gebhart/patrepeval huggingface dataset:
Preclinical human models and emerging therapeutics for advanced systemic mastocytosis (2018)

Mastocytosis is a term used to denote a group of rare diseases characterized by an abnormal accumulation of neoplastic mast cells in various tissues and organs. In most patients with systemic mastocytosis, the neoplastic cells carry activating mutations in <i>KIT</i> Progress in mastocytosis research has long been hindered by the lack of suitable <i>in vitro</i> models, such as permanent human mast cell lines. In fact, only a few human mast cell lines are available to date: HMC-1, LAD1/2, LUVA, ROSA and MCPV-1. The HMC-1 and LAD1/2 cell lines were derived from patients with mast cell leukemia. By contrast, the more recently established LUVA, ROSA and MCPV-1 cell lines were derived from CD34<sup>+</sup> cells of non-mastocytosis donors. While some of these cell lines (LAD1/2, LUVA, ROSA<sup>KIT WT</sup> and MCPV-1) do not harbor <i>KIT</i> mutations, HMC-1 and ROSA<sup>KIT D816V</sup> cells exhibit activating <i>KIT</i> mutations found in mastocytosis and have thus been used to study disease pathogenesis. In addition, these cell lines are increasingly employed to validate new therapeutic targets and to screen for effects of new targeted drugs. Recently, the ROSA<sup>KIT D816V</sup> subclone has been successfully used to generate a unique <i>in vivo</i> model of advanced mastocytosis by injection into immunocompromised mice. Such a model may allow <i>in vivo</i> validation of data obtained <i>in vitro</i> with targeted drugs directed against mastocytosis. In this review, we discuss the major characteristics of all available human mast cell lines, with particular emphasis on the use of HMC-1 and ROSA<sup>KIT D816V</sup> cells in preclinical therapeutic research in mastocytosis.
12-Channel &#x00D7; 20-Gbps on-board parallel optical modules using multi-chip visual alignment technique (2010)

We have developed 12-channel × 20-Gbps optical transmitter/receiver modules with 9 × 14-mm footprints. To achieve stable optical coupling efficiency, we also developed a precise multi-chip mounting technique. The three dies of 4-channel vertical-cavity surface-emitting laser (VCSEL)/photodiode (PD) arrays are mounted at the same time. The accuracy of the Z-axis can be controlled by monitoring the dies' positions for the optical reference plane. The coupling losses were less than 1.5 dB in the 12-channel transmitter/receiver modules. The standard deviations of the coupling losses were less than 1.0 dB in all samples. Error-free transmissions at a data rate of 20 Gbps were also demonstrated. A reliability test indicated that the modules are repairable and reliable.
Defining the Diversity of Phenotypic Respecification Using Multiple Cell Lines and Reprogramming Regimens (2013)

To better understand the basis of variation in cellular reprogramming, we performed experiments with two primary objectives: first, to determine the degree of difference, if any, in reprogramming efficiency among cells lines of a similar type after accounting for technical variables, and second, to compare the efficiency of conversion of multiple similar cell lines to two separate reprogramming regimens-induced neurons and induced skeletal muscle. Using two reprogramming regimens, it could be determined whether converted cells are likely derived from a distinct subpopulation that is generally susceptible to reprogramming or are derived from cells with an independent capacity for respecification to a given phenotype. Our results indicated that when technical components of the reprogramming regimen were accounted for, reprogramming efficiency was reproducible within a given primary fibroblast line but varied dramatically between lines. The disparity in reprogramming efficiency between lines was of sufficient magnitude to account for some discrepancies in published results. We also found that the efficiency of conversion to one phenotype was not predictive of reprogramming to the alternate phenotype, suggesting that the capacity for reprogramming does not arise from a specific subpopulation with a generally "weak grip" on cellular identity. Our findings suggest that parallel testing of multiple cell lines from several sources may be needed to accurately assess the efficiency of direct reprogramming procedures, and that testing a larger number of fibroblast lines--even lines with similar origins--is likely the most direct means of improving reprogramming efficiency.
My FVIII story (2020)

