gebhart/patrepeval huggingface dataset:
Molecular mimicry: Sensitization of Lewis rats with Campylobacter jejuni lipopolysaccharides induces formation of antibody toward GD3 ganglioside (2005)

Recently we have reported cases of demyelinating inflammatory neuropathy showing elevated titers of anti-GD3 antibodies, which occurs rarely in Guillain-Barré syndrome. To examine the correlation between the anti-GD3 antibody titer and Campylobacter jejuni infection, we sensitized female Lewis rats with lipopolysaccharides (LPSs) from serotype HS19 of C. jejuni and examined changes in nerve conduction velocity and nerve conduction block (P/D ratio). After 16 weeks of sensitization, animals revealed decreases of nerve conduction velocity and conduction block (P/D ratio) and high titer of anti-GD3 antibodies. These anti-GD3 antibodies also blocked transmission in neuromuscular junctions of spinal cord-muscle cells cocultures. The GD3 epitope was verified to be located on the Schwann cell surface and nodes of Ranvier in rat sciatic nerve. To determine the target epitope for GD3 antibodies in causing nerve dysfunction, the LPS fraction containing the GD3 epitope was purified from the total LPS by using an anti-GD3 monoclonal antibody-immobilized affinity column. Subsequently, chemical analysis of the oligosaccharide portion was performed and confirmed the presence of a GD3-like epitope as having the following tetrasaccharide structure: NeuAcalpha2-8NeuAc2-3Galbeta1-4Hep. Our data thus support the possibility of a contribution of GD3 mimicry as a potential pathogenic mechanism of peripheral nerve dysfunction.
Contributions of Stacking, Preorganization, and Hydrogen Bonding to the Thermodynamic Stability of Duplexes between RNA and 2′- O -Methyl RNA with Locked Nucleic Acids (2009)

Locked nucleic acids (LNA) considerably enhance the thermodynamic stability of DNA and RNA duplexes. We report the thermodynamic stabilities of LNA-2'-O-methyl RNA/RNA duplexes designed to provide insight into the contributions of stacking and hydrogen bonding interactions to the enhanced stability. The results show that hydrogen bonding of LNA nucleotides is similar to that of 2'-O-methyl RNA nucleotides, whereas the 3'-stacking interactions are on average approximately 0.7 kcal/mol more favorable at 37 degrees C than for 2'-O-methyl or RNA nucleotides. Moreover, NMR spectra suggest helical preorganization of the single-stranded tetramer, C(L)A(M)A(L)U(M), probably due to restriction of some torsion angles. Thus, enhanced stacking interactions and helical preorganization of single-stranded oligonucleotides contribute to the extraordinary stabilization of duplexes by LNA nucleotides.
Effect of collisional damping and reactions in a dynamic reaction cell on the precision of isotope ratio measurements (2000)

Collisional damping of ion density fluctuations of an ion beam extracted from an ICP in a linear rf quadrupole cell [dynamic reaction cell (DRC)] is studied. Target gas pressure, parameter q, entrance and exit lens potentials and DRC rod offset were optimized to broaden the 107Ag+ ion packets of 0.2 ms duration to 2–4 ms (FWHM). It is shown that operating the DRC under such optimized conditions reduces the RSD of isotope ratio measurements obtained with a downstream quadrupole mass analyzer to the theoretical limit defined by the counting statistics error. For Ag and Pb samples at 40 ng ml−1, measured with the cell pressurized by Ne, isotope ratio RSDs of 0.02–0.03% at a counting statistics error of 0.01–0.02% are shown. All 4 isotopes of Pb were measured in the same acquisition. For NIST 982 Isotope Standard at a concentration of 10 ng ml-1, 204Pb/206Pb, 207Pb/206Pb and 208Pb/206Pb isotope ratios were determined with an external precision (n = 7) of 0.056–0.117%, 0.022–0.034% and 0.014–0.028% RSD, and with an average inaccuracy of 340 ppm, 781 ppm and 180 ppm, respectively. NIST 981 at 10 ng ml−1 was used as an external standard. Reactive elimination of isobaric interferences in the DRC is shown to allow precise isotope ratio measurement of normally interfered isotopes of Fe by a quadrupole ICP-MS. ArN+ and ArO+ interferences on Fe+ were removed by ion–molecule reactions with NH3. Collisional damping of the ion beam fluctuations was sustained and internal precision is shown to be limited only by counting statistics. For Fe at 50 ng ml−1, the average internal precision for 19 samples (9 replicates per sample) of 54Fe/56Fe and 57Fe/56Fe ratios was 0.068% and 0.1% RSD, with a corresponding average counting statistics error of 0.053% and 0.082% and external precision of 0.055% and 0.056% RSD, respectively.
Tracking people with probabilistic appearance models (2002)

