gebhart/patrepeval huggingface dataset:
Mutations in the human forkhead transcription factor FOXE3 associated with anterior segment ocular dysgenesis and cataracts (2001)

Dysgenesis of the anterior segment of the eye delineates a spectrum of human developmental disorders that show wide phenotypic and genetic heterogeneity. It is also frequently associated with cataracts and glaucoma resulting in visual disability in childhood. The recently described forkhead transcription factor gene Foxe3 was shown to be involved in the dysgenetic lens phenotype in mice, which is characterized by small cataractic lens and anterior segment anomalies. Here we report an identification and characterization of the human ortholog of this gene, FOXE3. The gene was found to be expressed in the anterior lens epithelium and to be mutated in patients with ocular disorders. An insertion of G in the coding region of the FOXE3 gene that occurred 15 nucleotides upstream of the stop codon was identified in a family with anterior segment ocular dysgenesis and cataracts. The mutation causes a frameshift that results in an abnormal sequence of five terminal amino acids and an addition of 111 amino acids to the predicted protein. The mutation was present in two affected individuals from this family and was not identified in 180 normal control chromosomes.
Handheld skin printer: <i>in situ</i> formation of planar biomaterials and tissues (2018)

We present a handheld skin printer that enables the in situ formation of biomaterial and skin tissue sheets of different homogeneous and architected compositions. When manually positioned above a target surface, the compact instrument (weight <0.8 kg) conformally deposits a biomaterial or tissue sheet from a microfluidic cartridge. Consistent sheet formation is achieved by coordinating the flow rates at which bioink and cross-linker solution are delivered, with the speed at which a pair of rollers actively translate the cartridge along the surface. We demonstrate compatibility with dermal and epidermal cells embedded in ionically cross-linkable biomaterials (e.g., alginate), and enzymatically cross-linkable proteins (e.g., fibrin), as well as their mixtures with collagen type I and hyaluronic acid. Upon rapid crosslinking, biomaterial and skin cell-laden sheets of consistent thickness, width and composition were obtained. Sheets deposited onto horizontal, agarose-coated surfaces were used for physical and in vitro characterization. Proof-of-principle demonstrations for the in situ formation of biomaterial sheets in murine and porcine excisional wound models illustrate the capacity of depositing onto inclined and compliant wound surfaces that are subject to respiratory motion. We expect the presented work will enable the in situ delivery of a wide range of different cells, biomaterials, and tissue adhesives, as well as the in situ fabrication of spatially organized biomaterials, tissues, and biohybrid structures.
<title>Fuzzy-assignment-based color interpolation algorithm</title> (2000)

In an electronic color imaging device such as a digital camera using a single CCD or CMOS sensor, the color information is usually acquired in sub-sampled patterns of red (R), green (G) and blue (B) pixels. Full resolution color is subsequently generated from this sub-sampled image. This is popularly called Color Interpolation or Color Demosaicing. In this paper, we present a color interpolation algorithm using the method of fuzzy membership assignment along with the concept of smooth hue transition. The algorithm is adaptive in nature and produces superior quality full resolution color images compared to most of the popularly known color interpolation algorithms in the literature. Performance of the algorithm has been compared with a previously proposed block matching algorithm for color interpolation by the authors as well as the popularly used bilinear color interpolation. We present the results of comparison with some challenging sub-sampled images for color interpolation.
Development of Non-Birefrmgent Optical Adhesives (1997)

Abstract The birefringence compensation technique1 has been employed through polymer blending for the development of non-birefringent optical adhesives. It has been found that trimellitic anhydride(TMA)-cured polymethylmethacylate(PMMA)/Epoxy EPON-828) as a possible system resulted in phase separation due to polymerization2. To circumvent the problem of polymerization-induced phase separation, a copolymer system comprised of methylmethacrylate(MMA) and glycidylmethacrylate(GMA) was synthesiztd3. The MMA-co-GMA copolymer was subsequently blended with EPON-828, then cured thermally with TMA. The cured blend films showed single glass transition at all compositions and optical transparency suggestive of miscible character. These optical adhesive blends showed zero birefringence or zero optical retardation at compositions between 60–70-wt% copolymer. The zero Birefringence afforded by the compensation of the intrinsic birefringence of the constituent polymer chains may be attributed to the complete miscibility of the blends in the cured state.
Assessing corneal biomechanics without external excitation: heartbeat optical coherence elastography (Conference Presentation) (2020)

