gebhart/patrepeval huggingface dataset:
Rapid design and fielding of four diagnostic technologies in Sierra Leone, Thailand, Peru, and Australia: Successes and challenges faced introducing these biosensors (2018)

Febrile illnesses are among the most common reasons for visits to hospitals and clinics worldwide. Since fevers can arise from a wide range of diseases, identifying the causative pathogen is essential not only for effective personal treatment but also for early detection of outbreaks. The Defense Threat Reduction Agency (DTRA) tasked a coalition of commercial, academic, and government researchers with moving diagnostic technology concepts from ideation to field use as rapidly as possible using scientifically sound evaluations. DTRA's 24 Month Challenge program examined >30 technologies before fielding four technologies on four continents. >10,000 in field test results were recorded. Here we discuss our tiered evaluation system to assess candidate technologies developed by commercial partners and the process of field testing those technologies at various front-line clinics in Sierra Leone, Thailand, Peru, and Australia. We discuss successes and challenges for introducing two multiplexed lateral flow immunoassay (LFI) tests that detect malaria, dengue fever, melioidosis, and the plague. Additionally we discuss the use of a LFI reader that assisted the interpretation of the assay, communicated results to a data cloud, and greatly facilitated reach-back support. Lastly, we discuss the concurrent field testing of a multiplexed PCR assay on the FilmArray platform, which had an assay pouch specially designed for the 24 Month Challenge. Either standard-of-care or gold-standard testing were run alongside our fielded technologies to benchmark their performance.
Structure–electrical property study of anisotropic polyaniline films (2003)

Abstract The relationships of the structure and electrical properties of anisotropic HCl‐doped polyaniline (PANI) films cast from N,N ′‐dimethylpropylene urea (DMPU) solutions and stretched to different draw ratios were studied. The anisotropic structure of the stretched PANI films was examined by X‐ray diffraction, near‐infrared wave‐guide coupling, and polarized infrared measurements. The PANI emeraldine base (EB) films cast from DMPU solutions had a single‐phase noncrystalline structure, and stretching of the films did not cause crystallization to occur. The transition moment angles of two weakly absorbing infrared bands were determined, and the Hermans' orientation functions for the PANI EB films were calculated. The PANI films were then doped with HCl, and the electrical properties were determined by impedance spectroscopy. With a specially designed test fixture, the in‐plane and through‐plane impedance was obtained. The conductivity along the stretch direction increased with orientation. The in‐plane conductivity was significantly higher than the through‐plane conductivity. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 823–841, 2003
A Comparison Between Conversion Of Pericarp And Endosperm Fiber From Corn Into Ethanol (2004)

A modified dry grind corn process has been developed that allows recovery of bothpericarp and endosperm fiber as coproducts at the front end of the process, prior to fermentation.The modified process is called enzymatic milling (E-Mill) dry grind process. In a conventional dry grind corn process, only the starch component of corn kernel is converted into ethanol. Additionalethanol can be produced from corn if fiber component can also be converted into ethanol. In thisstudy, pericarp and endosperm fiber recovered in E-Mill dry grind process were evaluated as apotential ethanol feedstock. Both fractions were tested for their fermentability and potential ethanolyield. Total ethanol yield recovered from corn by fermenting starch, pericarp fiber and endospermfiber was also determined.<br><br>Results show that ethanol produced in g/100 g of fiber processed was 20% more for fine fibercompared to the coarse fiber. Total ethanol yield obtained by fermenting starch and both fiberfractions was 2.84 gal/bushel compared to ethanol yield of 2.58 gal/bushel obtained by fermentingstarch only.
Design, synthesis and biological evaluation of imidazopyridine–propenone conjugates as potent tubulin inhibitors (2017)

A library of imidazopyridine-propenone conjugates (<b>8a-8u</b>) were synthesized and evaluated for their antitumor activity against four human cancer cell lines, namely, prostate (DU-145), lung (A549), cervical (Hela) and breast (MCF-7) cancer cell lines. These conjugates showed good to moderate activity against the tested cell lines. Among them, two conjugates (<b>8m</b> and <b>8q</b>) showed significant antiproliferative activity against the human lung cancer cell line (A549) with IC<sub>50</sub> values of 0.86 μM and 0.93 μM, respectively. Flow cytometry analysis revealed that these compounds arrested the cell cycle at the G<sub>2</sub>/M phase in the human lung cancer cell line (A549), inhibiting tubulin polymerization leading to apoptosis. Further, Hoechst staining, decrease in mitochondrial membrane potential and Annexin V-FITC assay suggested that the cell death was due to apoptosis induction. Overall, the present investigation demonstrated that the synthesized imidazopyridine-propenone conjugates are promising tubulin inhibitors and apoptotic inducers.
Evidence for localized Si-donor state and its metastable properties in AlGaN (1999)

