gebhart/patrepeval huggingface dataset:
Molecular cloning of DNA complementary to Drosophila melanogaster α-amylase mRNA (1987)

Several lambda clones containing cDNAs from Drosophila melanogaster were identified in a lambda cDNA bank using two different approaches: (i) cross-species hybridization using a mouse amylase cDNA probe, and (ii) probing with a differential probe, generated from Drosophila RNA. An amylase cDNA fragment was used, in turn, for the isolation and characterization of amylase genomic clones. The size of the Drosophila amylase mRNA was estimated at 1650 b. This is comparable with the size of the murine amylase messenger that encodes a protein of similar molecular weight. In Drosophila larvae, amylase mRNA can account for as little as 0.01% of the poly(A)+ RNA under conditions of dietary glucose repression or greater than 1% of poly(A)+ RNA under derepressing dietary conditions.
GaN Field Emitter Arrays with JA of 10 A/cm2 at VGE = 50 V for Power Applications (2022)

III-Nitrides are attractive as field emission devices for high frequency, high power, and harsh environment applications. A wet-based digital etching and a novel device geometry was used to demonstrate GaN vertical self-aligned-gate (SAG) field emitter arrays (FEA) with uniform tips of sub-10 nm tip radius. The best GaN FEA has a current density $(J_{A})$ of 10 A/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> at $V_{GE} =50V$, which is better than the state-of-the-art Si field emitter arrays at the same bias condition.
Rapid and Automatic Annotation of Multiple On-Tissue Chemical Modifications in Mass Spectrometry Imaging with Metaspace (2022)

On-tissue chemical derivatization is a valuable tool for expanding compound coverage in untargeted metabolomic studies with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Applying multiple derivatization agents in parallel increases metabolite coverage even further but results in large and more complex datasets that can be challenging to analyze. In this work, we present a pipeline to provide rigorous annotations for on-tissue derivatized MSI data using Metaspace. To test and validate the pipeline, maize roots were used as a model system to obtain MSI datasets after chemical derivatization with four different reagents, Girard's T and P for carbonyl groups, coniferyl aldehyde for primary amines, and 2-picolylamine for carboxylic acids. Using this pipeline helped us annotate 631 unique metabolites from the CornCyc/BraChem database compared to 256 in the underivatized dataset, yet, at the same time, shortening the processing time compared to manual processing and providing robust and systematic scoring and annotation. We have also developed a method to remove false derivatized annotations, which can clean 5-25% of false derivatized annotations from the derivatized data, depending on the reagent. Taken together, our pipeline facilitates the use of broadly targeted spatial metabolomics using multiple derivatization reagents.
Integrated Field Study Involving Downhole Fluid Analyzer DFA for Reservoir Connectivity in Thin Complex Lithology Formation: Case Study from Oman (2016)

Abstract Early information about reservoir fluid complexity, dynamic behavior, and reservoir connectivity is crucial for development planning and production optimization of new plays. Such impact is manifested in three main areas: (1) reservoir presence and connectivity to understand the extent of the play (2) reservoir fluid variation to understand the charge history and devise production strategy (3) completion optimization in exploration wells to maximize early production. Petroleum Development of Oman pursued an ambitious exploration campaign firstly consisting of 8 wells targeting a shallow, thin, complex lithology formation to better understand a new play, especially from reservoir extension and connectivity viewpoints. In addition to advanced formation evaluation logging consisting of elemental spectroscopy and nuclear magnetic resonance, an advanced Downhole Fluid Analyzer (DFA) was deployed with Wireline Formation Testers (FT) aimed to obtain formation pressure and fluid samples. The fluid scanning using in-situ fluid analysis was also performed to obtain reservoir fluid information in real time and at reservoir condition. In addition, Interval Pressure Transient Tests (IPTT) was conducted to evaluate permeability of each well. This paper provides the workflow of using the DFA and laboratory data for full field development. This will include discussion of DFA data such as asphaltene, fluid composition, Gas-Oil-Ratio (GOR), density, viscosity, and fluorescence yield to help draw a full picture towards reservoir connectivity. Having detailed fluid properties data available in real time allows to optimize the completion decisions (pump selection as one example) in order to maximize early production while allowing longer term reservoir management planning. This paper also discusses the use of in-situ fluid viscosity and pressure transient data to estimate zone permeability during the FT operation, which will later be compared to actual well test data. Results show a good comparison and provide comfort to use FT pressure transient data to evaluate zone permeability at early stage of the operation. The DFA data from the first 4 wells suggested the presence of subtle but distinct fluid differences in terms of composition, oil color, and fluorescence yields. This DFA data was then supported by full PVT laboratory results. The differences in fluids will be examined in more details. This paper will present an effective workflow to integrate pressure, DFA, and PVT data to understand reservoir connectivity issue in this newly discovered formation. In addition, the DFA color gradient model was then used to help supporting other available information.
Faculty Opinions recommendation of Absence of mucosal-associated invariant T cells in a person with a homozygous point mutation in MR1. (2020)

