gebhart/patrepeval huggingface dataset:
A scalable solution for tumor mutational burden from formalin-fixed, paraffin-embedded samples using the Oncomine Tumor Mutation Load Assay (2018)

These results show that the TML assay targeting a 1.7-Mb genomic footprint can accurately predict TMB values that are comparable to the WES. The TML assay workflow incorporates a simple workflow using the Ion GeneStudio S5 System. Further, the AmpliSeq chemistry allows the use of low input DNA to estimate mutational burden from FFPE samples. This TMB assay enables scalable, robust research into immuno-oncology biomarkers with scarce samples.
Photovoltaically Self-Charging Battery (2002)

S.A1208-A1211
Improved Measurement of Vascular Access Pressure (2002)

Vascular access stenosis and thrombosis is one of the key problems for hemodialysis patients. Prospective monitoring of static venous dialysis pressures can be applied to detect outflow stenoses in a vascular access. However, the location of stenoses within the access may influence the diagnostic value of venous pressure measurements. Whereas a decrease in access flow occurs with all types of stenosis, strictures within the arterial anastomosis or between arterial and venous dialysis needle cannot be detected with venous pressure measurements alone. A new approach is discussed, which bases on the improved measurement of static venous and arterial extracorporeal pressures. Extracorporeal pressure at zero blood flow depends on both the position of the heart relative to the extracorporeal blood circuit and the vertical offset between access site and fluid level in the bloodline. After hydrostatic correction of each pressure signal the normalized arterial and venous intra-access pressure ratio AP/MAP can be calculated. A venous stenosis leads to an increase in both arterial and venous pressure ratio. In case of access stenosis between arterial and venous needle the ratio of venous pressure to mean arterial pressure is normal, and only the arterial pressure ratio is elevated. In summary, a combination of arterial and venous pressure measurement is more sensitive and allows differentiation between mid-access and venous stenosis. Hydrostatic correction of the dialysis pressure signal is inevitable. To minimize the rate of access thrombosis, venous and arterial intra-access pressure should be considered when evaluating dialysis pressures as part of any access monitoring program.
Hydrodesulfurization of Catalytic Cracked Gasoline. Selective Catalytic Cracked Gasoline Hydrodesulfurization Using Co-Mo/.GAMMA.-Al2O3 Catalyst Modified by Pyridine. (2001)

The effects of pyridine modification on the catalyst activity and selectivity of Co-Mo/γ-Al2O3 were investigated in thiophene hydrodesulfurization (HDS) and olefin hydrogenation (HG). Pyridine injection into the reactant flow caused strong inhibition of thiophene HDS, diisobutylene HG and 1-octene HG reactions on Co-Mo/γ-Al2O3 at 150°C. Inhibition of thiophene HDS was totally recovered after the temperature was raised to 300°C for a while. However, inhibition of diisobutylene and 1-octene HG persisted after the same temperature rise.The possibility of improving the HDS selectivity (higher activity for HDS and lower activity for olefin HG) by pyridine modification (i.e. pyridine injection at 150°C and partial pyridine desorption at 300°C) was investigated for HDS reactions of model gasolines and catalytic cracked gasoline (CCG). Thiophene HDS was little affected, but benzothiophene HDS was slightly inhibited. Olefin HG and thiol production reaction were strongly inhibited. Improvement of HDS selectivity was observed in the reactions of model gasolines and CCG after pyridine modification. The fall in octane value became smaller. Improvement of HDS selectivity by pyridine modification was considered to result from the selective deactivation of the active sites for olefin reactions (HG and thiol production).
Image reconstruction and system optimization for three-dimensional speed of sound tomography using laser-induced ultrasound (2013)

