gebhart/patrepeval huggingface dataset:
Heterogeneity Confounds Establishment of “a” Model Microbial Strain (2017)

<i>Aspergillus fumigatus</i> is a ubiquitous environmental mold and the leading cause of diverse human diseases ranging from allergenic bronchopulmonary aspergillosis (ABPA) to invasive pulmonary aspergillosis (IPA). Experimental investigations of the biology and virulence of this opportunistic pathogen have historically used a few type strains; however, it is increasingly observed with this fungus that heterogeneity among isolates potentially confounds the use of these reference isolates. Illustrating this point, Kowalski et al. (mBio 7:e01515-16, 2016, https://doi.org/10.1128/mBio.01515-16) demonstrated that variation in 16 environmental and clinical isolates of <i>A. fumigatus</i> correlated virulence with fitness in low oxygen, whereas Fuller et al. (mBio 7:e01517-16, 2016, https://doi.org/10.1128/mBio.01517-16) showed wide variation in light responses at a physiological and protein functionality level in 15 <i>A. fumigatus</i> isolates. In both studies, two commonly used type strains, Af293 and CEA10, displayed significant differences in physiological responses to abiotic stimuli and virulence in a murine model of IPA.
Stable Carbon Isotope Evidence for Intrinsic Bioremediation of Tetrachloroethene and Trichloroethene at Area 6, Dover Air Force Base (2000)

Area 6 at Dover Air Force Base (Dover, DE) has been the location of an in-depth study by the RTDF (Remediation Technologies Development Forum Bioremediation of Chlorinated Solvents Action Team) to evaluate the effectiveness of natural attenuation of chlorinated ethene contamination in groundwater. Compound-specific stable carbon isotope measurements for dissolved PCE and TCE in wells distributed throughout the anaerobic portion of the plume confirm that stable carbon isotope values are isotopically enriched in 13C consistent with the effects of intrinsic biodegradation. During anaerobic microbial reductive dechlorination of chlorinated hydrocarbons, the light (12C) versus heavy isotope (13C) bonds are preferentially degraded, resulting in isotopic enrichment of the residual contaminant in 13C. To our knowledge, this study is the first to provide definitive evidence for reductive dechlorination of chlorinated hydrocarbons at a field site based on the delta13C values of the primary contaminants spilled at the site, PCE and TCE. For TCE, downgradient wells show delta13C values as enriched as -18.0/1000 as compared to delta13C values for TCE in the source zone of -25.0 to -26.0/1000. The most enriched delta13C value on the site was observed at well 236, which also contains the highest concentrations of cis-DCE, VC, and ethene, the daughter products of reductive dechlorination. Stable carbon isotope signatures are used to quantify the relative extent of biodegradation between zones of the contaminant plume. On the basis of this approach, it is estimated that TCE in downgradient well 236 is more than 40% biodegraded relative to TCE in the proposed source area.
Validity Estimation of Functionally Gradient of Porous Aluminum by X-Ray CT Image Based FEM (2013)

Porous aluminum is a multifunctional material with both lightweight and high energy absorption properties. In this study, functionally graded (FG) porous aluminum was fabricated by spacer method varying pore structures. The obtained FG porous aluminum was observed non-destructively by X-ray computed tomography (CT). Image-based finite element (FE) analysis of compression tests of FG porous aluminum using X-ray CT images was conducted. By comparing the results of FE analysis and the deformation behavior of actual compressive tests of FG porous aluminum, it was shown that deformation behavior can be controlled by varying pore structures.
Ultra-rapid elimination of biofilms via the combustion of a nanoenergetic coating (2013)