The role unconventional T cells play in protective immunity in humans is unclear. Mucosal-associated invariant T (MAIT) cells are an unconventional T cell subset restricted to the antigen-presenting molecule MR1. Here, we report the discovery of a patient homozygous for a rare Arg31His (R9H in the mature protein) mutation in MR1 who has a history of difficult-to-treat viral and bacterial infections. MR1R9H was unable to present the potent microbially derived MAIT cell stimulatory ligand. The MR1R9H crystal structure revealed that the stimulatory ligand cannot bind due to the mutation lying within, and causing structural perturbation to, the ligand-binding domain of MR1. While MR1R9H could bind and be up-regulated by a MAIT cell inhibitory ligand, the patient lacked circulating MAIT cells. This shows the importance of the stimulatory ligand for MAIT cell selection in humans. The patient had an expanded γδ T cell population, indicating a compensatory interplay between these unconventional T cell subsets.
Long-Term Dosing of Arzoxifene Lowers Cholesterol, Reduces Bone Turnover, and Preserves Bone Quality in Ovariectomized Rats (2002)

Long-term effects of a new selective estrogen receptor modulator (SERM) arzoxifene were examined in ovariectomized (OVX) rats. Arzoxifene was administered postoperatively (po) at 0.1 mg/kg per day or 0.5 mg/kg per day to 4-month-old rats, starting 1 week after OVX for 12 months. At study termination, body weights for arzoxifene groups were 16-17% lower than OVX control, which was caused by mainly reduced gain of fat mass. Longitudinal analysis of the proximal tibial metaphysis (PTM) by computed tomography (CT) at 0, 2, 4, 6,9, and 12 months showed that OVX induced a 22% reduction in bone mineral density (BMD) at 2 months, which narrowed to a 12% difference between sham-operated (sham) and OVX rats by 12 months. Both doses of arzoxifene prevented the OVX-induced decline in BMD. Histomorphometry of the PTM showed that arzoxifene prevented bone loss by reducing osteoclast number in OVX rats. Arzoxifene maintained bone formation indices at sham levels and preserved trabecular number above OVX controls. Micro-CT analysis of lumbar vertebrae showed similar preservation of BMD compared with OVX, which were not different from sham. Compression testing of the vertebra and three-point bending testing of femoral shaft showed that strength and toughness were higher for arzoxifene-treated animals compared with OVX animals. Arzoxifene reduced serum cholesterol by 44-59% compared with OVX. Uteri wet weight from arzoxifene animals was 38-40% of sham compared with OVX rats, which were 29% of sham. Histology of the uterine endometrium showed that cell heights from both doses of arzoxifene were not significantly different from OVX controls. In summary, treatment of OVX rats with arzoxifene for nearly one-half of a lifetime maintained beneficial effects on cholesterol and the skeleton. These data suggest that arzoxifene may be a useful therapeutic agent for osteoporosis in postmenopausal women.
Phase cycle-slip replacement via data fitting (2004)

