gebhart/patrepeval huggingface dataset:
In Vitro Activity of Pentamidine Alone and in Combination with Antibiotics against Multidrug-Resistant Clinical Pseudomonas aeruginosa Strains (2020)

Multidrug-resistant (MDR) <i>Pseudomonas aeruginosa</i> is a public health problem causing both community and hospital-acquired infections, and thus the development of new therapies for these infections is critical. The objective of this study was to analyze in vitro the activity of pentamidine as adjuvant in combinations to antibiotics against seven clinical <i>P. aeruginosa</i> strains. The Minimum Inhibitory Concentration (MIC) was determined following standard protocols, and the results were interpreted according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints; however, the gentamicin activity was interpreted according to the Clinical and Laboratory Standards Institute (CLSI) recommendations. The bactericidal in vitro activity was studied at 1×MIC concentrations by time-kill curves, and also performed in three selected strains at 1/2×MIC of pentamidine. All studies were performed in triplicate. The pentamidine MIC range was 400-1600 μg/mL. Four of the strains were MDR, and the other three were resistant to two antibiotic families. The combinations of pentamidine at 1×MIC showed synergistic activity against all the tested strains, except for pentamidine plus colistin. Pentamidine plus imipenem and meropenem were the combinations that showed synergistic activity against the most strains. At 1/2×MIC, pentamidine plus antibiotics were synergistic with all three analyzed strains. In summary, pentamidine in combination with antibiotics showed in vitro synergy against multidrug-resistant <i>P. aeruginosa</i> clinical strains, which suggests its possible use as adjuvant to antibiotics for the therapy of infections from MDR <i>P. aeruginosa</i>.
Evaluation of Parallel Communication Models in Nekbone, a Nek5000 Mini-Application (2015)

Nekbone is a proxy application of Nek5000, a scalable Computational Fluid Dynamics (CFD) code used for modelling incompressible flows. The Nekbone mini-application is used by several international co-design centers to explore new concepts in computer science and to evaluate their performance. We present the design and implementation of a new communication kernel in the Nekbone mini-application with the goal of studying the performance of different parallel communication models. First, a new MPI blocking communication kernel has been developed to solve Nekbone problems in a three-dimensional Cartesian mesh and process topology. The new MPI implementation delivers a 13% performance improvement compared to the original implementation. The new MPI communication kernel consists of approximately 500 lines of code against the original 7,000 lines of code, allowing experimentation with new approaches in Nekbone parallel communication. Second, the MPI blocking communication in the new kernel was changed to the MPI non-blocking communication. Third, we developed a new Partitioned Global Address Space (PGAS) communication kernel, based on the GPI-2 library. This approach reduces the synchronization among neighbor processes and is on average 3% faster than the new MPI-based, non-blocking, approach. In our tests on 8,192 processes, the GPI-2 communication kernel is 3% faster than the new MPI non-blocking communication kernel. In addition, we have used the OpenMP in all the versions of the new communication kernel. Finally, we highlight the future steps for using the new communication kernel in the parent application Nek5000.
Frequency- and Time-Domain Dependency of Electrical Properties of Cement-Based Materials during Early Hydration (2017)

Abstract The electrical properties of Portland cement, and cements containing supplementary cementitious materials (SCM), were obtained over the frequency range 1 kHz–10 MHz during the initial 24 h after gauging with water. The response was measured in terms of conductivity and permittivity with both parameters exhibiting significant temporal changes during this period. It was also evident that while the conductivity increased only marginally with increasing frequency of applied electrical field, the permittivity decreased by several orders of magnitude over this frequency range. Moreover, certain features of the permittivity response, which are related to bulk polarization processes, only revealed themselves in the higher frequency range (100 kHz–1 MHz), and went undetected at lower frequencies. The detailed frequency- and time-domain measurements allowed identification of several stages in the early hydration of cement-based materials and the response can be interpreted in terms of hydration kinetics, physico-chemical processes and microstructural development. It is shown that the methodology can be equally applied to cement pastes and concretes.
Localization of ultracold atoms in disorder: 3D Localization and Coherent Backscattering. (2012)

Poster
Spectroscopy and Reactivity of Dialkoxy Acenes (2019)