This novel method of biofilm removal is currently in the early stage of development. However, it has potential to be used in offline biofilm elimination as a rapid, easy and environmentally friendly method.
A Wide-Range Mixed-Mode DLL for a Combination 512 Mb 2.0 Gb/s/pin GDDR3 and 2.5 Gb/s/pin GDDR4 SDRAM (2008)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A mixed-mode delay-locked loop (MDLL) for a 512 Mb graphics SDRAM is presented in this paper. The MDLL extends its lock range into the gigahertz realm by applying clock division and analog phase generation (APG). The divided clock from the MDLL is used for clocking logic and tracking deterministic access latency in the SDRAM. A short discussion of some of the side effects and advantages of using a divided, multi-phase clock for logic operation is presented. A low-power clock distribution network (CDN) based on the presented MDLL is also disclosed. Fabricated in a 1.5 V 95 nm triple-metal CMOS process, the MDLL achieves a measured RMS jitter of 4.6 ps and peak-to-peak jitter of 38 ps at GDDR4 mode with a 1 GHz clock. Power consumption for the entire MDLL-based CDN is 107 mW at 800 MHz and 1.5 V. </para>
Grand Rounds (2009)

Objective: The paper describes the case of a 27-year-old, right-handed woman, KF, who sustained a left thalamic ischemic infarct. KF's case is unusual in that she presented with ipsilateral hemiparesis. No similar cases were found in the existing literature. Young-Mok et al. (2005) describe two cases of ipsilateral hemiparesis following a corona radiata infarct that they attribute to re-organization of the brain following previous right-sided supratentorial stroke; however, there is no radiologic evidence of prior stroke for KF. Method: KF reported that on July 15, 2008 she had difficulty awakening and problems with vision and comprehension. Her mother noted that KF was disoriented, had slurred speech, and did not understand the seriousness of her situation. She presented to the emergency department with visual disturbance and unsteady gate. An MRI (July 15, 2008) revealed subacute left thalamic ischemic infarct. Results: Results of neuropsychologic evaluation suggest characteristic cognitive difficulties consistent with left thalamic infarct: verbal expression impairment (mildly impaired verbal abstract reasoning, mildly impaired vocabulary, borderline semantic fluency), memory deficits (visual memory mildly impaired initially and profoundly impaired following delay, word list learning severely impaired and delayed word list recall profoundly impaired), as well as exacerbation of premorbid attentional difficulties (sustained visual attention profoundly impaired). She also presented with characteristic right-hand fine motor dexterity deficits (borderline) and uncharacteristic left hemiparesis (severely impaired left hand strength and fingertip dexterity). Conclusions: KF's case offers the opportunity to discuss possible explanations for the observed deficits that are previously not described in the literature. This case allows for further understanding of the motor pathways through the thalamus.
ChemInform Abstract: Structural Basis of Protein Kinase C Activation by Tumor Promoters (1998)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comparison of Upper Limit of Vulnerability and Defibrillation Probability of Success Curves Using a Nonthoracotomy Lead System (1995)

ULV approximately equaled DF at V97. This is fortunate because it is clinically important to set the device voltage at the uppermost portion of the probability of success curve. Estimating DF V97 from ULV V97 would reduce the number of fibrillation inductions needed to establish defibrillation shock strength requirements. However, the large difference between ULV V97 and DF in a few animals indicates that further improvement and testing of algorithms for determining ULV V97 must be developed before the technique is used clinically.
Integration of MEMS phase shifters with CMOS control circuitry (2006)

A CMOS digital microcircuit, utilizing sub-micron technology, was designed for the purpose of providing integrated control circuitry to an array of high-voltage micro-electromechanical systems (MEMS) switch based phase shifter devices. The grid of MEMS phase shifters is part of a phased array antenna system. The phase of each element of the array is controlled via the CMOS microcircuit. This paper presents the design, physical layout, and the measured test results for CMOS digital control circuit that has been fabricated using the MOSIS Integrated Circuit Fabrication Service. The circuit converts serial data to parallel outputs to reduce number of control lines and lower the cost of wiring the phased array. In addition, discrete digital control circuitry for loading phase shifts into each MEMS device is presented.
Enhancement of slope efficiency and output power in GaN-based vertical-cavity surface-emitting lasers with a SiO2-buried lateral index guide (2018)