Transport studies of AlxGa1−xN (0.5&amp;lt;x&amp;lt;0.6) doped with Si have been performed in the pressure range up to 1.4 GPa. For these alloys, the Si dopant forms two donor states. One of them has an effective mass character and the other one represents the localized state strongly coupled to the crystal lattice (metastable state). The localized state of Si forms the corresponding level in the gap for x exceeding 0.5. For the higher x, an increase of the activation energy of this state occurs. Metastable properties of the localized state of Si lead to a persistent photoconductivity effect and to a pressure induced freeze-out of electrons.
EURETILE D7.3 - Dynamic DAL benchmark coding, measurements on MPI version of DPSNN-STDP (distributed plastic spiking neural net) and improvements to other DAL codes (2014)

The EURETILE project required the selection and coding of a set of dedicated benchmarks. The project is about the software and hardware architecture of future many-tile distributed fault-tolerant systems. We focus on dynamic workloads characterised by heavy numerical processing requirements. The ambition is to identify common techniques that could be applied to both the Embedded Systems and HPC domains. This document is the first public deliverable of Work Package 7: Challenging Tiled Applications.
Sparsity Controlled Random Multiple Access With Compressed Sensing (2014)

This paper considers random multiple access in a network where only a small portion of users have data to forward and transmit packets in each time slot because the user activity ratio is not high in practice. For this reason, the access point (AP) has to not only identify the users who transmitted but also decode the received data codewords. Exploiting the sparsity of transmitting users, Lasso, which is a well-known practical compressed sensing algorithm, is applied for efficient user identification. The compressed sensing algorithm enables the AP to handle more users than the conventional random multiple access schemes do. We develop distributed scheduling methods for maximizing the system sum throughput, and we analyze the corresponding optimal throughput for three different cases of channel knowledge, i.e., the channel state information at the transmitter (CSIT), the channel state information at the receiver (CSIR), and the imperfect channel state information at the receiver (ImCSIR). We also derive the closed-form expressions of asymptotically optimal scheduling parameters and the corresponding maximum sum throughput for each CSI assumption. The results show the effects of system parameters on the sum throughput and provide useful insights on using compressed sensing for throughput maximization in random multiple access schemes.
Enhancement technologies and physical understanding of electron mobility in III&#x2013;V n-MOSFETs with strain and MOS interface buffer engineering (2011)

In this paper, we have investigated the electron transport properties under two types of mobility enhancement engineering, which are channel strain and MOS interface buffer engineering. We have demonstrated epitaxial-based biaxially strained In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</sub> As MOSFETs. Tensile strained In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.53</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.47</sub> As MOSFETs shows high peak mobility of 2150 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs. Furthermore, we have demonstrated high performance InAs-OI(-on insulator) MOSFETs on Si substrate with MOS interface buffer layer by direct wafer bonding, showing high peak mobility of 3180 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /Vs. The scattering mechanisms for the electron mobility in thin body In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> Ga <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</sub> As(InAs)-OI MOSFETs have been systematically analyzed and identified, for the first time.
Fluoroquinolone-resistant bacteria and methicillin-resistant Staphylococci from normal preoperative conjunctiva (2008)

Journal of Cataract & Refractive Surgery 34(4):p 711-712, April 2008. | DOI: 10.1016/j.jcrs.2007.12.028
Prediction of Oral Bioavailability in Rats: Transferring Insights from in Vitro Correlations to (Deep) Machine Learning Models Using in Silico Model Outputs and Chemical Structure Parameters (2019)

Oral administration of drug products is a strict requirement in many medical indications. Therefore, bioavailability prediction models are of high importance for prioritization of compound candidates in the drug discovery process. However, oral exposure and bioavailability are difficult to predict, as they are the result of various highly complex factors and/or processes influenced by the physicochemical properties of a compound, such as solubility, lipophilicity, or charge state, as well as by interactions with the organism, for instance, metabolism or membrane permeation. In this study, we assess whether it is possible to predict intravenous (iv) or oral drug exposure and oral bioavailability in rats. As input parameters, we use (i) six experimentally determined in vitro and physicochemical endpoints, namely, membrane permeation, free fraction, metabolic stability, solubility, p<i>K</i><sub>a</sub> value, and lipophilicity; (ii) the outputs of six in silico absorption, distribution, metabolism, and excretion models trained on the same endpoints, or (iii) the chemical structure encoded as fingerprints or simplified molecular input line entry system strings. The underlying data set for the models is an unprecedented collection of almost 1900 data points with high-quality in vivo experiments performed in rats. We find that drug exposure after iv administration can be predicted similarly well using hybrid models with in vitro- or in silico-predicted endpoints as inputs, with fold change errors (FCE) of 2.28 and 2.08, respectively. The FCEs for exposure after oral administration are higher, and here, the prediction from in vitro inputs performs significantly better in comparison to in silico-based models with FCEs of 3.49 and 2.40, respectively, most probably reflecting the higher complexity of oral bioavailability. Simplifying the prediction task to a binary alert for low oral bioavailability, based only on chemical structure, we achieve accuracy and precision close to 70%.
Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants (2001)