This paper addresses the problem of phase cycle-slip (FM click noise) elimination. For analyses and application demonstration, the signal of interest is a commercial FM transmission, received and sampled for subsequent demodulation as typical in software defined radios. There are two parts to this paper. The first part will investigate the advantages of using data fitting to repair the time series in the neighbourhood of a detected click. Previous papers (e.g., [1]) have considered time series which have neighbourhoods in which only one point was considered as a click, and hence, only one point needed to be repaired. We will consider the more difficult and practical case where there is a frequency modulated signal passed through a band-pass filter and a (software/digital) FM limiter discriminator used for demodulation. This receive system has the effect of causing click distortion over multiple samples, making the repairing that much more difficult. The methods of forward-backward linear prediction (FBLP or Wiener filtering), least squares polynomial fitting (LSPOLY), and twin Tukey window (TTW) filtering are discussed. The results are shown empirically, and will show that the TTW technique outperforms the FBLP and LSPOLY techniques for the presented application. The second part of this paper will discuss potential techniques to discern samples which are clicks, from samples which are normal yet click-like. We will consider the combination of autocorrelation, kurtosis, 4th order moment, and spectral characteristics, to form a threshold detection level to identify clicks.
Controlling Electron Trap Depth To Enhance Optical Properties of Persistent Luminescence Nanoparticles for In Vivo Imaging ThomasMaldiney, † AurelieLecointre, ‡ BrunoViana,* ,‡ AurelieBessiere, ‡ MichelBessodes, † DidierGourier, ‡ (2011)

Focusing on the use of nanophosphors for in vivo imaging and diagnosis applications, we used thermally stimulated luminescence (TSL) measurements to study the influence of triva- lent lanthanide Ln 3+ (Ln = Dy, Pr, Ce, Nd) electron traps on the optical properties of Mn 2+ -doped diopside-based persistent lumi- nescence nanoparticles. This work reveals that Pr 3+ is the most suitable Ln 3+ electron trap in the diopside lattice, providing optimal trap depth for room temperature afterglow and resulting in the most intense luminescence decay curve after X-ray irradiation. This luminescence dependency toward the electron trap is maintained through additional doping with Eu 2+ , allowing UV-light excitation, critical for bioimaging applications in living animals. We finally identify a novel composition (CaMgSi2O6:Eu 2+ ,Mn 2+ ,Pr 3+ ) for in vivo imaging, displaying a strong near-infrared afterglow centered on 685 nm, and present evidence that intravenous injection ofsuchpersistentluminescencenanoparticlesinmiceallowsnotonlyimprovedbuthighlysensitivedetectionthroughlivingtissues.
Label-free molecular imaging of immunological synapses between dendritic and T cells by Raman micro-spectroscopy (2010)

Confocal Raman micro-spectroscopy (CRMS) was used to measure spectral images of immunological synapse formation between dendritic and T cells without using molecular labels or other invasive procedures. The purpose-built inverted CRMS instrument integrated an environmental enclosure and a near-infrared laser to allow measurements on live cells maintained under physiological conditions. The integration of the wide-field fluorescence also enabled viability assays and direct comparison between Raman spectral images and gold-standard immuno-fluorescence images for specific molecules. Raman spectral images of nucleus and proteins were built by fuzzy c-mean clustering method. The Raman images were found to be in good correspondence with the immuno-fluorescence images of DNA and actin. These results indicate that actin is a main contributor to the Raman spectrum of the cytoplasm of dendritic and T cells. While for control cells the Raman spectral images of proteins indicated a more homogeneous distribution of proteins in the cytoplasm of dendritic cells, they indicated a higher accumulation of proteins at the immunological synapses when dendritic cells were pre-treated with laminin. These conclusions were also supported by confocal immuno-fluorescence imaging after cell fixation and labelling. This study demonstrates the potential of CRMS for label-free non-invasive imaging of junctions between live cells. Therefore, this technique may become a useful tool for studying cellular processes in live cells and where non-invasive molecular specific imaging is desirable, such as cell-cell interactions.
High Temperature VARTM of Phenylethynyl Terminated Imides (PETI) Resins (2010)

