gebhart/patrepeval huggingface dataset:
Genome‐wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm (2003)

We have taken a genomic approach to examine global gene expression in the maize endosperm in relation to dosage and parental effects. Endosperm of eight hybrids generated by reciprocal crosses and their seven inbred parents were sampled at three developmental stages: 10, 14, and 21 days after pollination (DAP). These samples were subjected to GeneCalling, an open-ended mRNA-profiling technology, which simultaneously analyzes thousands of genes. Results indicated that the overall level of gene expression in the maize endosperm was dosage-dependent, that is, the gene expression was proportional to the parental genome contribution of 2n maternal : 1n paternal. However, approximately 8% of the genes deviated from such allelic additive expression and exhibited differential expression in hybrids of reciprocal crosses, resembling either maternally or paternally expressed genes. There were more genes with maternal-like expression (MLE) than those with paternal-like expression (PLE). Allele-specific expression analysis of four selected genes using the WAVE denaturing HPLC (dHPLC) system revealed several mechanisms responsible for the deviation from the allelic additive expression in the hybrid endosperm: heterochronic allelic variation, allelic variation in the level of expression, and genomic imprinting. We discovered a novel imprinted gene no-apical-meristem (NAM) related protein1 (nrp1) that was expressed only in the endosperm and regulated by gene-specific imprinting. The nrp1 gene, a putative transcriptional factor, may play an important role in endosperm development.
DNA Vaccine Expressing the Mimotope of GD2 Ganglioside Induces Protective GD2 Cross-reactive Antibody Responses (2005)

The GD2 ganglioside expressed on neuroectodermally derived tumors, including neuroblastoma and melanoma, is weakly immunogenic in tumor-bearing patients and induces predominantly immunoglobulin (Ig)-M antibody responses in the immunized host. Here, we investigated whether interconversion of GD2 into a peptide mimetic form would induce GD2 cross-reactive IgG antibody responses in mice. Screening of the X(15) phage display peptide library with the anti-GD2 monoclonal antibody (mAb) 14G2a led to isolation of mimetic peptide 47, which inhibited the binding of 14G2a antibody to GD2-positive tumor cells. The peptide was also recognized by GD2-specific serum antibodies from a patient with neuroblastoma, suggesting that it bears an internal image of GD2 ganglioside expressed on the tumor cells. The molecular basis for antigenicity of the GD2 mimetic peptide, established by molecular modeling and mutagenesis studies, led to the generation of a 47-LDA mutant with an increased mimicry to GD2. Immunization of mice with peptide 47-LDA-encoded plasmid DNA elicited GD2 cross-reactive IgG antibody responses, which were increased on subsequent boost with GD2 ganglioside. The vaccine-induced antibodies recognized GD2-positive tumor cells, mediated complement-dependent cytotoxicity, and exhibited protection against s.c. human GD2-positive melanoma growth in the severe combined immunodeficient mouse xenograft model. The results from our studies provide insights into approaches for boosting GD2 cross-reactive IgG antibody responses by minigene vaccination with a protective epitope of GD2 ganglioside.
023 Moving Beyond Hydraulics: Safety and Efficacy of Magnetic Induction for a New Penile Prosthesis in Human Cadavers and Animal Tissue (2018)

We previously developed a novel shape memory alloy prosthesis using a lasercut Nitinol extruded tube that expands and becomes rigid when activated to simulate an erection. We also described how it is possible to activate it using magnetic induction (MI) in vitro without the use of pumps or reservoirs. To better understand the thermal safety and efficacy of this approach in tissue, we tested MI activation using an in vitro animal tissue model and human cadavers. We used a commercially available magnetic inductor with a power of 1000W and a custom made 2mm copper coil of 3 turns of 4cm diameter. The prosthesis or nitinol tube was inserted down the length of a pork-product sausage or implanted in the corpora cavernosa of a human cadver. Two thermocouples were placed to measure temperature changes: (1) on the exoskeleton, and (2) 2 mm away in the tissue. The miniductor was waved over the embedded prosthesis and activated. Temperature tracings were recorded over time. As a control, the same setup was placed on a laboratory hot plate with temperature set at 43C.
Quantum-confined-atom-based nanophosphors for solid state lighting (2004)

