gebhart/patrepeval huggingface dataset:
Cytotoxicity of Cadmium-Free Quantum Dots and Their Use in Cell Bioimaging (2014)

The use of quantum dots (QDots) as bright and photostable probes for long-term fluorescence imaging is gaining more interest. Thus far, (pre)clinical use of QDots remains limited, which is primarily caused by the potential toxicity of QDots. Most QDots consist of Cd2+ ions, which are known to cause high levels of toxicity. In order to overcome this problem, several strategies have been tested, such as the generation of cadmium-free QDots. In the present study, two types of cadmium-free QDots, composed of ZnSe/ZnS (QDotZnSe) and InP/ZnS (QDotInP), were studied with respect to their cytotoxicity and cellular uptake in a variety of cell types. A multiparametric cytotoxicity approach is used, where the QDots are studied with respect to cell viability, oxidative stress, cell morphology, stem cell differentiation, and neurite outgrowth. The data reveal slight differences in uptake levels for both types of QDots (maximal for QDotZnSe), but clear differences in cytotoxicity and cell functionality effects exist, with highest toxicity for QDotZnSe. Differences between cell types and between both types of QDots can be explained by the intrinsic sensitivity of certain cell types and chemical composition of the QDots. At concentrations at which no toxic effects can be observed, the functionality of the QDots for fluorescence cell visualization is evaluated, revealing that the higher brightness of QDotZnSe overcomes most of the toxicity issues compared to that of QDotInP. Comparing the results obtained with common Cd2+-containing QDots tested under identical conditions, the importance of particle functionality is demonstrated, revealing that cadmium-free QDots tested in this study are not significantly better than Cd2+-containing QDots for long-term cell imaging and that more work needs to be performed in optimizing the brightness and surface chemistry of cadmium-free QDots for them to replace currently used Cd2+-containing QDots.
Compositional depth profiling of TaCN thin films (2012)

The composition profiling of thin TaCN films was studied. For the composition profile determination using x-ray photoemission spectrometry (XPS) in combination with Ar sputtering, preferential sputtering effects of N with respect to Ta and C were found to lead to inaccurate elemental concentrations. Sputter yield calculations for the given experimental conditions allowed for the correction of a part of the error, leading to fair accuracy by reference-free measurements. Further improvement of the accuracy was demonstrated by the calibration of the XPS compositions against elastic recoil detection analysis (ERDA) results. For Auger electron spectrometry (AES) in combination with Ar sputtering, accurate results required the calibration against ERDA. Both XPS and AES allowed for a reliable and accurate determination of the compositional profiles of TaCN-based thin films after calibration. Time-of-flight secondary-ion mass spectrometry was also used to assess the composition of the TaCN films. However, the analysis was hampered by large matrix effects due to small unintentional oxygen contents in the films. Energy-dispersive x-ray spectrometry is also discussed, and it is shown that an accurate reference-free measurement of the average film concentration can be achieved.
Pump-linewidth-tolerant optical wavelength conversion for high-order QAM signals using coherent pumps (2014)

Optical wavelength conversion (OWC) is expected to be a desirable function in future optical transparent networks. Since high-order quadrature amplitude modulation (QAM) is more sensitive to the phase noise, in the OWC of high-order QAM signals, it is crucial to suppress the extra noise introduced in the OWC subsystem, especially for the scenario with multiple cascaded OWCs. Here, we propose and experimentally demonstrate a pump-linewidth-tolerant OWC scheme suitable for high-order QAM signals using coherent two-tone pumps. Using 3.5-MHz-linewidth distributed feedback (DFB) lasers as pump sources, our scheme enables wavelength conversion of both 16QAM and 64QAM signals with negligible power penalty, in a periodically-poled Lithium Niobate (PPLN) waveguide based OWC. We also demonstrate the performance of pump phase noise cancellation, showing that such coherent two-tone pump schemes can eliminate the need for ultra-narrow linewidth pump lasers and enable practical implementation of low-cost OWC in future dynamic optical networks.
Effect of Elemental-Sulfur Deposition on the Rock Petrophysical Properties in Sour-Gas Reservoirs (2013)

