gebhart/patrepeval huggingface dataset:
Integrated Flue Gas Purification and Latent Heat Recovery for Pressurized Oxy-Combustion (Final Scientific/Technical Report) (2019)

Pressurized oxy-combustion has been identified by DOE as a transformational technology for coal power with carbon capture due to the advantages that are realized when the combustion process is pressurized. The staged pressurized oxy-combustion (SPOC) process is particularly attractive as the efficiency of the process is almost 6 percentage points greater than that of first generation oxy-combustion. A critical component of the SPOC process, and potentially other pressurized combustion processes, is the Direct Contact Cooler (DCC) where the latent heat of the flue gas moisture is recovery to improve plant efficiency while simultaneously removing SOx and NOx from the flue gas, so that the FGD and de-NOx processes can be eliminated, and the cost of electricity minimized. The objective of this R&D effort was to advance the TRL of the DCC technology, which included performance testing at a 100 kW scale to validate the process and obtain key engineering data for scale-up. A collateral objective was to study the gas- and liquid-phase kinetics, and the development of a systematic chemical mechanism validated by experimental data. Experiments in a bench-scale stirred reactor provided an updated understanding of the liquid chemistry and the effects of temperature and pH. This information was used to develop a reduced reaction mechanism, which was subsequently incorporated in an ASPENbased process model, to allow for evaluation of the DCC at full scale. A small-pilot DCC column was designed, constructed and tested using simulated flue gas at the pressurized oxy-combustion test facility at Washington University in St. Louis. In the majority of tests, the SO2 capture approached 100%, making the NOx capture the primary metric of capture efficiency. An NOx capture efficiency of 90% was achieved when the gas residence time was 95 seconds, demonstrating that high capture rates can be attained with reasonable reactor size. At higher temperatures (up to 200°C inlet gas temperature) the total NOx scrubbing efficiency was reduced by approximately 10% (compared to room temp.) and this was attributed to a reduced NO oxidation rate. A significant amount of SO2 was present in the gas outlet (10%) only when the temperature was high and the N:S ratio was low (N/S < 1), which highlights the necessity of controlling the NOx concentration in the flue gas for complete sulfur scrubbing. After incorporated our optimized chemical mechanism into an ASPEN process model, various full-scale configurations of the DCC were evaluate, and the results indicate that the proposed DCC can accomplish its intended goals at full scale and at a modest size. Thus, the results of this project indicate that the DCC is a promising technology for recovery of the latent heat of the moisture in the flue gas while simultaneously scrubbing the nitrogen and sulfur oxides, thus enabling pressurized oxy-combustion, in general, and the SPOC process, in particular.
Biodegradation of the Hexahydro-1,3,5-Trinitro-1,3,5-Triazine Ring Cleavage Product 4-Nitro-2,4-Diazabutanal by Phanerochaete chrysosporium (2004)

Initial denitration of hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) by Rhodococcus sp. strain DN22 produces CO2 and the dead-end product 4-nitro-2,4-diazabutanal (NDAB), OHCNHCH2NHNO2, in high yield. Here we describe experiments to determine the biodegradability of NDAB in liquid culture and soils containing Phanerochaete chrysosporium. A soil sample taken from an ammunition plant contained RDX (342 micromol kg(-1)), HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine; 3,057 micromol kg(-1)), MNX (hexahydro-1-nitroso-3,5-dinitro-1,3,5-triazine; 155 micromol kg(-1)), and traces of NDAB (3.8 micromol kg(-1)). The detection of the last in real soil provided the first experimental evidence for the occurrence of natural attenuation that involved ring cleavage of RDX. When we incubated the soil with strain DN22, both RDX and MNX (but not HMX) degraded and produced NDAB (388 +/- 22 micromol kg(-1)) in 5 days. Subsequent incubation of the soil with the fungus led to the removal of NDAB, with the liberation of nitrous oxide (N2O). In cultures with the fungus alone NDAB degraded to give a stoichiometric amount of N2O. To determine C stoichiometry, we first generated [14C]NDAB in situ by incubating [14C]RDX with strain DN22, followed by incubation with the fungus. The production of 14CO2 increased from 30 (DN22 only) to 76% (fungus). Experiments with pure enzymes revealed that manganese-dependent peroxidase rather than lignin peroxidase was responsible for NDAB degradation. The detection of NDAB in contaminated soil and its effective mineralization by the fungus P. chrysosporium may constitute the basis for the development of bioremediation technologies.
A chromosome-length genome assembly and annotation of blackberry ( Rubus argutus , cv. ‘Hillquist’) (2022)

