gebhart/patrepeval huggingface dataset:
Hydrophilic interaction and reversed‐phase ultra‐performance liquid chromatography TOF‐MS for metabonomic analysis of Zucker rat urine (2008)

Hydrophilic interaction chromatography (HILIC) provides a complementary technique to RP methods for the retention of polar analytes for LC-MS-based metabonomic studies. Combining the advantages of both RP and HILIC separations with the efficient and rapid separations obtained using sub-2 mum particles via the recently introduced ultra-performance LC (UPLC) enables increased coverage of the metabolites present in biological samples to be achieved. Here an HILIC-UPLC-MS method was developed to provide metabolite profiles for urine samples obtained from male Zucker rats. The resulting data were compared with results obtained for the same samples by RP-UPLC-MS and demonstrated the complementary nature of the two separations with both methods enabling discrimination between the different sample types. Interestingly sample type differentiation was based on different markers.
Run-time adaptation in river (2003)

We present the design, implementation, and evaluation of run-time adaptation within the River dataflow programming environment. The goal of the River system is to provide adaptive mechanisms that allow database query-processing applications to cope with performance variations that are common in cluster platforms. We describe the system and its basic mechanisms, and carefully evaluate those mechanisms and their effectiveness. In our analysis, we answer four previously unanswered and important questions. Are the core run-time adaptive mechanisms effective, especially as compared to the ideal? What are the keys to making them work well? Can applications easily use these primitives? And finally, are there situations in which run-time adaptation is not sufficient? In performing our study, we utilize a three-pronged approach, comparing results from idealized models of system behavior, targeted simulations, and a prototype implementation. As well as providing insight on the positives and negatives of run-time adaptation both specifically in River and in a broader context, we also comment on the interplay of modeling, simulation, and implementation in system design.
The T Cell Costimulator TL1A Is Induced by FcγR Signaling in Human Monocytes and Dendritic Cells (2007)

The recently described TL1A/DR3 ligand/receptor pair mediates strong costimulation of Th1 cells. Activation of T and NK cells induces DR3 expression, permitting soluble recombinant TL1A to increase IFN-gamma production and proliferation of these cells. Gut T cells and macrophages express TL1A, especially in Crohn's disease (CD), and there is a strong association between CD and tl1a single nucleotide polymorphisms. Murine studies implicate TL1A in gut inflammation. To determine whether professional T cell-activating cells can express TL1A, fresh blood monocytes and monocyte-derived dendritic cells were stimulated with various activating ligands, including TLR agonists, IFN-gamma, and immune complexes. FcgammaR stimulation strongly induced TL1A mRNA in both cell types, which correlated with the detection of TL1A on the cell surface and in cell culture medium. TLR agonists capable of inducing IL-6 and TNF-alpha in monocytes and dendritic cells did not induce surface nor soluble TL1A. Furthermore, we demonstrate that TL1A production in monocytes leads to enhancement of T cell responses. The induction of TL1A on APCs via specific pathway stimulation suggests a role for TL1A in Th1 responses to pathogens, and in CD.
Expression of the Escherichia coli yfiD gene responds to intracellular pH and reduces the accumulation of acidic metabolic end products (2002)

The YfiD protein of Escherichia coli has been reported to be an acid-inducible protein. Here it is shown that expression of a yfiD::lac reporter fusion is enhanced up to 3 small middle dot5-fold during acidic growth. The anaerobic transcription factor FNR was confirmed as the major regulator of yfiD expression, and ArcA was found to enhance anaerobic yfiD expression, probably by displacing a repressing FNR dimer in the -93 small middle dot5 region of the promoter. Moreover, the pyruvate sensor PdhR was shown to act as a minor anaerobic repressor of yfiD expression. On the basis of its strong homology to the C-terminal region of pyruvate formate-lyase (PFL) it was predicted that YfiD would be a radical-containing enzyme. The YfiD radical was found to be introduced by the PFL-activase enzyme, but unlike PFL, AdhE did not deactivate radicalized YfiD. The extent of radical activation of YfiD was enhanced by low intracellular pH, and thus it was concluded that both yfiD expression and YfiD activity are affected by growth at low pH. The yfiD mutant strain JRG4033 excreted increased levels of organic acids compared to the parental strain when grown in chemostat culture under oxygen-starved conditions, consistent with the acid-inducibility of yfiD expression and the recently reported ability of YfiD to rescue the activity of oxygenolytically cleaved PFL.
Experience in 118 Consecutive Patients undergoing CT-Guided Stereotactic Surgery utilizing the Cosman-Robert-Wells (CRW) Frame (2003)