Quantifying the biomechanical properties of the cornea is required for accurate assessment of tissue health. In this work, we evaluate cornea biomechanical properties during intraocular pressure fluctuation. This method results in a more physiologically relevant assessment of tissue mechanics, and thus diverges from typical elastography techniques that use externally induced deformation. Optical coherence elastography is used to detect displacements in the cornea as IOP is cycled during the heartbeat. The axial strains within the cornea are calculated from these displacements, so that dynamic changes in stiffness can be determined. The results indicate a gradient in axial strain within the cornea.
Controlling evanescent waves on-chip using all-dielectric metamaterials for dense photonic integration (2017)

Miniaturization of optical components with low power consumption fabricated using a CMOS foundry process can pave the way for dense photonic integrated circuits within nanoelectronic platforms. However, the large spatial extent of evanescent light waves generated during nanoscale light confinement are ubiquitous in silicon photonic devices and are the stumbling roadblock to miniaturization. Here, we demonstrate the control of evanescent waves using all-dielectric metamaterials on a chip. We demonstrate that anisotropic metamaterials open a new degree of freedom in total internal reflection (TIR) to reduce the decay length of evanescent waves. This counterintuitive approach uses optical devices which can have a cladding with a higher average index than the core and marks a departure from interference based confinement as in photonic crystal waveguides or slot waveguides which utilize nanoscale field enhancement. We experimentally show that all-dielectric anisotropic metamaterials can help to reduce the cross-talk more than 30 times and bending loss more than 3 times in ultra-compact photonic circuits, two major attributes that limit the integration density in photonic circuits. We verify our all-dielectric metamaterial platform fabricated on a scalable process with a relatively negligible propagation loss of 3.67 dB/cm paving the way to impact future device designs for dense photonic integration
A Parfocality Measurement Method of a Continuous Zoom Stereo Microscope (2013)

Abstract To satisfy the demands of the continuous zoom stereo microscope, a parfocality measurement method is proposed. First, the mechanical parameters of the focusing system are estimated by testing the highest and the lowest displacements of the lens group and the rotation angle of the knob simultaneously. Second, by analyzing images captured under different zoom rates, the relatively sharpest displacement under a specified zoom rate is obtained according to the values of the four definition functions, including the variance function, the gradient square function, the discrete Fourier transform function and the Walsh-Hadamard transform function. Then, an in-focus model is presented and implemented to determine whether or not the relatively sharpest displacement under a specified zoom rate is an in-focus displacement, and to obtain the discrete in-focus displacements under multirates. Finally, by using discrete in-focus displacements, a continuous zoom in-focus curve is fitted. Results from the experiments show that the proposed method can accurately and effectively measure the parfocality of a continuous zoom stereo microscope.
An efficient on-the-fly cycle collection (2007)

A reference-counting garbage collector cannot reclaim unreachable cyclic structures of objects. Therefore, reference-counting collectors either use a backup tracing collector infrequently, or employ a cycle collector to reclaim cyclic structures. We propose a new concurrent cycle collector, one that runs concurrently with the program threads, imposing negligible pauses (of around 1ms) on a multiprocessor. Our new collector combines a state-of-the-art cycle collector [Bacon and Rajan 2001] with sliding-views collectors [Levanoni and Petrank 2001, 2006; Azatchi et al. 2003]. The use of sliding views for cycle collection yields two advantages. First, it drastically reduces the number of cycle candidates, which in turn drastically reduces the work required to record and trace these candidates. Consequentially, a large improvement in cycle collection efficiency is achieved. Second, it eliminates the theoretical termination problem that appeared in the earlier concurrent cycle collector. There, a rare race may delay the reclamation of an unreachable cyclic structure forever. The sliding-views cycle collector guarantees reclamation of all unreachable cyclic structures. The proposed collector was implemented on the Jikes RVM and we provide measurements including a comparison between the use of backup tracing and the use of cycle collection with reference counting. To the best of our knowledge, such a comparison has not been reported before.
The frequency of druggable targets in localized prostate cancer: Initial analysis from the Decipher GRID. (2016)