When an atomic impurity is incorporated in a nanoparticle of size 2 to 10 nm, the quantum-confinement provided by the dielectric-boundary of the host-nanoparticle modulates the properties of the atom. This Quantum Confined Atom (QCA) shows extraordinary changes in its luminescent properties and is associated with the modulation of the excited states of the caged atom. These “atomically engineered nanomaterials,” pioneered and developed by Nanocrystals Technology, yield several novel properties and are expected to be a major contributor to the future of nanotechnology. Efficient QCA-Nanophosphors that emit different colors depending on the specific choice of the 'caged atom' are being developed for applications to solid-state lighting. We have made two key contributions to development of SSL. (1) By embedding nanoparticles in the encapsulant, the refractive index is enhanced to 1.8 that allows us to enhance Light Extraction Efficiency (LEE) of the LED chip. (2) Incorporation of appropriate nanophosphors enables efficient down-conversion with high color-quality. The combination of an optically transparent downconverter and high refractive index in an encapsulant has yielded Phosphor-Converted LEDs (PC-LEDs) that yield higher package optical efficiency at lower package-level cost. The LEE and wall plug efficiency enhancement due to the HRI encapsulant is applicable across the entire visible spectrum of monochromatic HB-LED lamps.
Damage Assessment in Metal Plates by Using Laser Vibrometer Measurements (2014)

Lamb waves, the ultrasonic guided waves in plates, have been increasingly used for long range damage detection in plate-like structures. They have been considered as the new generation ultrasonic structural health monitoring (SHM) and nondestructive evaluation (NDE) approaches that are able to provide efficient and effective sensing for critical structural components. In this paper, the laser Doppler vibrometer measurements are used for the damage detection. The laser Doppler vibrometer provides a non-contact means to acquire the ultrasonic wavefield and visualize the wave propagation. The ultrasonic wavefield as a function of time and space contains a wealth of information regarding the wave propagation in the structure and wave interaction with the damage. The frequency–wavenumber analysis and phased array beamforming are adopted to process the ultrasonic wavefield and visualize the damage. The proposed methodology was verified through an experimental test on an aluminum plate with a bonded quartz rod as a simulated damage.
Multimedia Collaborative Content Creation (mc<sup>3</sup>): The MSU Lecture Online System* (1999)

Abstract Putting lecture material on‐line is a time‐consuming undertaking. Before communicating any subject matter, faculty must invest time and effort in dealing with computer‐related administrative overhead. Also, in traditional lecture preparations, faculty can profit from years of previously prepared written material, while for on‐line classes, they often unnecessarily re‐create learning modules that already exist on‐line. Lecture Online is a means for faculty to develop modular on‐line resources collaboratively and share them with each other. The Learning Online Network, which is currently under development, implements a distributed server network with a strong emphasis on cross‐institutional collaborations with intellectual property rights management and optional usage‐based royalty mechanisms.
TH-C-17A-01: Imaging Sensor Comparison for Real-Time Cherenkov Signal Detection From Tissue for Treatment Verification (2014)