Aims: To evaluate the efficacy of CT-guided neurosurgical procedures done on patients operated by this modality.Methods: Between January 1997 and March 2000, 118 patients undergoing CT-guided stereotactic procedures were recruited to the study. The CRW III stereotactic system (Radionics, USA) and the TSX-00ZA CT Scanner (Toshiba, Japan) were used for all the procedures in the series. These procedures were directed to symptomatic brain lesions or for the treatment of Parkinsonian tremor.Results: Of 118 patients, 109 had intra-cranial lesions and 9 had Parkinson's Disease. The stereotactic procedures performed on these patients were: biopsies in 62, guided mini-craniotomies in 22, haematoma evacuation in 11 cases, aspiration of abscess in 8 cases, 2 biopsy/aspiration of cysts, 4 placement of catheters and 9 thalamotomies. A histological diagnosis was made in 98.15% while no diagnosis was reached in 1.85%. Morbidity and mortality were 5.92% and 2.55% respectively.Conclusion: CT-guided stereotactic surgery using the CRW frame is accurate, quick, safe and highly effective.
Quantitative Analyses of Core Promoters Enable Precise Engineering of Regulated Gene Expression in Mammalian Cells (2016)

Inducible transcription systems play a crucial role in a wide array of synthetic biology circuits. However, the majority of inducible promoters are constructed from a limited set of tried-and-true promoter parts, which are susceptible to common shortcomings such as high basal expression levels (i.e., leakiness). To expand the toolbox for regulated mammalian gene expression and facilitate the construction of mammalian genetic circuits with precise functionality, we quantitatively characterized a panel of eight core promoters, including sequences with mammalian, viral, and synthetic origins. We demonstrate that this selection of core promoters can provide a wide range of basal gene expression levels and achieve a gradient of fold-inductions spanning 2 orders of magnitude. Furthermore, commonly used parts such as minimal CMV and minimal SV40 promoters were shown to achieve robust gene expression upon induction, but also suffer from high levels of leakiness. In contrast, a synthetic promoter, YB_TATA, was shown to combine low basal expression with high transcription rate in the induced state to achieve significantly higher fold-induction ratios compared to all other promoters tested. These behaviors remain consistent when the promoters are coupled to different genetic outputs and different response elements, as well as across different host-cell types and DNA copy numbers. We apply this quantitative understanding of core promoter properties to the successful engineering of human T cells that respond to antigen stimulation via chimeric antigen receptor signaling specifically under hypoxic environments. Results presented in this study can facilitate the design and calibration of future mammalian synthetic biology systems capable of precisely programmed functionality.
Cloning and characterization of KAP2 : a novel kinesin superfamily associated protein of KIF3A/3B (1996)

We previously reported that KIF3A and KIF3B form a heterodimer that functions as a microtubule-based fast anterograde translocator of membranous organelles. We have also shown that this KIF3A/3B forms a complex with other associated polypeptides, named kinesin superfamily-associated protein 3 (KAP3). In the present study, we purified KAP3 protein by immunoprecipitation using anti-KIF3B antibody from mouse testis. Microsequencing was carried out, and we cloned the full-length KAP3 cDNA from a mouse brain cDNA library. Two isoforms of KAP3 exist [KAP3A (793 aa) and KAP3B (772 aa)], generated by alternative splicing in the carboxyl terminus region. Their amino acid sequences have no homology with those of any other known proteins, and prediction of their secondary structure indicated that almost the entire KAP3 molecule is alpha-helical. We produced recombinant KAP3 and KIF3A/3B using a baculovirus-Sf9 expression system. A reconstruction study in Sf9 cells revealed that KAP3 is a globular protein that binds to the tail domain of KIF3A/3B. The immunolocalization pattern of KAP3 was similar to that of KIF3A/3B in nerve cells. In addition, we found that KAP3 does not affect the motor activity of KIF3A/3B. KAP3 was associated with a membrane-bound form of KIF3A/3B in a fractional immunoprecipitation experiment, and since the KIF3 complex was found to bind to membranous organelles in an EM study, KAP3 may regulate membrane binding of the KIF3 complex.
Allelic loss on chromosome 6Q in primary prostate cancer (1999)

Molecular genetic analyses of human prostate cancer (CaP) has revealed frequent loss of specific chromosome regions suggesting the presence of putative tumor suppressor gene(s) (TSG) on these chromosome loci whose inactivation may play a role in prostate tumorigenesis. To understand the role of 6q alterations in CaP, we have undertaken a comprehensive analysis of proximal 6q. Genomic DNA from tumor and normal prostate tissues from radical prostatectomy specimens of 38 patients were analyzed by polymerase chain reaction (PCR) for 13 polymorphic microsatellite loci on 6q. Allelic losses of 1 or more polymorphic loci were detected in 11 of 38 patients (29%). Six of 11 tumors showing any 6q deletion were found to have allelic losses at D6S1056 and D6S300 loci. Our results revealed a 1.5 megabase interval between D6S1056 and D6S300 at 6q16.3-21 as the minimal region of deletion, which may contain the putative TSG involved in prostate tumorigenesis. One of the tumor samples demonstrated homozygous deletion at a distal location D6S314 (6q23-24), suggesting another locus potentially associated with CaP. Although the relationship of 6q loss of heterozygosity (LOH) with various clinico-pathologic variables, i.e., cancer recurrence or pathologic stage, did not reveal a statistically significant association, the risk for 6q LOH to non-organ confined (pT3) disease was 5-fold higher than for organ confined disease.
3D angle gathers from reverse time migration (2011)