VIII VIII VIII VIII (FVIII) A FVIII X (tenase) IX (FIXa) X (FX) Vmax 10 5 1) FVIII FVIII FVIII von Willebrand (VWF)FVIII
Nanoparticle-Mediated Measurement of Target–Drug Binding in Cancer Cells (2011)

Responses to molecularly targeted therapies can be highly variable and depend on mutations, fluctuations in target protein levels in individual cells, and drug delivery. The ability to rapidly quantitate drug response in cells harvested from patients in a point-of-care setting would have far reaching implications. Capitalizing on recent developments with miniaturized NMR technologies, we have developed a magnetic nanoparticle-based approach to directly measure both target expression and drug binding in scant human cells. The method involves covalent conjugation of the small-molecule drug to a magnetic nanoparticle that is then used as a read-out for target expression and drug-binding affinity. Using poly(ADP-ribose) polymerase (PARP) inhibition as a model system, we developed an approach to distinguish differential expression of PARP in scant cells with excellent correlation to gold standards, the ability to mimic drug pharmacodynamics ex vivo through competitive target-drug binding, and the potential to perform such measurements in clinical samples.
40 Gbit/s packet-wavelength-selective, reconfigurable optical add/drop multiplexing using label-selectivity-enhanced optical en/decoder and wide-passband AOTF (2006)

We demonstrate the packet-wavelength-selective reconfigurable OADM network on 16-wavelength /spl times/ 40-Gbit/s NRZ signal using a label-selectivity-enhanced optical en/decoder and wide-passband AOTF. Error-free operations for all 16-wavelength channels at three nodes with 100-km transmission are realized.
Electrochemical Reactions During Ru Chemical Mechanical Planarization and Safety Considerations (2011)

We analyzed electrochemical reactions during ruthenium (Ru) chemical mechanical planarization (CMP) using a potentiostat and a quartz crystal microbalance, and considered the potential safety issues. We evaluated the valence number derived from Faraday's law using the dissolution mass change of Ru and total coulomb consumption in the electrochemical reactions for Ru in acidic solution and slurry. The valence numbers of dissolved Ru ions were distributed in the range of 2 to 3.5. As toxic ruthenium tetroxide (RuO4) has a valence number of 8, we were able to conclude that no toxic RuO4 was produced in the actual Ru CMP.
Binding of Gadobenate Dimeglumine to Proteins Extravasated into Interstitial Space Enhances Conspicuity of Reperfused Infarcts (1994)

Cavagna FM, Marzola P, Daprà M, Maggioni F, Vicinanza E, Castclli PM, de Haën C, Luchinat C, Wendland MF, Saeed M, Higgins CB. Binding of gadobenate dimeglumine to proteins extravasated into interstitial space enhances conspicuity of reperfused infarcts. Invest Radiol 1994;29:S50–S53.
Postinfarction Ventricular Septal Defect - Surgical Strategies and Results (1989)

Twenty consecutive patients with postinfarction ventricular septal defect (VSD) were subjected to surgery: there were 8 females and 12 males with a mean age of 67 +/- 9 years. Nine acute patients developed cardiogenic shock, and intra-aortic balloon pump was started before surgery (with IABP). Eight acute patients showed preoperatively relatively stable hemodynamics, and surgery was feasible without previous use of the intra-aortic balloon pump (without IABP). The interval between myocardial infarction and surgery was 13 days for 17 acute cases. In the group with IABP the interval was 8 +/- 5 days versus 19 +/- 11 days in the group without IABP (p less than 0.025). VSD patch closure was performed in 20/20, resection of infarct in 10/20, transventricular approach without resection of infarct in 3/20, patch enlargement of the left ventricle in 2/20, plicature of an aneurysm in 3/20, aorto-coronary bypass in 10/20 (number of bypasses: 2.1 +/- 1.3) and mitral annuloplasty in 1/20. The perioperative 30 days mortality was 5/20 (25%) for the whole series. In the group with IABP mortality was 4/9 (44%) versus 1/8 (13%) in the group of acute patients without IABP (p less than 0.05). Mean follow-up for the 15 surviving patients was 1.7 +/- 1.0 years. Two patients died during the first year, one of them due to carcinoma. After 1 year, mean NYHA functional class was assessed 1.5 +/- 0.6. One patient showed a residual VSD which was closed surgically. Immediate closure of a postinfarction ventricular septal defect is the therapy of choice of this complication of acute myocardial infarct with a natural history showing an extremely high mortality.
An innovative strategy to identify new targets for delivering antibodies to the brain has led to the exploration of the integrin family (2022)

