gebhart/patrepeval huggingface dataset:
CD63-Mediated Antigen Delivery into Extracellular Vesicles via DNA Vaccination Results in Robust CD8+ T Cell Responses (2017)

DNA vaccines are attractive immunogens for priming humoral and cellular immune responses to the encoded Ag. However, their ability to induce Ag-specific CD8<sup>+</sup> T cell responses requires improvement. Among the strategies for improving DNA vaccine immunogenicity are booster vaccinations, alternate vaccine formulations, electroporation, and genetic adjuvants, but few, such as extracellular vesicles (EVs), target natural Ag delivery systems. By focusing on CD63, a tetraspanin protein expressed on various cellular membranes, including EVs, we examined whether a DNA vaccine encoding an Ag fused to CD63 delivered into EVs would improve vaccine immunogenicity. In vitro transfection with plasmid DNA encoding an OVA Ag fused to CD63 (pCD63-OVA) produced OVA-carrying EVs. Immunizations with the purified OVA-carrying EVs primed naive mice to induce OVA-specific CD4<sup>+</sup> and CD8<sup>+</sup> T cells, whereas immunization with EVs purified from cells transfected with control plasmids encoding OVA protein alone or a calnexin-OVA fusion protein delivered into the endoplasmic reticulum failed to do so. Vaccinating mice with pCD63-OVA induced potent Ag-specific T cell responses, particularly those from CD8<sup>+</sup> T cells. CD63 delivery into EVs led to better CD8<sup>+</sup> T cell responses than calnexin delivery into the endoplasmic reticulum. When we used a mouse tumor implantation model to evaluate pCD63-OVA as a therapeutic vaccine, the EV-delivered DNA vaccination significantly inhibited tumor growth compared with the control DNA vaccinations. These results indicate that EV Ag delivery via DNA vaccination offers a new strategy for eliciting strong CD8<sup>+</sup> T cell responses to the encoded Ag, making it a potentially useful cancer vaccine.
A low power and delay multi-protocol switch with IO and network virtualization (2013)

Data centers connect a larger number of servers requiring IO and switches with low power and delay. Virtualization of IO and network is crucial for these servers, which run virtual processes for computing, storage, and applications. We propose using the PCI Express (PCIe) protocol and a new PCIe switch fabric for IO and switch virtualization. The switch fabric has little data buffering, allowing up to 512 physical 10 Gb/s PCIe 2.0 lanes to be connected via a switch fabric on a chip. The switch is scalable with adapters running multiple adaptation protocols, such as Ethernet over PCIe, PCIe over Internet, or FibreChannel over Ethernet. Such adaptation protocols allow integration of IO often required for disjoint data center applications such as storage and networking. The novel switch fabric based on space-time carrier sensing facilitates high bandwidth, low power, and low delay multiprotocol switching. To achieve Terabit switching, both time (high transmission speed) and space (multi-stage interconnection network) technologies are required. In this paper, we present the design of an up to 256 lanes Close-network of multistage crossbar switch fabric for PCIe system. The switch core consists of 32 16x16 crossbar sub-switches. We also propose a new output contention resolution algorithm utilizing an out-of-band protocol of Request-To-Send (RTS), Clear-To-Send (CTS) before sending PCIe packets through the switch fabric. Preliminary power and delay estimates are provided.
A-type potassium channels expressed from Shaker locus cDNA. (1988)

A-type K+ currents are expressed in Xenopus oocytes injected with in vitro-synthesized transcripts from cDNAs for the Drosophila Shaker (Sh) locus. A single Sh gene product, possibly as a multimer, is sufficient for formation of functional A channels. Various Sh RNAs express A currents with distinct kinetic properties. An analysis of structure-function relationships shows that the conserved central region of Sh polypeptides determines ionic selectivity and overall channel behavior, whereas the divergent amino and carboxyl termini can modify channel kinetics. Alternative splicing of Sh gene transcripts may provide one mechanism for the generation of K+ channel diversity.
Simultaneous Synthesis of a Biogas Process and Heat Exchanger Network for a Large-scale Meat Company (2011)

Abstract preview not available - see full-text PDF article.
<title>Resist metrology for lithography simulation, part 2: development parameter measurements</title> (1996)

