gebhart/patrepeval huggingface dataset:
Retinoid‐binding proteins: structural determinants important for function (1995)

The transport and functions of biologically active naturally occurring retinoids (Vitamin A, retinol, and its metabolites) are mediated by extracellular, intracellular, and nuclear proteins. X-ray crystallographic studies to date on the extra- and intracellular proteins have helped to define distinct protein retinoid recognition mechanisms, each with a characteristic structural motif. The extracellular proteins (serum retinol-binding protein and a retinoic acid-binding protein from rat epididymis) bind retinoids with a hand-in-glove like fit in deep, hydrophobic-binding cavities. The intracellular proteins (cellular retinol-binding proteins types I and II) encapsulate the ligand in an aqueous internal cavity. The details of the mechanisms of retinoid recognition, and how they result as a consequence of the different protein structures, are described in this review.
A gesture-based design tool: Assessing 2DOF vs. 4DOF steerable instrument control (2018)

Iterative prototyping is costly and time-consuming. Particularly when designing medical instruments, human factors related design choices significantly impact performance and safety. A tool is presented that allows for the evaluation of steerable instrument controls before the onset of the prototyping stage. The design tool couples gestural input to virtually simulated instrument motions using hand motion tracking. We performed a human-subject evaluation of two manual control strategies that differed in their degrees of freedom (DOF). 2DOF thumb control was compared to 4DOF thumb-index finger control. Results identified regions within the instrument workspace that are difficult to reach and showed participants to favor using the thumb for gross and fine-tuning motions at both control strategies. Index finger ab/adduction was found to be least functional. A strong learning effect was observed at 4DOF control. Based on the results, gesture-based instrument design is a viable design tool.
Changes in Polyphenol Concentrations and Polyphenol Oxidase Activity of Loquat (Eriobotrya japonica Lindl.) Fruits in Relation to Browning. (1998)

Polyphenols and polyphenol oxidase (PPO) activity in the fruits of loquat (cv. Mogi) during development and storage were studied in relation to browning of the pulp. The concentration of total phenolics decreased sharply during fruit growth and then increased significantly during maturation and ripening. But, it varied slightly during the two months of cold storage. Chlorogenic acid increased rapidly during fruit maturation and ripening and became a predominant compound in ripe fruits. Chlorogenic acid decreased slightly while the fruit was stored at 5°C. PPO activity declined concurrent to fruit growth and ripening. In cold storage, PPO activity decreased gradually, but from 68.8 to 92.2% of the browning in the reaction mixture prepared from pulp juice occurred within the first hour. Chlorogenic acid oxidation proceeded quickly and played an important role in browning of ripe fruit. Total phenolics was highly related to the degree of browning.
Fullerene bisadduct as an effective phase-separation inhibitor in preparing poly(3-hexylthiophene)–[6,6]-phenyl-C61-butyric acid methyl ester blends with highly stable morphology (2012)

This work demonstrates that the bis-adduct of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) is an effective inhibitor of the aggregation of PCBM inside the poly(3-hexylthiophene) (P3HT) matrix. Substituting some of the PCBM with bis-PCBM apparently reduces the size of PCBM-rich clusters, enhancing both the short-circuit current density (JSC) and the fill factor (FF), leading to a ∼17% increment in power conversion efficiency (PCE) for a cell with 8.3 wt% bis-PCBM replacement. More importantly, a tiny amount of bis-PCBM significantly improves the morphological stability of P3HT–PCBM blend against high-temperature aging. All P3HT–PCBM:bis-PCBM devices exhibit extremely stable PCEs, which do not visibly change upon heating at 150 °C for 15 hours.
CRISPR/Cas9 Targeted Gene Editing and Cellular Engineering in Fanconi Anemia (2016)