Photochemical oxidation of acenes can benefit or impede their function, depending on the application. Although acenes with alkoxy substituents on reactive sites are important for applications as diverse as drug delivery and organic optoelectronics, the influence of chemical structure on their photochemical oxidation remains unknown. This paper therefore describes the synthesis, spectroscopic properties, and reactivity with singlet oxygen (<sup>1</sup> O<sub>2</sub> ) of a series of dialkoxyacenes that vary in the number and types of fused rings in the (hetero)acene cores. Reductive alkylation of quinone precursors yielded target dialkoxyacenes with fused backbones ranging from benzodithiophene to tetracenothiophene. Trends of their experimental spectroscopic characteristics were consistent with time-dependent density functional theory (TD-DFT) calculations. NMR studies show that photochemically generated <sup>1</sup> O<sub>2</sub> oxidizes all but one of these acenes to the corresponding endoperoxides in organic solvent. The rates of these oxidations correlate with the number and types of fused arenes, with longer dialkoxyacenes generally oxidizing faster than shorter derivatives. Finally, irradiation of these acenes in acidic, oxidizing environments cleaves the ether bonds. This work impacts those working in organic optoelectronics, as well as those interested in harnessing photogenerated reactive oxygen species in functional materials.
Benchmarking local motion planners for navigation of mobile manipulators (2022)

There are various trajectory planners for mobile manipulators. It is often challenging to compare their performance under similar circumstances due to differences in hardware, dissimilarity of tasks and objectives, as well as uncertainties in measurements and operating environments. In this paper, we propose a simulation framework to evaluate the performance of the local trajectory planners to generate smooth, and dynamically and kinematically feasible trajectories for mobile manipulators in the same environment. We focus on local planners as they are key components that provide smooth trajectories while carrying a load, react to dynamic obstacles, and avoid collisions. We evaluate two prominent local trajectory planners, Dynamic-Window Approach (DWA) and Time Elastic Band (TEB) using the metrics that we introduce. Moreover, our software solution is applicable to any other local planners used in the Robot Operating System (ROS) framework, without additional programming effort.
Outcomes of acute leukemia patients transplanted with naive T cell–depleted stem cell grafts (2015)

ClinicalTrials.gov (NCT 00914940).
Multimodal Sentiment Analysis using Hierarchical Fusion with Context Modeling (2018)

Multimodal sentiment analysis is a very actively growing field of research. A promising area of opportunity in this field is to improve the multimodal fusion mechanism. We present a novel feature fusion strategy that proceeds in a hierarchical fashion, first fusing the modalities two in two and only then fusing all three modalities. On multimodal sentiment analysis of individual utterances, our strategy outperforms conventional concatenation of features by 1%, which amounts to 5% reduction in error rate. On utterance-level multimodal sentiment analysis of multi-utterance video clips, for which current state-of-the-art techniques incorporate contextual information from other utterances of the same clip, our hierarchical fusion gives up to 2.4% (almost 10% error rate reduction) over currently used concatenation. The implementation of our method is publicly available in the form of open-source code.
The Use of Slotted Expandable Liners in Multizone Openhole Frac-Packs: A New Completion Concept (2011)

Abstract Sand production is becoming increasingly problematic due to the exploitation of poorer quality reservoirs and depletion of existing reservoirs. Cased hole frac-packs (CHFP) combine reliable sand control with potential for high productivity, and have become the completion of choice in many provinces. However, CHFP completions manifest in limited flow entry area into the well. This may cause two problems; a loss of productivity and potential screen erosion. In CHFP designs it is common to perforate the casing with high shot density big hole charges, but due to shot orientation and phasing, only a relatively few perforations connect with the fracture. Entire well production therefore originates from 4spf or less. Detailed modeling shows that this will not cause productivity impairment if the proppant pack is undamaged. Predicted skins for undamaged CHFP should be slightly negative, but field observations in one particular region show typical skins of 2 to 5, but with skins above 10 also reported. This tends to suggest that proppant permeability is being reduced in-situ. By contrast, productivity of open hole frac-packs (OHFP) is significantly less impacted by proppant damage and they also greatly reduce screen erosion risk. The productivity enhancement is revealed through detailed inflow modeling and laboratory experiments. However, it is difficult to engineer multi-zone OHFP completions, and wellbore stability issues complicate implementation. These limitations can be resolved by setting field-proven expandable completion liner (ECL) in the openhole section, prior to running the inner sand screen completion and frac-pack tools. Experiments on large scale samples show that ECL stabilizes the borehole. ECL slot geometry also results in 3-5 fold increase in fracture connection area compared to CHFP. ECL technology can also be combined with a number of different zonal isolation packer technologies, such as expandable, mechanical, swell and combo packer designs, to segment zones. This gives ECL frac-packs (EFP) the functionality of a multi-zone CHFP, but mitigates productivity impairment through proppant plugging and also screen erosion risk. The EFP completion concept also removes a casing string and eliminates perforating, and so also reduces HSE risks. It also has the potential to accommodate larger screen sizes, slim well designs and to reach deeper targets. The EFP completion concept also relies on integration of existing technologies, while offering the potential for a step change in well performance.
A predictive high‐throughput scale‐down model of monoclonal antibody production in CHO cells (2009)