Summary The deposition of elemental sulfur as a solid phase results in plugging the pore space available for gas flow and reduces the reservoir productivity. Elemental sulfur also can be deposited as a liquid phase if the reservoir temperature is greater than 115°C. The liquid sulfur restricts the inflow of gas because of the big density difference between liquid sulfur and gas, which could be 20 times or more. For isothermal conditions in the reservoir, the reduction in reservoir pressure to lower than a critical value causes the elemental sulfur to deposit in the formation, and in turn the gas-well productivity is affected. Accurate prediction of sulfur deposition will help better manage sour-gas reservoirs with potential sulfur-deposition problems. In this paper, a new analytical model was developed to predict the effect of sulfur deposition on the damage of the near-wellbore region. The damage was quantified through the investigation of the effect of sulfur deposition on rock porosity, relative permeability of the gas phase, and the change in rock wettability. The main objective of this model is to investigate the effect of radial distance on formation damage. Different rock- and fluid-property correlations were used in the model. Previous studies did not consider the change in gas properties with pressure, and numerically modeled the sulfur deposition as a condensate in a gas/condensate reservoir. This paper will consider sulfur adsorption, and the actual physical properties of the sulfur will be used in the developed model. The optimum gas-flow velocity that will maximize the sulfur solubility in the gas will be determined. A coreflood experiment was performed to determine the effect of sulfur deposition on the carbonate-rock permeability, porosity, and wettability. The experiment was used to determine the effect of sulfur adsorption on the rock petrophysical properties. The contact angle was measured for a carbonate core saturated with sulfur by use of a pendant-drop tensiometer. Analytical and numerical solutions showed that the deposition of sulfur was affected by the radial distance from the wellbore and sulfur-solubility changes as a function of the pressure drop. Sulfur deposition was found to have a great effect on the rock wettability, and in turn the gas production will be affected. The model can be used to predict the critical flow velocity that the gas can flow without precipitating sulfur. The optimum gas-flow velocity was estimated to be a range that maximizes the sulfur solubility in the gas. It was confirmed experimentally that the sulfur deposition reduced the carbonate-core porosity and permeability, and changed the contact angle (rock wettability). The contact angle increased, which means sulfur adsorption on the rock surfaces changed the rock toward more-gas-wet rock.
π-Facial selectivity in Diels–Alder reactions of C-2-vinyl glycals. Stereocontrolled route to annulated C-glycopyranosides (1990)

An allylic methoxy substituent at C-3 in C-2 vinyl glycals (1b,c) induces complete antiπ-facial selectivity in the thermal Diels–Alder reaction with malefic anhydride; in contrast, products resulting from anti and syn approaches are observed when linear acetylenic compounds are employed as dienophiles; the latter adducts readily aromatize to afford a mixture of products with the pyranose ring unchanged (8) and opened (9).
Diets containing inulin but not lupins help to prevent swine dysentery in experimentally challenged pigs1 (2010)

Swine dysentery is a contagious mucohemorrhagic diarrheal disease caused by the intestinal spirochete Brachyspira hyodysenteriae that colonizes and induces inflammation of the cecum and colon. It has been reported that a diet containing chicory root and sweet lupin can prevent swine dysentery. This experiment was conducted to test the hypothesis that inulin in the chicory root rather than galactans in lupins was responsible for protective effects. An experiment with a 2 × 2 factorial arrangement of treatments was undertaken using pigs fed barley- and triticale-based diets, with the main effects being protein source [185 g/kg of canola meal (decreased galactans) or 220 g/kg of lupins (greater galactans)] and inulin supplementation (0 or 80 g/kg). Forty Large White × Landrace pigs weighing 21 ± 3 kg, with 10 pigs per diet, were allowed to adapt to the diets for 2 wk, and then each pig was challenged orally 4 times with a broth culture containing B. hyodysenteriae on consecutive days. Pigs were killed when they showed clinical signs of dysentery or 6 wk postchallenge. Pigs fed diets without inulin had 8.3 times greater risk (P = 0.017) of developing swine dysentery and were 16 times more likely (P = 0.004) to have colon contents that were culture-positive for B. hyodysenteriae, compared with the pigs fed a diet with 80 g/kg of inulin. Diets containing lupins did not prevent pigs from developing clinical swine dysentery; however, inclusion of lupins or inulin or both in the diets delayed the onset of disease compared with the diet based mainly on canola meal (P < 0.05). Diet did not influence the total concentration of organic acids in the ileum, cecum, or upper and lower colon; however, the molar proportions of the organic acids were influenced (P < 0.05). Consequently the pH values in the cecum, and upper and lower colon were not influenced (P > 0.05) by diet. However the pH values of the ileal digesta were decreased in pigs fed the diet with both lupins and inulin compared with the diet containing only lupins (P < 0.05). In conclusion, this study shows that diets supplemented with highly fermentable carbohydrates from inulin protected pigs against developing swine dysentery.
On The Performance of a Hybrid Mode Beamforming in A Two-Cell System (2012)

