galactosyl binding specificity has been found in large amounts (0.5 - 1.0% of serum IgG) in all individuals tested. It has been purified by affinity chromatography on a column of melibiose-Sepharose. In addition to its affinity for normal and pathological senescent human red cells, the antibody readily interacts with rabbit red blood cell (RRBC) glycolipids with alpha-galactosyl terminal residues. Two types (glycosidic linkages of 1----3 vs. 1----4) of rabbit red cells glycolipids with terminal alpha-galactosyl residues were tested for antibody binding. The antibody specifically bound to glycolipids with Gal alpha 1----3 terminal residues, and treatment of these glycolipids with alpha-galactosidase abolished binding. Hemagglutination inhibition studies with oligosaccharides of known structure also showed that the antibody binds specifically to glycoconjugates with an alpha 1----3 terminal galactose residue. Anti-Gal did not bind to a human B-active glycolipid, indicating that fucose-linked alpha 1----2 to the penultimate galactose prevents anti-Gal binding. The anti-Gal specificity for RRBC glycolipids also paralleled that of the alpha-galactosyl-specific Bandeiraea simplicifolia lectin. The possible reasons for the occurrence of this unique antibody in human serum are discussed.
Human Liver Serine Dehydratase (1989)

Rat liver serine dehydratase cDNA was used to screen a human liver cDNA library in lambda gt11. One positive clone occurred in every 5,000 clones. Fifteen positive clones were plaque purified. The largest cDNA obtained contained an open reading frame of 987 base pairs, and 5' and 3' noncoding regions of 89 and 317 base pairs, respectively. The deduced amino acid sequence, with a calculated Mr of 34,615, was similar to that of rat liver serine dehydratase except for the absence of a segment consisting of 36 amino acid residues. In vitro transcription/translation with the cDNA resulted in the formation of a polypeptide with an Mr of approximately 35,000, which cross-reacted with the anti-rat serine dehydratase antibody. These results suggest that the human serine dehydratase is structurally cognate with the rat enzyme. Moreover, portions of the sequence postulated to be essential for activity in microbial threonine dehydratases are found in the mammalian serine dehydratases, suggesting that hydroxyamino and dehydratases may have originated from a common ancestor.
Design and Dynamic Culture of 3D-Scaffolds for Cartilage Tissue Engineering (2009)

Engineered scaffolds for tissue-engineering should be designed to match the stiffness and strength of healthy tissues while maintaining an interconnected pore network and a reasonable porosity. In this work, we have used 3D-plotting technique to produce poly-L-Lactide macroporous scaffolds with two different pore sizes. The ability of these macroporous scaffolds to support chondrocyte attachment and viability were compared under static and dynamic loading in vitro. Moreover, the 3D-plotting technique was combined with porogen-leaching, leading to macro/microporous scaffolds, so as to examine the effect of microporosity on the level of cell attachment and viability under similar loading condition. Canine chondrocytes' cells were seeded onto the scaffolds with different topologies, and the constructs were cultured for up to 2 weeks under static conditions or in a bioreactor under dynamic compressive strain of 10% strain, at a frequency of 1 Hz. The attachment and cell growth of chondrocytes were examined by scanning electron microscopy and by 3-(4,5-dimethythiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay. A significant difference in cell attachment was observed in macroporous scaffolds with different pore sizes after 1, 7, and 14 days. Cell viability in the scaffolds was enhanced with decreasing pore size and increasing microporosity level throughout the culture period. Chondrocyte viability in the scaffolds cultured under dynamic loading was significantly higher (p<0.05) than the scaffolds cultured statically. Dynamic cell culture of the scaffolds improved cell viability and decreased the time of in vitro culture when compared to statically cultured constructs. Optimizing the culture conditions and scaffold properties could generate optimal tissue/constructs combination for cartilage repair.
Is Escherichia coli growing in glucose-limited chemostat culture able to utilize other sugars without lag? (1995)

It was investigated whether Escherichia coli cultured in a glucose-limited chemostat is able to grow with a series of sugars whose utilization is normally repressed during batch growth with glucose. Cells growing at dilution rates of 0.2, 0.3 and 0.6h-1 were able to immediately utilize and grow with fructose, mannose, maltose and ribose. Galactose was transported instantaneously but growth started only after a considerable lag. Arabinose was the only sugar tested which was neither transported nor utilized immediately. The results give experimental evidence that in vivo catabolite repression by glucose is absent at the very low glucose concentrations present in chemostat culture. Additionally, the results demonstrate that chemostat-grown cells of E. coli are able to substitute glucose as a carbon and energy source by several other sugars with no lag period.
Electrical and Ionic Conductivity of Gd-Doped Ceria (1999)

Electrical Conductivity of GdyCe1−yO2-y/2-x(y=0.1, 0.2), as a function of temperature and oxygen partial pressure, was measured with a complex impedance method. It is shown that the increase of electrical conductivity with reducing oxygen partial pressure can be described well by a model that assumes constant mobility of both oxygen vacancy and electron, based on ideal solution model of nonstoichiometry of Gd-doped ceria. Ionic conductivity is calculated and its activation energy is discussed. Electronic conductivity is discussed also.
Measuring Mast Cell Mediator Release (2010)

Mediators released from activated mast cells are responsible for the allergic inflammatory reactions associated with disease states such as anaphylaxis and atopy. These mediators are released as a consequence of immediate degranulation and phospholipid metabolism upon mast cell activation, followed by delayed cytokine gene expression. Thus, techniques that monitor indices of these events in mast cell culture systems, in association with biochemical analysis of parameters of cell signaling, are critical to our understanding of the molecular mechanisms regulating mast cell-mediated disease. Furthermore, these systems can be adapted for high-throughput screens to identify potential inhibitors of mast cell activation that may provide potential leads for novel therapies for these diseases. In this unit, we describe approaches that can be readily used or adapted to a variety of rodent and human mast cell culture systems for the determination of degranulation, phospholipid-derived inflammatory mediator production, and cytokine generation.
The Immunoglobulin Superfamily: Domains For Cell Surface Recognition (1988)

Exhausted CD8 T (Tex) cells are a distinct cell lineage that arise during chronic infections and cancers in animal models and humans. Tex cells are characterized by progressive loss of effector functions, high and sustained inhibitory receptor expression, ...Read More
Query understanding enhanced by hierarchical parsing structures (2013)

Query understanding has been well studied in the areas of information retrieval and spoken language understanding (SLU). There are generally three layers of query understanding: domain classification, user intent detection, and semantic tagging. Classifiers can be applied to domain and intent detection in real systems, and semantic tagging (or slot filling) is commonly defined as a sequence-labeling task - mapping a sequence of words to a sequence of labels. Various statistical features (e.g., n-grams) can be extracted from annotated queries for learning label prediction models; however, linguistic characteristics of queries, such as hierarchical structures and semantic relationships, are usually neglected in the feature extraction process. In this work, we propose an approach that leverages linguistic knowledge encoded in hierarchical parse trees for query understanding. Specifically, for natural language queries, we extract a set of syntactic structural features and semantic dependency features from query parse trees to enhance inference model learning. Experiments on real natural language queries show that augmenting sequence labeling models with linguistic knowledge can improve query understanding performance in various domains.