Resist simulation technology began with the presentation of Dill's lithography models over 20 years ago, and in the ensuing years has undergone various improvements. Basic parameters in resist modeling include the exposure parameters, bulk development parameters, diffusion length of the photoactive compound (PAC) due to post-exposure baking (PEB), and surface inhibition factors. (The exposure parameters are discussed in detail in 'Resist Metrology for Lithography Simulation, Part 1.') In this report, equipment and data analysis software capable of efficient and accurate determination of development parameters, the diffusion lengths of PAC due to PEB, and surface inhibition factors are discussed. In particular, the construction of equipment for the measurement of development rates is described, and techniques for extraction of development parameters, PAC diffusion lengths, and surface inhibition factors are discussed in detail and examples are given for a high resolution i-line resist.
Parallel out-of-core sorting and fast accesses to disks (2005)

The paper addresses two problems. We investigate the problem of parallel external sorting in the context of a form of heterogeneous clusters then we investigate the impact of efficient disk remote accesses on the performance of external sorting. We explore three techniques to show how they can be deployed for clusters with proportional processor performances. We also validate the READ2 library, an efficient implementation of remote SCSI disk accesses. We derive a new parallel sorting algorithm that is adapted to the READ2 interface. The expected gain of using READ2 is compared to the measured gain for one external sorting implementation.
Molecular-Mechanics Modelling of Drug-DNA Structures; the Effects of Differing Dielectric Treatment on Helix Parameters and Comparison with a Fully Solvated Structural Model (1990)

This study analyses the influence that the nature of the dielectric constant has on the final structures obtained from in vacuo molecular mechanics calculations on a drug-DNA complex and compares these structures with the energy minimised complex including explicit solvent molecules. Minimisations have been performed on a proflavine-decanucleotide structure, where the drug was intercalated at the d(CpG) site of the d(GpApTpApCpGpApTpApC) decamer duplex, using two expressions for the dielectric constant: a distance-independent, epsilon ij = EPS, and a distance-dependent, epsilon ij = EPS*Rij, form and for values of EPS from 1 to 8. Significantly different structures are obtained for the distance-independent and the distance-dependent expressions of the dielectric constant. The use of a distance-independent dielectric constant leads to distorted structures, which are very sensitive to slight changes in the value of EPS. The use of a distance-dependent dielectric constant leads to less distorted and more stable structures. The effects on helical parameters are analysed in detail. The structures obtained for different values of EPS (within the distance-dependent formalism) seem to converge for values of EPS equal to 4 or greater. Based on these results a distance-dependent form of the dielectric with an EPS value of 4 is recommended in order to produce reliable refined nucleic acid structures by molecular mechanics. These conclusions have been supported by molecular-mechanics minimisation of the same structure with the inclusion of explicit water molecules and counter-ions.
Therapy of Treatment Resistant Depression: Focus on the Management of TRD with Atypical Antipsychotics (2004)

Treatment-resistant depression (TRD) represents a significant challenge for physicians. About one third of patients with major depressive disorder fail to experience sufficient symptom improvement despite adequate treatment. Despite this high occurrence of TRD there was no general consensus on diagnosis criteria for TRD until 1997 when researchers proposed a model of defining and staging TRD. In 1999, others defined operational criteria for the definition of TRD. Treatment of TRD is commonly separated into pharmacologic and nonpharmacologic methods. This review gives a short overview of these two methods. The nonpharmacologic methods include psychotherapy, electroconvulsive therapy, and vagus nerve stimulation. Pharmacologic methods include switching to another antidepressant monotherapy, and augmentation or combination with two or more antidepressants or other agents. This review especially focuses on the augmentation of the antidepressant therapy with atypical antipsychotics.
Ultrasonic root‐end preparation Part 1. SEM analysis (1994)

