gebhart/patrepeval huggingface dataset:
Chronic Lymphocytic Leukemia Cells Can Induce Monocytes to Express High Levels of BAFF and Assume Properties of Nurselike Cells In Vitro. (2006)

Abstract CD14+ blood mononuclear cells co-cultured with chronic lymphocytic leukemia (CLL) B cells differentiate into nurselike cells (NLCs) that in turn can support CLL-cell survival in vitro and possibly in vivo. These cells appear similar to lymphoma-associated macrophages, which were identified in secondary lymphoid tissue of patients with follicular lymphoma and appear more prevalent in patients with therapy-resistant disease. To investigate the relationship between NLC and macrophages, we performed studies on macrophages and NLCs that were induced to differentiate from CD14+ blood mononuclear cells in vitro. Consistent with prior studies, we found that NLCs express significantly higher levels of CD68 than macrophages, as assessed via cytoplasmic flow cytometry. However, Affymatrix U113A microarray analysis of gene expression by NLC, macrophages, and monocytes-derived dendritic cells (DCs) from 3 donors revealed major differences in gene expression between DCs versus macrophages or NLCs, but no major differences in gene expression profiles between NLCs and macrophages. Flow cytometric analyses of NLCs and macrophages revealed that these two cell types also shared similar expression levels of CD16, CD32, CD35, CD86, CD58, MHC-II, CD40, and CD54. However, using flow cytometry we found that NLCs (n=9) expressed significantly higher levels than macrophages of the B-cell activating factor belonging to the tumor necrosis factor family (BAFF). Deconvolution microscopy confirmed the differences in BAFF expression and also revealed that NLCs express higher levels of a proliferation-inducing ligand (APRIL) than macrophages. These are two key factors involved in promoting leukemia/lymphoma B cell survival. Moreover, NLCs maintained high-level expression of BAFF even when cultured apart from CLL cells in fresh medium. We investigated whether co-culture of differentiated macrophages with CLL cells could induce the macrophages to express high-levels of BAFF. Although such co-culture induced progressive increase in macrophages-expression of BAFF, the levels of BAFF induced after even 7 days of co-culture were lower than those noted for NLCs. We cultured CD14+ blood monocytes and CLL cells separated across a transwell membrane to determine whether a soluble factor(s) was responsible for the induction of high BAFF levels noted on NLCs. Following several days in culture, the cultured monocytes acquired expression levels of BAFF similar to those detected for NLCs. These studies indicate that monocytes can respond to a soluble factor(s) elaborated by CLL cells to assume properties similar to those of NLCs. Moreover they suggest that NLCs may be a peculiar type of terminally differentiated macrophages-like cells induced by the leukemia-cell population to have properties that promote CLL cell survival. Agents that can block the maturation of monocytes into NLCs or that inhibit the capacity of NLCs to promote leukemia-cell survival may be effective in the treatment of CLL and related lymphoid malignancies.
Expression of AMPA, kainate, and NMDA receptor subunits in cochlear and vestibular ganglia (1995)

Glutamate is believed to be the principal afferent neurotransmitter in the peripheral auditory and vestibular systems. In this report, we present a comprehensive molecular analysis of ionotropic glutamate receptor gene expression in the cochlear and vestibular ganglia of the rat. Fourteen glutamate receptor subunits were studied: GluR1-4 (including flip and flop variants), GluR5-7, KA1&2, NR1, and NR2A-D. Reverse transcription of RNA followed by DNA amplification with the polymerase chain reaction was used for the initial analysis. Immunocytochemistry and in situ hybridization with subunit-specific oligonucleotides were subsequently used for cellular localization of receptor expression. AMPA (GluR2-4), kainate (GluR5&6 and KA1&2), and NMDA receptor (NR1 and NR2A-D) subunit expression was detected. Based on the relative amounts of mRNA detected by in situ hybridization, the predominant receptors expressed by cochlear and vestibular ganglion cells appear to be GluR2, GluR3, GluR4, GluR5, and NR1. At a moderate level were GluR6, NR2B, and NR2D. KA1, KA2, NR2A, and NR2C mRNAs were also expressed in ganglion cells, but at lower levels. Only the AMPA receptor subunit GluR1 and the kainate receptor subunit GluR7 were not found to be expressed in vestibulocochlear neurons. These studies suggest that functional AMPA, kainate, and NMDA receptors are present at the hair cell/vestibulocochlear nerve synapse.
Develop once deploy anywhere achieving adaptivity with a runtime linker/loader framework (2005)