Common-image gathers are an important output of prestack depth migration. They provide information needed for velocity model building and amplitude and phase information for subsurface attribute interpretation. Conventionally, common-image gathers are computed using Kirchhoff migration on common-offset/azimuth data volumes. When geologic structures are complex and strong contrasts exist in the velocity model, the complicated wave behaviors will create migration artifacts in the image gathers. As long as the gather output traces are indexed by any surface attribute, such as source location, receiver location, or surface plane-wave direction, they suffer from the migration artifacts caused by multiple raypaths. These problems have been addressed in a significant amount of work, resulting in common-image gathers computed in the reflection angle domain, whose traces are indexed by the subsurface reflection angle and/or the subsurface azimuth angle. Most of these efforts have concentrated on Kirchhoff and one-way wave-equation migration methods. For reverse time migration, subsurface angle gathers can be produced using the same approach as that used for one-way wave-equation migration. However, these approaches need to be revisited when producing high-quality subsurface angle gathers in three dimensions (reflection angle/azimuth angle), especially for wide-azimuth data. We have developed a method for obtaining 3D subsurface reflection angle/azimuth angle common-image gathers specifically for the amplitude-preserved reverse time migration. The method builds image gathers with a high-dimensional convolution of wavefields in the wavenumber domain. We have found a windowed antileakage Fourier transform method that leads to an efficient and practical implementation. This approach has generated high-resolution angle-domain gathers on synthetic 2.5D data and 3D wide-azimuth real data.
Sequential Immunization with Vesicles Prepared from HeterologousNeisseria meningitidisStrains Elicits Broadly Protective Serum Antibodies to Group B Strains (2002)

The capsular polysaccharide of Neisseria meningitidis group B is an autoantigen, whereas noncapsular antigens are highly variable. These factors present formidable challenges for development of a broadly protective and safe group B vaccine. Mice and guinea pigs were sequentially immunized with three doses of micovesicles or outer membrane vesicles prepared from three meningococcal strains that were each antigenically heterologous with respect to the two major porin proteins, PorA and PorB, and the group capsular polysaccharide. The resulting antisera conferred passive protection against meningococcal group B bacteremia in infant rats and elicited complement-mediated bactericidal activity against genetically diverse group B strains that were either homologous or heterologous with respect to PorA of the strains used to prepare the vaccine. By using knockout strains, a portion of the bactericidal antibody was directed against the highly conserved protein, neisserial surface protein A (NspA). Further, an anti-NspA monoclonal antibody elicited by the sequential immunization was highly bactericidal against strains that were previously shown to be resistant to bacteriolysis by anti-NspA antibodies produced by immunization with recombinant NspA. Sequential immunization with heterologous vesicle preparations offers a novel approach to eliciting broadly protective immunity against N. meningitidis strains. An NspA-based vaccine prepared from protein expressed by Neisseria also may be more effective than the corresponding recombinant protein made in Escherichia coli.
Allogeneic immunotherapy to optimize the graft-versus-tumor effect: concepts and controversies (2010)

This article focuses on the recent evolution of novel conditioning regimens in combination with adoptive cellular therapy in the allogeneic transplant setting for hematologic malignancies. Building on data from animal models, the field of allogeneic transplantation is undergoing a paradigm shift toward immunosuppressive regimens with less toxicity that allow donor hematopoietic engraftment in order to provide a graft-versus-tumor effect as the primary goal of transplantation, rather than chemoablation. In addition, the strategies described in this article, including the use of T-cell subsets as adoptive therapy, will apply to a much broader pool of patients than traditional transplant approaches, thereby allowing more patients with life-limiting illnesses, previously deemed ineligible, to pursue therapy with curative intent.
The small, dense LDL phenotype and the risk of coronary heart disease: epidemiology, patho-physiology and therapeutic aspects. (1999)