Purpose: To identify the optimum imaging sensor for a clinical system that would provide real-time imaging of the surface beam profile on patients as novel visual information to radiation therapy technologists, and more rapidly collect clinical data for large-scale studies of Cherenkov applications in radiotherapy. Methods: Four camera types, CMOS, CCD, ICCD and EMICCD, were tested to determine proficiency in the detection of Cherenkov signal in the clinical radiotherapy setting, and subsequent maximum supportable frame rate. Where possible, time-gating between the trigger signal from the LINAC and the intensifiers was implemented to detect signal with room lighting conditions comparable to patient treatment scenarios. A solid water phantom was imaged by the EM-ICCD and ICCD to evaluate the minimum number of accumulations-on-chip required for adequate Cherenkov detection, defined as >200% electron count s per pixel over background signal. Additionally, an ICCD and EM-ICCD were used clinically to image patients undergoing whole-breast radiation therapy, to understand the impact of the resolution limitation of the EM-ICCD. Results: The intensifier-cou pled cameras performed best at imaging Cherenkov signal, even with room lights on, which is essential for patient co mfort. The tested EM-ICCD was able to support single-shot imaging and frame rates of 30 fps, however, the current maximum resolution of 512 × 512 pixels was restricting. The ICCD used in current clinical trials was limited to 4.7 fps at a 1024 × 1024 resolution. An intensifier with higher quantum efficiency at the entrance photocathode in the red wavelengths (30% QE vs current 7%) promises 16 fps at the same resolution at lower co st than the EM-ICCD. Co nclusion: The ICCD with the better red wavelength QE intensifier was determined to be the best suited co mmercial-off-the-shelf camera to detect real-time Cherenkov signal and provide the best potential for real-time display of radiation dose on the skin during treatment. Funding is from grants from the NIH numbers R01CA109558 and R21EB017559.
Characterization of two novel LPS‐binding sites in leukocyte integrin βA domain (2007)

Lipopolysaccharide (LPS), a bacterial endotoxin, triggers deleterious systemic inflammatory responses when released into blood circulation, causing organ dysfunction and death. In response to LPS stimulation, CD14 and toll-like receptor (TLR)-4 elicit inflammatory signaling cascades. Although leukocyte integrins (CD11b/CD18 and CD11c/CD18) were reported to bind LPS and induce NF-kappaB translocation, the evidence on such epitope location remains elusive. The present study aims to delineate the LPS-binding sites on the integrin CD18 antigen and to design peptide(s) as potential prophylactic and/or therapeutic agents to modulate LPS effects in activated Jurkat cells. Epitope mapping analysis using a series of CD18 truncated variants revealed two putative LPS-binding sites within the betaA region (216-248 and 266-318 a.a.), which were further confirmed by point mutation studies. Inhibition assay demonstrated that the CD18-betaA(266-318) peptide could block LPS binding in a dose-dependent manner. Our data also indicated that treatment with the CD18-peptide modulated TNF-alpha mRNA transcription via the NF-kappaB signaling pathway in LPS-activated Jurkat cells. In conclusion, we have identified two novel LPS-binding sites located at the CD18 betaA domain of leukocyte integrin, and the integrin peptide betaA(266-318) is shown to inhibit LPS binding and subsequent inflammatory events, having therapeutic implications to cure gram-negative endotoxemia.
TCP with faster recovery (2002)

Among the problems affecting the current version of TCP are the slow recovery upon a coarse timeout expiration on long, fat pipes, and the reaction to random segment losses. Both problems are known to reduce the throughput of a connection. We propose and evaluate the merits of a class of TCP modifications obtained through a source-based estimate of the available bandwidth by measuring the rate of received ACKs. The estimated bandwidth is used to set the slow start threshold and the congestion window after a timeout or 3 duplicate ACKs. The goal is to allow sources to recover quickly after sporadic losses over high bandwidth-delay links. It is worth noting that only a slight modification of the protocol stack at the source is needed. In our algorithms, a TCP source estimates the bandwidth available to it using an exponential averaging. Whenever an ACK is received, the bandwidth estimate is updated based on the amount of data that clears the transmission buffer following the ACK reception, divided by the current RTT estimate. After a timeout or 3 duplicate ACKs, the available bandwidth estimate is used to reset the TCP congestion window and the slow start threshold. Simulation results show that TCP with "faster recovery" exhibits higher goodput than other flavors of TCP, notably TCP Reno and TCP SACK (selective acknowledgement) in specific scenarios.
Models for objective evaluation of dysarthric speech from data annotated by multiple listeners (2016)

In subjective evaluation of dysarthric speech, the inter-rater agreement between clinicians can be low. Disagreement among clinicians results from differences in their perceptual assessment abilities, familiarization with a client, clinical experiences, etc. Recently, there has been interest in developing signal processing and machine learning models for objective evaluation of subjective speech quality. In this paper, we propose a new method to address this problem by collecting subjective ratings from multiple evaluators and modeling the reliability of each annotator within a machine learning framework. In contrast to previous work, our model explicitly models the dependence of the speaker on an evaluators reliability. We evaluate the model on a series of experiments on a dysarthric speech database and show that our method outperforms other similar approaches.
High-fiber, noncaloric flour substitute for baked foods. Properties of alkaline peroxide-treated lignocellulose (1989)