Fabrication of composite structures using vacuum assisted resin transfer molding (VARTM) is generally more affordable than conventional autoclave techniques. Recent efforts have focused on adapting VARTM for the fabrication of high temperature composites. Due to their low melt viscosity and long melt stability, certain phenylethynyl terminated imides (PETI) can be processed into composites using high temperature VARTM (HT-VARTM). However, one of the disadvantages of the current HT-VARTM resin systems has been the high porosity of the resultant composites. For aerospace applications a void fraction of less than 2% is desired. In the current study, two PETI resins, LARCTM PETI-330 and LARCTM PETI-8 have been used to fabricate test specimens using HT-VARTM. The resins were infused into carbon fiber preforms at 260 C and cured between 316 C and 371 C. Modifications to the thermal cycle used in the laminate fabrication have reduced the void content significantly (typically < 3%) for carbon fiber biaxially woven fabric. Photomicrographs of the panels were taken and void contents were determined by acid digestion. For carbon fiber uniaxial fabric, void contents of less than 2% have been obtained using both PETI-8 and PETI-330. Mechanical properties of the panels were determined at both room and elevated temperatures. These include short beam shear and flexure tests. The results of this work are presented herein.
Frequency, onset and clinical impact of somatic DNMT3A mutations in therapy-related and secondary acute myeloid leukemia (2011)

The recent identification of DNMT3A mutations in de novo acute myeloid leukemia prompted us to determine their frequency, patterns and clinical impact in a cohort of 98 patients with either therapy-related or secondary acute myeloid leukemia developing from an antecedent hematologic disorder. We identified 24 somatic mutations in 23 patients with a significantly higher frequency in secondary acute myeloid leukemia (35.1%) as compared to therapy-related acute myeloid leukemia (16.4%, P=0.0486). DNMT3A mutations were associated with a normal karyotype and IDH1/2 mutations, but did not affect survival. In contrast to de novo acute myeloid leukemia, most mutations did not affect arginine on position 882, but were predominantly found in the methyltransferase domain. All DNMT3A mutations identified in secondary acute myeloid leukemia were already present in the antecedent disorders indicating an early event. Reduction to homozygosity by uniparental disomy was observed in 2 patients with secondary acute myeloid leukemia during disease progression.
High characteristic temperature for ridge-waveguide laser with a highly stacked InAs quantum dot structure (2016)

A ridge-waveguide laser with highly stacked InAs quantum dot structure based on strain compensation technique was fabricated. The threshold current of this laser was decreased to approximately 75 mA without coating the facet mirror. A high characteristic temperature of over 100 K was obtained using this laser.
Response reduction methods for base isolated buildings with collision to retaining walls (2017)

This paper proposes a new damper that can change the damping force depending on the response displacement and response velocity. The proposed damper reduces the damage of seismic-isolated structures which undergo excessive deformation during huge earthquakes, without lowering the performance of the seismic-isolation system during medium to small magnitude earthquakes. We investigate the effects of using the proposed attenuator on the responses of a superstructure model to seismic motion that causes collision with retaining walls. An experiment using a shaking table is conducted, and the results from the test are compared with those from numerical analyses. The test results agree approximately with the numerical analysis results except for the absolute acceleration results in collision cases.
MO274: Vancomycin Adsorption During In Vitro Model of Hemoperfusion with Mini-Module of HA380 Cartridge (2022)