The role of active-site residues in the dealkylation reaction in the P(S)C(S) diastereomer of 2-(3,3-dimethylbutyl)methylphosphonofluoridate (soman)-inhibited Torpedo californica acetylcholinesterase (AChE) was investigated by full-scale molecular dynamics simulations using CHARMM: >400 ps equilibration was followed by 150-200 ps production runs with the fully solvated tetracoordinate phosphonate adduct of the wild-type, Trp84Ala and Gly199Gln mutants of AChE. Parallel simulations were carried out with the tetrahedral intermediate formed between serine-200 Ogamma of AChE and acetylcholine. We found that the NepsilonH in histidine H(+)-440 is positioned to protonate the oxygen in choline and thus promote its departure. In contrast, NepsilonH in histidine H(+)-440 is not aligned for a favourable proton transfer to the pinacolyl O to promote dealkylation, but electrostatic stabilization by histidine H(+)-440 of the developing anion on the phosphonate monoester occurs. Destabilizing interactions between residues and the alkyl fragment of the inhibitor enforce methyl migration from Cbeta to Calpha concerted with C-O bond breaking in soman-inhibited AChE. Tryptophan-84, phenyalanine-331 and glutamic acid-199 are within 3.7-3.9 A (1 A=10(-10) m) from a methyl group in Cbeta, 4.5-5.1 A from Cbeta and 4.8-5.8 A from Calpha, and can better stabilize the developing carbenium ion on Cbeta than on Calpha. The Trp84Ala mutation eliminates interactions between the incipient carbenium ion and the indole ring, but also reduces its interactions with phenylalanine-331 and aspartic acid-72. Tyrosine-130 promotes dealkylation by interacting with the indole ring of tryptophan-84. Glutamic acid-443 can influence the orientation of active-site residues through tyrosine-421, tyrosine-442 and histidine-440 in soman-inhibited AChE, and thus facilitate dealkylation.
18 GHz 3 dB bandwidth SiGe resonant photodetector in 45 nm SOI CMOS (2020)

We present a SiGe resonant photodetector fabricated in commercial 45 nm SOI CMOS with a 3-dB bandwidth of 17.8 GHz, the highest reported for such devices. This is achieved by using high doping concentrations to reduce the resistance of the regions accessing the active area.
Late-Stage 18O Labeling of Primary Sulfonamides via a Degradation-Reconstruction Pathway (2020)

A late-stage 18O labeling approach of sulfonamides that employs the corresponding unlabeled molecule as the starting material was developed. Upon deamination of the sulfonamide, a sulfinate intermediate was isotopically enriched using eco-friendly reagents H218O and 15NH3(aq) to afford a M+5 isotopologue of the parent compound. This degradation-reconstruction approach afforded isolated yields of up to 96% for the stable isotope labeled (SIL) sulfonamides, and was compatible with multiple marketed therapeutics, including celecoxib, on a gram scale. The SIL products also exhibited no 18O/16O back exchange under extreme conditions, further validating the utility of this green strategy for drug labeling for both in vitro and in vivo use. This procedure was also adapted to include pharmaceutically relevant methyl sulfones by using 13CH3, affording M+5 isotopic enrichment, thereby illustrating the broad utility of this methodology.
A continuous, low-glitch, low-offset, programmable gain and bandwidth Gm-C filter (2005)

A programmable gain and bandwidth first-order low-pass Gm-C filter is proposed, designed, and simulated. Continuous low-offset operation is achieved by combining the continuity and low offset features of the ping-pong and auto-zeroing schemes. In the proposed strategy, clock feedthrough and charge injection are also reduced by decoupling the holding capacitor from the ac-signal path and increasing its value without affecting filter response. The ping-pong operation is designed to occur on the dominant pole-setting node, where a large capacitor resides, thereby also attenuating the glitches normally associated with "hand-over" events. The gain and bandwidth are programmed by adjusting the transconductance and loading resistance of the filter, achieving gain and bandwidth ranges and resolutions of 2-40 V/V, 75 mV/V, 1-5 KHz, and 32 Hz, respectively. Worst-case Monte Carlo simulations of the proposed 0.5 mum CMOS IC resulted in an input-referred offset of less than 0.5 mV and hand-over glitches below 5 mV
Verification and Calibration of Antenna Cross-Polarization Discrimination and Penetration Loss for Millimeter Wave Communications (2018)