This transcytotic behavior has not previously been reported for anti-integrin antibodies. Further studies should be undertaken to validate this new mechanism in vivo and to evaluate its potential in brain delivery.
Gas position effect on single attosecond pulse generation in crossed metal nanostructure (2018)

An effect method to obtain the single attosecond pulses (SAPs) by using the inhomogeneous polarization gating (PG) technology in the crossed metal nanostructure has been proposed and investigated. It is found that by properly injecting the gas into the negative position of the nanostructure, the emitted harmonics at the very highest orders used for the SAPs only occurs at one side of the region inside the nanostructure. As a result, not only the extension of the harmonic cutoff can be achieved, but also the modulations of the harmonics can be decreased. Further, with the introduction of a weak near-infrared field, the harmonic yield can be enhanced by 3.5 orders of magnitudes in comparison with that from the single PG technology. Finally, by superposing the selected harmonics from the inhomogeneous PG scheme, a 32 as SAP with the high signal intensity can be obtained.
Supplementary Table 6 from Comprehensive Genome Methylation Analysis in Bladder Cancer: Identification and Validation of Novel Methylated Genes and Application of These as Urinary Tumor Markers (2023)

&lt;p&gt;PDF file - 56K&lt;/p&gt;
Performance Improvement of a Return Channel in a Multistage Centrifugal Compressor Using Multiobjective Optimization (2013)

The effect of the design parameters of a return channel on the performance of a multistage centrifugal compressor was numerically investigated, and the shape of the return channel was optimized using a multiobjective optimization method based on a genetic algorithm to improve the performance of the centrifugal compressor. The results of sensitivity analysis using Latin hypercube sampling suggested that the inlet-to-outlet area ratio of the return vane affected the total pressure loss in the return channel, and that the inlet-to-outlet radius ratio of the return vane affected the outlet flow angle from the return vane. Moreover, this analysis suggested that the number of return vanes affected both the loss and the flow angle at the outlet. As a result of optimization, the number of return vane was increased from 14 to 22 and the area ratio was decreased from 0.71 to 0.66. The radius ratio was also decreased from 2.1 to 2.0. Performance tests on a centrifugal compressor with two return channels (the original design and optimized design) were carried out using two-stage test apparatus. The measured flow distribution exhibited a swirl flow in the center region and a reversed swirl flow near the hub and shroud sides. The exit flow of the optimized design was more uniform than that of the original design. For the optimized design, the overall two-stage efficiency and pressure coefficient were increased by 0.7% and 1.5%, respectively. Moreover, the second-stage efficiency and pressure coefficient were respectively increased by 1.0% and 3.2%. It is considered that the increase in the second-stage efficiency was caused by the increased uniformity of the flow, and the rise in the pressure coefficient was caused by a decrease in the residual swirl flow. It was thus concluded from the numerical and experimental results that the optimized return channel improved the performance of the multistage centrifugal compressor.
Uncertainty-Aware Estimation of Vehicle Orientation for Self-Driving Applications (2021)

