gebhart/patrepeval huggingface dataset:
Dual SMN inducing therapies can rescue survival and motor unit function in symptomatic ∆7SMA mice (2021)

Spinal muscular atrophy (SMA) is an autosomal recessive disease characterized by survival motor neuron (SMN) protein deficiency which results in motor neuron loss and muscle atrophy. SMA is caused by a mutation or deletion of the survival motor neuron 1 (SMN1) gene and retention of the nearly identical SMN2 gene. SMN2 contains a C to T change in exon 7 that results in exon 7 exclusion from 90% of transcripts. SMN protein lacking exon 7 is unstable and rapidly degraded. The remaining full-length transcripts from SMN2 are insufficient for normal motor neuron function leading to the development of SMA. Three different therapeutic approaches that increase full-length SMN (FL-SMN) protein production are approved for treatment of SMA patients. Studies in both animal models and humans have demonstrated increasing SMN levels prior to onset of symptoms provides the greatest therapeutic benefit. Treatment of SMA, after some motor neuron loss has occurred, is also effective but to a lesser degree. The SMN∆7 mouse model is a well characterized model of severe or type 1 SMA, dying at 14 days of age. Here we treated three groups of ∆7SMA mice starting before, roughly during, and after symptom onset to determine if combining two mechanistically distinct SMN inducing therapies could improve the therapeutic outcome both before and after motor neuron loss. We found, compared with individual therapies, that morpholino antisense oligonucleotide (ASO) directed against ISS-N1 combined with the small molecule compound RG7800 significantly increased FL-SMN transcript and protein production resulting in improved survival and weight of ∆7SMA mice. Moreover, when give late symptomatically, motor unit function was completely rescued with no loss in function at 100 days of age in the dual treatment group. We have therefore shown that this dual therapeutic approach successfully increases SMN protein and rescues motor function in symptomatic ∆7SMA mice.
In vivo time-resolved autofluorescence measurements to test for glycation of human skin (2008)

We present an evaluation of time-resolved fluorescence measurements on human skin for screening type 2 diabetes. In vivo human skin is excited with a pulse diode at 375 nm and pulse width of 700 ps. Fluorescence decays are recorded at four different emission wavelengths: 442, 460, 478, and 496 nm. Experiments are performed at various locations, including the palms, arms, legs, and cheeks of a healthy Caucasian subject to test single-subject variability. The fluorescence decays obtained are modeled using a three-exponential decay. The variations in the lifetimes and amplitudes from one location to another are minimal, except on the cheek. We compare the fluorescent decays of 38 diabetic subjects and 37 nondiabetic subjects, with different skin complexions and of ages ranging from 6 to 85 yr. The average lifetimes for nondiabetic subjects were 0.5, 2.6, and 9.2 ns with fractional amplitudes of 0.78, 0.18, and 0.03, respectively. The effects of average hemoglobin A1c (HbA1c) from the previous 4 yr and diabetes duration are evaluated. While no significant differences between the fluorescence lifetimes of nondiabetic and diabetic subjects are observed, two of the fractional amplitudes are statistically different. Additionally, none of the six fluorescence parameters correlated with diabetes duration or HbA1c. One of the lifetimes as well as two of the fractional amplitudes differ between diabetic subjects with foot ulcers and nondiabetic subjects.
Giant resonant light forces in microspherical photonics (2013)