Treatment of lignocellulosic materials such as wheat straw, corn stalks, cereal brans, or vegetable and fruit pulps with an alkaline (pH 11.5) solution of hydrogen peroxide dramatically increased their ability to absorb water, soften, and swell when hydrated. Substitution of alkaline hydrogen peroxide treated lignocellulose for cornstarch-dextrose mixtures in the diets of nonruminant animals (rats, chicks) reduced the digestibility of the diets without increasing the amount of feed consumed. As a result, the rate and efficiency and weight gain were reduced for animals consuming the diets containing treated lignocellulose. The low digestibility of alkaline peroxide-treated lignocellulose by nonruminants, in conjunction with its enhanced physical properties compared with other cellulosic ingredients for baked foods, suggests that this material may be useful as an ingredient for reducing caloric density and/or increasing dietary fiber content of baked products.
Wavelength Locking and Thermally Stabilizing Microring Resonators Using Dithering Signals (2014)

The bandwidth bottleneck looming for traditional electronic interconnects has driven the consideration of optical communications technologies as realized through the complementary metal-oxide-semiconductor-compatible silicon nanophotonic platform. Within the silicon photonics platform, silicon microring resonators have received a great deal of attention for their ability to implement the critical functionalities of an on-chip optical network while offering superior energy-efficiency and small footprint characteristics. However, silicon microring-based structures have a large susceptibility to fabrication errors and changes in temperature. Integrated heaters that provide local heating of individual microrings offer a method to correct for these effects, but no large-scale solution has been achieved to automate their tuning process. In this context, we present the use of dithering signals as a broad method for automatic wavelength tuning and thermal stabilization of microring resonators. We show that this technique can be manifested in low-speed analog and digital circuitry, lending credence to its ability to be scaled to a complete photonic interconnection network.
Total Synthesis of Hematoporphyrin and Protoporphyrin: A Conceptually New Approach (2010)

The total synthesis of protoporphyrin IX and its disodium salt using a new alternative method to the classical MacDonald condensation is reported. The key step is the reaction of the new unsymmetrical diiodo dipyrrylmethane 1 with the known dipyrrylmethane 2. Coupling of the two fragments leads directly to porphyrin 3 without the need of an oxidizing agent. The new methodology is well suited for the synthesis of protoporphyrin IX derivatives on a multi 100 g scale in good quality without the need for chromatography. Furthermore, these preparations are completely free of any contaminant of animal origin, which represents a real improvement in the manufacturing of protoporphyrin IX derivatives.
Wavelength Shift Analysis: A Simple Method to Determine the Contribution of Hemoglobin and Myoglobin to <i>In Vivo</i> Optical Spectra (2007)

The ability to quantify the contributions of hemoglobin (Hb) and myoglobin (Mb) to in vivo optical spectra has many applications for clinical and research use such as noninvasive measurement of local tissue O(2) uptake rates and regional blood content. Recent work has demonstrated an approach to independently measure oxygen saturations of Hb and Mb in optical spectra collected in vivo. However, the utility of this approach is limited without information on tissue concentrations of these species. Here we describe a strategy to quantify the contributions of Hb and Mb to in vivo optical spectra. We have found that the peak position of the deoxy-heme peak around 760 nm in the optical spectra of the deoxygenated tissue is a linear function of the relative contributions of Hb and Mb to the optical spectra. Therefore, analysis of this peak position, hereafter referred to as wavelength shift analysis, reveals the relative concentration of Hb to Mb in solutions and intact tissue. Biochemical analysis of muscle homogenates confirmed that the wavelength shift of the combined Hb/Mb peak in in vivo spectra reflects the ratio of concentrations (Hb/Mb) in muscle. The importance of quantifying the Hb contribution is illustrated by our data demonstrating that Hb accounts for approximately 80% of the optical signal in mouse skeletal muscle but only approximately 20% in human skeletal muscle. This advance will facilitate comparison of the metabolic properties between individual muscles and provides a fully noninvasive approach to measuring local respiration that can be adapted for clinical use.
Measurement of single electron and nuclear spin states based on optically detected magnetic resonance (2006)