Object detection is a critical component of a self-driving system, tasked with inferring the current states of the surrounding traffic actors. While there exist a number of studies on the problem of inferring the position and shape of vehicle actors, understanding actors' orientation remains a challenge for existing state-of-the-art detectors. Orientation is an important property for downstream modules of an autonomous system, particularly relevant for motion prediction of stationary or reversing actors where current approaches struggle. We focus on this task and present a general method that allows us to more accurately infer vehicle orientations, which we apply to the state-of-the-art models that perform joint object detection and motion prediction. In addition, the approach is able to quantify prediction uncertainty, outputting the probability that the inferred orientation is flipped, which allows for improved motion prediction and safer autonomous operations. Empirical results show the benefits of the approach, obtaining state-of-the-art performance on the open-sourced nuScenes data set.
Bayesian filtering of Poisson noise using local statistics (1988)

Images recorded at low-light levels inherently suffer from Poisson noise. A filter based on the maximum a posteriori probability (MAP) criterion is developed to remove this noise. The filter is adaptive; it responds to local changes in image statistics and, thus, removes the noise along the edges without significantly affecting the edge sharpness. It does not require any a priori information about the original image because all the parameters needed for the filter are estimated from the noisy image by assuming local stationarity. Additionally, the simple structure of the filter can be easily implemented in hardware.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Solution structure of αtα, a helical hairpin peptide of de novo design (1997)

Abstract αtα is a 38‐residue peptide designed to adopt a helical hairpin conformation in solution (Fezoui Y, Weaver DL, Osterhout JJ, 1995, Protein Sci 4286‐295). A previous study of the carboxylate form of αtα by CD and two‐dimensional NMR indicated that the peptide was highly helical and that the helices associated in approximately the intended orientation (Fezoui Y, Weaver DL, Osterhout JJ, 1994, Proc Natl Acad Sci USA 91:3675‐3679). Here, the solution structure of αtα as determined by two‐dimensional NMR is reported. A total of 266 experimentally derived distance restraints and 20 dihedral angle restraints derived from J‐couplings were used. One‐hundred initial structures were generated by distance geometry and refined by dynamical simulated annealing. Twenty‐three of the lowest‐energy structures consistent with the experimental restraints were analyzed. The results presented here show that αtα is comprised of two associating helices connected by a turn region.
Modelling single- and tandem-bubble dynamics between two parallel plates for biomedical applications (2013)

Carefully timed tandem microbubbles have been shown to produce directional and targeted membrane poration of individual cells in microfluidic systems, which could be of use in ultrasound-mediated drug and gene delivery. This study aims at contributing to the understanding of the mechanisms at play in such an interaction. The dynamics of single and tandem microbubbles between two parallel plates is studied numerically and analytically. Comparisons are then made between the numerical results and the available experimental results. Numerically, assuming a potential flow, a three-dimensional boundary element method (BEM) is used to describe complex bubble deformations, jet formation, and bubble splitting. Analytically, compressibility and viscous boundary layer effects along the channel walls, neglected in the BEM model, are considered while shape of the bubble is not considered. Comparisons show that energy losses modify the bubble dynamics when the two approaches use identical initial conditions. The initial conditions in the boundary element method can be adjusted to recover the bubble period and maximum bubble volume when in an infinite medium. Using the same conditions enables the method to recover the full dynamics of single and tandem bubbles, including large deformations and fast re-entering jet formation. This method can be used as a design tool for future tandem-bubble sonoporation experiments.
Immortalization of human small airway epithelial cells with characteristics of bronchioalveolar stem cells (2009)