This paper presents Load and Let Link -- a framework for flexible runtime loading and linking of procedural native code components. LLL has several novel aspects. First, it provides componentization without requiring an object-oriented language. Second, LLL performs linking at runtime, providing arbitrary code expansion, contraction and substitution. This enables (a) adaptive applications that can rewire themselves in response to dynamic conditions, (b) code patching for mission critical systems and (c) automatic overlaying in memory constrained environments. LLL is language neutral and orthogonal to current software development methodologies, thus providing the substrate for the next generation of develop once deploy anywhere software. In this paper, we present the LLL framework, its implementation on 32 bit x86 architectures and two case studies that showcase the capabilities of the framework.
A preliminary assessment of the risks associated with engine immobilisers (1993)

It is generally perceived that motor vehicles are easy to break into and manufacturers have been slow to provide high quality locks for doors and tailgates. Various security devices are now available either as part of the new vehicle package or as after-market accessories. There are fundamentally two types of immobiliser system, the simple mechanical lock, for example that may clamp the steering wheel to the pedals, which is intended to prevent the vehicle from being driven away, and electronic devices that may provide various means of immobilising the vehicle and can have warning alarms fitted. It is unlikely that any of these devices are thief-proof but they may slow the thief down or discourage him from selecting a particular vehicle. This paper provides a summary of a preliminary study of the factors affecting the reliability of engine immobiliser systems which was carried out for the Police Scientific Development Branch, PSDB, in February 1993. >
Automated de novo sequencing of proteins using the differential scanning technique (2001)

Despite the progress in genomic DNA sequencing de novo sequencing of peptides is still required in a biological research environment since many experiments are done in organisms whose genomes are not sequenced. A way to unambiguously retrieve a peptide sequence from a tandem mass spectrum is to assign the correct ion type to the fragments. Here we describe a method which improves the specificity in y-ion assignment throughout the spectrum. The differential scanning technique requires that the peptides are partially 18O labelled at their C-terminus and that two fragment spectra are acquired for each peptide, one selecting the 16O/18O isotopic cluster and a second fragmenting only the 18O labelled ions. When the spectra are acquired with a quadrupole time of flight mass spectrometer y-ions can be very specifically filtered from the spectrum using a computer algorithm. Partial or complete peptide sequences can be assigned automatically simply by finding the most abundant series of fragments spaced by amino acid residue masses. This method was used extensively in a project investigating vesicular transport in bovine brain cells. Human or mouse homologues to the bovine proteins were found in EST databases facilitating rapid cloning of the human homologues.
Low overhead program monitoring and profiling (2005)

Program instrumentation, inserted either before or during execution, is rapidly becoming a necessary component of many systems. Instrumentation is commonly used to collect information for many diverse analysis applications, such as detecting program invariants, dynamic slicing and alias analysis, software security checking, and computer architecture modeling. Because instrumentation typically has a high run-time overhead, techniques are needed to mitigate the overheads. This paper describes "instrumentation optimizations" that reduce the overhead of profiling for program analysis. Our approach applies transformations to the instrumentation code that reduce the (1) number of instrumentation points executed, (2) cost of instrumentation probes, and (3) cost of instrumentation payload, while maintaining the semantics of the original instrumentation. We present the transformations and apply them for program profiling and computer architecture modeling. We evaluate the optimizations and show that the optimizations improve profiling performance by 1.26-2.63x and architecture modeling performance by 2-3.3x.
Optical beam guidance in monolithic polymer chips for miniaturized colorimetric assays (2005)

For the first time, we present a simple and robust optical concept to enable precise and sensitive read-out of colorimetric assays in flat lab-on-a-chip devices. The optical guidance of the probe beam through an incorporated measurement chamber to the detector is based on the total internal reflection at V-grooves in the polymer chip. This way, the optical path length through the flat measurement chamber and thus the performance of the measurements are massively enhanced compared to direct (perpendicular) beam incidence. This is demonstrated by a chip-based, colorimetric glucose-assay on serum. Outstanding features are an excellent reproducibility (CV= 1.91 %), a competitive lower limit of detection (c/sub min/ = 124 /spl mu/M), and a high degree of linearity (R/sup 2/ = 0.998) within a working range extending over nearly three orders of magnitude.
Log-only temporal object storage (2002)