Preparations of apical cavities in resected root ends using rotary burs, with and without citric acid rinse, and ultrasonic tips were compared based on the presence or absence of superficial debris and smear layer. Three groups of 20 extracted teeth each were prepared as follows; I, a size 010 round bur was used to prepare an apical cavity 2-3 mm down the long axis of the root; II, treatment as per group I followed by a 60-s rinse with a solution of 10:3 (10% citric acid, 3% Fe2Cl3); and III, an ultrasonic retrotip was used to prepare a 2-3 mm deep apical cavity. Roots were grooved longitudinally, split and prepared for SEM analysis at x100 and x780 magnification. Examiners were calibrated to a standardized grading system. Extensive statistical analyses indicated statistically significant differences within and among the groups (P < 0.05). Root-end preparation with a bur created a heavy smear layer at all levels of the preparation. This layer was partially removed during ultrasonic preparation in the apical two-thirds. A greater removal of the smear layer was achieved with the citric acid rinse (P < 0.05). Coronally, root-end preparations were contaminated with moderate to heavy amounts of debris with all techniques.
Hematopoietic stem cells (2003)

Considerable effort has been made in recent years in defining the embryonic origin of the hematopoietic stem cell (HSC). Using transgenic mouse models, a number of genes that regulate the formation, self-renewal, or differentiation of HSCs have been identified. Of particular interest, it has recently been shown that key regulators of definitive blood formation played a crucial role in adult HSC development. Specifically, the use of some of these regulatory molecules has dramatically improved the potential of adult HSC expansion. Furthermore, the elucidation of the molecular phenotype of the HSC has just begun. Finally, unexpected degrees of HSC developmental or differentiation plasticity have emerged. In this review, we will summarize the recent advances made in the human HSC field, and we will examine the impacts these discoveries may have clinically and on our understanding of the organization of the human hematopoietic system.
KPNB1, XPO7 and IPO8 Mediate the Translocation ofNF‐κB/p65 into the Nucleus (2013)

NF-κB/p65 is retained in the cytoplasm until it is activated in response to stress. Nuclear import of p65 is regulated by importin α in a nuclear localization signal (NLS)-dependent manner. However, the role of importin β family members in the nuclear translocation of p65 is largely unclear. In this study, using high-content siRNA screening, we identified three of 17 importin β family members that are involved in the nuclear import of p65. Our data showed that knockdown of KPNB1, XPO7 and IPO8 reduced the amount of nuclear p65 following tumor necrosis factor-α (TNF-α) stimulation, resulting in lower NF-κB activity. KPNB1 was the major importin β receptor for p65 import, and this import was dependent on the NLS of p65. However, NLS-mutated p65 still entered the nucleus and bound to XPO7 and IPO8. Interestingly, among the six members of the importin α family, KPNA2 was most important for p65 import. Taken together, our results show that the import of p65 mainly relies on the canonical KPNA2/KPNB1 pathway; however, p65 is also imported by an alternative pathway that is independent of its NLS. Redundant importin receptors are likely to maintain the important function of p65 according to need.
Valproic Acid Teratogenicity: A Toxicogenomics Approach (2004)

Embryonic development is a highly coordinated set of processes that depend on hierarchies of signaling and gene regulatory networks, and the disruption of such networks may underlie many cases of chemically induced birth defects. The antiepileptic drug valproic acid (VPA) is a potent inducer of neural tube defects (NTDs) in human and mouse embryos. As with many other developmental toxicants however, the mechanism of VPA teratogenicity is unknown. Using microarray analysis, we compared the global gene expression responses to VPA in mouse embryos during the critical stages of teratogen action in vivo with those in cultured P19 embryocarcinoma cells in vitro. Among the identified VPA-responsive genes, some have been associated previously with NTDs or VPA effects [vinculin, metallothioneins 1 and 2 (Mt1, Mt2), keratin 1-18 (Krt1-18)], whereas others provide novel putative VPA targets, some of which are associated with processes relevant to neural tube formation and closure [transgelin 2 (Tagln2), thyroid hormone receptor interacting protein 6, galectin-1 (Lgals1), inhibitor of DNA binding 1 (Idb1), fatty acid synthase (Fasn), annexins A5 and A11 (Anxa5, Anxa11)], or with VPA effects or known molecular actions of VPA (Lgals1, Mt1, Mt2, Id1, Fasn, Anxa5, Anxa11, Krt1-18). A subset of genes with a transcriptional response to VPA that is similar in embryos and the cell model can be evaluated as potential biomarkers for VPA-induced teratogenicity that could be exploited directly in P19 cell-based in vitro assays. As several of the identified genes may be activated or repressed through a pathway of histone deacetylase (HDAC) inhibition and specificity protein 1 activation, our data support a role of HDAC as an important molecular target of VPA action in vivo.
Rapid Fuel Quality Surveillance through Chemometric Modeling of Near-Infrared Spectra (2009)