Abstract BACKGROUND AND AIMS Septic shock is one of the most frequent causes in Intensive Care Unit (ICU) admission and is related to a very high risk of mortality. About one-third of patients with sepsis develops AKI which contributes to a worsening prognosis. AKI due to sepsis is the result of a dysregulated host immune response to infection, with the production of inflammatory mediators and cytokines that cause haemodynamic alterations, endothelial damage, apoptosis and, finally, immunoparalysis. The new Jafron HA380 cartridge has been specifically designed for use in clinical conditions characterized by cytokine storm such as sepsis. Given the growing application of these devices in cases of septic AKI in ICU, an unsolved problem is whether these polymers adsorb drugs, including antibiotics. In vitro experiments were conducted to determine its adsorption capacity toward Vancomycin antibiotic. METHOD In vitro circulation was performed using a dedicated testing platform Galileo. A customized cartridge was built assembling mini-module components scaled in dimension toward HA380 and filled with 75 g of HA380 beads (25% of the regular size cartridge). Peristaltic pump was set at 250 mL/min. we performed two circulation containing extremely high quantity of Vancomycin (5 g in 500 mL and 10 g in 1000 mL) for 300 minutes. Samples were collected every 20 minutes. Vancomycin concentrations were measured. The adsorption isotherm was represented using the equation: Massadsorbed = RR × Massinjected, where the RR in the Vancomycin removal ratio. RESULTS In vitro circulation confirms the affinity of beads material in binding Vancomycin molecules. The kinetics of vancomycin adsorption shows a rapid decay of the concentration in the first part of the experiments, after which we can observed a plateau (Fig. 1a). A total of 4500 mg of the 5000 mg were adsorbed in the end of the experiment (RR = 94%), of which 90% in the first 40 minutes (RR = 87%); after this period the curve became flat and the adsorption phenomenon negligible (Fig. 1b). In the experiment with 10 000 mg, after 60 minutes of rapid adsorption (RR = 55%), the curve reached a plateau converging to a RR higher than 60% (Fig.). The sorbent beads were able to bind 6100 mg toward 10 000 mg injected. This amount saturated the mini-module binding sites. CONCLUSION The application of HA380 mini-modules allowed to determine the amount of Vancomycin necessary to reach the saturation of the sorbent material. Based on the obtained results, we estimated that the cartridge HA380 could retain more than 24 g of Vancomycin during HP circulation. Further investigation is needed to validate our results and to better understand HA380 performance in clinical practice.
Instantaneous availability for the protection devices based on non-homogeneous Markov model and a case study (2014)

While evaluating the reliability of protection devices, the instantaneous availability (IA) is more applicable than the steady-state availability. This paper first proposes a general formulation to calculate the IA of relay protection device with the non-homogeneous Markov model. Then, it presents a 4-state Markov model, including the self-test and preventive maintenance, together with time-varying failure rate (TFR) as a case study. Furthermore, based on the field data, it analyzes the variation of IA with respect to different self-test efficiency and repair cycle.
Active abstractions (1994)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1994.
A framework for designing patient‐specific bioprosthetic heart valves using immersogeometric fluid–structure interaction analysis (2017)

Numerous studies have suggested that medical image derived computational mechanics models could be developed to reduce mortality and morbidity due to cardiovascular diseases by allowing for patient-specific surgical planning and customized medical device design. In this work, we present a novel framework for designing prosthetic heart valves using a parametric design platform and immersogeometric fluid-structure interaction (FSI) analysis. We parameterize the leaflet geometry using several key design parameters. This allows for generating various perturbations of the leaflet design for the patient-specific aortic root reconstructed from the medical image data. Each design is analyzed using our hybrid arbitrary Lagrangian-Eulerian/immersogeometric FSI methodology, which allows us to efficiently simulate the coupling of the deforming aortic root, the parametrically designed prosthetic valves, and the surrounding blood flow under physiological conditions. A parametric study is performed to investigate the influence of the geometry on heart valve performance, indicated by the effective orifice area and the coaptation area. Finally, the FSI simulation result of a design that balances effective orifice area and coaptation area reasonably well is compared with patient-specific phase contrast magnetic resonance imaging data to demonstrate the qualitative similarity of the flow patterns in the ascending aorta.
Solubility Increases Associated with Crystalline Drug Nanoparticles: Methodologies and Significance (2010)

In this manuscript, the determination of solubility of crystalline drug nanosuspensions by a range of methods is critically investigated. As the determinations of solubility were performed in the presence of the solubilizing nanosuspension stabilizer d-α-tocopherol polyethylene glycol 1000 succinate (TPGS), the potential effects of this excipient on the measurements were studied first. Solubility data of nanosuspensions of itraconazole, loviride, phenytoin and naproxen were generated using different methodologies. Data obtained using separation-based methodologies (centrifugation, filtration and ultracentrifugation) proved to be of limited use, due to poor nanoparticle separation efficiencies and/or significant adsorption of TPGS onto the nanoparticle surfaces. Light scattering and turbidity were found to be more suitable for the determination of nanosuspension solubility. The obtained data show that, unlike earlier reports, the solubility increases due to nanosizing are small, with measured increases of only 15%. These solubility increases are in fair agreement with what would be predicted based on the Ostwald-Freundlich equation.