We developed the first prototype of dual-modality imager combining optoacoustic tomography (OAT) and laser ultrasound tomography (UST) using computer models followed by experimental validation. The system designed for preclinical biomedical research can concurrently yield images depicting both the absorbed optical energy density and acoustic properties (speed of sound) of an object. In our design of the UST imager, we seek to replace conventional electrical generation of ultrasound waves by laser-induced ultrasound (LU). While earlier studies yielded encouraging results [Manohar, et al., Appl. Phys. Lett, 131911, 2007], they were limited to two-dimensional (2D) geometries. In this work, we conduct computer-simulation studies to investigate different designs for the 3D LU UST imager. The number and location of the laser ultrasound emitters, which are constrained to reside on the cylindrical surface opposite to the arc of detectors, are optimized. In addition to the system parameters, an iterative image reconstruction algorithm was optimized. We demonstrate that high quality volumetric maps of the speed of sound can be reconstructed when only 32 emitters and 128 receiving transducers are employed to record time-of-flight data at 360 tomographic view angles. The implications of the proposed system for small animal and breast-cancer imaging are discussed.
An Organometallic Inhibitor for Glycogen Synthase Kinase 3 (2004)

Replacing natural products with kinetically inert metal complexes may lead to a new class of therapeutics in which a metal center plays the role of an innocent bystander, organizing the orientation of the organic ligands in the receptor space. As an example of this approach, a ruthenium complex is described that copies the binding mode of indolocarbazole protein kinase inhibitors and serves as a reversible, low-nanomolar inhibitor for glycogen synthase kinase 3 (GSK-3).
Matrix addressable vertical cavity surface emitting laser array (1991)

The design, fabrication and characterisation of 1024-element matrix addressable vertical cavity surface emitting laser (VCSEL) arrays are described. A strained InGaAs quantum well VCSEL structure was grown by molecular beam epitaxy and an array of 32×32 lasers was defined using a proton implantation process. A matrix addressing architecture was employed, which enables the individual addressing of each of the 1024 lasers using only 64 electrical contacts. All the lasers in the array, measured after the laser definition step, were operating with fairly homogeneous characteristics; threshold current of 6.8 mA and output quantum differential efficiency of about 8%.
Indium Phosphide‐Based Quantum Dots with Shell‐Enhanced Absorption for Luminescent Down‐Conversion (2017)

It is shown that admixing small amounts of cadmium into the shell of InP/ZnSe core/shell quantum dots results in an increased absorption of blue light and a limited redshift of the band-edge emission. These effects reflect the reduced bandgap of (Zn,Cd)Se alloys and their smaller conduction-band offset with InP. Nevertheless, adjusting the InP core size enables InP/ZnSe and InP/(Zn,Cd)Se quantum dots with identical emission characteristics to be made. Processing both materials into remote phosphor disks, it is demonstrated that the shell-enhanced absorbance of InP/(Zn,Cd)Se has the double benefit of suppressing self-absorption and reducing the amount of quantum dots by weight needed to attain a given blue-to-red color conversion.
Local and systemic delivery of a stable aspirin-triggered lipoxin prevents neutrophil recruitment<i>in vivo</i> (1999)

Aspirin (ASA) triggers a switch in the biosynthesis of lipid mediators, inhibiting prostanoid production and initiating 15-epi-lipoxin generation through the acetylation of cyclooxygenase II. These aspirin-triggered lipoxins (ATL) may mediate some of ASA's beneficial actions and therefore are of interest in the search for novel antiinflammatories that could manifest fewer unwanted side effects. Here, we report that design modifications to native ATL structure prolong its biostability in vivo. In mouse whole blood, ATL analogs protected at carbon 15 [15(R/S)-methyl-lipoxin A4 (ATLa1)] and the omega end [15-epi-16-(para-fluoro)-phenoxy-LXA4 (ATLa2)] were recoverable to approximately 90 and 100% at 3 hr, respectively, compared with a approximately 40% loss of native lipoxin A4. ATLa2 retains bioactivity and, at levels as low as approximately 24 nmol/mouse, potently inhibited tumor necrosis factor-alpha-induced leukocyte recruitment into the dorsal air pouch. Inhibition was evident by either local intra-air pouch delivery (approximately 77% inhibition) or systemic delivery by intravenous injection (approximately 85% inhibition) and proved more potent than local delivery of ASA. Rank order for inhibiting polymorphonuclear leukocyte infiltration was: ATLa2 (10 micrograms, i.v.) approximately ATLa2 (10 micrograms, local) approximately dexamethasone (10 micrograms, local) >ASA (1.0 mg, local). Applied topically to mouse ear skin, ATLa2 also inhibited polymorphonuclear leukocyte infiltration induced by leukotriene B4 (approximately 78% inhibition) or phorbol ester (approximately 49% inhibition), which initiates endogenous chemokine production. These results indicate that this fluorinated analog of natural aspirin-triggered lipoxin A4 is bioavailable by either local or systemic delivery routes and is a more potent and precise inhibitor of neutrophil accumulation than is ASA.
Semi-automatic customization of internal fracture fixation plates (2011)