Resonant light pressure effects can open new degrees of freedom in optical manipulation with microparticles, but they have been traditionally considered as relatively subtle effects. Using a simplified two-dimensional model of surface electromagnetic waves evanescently coupled to whispering gallery modes (WGMs) in transparent circular cavities, we show that under resonant conditions the peaks of the optical forces can approach theoretical limits imposed by the momentum conservation law on totally absorbing particles. Experimentally, we proved the existence of strong peaks of the optical forces by studying the optical propulsion of dielectric microspheres along tapered microfibers. We observed giant optical propelling velocities ∼0.45 mm s−1 for some of the 15-20 µm polystyrene microspheres in water for guided powers limited at ∼43 mW. Such velocities exceed previous observations by more than an order of magnitude, thereby providing evidence for the strongly enhanced resonant optical forces. We analyzed the statistical properties of the velocity distribution function measured for slightly disordered (∼1% size variations) ensembles of microspheres with mean diameters varying from 3 to 20 µm. These results demonstrate a principal possibility of optical sorting of microspheres with the positions of WGM resonances overlapped at the wavelength of the laser source. They can be used as building blocks of the lossless coupled resonator optical waveguides and various integrated optoelectronics devices. Researchers have developed a way of accelerating microscopic particles to high speeds using light beams. Vasily Astratov and colleagues, from the University of North Carolina at Charlotte in the USA, in collaboration with researchers from Russia and the UK, have shown theoretically and experimentally that a spherical particle whose circumference matches an integer multiple of the wavelength of the light experiences significantly stronger optical force compared to that felt by a slightly larger or smaller particle. In experiments with micrometre-sized polystyrene particles, spheres in resonance with the light beam travelled through water up to ten times faster than those of other sizes, thanks to their enhanced ability to trap and subsequently scatter light. This effect could be useful for sorting particles according to their resonances or sizes and for other optical manipulation schemes.
Compressed ultrafast photography by multi-encoding imaging (2018)

<p>Imaging ultrafast dynamic scenes has been long pursued by scientists. As a two-dimensional dynamic imaging technique, compressed ultrafast photography (CUP) provides the fastest receive-only camera to capture transient events. This technique is based on three-dimensional image reconstruction by combining streak imaging with compressed sensing (CS). However, the image quality and the frame rate of CUP are limited by the CS-based image reconstruction algorithms and the inherent temporal and spatial resolutions of the streak camera. Here, we report a new method to improve the temporal and spatial resolutions of CUP. Our numerical simulation and experimental verification show that by using a multi-encoding imaging method, both the image quality and the frame rate of CUP can be significantly improved beyond the intrinsic technical parameters. Importantly, the temporal resolution by our scheme can break the limitation of the streak camera. Therefore, this new technology has potential benefits in many applications that require the ultrafast dynamic scene image with high temporal and spatial resolutions.</p>
Privacy-Enabled Biometric Search (2017)

Biometrics have a long-held hope of replacing passwords by establishing a non-repudiated identity and providing authentication with convenience. Convenience drives consumers toward biometrics-based access management solutions. Unlike passwords, biometrics cannot be script-injected; however, biometric data is considered highly sensitive due to its personal nature and unique association with users. Biometrics differ from passwords in that compromised passwords may be reset. Compromised biometrics offer no such relief. A compromised biometric offers unlimited risk in privacy (anyone can view the biometric) and authentication (anyone may use the biometric). Standards such as the Biometric Open Protocol Standard (BOPS) (IEEE 2410-2016) provide a detailed mechanism to authenticate biometrics based on pre-enrolled devices and a previous identity by storing the biometric in encrypted form. This paper describes a biometric-agnostic approach that addresses the privacy concerns of biometrics through the implementation of BOPS. Specifically, two novel concepts are introduced. First, a biometric is applied to a neural network to create a feature vector. This neural network alone can be used for one-to-one matching (authentication), but would require a search in linear time for the one-to-many case (identity lookup). The classifying algorithm described in this paper addresses this concern by producing normalized floating-point values for each feature vector. This allows authentication lookup to occur in up to polynomial time, allowing for search in encrypted biometric databases with speed, accuracy and privacy.
Antibodies against the melanocortin-4 receptor act as inverse agonists in vitro and in vivo (2007)

