gebhart/patrepeval huggingface dataset:
Human Immunodeficiency Virus Type 2 Reverse Transcriptase Activity in Model Systems That Mimic Steps in Reverse Transcription (2003)

Human immunodeficiency virus type 2 (HIV-2) infection is a serious problem in West Africa and Asia. However, there have been relatively few studies of HIV-2 reverse transcriptase (RT), a potential target for antiviral therapy. Detailed knowledge of HIV-2 RT activities is critical for development of specific high-throughput screening assays of potential inhibitors. Here, we have conducted a systematic evaluation of HIV-2 RT function, using assays that model specific steps in reverse transcription. Parallel studies were performed with HIV-1 RT. In general, under standard assay conditions, the polymerase and RNase H activities of the two enzymes were comparable. However, when the RT concentration was significantly reduced, HIV-2 RT was less active than the HIV-1 enzyme. HIV-2 RT was also impaired in its ability to catalyze secondary RNase H cleavage in assays that mimic tRNA primer removal during plus-strand transfer and degradation of genomic RNA fragments during minus-strand DNA synthesis. In addition, initiation of plus-strand DNA synthesis was much less efficient with HIV-2 RT than with HIV-1 RT. This may reflect architectural differences in the primer grip regions in the p66 (HIV-1) and p68 (HIV-2) palm subdomains of the two enzymes. The implications of our findings for antiviral therapy are discussed.
Semantic Hierarchy Emerges in Deep Generative Representations for Scene Synthesis (2019)

Despite the success of Generative Adversarial Networks (GANs) in image synthesis, there lacks enough understanding on what generative models have learned inside the deep generative representations and how photo-realistic images are able to be composed of the layer-wise stochasticity introduced in recent GANs. In this work, we show that highly-structured semantic hierarchy emerges as variation factors from synthesizing scenes from the generative representations in state-of-the-art GAN models, like StyleGAN and BigGAN. By probing the layer-wise representations with a broad set of semantics at different abstraction levels, we are able to quantify the causality between the activations and semantics occurring in the output image. Such a quantification identifies the human-understandable variation factors learned by GANs to compose scenes. The qualitative and quantitative results further suggest that the generative representations learned by the GANs with layer-wise latent codes are specialized to synthesize different hierarchical semantics: the early layers tend to determine the spatial layout and configuration, the middle layers control the categorical objects, and the later layers finally render the scene attributes as well as color scheme. Identifying such a set of manipulatable latent variation factors facilitates semantic scene manipulation.
Service-Tailored User-Plane Design Framework and Architecture Considerations in 5G Radio Access Networks (2017)

This paper presents a novel user plane framework, tailored for different 5G services with diverse and conflicting key performance indicators. Initially, this paper identifies the major challenges in the legacy user-plane approaches and highlights the up-to-date 5G standardization activities in this area. It further analyzes new functional requirements related to service-oriented design and the introduction of new mechanisms to address them. Subsequently, this paper discusses how various user plane design decisions related to the control/user plane split options, network slicing, and radio access network (RAN)core network (CN) interfacing can potentially impact the overall 5G architecture. For the latter, some key RAN/CN interface considerations and the interactions with CN given different protocols and quality of service models are investigated.
Freestanding vertically aligned arrays of individual carbon nanotubes on metallic substrates for field emission cathodes (2004)

Direct growth of individual and vertically aligned carbon nanotubes (CNTs) onto a metallic tip apex using a two-chamber radio-frequency plasma-enhanced chemical vapor deposition is reported. Individual Ni nanocatalysts, obtained by a sol–gel combustion technique, were dots for the nucleation of individual CNTs that were freestanding, clean, and vertically aligned by the presence of a controlled applied field. The arrays of CNTs obtained, having a low-density spatial distribution to avoid mutual electrostatic field screening, gave uniform stable overall field emission patterns after a conditioning process. Effective total current densities up to 1A∕cm2 can be extracted.
A Fourier Transform Infrared Study of Mineral Matter in Coal: The Application of a Least Squares Curve-Fitting Program (1981)

The application of Fourier transform infrared spectroscopy to the quantitative determination of mineral matter in coal is discussed. The use of a least squares curve-fitting program allows a choice between standards to be made. The results of an analysis of mineral mixtures and a coal low temperature ash are presented. The results are in good agreement with known concentrations and those obtained by other methods of analysis.
Feature Engineering and Classifier Ensemble for KDD Cup 2010 (2010)