This paper describes a real-time computer vision system for tracking people in monocular video sequences. The system tracks people as they move through the camera’s field of view, by a combination of background subtraction and the learning of appearance models. The appearance models allow objects to be tracked through occlusions using a probabilistic pixel reclassification algorithm. The system is evaluated on the three test sequences of the PETS 2002 dataset, for which tracking results and processing time requirements are presented.
Structural analysis of the promoter of tomato 1-aminocyclopropane-l-carboxylate synthase 6 gene （Le-ACS6） (2007)

乙烯在许多生长的规定和更高的植物的发展过程起一个重要作用。在西红柿， Le-ACS6， ACC synthase 的一个成员 multigenefamily 在水果成熟期间在系统 1 乙烯生合成包含了，由乙烯服从于否定反馈规定。识别为否定反馈控制负责的 cis 元素，我们建立了一在里面 vitro 在成熟绿色的西红柿水果果皮上采用粒子轰炸检验由 5'-serially 的记者 gened rive 的过去分词删除了的酶(LUC ) 的表达式的短暂试金系统 Le-ACS6 倡导者。结果为在从 translationalstartsite ATG 的 -347 和 -266 upstream 之间的否定乙烯反应的局部性的通常认为的 cis-elementsrequired。Le-ACS6 倡导者和从 -347 包含内部删除到 -266 的 GUS 记者熔化基因的稳定的转变的几根线被产生。GUS 记者的表示模式证明到 -266 的从 -347 的核苷酸的那移动完全消除了 Le-ACS6 倡导者的反应到外长的乙烯。
Role of the N-terminal Amino Acid for the Biological Activities of Angiotensin and Inhibitory Analogues (1974)

Aspartic acid was replaced in position 1 of angiotensin II (AT II ) with several amino acids, to assess the possible influence of the N-terminal amino acid for (a) the intrinsic activity, (b) the affinity, and (c) the metabolic degradation of agonist analogues of AT II . Some of the substitutions in position 1 were used in combination with replacement of Phe by Gly or Leu in position 8, to obtain the corresponding antagonist.The compounds were tested in vivo (rat blood pressure) and in two in vitro preparations (rat stomach and rabbit aorta strips). The oil immersion technique, described by Kalsner and Nickerson (1968) (Can. J. Physiol. Pharmacol. 46, 719–730), was used to study the disposition of the peptides by vascular smooth muscles (rabbit aorta strips). Degradation of the peptides by purified aminopeptidases was evaluated in vitro by measuring the fragments on paper chromatography. Potency of antagonists was estimated in vivo (ID 50 ) and in vitro (pA 2 values): duration of action was established by infusing the inhibitors intravenously into anesthetized rats and testing the effect of standard doses of angiotensin before and after.The results indicate that replacement of Asp with other amino acids does not influence the intrinsic activity, but can either increase or decrease the affinity in vitro or the potency in vivo. 1-Sar-AT II , and 1-D-Ala-AT II are more potent and longer acting than 1-Asp-AT II on isolated intestinal and vascular smooth muscles, but not in vivo. On the contrary, 1-β-Asp-AT II and 1-β-D-Asp-AT II are more potent than 1-Asp-AT II in vivo, but not on rabbit aorta strips. Rate of relaxation of rabbit aorta strips suspended in oil, after contraction with submaximal doses of several analogues of AT II , are significantly slower than relaxation after 1-Asn 2 -AT II and 1-Asp-AT II . A close parallelism between the diminution of the relaxation rate in oil and the degradation by aminopeptideses in vitro was observed, suggesting that metabolic degradation may be the major factor determining relaxation of rabbit aorta in oil after contraction with one of these peptides. Potencies of antagonists in vivo and in vitro are increased by replacing Asp with Sar. Substitution of Asp with β-Asp or β-D-Asp brings about a slight increase of potency in vivo but not in vitro. It appears that firm binding and prolonged occupation of receptors by sarcosyl derivatives are the primary factors contributing to increase the potency and to prolong the duration of action of antagonists, while prevention or reduction of metabolic breakdown by aminopeptidases is much less efficient.
Systematic synthesis and biological evaluation of .alpha.- and .beta.-D-lyxofuranosyl nucleosides of the five naturally occurring nucleic acid bases (1987)