Functionally active antibodies (Abs) against central G-protein-coupled receptors have not yet been reported. We selected the hypothalamic melanocortin-4 receptor (MC4-R) as a target because of its crucial role in the regulation of energy homeostasis. A 15 amino acid sequence of the N-terminal (NT) domain was used as an antigen. This peptide showed functional activity in surface plasmon resonance experiments and in studies on HEK-293 cells overexpressing the human MC4-R (hMC4-R). Rats immunized against the NT peptide produced specific antibodies, which were purified and characterized in vitro. In HEK-293 cells, rat anti-NT Abs showed specific immunofluorescence labeling of hMC4-R. They reduced the production of cAMP under basal conditions and after stimulation with a synthetic MC4-R agonist. Rats immunized against the NT peptide developed a phenotype consistent with MC4-R blockade, that is, increased food intake and body weight, increased liver and fat pad weight, and elevated plasma triglycerides. In a separate experiment in rats, an increase in food intake could be produced after injection of purified Abs into the third ventricle. Similar results were obtained in rats injected with anti-NT Abs raised in rabbits. Our data show for the first time that active immunization of rats against the NT sequence of the MC4-R results in specific Abs, which appear to stimulate food intake by acting as inverse agonists in the hypothalamus.
In Vivo Residue‐Specific Dopa‐Incorporated Engineered Mussel Bioglue with Enhanced Adhesion and Water Resistance (2014)

Abstract Misaminoacylation of 3,4‐dihydroxyphenylalanine (Dopa) molecules to tRNA Tyr by endogenous tyrosyl‐tRNA synthetase allowed the quantitative replacement of tyrosine residues with a yield of over 90 % by an in vivo residue‐specific incorporation strategy, to create, for the first time, engineered mussel adhesive proteins (MAPs) in Escherichia coli with a very high Dopa content, close to that of natural MAPs. The Dopa‐incorporated MAPs exhibited a superior surface adhesion and water resistance ability by assistance of Dopa‐mediated interactions including the oxidative Dopa cross‐linking, and furthermore, showed underwater adhesive properties comparable to those of natural MAPs. These results propose promising use of Dopa‐incorporated engineered MAPs as bioglues or adhesive hydrogels for practical underwater applications.
CCR6 is a receptor for CCL18 expressed on human lung fibroblasts from IPF lungs (2011)

Background: CCL18 is a chemokine released by alternatively activated macrophages binding to a yet unknown receptor. CCL18 induces collagen synthesis by fibroblasts thus indicating that the putative CCL18 receptor is expressed by human lung fibroblasts. Methods: To identify the receptor we screened a phage display library; the expression of the receptor was confirmed using conventional antibodies. FGF2 Release was measured by ELISA and expression of collagen and α-smooth muscle actin was estimated by quantitative PCR. Results: Phage-display experiments pointed to the CC-chemokine receptor 6 (CCR6) as CCL18-receptor. Staining lung tissue indicated CCR6 expression by AEC-II and fibroblasts in IPF lungs but not in tumour-free areas of resected lungs from SqC-patients. CCR6 was expressed by lung fibroblast lines derived from IPF lungs but was almost absent in lines from healthy areas of lung tissue from squamous carcinoma (SqC) patients. Spontaneous release of fibroblast growth factor 2 (FGF2) was very low in SqC-fibroblasts (71±25pg/ml) but significantly increased in IPF-fibroblasts (603±463pg/ml). Stimulation of fibroblasts with CCL18 induced a non-significant increase in FGF2 release in SqC-fibroblast lines (143±77pg/ml) but led to a significant increase in IPF lines (1194±601pg/ml) which was blocked by an anti-CCR6 antibody in IPF-fibroblast lines (783±632pg/ml) but not in SqC-lines (112±66pg/ml). Likewise, CCL18 induced an up-regulation of collagen I (coll-1) and αSMA expression. Again, induction of coll-I and αSMA expression was blocked by an anti-CCR6 antibody. Conclusion: Our data indicate that stimulatory effects of CCL18 on human lung fibroblasts are mediated via CCR6 (patent pending).
Image performance of a new amorphous selenium flat panel x-ray detector designed for digital breast tomosynthesis (2005)