The ability to rationally target disease-causing mutations has been made possible with programmable nucleases with the CRISPR/Cas9 system representing a facile platform for individualized gene-based medicine. In this study we employed footprint free reprogramming of fibroblasts from a patient with mutations to the Fanconi anemia I (FANCI) gene to generate induced pluripotent stem cells (iPSC). This process was accomplished without gene complementation and the resultant iPSC were able to be gene corrected in a robust manner using the Cas9 nickase. The self-renewing iPSC that were maintained under feeder free conditions were differentiated into cells with characteristics of definitive hematopoiesis. This defined and highly efficient procedure employed small molecule modulation of the hematopoietic differentiation pathway and a vascular induction technique to generate hematopoietic progenitors. In sum, our results demonstrate the ability to induce patient derived FA cells to pluripotency for patient specific therapeutic cell derivation.
Patient-reported distress in adults with myelodysplastic syndromes (MDS). (2016)

80 Background: MDS are hematopoietic malignancies that are incurable in most patients. The National Comprehensive Cancer Network (NCCN) defines distress as an unpleasant emotional experience associated with the psychosocial complications of cancer that may interfere with quality of life. Distress is not well described in MDS and may be useful to screen for palliative care needs. Methods: We conducted a retrospective review of distress in ambulatory adult MDS patients visiting our clinics from July 2013 to September 2015. We abstracted demographic, diagnostic, and comorbidity data from records along with the 10-point ordinal NCCN Distress Thermometer (DT) and its 39-item Problem List (PL). NCCN guidelines suggest DT scores ≥ 4 be evaluated for referral to psychosocial resources. Results: We included 119 patients (median age = 68, range = 30-88 years; 73.9% White; 67.2% male; 29.4% with prior cancer). Half were low-risk and 5 progressed to AML. Twenty-three (19.3%) had ≥ 1 hospitalization and 10.9% had &gt; = 1 emergency department visit. Ten patients died; 1 was referred to counseling and 1 used hospice. Three others were referred to counseling and no patients had a palliative care consult. There were 366 DT (median distress = 1, range = 0-10) across 580 visits and 106 patients (median = 2 DT/patient, range = 1-16). Fifty-two patients had at least 1 DT ≥ 4 and 19 had 2 or more DT ≥ 4. With patients classified by their maximum DT (median = 3, interquartile range = 1-7) ever-use of therapy (hypomethylating agents/lenalidomide/growth factors/transfusions/chelation) was associated with greater maximum DT (median = 4, range = 0-10, N = 73) compared with no therapy (median = 2, range = 0-9, N = 33; P = 0.03, 2-sample Wilcoxon test). Ninety-five patients reported 1,335 problems during 22,846 person-days of follow-up (median = 4 problems/patient/visit, range = 1-23). The 5 most frequent problems were fatigue (176 times; 76 patients), pain (92 times; 44 patients), worry (77 times; 43 patients), sleep (75 times; 39 patients), and tingling hands/feet (68 times; 33 patients). Conclusions: MDS patients experience frequent and substantial distress yet referrals to counseling and use of palliative care are rare. These findings point to unmet palliative care needs in MDS.
Characterization and correction of data loss in a high bandwidth passive radar system (2014)

Passive radar receivers use transmitters of opportunity such as digital television (DTV) broadcast to detect targets. The next generation Manastash Ridge Radar (MRR) is designed without the use of an analog downconverter to observe transmitters up to 1.5 GHz. In addition to fast sampling, the receiver is built around a Xilinx Virtex-5 field programmable gate array (FPGA) for software-defined, flexible, and real-time, low latency processing. The FPGA channelizes data from up to four antennas and streams 8-bit IQ data through a 10 GbE link to a data recorder. Challenging the capacity of this link is extremely desirable, as it will allow the user to save a wide RF spectrum to disk for experimental processing. In the fastest use of this link, we observe up to 10 frequency-adjacent DTV stations simultaneously, however packet loss occurs. We present here characterization of this loss in real data, simulations of how this loss propagates through the processing chain and affects the final data product, suggestions for correcting this loss, and apply these strategies to real detections of aircraft on each of four antennas. The results of the simulations suggest that the radar system can absorb even 50% data loss while losing only 3 dB in detectability of targets and completely recover accurate range and Doppler velocity estimates. The detection of an aircraft with our system in the presence of 12% data loss follows the trends observed in simulation. This encouraging result shows that systems with high processing gain are incredibly robust to noise and the sacrifice of lost data in the face of observing more RF spectrum (more transmitters) is truly not a sacrifice at all.
JWST microshutter array system and beyond (2010)

