gebhart/patrepeval huggingface dataset:
Changes in cardiac gene expression after pig‐to‐primate orthotopic xenotransplantation (2011)

This is the first genome wide assessment of changes in cardiac gene expression after OCXTx. Hierarchical cluster analysis indicates a unique gene profile for each transplant outcome but additional samples will be required to define the unique classifier probe sets. Quantitative RT-PCR confirmed that all transplants exhibited strong evidence of ongoing inflammation and myocardial injury consistent with the effects of cytokines and vascular antibody-mediated inflammation. This was also consistent with bioinformatic analysis suggesting ongoing tissue repair in survivor and PCXD samples. Bioinformatics analysis suggests for the first time that xenotransplantation may affect cardiac metabolism in survivor and rejected samples. This study highlights the potential utility of molecular analysis to monitor xenograft function, to identify new molecular markers and to understand processes, which may contribute to DXR.
CollaVR (2017)

Collaborative review and feedback is an important part of conventional filmmaking and now Virtual Reality (VR) video production as well. However, conventional collaborative review practices do not easily translate to VR video because VR video is normally viewed in a headset, which makes it difficult to align gaze, share context, and take notes. This paper presents CollaVR, an application that enables multiple users to review a VR video together while wearing headsets. We interviewed VR video professionals to distill key considerations in reviewing VR video. Based on these insights, we developed a set of networked tools that enable filmmakers to collaborate and review video in real-time. We conducted a preliminary expert study to solicit feedback from VR video professionals about our system and assess their usage of the system with and without collaboration features.
Reinforcement Learning Control for Water-Efficient Agricultural Irrigation (2017)

Modern sensor technologies, internet and advanced irrigation equipment allow a relative precise control of agricultural irrigation that leads to high water-use efficiency. However, the core control algorithms that make use of these technologies have not been well studied. In this work, a reinforcement learning based irrigation control technique is investigated. The delayed reward of crop yield is handled by the temporal difference technique. The learning process can be based on both off-line simulation and real data from sensors and crop yield. Neural network based fast models for soil water level and crop yield are developed to improve the scalability of learning. Simulations for various geographic locations and crop types show that the proposed method can significantly increase net return considering both crop yield and water expense.
Two-Dimensional Ion Mobility Analyses of Proteins and Peptides (2009)

Ion mobility separations have emerged as a major tool for mass spectrometry of proteins and peptides. The high speed of ion mobility spectrometry (IMS) compared with chromatography enables accelerating proteomic analyses at same separation power or raising the peak capacity at equal throughput. Of interest to structural biology, tractable physics of ion transport in gases permits characterizing the structure of macromolecules by matching measured mobilities to values calculated for candidate geometries. The two known experimental methods are drift-tube IMS based on absolute mobility and field asymmetric waveform IMS (FAIMS) based on differential mobility as a function of electric field. Here, we describe combining them into 2D separations coupled to time-of-flight MS, a development made practical by electrodynamic ion funnel interfaces that effectively convey ions in and out of IMS, including "hourglass" funnels to accumulate ions filtered by FAIMS between pulsed injections into IMS. For peptide separations, the peak capacity of FAIMS/IMS is ~500 and potentially higher, a metric close to that of top capillary LC systems. In structural investigations, FAIMS/IMS allows more protein conformers to be distinguished than either stage alone, and extends the dynamic range of detection by an order of magnitude over 1D IMS. A controlled heating of ions by rf field over a variable time in the funnel trap between FAIMS and IMS stages allows following the evolution of selected isomers in both thermodynamic and kinetic aspects, which opens a new approach to mapping the pathways and energy surfaces of protein folding.
Simple gain control method for broadband Raman amplifiers gain-flattened by multi-wavelength pumping (2002)

We propose and experimentally demonstrate that, for broadband Raman amplifiers with five wavelength pump channels, gain flatness can be preserved at different gain levels by means of changing only two parameters to control the launched pump power.
Generation of Shear Adhesion Map Using SynVivo Synthetic Microvascular Networks (2014)