Most of our current understanding of stem cells in the adult lung is based on mouse models while information in the human lung remains poorly defined. A major advance would be the ability to reproducibly grow human lung stem or progenitor cells to allow their systematic study and genetic manipulation. Toward this goal, we have worked out conditions to routinely immortalized (NB = 9) human small airway epithelial cells (HSAECs) from peripheral lung using Cdk4 and hTERT expression vectors in these cells. As an example strain HSAEC1 grows in serum free SAGM medium (Clonetics), forms colonies in liquid media efficiently, but does not form colonies in soft agar or tumors in SCID/NOD mice. HSAEC1 expresses lung basal/stem cell markers (aldehyde dehydrogenase, p63, Cytokeratin14 and 17, and is resistant to 1 mM naphthalene) but very low or undetectable Clara cell, Type1 and Type2 cell markers in SAGM, which are then expressed when grown in Matrigel culture or in serum. Finally, the cells can be genetically manipulated toward oncogenesis (with KRASV12, and or missense p53). We conclude, that we have prepared multiple, immortalized strains of human peripheral lung epithelial cells with many characteristics of lung stem or progenitor cells that are experimentally tractable for studying lung differentiation and tumorigenesis. This work is supported by NCI SPORE P50CA70907, and NASA/DOE NSCOR NNJ05HD36G, DE‐AI02‐05ER64068
A protocatechuate biosensor for Pseudomonas putida KT2440 via promoter and protein evolution (2018)

Robust fluorescence-based biosensors are emerging as critical tools for high-throughput strain improvement in synthetic biology. Many biosensors are developed in model organisms where sophisticated synthetic biology tools are also well established. However, industrial biochemical production often employs microbes with phenotypes that are advantageous for a target process, and biosensors may fail to directly transition outside the host in which they are developed. In particular, losses in sensitivity and dynamic range of sensing often occur, limiting the application of a biosensor across hosts. Here we demonstrate the optimization of an <i>Escherichia coli-</i>based biosensor in a robust microbial strain for the catabolism of aromatic compounds, <i>Pseudomonas putida</i> KT2440, through a generalizable approach of modulating interactions at the protein-DNA interface in the promoter and the protein-protein dimer interface. The high-throughput biosensor optimization approach demonstrated here is readily applicable towards other allosteric regulators.
Superprism Effect of a Triangular One-Dimensional Photonic Crystal Embedded in a Slab Waveguide of a Ta2O5 Core with SiO2 Cladding (2006)

We first embedded a triangular one-dimensional photonic crystal in a slab waveguide of a Ta2O5 core with SiO2 cladding. The change in the output angle was 4.8° with the incident wavelength change of 1% for wavelengths of 1400–1500 nm. This value was 1.7 times larger than that of our previous photonic crystal with a SiO2 core. In addition, the maximum diffraction efficiency of 25% was achieved, which was a considerable improvement over the efficiency of our previous one.
GDMT-T: Superconducting Linear Device for PMI Studies (2013)

AbstractThe prospect of a new facility for plasma-surface interaction studies is presented. The unique features of this facility named GDMT-T are ability to generate both stationary plasma flux and transient events which simulate ITER ELM-mode operation and strong magnetic field on the target important for studies of dust and impurity migration. The experimental program of GDMT-T will include testing of plasma-facing components at ITER-relevant conditions and investigations of electron beam generation and beam-plasma interaction for application in the next generation of linear fusion facilities.
Trivariate, Stereological Length–Radius–Orientation Unfolding Derived and Applied to Alumina–Silicon Carbide Whisker Composites (2005)

A new method of simultaneously unfolding lengths, radii, and orientations of chopped fibers or whiskers embedded in composites with an axis of symmetry is presented. The technique makes use of previously derived stereological results for the unfolding of lengths and radii of chopped fibers that are randomly oriented. An equation relating the trivariate size–shape–orientation distribution to the orientation of elliptical sections appearing on a vertical plane is derived. The procedure is demonstrated on an alumina–silicon carbide whisker composite material. A functional form for the distribution of whiskers in hot pressed ceramic matrix composites is proposed.
Modelling and Control of a Quad-Rotor Robot (2006)

To date, most quad-rotor aerial robots have been based on flying toys. Although such systems can be used as prototypes, they are not sufficiently robust to serve as experimental robotics platforms. We have developed the X-4 Flyer, a quad-rotor robot using custom-built chassis and avionics with off-the-shelf motors and batteries, to be a highly reliable experimental platform. The vehicle uses tuned plant dynamics with an onboard embedded attitude controller to stabilise flight. A linear SISO controller was designed to regulate flyer attitude. 1