We have developed the Microshutter Array (MSA) system at NASA Goddard Space Flight Center (GSFC) as a multi-object aperture array for the Near Infrared Spectrograph (NIRSpec) instrument on the James Webb Space Telescope (JWST). The MSA system will enable NIRSpec to simultaneously obtain spectra from more than 100 targets, which, in turn, increases instrument efficiency one-hundred fold. Consequently, this system represents one of the three major innovations on the JWST, which has been selected by the National Research Council's 2001 decadal survey as the top-ranked space-based mission and is scheduled to be the successor to the Hubble Space Telescope. Furthermore, the MSA system will be one of the first MEMS devices serving observation missions in space. Microshutters are designed for the selective transmission of light with high efficiency and contrast and feature torsion hinges, light shields, deep-reactive ion-etched silicon windows, magnetic actuation, and electrostatic latching and addressing. Complete MSA quadrant assemblies consisting of 365 x 181 microshutters have been successfully fabricated. The assemblies have passed a series of critical reviews, which include programmable 2-D addressing, life tests, optical contrast tests, and environmental tests, required by the design specifications of JWST. Both the MSA and NIRSpec will be delivered to ESA for final assembly, and JWST is scheduled to launch in 2014. During final assembly and testing of the MSA system, we have begun to develop the Next Generation Microshutter Arrays (NGMSA) for future telescopes. These telescopes will require a much larger field of view than JWST's, and we discuss strategies for fabrication of a proof-of-concept NGMSA which will be modular in design and electrostatically actuated.
Guided growth of auditory neurons: Bioactive particles towards gapless neural – electrode interface (2016)

Cochlear implant (CI) is a successful device to restore hearing. Despite continuous development, frequency discrimination is poor in CI users due to an anatomical gap between the auditory neurons and CI electrode causing current spread and unspecific neural stimulation. One strategy to close this anatomical gap is guiding the growth of neuron dendrites closer to CI electrodes through targeted slow release of neurotrophins. Biodegradable calcium phosphate hollow nanospheres (CPHSs) were produced and their capacity for uptake and release of neurotrophins investigated using <sup>125</sup>I-conjugated glia cell line-derived neurotrophic factor (GDNF). The CPHSs were coated onto CI electrodes and loaded with neurotrophins. Axon guidance effect of slow-released neurotrophins from the CPHSs was studied in an in vitro 3D culture model. CPHS coating bound and released GDNF with an association rate constant 6.3 × 10<sup>3</sup> M<sup>-1</sup>s<sup>-1</sup> and dissociation rate 2.6 × 10<sup>-5</sup> s<sup>-1</sup>, respectively. Neurites from human vestibulocochlear ganglion explants found and established physical contact with the GDNF-loaded CPHS coating on the CI electrodes placed 0.7 mm away. Our results suggest that neurotrophin delivery through CPHS coating is a plausible way to close the anatomical gap between auditory neurons and electrodes. By overcoming this gap, selective neural activation and the fine hearing for CI users become possible.
Monitoring aerosol optical properties over the Mediterranean from SeaWiFS images using a neural network inversion (2004)

The SeaWiFS archive provides a unique opportunity to study aerosol optical properties over oceans since October 1997. Standard SeaWiFS aerosol products are however not suitable because optical thicknesses are limited to 0.35 and Angström exponents to 1.5. We developed an inversion based on neural networks to retrieve both optical thickness and Angström exponent from SeaWiFS red and near infrared channels. Neural networks are capable of approximating non‐linear inverse functions and of processing efficiently large amounts of data. Neural networks were trained with radiative transfer computations for wide ranges of optical thickness and Angström exponent. All SeaWiFS images of the Mediterranean for year 2000 were processed and monthly mean maps of aerosol optical thickness and Angström exponent were derived. A comparison with ground‐based measurements at three AERONET stations in the Mediterranean shows the good accuracy of the method, as well as the improvement compared to operational SeaWiFS aerosol products.
<title>Corrals, hubcaps, and crystal balls: some new designs for very-wide-angle visible-light heliospheric imagers</title> (1998)