As main memory capacity increases, more of the database read requests will be satisfied from the buffer system. Consequently, the amount of disk write operations relative to disk read operations will increase. This calls for a focus on write optimized storage managers. We show how the Vagabond object storage manager uses no-overwrite sequential writing of long blocks to achieve high write performance. Vagabond also supports versioned/temporal objects, with the no-overwrite policy used, this does not imply any extra cost. Large objects, e.g., video and matrices, are divided into large chunks. This makes it easy to achieve high read and write bandwidth. This is important, since in many application areas, high data bandwidth is just as important as high transaction throughput. The buffer system in Vagabond is object based, rather than page based. This gives better utilization of main memory. Transparent compression of objects on disk is supported.
Transfer of 5′-terminal cap of globin mRNA to influenza viral complementary RNA during transcription <i>in vitro</i> (1979)

We have recently demonstrated that globin mRNAs are effective primers for influenza viral RNA transcription in vitro catalyzed by the virion transcriptase [Bouloy, M., Plotch, S. J. & Krug, R. M. (1978) Proc. Natl. Acad. Sci. USA 75, 4886-4890]. Here, we present direct evidence that the 5'-terminal methylated cap of the globin mRNAs is transferred to viral complementary RNA (cRNA) during transcription. Chemical (beta-elimination) or enzymatic removal of the cap of globin mRNAs eliminated essentially all their priming activity. Much of this activity could be restored by recapping the beta-eliminated globin mRNAs with the vaccinia virus guanylyl and methyl transferases. Globin mRNAs containing (32)P label only in the cap (m(7)G(32)pppm(6)A(m)-) were prepared by recapping beta-eliminated globin mRNAs with the vaccinia virus enzymes, [alpha-(32)P]GTP, and unlabeled S-adenosylmethionine. By using this labeled globin mRNA as primer and unlabeled nucleoside triphosphates as precursors, the viral cRNA segments that were synthesized were shown to contain a (32)P-labeled 5'-terminal cap structure. Gel electrophoretic analysis indicated that the globin mRNA-primed cRNA segments were 10-15 nucleotides longer at their 5' end than ApG-primed cRNA segments, which initiate exactly at the 3' end of the virion RNA templates. This suggests that, in addition to the cap, about 10-15 other nucleotides are also transferred from the globin mRNA to viral cRNA. A mechanism for the priming of influenza viral cRNA synthesis by globin mRNA is proposed.
002.6 A low-cost mobile naat platform for<i>chlamydia trachomatis</i> (2015)

<h3></h3> We report the development of a low-cost mobile nucleic acid analysis platform (mobiLab) utilising a smartphone-enabled microfluidic device for streamlined analysis of biological samples. Using magnetic particles as a mobile solid phase for nucleic acid capture and transport, fluidic processing is simplified to particle translocation on a robust and scalable cartridge. Process integration facilitated by Bluetooth-enabled microcontrollers enables full control of the instrument by the user with a smartphone application. Each cartridge costs less than $2 using off-the-shelf reagents and materials, an order of magnitude cheaper than $9.98/test for a GeneXpert cartridge. The instrument utilises a microcontroller which controls the rotary bead manipulator, thermal incubation and Bluetooth-based communication with the smartphone application. Each assay consumes approximately 10% of the battery capacity, allowing up to 10 assays to be performed consecutively without access to a power outlet. We designed a single-stream loop-mediated isothermal amplification (LAMP) assay to operate in tandem with the mobiLab platform. We tested the single-stream assay using plasmid targets and were able to capture and amplify 10<sup>3</sup> copies of gene targets. Absence of cross-reactivity with human genomic DNA or other vaginal flora was verified. The platform was validated by testing <i>Chlamydia trachomatis</i> infection from patient-collected vaginal swab samples. Volunteers enrolled in an internet-based Chlamydia screening program, where two sets of swabs were self-collected and mailed back to our lab. One set of swabs was analysed using the gold standard Gen-Probe AC2 CT assay. The second set of swabs was tested using the mobiLab platform. The two results were in agreement for 20 out of 20 samples at a time threshold of 30 min, demonstrating that the droplet assay performance is comparable to the gold standard for the samples tested. To our knowledge, this abstract presents the first smartphone-based NAAT platform that integrates sample preparation, amplification and data processing. <h3>Disclosure of interest statement</h3> None to disclose.
Eosinophil transendothelial migration induced by cytokines. I. Role of endothelial and eosinophil adhesion molecules in IL-1 beta-induced transendothelial migration (1992)