We have achieved a high output power of 6 mW from a 441 nm GaN-based vertical-cavity surface-emitting laser (VCSEL) under continuous wave (CW) operation, by reducing both the internal loss and the reflectivity of the front cavity mirror. A preliminary analysis of the internal loss revealed an enormously high transverse radiation loss in a conventional GaN-based VCSEL without lateral optical confinement (LOC). Introducing an LOC structure enhanced the slope efficiency by a factor of 4.7, with a further improvement to a factor of 6.7 upon reducing the front mirror reflectivity. The result was a slope efficiency of 0.87 W/A and an external differential quantum efficiency of 32% under pulsed operation. A flip-chip-bonded VCSEL also exhibited a high slope efficiency of 0.64 W/A and an external differential quantum efficiency of 23% for the front-side output under CW operation. The reflectivity of the cavity mirror was adjusted by varying the number of AlInN/GaN distributed Bragg reflector pairs from 46 to 42, corresponding to reflectivity values from 99.8% to 99.5%. These results demonstrate that a combination of internal loss reduction and cavity mirror control is a very effective way of obtaining a high output GaN-based VCSEL.
Role of Gallium Doping in Dramatically Lowering Amorphous‐Oxide Processing Temperatures for Solution‐Derived Indium Zinc Oxide Thin‐Film Transistors (2009)

Ga doping in indium zinc oxide (IZO)-based amorphous-oxide semiconductors (AOSs) promotes the formation of oxide-lattice structures with oxygen vacancies at low annealing temperatures, which is essential for acceptable thin-film-transistor performance (see figure). The mobility dependence on annealing temperature and AOS composition are analyzed and the chemical role of Ga is clarified, as required for solution-processed, low-temperature-annealed AOSs. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Type I and Type II mechanisms of antimicrobial photodynamic therapy: An in vitro study on gram‐negative and gram‐positive bacteria (2012)

Azidyl radicals may be formed from NaN(3) and HO(.). It may be that Gram-negative bacteria are more susceptible to HO(.) while Gram-positive bacteria are more susceptible to (1) O(2). The differences in NaN(3) inhibition may reflect differences in the extent of PS binding to bacteria (microenvironment) or differences in penetration of NaN(3) into cell walls of bacteria.
Comparison Of Techniques For Gate Oxide Damage Measurements (1997)

A comparison of oxide charging damage measurements is made. Gate leakage, threshold voltage and total charge-tobreakdown techniques are described in detail including measurement issues and results. Each technique is proven to be valuable in exposing latent oxide damage. Deeper understanding of the trapping nature of the oxide is achieved. Correlations between each technique are made.
ChemInform Abstract: STUDIES OF HETEROCYCLIC COMPOUNDS. PART 22. REACTIONS OF 1,6‐DIOXA‐6AΛ4‐THIAPENTALENES (1977)

Abstract Aus der Titelverbindung (I) entstehen bei Bromierung, Jodierung, Tritylierung bzw. Acetoxymercurierung 3‐mono‐ oder 3,4‐disubstituierte Produkte (II)‐(V) (die Bildung von (IIIa) oder (IIIb) hängt von den verwendeten Mengen von Substrat und Reagenz ab).
Harnessing Human Dendritic Cell Subsets to Design Novel Vaccines (2009)

Dendritic cells (DCs) orchestrate a repertoire of immune responses that endow resistance to infection and tolerance to self. DC plasticity and subsets are prominent determinants of the quality of elicited immune responses. Different DC subsets display different receptors and surface molecules and express different sets of cytokines/chemokines, all of which lead to distinct immunological outcomes. Recent findings on human DC subsets and their functional specialization have provided insights for the design of novel human vaccines.
Temperature-Regulated Microcolony Formation byBurkholderia pseudomalleiRequirespilAand Enhances Association with Cultured Human Cells (2006)