The purpose of this work is to report the performance of an amorphous selenium (a-Se) based flat-panel x-ray imager under development for application in digital breast tomosynthesis. This detector is designed to perform both in the conventional Full Field Digital Mammography (FFDM) mode and the tomosynthesis mode. The large area 24 x 29 cm detector achieves rapid image acquisition rates of up to 4 frames per second with minimal trapped charge induced effects such as ghost or lag images of previously acquired objects. In this work, a new a-Se/TFT detector layer structure is evaluated. The design uses a top conductive layer in direct contact with the a-Se x-ray detection layer. The simple structure has few layers and minimal hole and electron trapping effects. Prototype detectors were built to investigate the basic image performance of this new a-Se/TFT detector. Image signal generation, image ghosting, image lag, and detector DQE were studied. For digital mammography applications, the residual image ghosting was less than 1% at 30 seconds elapsed time. DQE, measured at a field of 5.15 V/um, showed significantly higher values over previously reported data, especially at low exposure levels. For digital breast tomosynthesis, the image lag at dynamic readout rate was < 0.6 % at 0.5-second elapsed time. A prototype tomosynthesis system is being developed utilizing this new a-Se/TFT detector.
Interfacial microfluidic processing of metal-organic framework hollow fiber membranes (2014)

Molecular sieving metal-organic framework (MOF) membranes have great potential for energy-efficient chemical separations, but a major hurdle is the lack of a scalable and inexpensive membrane fabrication mechanism. We describe a route for processing MOF membranes in polymeric hollow fibers, combining a two-solvent interfacial approach for positional control over membrane formation (at inner and outer surfaces, or in the bulk, of the fibers), a microfluidic approach to replenishment or recycling of reactants, and an in situ module for membrane fabrication and permeation. We fabricated continuous molecular sieving ZIF-8 membranes in single and multiple poly(amide-imide) hollow fibers, with H2/C3H8 and C3H6/C3H8 separation factors as high as 370 and 12, respectively. We also demonstrate positional control of the ZIF-8 films and characterize the contributions of membrane defects and lumen bypass.
LDPC codes and stochastic decoding for beyond 100 Gb/s optical transmission (2008)

We present a modified stochastic LDPC decoding algorithm suitable for implementation at 100-Gb/s and above. The stochastic decoding is invented for low-precision digital circuits, and as such is suitable for beyond 100-Gb/s implementation to avoid the problem of nonexistence of high-precision analog-to-digital converters operating at those speeds.
Cloning and expression of Treponema pallidum (Nichols) antigen genes in Escherichia coli (1983)

Hybrid pBR322 plasmid clone banks comprised of more than 125,000 recombinant DNA clones and representing the entire Treponema pallidum Nichols genome were constructed in Escherichia coli K-12 RR1. The two clone banks individually contain over 53,000 and 72,000 recombinant clones. The number average and mass average sizes of the cloned DNA inserts were found to be approximately 12 and 13 kilobase pairs, respectively, indicating the presence of large treponemal DNA inserts in a majority of recombinant clones. To detect E. coli clones synthesizing T. pallidum antigens as hybrid plasmid gene translation products in the clone bank, a simplified, direct, solid-phase radioimmuno-colony blot (RICB) assay was developed employing immunoglobulin G antibody isolated from anti-T. pallidum immune rabbit serum. Clones with positive reactivities in the RICB assay were isolated at frequencies of 0.1 to 0.2%. One isolated RICB-positive clone, designated RICB2-1, produced a very strong signal in the RICB assay and was subsequently found through E. coli cell-free in vitro transcription/translation analysis to encode the synthesis of two gene translation products with apparent molecular weights of 77,000 and 44,000. The 44,000-dalton protein was effectively immunoprecipitated from [35S]methionine-labeled E. coli clone cells by using either immune rabbit serum (preabsorbed with Treponema phagedenis biotype Reiter antigens) or selected human syphilitic serum, whereas the 77,000-dalton protein was never immunoprecipitable by similar methods. Purified plasmid DNA from clone RICB2-1 contained a treponemal DNA insert of 3.70 kilobase pairs, which was of suitable size to code for the 121-dalton (44 + 77) protein. The insert was also flanked on each end by PstI sites and possessed three internal PstI sites with fragment sizes of 2.15, 1.18, 0.20, and 0.17 kilobase pairs. Purified clone RICB2-1 plasmid DNA was capable of transforming recipient E. coli cells to virtually 100% RICB reactivity, thus substantiating the plasmid-encoded characteristic. Further experiments employing various antisera in radioimmunoprecipitation systems utilizing cell-free in vitro synthesized gene translation products from clone RICB2-1 also provided the first evidence that E. coli may be capable of using endogenous T. pallidum DNA promotors for genetic expression. These studies, amplified by the isolation of a potentially significant immunoprecipitable 44,000-dalton recombinant protein antigen, point to the importance of the "cloned antigen gene" approach for the eventual eludication of specific antigens or immunogens operative in the pathogenesis, immunology, and serodiagnosis of T. pallidum infection.
Determination of optimum resistor sequence in a ballistic breaker (2012)