The alpha- and beta-D-lyxofuranosyl analogues of the naturally occurring nucleosides have been synthesized and their antiviral properties examined. The alpha anomers were prepared by glycosylation of purine and pyrimidine aglycons with tetra-O-acetyl-alpha-D-lyxofuranose, followed by removal of the blocking groups. The beta anomers were obtained by sequential oxidation and reduction of 3',5'-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-beta-D-x ylofuranosyl nucleosides. The lyxofuranosyl nucleosides were tested for their activity against a variety of RNA and DNA viruses and for inhibition of cell growth. One compound, 9-alpha-D-lyxofuranosyladenine, showed activity against herpes simplex virus types 1 and 2 both in vitro and in vivo.
Evaluation of the Use of the TobaccoPR-1aPromoter to Monitor Defense Gene Expression by the Luciferase Bioluminescence Reporter System (2011)

Because of their marked responsiveness to induction signals, genes encoding pathogenesis-related proteins are used as markers to monitor defense gene expression in plants. To develop a non-invasive bioluminescence reporter assay system, we tested acidic PR-1 gene promoters from tobacco and Arabidopsis. These two promoters share common regulatory elements and are believed to show similar responsiveness to various stimuli but the results of transient expression assays by microprojectile bombardment of various plant cells and npr1 mutant Arabidopsis suggest that the tobacco PR-1a promoter is superior to its Arabidopsis counterpart in terms of responsiveness to salicylic acid treatment. Transgenic Arabidopsis seedlings harboring the tobacco PR-1a promoter fused to firefly luciferase showed marked induction in response to treatment with chemicals that induce defense gene expression in plants. These results suggest that the tobacco PR-1a promoter is applicable in monitoring defense-gene expression in various plant species.
ST2 blockade reduces sST2-producing T cells while maintaining protective mST2-expressing T cells during graft-versus-host disease (2015)

Graft-versus-host disease (GVHD) remains a devastating complication after allogeneic hematopoietic cell transplantation (HCT). We previously identified high plasma soluble suppression of tumorigenicity 2 (sST2) as a biomarker of the development of GVHD and death. sST2 sequesters interleukin-33 (IL-33), limiting its availability to T cells expressing membrane-bound ST2 (mST2) [T helper 2 (TH2) cells and ST2(+)FoxP3(+) regulatory T cells]. We report that blockade of sST2 in the peritransplant period with a neutralizing monoclonal antibody (anti-ST2 mAb) reduced GVHD severity and mortality. We identified intestinal stromal cells and T cells as major sources of sST2 during GVHD. ST2 blockade decreased systemic interferon-γ, IL-17, and IL-23 but increased IL-10 and IL-33 plasma levels. ST2 blockade also reduced sST2 production by IL-17-producing T cells while maintaining protective mST2-expressing T cells, increasing the frequency of intestinal myeloid-derived suppressor cells, and decreasing the frequency of intestinal CD103 dendritic cells. Finally, ST2 blockade preserved graft-versus-leukemia activity in a model of green fluorescent protein (GFP)-positive MLL-AF9 acute myeloid leukemia. Our findings suggest that ST2 is a therapeutic target for severe GVHD and that the ST2/IL-33 pathway could be investigated in other T cell-mediated immune disorders with loss of tolerance.
SSL1, a suppressor of a HIS4 5'-UTR stem-loop mutation, is essential for translation initiation and affects UV resistance in yeast. (1992)

The SSL1 locus was identified as a trans-acting suppressor that restores HIS4 expression despite a stem-loop structure in the 5'-UTR. SSL1 encodes an essential protein of 52 kD with features characteristic of a protein with multiple zinc fingers. The mechanism of SSL1 suppression is not related to altering his4 transcription or removing the stem-loop sequence from the 5'-UTR; rather, 3- to 5-fold increases in His4 translational expression are observed indicating a post-transcriptional mechanism for SSL1 suppression. SSL1 suppressor mutants that are conditional for growth have altered polysome profiles at the restrictive temperature, and their cell-free extracts are thermolabile in their ability to translate exogenously added mRNA. In addition, the mechanism of suppression appears to be specific for stem-loop structures placed near the 5' end of the message as opposed to a stem-loop located at a downstream position in the 5'-UTR. These observations suggest a role for this protein in promoting translation initiation presumably at the level of ribosomal binding to mRNA. Surprisingly, SSL1 suppressor mutations that are shown to confer an in vivo and in vitro defect in translation initiation also rendered yeast hypersensitive to UV irradiation. This latter phenotype was observed previously with a mutation in the SSL2 suppressor gene, which encodes the yeast homolog of the human gene ERCC-3, for which a defective form causes xeroderma pigmentosum. In light of the related effects of mutations in the SSL1 and SSL2 genes, the encoded proteins may functionally interact both to promote DNA repair and perform an essential function during translation initiation.
Sketch-a-Net that Beats Humans (2015)