본 논문에서는 연계 빔형성과 비연계 빔형성 방법이 동시에 가능한 하이브리드 모드 빔형성 (HMB) 방법을 제안한다. HMB는 점근적으로 합 전송 증가율에 있어서 최적의 빔형성 방법임을 증명한다. 다양한 모의 실험을 통해서 HMB는 대칭 간섭 채널 환경에서 연계 빔형성 방법과 거의 동일한 성능을 달성함을 보인다. 또한, 보다 현실적인 비대칭적 간섭 채널 환경에서는 비대칭 채널 환경에서 연계 빔형성의 전력 비효율성으로 인한 성능의 저하를 갖지만, 연계 빔형성 방법보다는 우수한 성능을 갖는다는 것을 보인다. In this paper, hybrid mode beamforming (HMB) which allows simultaneous transmission of joint beamforming and disjoint beamforming is proposed. HMB is proven to be asymptotically optimal beamforming for sum rate growth. Extensive simulations show that HMB achieves nearly the same performance as joint encoding (JE) in symmetric interference channel. It is also shown that it outperforms JE in a more realistic asymmetric interference channel environment, though it still experiences some performance degradation due to power inefficiency of joint beamforming in asymmetric channel.
Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes (2020)

Nef is an HIV-encoded accessory protein that enhances pathogenicity by down-regulating major histocompatibility class I (MHC-I) expression to evade killing by cytotoxic T lymphocytes (CTLs). A potent Nef inhibitor that restores MHC-I is needed to promote immune-mediated clearance of HIV-infected cells. We discovered that the plecomacrolide family of natural products restored MHC-I to the surface of Nef-expressing primary cells with variable potency. Concanamycin A (CMA) counteracted Nef at subnanomolar concentrations that did not interfere with lysosomal acidification or degradation and were nontoxic in primary cell cultures. CMA specifically reversed Nef-mediated down-regulation of MHC-I, but not CD4, and cells treated with CMA showed reduced formation of the Nef:MHC-I:AP-1 complex required for MHC-I down-regulation. CMA restored expression of diverse allotypes of MHC-I in Nef-expressing cells and inhibited Nef alleles from divergent clades of HIV and simian immunodeficiency virus, including from primary patient isolates. Lastly, we found that restoration of MHC-I in HIV-infected cells was accompanied by enhanced CTL-mediated clearance of infected cells comparable to genetic deletion of Nef. Thus, we propose CMA as a lead compound for therapeutic inhibition of Nef to enhance immune-mediated clearance of HIV-infected cells.
Ubc13 haploinsufficiency protects against age-related insulin resistance and high-fat diet-induced obesity (2016)