A novel design for a DC circuit breaker based on commutating the current over a series of different resistive paths through a variable resistance commutating shuttle was first described in a 2011 paper <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1</sup> . Since then, it has been recognized that the concept can be generalized to stationary resistors as well as moving resistors, to rotating shuttles as well as shuttles that move axially; and to stepper motors or other drives to actuate the motion of the shuttle, in addition to methods which are capable of driving the shuttle ballistically (as was initially envisioned).
Combined Effects of Shunt and Luminescence Coupling on External Quantum Efficiency Measurements of Multijunction Solar Cells (2011)

The combined effects of shunt and luminescence coupling on the measurement artifact of external quantum efficiency (EQE) of multi-junction solar cells are studied. The EQE measurement artifact is modeled using DC and small-signal equivalent circuits under voltage and light bias conditions. The modeling results are verified with EQE measurements of a Ge bottom cell of a triple-junction solar cell. It is found that the optimal bias light intensity to minimize the EQE measurement artifact is the result of the tradeoff between the shunt and the luminescence coupling effects.
New design for wavelength-flattened 2×2 tapered fused couplers for single- and few-mode fibers (1991)

A well-known way of realizing wavelength-flattened couplers is to fuse and taper two different optical fibers. 1,2 These couplers, however, are difficult to realize because of the control required in the asymmetry as well as with the usual coupler parameters. We propose an alternate method using identical fibers.
Application performance of elements in a floating-gate FPAA (2004)

Field-programmable analog arrays (FPAAs) provide a method for rapidly prototyping analog systems. Currently available commercial and academic FPAAs are typically based on operational amplifiers (or other similar analog primitives) with only a few computational elements per chip. While their specific architectures vary, their small sizes and often restrictive interconnect designs leave current FPAAs limited in functionality, flexibility, and usefulness. In this paper, we explore the use of floating-gate devices as the core programmable element in a signal processing FPAA. A generic FPAA architecture is presented that offers increased functionality and flexibility in realizing analog systems. In addition, the computational analog elements are shown to be widely and accurately programmable while remaining small in area.
High capacity image barcodes using color separability (2010)

Two-dimensional barcodes are widely used for encoding data in printed documents. In a number of applications, the visual appearance of the barcode constitutes a fundamental restriction. In this paper, we propose high capacity color image barcodes that encode data in an image while preserving its basic appearance. Our method aims at high embedding rates and sacrifices image fidelity in favor of embedding robustness in regions where these two goals conflict with each other. The method operates by utilizing cyan, magenta, and yellow printing channels with elongated dots whose orientations are modulated in order to encode the data. At the receiver, by using the complementary sensor channels to estimate the colorant channels, data is extracted in each individual colorant channel. In order to recover from errors introduced in the channel, error correction coding is employed. Our simulation and experimental results indicate that the proposed method can achieve high encoding rates while preserving the appearance of the base image.