Abstract Background Blackberries ( Rubus spp.) are the fourth most economically important berry crop worldwide. Genome assemblies and annotations have been developed for Rubus species in subgenus Idaeobatus , including black raspberry ( R. occidentalis ), red raspberry ( R. idaeus ), and R. chingii , but very few genomic resources exist for blackberries and their relatives in subgenus Rubus . Findings Here we present a chromosome-length assembly and annotation of the diploid blackberry germplasm accession ‘Hillquist’ ( R. argutus ). ‘Hillquist’ is the only known source of primocane-fruiting (annual-fruiting) in tetraploid fresh-market blackberry breeding programs and is represented in the pedigree of many important cultivars worldwide. The ‘Hillquist’ assembly, generated using PacBio long reads scaffolded with Hi-C sequencing, consisted of 298 Mb, of which 270 Mb (90%) was placed on seven chromosome-length scaffolds with an average length of 38.6 Mb. Approximately 52.8% of the genome was composed of repetitive elements. The genome sequence was highly collinear with a novel maternal haplotype-resolved linkage map of the tetraploid blackberry selection A-2551TN and genome assemblies of R. chingii and red raspberry. A total of 38,503 protein-coding genes were predicted using the assembly and Iso-Seq and RNA-seq data, of which 72% were functionally annotated. Conclusions The utility of the ‘Hillquist’ genome has been demonstrated here by the development of the first genotyping-by-sequencing based linkage map of tetraploid blackberry and the identification of several possible candidate genes for primocane-fruiting within the previously mapped locus. This chromosome-length assembly will facilitate future studies in Rubus biology, genetics, and genomics and strengthen applied breeding programs.
Physicochemical Property Correlations with Ionization Efficiency in Capillary Vibrating Sharp-Edge Spray Ionization (cVSSI) (2020)

The relative contributions to ionization efficiency by three molecular chemical properties have been examined for field-free and field-enabled capillary vibrating sharp-edge spray ionization (cVSSI) using mass spectrometry (MS) analysis. Ion intensities have been recorded for model compounds under each operational ionization mode as well as for aqueous and nonaqueous (methanol) solvent systems. Multiple regression analysis suggests that for field-free cVSSI, ion intensity is mostly associated with the log of the base dissociation constant (p<i>K</i><sub>b</sub>) and proton affinity (PA) for both aqueous and methanol solutions. Comparatively, for field-enabled cVSSI using aqueous solutions, the dominant factor correlated with ion intensity is the log of the partition coefficient (log <i>P</i>). To a lesser degree, this is observed for methanol solutions as well. For ESI, p<i>K</i><sub>b</sub> is the dominant factor associated with ion signal levels from methanol and aqueous solutions. These results are supported by studies conducted on two different mass spectrometers employing different cVSSI emitter tips. The relationship of ion intensity and p<i>K</i><sub>b</sub> in ESI is supported by multiple studies; however, the shift to other chemical properties with the addition of cVSSI suggests the possibility that a different (or combinations of) ionization mechanism(s) may be operative for these ionization modes. These results are briefly considered in light of the different ESI mechanisms.
Temperature dependence of optical properties of GaAs (1991)