Cell/particle adhesion assays are critical to understanding the biochemical interactions involved in disease pathophysiology and have important applications in the quest for the development of novel therapeutics. Assays using static conditions fail to capture the dependence of adhesion on shear, limiting their correlation with in vivo environment. Parallel plate flow chambers that quantify adhesion under physiological fluid flow need multiple experiments for the generation of a shear adhesion map. In addition, they do not represent the in vivo scale and morphology and require large volumes (~ml) of reagents for experiments. In this study, we demonstrate the generation of shear adhesion map from a single experiment using a microvascular network based microfluidic device, SynVivo-SMN. This device recreates the complex in vivo vasculature including geometric scale, morphological elements, flow features and cellular interactions in an in vitro format, thereby providing a biologically realistic environment for basic and applied research in cellular behavior, drug delivery, and drug discovery. The assay was demonstrated by studying the interaction of the 2 µm biotin-coated particles with avidin-coated surfaces of the microchip. The entire range of shear observed in the microvasculature is obtained in a single assay enabling adhesion vs. shear map for the particles under physiological conditions.
Effect of Tooth–Bound Fluoride on Enamel Demineralization/ Remineralization in vitro (2000)

The effect of tooth-bound fluoride (F) on enamel caries formation was investigated under the condition that loosely bound F was essentially absent. Eighteen thin enamel sections, prepared from the lingual or buccal surfaces of extracted human molars, were embedded in acrylic resin with the enamel surfaces exposed. The sections were placed in a pH 7 remineralizing solution (RS; 1.2 mmol/l Ca, 0.72 mmol/l P, 30 mmol/l KCl, 50 mmol/l HEPES) for 5 days, and were randomly divided into 3 groups: (1) control group that received no treatment, (2) acidulated phosphate fluoride (APF) group that received 5 cycles of a 4 min treatment with APF gel followed by immersion in the RS for 2 days (RS changed daily) and (3) dicalcium phosphate dihydrate (DCPD) - APF group that received 5 cycles of a 4-min pH 2.1 DCPD-forming solution followed by 4 min APF gel and then placed in the RS for 2 days. After the treatment cycles, the sections were washed in a constant composition F titration system to remove loosely bound F. An in vitro model, which consisted of cycles of de- (6 h) and remineralization (18 h) each day for 5 days, was used to produce caries-like lesions in the specimens. The DeltaZ (mineral loss) values, measured by quantitative microradiography, of the lesions formed in the three groups were (mean +/- standard deviation; n = 6) 91.2+/-12.3 microm for the control group, 41.3+/-10.1 microm for the APF group and 21.2+/-4.8 microm for the DCPD-APF group. The same system produced lesions in untreated shark enamel with a mean DeltaZ of 4.4+/-0.3 microm (n = 12). One-way fixed-effects ANOVA indicated that mineral loss was significantly different among the different groups (p<0.05). The results showed that enamel resistance to lesion formation increased with increasing tooth-bound F content. Shark enamel was much more resistant to demineralization than human enamel.
Nonlinear approximation based image recovery using adaptive sparse reconstructions (2004)

We study the robust estimation of missing regions in images and video using adaptive, sparse reconstructions. We assume that we are given a linear transform that is expected to provide sparse decompositions over missing regions such that a portion of the transform coefficients over missing regions are zero or close to zero. We adaptively determine these small magnitude coefficients through thresholding, establish sparsity constraints, and estimate missing regions in images using information surrounding these regions. We show that the region types we can effectively estimate in a mean squared error sense are those for which the given transform provides a close approximation using nonlinear approximation. We show the nature of the constructed estimators and how these estimators relate to the utilized transform and its sparsity over regions of interest. For images the developed algorithms are applicable over locally uniform (smooth, high frequency, texture, etc.) regions separated by edges or edge-like singularities. However, the developed estimation framework is general, and can readily be applied to other nonstationary signals with a suitable choice of linear transforms. Equations are derived and extensive simulation examples included.
Mechanical Ventilator for Delivery of 17O2 in Brief Pulses (2008)