KDD Cup 2010 is an educational data mining competition. Participants are asked to learn a model from students ’ past behavior and then predict their future performance. At National Taiwan University, we organized a course for this competition. Most student sub-teams expanded features by various binarization and discretization techniques. The resulting sparse feature sets were trained by logistic regression (using LIBLINEAR). One sub-team considered condensed features using simple statistical techniques and applied Random Forest (through Weka) for training. Initial development was conducted on an internal split of training data for training and validation. We identified some useful feature combinations to improve performance. For the final submission, we combined results of student sub-teams by regularized linear regression. Our team is the first prize winner of both tracks (all teams and student teams) of KDD Cup 2010.
Rindopepimut: an evidence-based review of its therapeutic potential in the treatment of EGFRvIII-positive glioblastoma (2012)

Glioblastoma multiforme (GBM) is the most common primary brain tumor in adults and is universally fatal. Despite surgical resection, radiotherapy, and systemic chemotherapy, the median overall survival is less than 15 months. As current therapies are not tumor-specific, treatment commonly results in toxicity. The epidermal growth factor receptor variant III (EGFRvIII) is a naturally occurring mutant of EGFR and is expressed on approximately 20% to 30% of GBMs. As it is not expressed on normal cells, it is an ideal therapeutic target. Rindopepimut is a peptide vaccine which elicits EGFRvIII-specific humoral and cellular immune responses. Phase I and II clinical trials have demonstrated significantly higher progression-free and overall survival times in vaccinated patients with EGFRvIII-expressing GBM tumors. Side effects are minimal and mainly consist of hypersensitivity reactions. Due to the efficacy and safety of rindopepimut, it is a promising therapy for patients with GBM. Currently, rindopepimut is undergoing clinical testing in an international Phase III trial for newly diagnosed GBM and a Phase II trial for relapsed GBM.
Disilane Photo-Epitaxy for VLSI (1984)

The low-temperature photo-epitaxy technique has been developed using Si2H6 source gas. The Si2H6 gas is directly dissociated under UV light irradiation resulting in increase of growth rate. The epitaxial growth has been possible at a substrate temperature of 630°C. The nearly abrupt impurity profile is obtained which is advantageous for production of VLSI devices with small dimensions.
Copper/low-k process characterization for 90nm technology using SEM and TEM imaging (2005)

Artificial vertical and lateral shrinkage of different carbon-doped oxide (CDO) low-k materials is observed for electron beam exposure. The effect depends on SEM and TEM imaging conditions and sample preparation procedures. Typical artifacts include layer thinning and delamination of the CDO material from surrounding materials. TEM imaging is less critical compared to SEM. This is partly due to the favorable conditions during TEM sample preparation employing ion milling steps, which avoid the mechanical stress of conventional SEM sample cross-sectioning. Samples also absorb less energy from the electron beam during TEM scanning, which minimizes the impact of CDO shrink. Some artifacts are difficult to distinguish from real process issues, e.g. de-lamination caused by poor layer adhesion. Therefore, careful sample preparation and imaging are necessary to provide meaningful information.
Nitric oxide and salicylic acid signaling in plant defense (2000)

Salicylic acid (SA) plays a critical signaling role in the activation of plant defense responses after pathogen attack. We have identified several potential components of the SA signaling pathway, including (i) the H(2)O(2)-scavenging enzymes catalase and ascorbate peroxidase, (ii) a high affinity SA-binding protein (SABP2), (iii) a SA-inducible protein kinase (SIPK), (iv) NPR1, an ankyrin repeat-containing protein that exhibits limited homology to IkappaBalpha and is required for SA signaling, and (v) members of the TGA/OBF family of bZIP transcription factors. These bZIP factors physically interact with NPR1 and bind the SA-responsive element in promoters of several defense genes, such as the pathogenesis-related 1 gene (PR-1). Recent studies have demonstrated that nitric oxide (NO) is another signal that activates defense responses after pathogen attack. NO has been shown to play a critical role in the activation of innate immune and inflammatory responses in animals. Increases in NO synthase (NOS)-like activity occurred in resistant but not susceptible tobacco after infection with tobacco mosaic virus. Here we demonstrate that this increase in activity participates in PR-1 gene induction. Two signaling molecules, cGMP and cyclic ADP ribose (cADPR), which function downstream of NO in animals, also appear to mediate plant defense gene activation (e.g., PR-1). Additionally, NO may activate PR-1 expression via an NO-dependent, cADPR-independent pathway. Several targets of NO in animals, including guanylate cyclase, aconitase, and mitogen-activated protein kinases (e.g., SIPK), are also modulated by NO in plants. Thus, at least portions of NO signaling pathways appear to be shared between plants and animals.
[Increase of the QT interval dispersion in diabetes mellitus]. (1997)