Burkholderia pseudomallei is the causative agent of melioidosis, a potentially fatal disease that is endemic to Northern Australia and Southeast Asia and is acquired from soil or water. Adherence of B. pseudomallei 08 to cultured cells increases dramatically following prior growth at 30 degrees C or less compared to that following prior growth at 37 degrees C. Here, we show that this occurs almost entirely as the result of microcolony formation (bacterium-bacterium interactions) following growth at 27 degrees C but not at 37 degrees C, which considerably enhances bacterial association with eukaryotic cells. Further, we demonstrate that the type IVA pilin-encoding gene, pilA, is essential for microcolony development by B. pseudomallei 08, and thus optimum association with eukaryotic cells, but is not required for direct adherence (bacterium-cell interactions). In contrast, although the B. pseudomallei genome sequence strain, K96243, also contains transcriptionally active pilA, microcolony formation rarely occurs following growth at either 27 degrees C or 37 degrees C and cell association occurs significantly less than with strain 08. Analysis of pilA transcription in 08 identified that pilA is dramatically upregulated under microcolony-forming conditions, viz., growth at low temperature, and association with eukaryotic cells; the pattern of transcription of pilA in K96243 differed from that in 08. Our study also suggests that biofilm formation by B. pseudomallei 08 and K96243 on polyvinylchloride is not mediated by pilA. Adherence and microcolony formation, and pilA transcription, vary between strains, consistent with known genomic variation in B. pseudomallei, and these phenotypes may be relevant to colonization from the environment.
Trilevel‐Structured Superhydrophobic Pillar Arrays with Tunable Optical Functions (2014)

Water‐repelling surfaces inspired by lotus leaves have been developed for their commercial needs in superhydrophobic and self‐cleaning coatings on glasses and windows. The extraordinary properties originate from their multiscale structures with waxy materials. To obtain high transparency as well as superhydrophobicity, microhair arrays are designed with large spacing to reduce optical scattering effects caused by microstructures, but with a trilevel hierarchical structure to compensate for the loss of superhydrophobicity. In this study, a soft molding technique on wet pastes consisting of nanoparticles (NPs) is proposed to create a multilevel hierarchical structure of sub‐100 nm nanoparticles, which demonstrates excellent water repellency. Additionally, full advantage is taken of the TiO 2 NP mesoporous structure for UV protection and for its ability to attach to various kinds of functional (for example, photoresponsive) dyes. Furthermore, the stability of fluorinated surfaces against UV light is enhanced by the passivation of the TiO 2 surface with a thin silica coating.
Bit error rate of free-space optical communication systems through exponentiated Weibull turbulent channels: impact of atmospheric aerosol induced warming (2021)

Wavefront distortion of data-carrying laser beam propagating through the atmosphere has been reported to have detrimental effects on the performance of Free-Space Optical (FSO) communication systems. Optical intensity fluctuation models generally assume clear air optical turbulence where atmospheric aerosols warming effects are neglected. This variation of the refractive index structure parameter (C<sub>n</sub><sup>2</sup>) of the atmosphere due to the aerosol induced warming and its influence on Bit Error Rate (BER) performance of FSO systems are studied in this paper using high-resolution radiosonde and multi-satellite observations of aerosols and atmospheric thermodynamics. Based on an approximate mathematical expression built on Gauss-Laguerre quadrature rule, and a radiative transfer model-based analysis, the BER of a Differential Phase Shift Keying (DPSK) FSO communication link through Exponentiated Weibull modelled turbulence with aperture averaging has been investigated. Our results show significant signal deterioration with the aerosol-induced turbulence taking a toll on the signal to noise ratio (SNR) over more than 15 dB. BER analysis under different receiver aperture dimensions is performed with the selected intensity fluctuation model. We show that aperture averaging does not have significant influence on the performance enhancement under aerosol perturbed atmospheric conditions.
Nearfield Hydrophone Driven 3D Source Designature and Deghosting for Multi-Level Source Data (2015)

Summary Combined with recent receiver deghosting strategies, the use of multi-level sources can provide further uplift to the ever broadening bandwidth of seismic data. While multi-level sources help mitigate source notches in the output spectrum, the resulting emitted wavelet still exhibits residual ghosts, directivity, and bubble energy which must be handled in processing. We highlight the compatibility of Ziolkowski’s notional source method with multi-level source acquisition. We continue by showing how the directional signatures may be used for 3D directional designature and deghosting on shallow water towed streamer data. The results show a significant improvement in the level of ringing relating to source wavelet directivity effects.
Equivalent Quasi-Static Estimation of Dynamic Penetration Force for Near Surface Soil Characterization (2011)