IL-1 beta promotes adhesiveness in human umbilical vein endothelial cells (HuVEC) for eosinophils through expression of adhesion molecules including intercellular adhesion molecules-1 (ICAM-1), E-selectin, and vascular cell adhesion molecule-1 (VCAM-1). Using an in vitro endothelial monolayer system, we examined whether IL-1 beta or TNF-alpha can promote eosinophil transendothelial migration. We also evaluated the contributions of ICAM-1, E-selectin, VCAM-1, leukocyte adhesion complex (CD11/18), and very late Ag-4 (CD11b/18) (VLA-4) in this process using blocking mAb, and determined the changes in expression of CD11b and L-selectin on eosinophils that had undergone transmigration. IL-1 beta and TNF-alpha treatment of HuVEC (4 h, 5 ng/ml) induced significant transendothelial migration of eosinophils (a 4.1 +/- 0.4-fold (IL-1 beta) and 2.0 +/- 0.9-fold (TNF-alpha) increase from the spontaneous value of 3.2 +/- 0.3%). Increased CD11b expression and shedding of L-selectin were observed on eosinophils following IL-1 beta-induced eosinophil transendothelial migration. Studies with mAb revealed that blockade of either ICAM-1 or CD11/18 inhibited transmigration, while antibodies against VCAM-1 and VLA-4 had no inhibitory effect. Among antibodies which block beta 2 integrins, anti-CD18 mAb had the best inhibitory effect (88% inhibition). The combined inhibitory effect of anti-CD11a mAb and anti-CD11b mAb was roughly equal to that of anti-CD18, although anti-CD11a (31% inhibition) and anti-CD11b (52% inhibition) were less effective individually. Anti-ICAM-1 by itself inhibited IL-1 beta-induced eosinophil transendothelial migration (24% inhibition) whereas neither anti-E-selectin nor anti-VCAM-1 were effective inhibitors. Interestingly, the combination of anti-E-selectin and anti-VCAM-1 with anti-ICAM-1 inhibited IL-1 beta-induced eosinophil transendothelial migration significantly better (53% inhibition) than anti-ICAM-1 alone. These results suggest that although the initial attachment of eosinophils to IL-1 beta-activated endothelial cells involves VCAM-1, E-selectin, and ICAM-1, the subsequent transendothelial migration process relies heavily on ICAM-1 and CD11/18. Finally, the changes that eosinophils have been observed to undergo during infiltration in vivo, namely increased expression of CD11/18 and shedding of L-selectin, appear to take place as a direct result of the interaction between eosinophils and endothelial cells.
Optimization of Timing Jitter Reduction by Optical Feedback for a Passively Mode-Locked Laser (2014)

We investigate the effect of optical self-feedback on the timing jitter of a passively mode-locked (ML) laser and compare the von Linde method with two pure time domain methods for calculating the timing jitter of such a system. We find that all three methods yield the same dependence of the timing jitter on the external cavity roundtrip time (delay time). Of these methods, the so-called long term jitter method is significantly less computationally expensive. We therefore use this method to investigate the influence of the delay time, feedback strength, and amplitude-phase coupling on the timing jitter. Our results show that, with vanishing amplitude-phase coupling, greater timing jitter reduction can be achieved with long delay times and larger feedback strengths, when feedback is near resonance. Off resonance, the timing jitter is increased. Non-vanishing amplitude-phase coupling can lead to destabilized pulse stream, even at the feedback main resonances.
Enhancing Photorealism Enhancement (2022)

We present an approach to enhancing the realism of synthetic images. The images are enhanced by a convolutional network that leverages intermediate representations produced by conventional rendering pipelines. The network is trained via a novel adversarial objective, which provides strong supervision at multiple perceptual levels. We analyze scene layout distributions in commonly used datasets and find that they differ in important ways. We hypothesize that this is one of the causes of strong artifacts that can be observed in the results of many prior methods. To address this we propose a new strategy for sampling image patches during training. We also introduce multiple architectural improvements in the deep network modules used for photorealism enhancement. We confirm the benefits of our contributions in controlled experiments and report substantial gains in stability and realism in comparison to recent image-to-image translation methods and a variety of other baselines.
공무원의 직무소진이 조직성과에 미치는 영향: 조직개입의 조절효과를 중심으로 (2019)