The QT dispersion, measured as the interlead variability of QT interval (QTd = QTmax-QTmin), reflects the spatial inhomogeneity of ventricular repolarization times. The authors studied QTd and heart rate-corrected QTd (QTc-d) in 81 patients with diabetes mellitus (IDDM: 39, NIDDM: 42) using Bazett's formula; 20 non-diabetic subjects acted as controls (means +/- SD). QTd (43 +/- 17 ms) and QT c-d (52 +/- 20 ms) were increased (p < 0.05) as compared to the control values (QTd = 32 +/- 17 and, QTc-d = 35 +/- 17 ms, respectively). A significant difference was also observed in QTc-d if the two diabetic groups were compared to the control separately (p < 0.05). Moreover, comparison of the diabetic groups (IDDM vs NIDDM) revealed that type I diabetes mellitus is accompanied by a more pronounced spatial dispersion of ventricular reporlarization (QTd = 49 +/- 16, and QTc-d = 59 +/- 19 ms) as compared to NIDDM (QTd = 38 +/- 16, QTc-d = 46 +/- 20 ms [p < 0.01]). The hypothesis that increased QTd/QTc-d is truly a predictive marker of sudden arrhythmic cardiac death in patients with diabetes mellitus needs further clinical investigation.
Potential assays for sperm capacitation in mammals (1994)

Sperm capacitation is an essential process in fertilization. It apparently involves a large number of processes, the common denominator of which is that they donate to sperm the potential to undergo the acrosome reaction, i.e., to release proteolytic enzymes enabling sperm penetration through the egg coat. Although the phenomenon of capacitation has been known for more than 40 years, it is far from understood, and, consequently, there is, as yet, no operational definition of it. The lack of an assay to identify capacitated spermatozoa is both the cause and the effect of this situation. Here we critically review the major changes that are thought to occur during sperm capacitation, and assess their potential use as markers for the identification of capacitated spermatozoa.
Establishment and Characterization of a High and Stable Porcine CD163-Expressing MARC-145 Cell Line (2018)

Isolation and identification of diverse porcine reproductive and respiratory syndrome viruses (PRRSVs) play a fundamental role in PRRSV research and disease management. However, PRRSV has a restricted cell tropism for infection. MARC-145 cells are routinely used for North American genotype PRRSV isolation and vaccine production. But MARC-145 cells have some limitations such as low virus yield. CD163 is a cellular receptor that mediates productive infection of PRRSV in various nonpermissive cell lines. In this study, we established a high and stable porcine CD163- (pCD163-) expressing MARC-145 cell line toward increasing its susceptibility to PRRSV infection. Indirect immunofluorescence assay (IFA) and Western blotting assays showed that pCD163 was expressed higher in pCD163-MARC cell line than MARC-145 cells. Furthermore, the ability of pCD163-MARC cell line to propagate PRRSV was significantly increased as compared with MARC-145 cells. Finally, we found that pCD163-MARC cell line had a higher isolation rate of clinical PRRSV samples and propagated live attenuated PRRS vaccine strains more efficiently than MARC-145 cells. This pCD163-MARC cell line will be a valuable tool for propagation and research of PRRSV.
Experimental Investigation of Single-Phase Microjet Array Heat Transfer (2010)