We propose a multi-scale multi-channel deep neural network framework that, for the first time, yields sketch recognition performance surpassing that of humans. Our superior performance is a result of explicitly embedding the unique characteristics of sketches in our model: (i) a network architecture designed for sketch rather than natural photo statistics, (ii) a multi-channel generalisation that encodes sequential ordering in the sketching process, and (iii) a multi-scale network ensemble with joint Bayesian fusion that accounts for the different levels of abstraction exhibited in free-hand sketches. We show that state-of-the-art deep networks specifically engineered for photos of natural objects fail to perform well on sketch recognition, regardless whether they are trained using photo or sketch. Our network on the other hand not only delivers the best performance on the largest human sketch dataset to date, but also is small in size making efficient training possible using just CPUs.
Mechanisms of Variable p44 Expression by Anaplasma phagocytophilum (2003)

The human intragranulocytic bacterium Anaplasma phagocytophilum promotes variation of P44s, which are surface-exposed proteins encoded by a p44 multigene family. In the present study, the specific p44 gene expression loci in four strains of A. phagocytophilum were identified and it was determined that each consisted of four tandem genes, tr1, omp-1X, omp-1N, and p44. A putative sigma(70)-type promoter was found upstream of tr1. The p44 genes include a central hypervariable region flanked by conserved regions. The hypervariable region sequence in the p44 expression locus was duplicated and, regardless of the expression status, conserved at another locus in both low- and high-passage cell cultures of strain NY-37. No significant differences in the hypervariable region were found when we compared p44 sequences, at the level of cDNA, within the expression locus and within other loci in the genomes of strains NY-37 and HZ. Similarly, in cDNA isolated from patients and from assorted cultures of strains NY-31, NY-36, and NY-37, hypervariable regions of 450 deduced amino acid sequences of various p44s within each strain were found to be identical, as were those of p44 sequences in the genome of strain HZ. These data suggest that variations in p44 sequences at the level of the p44 expression locus occur through unidirectional conversion of the entire (nonsegmental) p44 hypervariable region including flanking regions with a corresponding sequence copied from one of the conserved donor p44 genomic loci. The data suggest that the P44 antigenic repertoire within the hypervariable region is restricted.
The consensus concept for thermostability engineering of proteins: further proof of concept (2002)

Previously, we calculated a consensus amino acid sequence from 13 homologous fungal phytases. A synthetic gene was constructed and recombinantly expressed. Surprisingly, consensus phytase-1 was 15-26 degrees C more thermostable than all parent phytases used in its design [Lehmann et al. (2000)Protein Eng., 13, 49-57]. In the present study, inclusion of six further phytase sequences in the amino acid sequence alignment resulted in the replacement of 38 amino acid residues in either one or both of the new consensus phytases-10 and -11. Since consensus phytase-10, again, was 7.4 degrees C more thermostable than consensus phytase-1, the thermostability effects of most of the 38 amino acid substitutions were tested by site-directed mutagenesis. Both stabilizing and destabilizing mutations were identified, but all affected the stability of the enzyme by <3 degrees C. The combination of all stabilizing amino acid exchanges in a multiple mutant of consensus phytase-1 increased the unfolding temperature from 78.0 to 88.5 degrees C. Likewise, back-mutation of four destabilizing amino acids and introduction of an additional stabilizing amino acid in consensus phytase-10 further increased the unfolding temperature from 85.4 to 90.4 degrees C. The thermostabilization achieved is the result of a combination of slight improvements from multiple amino acid exchanges rather than being the effect of a single or of just a few dominating mutations that have been introduced by chance. The present findings support the general validity of the consensus concept for thermostability engineering of proteins.
A Phase II Trial of Gefitinib (Iressa, ZD1839) in Stage IV and Recurrent Renal Cell Carcinoma (2004)

Gefitinib is without significant conventional activity in renal cell carcinoma. The relation of "stable disease" to treatment or to disease-related prognostic heterogeneity remains to be defined.
Aggressive inlining (1997)