Pseudodielectric functions 〈ε〉=〈ε1〉+i〈ε2〉 of GaAs were measured by spectroscopic ellipsometry (SE), in the range of 1.6–4.45 eV, at temperatures from room temperature (RT) to ∼610 °C. A very clean, smooth surface was obtained by first growing an epitaxial layer of GaAs on a GaAs substrate and immediately capping it with a protective layer of arsenic. The cap prevented surface oxidation during transport to the measurement chamber, where it was evaporated under ultrahigh vacuum at ∼350 °C. Room-temperature SE results from this surface are in good agreement with those in the literature obtained by wet-chemical etching. A quantitative analysis of the 〈ε〉 spectrum was made using the harmonic-oscillator approximation (HOA). It is shown by the HOA that the E1 and E1+Δ1 energy-band critical points shift downward ∼300 meV as temperature increases from RT to ∼610 °C. An algorithm was developed, using the measured optical constants at a number of fixed temperatures, to compute the dielectric function spectrum at an arbitrary temperature in the range of 22–610 °C. Therefore, the ellipsometer can be utilized as an optical thermometer to determine the sample surface temperature.
In vitro and in vivo studies on the effects of the alpha‐adrenoceptor blocker IP/66 (1‐(2‐ethoxy‐2‐(3′ ‐pyridyl)ethyl)‐4‐(2′‐methoxy‐phenyl)piperazine) on urethral tone in rats (1991)

Abstract IP/66 (1‐(2‐ethoxy‐2‐(3′‐pyridyl)ethyl)‐4‐(2′‐methoxy‐phenyl))piperazine is a newly synthetized and stereoselective alpha‐adrenoceptor blocking drug. This compound exhibits preferential blocking activity in postjunctional as compared to prejunctional alpha‐adrenergic responses. Furthermore, IP/66 inhibits phenylephrine‐induced motor response in human and rat prostatic tissue and phenylephrine‐, DMPP‐ and EFS‐induced motor responses in rat urethral tissues, being equieffective or even more potent than prazosin. Like prazosin, intravenous administration of IP/66, at doses at which no hypotensive effect is observed, induces a marked inhibition of phenylephrine or DMPP‐induced increase in urethral perfusion pressure, in anaesthetized pithed rats. Finally, IP/66 administration exerts beneficial effects in animals with surgically‐ or pharmacologically‐induced urethral outflow obstruction. As a whole, the pharmacodynamic profile of IP/66 is promising and this drug might be proposed for clinical setting evaluating its efficacy for the treatment of lower urinary tract dysfunctions.
Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative (2022)

Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
Photonic crystal lasers: fabrication with AI-assisted technology and application to LiDAR system (2021)

We report on photonic crystal lasers (PCSELs) with high power and high beam quality. The PCSELs have been developed with AI-assisted technologies. The developed devices with a 500µm diameter successfully oscillated with a high, 10W-class peak output power and a very narrow divergence angle of 0.1°. This fact indicates that the devices operate in a complete single lateral and longitudinal mode even over the large area of 500µm diameter. The devices have been installed in time-of-flight LiDAR system. Very high-resolution operation has been successfully realized even though a lens system is not utilized, clearly demonstrating the advantage of high-brightness PCSELs.
PTU-118 A diagnostic accuracy meta-analysis of endoanal ultrasound and MRI for perianal fistula assessment (2012)