A new method for customization of fixation plates for repairing bone fractures is proposed. Digital models of plates are typically available as CAD models that contain smooth analytic geometry representations including NURBS. With the existing pre-operative planning solutions, these models are converted to polygonal meshes and adapted manually to the patient's bone geometry by the user. Based on the deformed model, physical bending is then performed by the surgeon in operating room. With the proposed approach, CAD models are semi-automatically adapted using NURBS to generate customized plates that conform to the desired region of the bone surface of patients. This enables an efficient and accurate approach that is also computationally suitable for interactive planning applications. Moreover, the patient-specific customized plates can then be produced directly from the adapted CAD models with a standard CNC machine before surgery. This may dramatically reduce time spent in OR, improve precision of the procedure and as a result improve the patient's outcome.
Pharmacokinetics and Exposure-Response Relationships of Dasotraline in the Treatment of Attention-Deficit/Hyperactivity Disorder in Adults (2015)

These results related dasotraline pharmacokinetics to pharmacological activity in ADHD, and support the novel concept that maintaining constant, steady-state dopamine and norepinephrine reuptake inhibition throughout a 24-h dosing interval is a novel pharmacological approach to the management of ADHD symptoms. Clinicaltrials.gov identifier: NCT01692782.
Duration and Spread of an Entomopathogenic Fungus, <I>Beauveria bassiana</I> (Deuteromycota: Hyphomycetes), Used to Treat Varroa Mites (Acari: Varroidae) in Honey Bee (Hymenoptera: Apidae) Hives (2007)

A strain of the fungus Beauveria bassiana (Balsamo) Vuillemin (Deuteromycota: Hyphomycetes) isolated from varroa mites, Varroa destructor Anderson & Trueman (Acari: Varroidae), was used to treat honey bees, Apis mellifera L. (Hymenoptera: Apidae), against varroa mites in southern France. Fungal treatment caused a significant increase in the percentage of infected varroa mites compared with control treatments in two field experiments. In the first experiment, hives were treated with a formulation containing 0.37 g of B. bassiana conidia per hive and in the second experiment with a dose of 1.0 g of conidia per hive. The percentage of infected varroa mites also increased in the nontreated (control) hives, suggesting a movement of conidia, probably via bee drift, among the hives. Mite fall was significantly higher among treated hives compared with control hives on the sixth and eighth days after treatment in the first experiment. These days correspond to previously published data on the median survivorship of mites exposed to that fungal solate. The interaction of treatment and date was significant in the second experiment with respect to mite fall. Increases in colony-forming unit (cfu) density per bee were observed in all treatments but were significantly higher among bees from treated hives than control hives for at least a week after treatment. The relationship between cfu density per bee and proportion infected was modeled using a sigmoid curve. High levels of infection (>80%) were observed for cfu density per bee as low as 5 x 102 per bee, but the cfu density in hives treated with 0.37 g generally dropped below this level less than a week after treatment.
Self‐Assembly of Perovskite for Fabrication of Semitransparent Perovskite Solar Cells (2015)

This work reports on the preparation of semitransparent perovskite solar cells. The cells transparency is achieved through a unique wet deposition technique that creates perovskite grids with various dimensions. The perovskite grid is deposited on a mesoporous TiO 2 layer, followed by hole transport material deposition and evaporation of a semitransparent gold film. Control of the transparency of the solar cells is achieved by changing the perovskite solution concentration and the mesh openings. The semitransparent cells demonstrate 20–70% transparency with a power conversion efficiency of 5% at 20% transparency. This is the first demonstration of the possibility to create a controlled perovskite pattern using a direct mesh‐assisted assembly deposition method for fabrication of a semitransparent perovskite‐based solar cell.
Fuzzy object modeling (2011)