The use of liquid fuels necessitates methods to assess the quality and suitability of these fuels for their intended use. Traditionally, this is performed through a series of chemical and physical tests. However, in some operational situations, streamlined methods to reliably evaluate fuel quality would offer distinct advantages. The Naval Research Laboratory has been engaged in a research program to explore and develop rapid automated fuel quality surveillance technologies. Chemometric modeling methodologies have been investigated as a means to derive mathematical relationships between spectroscopic measurements and measured fuel specification properties. While this is not a novel approach, the consistency and close quality control of today’s production fuels render them non-ideal as calibration sets for the construction of multivariate property prediction models, and thus can limit their precision. This paper describes a practical approach to identify and predict the properties of petroleum derived fuels, as well as blends with Fischer−Tropsch synthetic and biofuels. The performance of these property models is demonstrated in an example of a hardware implementation, that is, the Navy Fuel Property Monitor (NFPM). The NFPM will rapidly estimate a range of specification fuel properties of jet and Naval distillate fuels, from a single analysis by near-infrared (NIR) spectroscopy. This technology will form the basis for control, acquisition and data analysis instrumentation for shipboard and land-based use. A further implementation of this technology will be for in-line sensing applications to provide real-time fuel grade and specification property monitoring as the fuels are moved through supply pipelines.
Positron Emission Tomographic Analysis of Central D1 and D2 Dopamine Receptor Occupancy in Patients Treated With Classical Neuroleptics and Clozapine (1992)

Positron emission tomography and selective radioligands were used to determine D1 and D2 dopamine receptor occupancy induced by neuroleptics in the basal ganglia of drug-treated schizophrenic patients. In 22 patients treated with conventional dosages of classical neuroleptics, the D2 occupancy was 70% to 89%. Patients with acute extrapyramidal syndromes had a higher D2 occupancy than those without side effects. This finding indicates that neuroleptic-induced extrapyramidal syndromes are related to the degree of central D2 occupancy induced in the basal ganglia. In five patients treated with clozapine, the prototype atypical antipsychotic drug, a lower D2 occupancy of 38% to 63% was found. This finding demonstrates that clozapine is also "atypical" with respect to the central D2 occupancy in patients. During treatment with clozapine, there is a low frequency of extrapyramidal syndromes, which accordingly may reflect the comparatively low D2 occupancy induced by clinical doses of clozapine. Classical neuroleptics, like haloperidol or sulpiride, did not cause any evident D1 occupancy, but the thioxanthene flupentixol induced a 36% to 44% occupancy. In four patients treated with clozapine, the D1 occupancy was 38% to 52%. The D1 occupancy induced by clozapine and flupentixol may contribute to the antipsychotic effect of these drugs.
Experimental and human studies on antimony metabolism: their relevance for the biological monitoring of workers exposed to inorganic antimony. (1991)

Unlike inorganic arsenic, inorganic trivalent antimony (Sb) is not methylated in vivo. It is excreted in the bile after conjugation with glutathione and also in urine. A significant proportion of that excreted in bile undergoes an enterohepatic circulation. In workers exposed to pentavalent Sb, the urinary Sb excretion is related to the intensity of exposure. It has been estimated that after eight hours exposure to 500 micrograms Sb/m3, the increase of urinary Sb concentration at the end of the shift amounts on average to 35 micrograms/g creatinine.
Radiata pine pruning technology (1986)

SummaryRadiata pine trees are pruned either to increase the yield of clear timber or to improve fire-protection and access into plantations. The requirements for satisfactory pruning are reviewed, and aspects of methods, such as power source and cutter-head, are discussed. The chainsaw appears to be the most generally suitable motor-manual method available. The use of semi-automated and machine-mounted systems is discussed. None of these systems has gained much acceptance for pruning radiata pine. Some comments are made on the costs of the alternative methods, although a lack of data and the difficulty of separating pruning from the silvicultural system of which it is a part precludes a full cost analysis.
Using the random ball test to calibrate slope dependent errors in optical profilometry (2014)