The heat transfer performance of two microjet arrays was investigated using degassed deionized water and air. The inline jet arrays had diameters of 54 μm and 112 μm, a spacing of 250 μm, a standoff of 200 μm (S/d=2.2 and 4.6, H/d=1.8 and 3.7), and jet-to-heater area ratios from 0.036 to 0.16. Average heat transfer coefficients with deionized water were obtained for 150≤Red≤3300 and ranged from 80,000 W/m2 K to 414,000 W/m2 K. A heat flux of 1110 W/cm2 was attained with 23°C inlet water and an average surface temperature of 50°C. The Reynolds number range for the same arrays with air was 300≤Red≤4900 with average heat transfer coefficients of 2500 W/m2 K to 15,000 W/m2 K. The effect of the Mach number on the area-averaged Nusselt number was found to be negligible. The data were compared with available correlations for submerged jet array heat transfer.
A 240x180 120dB 10mW 12us‐latency sparse output vision sensor for mobile applications (2013)

This paper proposes a CMOS vision sensor that combines event-driven asynchronous readout of temporal contrast with synchronous frame-based active pixel sensor (APS) readout of intensity. The image frames can be used for scene content analysis and the temporal contrast events can be used to track fast moving objects, to adjust the frame rate, or to guide a region of interest readout. Therefore the sensor is suitable for mobile applications because it allows low latency at low data rate and low system-level power consumption. Sharing the photodiode for both readout types allows a compact pixel design that is 60% smaller than a comparable design. The 240x180 sensor has a power consumption of 10mW. It is built in 0.18um technology with 18.5um pixels. The temporal contrast pathway has a minimum latency of 12us, a dynamic range of 120dB, 12% contrast detection threshold and 3.5% contrast matching. The APS readout has 55dB dynamic range with 1% FPN.
The selective ROCK2 inhibitor KD025 reduces IL‐17 secretion in human peripheral blood mononuclear cells independent of IL‐1 and IL‐6 (2018)

Reducing the activities of the pro-inflammatory cytokine IL-17 is an effective treatment strategy for several chronic autoimmune disorders. Rho-associated coiled-coil containing kinase 2 (ROCK2) is a member of the serine-threonine protein kinase family that regulates IL-17 secretion in T cells via signal transducer and activator of transcription 3 (STAT3)-dependent mechanism. We reported here that the selective ROCK2 inhibitor KD025 significantly reduced in vitro production of IL-17 in unfractionated human peripheral blood mononuclear cells (PBMCs) stimulated with the dectin-1 agonist Candida albicans. C. albicans induced IL-17 was reduced by 70% (p < 0.0001); a similar reduction (80%) was observed in PBMC stimulated with the Toll-like receptor 2 agonist Staphylococcus epidermidis (p < 0.0001). Treatment of PBMC with KD025 was not associated with a reduction in IL-1β, IL-6 or IL-1α levels; in contrast, a 1.5 fold increase in the level of IL-1 receptor antagonist (IL-1Ra) was observed (p < 0.001). KD025 down-regulated C. albicans-induced Myosin Light Chain and STAT3, whereas STAT5 phosphorylation increased. Using anti-CD3/CD28 activation of the TCR, KD025 similarly suppressed IL-17 independent of a reduction in IL-1β. Thus, ROCK2 directly regulates IL-17 secretion independent of endogenous IL-1 and IL-6 supporting development of selective ROCK2 inhibitors for treatment of IL-17-driven inflammatory diseases.
Dynamic Properties of Functional Connectivity in the Rodent (2012)

Functional connectivity mapping with resting-state magnetic resonance imaging (MRI) has become an immensely powerful technique that provides insight into both normal cognitive function and disruptions linked to neurological disorders. Traditionally, connectivity is mapped using data from an entire scan (minutes), but it is well known that cognitive processes occur on much shorter time scales (seconds). Recent studies have demonstrated that the correlation between the blood oxygenation level-dependent (BOLD) MRI signal from different areas varies over time, motivating a further exploration of these fluctuations in apparent connectivity. However, it has also been shown that similar changes in correlation can arise when the timing relationships between voxels are randomized (Handwerker et al., 2012 ). In this work, we show that functional connectivity in the anesthetized rat exhibits dynamic properties that are similar to those previously observed in awake humans (Chang and Glover, 2010 ) and anesthetized monkeys (Hutchison et al., 2012 ). Sliding window correlation between BOLD time courses obtained from bilateral cortical and subcortical regions of interest results in periods of variable positive and negative correlation for most pairs of areas except homologous areas in opposite hemispheres, which exhibit a primarily positive correlation. A comparison with sliding window correlation of randomly matched time courses suggests that with the exception of homologous areas and sensorimotor connections, the dynamics cannot be distinguished from random fluctuations in correlation over time, supporting the idea that some of these dynamic patterns may be due to inherent properties of the signal rather than variations in neural coherence. Within the pairs of areas where the dynamics are most different from those of randomly matched time courses, ten common patterns of connectivity are identified, and their occurrence as a function of time is plotted for all animals. The observation of time-varying correlation in the rodent model will facilitate the future multimodal experiments needed to determine whether the changes in apparent connectivity are linked to underlying neural variability.
Antimicrobial, free radical scavenging activities and catalytic oxidation of benzyl alcohol by nano-silver synthesized from the leaf extract of Aristolochia indica L.: a promenade towards sustainability (2015)