Introduction Imaging modalities such as endoanal ultrasound or MRI can be useful preoperative adjuncts prior to the appropriate surgical intervention for perianal fistulas. We present a systematic review of published literature comparing endoanal ultrasound with MRI for the assessment of idiopathic and Crohn's perianal fistulas. Methods A meta-analysis was performed to obtain pooled values for specificity and sensitivity. Electronic databases were searched from January 1970 to October 2010 for published studies. Results Four studies were used in our analysis. There were 241 fistulas in the ultrasound group and 240 in the magnetic resonance group. The combined sensitivity and specificity of magnetic resonance for fistula detection were 0.87 (95% CI 0.63 to 0.96) and 0.69 (95% CI 0.51 to 0.82). There was a high degree of heterogeneity between studies reporting on MRI sensitivity (df=3, I 2 =93%). This compares to a sensitivity and specificity for endoanal ultrasound of 0.87 (95% CI 0.70 to 0.95) and 0.43 (95% CI 0.21 to 0.69) respectively. There was a high degree of heterogeneity between studies reporting on EAUS sensitivity (df=3, I 2 =92%). Conclusion From the available literature, the summarised performance characteristics for MRI and EAUS demonstrate comparable sensitivities at detecting perianal fistulas, although the specificity for MRI was higher than that for EAUS. Both specificity values are however considered to be diagnostically poor. The high degree of data heterogeneity and the shortage of applicable studies precludes any firm conclusions being made for clinical practice. Future trials with improved study design (including prospective data collection and consideration of verification bias) may help to further clarify the role of MRI in the assessment and treatment response monitoring of perianal fistulas (particularly in patients with Crohn's disease). Competing interests None declared.
Fused silica contamination layer removal using magnetic field‐assisted finishing (2020)

Abstract Fused silica optics used in lasing systems requires a high laser‐induced damage resistance. Processes typically used to polish fused silica lenses induce subsurface and surface damage that collect ceria abrasive, creating a layer of contamination. The contamination can be a precursor to laser damage during use. A preliminary study showed the feasibility of magnetic field‐assisted finishing (MAF) for polishing fused silica and suggested possible beneficial effects of the MAF‐polished surface on the laser‐induced damage threshold (LIDT). This paper proposes a method to examine the fundamental polishing characteristics of MAF for fused silica. Using the proposed method, this paper explores the material removal characteristics of the MAF process and improves the understanding of the MAF polishing mechanism. The 45% improvement of LIDT shows the efficacy of MAF for removing the contamination layer of fused silica surfaces with minimal changes in the surface roughness.
Development of a microfabricated cytometry platform for characterization and sorting of individual leukocytes (2004)

Organizing leukocytes into high-density arrays makes these cells amenable to rapid optical characterization and subsequent sorting, pointing to clinical and basic science applications. The present paper describes development of a cytometry platform for creating high-density leukocyte arrays and demonstrates retrieval of single cells from the array. Poly(ethylene glycol)(PEG) photolithography was employed to fabricate arrays of microwells composed of PEG hydrogel walls and glass attachment pads 20 microm x 20 microm and 15 microm x 15 microm in size. PEG micropatterned glass surfaces were further modified with cell-adhesive ligands, poly-L-lysine, anti-CD5 and anti-CD19 antibodies, in order to engineer specific cell-surface interactions within the individual wells. Localization of the fluorescently-labeled proteins in the glass attachment pads of PEG microwells was visualized by fluorescence microscopy. Glass slides micropatterned with PEG and cell-adhesive ligands were exposed to T-lymphocytes for 30 min. These anchorage-independent cells became selectively captured in the ligand-modified microwells forming high-density cell arrays. Cell occupancy in the microwells was found to be antibody-dependent, reaching 94.6 +/- 2.3% for microwells decorated with T-cell specific anti-CD5 antibodies. Laser capture microdissection (LCM) was investigated as a method for sorting cells from the array and retrieval of single selected cells was demonstrated.
Virtual enterprises: building blocks for dynamic e-business (2001)