Optical profilometers are susceptible to slope-dependent errors. The random ball test can be used for calibrating such errors. We demonstrate such a calibration on a 50× confocal microscopy in this paper.
Bow-tie surface-emitting lasers (2000)

We report a new design for surface emitting semiconductor lasers operating at 940 nm, incorporating a double-flare cavity, and distributed Bragg reflector (DBR) mirrors also providing surface emission. This design can take advantage of the modal behavior of the unstable resonator, and has shown very good mode control, with coherent emission from two facets in the same direction. We report preliminary performance results showing very promising characteristics including single-mode diffraction limited operation, and spectral behavior with 42 dB side-mode suppression. This design has exhibited promising results for increasing the current range between the lasing threshold and the filament threshold.
New Results on Multiple-Input Multiple-Output Broadcast Channels With Confidential Messages (2013)

This paper presents two new results on multiple-input multiple-output (MIMO) Gaussian broadcast channels with confidential messages. First, the MIMO Gaussian wiretap channel is revisited. A matrix characterization of the capacity-equivocation region is provided, which extends the previous result on the secrecy capacity to the more general imperfect secrecy setting. Next, the MIMO Gaussian broadcast channel with two receivers and three independent messages: a common message intended for both receivers, and two confidential messages each intended for one of the receivers but needing to be kept asymptotically perfectly secret from the other, is considered. A precise characterization of the capacity region is provided, generalizing the previous results which considered only two out of three possible messages.
A framework for marketing image management. (1991)

Managers know that the customer's impression of an organization is important. And sometimes companies attempt to determine just what that impression is. They conduct ad hoc surveys and focus groups. But too often the data is insubstantial, or difficult to analyze, or even inaccurate. Barich and Kotler introduce the concept of "marketing image" and describe a system of image management: designing a study, collecting data, analyzing image problems, modifying the image, and tracking responses to that image. They argue that only a systematic approach will yield useful and accurate information that a company can translate into action.
An enantioselective oxidative coupling reaction of 2-naphthol derivatives catalyzed by chiral diphosphine oxide–iron(ii) complexes (2019)

An enantioselective oxidative coupling of 2-naphthol derivatives is developed with the use of chiral Fe(ii)-diphosphine oxide complexes. Optically active 1,1-bi-2-naphthol derivatives can be synthesized in high yields when a 2 : 1 complex of (S)-xylyl-iPrO-BIPHEP-oxide and Fe(OTf)<sub>2</sub> is used in the presence of t-butyl hydroperoxide as an oxidant. The non-linear effect, X-ray crystal structure and ESI-MS suggest that a 2 : 1 complex of (S)-xylyl-iPrO-BIPHEP-oxide and Fe(OTf)<sub>2</sub> is a pre-catalyst for a Fe(iii)/Fe(iv) redox cycle.
Assisted reproduction in HIV-1-serodifferent couples (2002)

Selected spermatozoa may be positive for HIV RNA detection even in treated patients. Viral validation of processed semen is necessary in ART programmes for serodifferent couples, particularly in men with only partially or poorly controlled HIV infection.
<title>Speckle reduction by virtual spatial coherence</title> (1993)

Using highly coherent laser sources in interferometry often leads to speckles in the interferograms. These speckles constitute a noise on the fringe phase and, hence, lead to a reduction of wavefront measurement precision. They arise from the light scattered by random imperfections of the optical surfaces. A new technique was developed at Carl Zeiss to reduce the effects of speckles in the laser interferometer DIRECT 100 by a virtual reduction of the spatial coherence regarding the speckle contrast. In the technique presented here the direction of the illuminating light beam in the interferometer is modulated while averaging wavefronts (not intensities) with the real-time wavefront averaging capability of DIRECT 100, resulting in a virtually larger extent of the light source. The fringe contrast is independent of this beam modulation, whereas the speckle contrast in the accumulated wavefront is determined by the virtual extent of the light source. Thus, speckle effects not only from the imaging part of the optical train but also from the illuminating part are reduced.