This article presents measurement guidelines and verification procedures for antenna cross-polarization discrimination (XPD) and penetration loss measurements for millimeter wave (mmWave) channel sounder systems. These techniques are needed to ensure accurate and consistent measurements by different researchers at different frequencies and bandwidths. Measurements at 73 GHz are used to demonstrate and verify the guidelines, and show the consistency of the antenna XPD factor and the penetration loss at different transmitter-receiver (T-R) separation distances, thus providing a systematic method that may be used at any frequency for reliable field measurements.
Differential Gene Expression Patterns of EBV Infected EBNA-3A Positive and Negative Human B Lymphocytes (2009)

The genome of Epstein-Barr virus (EBV) encodes 86 proteins, but only a limited set is expressed in EBV-growth transformed B cells, termed lymphoblastoid cell lines (LCLs). These cells proliferate via the concerted action of EBV nuclear antigens (EBNAs) and latent membrane proteins (LMPs), some of which are rate limiting to establish a stable homeostasis of growth promoting and anti-apoptotic activities. We show here that EBV mutants, which lack the EBNA-3A gene, are impaired but can still initiate cell cycle entry and proliferation of primary human B cells in contrast to an EBNA-2 deficient mutant virus. Surprisingly, and in contrast to previous reports, these viral mutants are attenuated in growth transformation assays but give rise to permanently growing EBNA-3A negative B cell lines which exhibit reduced proliferation rates and elevated levels of apoptosis. Expression profiles of EBNA-3A deficient LCLs are characterized by 129 down-regulated and 167 up-regulated genes, which are significantly enriched for genes involved in apoptotic processes or cell cycle progression like the tumor suppressor gene p16/INK4A, or might contribute to essential steps of the viral life cycle in the infected host. In addition, EBNA-3A cellular target genes remarkably overlap with previously identified targets of EBNA-2. This study comprises the first genome wide expression profiles of EBNA-3A target genes generated within the complex network of viral proteins of the growth transformed B cell and permits a more detailed understanding of EBNA-3A's function and contribution to viral pathogenesis.
Dynamic and social behaviors of human pluripotent stem cells (2015)

Human pluripotent stem cells (hPSCs) can self-renew or differentiate to diverse cell types, thus providing a platform for basic and clinical applications. However, pluripotent stem cell populations are heterogeneous and functional properties at the single cell level are poorly documented leading to inefficiencies in differentiation and concerns regarding reproducibility and safety. Here, we use non-invasive time-lapse imaging to continuously examine hPSC maintenance and differentiation and to predict cell viability and fate. We document dynamic behaviors and social interactions that prospectively distinguish hPSC survival, self-renewal, and differentiation. Results highlight the molecular role of E-cadherin not only for cell-cell contact but also for clonal propagation of hPSCs. Results indicate that use of continuous time-lapse imaging can distinguish cellular heterogeneity with respect to pluripotency as well as a subset of karyotypic abnormalities whose dynamic properties were monitored.
Editorial: Cytokines and Intestinal Mucosal Immunity (2021)

EDITORIAL article Front. Immunol., 14 May 2021Sec. Cytokines and Soluble Mediators in Immunity Volume 12 - 2021 | https://doi.org/10.3389/fimmu.2021.698693
Solution-Processed Amorphous In–Zn–Sn Oxide Thin-Film Transistor Performance Improvement by Solution-Processed Y2O3Passivation (2016)

We report the effect of water-based Y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> passivation on the performances of solution-processed amorphous indium-zinc-tin oxide (a-IZTO) thin-film transistors (TFTs) employing a solution-processed ZrO <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sup> gate insulator. The Y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> passivation increases the saturation mobility (μ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sat</sub> ) and the current ratio (I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ON</sub> / <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">OFF</sub> ) from 1.64 ± 0.70 to 4.75 ± 0.87 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> V <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> s <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> and from 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sup> to 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">9</sup> , respectively, and decreases the hysteresis voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">H</sub> ), subthreshold swing, and threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) from 0.09 ± 0.09 to 0 V, from 147.44 ± 44.55 to 114.29 ± 15.06 mV/decade, and from 0.54 ± 0.21 to 0.42 ± 0.23 V, respectively. The threshold voltage shift under positive gate bias stress is also reduced from 1.78 to 0 V. The improvements can be explained by the diffusion of Y into a-IZTO. Yttrium concentration in the a-IZTO active layer is found to be ~16 at.%, which leads to the decrease in oxygen vacancy and hydroxyl group concentrations, and to the increase in M-O-M bond concentration at the a-IZTO/ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</sub> and a-IZTO/Y <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> interfaces.