This paper describes the application of maximum log-likelihood estimation to estimate the average force during a dynamic penetration. It is used to obtain a quasi- static equivalent of the dynamic force in Rapid Soil Characterization System (RapSochs). The force is measured at the tip and friction sleeve by strain gauges during hammer blows. The results are necessary for any analyses similar to Cone Penetration Test (CPT) data analysis. This method is proven to result in an acceptable estimation of the force (the soil resistance) in different soil types. It is shown that the cone resistance, friction resistance and friction ratio similar to CPT can be obtained and these are plotted versus depth. It is also shown that the estimated soil resistance does not depend on the applied energy and variable hammer drop height.
Return to Sport after Coracoid Bone Block Transfer for Shoulder Instability: A Systematic Review (2019)

Coracoid bone block transfer allows for a high rate of return to sport, although the rate of return to sport at athletes' pre-operative level is lower. The rate of return to sport after Latarjet procedure is higher in comparison with Bankart repair. Additionally, coracoid bone block transfer is associated with improvements in a number of clinical outcome measures. Common post-operative complications include non-union between bone block and glenoid, hematoma, and infection.
Highly Efficient Hydrotalcite/1-Butanol Catalytic System for the Production of the High-Yield Fructose Crystal from Glucose (2019)

Catalytic isomerization of glucose to fructose is a key step for the synthesis of bioplastics and biofuels as well as sweeteners. In this study, a record fructose yield of greater than 50% with selectivity exceeding 80% was obtained from glucose concentration of 10 wt % by adopting a 1-butanol/hydrotalcite catalytic system. In this novel process, Mg2+ leaching from hydrotalcite, which is an important issue when utilizing hydrotalcite for glucose isomerization in aqueous solution, was negligible during the reaction. NMR study confirmed that the absence of deuterium at the C-1 position of the fructose product as well as C-2 position of glucose-2-d clearly supports the base-catalyzed deprotonation of the C-2 position in glucose. Also, density functional theory (DFT) calculations supported the selective formation of fructose from glucose over hydrotalcite surface in 1-butanol than other solvents. Notably, after glucose isomerization, the highly pure glucose (91%) and fructose crystals (95%) were recovered easily from 1-butanol solvent by subsequent cooling and filtration without requiring chromatographic separation. Therefore, the hydrotalcite/1-butanol catalytic system is simple, inexpensive, and a green process for the high-yield fructose production from glucose when compared with current industrial procedures that rely on enzymatic isomerization reactions and chromatographic separations.
4G LTE Network Data Collection and Analysis along Public Transportation Routes (2020)

With the advancements in wireless network technologies over the past few decades and the deployment of 4G LTE networks, the capabilities and services provided to end-users have become seemingly endless. Users of smartphones utilize high-speed network services while commuting on public transit and hope to have a consistent, high-quality connection for the duration of their trip. Due to the massive load demand on cellular networks and frequent changes in the underlying radio channel, users often experience sudden unexpected variations in the connection quality. To overcome such variations and maintain a consistent connection, these variations need to be predicted before they occur. This can be accomplished by the spatio-temporal analysis of the different network quality parameters and the investigation of the main factors that affect the network's performance and QoS. To this end, we conducted a network survey via Kingston Transit in Kingston, Ontario, Canada. We used the Android network monitoring application G-NetTrack Pro to build a dataset of various client-side wireless network quality parameters. The dataset consists of 30 repeated public transit bus trips at three different times of the day, each lasting around one hour. In this paper, we describe the data collection process, present an analysis of the collected data, and investigate the effects of time and location on the network's measured throughput and signal strength. We made the collected data, including more than 190 thousand unique records, publicly available to researchers in a domain where open data is rare.