The ¹⁷O nucleus has been used recently by several groups for magnetic resonance (MR) imaging of cerebral metabolism. Inhalational delivery of ¹⁷O(2) in very brief pulses could, in theory, have significant advantages for determination of the cerebral metabolic rate for oxygen (CMRO₂) with MR imaging. Mechanical ventilators, however, are not typically capable of creating step changes in gas concentration at the airway. We designed a ventilator for large animal and human studies that provides mechanical ventilation to a subject inside an MR scanner through 25 feet of small-bore connecting tubing, and tested its capabilities using helium as a surrogate for ¹⁷O₂. After switching the source gas from oxygen to helium, the 0-90% response time for helium concentration changes at the airway was 2.4 seconds. The capability for creating rapid step changes in gas concentration at the airway in large animal and human studies should facilitate the experimental testing of the delivery ¹⁷O₂ in brief pulses, and its potential use in imaging CMRO₂.
On-line planning and scheduling for high-speed manufacturing (2005)

We describe a real manufacturing problem that lies between job shop scheduling and temporal planning. The setting is on-line in the sense that new jobs arrive asynchronously, perhaps several per second, while plans for previous jobs are being executed. We formalize the problem as a variant of STRIPS extended with action durations and resources. We present a hybrid algorithm for this problem that combines techniques from partial-order scheduling and state-space planning. No domain-specic search control is used. Our current imple-mentation successfully controls two prototype plants and our technology is anticipated to enable a new line of products. By integrating planning and scheduling, we enable high produc-tivity even for complex plants.
A Total Synthesis of Taxol (1995)

The intramolecular Heck reaction of 1 to 2 is the cornerstone of this total synthesis of taxol (see conversion below). The route starts with the (S)-Wieland Miescher ketone, and the oxetane ring is installed early in the synthesis. Elaboration to a CD ring fragment, addition of an A ring nucleophile, and further manipulations yield the appropriate starting material (1) for the Heck reaction. After this key step yielding 2, the synthesis of baccatin III (and thence taxol) concludes with the cleavage of the exo double bond at C-10 and oxygenation at C-9 and C-13.
Regulatory Bc200 Rna in Peripheral Blood of Patients with Invasive Breast Cancer (2018)

Regulatory brain cytoplasmic 200 RNA (BC200 RNA) is highly expressed in human mammary carcinoma cells. Here, we ask whether BC200 RNA becomes detectable in peripheral blood of patients with invasive breast cancer. Using quantitative reverse-transcription PCR (qRT-PCR) methodology, we observed that BC200 RNA blood levels were significantly elevated, in comparison with healthy subjects, in patients with invasive breast cancer prior to tumorectomy (p=0.001) and in patients with metastatic breast cancer (p=0.003). In patients with invasive breast cancer who had recently undergone tumorectomy, BC200 RNA blood levels were not distinguishable from levels in healthy subjects. However, normality analysis revealed a heterogeneous distribution of patients in this group, including a subgroup of individuals with high residual BC200 RNA blood levels. In blood from patients with invasive breast cancer, BC200 RNA was specifically detected in the mononuclear leukocyte fraction. The qRT-PCR approach is sensitive enough to detect as few as three BC200 RNA-expressing tumor cells. Our work establishes the potential of BC200 RNA detection in blood to serve as a molecular indicator of invasive breast malignancy.
Fault Detection and Faulted Line Identification in Active Distribution Networks Using Synchrophasors-Based Real-Time State Estimation (2016)

We intend to prove that phasor-measurement-unit (PMU)-based state estimation processes for active distribution networks exhibit unique time determinism and a refresh rate that makes them suitable to satisfy the time-critical requirements of protections as well as the accuracy requirements dictated by faulted line identification. In this respect, we propose a real-time fault detection and faulted line identification functionality obtained by computing parallel synchrophasor-based state estimators. Each state estimator is characterized by a different and augmented topology in order to include a floating fault bus. The selection of the state estimator providing the correct solution is performed by a metric that computes the sum of the weighted measurement residuals. The proposed process scheme is validated by means of a real-time simulation platform where an existing active distribution network is simulated together with a PMU-based monitoring system. The proposed process is shown to be suitable for active and passive networks, with solid-earthed and unearthed neutral, for low- and high-impedance faults of any kind (symmetric and asymmetric) occurring at different locations.
Suppression of pain‐related behavior in two distinct rodent models of peripheral neuropathy by a homopolyarginine‐conjugated <scp>CRMP</scp>2 peptide (2012)