Silver nanoparticles (Ag-NPs) were synthesized from aqueous silver nitrate through a simple route using the leaf extract of Aristolochia indica L. (LAIL) which acted as a reducing as well as capping agent. X-ray diffraction confirmed that the synthesized silver particles have a face centred cubic structure. EDS predicted the presence of elemental silver. The SEM images showed the synthesis of spherically mono-dispersed particles, with nano dimensions accounted by the TEM images. Infra-red spectrum adopted to the different organic functionalities present at the surface of the particles. TGA indicated an overall 11 % weight loss up to 1000 °C, suggesting desorption of biomolecules from the surface. X-ray photoelectron spectroscopy (XPS) analysis revealed the presence of metallic silver nanoparticles. The prepared material was utilized as catalyst in the oxidation of benzyl alcohol with molecular oxygen as the oxidant in methanol, under ambient conditions of temperature and pressure. Also Ag-NPs showed good to moderate anti-microbial activity employing the Agar disc diffusion method against various strains using Ciprofloxacin and Fluconazole as standard. Free radical scavenging activity of the nanoparticles were observed by modified 1,1-diphynyl-2-picrylhydrazyl, DPPH and 2,2-azinobis(3-ethylbenzothiazoline-6-sulfonic acid), ABTS in vitro assays. The work presented here demonstrates the adaptability of the synthesized Ag-NPs in participating as a disinfectant agent, free radical scavenger and an effective oxidation catalyst. The basic premise of attaining sustainability through the green synthesis of smart multifaceted materials has been consciously addressed.
A case of Churg-Strauss syndrome and central retinal artery occlusion with good visual recovery (2013)

Here we report a case of Churg-Strauss syndrome (CSS) and central retinal artery occlusion (CRAO), with good visual recovery. A 58-year-old Japanese man with CSS experienced acute painless loss of vision in his right eye. CRAO was diagnosed by fundoscopic findings (retinal whitening with a cherry-red spot). Steroid pulse therapy (methylprednisolone at 1 g daily for 3 days) followed by combined treatment with prednisolone (30 mg/day) and cyclophosphamide (150 mg/day) was administered; his visual acuity recovered to 20/30 in 1 month, and no recurrence has occurred for 1 year. Steroid pulse therapy may be effective for CRAO in CSS patients.
Polymerizable Ligands as Stabilizers for Nanoparticles (2014)

Monomers bearing functional groups that can get chemisorbed on nanoparticles to form polymerizable monolayers have emerged as an interesting class of stabilizer ligands for various nanoparticles. High-surface coverage, their ability to modify the properties of underlying nanoparticles, capability to form polymers of different molecular weights and possibility to make structural modifications make them attractive for their use as stabilizer ligands for nanoparticles. Both in situ and post-synthesis grafting methods for attaching polymerizable ligands to nanoparticles are frequently used. The advantage of grafting polymerizable stabilizer on the surface of nanoparticles is that initially the polymerizable molecule acts as a proper stabilizer for the nanoparticles and later their surface polymerization or co-polymerization with another suitable monomer can be carried out to generate the desired polymer scaffold around the nanoparticles, which ensures the increased stability of the resulting core-polymerized shell nanoparticles. This review discusses interesting reports from recent literature on grafting of polymerizable ligands and their polymerization on gold, silver, silica, and iron oxide nanoparticles.