Dynamic e-business, as envisioned by several industry analysts and corporate leaders, involves the rapid teaming of companies with both familiar and new business partners in pursuit of specific market opportunities. For realizing this new generation business model, the ability to form, operate, and disband virtual enterprises will be the single-most important requirement. These short-lived, opportunity-based organizations leverage the individual capabilities of several member companies to form virtual enterprises that have resources equivalent to a traditional vertically integrated corporation. Before successfully applying this business model, however, several issues need to be resolved, such as building trust and a collaborative attitude amongst member companies, developing the e-commerce infrastructure for handling engineered-to-order products and services, building optimal coalitions for the job, etc. This paper discusses our experiences in developing a web-based infrastructure for creating, operating, and eventually dissolving virtual enterprises. The primary operators of this infrastructure will be market makers offering custom products and services in various industries as well as corporations involved in bringing new products to the market.
COVID-19: a challenge for oncology services (2020)

ou non, manant des tablissements d'enseignement et de recherche franais ou trangers, des laboratoires publics ou privs.
Langmuir−Blodgett Mono- and Multilayers of Rodlike Oligo(cyclohexylidene) Derivatives Bearing an Oxime Headgroup (1996)

The Langmuir film-forming properties of rodlike oligo(cyclohexylidene) oximes and derivatives 1(n)−8 have been studied. It is shown that subtle structural modifications of their hydrocarbon framework, such as end-functionalization by a tert-butyl group or an n-alkyl group or (selective) hydrogenation of double bonds, markedly affect their propensity toward Langmuir monolayer formation and in particular monolayer film stability. Mean molecular areas (π−A isotherms) show that the oximes orient nearly perpendicular on the air−water interface. Film transfer of 5(2) onto moderately hydrophilic silicon (100) wafers gave predominantly Z-type deposition; for a monolayer a tilt angle of 26° was derived (atomic force microscopy). The quantitative elemental composition of a transferred multilayer assembly of 5(2) was determined using elastic recoil detection.
DNA Ligases (1989)

DNA ligases catalyze the formation of phosphodiester bonds between juxtaposed 5' phosphate and a 3'-hydroxyl terminus in duplex DNA. This activity can repair single-stranded nicks in duplex DNA and join duplex DNA restriction fragments having either blunt ends or homologous cohesive ends. Two ligases are used for nucleic acid research and their reaction conditions and applications are described in this unit: E. coli ligase and T4 ligase. These enzymes differ in two important properties. One is the source of energy: T4 ligase uses ATP, while E. coli ligase uses NAD. Another important difference is their ability to ligate blunt ends; under normal reaction conditions, only T4 DNA ligase will ligate blunt ends.
Privacy-Preserving Ridge Regression on Hundreds of Millions of Records (2013)

Ridge regression is an algorithm that takes as input a large number of data points and finds the best-fit linear curve through these points. The algorithm is a building block for many machine-learning operations. We present a system for privacy-preserving ridge regression. The system outputs the best-fit curve in the clear, but exposes no other information about the input data. Our approach combines both homomorphic encryption and Yao garbled circuits, where each is used in a different part of the algorithm to obtain the best performance. We implement the complete system and experiment with it on real data-sets, and show that it significantly outperforms pure implementations based only on homomorphic encryption or Yao circuits.
Carbon-Based Liner for RESET Current Reduction in Self-Heating Phase- Change Memory Cells (2020)

The use of carbon-based (C-based) liners is investigated for RESET current reduction in self-heating, pillar-shaped phase-change memory (PCM) cells for storage class memory (SCM) technologies. The liner is inserted between the top electrode and the phase-change layer. A finite element analysis (FEA) is done to simulate the effect of this liner on the RESET current, using the melting current as a proxy. From this FEA, we see that the high resistance of the C-based liner increases the heat generation at the interface with the phase-change layer, changing the cell from being solely self-heated by the phase-change layer to a combination of the phase-change layer's self-heating and heating from the C-based liner. The simulation results are validated against experimental results from fabricated pillar cells. We show the liner reduces the melting current of the pillar cell by 60%. The effect of the thickness of the C-based liner and the phase-change layer on the melting current is quantified, showing a strong dependence on the liner thickness and a weak dependence on the phase-change layer thickness. These findings can guide the design of PCM cells with high-resistance liners between the electrode and phase-change layer for RESET current reduction.