Existing research understates the benefits that can be obtained from inlining and cloning, especially when guided by profile information. Our implementation of inlining and cloning yields excellent results on average and very rarely lowers performance. We believe our good results can be explained by a number of factors: inlining at the intermediate-code level removes most technical restrictions on what can be inlined; the ability to inline across files and incorporate profile information enables us to choose better inline candidates; a high-quality back end can exploit the scheduling and register allocation opportunities presented by larger subroutines; an aggressive processor architecture benefits from more predictable branch behavior; and a large instruction cache mitigates the impact of code expansion. We describe the often dramatic impact of our inlining and cloning on performance: for example, the implementations of our inlining and cloning algorithms in the HP-UX 10.20 compilers boost SPECint95 performance on a PA8000-based workstation by a factor of 1.32.
Chronic Pruritus: Clinics and Treatment (2011)

Chronic pruritus, one of the main symptoms in dermatology, is often intractable and has a high impact on patient's quality of life. Beyond dermatologic disorders, chronic pruritus is associated with systemic, neurologic as well as psychologic diseases. The pathogenesis of acute and chronic (>6 weeks duration) pruritus is complex and involves in the skin a network of resident (e.g., sensory neurons) and transient inflammatory cells (e.g., lymphocytes). In the skin, several classes of histamine-sensitive or histamine-insensitve C-fibers are involved in itch transmission. Specific receptors have been discovered on cutaneous and spinal neurons to be exclusively involved in the processing of pruritic signals. Chronic pruritus is notoriously difficult to treat. Newer insights into the underlying pathogenesis of pruritus have enabled novel treatment approaches that target the pruritus-specific pathophysiological mechanism. For example, neurokinin-1 antagonists have been found to relieve chronic pruritus.
Towards Self-Powered Cameras (2015)

We propose a simple pixel design, where the pixel's photodiode can be used to not only measure the incident light level, but also to convert the incident light into electrical energy. A sensor architecture is proposed where, during each image capture cycle, the pixels are used first to record and read out the image and then used to harvest energy and charge the sensors' power supply. We have conducted several experiments using off-the-shelf discrete components to validate the practical feasibility of our approach. We first developed a single pixel based on our design and used it to physically scan images of scenes. Next, we developed a fully self-powered camera that produces 30×40 images. The camera uses a supercap rather than an external source as its power supply. For a scene that is around 300 lux in brightness, the voltage across the supercap remains well above the minimum needed for the camera to indefinitely produce an image per second. For scenarios where scene brightness may vary dramatically, we present an adaptive algorithm that adjusts the framerate of the camera based on the voltage of the supercap and the brightness of the scene. Finally, we analyze the light gathering and harvesting properties of our design and explain why we believe it could lead to a fully self-powered solid-state image sensor that produces a useful resolution and framerate.
The contribution of classical (beta1/2-) and atypical beta-adrenoceptors to the stimulation of human white adipocyte lipolysis and right atrial appendage contraction by novel beta3-adrenoceptor agonists of differing selectivities. (1998)

The role of beta3- and other putative atypical beta-adrenoceptors in human white adipocytes and right atrial appendage has been investigated using CGP 12177 and novel phenylethanolamine and aryloxypropanolamine beta3-adrenoceptor (beta3AR) agonists with varying intrinsic activities and selectivities for human cloned betaAR subtypes. The ability to demonstrate beta1/2AR antagonist-insensitive (beta3 or other atypical betaAR-mediated) responses to CGP 12177 was critically dependent on the albumin batch used to prepare and incubate the adipocytes. Four aryloxypropanolamine selective beta3AR agonists (SB-226552, SB-229432, SB-236923, SB-246982) consistently elicited beta1/2AR antagonist-insensitive lipolysis. However, a phenylethanolamine (SB-220646) that was a selective full beta3AR agonist elicited full lipolytic and inotropic responses that were sensitive to beta1/2AR antagonism, despite it having very low efficacies at cloned beta1- and beta2ARs. A component of the response to another phenylethanolamine selective beta3AR agonist (SB-215691) was insensitive to beta1/2AR antagonism in some experiments. Because no [corrected] novel aryloxypropanolamine had a beta1/2AR antagonist-insensitive inotropic effect, these results establish more firmly that beta3ARs mediate lipolysis in human white adipocytes, and suggest that putative 'beta4ARs' mediate inotropic responses to CGP 12177. The results also illustrate the difficulty of predicting from studies on cloned betaARs which betaARs will mediate responses to agonists in tissues that have a high number of beta1- and beta2ARs or a low number of beta3ARs.