The N-type voltage-gated calcium channel (CaV2.2) is a clinically endorsed target in chronic pain treatments. As directly targeting the channel can lead to multiple adverse side effects, targeting modulators of CaV2.2 may prove better. We previously identified ST1-104, a short peptide from the collapsin response mediator protein 2 (CRMP2), which disrupted the CaV2.2-CRMP2 interaction and suppressed a model of HIV-related neuropathy induced by anti-retroviral therapy but not traumatic neuropathy. Here, we report ST2-104 -a peptide wherein the cell-penetrating TAT motif has been supplanted with a homopolyarginine motif, which dose-dependently inhibits the CaV2.2-CRMP2 interaction and inhibits depolarization-evoked Ca(2+) influx in sensory neurons. Ca(2+) influx via activation of vanilloid receptors is not affected by either peptide. Systemic administration of ST2-104 does not affect thermal or tactile nociceptive behavioral changes. Importantly, ST2-104 transiently reduces persistent mechanical hypersensitivity induced by systemic administration of the anti-retroviral drug 2',3'-dideoxycytidine (ddC) and following tibial nerve injury (TNI). Possible mechanistic explanations for the broader efficacy of ST2-104 are discussed.
Organometal Trihalide Perovskite Single Crystals: A Next Wave of Materials for 25% Efficiency Photovoltaics and Applications Beyond? (2015)

Hybrid perovskite single crystals have been recently revealed to have superior optoelectronic properties to perovskite polycrystalline thin films, especially the extraordinarily long carrier diffusion length due to the eliminated grain boundaries. One question that naturally arises is whether the single crystal hybrid perovskites can be a next wave of photoactive materials for even higher-efficiency devices. This Perspective presents an overview of the historic evolution in understanding of carrier diffusion length in CH3NH3PbI3, the initial investigations of the synthesis of single crystalline hybrid perovskites, and the characterization of their optoelectronic properties. Our analysis indicates that single crystalline perovskite materials have potential to further boost photovoltaic device power conversion efficiency to 25%. The potential opportunities for the fundamental study of the perovskite intrinsic properties, particularly the carrier mobility and carrier recombination lifetime, and other fields such as radiation detectors are also briefed.
A Class of Tricyclic Compounds Blocking Malaria Parasite Oocyst Development and Transmission (2012)

Malaria is a deadly infectious disease in many tropical and subtropical countries. Previous efforts to eradicate malaria have failed, largely due to the emergence of drug-resistant parasites, insecticide-resistant mosquitoes and, in particular, the lack of drugs or vaccines to block parasite transmission. ATP-binding cassette (ABC) transporters are known to play a role in drug transport, metabolism, and resistance in many organisms, including malaria parasites. To investigate whether a Plasmodium falciparum ABC transporter (Pf14_0244 or PfABCG2) modulates parasite susceptibility to chemical compounds or plays a role in drug resistance, we disrupted the gene encoding PfABCG2, screened the recombinant and the wild-type 3D7 parasites against a library containing 2,816 drugs approved for human or animal use, and identified an antihistamine (ketotifen) that became less active against the PfABCG2-disrupted parasite in culture. In addition to some activity against asexual stages and gametocytes, ketotifen was highly potent in blocking oocyst development of P. falciparum and the rodent parasite Plasmodium yoelii in mosquitoes. Tests of structurally related tricyclic compounds identified additional compounds with similar activities in inhibiting transmission. Additionally, ketotifen appeared to have some activity against relapse of Plasmodium cynomolgi infection in rhesus monkeys. Further clinical evaluation of ketotifen and related compounds, including synthetic new derivatives, in blocking malaria transmission may provide new weapons for the current effort of malaria eradication.
Antiinflammatory activity of 5,6-diaryl-2,3-dihydroimidazo[2,1-b]thiazoles. Isomeric 4-pyridyl and 4-substituted-phenyl derivatives (1984)