To make Quantitative Radiology (QR) a reality in routine clinical practice, computerized automatic anatomy recognition (AAR) becomes essential. As part of this larger goal, we present in this paper a novel fuzzy strategy for building bodywide group-wise anatomic models. They have the potential to handle uncertainties and variability in anatomy naturally and to be integrated with the fuzzy connectedness framework for image segmentation. Our approach is to build a family of models, called the Virtual Quantitative Human, representing normal adult subjects at a chosen resolution of the population variables (gender, age). Models are represented hierarchically, the descendents representing organs contained in parent organs. Based on an index of fuzziness of the models, 32 thorax data sets, and 10 organs defined in them, we found that the hierarchical approach to modeling can effectively handle the non-linear relationships in position, scale, and orientation that exist among organs in different patients.
Transgene‐triggered, epigenetically regulated ectopic expression of a flower homeotic gene <i>pMADS3</i> in <i>Petunia</i> (2005)

Summary pMADS3 is a class C floral homeotic gene of Petunia that is specifically expressed in stamens and carpels of developing flowers. We previously reported that introduction of a part of the pMADS3 genomic sequence silenced endogenous pMADS3 (sil‐ pMADS3 ) in transgenic Petunia hybrida . Here we report that introduction of the same sequence triggers ectopic expression of endogenous pMADS3 in sepals, petals and leaves (ect‐ pMADS3 ), accompanied by homeotic conversion of the floral organs and altered leaf morphology similar to that of an Arabidopsis curly leaf mutant. The occurrence of the ect‐ pMADS3 phenotype depended on the presence of pMADS3 intron 2 in the transgenes. Occasionally, sil‐ pMADS3 and ect‐ pMADS3 phenotypes somatically interconverted. Some T 1 progeny inherited their parent's pMADS3 expression pattern, while others switched from sil‐ pMADS3 to ect‐ pMADS3 and vice versa . Both phenotypes occasionally occurred even after the transgenes were segregated away. RT‐PCR analyses of ectopically expressed pMADS3 transcripts indicated that two pMADS3 alleles were often differently regulated. Furthermore, reciprocal crosses with untransformed Petunia indicated that pMADS3 alleles other than the one ectopically expressed in T 0 plants were sometimes expressed ectopically in T 1 plants: the paramutation‐like transmission of epigenetic regulation between alleles. We detected in the transformants aberrant transcripts, including sense and antisense pMADS3 intron 2 sequences of heterogeneous molecular sizes, irrespective of the pMADS3 phenotypes. We speculate on possible molecular mechanisms underlying these epigenetic phenomena.
Tear film imager for dynamic mapping of the human tear film (2019)

Dry eye (DE) disease is a multifactorial disease of the outer ocular surface characterized by several ocular symptoms and mainly by tear film instability. We have developed an optical imaging system, the tear film imager (TFI), which is the first instrument that can directly image the muco-aqueous tear layer physical dimension in vivo and evaluate its parameters in a noninvasive mode with nanometer axial resolution. This instrument provides quantified information about many attributes of the tear film, including muco-aqueous layer thickness, lipid layer thickness, thickness change rate, and the break-up time. The TFI performances are based on simultaneous acquisition of large field of view (FOV) imagery and fast spectrometric measurement of the interference from the thin tear film sublayers. Herein, after describing the instrument and the methodology of the measurements, we use a tear film mock-up to quantify device accuracy (2.2 nm) and repeatability (0.25 nm standard deviation). In conclusion, we present a new technology for the assessment of the tear film with an unprecedented axial resolution and excellent accuracy and reproducibility.
Hydrogenation process for solid carbonaceous materials. [DOE patent] (1979)

Coal or other solid carbonaceous material is contacted with an organic solvent containing both hydrogen and a transition metal catalyst in solution to hydrogenate unsaturated bonds within the carbonaceous material. This benefaction step permits subsequent pyrolysis or hydrogenolysis of the carbonaceous fuel to form gaseous and liquid hydrocarbon products of increased yield and quality.
Performance of DC SQUIDs fabricated on 4-inch silicon wafer (1993)