Multi-factorial experimentation is essential in understanding the link between mammalian cell culture conditions and the glycoprotein product of any biomanufacturing process. This understanding is increasingly demanded as bioprocess development is influenced by the Quality by Design paradigm. We have developed a system that allows hundreds of micro-bioreactors to be run in parallel under controlled conditions, enabling factorial experiments of much larger scope than is possible with traditional systems. A high-throughput analytics workflow was also developed using commercially available instruments to obtain product quality information for each cell culture condition. The micro-bioreactor system was tested by executing a factorial experiment varying four process parameters: pH, dissolved oxygen, feed supplement rate, and reduced glutathione level. A total of 180 micro-bioreactors were run for 2 weeks during this DOE experiment to assess this scaled down micro-bioreactor system as a high-throughput tool for process development. Online measurements of pH, dissolved oxygen, and optical density were complemented by offline measurements of glucose, viability, titer, and product quality. Model accuracy was assessed by regressing the micro-bioreactor results with those obtained in conventional 3 L bioreactors. Excellent agreement was observed between the micro-bioreactor and the bench-top bioreactor. The micro-bioreactor results were further analyzed to link parameter manipulations to process outcomes via leverage plots, and to examine the interactions between process parameters. The results show that feed supplement rate has a significant effect (P < 0.05) on all performance metrics with higher feed rates resulting in greater cell mass and product titer. Culture pH impacted terminal integrated viable cell concentration, titer and intact immunoglobulin G titer, with better results obtained at the lower pH set point. The results demonstrate that a micro-scale system can be an excellent model of larger scale systems, while providing data sets broader and deeper than are available by traditional methods.
Chloroplast DNA variation among and within taxonomic varieties of Pinuscaribaea and Pinuselliottii (1994)

Chloroplast DNA BamHI restriction fragments were studied in Pinuselliottii Engelm. var. elliottii (11 trees), P. elliottii var. densa (2 trees), the three taxonomic varieties of Pinuscaribaea Morelet (39 trees), and Pinusoocarpa Schiede (9 trees). Polymorphism was detected within both P. elliottii varieties, but not within P. oocarpa. Each of the P. caribaea varieties was monomorphic, but the Cuban variety, P. caribaea var. caribaea, differed clearly from the Bahamian (P. caribaea var.bahamensis) and Honduran (P. caribaea var. hondurensis) varieties. Variety caribaea shared the most frequent chloroplast genotype of P. elliottii var. elliottii, while varieties bahamensis and hondurensis shared the second most frequent genotype of P. elliottii var. elliottii. The P. oocarpa chloroplast genotype was not found in other taxa of the present study, but was found previously in Pinusechinata Mill, and Pinuspalustris Mill. The results of this study, taken together with other chloroplast data from subsection Australes, suggest a close relationship between P. caribaea and P. elliottii. This confirms previous morphological and biochemical evidence, but several discrepancies were apparent and are discussed.
Brucellosis: An Unusual Diagnosis for a Seronegative Patient with Abscesses, Osteomyelitis, and Ulcerative Colitis (1991)

A 16-year-old girl developed multiple subcutaneous abscesses, osteomyelitis, and severe colitis. On the patient's second admission, a single blood culture--and, subsequently, a specimen of pus--yielded Brucella melitensis biovar 1. A second set of serologic tests, including the rose bengal test, the standard tube agglutination test, the CF test, and Coombs' test, were all negative for Brucella on the patient's second admission and 1 month later. However, a lymphocyte proliferation assay with extracted antigen of Brucella was markedly positive. Thus, this case illustrates that patients with B. melitensis infection may have a unique clinical presentation and that the lymphocyte proliferation assay is an important diagnostic tool for patients whose serologic test results are negative but for whom brucellosis is suspected.
Bit-error rate for a lightwave communication system incorporating an erbium-doped fibre amplifier (1991)

The photon-number distribution at the output of an erbium-doped fibre amplifier (EDFA) with coherent light at the input is shown to obey the noncentral-negative-binomial (NNB) distribution. The use of this distribution in a binary on/off keying system gives rise to a lower bit-error rate (BER) than the Gaussian distribution, because the tails of these distributions differ (even for large mean input photon numbers).
STRING-MATCHING AND OTHER PRODUCTS (1974)

The string-matching problem considered here is to find all occurrences of a given pattern as a substring of another longer string. When the pattern is simply a given string of symbols, there is an algorithm due to Morris, Knuth and Pratt which has a running time proportional to the total length of the pattern and long string together. This time may be achieved even on a Turing machine. The more difficult case where either string may have "don't care" symbols which are deemed to match with all symbols is also considered. By exploiting the formal similarity of string-matching with integer multiplication, a new algorithm has been obtained with a running time which is only slightly worse than linear.
A 2.3-μW Capacitively Coupled Chopper-Stabilized Neural Amplifier With Input Impedance of 6.7 GΩ (2021)