A novel approach for measurement of single electron and nuclear spin states is suggested. Our approach is based on optically detected magnetic resonance in a nano-probe located at the apex of an AFM tip. The method provides single electron spin sensitivity with nano-scale spatial resolution.
Phoneme-Based Contextualization for Cross-Lingual Speech Recognition in End-to-End Models (2019)

A method (500) includes receiving audio data encoding an utterance (106) spoken by a native speaker (110) of a first language, and receiving a biasing term list (105) including one or more terms in a second language different than the first language. The method also includes processing, using a speech recognition model (200), acoustic features (105) derived from the audio data to generate speech recognition scores for both wordpieces and corresponding phoneme sequences in the first language. The method also includes rescoring the speech recognition scores for the phoneme sequences based on the one or more terms in the biasing term list, and executing, using the speech recognition scores for the wordpieces and the rescored speech recognition scores for the phoneme sequences, a decoding graph (400) to generate a transcription (116) for the utterance.
Optimal Scheduling of Demand Response Events for Electric Utilities (2013)

Electric utilities have been investigating methods to reduce peak power demand. Demand response (DR) is one such method which intends to reduce peak electricity demand. DR programs typically have limits on the number and timing of events that may be triggered for a selected group of customers. This paper presents a methodology for optimizing the scheduling of DR events for various DR programs. The proposed optimization mechanism establishes a policy that triggers DR events according to the criteria that govern the cost to the utility and based on probability distributions of exogenous information that is accessible to utilities a priori, for decision making. The policy determines a dynamic threshold for triggering events that optimizes the expected savings over the planning horizon. Case studies using real utility data show that our solutions are better than current industrial practices, and close to ex-post optimality.
SiC symmetric blocking terminations using orthogonal positive bevel termination and Junction Termination Extension (2013)

Symmetric blocking power semiconductor switches require two edge terminations, one for the reverse blocking junction and the other one for the forward blocking junction. In this work, we demonstrated 1100V SiC symmetric blocking edge terminations using orthogonal positive bevel (OPB) termination and a one-zone Junction Termination Extension (JTE). The OPB was formed by orthogonally sawing 45° V-shape trenches into the SiC wafer with a diamond-coated dicing blade. The surface damage was then repaired with dry-etch in SF <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sub> /O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> plasma, which reduced the leakage current by around two orders of magnitude. As limited by field reach-through, both the OPB and the JTE terminations show breakdown voltage of 1100V. The P <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> P <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> N <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> diodes fabricated on the same wafer with the OPB termination showed 1610V avalanche breakdown which was around 83% of ideal value.
Microwave measurement of the mass of frozen hydrogen pellets (1988)

A nondestructive method for measuring the mass of high-speed, frozen hydrogen pellets is described. The measurement technique is an improvement on previous methods based on the perturbation to a resonant cavity caused by a dielectric pellet passing through the cavity. In the new method, an oscillator circuit is formed with a resonant cavity in the positive feedback loop of a microwave power amplifier. An injected pellet perturbs the resonance characteristics of the cavity causing a shift in the operating frequency of the oscillator proportional to the ratio of the pellet volume to the volume of the cavity. Through digital measurement of the frequency shift the size of the pellet is determined automatically. In a ‘‘proof-of-principle’’ experiment it was shown that polyethylene pellets, with an average volume of 0.26 mm3 and velocity ≊500 m/s, caused a shift in the operating frequency of the oscillator circuit that was within 10% of the predicted value. The hydrogen pellets (of interest to us) will have 4–10× the volume of the plastic pellets. Thus with a dielectric constant of about 1.26 for frozen hydrogen, the signals in the actual experiment would be 1–2× those described here.