A Nb/AlO/sub x//Nb Josephson process has been developed to fabricate DC superconducting quantum interference devices (SQUIDs) for biomagnetic measurements on 4-in silicon wafers. The purpose of the process is to fabricate high-quality junctions and to keep the quality uniform over a silicon wafer. All the films were deposited using magnetron sputtering. The components of the SQUID, except the junctions, were formed by taper etching to improve the step coverage. The uniformity of the SQUID characteristics (critical current, modulation depth, and mutual inductance between SQUID and modulation coil) was measured, and an excellent value of less than +or-5% was obtained. Three different configurations of SQUIDs, single washer (SW), double washer series (DWS), double washer parallel (DWP) have been fabricated with the same characteristics. The SW (single washer) had a white noise level of 6.3*10/sup -6/ Phi /sub 0// square root Hz, lower than those of DWS and DWP. 1/f crossover frequencies were below 1 Hz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Optimal Power Control of Inverter-Based Distributed Generations in Grid-Connected Microgrid (2019)

Distributed generation (DG) units are utilized to feed their closed loads in the autonomous microgrid. While in the grid-connected microgrid, they are integrated to support the utility by their required real and reactive powers. To achieve this goal, these integrated DGs must be controlled well. In this paper, an optimal PQ control scheme is proposed to control and share a predefined injected real and reactive powers of the inverter based DGs. The control problem is optimally designed and investigated to search for the optimal controller parameters by minimizing the error between the reference and calculated powers using particle swarm optimization (PSO). Microgrid containing inverter-based DG, PLL, coupling inductance, LC filter, power and current controllers is implemented on MATLAB. Two microgrid cases with different structure are studied and discussed. In both cases, the microgrid performance is investigated under different disturbances such as three-phase fault and step changes. The simulation results show that the proposed optimal control improves the microgrid dynamic stability. Additionally, the considered microgrids are implemented on real time digital simulator (RTDS). The experimental results verify the effectiveness and tracking capability of the proposed controllers and show close agreement with the simulation results. Finally, the comparison with the literature confirms the effectiveness of the proposed control scheme.
Multimodal Transfer: A Hierarchical Deep Convolutional Neural Network for Fast Artistic Style Transfer (2016)

Transferring artistic styles onto everyday photographs has become an extremely popular task in both academia and industry. Recently, offline training has replaced on-line iterative optimization, enabling nearly real-time stylization. When those stylization networks are applied directly to high-resolution images, however, the style of localized regions often appears less similar to the desired artistic style. This is because the transfer process fails to capture small, intricate textures and maintain correct texture scales of the artworks. Here we propose a multimodal convolutional neural network that takes into consideration faithful representations of both color and luminance channels, and performs stylization hierarchically with multiple losses of increasing scales. Compared to state-of-the-art networks, our network can also perform style transfer in nearly real-time by conducting much more sophisticated training offline. By properly handling style and texture cues at multiple scales using several modalities, we can transfer not just large-scale, obvious style cues but also subtle, exquisite ones. That is, our scheme can generate results that are visually pleasing and more similar to multiple desired artistic styles with color and texture cues at multiple scales.
Design of high-energy terahertz sources based on optical rectification (2010)

Detailed analysis of the tilted-pulse-front pumping scheme used for ultrashort THz pulse generation by optical rectification of femtosecond laser pulses is presented. It is shown that imaging errors in a pulse-front-tilting setup consisting of a grating and a lens can lead to a THz beam with strongly asymmetric intensity profile and strong divergence, thereby limiting applications. Optimized setup parameters are given to reduce such distortions. We also show that semiconductors can offer a promising alternative to LiNbO(3) in high-energy THz pulse generation when pumped at longer wavelengths. This requires tilted-pulse-front pumping, however the small tilt angles allow semiconductors to be easily used in such schemes. Semiconductors can be advantageous for generating THz pulses with high spectral intensity at higher THz frequencies, while LiNbO(3) is better suited to generate THz pulses with very large relative spectral width. By using optimized schemes the upscaling of the energy of ultrashort THz pulses is foreseen.