98 Background: Prostate cancers patient management has been enhanced with commercially available genomic prognostic tests such as the Decipher prostate cancer classifier that are useful for making treatment decision-making. In addition to being the most validated predictor of metastasis in prostate cancer, Decipher is also a genome-wide assay that measures the expression of many druggable targets. Methods: Decipher GRID (Genomic Resource Information Database), was queried to assess the expression patterns of 14 genes from 5 biological pathways (Table) in 1,850 patients from previously published Decipher validation studies. The frequency of high (or low) expression of each gene was ascertained using a standard and more conservative thresholds based on the median absolute deviation (MAD) metric. For the standard threshold, genes whose high expression is of clinical relevance, patients with gene expression above the median + 1.48*MAD were annotated as high expression and for genes whose low expression is of clinical relevance, patients with gene expression below the median - 1.48*MAD were annotated as low expression. For the conservative threshold, median +/- 2*1.48*MAD was used. Results: See Table. Conclusions: Since every patient receiving the Decipher test also has a genome-wide expression profile, the Decipher GRID will allow researchers to evaluate on a systematic population-level the expression of genes that may be targeted with existing therapies. Such information may be useful for selection of optimal systemic therapy and inclusion into clinical trials of novel targeted agents. This rich genomic resource is being made available on a research use only basis to prostate cancer researchers and to clinicians seeking to uncover individualized genomic insights for patients to advance precision medicine. [Table: see text]
Noncontact orientation of objects in three-dimensional space using magnetic levitation (2014)

This paper describes several noncontact methods of orienting objects in 3D space using Magnetic Levitation (MagLev). The methods use two permanent magnets arranged coaxially with like poles facing and a container containing a paramagnetic liquid in which the objects are suspended. Absent external forcing, objects levitating in the device adopt predictable static orientations; the orientation depends on the shape and distribution of mass within the objects. The orientation of objects of uniform density in the MagLev device shows a sharp geometry-dependent transition: an analytical theory rationalizes this transition and predicts the orientation of objects in the MagLev device. Manipulation of the orientation of the levitating objects in space is achieved in two ways: (i) by rotating and/or translating the MagLev device while the objects are suspended in the paramagnetic solution between the magnets; (ii) by moving a small external magnet close to the levitating objects while keeping the device stationary. Unlike mechanical agitation or robotic selection, orienting using MagLev is possible for objects having a range of different physical characteristics (e.g., different shapes, sizes, and mechanical properties from hard polymers to gels and fluids). MagLev thus has the potential to be useful for sorting and positioning components in 3D space, orienting objects for assembly, constructing noncontact devices, and assembling objects composed of soft materials such as hydrogels, elastomers, and jammed granular media.
Identification and functional characterization of eight CYP3A4 protein variants. (2001)

The genetic component of the inter-individual variability in CYP3A4 activity has been estimated to be between 60% and 90%, but the underlying genetic factors remain largely unknown. A study of 213 Middle and Western European DNA samples resulted in the identification of 18 new CYP3A4 variants, including eight protein variants. A total of 7.5% of the population studied was found to be heterozygous for one of these variants. In a bacterial heterologous expression system, two mutants, R130Q and P416L, did not result in detectable P450 holoprotein. One mutant, T363M, expressed at significantly lower levels than wild-type CYP3A4. G56D, V170I, D174H and M445T were not significantly different when compared with wild-type CYP3A4 in expression or steroid hydroxylase activity. L373F displayed a significantly altered testosterone metabolite profile and a four-fold increase in the Km value for 1'-OH midazolam formation. The results suggest a limited contribution of CYP3A4 protein variants to the inter-individual variability of CYP3A4 activity in Caucasians. Some variants may, however, play a role in the atypical response to drugs or altered sensitivity to carcinogens.
An Importance Sampling Approach for Time-Dependent Reliability (2011)