본 연구는 악성민원으로 인한 공무원들의 직무소진이 조직성과에 미치는 부(-)적인 영향을 줄이기 위한 방안으로, 각 기관이 활용하고 있는 조직개입 수단의 효과성을 확인하기 위한 목적이다. 조직개입 수단 중에 보상의 조절효과는 존재했고, 가설은 채택되었다. 하지만, 교육의 조절효과에 대한 가설은 기각되었다.
모든 연구대상 집단에서 악성민원처리로 인한 보상인식 수준은 낮았다. 보상의 수준을 높여주거나 관리자와 직원 사이에 일대일 성과면담을 통해서, 직원들이 보상을 받고 있다는 인식을 높여줄 필요가 있었다.
개별집단 분석결과에서, 악성민원처리와 관련된 교육과 임파워먼트는 소방공무원의 이직의도에 정(+)적이었고, 국세공무원은 조직몰입에 부(-)적인 영향을 미치고 있었다. 또한, 모든 연구대상 기관에 대한 악성민원처리 관련 교육의 효과는 유의미하지 않거나 부(-)적이었다. 해당 공무원들이 교육을 받을 마음의 여유가 없을 만큼 직무부담이 크다는 것을 양적분석 결과에 대한 질적 해석을 통해서 알 수 있었다. 세 가지 조직개입 수단이외에 추가적인 조직개입 방안이 필요하다는 것을 알 수 있었다.
Regulation of ion channels in smooth muscles by calcium (1996)

Intracellular Ca2+ concentration ([Ca2+]i) plays a central role in regulating tone and contractility of smooth muscle cells. In contrast to the "classic" model of electromechanical coupling where membrane potential determines [Ca2+]i, it is now well established that [Ca2+]i in turn may also affect membrane potential by modulating open probabilities of ion channels. Activation by [Ca2+]i of large-conductance K+ channels, Cl- channels, and nonselective cation channels has been described, as well as block of delayed rectifier K+ channels by [Ca2+]i and [Ca2+]i-induced inactivation of Ca2+ channels. Therefore, a network consisting of positive- and negative-feedback loops regulates [Ca2+]i as well as membrane potential. In this context, we review the properties of Ca(2+)-dependent ion channels and their functional role in vascular and visceral smooth muscles. Any alteration of the "Ca2+ sensitivity" of ion channels is expected to have a profound effect on the reciprocal relationship between membrane potential and [Ca2+]i. Already several molecular factors determining Ca2+ sensitivity of Ca(2+)-activated K+ channels have been identified. We provide a working definition for Ca2+ sensitivity.
<i>Yersinia pestis</i> YopJ Suppresses Tumor Necrosis Factor Alpha Induction and Contributes to Apoptosis of Immune Cells in the Lymph Node but Is Not Required for Virulence in a Rat Model of Bubonic Plague (2006)

The virulence of the pathogenic Yersinia species depends on a plasmid-encoded type III secretion system that transfers six Yop effector proteins into host cells. One of these proteins, YopJ, has been shown to disrupt host cell signaling pathways involved in proinflammatory cytokine production and to induce macrophage apoptosis in vitro. YopJ-dependent apoptosis in mesenteric lymph nodes has also been demonstrated in a mouse model of Yersinia pseudotuberculosis infection. These results suggest that YopJ attenuates the host innate and adaptive immune response during infection, but the role of YopJ during bubonic plague has not been completely established. We evaluated the role of Yersinia pestis YopJ in a rat model of bubonic plague following intradermal infection with a fully virulent Y. pestis strain and an isogenic yopJ mutant. Deletion of yopJ resulted in a twofold decrease in the number of apoptotic immune cells in the bubo and a threefold increase in serum tumor necrosis factor alpha levels but did not result in decreased virulence, systemic spread, or colonization levels in the spleen and blood. Our results indicate that YopJ is not essential for bubonic plague pathogenesis, even after peripheral inoculation of low doses of Y. pestis. Instead, the effects of YopJ appear to overlap and augment the immunomodulatory effects of other Y. pestis virulence factors.