Recording electrical activities through high-density electrodes using neural amplifiers plays a crucial role in the successful implementation of a data acquisition system targeting deep-brain regions. To advance the concept of high-density electrodes, neural amplifiers with not only minimum area but also high-power efficiency are needed. This letter presents a neural recording chopper amplifier using the auxiliary path and gain revision techniques to boost the input impedance to a dc value of 6.7 GΩ that meets the requirements of an implantable multichannel recording system. The front-end fabricated in 180-nm CMOS technology occupies an area of 0.051 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , and consumes a total power consumption of 2.1 μW drawn from a 1-V supply. The proposed work increases the dc input impedance ( 18×) and decreases the area by 25% in comparison with conventional auxiliary path impedance boosting with a CMRR of -75 dB, and the input-referred noise of 2.1 μV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> rms</sub> .
Polymorphism in Squaraine Dye Aggregates by Self‐Assembly Pathway Differentiation: Panchromatic Tubular Dye Nanorods versus J‐Aggregate Nanosheets (2021)

A bis(squaraine) dye equipped with alkyl and oligoethyleneglycol chains was synthesized by connecting two dicyanomethylene substituted squaraine dyes with a phenylene spacer unit. The aggregation behavior of this bis(squaraine) was investigated in non-polar toluene/tetrachloroethane (98:2) solvent mixture, which revealed competing cooperative self-assembly pathways into two supramolecular polymorphs with entirely different packing structures and UV/Vis/NIR absorption properties. The self-assembly pathway can be controlled by the cooling rate from a heated solution of the monomers. For both polymorphs, quasi-equilibrium conditions between monomers and the respective aggregates can be established to derive thermodynamic parameters and insights into the self-assembly mechanisms. AFM measurements revealed a nanosheet structure with a height of 2 nm for the thermodynamically more stable polymorph and a tubular nanorod structure with a helical pitch of 13 nm and a diameter of 5 nm for the kinetically favored polymorph. Together with wide angle X-ray scattering measurements, packing models were derived: the thermodynamic polymorph consists of brick-work type nanosheets that exhibit red-shifted absorption bands as typical for J-aggregates, while the nanorod polymorph consists of eight supramolecular polymer strands of the bis(squaraine) intertwined to form a chimney-type tubular structure. The absorption of this aggregate covers a large spectral range from 550 to 875 nm, which cannot be rationalized by the conventional exciton theory. By applying the Essential States Model and considering intermolecular charge transfer, the aggregate spectrum was adequately reproduced, revealing that the broad absorption spectrum is due to pronounced donor-acceptor overlap within the bis(squaraine) nanorods. The latter is also responsible for the pronounced bathochromic shift observed for the nanosheet structure as a result of the slip-stacked arranged squaraine chromophores.
Selective light-induced desorption: The mechanism of photoalignment of liquid crystals at adsorbing solid surfaces (2006)

We demonstrate experimentally that bare solid surfaces with adsorbed organic molecules can orient liquid crystals after UV light irradiation. The detailed structure and behavior of the surface-adsorbed molecules are not important to the effect: just their UV light absorption should depend on their orientation. The only requirement to the solid substrates is their transparency to the UV light. The universal reason for the photoinduced anisotropy in such systems is that photons clean from the surface those molecules that absorb them most intensively. This is a kind of light rubbing resulting in the anisotropic ablation of the adsorbed material.
Analysis of Lipids in Caveolae (2003)

Caveolae are small invaginated microdomains located on the surface of many cells that form in part through the oligomerization of a rather unusual protein called caveolin (1,2). Caveolin appears to be embedded only partially in the lipid membrane with its N- and C-terminals exposed to the cytoplasm (3). Caveolin can form large homooligomeric spherical structures in solution and interacts with a variety of lipids and lipid-anchored proteins (4–6). Caveolae are rich in certain lipid-anchored proteins, such as nonreceptor tyrosine kinases and endothelial nitric oxide synthase (7,8), as well as lipids, such as, sphingomyelin, phosphoinositides and gangliosides, GM1 (7,9). Many of these same molecules have also been detected in various cell types in isolated Triton-insoluble membranes (10–13), which contain caveolae as well as various other membrane microdomains including those rich in GPI-anchored proteins or cytoskeletal elements (14). Interestingly, caveolae appear capable of discriminating between lipid-anchored proteins by excluding many GPI-anchored proteins under normal, nonperturbed conditions (14). However, after clustering induced by molecules that crosslink GPI-anchored proteins, they may enter caveolae to be internalized (15,16). The unusual lipid composition of caveolae may result not only from the presence of caveolin, which may act as a scaffolding protein for various signaling molecules (6), but also the inherent properties of these lipids that can self-associate and cluster into microdomains, thereby, creating a local environment that is distinct from the remaining membrane.