Obesity is associated with low-grade inflammation that leads to insulin resistance and type 2 diabetes via Toll-like Receptor (TLR) and TNF-family cytokine receptor (TNFR) signaling pathways. Ubc13 is an ubiquitin-conjugating enzyme responsible for non-canonical K63-linked polyubiquitination of TNF receptor-associated factor (TRAF)-family adapter proteins involved in TLR and TNFR pathways. However, the relationship between Ubc13 and metabolic disease remains unclear. In this study, we investigated the role of Ubc13 in insulin resistance and high-fat diet (HFD)-induced obesity. We compared wild-type (WT) and Ubc13 haploinsufficient (ubc13<sup>+/-</sup>) mice under normal diet (ND) and HFD, since homozygous knockout mice (ubc13<sup>-/-</sup>) are embryonic lethal. Male and female ubc13<sup>+/-</sup> mice were protected against age-related insulin resistance under ND and HFD compared to WT mice. Interestingly, only female ubc13<sup>+/-</sup> mice were protected against HFD-induced obesity and hepatic steatosis. Moreover, only female HFD-fed ubc13<sup>+/-</sup> mice showed lower expression of inflammatory cytokines that was secondary to reduction in weight gain not present in the other groups. In summary, our results indicate that suppression of Ubc13 activity may play a metabolic role independent of its inflammatory function. Thus, Ubc13 could represent a therapeutic target for insulin resistance, diet-induced obesity, and associated metabolic dysfunctions.
Human cord blood CD34+ cells and behavioral recovery following focal cerebral ischemia in rats (2006)

The present study investigated effects of human umbilical cord blood derived CD34+ cells on sensorimotor, cognitive, and histological outcome in rats following focal cerebral ischemia. Halothane anesthetized adult male Wistar rats were subjected to transient or permanent occlusion of the middle cerebral artery (MCAO) followed by intravenous administration of CD34+ cells (5 x 10(5) or 2 x 10(6)) after 24 h recovery. The beam-walking and cylinder tests were used to assess sensorimotor function, and Morris water-maze examined cognitive performance during a 25 day follow-up period. Subsequently, rats were perfused for measurement of infarct volumes and detection of CD34' cells in the brain by immunohistochemistry (MAB1281). MCAO rats showed minor or no spontaneous recovery in sensorimotor function during the follow-up. The recovery profile was similar in MCAO controls and in MCAO rats that received CD34+ cells, although CD34+ cells seemed to improve the use of impaired forelimb. There was also a trend toward improved water-maze performance by CD34+ cells in transient MCAO rats. Infarct volumes assessed from Nissl-stained sections on postoperative day 25 did not differ between the experimental groups. MAB 1281-positive cells were not detected in the brain of MCAO rats that received CD34+ cells. The present study suggests that CD34+ cells might improve functional outcome in MCAO rats after systemic administration, but do not significantly provide neuroprotection.
Pest risk assessment for the European Community plant health: A comparative approach with case studies (2012)

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A Major Combustion Aerosol Event Had a Negligible Impact on the Atmospheric Ice‐Nucleating Particle Population (2020)

Abstract Clouds containing supercooled water are important for both climate and weather, but our knowledge of which aerosol particle types nucleate ice in these clouds is far from complete. Combustion aerosols have strong anthropogenic sources, and if these aerosol types were to nucleate ice in clouds, they might exert a climate forcing. Here, we quantified the atmospheric ice‐nucleating particle (INP) concentrations during the United Kingdom's annual Bonfire Night celebrations, which are characterized by large amounts of combustion aerosol from bonfires and fireworks. We used three immersion mode techniques covering more than 6 orders of magnitude in INP concentration over the temperature range from −10°C to homogeneous freezing. We found no observable systematic change in the INP concentration on three separate nights, despite more than a factor of 10 increase in aerosol number concentrations, up to a factor of 10 increase in PM 10 concentration, and more than a factor of 100 increase in black carbon (BC) mass concentration relative to pre‐event levels. This implies that BC and other combustion aerosol such as ash did not compete with the INPs present in the background air. Furthermore, the upper limit of the ice‐active site surface density, n s ( T ), of BC generated in these events was shown to be consistent with several other recent laboratory studies, showing a very low ice‐nucleating activity of BC. We conclude that combustion aerosol particles similar to those emitted on Bonfire Night are at most of secondary importance for the INP population relevant for mixed‐phase clouds in typical midlatitude terrestrial locations.
Spatially invariant embeddings of systems with boundaries (2016)