Emerging techniques allow instruments to view very large sky areas, a hemisphere or more, in visible light. In space, such wide-angle coverage enables observation of heliospheric features form close to the Sun to well beyond Earth. Observations from deep-space missions such as Solar Probe, Stereo, and Solar Polar Sail, coupled with observations near Earth, permit 3D reconstruction of solar mass ejections and co-rotating structures, discovery and study of new comets and asteroids, and detailed measurements of brightness variations in the zodiacal cloud. Typical heliospheric features have 1 percent or less of ambient brightness, so visible-light cameras must deliver &lt; 0.1 percent photometry and be well protected from stray background light. When more than a hemisphere of viewing area is free of bright background-light sources, we have shown that corral-like structures with several vane-like walls reduces background light illuminating to wide-angle optical system by up to ten orders of magnitude. The optical system itself typically provides another five orders of surface-brightness reduction. With CCDs as the light-detection device, images of point-like sources must cover typically 100 pixels to average down sub-pixel response gradients and provide the above 0.1 percent photometry. With present-day CCDs this requires images of order 1 degree in angular size. Tolerating such large images in turn enables wide-angle sky coverage using simple reflecting and refracting optical systems such as convex spherical reflectors, toroids and thick lenses. We show that combining these with light- reducing corrals yields practical, light-weight instruments suitable for inclusion on deep-space probes.
Neuromedical Complications in Stroke Patients Transferred for Rehabilitation Before and After Diagnostic Related Groups (1987)

Among 100 Medicare stroke patients in 1980 and 100 stroke patients in 1985 who were transferred to a rehabilitation center, no differences were found in type of stroke, comorbidity, functional level at admission and discharge, or length of stay. Time from onset of stroke to time of transfer to the rehabilitation service decreased significantly, and the number of neuromedical complications within 24 h of the transfer of patients from other acute care hospitals rose significantly from 22 to 48%. Subsequently, about 40% of patients in each period developed medical complications of their stroke or comorbid conditions that led to a temporary acute hospital transfer, ongoing manipulation of medication and biochemical monitoring, or modification of rehabilitation therapies. More intensive neuromedical care of patients transferred into rehabilitation centers may be needed under the pressures for early acute hospital discharge fostered by the diagnostic related groups system.
Muscle strength, size and composition following 12 months of gender-affirming treatment in transgender individuals: retained advantage for the transwomen (2019)

Abstract Objectives This study explored the effects of gender-affirming treatment, which includes inhibition of endogenous sex hormones and replacement with cross-sex hormones, on muscle function, size and composition in 11 transwomen (TW) and 12 transmen (TM). Methods Isokinetic knee extensor and flexor muscle strength was assessed at baseline (T00), 4 weeks after gonadal suppression of endogenous hormones but before hormone replacement (T0), and 3 (T3) and 11 (T12) months after hormone replacement. In addition, at T00 and T12, we assessed lower-limb muscle volume using MRI, and cross-sectional area (CSA) and radiological density using CT. Results Thigh muscle volume increased (15%) in TM, which was paralleled by increased quadriceps CSA (15%) and radiological density (6%). In TW, the corresponding parameters decreased by −5% (muscle volume) and −4% (CSA), while density remained unaltered. The TM increased strength over the assessment period, while the TW generally maintained or slightly increased in strength. Baseline muscle volume correlated highly with strength (R&gt;0.75), yet the relative change in muscle volume and strength correlated only moderately (R=0.65 in TW and R=0.32 in TM). The absolute levels of muscle volume and knee extension strength after the intervention still favored the TW. Conclusion Cross-sex hormone treatment markedly affects muscle strength, size and composition in transgender individuals. Despite the robust increases in muscle mass and strength in TM, the TW were still stronger and had more muscle mass following 12 months of treatment. These findings add new knowledge that could be relevant when evaluating transwomen’s eligibility to compete in the women’s category of athletic competitions.
The design of thermal tunnel energy segments for Crossrail, UK (2014)