More than decade ago, several cross-sectional studies have reported differences in LDL particle size, density and composition between coronary heart disease (CHD) patients and healthy controls. Three recent prospective, nested case-control studies have since confirmed that the presence of small, dense LDL particles was associated with more than a three-fold increase in the risk of CHD. The small, dense LDL phenotype rarely occurs as an isolated disorder. It is most frequently accompanied by hypertriglyceridemia, reduced HDL cholesterol levels, abdominal obesity, insulin resistance and by a series of other metabolic alterations predictive of an impaired endothelial function and increased susceptibility to thrombosis. Whether or not the small, dense LDL phenotype should be considered an independent CHD risk factor remains to be clearly established. The cluster of metabolic abnormalities associated with small, dense LDL particles has been referred to as the insulin resistance-dyslipidemic phenotype of abdominal obesity. Results from the Québec Cardiovascular Study have indicated that individuals displaying three of the numerous features of insulin resistance (elevated plasma insulin and apolipoprotein B concentrations and small, dense LDL particles) showed a remarkable increase in CHD risk. Our data suggest that the increased risk of CHD associated with having small, dense LDL particles may be modulated to a significant extent by the presence/absence of insulin resistance, abdominal obesity and increased LDL particle concentration. We suggest that the complex interactions among the metabolic alterations of the insulin resistance syndrome should be considered when evaluating the risk of CHD associated with the small, dense LDL phenotype. From a therapeutic standpoint, the treatment of this condition should not only aim at reducing plasma triglyceride levels, but also at improving all features of the insulin resistance syndrome, for which body weight loss and mobilization of abdominal fat appear as key elements. Finally, interventions leading to reduction in fasting triglyceride levels will increase LDL particle size and contribute to reduce CHD risk, particularly if plasma apolipoprotein B concentration (as a surrogate of the number of atherogenic particles) is also reduced.
Oligosaccharide modification by swainsonine treatment inhibits pulmonary colonization by B16-F10 murine melanoma cells. (1986)

Oligosaccharide moieties of cell-surface glycoconjugates are thought to be involved in recognition events associated with tumor metastasis and invasion. Using swainsonine (SW), an inhibitor of Golgi alpha-mannosidase II that results in the formation of hybrid-type oligosaccharides on N-linked glycoproteins, we have tested the hypothesis that specific glycan structures are required for pulmonary colonization by tumor cells. B16-F10 murine melanoma cells were treated with SW in growth medium and then injected intravenously into syngeneic C57BL/6 mice. This treatment resulted in dramatic inhibition of colonization, but it had no effect on B16-F10 viability or on cellular tumorigenicity after subcutaneous implantation. SW-treated radiolabeled B16-F10 cells were cleared from the lungs at a greater rate than control cells, suggesting that one effect of treatment is to alter tumor cell retention in the target organ. Our results implicate specific glycan structures in pulmonary colonization and offer a potential approach for identification of specific macromolecules involved in tumor cell-organ recognition during metastasis.
Carbon-Nanotube Growth in Alcohol-Vapor Plasma (2009)

We have successfully grown carbon nanotubes (CNTs) by plasma-enhanced chemical vapor deposition (PECVD) using alcohol. When 0.01-wt% ferrocene was added to the alcohol, vertically aligned CNTs grew at 650degC. By contrast, a few CNTs and mostly carbon nanoparticles were obtained by pure alcohol PECVD even though the Fe catalyst was coated on Si substrates. Comparing this PECVD experiment with thermal alcohol CVD showed that only the PECVD method can be used to grow CNTs under the reported experimental conditions. To understand the plasma properties for CNT growth, particularly plasma species contained in a gas phase of alcohol plasma, the plasma was analyzed using optical-emission spectroscopy (OES) and quadrupole mass spectrometry (QMS). From the OES measurement, emission peaks from the excitation states of C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , CH, CHO, CH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O, CO, H, O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> , and CO <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> were identified, while the QMS measurement also showed the existence of H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , O, and CO. These results indicate that, in alcohol plasma, oxidants and reductants exist together and potentially promote/suppress CNT growth depending on the process conditions. The contribution of C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">y</sub> (x ges 1, y ges 3) radicals, which were produced by decomposition reactions in alcohol plasma as a CNT precursor, is discussed.
Facial expression transformation based on sketch image and multiscale edges (2001)

Abstract This paper proposes a new method of transforming facial expression based on facial sketch image and multi‐scale edges. Multiscale edges, which are defined as local maxima of high‐frequency signal of facial images, are generally located on the edges of facial parts. Facial sketch images defined as line drawings of edges of facial parts are extracted by morphological processing, the generalized symmetry operator, the rectangle filter, and a geometrical template. Therefore, it is possible to transform the binary sketch image into gray‐tone multiscale edge images which are called characterized sketch images. The expression of the characterized facial image can be transformed easily based on FACS (Facial Action Coding System). By reconstruction based on Mallat's method of reconstruction of multiscale edges, facial images with different expressions can be obtained easily. © 2001 Scripta Technica, Electron Comm Jpn Pt 3, 84(9): 67–75, 2001