We consider certain spatially distributed optimal control problems where the spatial domains are finite intervals with boundaries. The optimal control design procedures for spatially invariant systems are normally not applicable to such bounded spatial domains. For problems that possess certain symmetries, we show how to apply spatially invariant techniques using embeddings. In this note, we report on such “embeddable” problems. As an application, we consider LQR problems for systems posed as PDEs on finite intervals, where it will turn out that the solution for the finite-extent system equals that of its spatially invariant counterpart plus a term that corrects for the boundary conditions. We also show that this decomposition can be understood as a Toeplitz plus Hankel decomposition of the state feedback gain operator, with the Toeplitz part governing the feedback in the interior domain, while the Hankel part provides the needed corrections near the boundaries.
Artificial intelligence–coupled plasmonic infrared sensor for detection of structural protein biomarkers in neurodegenerative diseases (2023)

Diagnosis of neurodegenerative disorders (NDDs) including Parkinson's disease and Alzheimer's disease is challenging owing to the lack of tools to detect preclinical biomarkers. The misfolding of proteins into oligomeric and fibrillar aggregates plays an important role in the development and progression of NDDs, thus underscoring the need for structural biomarker-based diagnostics. We developed an immunoassay-coupled nanoplasmonic infrared metasurface sensor that detects proteins linked to NDDs, such as alpha-synuclein, with specificity and differentiates the distinct structural species using their unique absorption signatures. We augmented the sensor with an artificial neural network enabling unprecedented quantitative prediction of oligomeric and fibrillar protein aggregates in their mixture. The microfluidic integrated sensor can retrieve time-resolved absorbance fingerprints in the presence of a complex biomatrix and is capable of multiplexing for the simultaneous monitoring of multiple pathology-associated biomarkers. Thus, our sensor is a promising candidate for the clinical diagnosis of NDDs, disease monitoring, and evaluation of novel therapies.
Effect of Equal Channel Angular Pressing on the Pitting Corrosion Resistance on the Aluminum Alloys with/without Anodization (2010)

The effect of equal-channel angular pressing (ECAP) on the pitting corrosion resistance of Al (AA1100) and Al-Mg (AA5052) alloy with anodization and without was investigated by means of polarization curves in solutions containing 300 ppm or 0.6 mol/L of Cl- and by surface analysis. In Al and Al-Mg alloy without anodization, the potentials for pitting corrosion were evidently shifted to the noble direction by ECAP process, indicating that this process improves resistance to pitting corrosion. SEM observation revealed that the pitting corrosion occurred near the impurity precipitates and the size of impurity precipitated decreased with ECAP process. The time-dependence of corrosion potential and the polarization resistance determined by AC impedance technique suggested that the formation rate of Al oxide films was increased with ECAP process. The improvement in pitting corrosion resistance of Al and Al-Mg by ECAP seems to be attributable to the decrease in the size of impurity precipitates and the increase in the formation rate of Al oxide films. On the other hand, the time required for initiating pitting corrosion of anodised Al was longer with ECAP than without, indicating improvement in the pitting corrosion resistance by application of ECAP. However, the pitting corrosion of anodized Al-Mg alloy occurred earlier with ECAP than without, showing that the corrosion resistance was worse with ECAP than without. In anodized Al-Mg alloy, cracks occurred in the anodic oxide films during initial corrosion and the cracks were larger with ECAP than without. It is assumed that the pitting corrosion was promoted by the cracks due to the higher internal stress resulting from ECAP.
Significance of True-Positive and False-Positive Pretransplantation Lymphocytotoxic Crossmatch in Primary Liver Allograft Outcomes (2013)

Our findings demonstrate that t+CXM transplants show increased aspartate aminotransferase and alanine aminotransferase peak immediately after transplantation, which influences liver-specific graft outcomes. Additionally, the presence of circulating immunoglobulin M autoantibodies against recipients' own antigens may be protective in liver grafts. However, this may be a predisposing factor for de novo malignancies.
Linewidth broadening of a quantum dot coupled to an off-resonant cavity (2010)

We study the coupling between a photonic crystal cavity and an off-resonant quantum dot under resonant excitation of the cavity or the quantum dot. Linewidths of the quantum dot and the cavity as a function of the excitation laser power are measured. We show that the linewidth of the quantum dot, measured by observing the cavity emission, is significantly broadened compared to the theoretical estimate. This indicates additional incoherent coupling between the quantum dot and the cavity.