Significant heat is generated by underground trains, particularly when braking, stopping at platforms and accelerating away from stations. A complex ventilation system including shaft, fans and under-platform extraction thus has to be designed to manage the rising temperature in tunnels and stations. This conventional approach results in high energy consumption for running the fans and neglects the possibility to use the extracted heat above ground in buildings. Lining underground rail tunnels with heat-exchange segments can provide an alternative solution to cool the tunnels and surrounding ground, and transfer the harvested heat to adjacent buildings for heating. It will also bring benefits in terms of reduction of energy consumption for tunnel ventilation operations. This paper reports on the work carried out in designing thermal energy segments for use on the tunnelled sections of the Crossrail project in London, UK.
Automated coregistered imaging using a hand-held probe-based optical imager (2010)

Near-infrared optical imaging holds a promise as a noninvasive technology toward cancer diagnostics and other tissue imaging applications. In recent years, hand-held based imagers are of great interest toward the clinical translation of the technology. However hand-held imagers developed to date are typically designed to obtain surface images and not tomography information due to lack of coregistration facilities. Herein, a recently developed hand-held probe-based optical imager in our Optical Imaging Laboratory has been implemented with novel coregistration facilities toward real-time and tomographic imaging of tissue phantoms. Continuous-wave fluorescence-enhanced optical imaging studies were performed using an intensified charge coupled device camera based imaging system in order to demonstrate the feasibility of automated coregistered imaging of flat phantom surfaces, using a flexible probe that can also contour to curvatures. Three-dimensional fluorescence tomographic reconstructions were also demonstrated using coregistered frequency-domain measurements obtained using the hand-held based optical imager. It was also observed from preliminary studies on cubical phantoms that multiple coregistered scans differentiated deeper targets (approximately 3 cm) from artifacts that were not feasible from a single coregistered scan, demonstrating the possibility of improved target depth detectability in the future.
A study of current transport in (BaxSr1−x)Ti1+yO3+z thin-film capacitors containing a voltage-dependent interface state charge distribution (2005)

J – V – T characteristics, measured over a very wide temperature (50–441 K) range, are analyzed simultaneously with C–V measurements to investigate conduction mechanisms and the state of charge of Pt/BaxSr1−xTi1+yO3+z(BST)/Pt thin-film capacitors during an applied voltage or current stress. A time- and voltage-dependent state of charge of the Pt/BST/Pt capacitors is inferred from stress-induced voltage shifts in the C–V curves. The voltage and temperature dependence of the C–V curve shifts is shown to be consistent with a voltage-dependent charge in interface states resulting from a change in potential across interfacial dipole layers. An intimate contact Schottky barrier model incorporating a voltage-dependent charge in interface states at both cathode and anode contacts is used to investigate conduction mechanisms in Pt/BST/Pt thin-film capacitors. The basic transport mechanisms of drift-diffusion, thermionic field emission, and Fowler–Nordeim tunneling are shown to dominate leakage in limiting voltage and temperature regimes. Thermionic emission is not predicted to control current flow at any investigated voltage and temperature.
Analog Pre-Distortion Linearizer Using Self Base Bias Controlled Amplifier (2010)

An analog pre-distortion linearizer employing a radio frequency (RF) transistor with a self base bias control circuit is proposed. The self base bias control circuit extracts the envelope from the modulated input RF signal of the RF transistor and automatically controls its base current according to the extracted envelope. As a result, the proposed linearizer realizes positive gain deviation at high input power level. By adding a resistor between the RF transistor and the self base bias control circuit, the negative gain deviation can be derived. The design of the proposed lineaizer is described with taking the envelope frequency response of the self base bias control circuit into consideration. The fabricated linearizer achieves the adjacent channel power leakage ratio (ACLR) improvement of 8.1dB for a 2GHz-band, 10W-class GaAs FET high-power amplifier (HPA) with negative gain deviation for W-CDMA base stations. It also achieves the ACLR improvement of 8.3dB for a LDMOS HPA with positive gain deviation for the same application.