Reliability is an important engineering requirement for consistently delivering acceptable product performance through time. The reliability usually degrades with time increasing the lifecycle cost due to potential warranty costs, repairs and loss of market share. Reliability is the probability that the system will perform its intended function successfully for a specified time. In this article, we consider the first-passage reliability which accounts for the first time failure of non-repairable systems. Methods are available which provide an upper bound to the true reliability which may overestimate the true value considerably. The traditional Monte-Carlo simulation is accurate but computationally expensive. A computationally efficient importance sampling technique is presented to calculate the cumulative probability of failure for random dynamic systems excited by a stationary input random process. Time series modeling is used to characterize the input random process. A detailed example demonstrates the accuracy and efficiency of the proposed importance sampling method over the traditional Monte Carlo simulation.
<i>BCR-ABL</i>alternative splicing as a common mechanism for imatinib resistance: evidence from molecular dynamics simulations (2008)

Rare cases of chronic myelogenous leukemia (CML) express high levels of alternatively spliced BCR-ABL mRNA with a 35-bp insertion (35INS) between ABL kinase domain exons 8 and 9. This insertion results in a frameshift leading to the addition of 10 residues and truncation of 653 residues due to early termination. Sensitive PCR-based testing showed that 32 of 52 (62%) imatinib-resistant CML patients in chronic phase and 8 of 38 (21%) in accelerated or blast crisis expressed varying levels of the alternatively spliced BCR-ABL mRNA. A three-dimensional structural model of the 35INS ABL kinase domain complexed with imatinib was built using homology modeling, followed by molecular dynamics simulations. Simulation results showed that the new residues cause a significant global conformational change, altering imatinib binding in a way similar to that of the T315I mutation and, therefore, providing resistance to imatinib that depends on the level of expression.
Analog-to-Digital Converter Error Correction using Frequency Selective Tables (2002)

Error correction for analog-to-digital converters (ADCs) is considered. The frequency-dependent nature of ADC errors motivates the proposal of a novel scheme, incorporating look-up table correction and fast frequency estimation. The method is evaluated using experimental converter data, and the performance, measured in SFDR and SINAD, is found to be superior to that of non frequency-dependent correction methods.
Development of a validated LC- MS/MS method for the quantification of 19 endogenous asthma/COPD potential urinary biomarkers (2017)

Obstructive airways inflammatory diseases sometimes show overlapping symptoms that hinder their early and correct diagnosis. Current clinical tests are tedious and are of inadequate specificity in special population such as the elderly and children. Therefore, we are developing tandem mass spectrometric (MS/MS) methods for targeted analysis of urine biomarkers. Recently, proton-nuclear magnetic resonance (<sup>1</sup>H-NMR) analysis proposed 50 urinary metabolites as potential diagnostic biomarkers among asthma and chronic obstructive pulmonary disease (COPD) patients. Metabolites are divided into 3 groups based on chemical nature. For group 1 (amines and phenols, 19 urinary metabolites), we developed and validated a high performance liquid chromatographic (HPLC)-MS/MS method using differential isotope labeling (DIL) with dansyl chloride. Method development included the optimization of the derivatization reaction, the MS/MS conditions, and the chromatographic separation. Linearity varied from 2 to 4800 ng/mL and the use of <sup>13</sup>C<sub>2</sub>-labeled derivatives allowed for the correction of matrix effects as well as the unambiguous confirmation of the identity of each metabolite in the presence of interfering isomers in urine. Despite the challenges associated with method validation, the method was fully validated as per the food and drug administration (FDA) and the European medicines agency (EMA) recommendations. Validation criteria included linearity, precision, accuracy, dilution integrity, selectivity, carryover, and stability. Challenges in selectivity experiments included the isotopic contributions of the analyte towards its internal standard (IS), that was addressed via the optimization of the IS concentration. In addition, incurred sample analysis was performed to ensure that results from patient samples are accurate and reliable. The method was robust and reproducible and is currently being applied in a cohort of asthma and COPD patient urine samples for biomarker discovery purposes.
ChemInform Abstract: STRUCTURAL MODIFICATION STUDY OF BIS(SUBSTITUTED AMINOALKYLAMINO)ANTHRAQUINONES. AN EVALUATION OF THE RELATIONSHIP OF THE (2‐((2‐HYDROXYETHYL)AMINO)ETHYL)AMINO SIDE CHAIN WITH ANTINEOPLASTIC ACTIVITY (1979)