Isomeric 5(6)-(4-pyridyl)- and 6(5)-(4-substituted-phenyl)-2,3-dihydroimidazo[2,1-b]thiazoles were prepared by a mixed benzoin-imidazothione route, and their structures were assigned by spectral comparison to compounds of established substitution pattern. The structural assignment was confirmed by X-ray analysis. Examination of the compounds for antiinflammatory activity by an adjuvant arthritic rat assay revealed strikingly higher potencies for one analogous series than for their isomers. This selectivity was paralleled in the ability to stimulate cell-mediated immunity, as reflected in an oxazolone-induced contact sensitivity model. A drug-receptor complex is proposed that requires at least three sites of interactions.
Optical Phased Arrays for Integrated Beam Steering (2018)

We present 512-element integrated optical phased arrays with low power operation (<;1 mW total), large steering ranges (56°×15°), and high-speed beam steering (10 ns phase shifter time constants). Co-packaging with an integrated III/V laser is shown, enabling compact beam steering capabilities for LiDAR and data-communications.
Effects of Parent Coal Properties on the Pyrolytic Char Chemical Structure: Insights from Micro-Raman Spectroscopy Based on 32 Kinds of Chinese Coals (2021)

The chemical structures of pyrolytic chars prepared from 32 kinds of Chinese coals were investigated with micro-Raman spectroscopy in this study. Both first-order and second-order Raman spectra of the chars were curve-fitted and analyzed. The effects of the parent coal properties, including coal rank, volatile, fixed carbon, and ash content, on the pyrolytic char structures were detailed discussed and the correlations between these coal properties and pyrolytic char chemical structures were set up. Multiple-factor analysis was done to propose a comprehensive coal property index that relates well to the pyrolytic char chemical structure. The results indicate that the aromatization degree is the key distinguishable structure of pyrolytic chars prepared from coals with various rank, and the alkyl C−H and aryl C−H structures have no significant difference. The aromatization degree of pyrolytic char decreases with the increase of coal rank, while it increases with the increase of the fixed carbon content in parent coals. The high content of moisture in parent coal can induce condensation of the pyrolytic char, but the inorganic composition probably prevents the condensation of the char. Limited correlations between the coal rank, fixed carbon, moisture and ash content, and the aromatization degree of pyrolytic chars were found. A comprehensive coal property index: (fixed carbon content + moisture content)/(volatile content + ash content) (in air dry basis) combining the coal properties together relates well to the aromatization degree of pyrolytic char and can act as a good indicator for the pyrolytic char chemical structure. This study reveals the effects of the parent coal properties, including coal rank, fixed carbon, moisture, and ash content, on the pyrolytic char chemical structure, and provides a new comprehensive coal property index to predict the pyrolytic char chemical structure.
Velocity-matching techniques for integrated optic traveling wave switch/modulators (1984)

We propose and analyze a new technique for achieving velocity match between the traveling wave electrical drive and guided optical signal for modulators in substrates for which there is an inherent mismatch. The traveling wave electrodes are laterally shifted periodically to reverse the direction of the applied electric field within the optical waveguide which exactly compensates for the polarity reversal caused by the microwave-optical walkoff. Consequently, the electrooptically induced phase shifts of each section add in phase and several sections can be used to reduce the required drive voltage at the design frequency. This artificial velocity-matching technique moves the mismatch-limited bandwidth to an arbitrarily high design frequency. In addition, we extend the new concept of phase reversal and the previously suggested technique of intermittent interaction by proposing electrode structures with large inactive to active aspect ratios. This generalization provides increased flexibility for manipulating the total available bandwidth to, for example, allow efficient modulation by a train of arbitrarily short electrical pulses. These techniques are ideally suited for several proposed integrated optic devices, including picosecond samplers and gates, which require strong overmodulation at a single high frequency.