Abstract Von den im Formelschema aufgeführten Verbindungen werden (II), (IIIb), (IV)‐(VIIa) dargestellt.
Horizon nulling helix antennas for GPS timing (2017)

Global Positioning System (GPS) antennas installed at fixed site infrastructure are susceptible to interference incident along the direction of the horizon. In this paper, a series of quadrifilar helical antennas are presented for the application of GPS timing. The first antenna employs a novel method of reactive loading along the length of the multi-turn helix. The phase distribution along the helix creates a deep null in the gain pattern at the horizon while maintaining sufficient beam width in the zenith direction. The horizon null minimizes ground based interference. The second antenna achieves similar performance by varying the pitch of the helix arms along the length of the antenna. The third antenna operates over L1 and L2 frequencies using concentric helices. A novel method is presented to decouple the concentric helices based on distributed trap circuits along the length of the helix arms, which preserves the horizon nulling patterns at both frequencies. The proposed antennas offer improved performance over previous horizon-nulling designs. Additionally, the proposed antennas can be manufactured at a lower cost compared to other interference mitigating antennas based on the simple architecture.
Germanium-on-SOI Infrared Detectors for Integrated Photonic Applications (2006)

An overview of recent results on high-speed germanium-on-silicon-on-insulator (Ge-on-SOI) photodetectors and their prospects for integrated optical interconnect applications are presented. The optical properties of Ge and SiGe alloys are described and a review of previous research on SOI and SiGe detectors is provided as a motivation for the Ge-on-SOI detector approach. The photodetector design is described, which consists of lateral alternating p- and n-type surface contacts on an epitaxial Ge absorbing layer grown on an ultrathin-SOI substrate. When operated at a bias voltage of -0.5 V, 10mumtimes10 mum devices have dark current I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dark</sub> , of only ~10 nA, a value that is nearly independent of finger spacing S, between S=0.3mum and 1.3mum. Detectors with S=1.3mum have external quantum efficiencies eta, of 52% (38%) at lambda=895 nm (850 nm) with corresponding responsivities of 0.38 A/W (0.26 A/W). The wavelength-dependence of eta agrees fairly well with expectations, except at longer wavelengths, where Si up-diffusion into the Ge absorbing layer reduces the efficiency. Detectors with 10 mumtimes10 mum area and S=0.6mum have -3-dB bandwidths as high as 29 GHz, and can simultaneously achieve a bandwidth of 27 GHz with I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dark</sub> =24 nA, at a bias of only -1 V, while maintaining high efficiency of eta=46%(33%), at lambda=895 nm (850 nm). Analysis of the finger spacing and area-dependence of the device speed indicates that the performance at large finger spacing is transit-time-limited, while at small finger spacing, RC delays limit the bandwidth. Methods to improve the device performance are presented, and it is shown that significant improvement in the speed and efficiency both at lambda=850 and 1300 nm can be expected by optimizing the layer structure design