gebhart/patrepeval huggingface dataset:
Abstract 039: Oral Delivery of Angiotensin Converting Enzyme2 and Angiotensin-(1-7) Bioencapsulated in Plant Cells Attenuates Pulmonary Hypertension (2014)

Rationale: Emerging evidences indicate that diminished activity of the vasoprotective axis of the renin-angiotensin system, constituting angiotensin converting enzyme2 (ACE2) and its enzymatic product, angiotensin-(1-7) [Ang-(1-7)] contribute to the pathogenesis of pulmonary hypertension (PH). However, long-term repetitive delivery of ACE2 or Ang-(1-7) would require enhanced protein stability and ease of administration to improve patient compliance. Objective: To develop a low-cost oral delivery system for ACE2 and Ang-(1-7), and demonstrate their therapeutic efficacy in an experimental model of PH. Methods: We have taken advantage of transplastomic technology, which enables chloroplasts to generate high levels of therapeutic proteins within plant leaves. Transplastomic plants expressing ACE2 or Ang-(1-7) were created using biolistic delivery of chloroplast vectors. Male rats were given a single subcutaneous injection of monocrotaline (MCT, 50mg/Kg) to induce PH. Oral gavage of the frozen powdered leaves (500mg in phosphate buffered saline) expressing either ACE2 or Ang-(1-7) was performed twice daily for 4-weeks in MCT rats. Results: MCT injected rats exhibited marked increase in right ventricular systolic pressure (RVSP; Control: 33±1mmHg; MCT: 89±4mmHg),signifying development of PH, which was associated with right ventricular hypertrophy (RVH; Control: 0.28±0.01; MCT: 0.63±0.03).However, oral feeding of MCT rats with bioencapsulated ACE2 or Ang-(1-7) showed significant decreases in RVSP (MCT+ACE2: 55±8mmHg, MCT+Ang-(1-7): 62±7mmHg ) and RVH (MCT+ACE2: 0.39±0.05, MCT+Ang-(1-7): 0.4±0.03). Similarly, echocardiography data revealed significant improvement in right heart function, along with enhanced pulmonary blood flow in MCT animals fed with ACE2 or Ang-(1-7). Furthermore, histological studies revealed considerable reduction in right ventricular fibrosis and pulmonary vessel wall thickness in ACE2 or Ang-(1-7) fed animals.These protective effects were associated with decreased inflammation. Conclusion: Our study provides the first proof-of-concept for a novel low-cost oral ACE2 and Ang-(1-7) delivery system, using transplastomic technology that has significant clinical implications for treating PH.
Design of multi-ghz resonant global clock distributions (2005)

The global clock on a microprocessor has traditionally been distributed using a tree-driven grid. Ensuring that this large global network distributes the clock with low-skew and low-jitter in the presence of process, voltage, and temperature (PVT) variation is a significant challenge. With global clock latency on high-performance multi-GHz designs approaching four to five cycles, a skew and jitter budget of 10% of cycle time translates into a delay variation of no more than 2% across PVT corners, a realistically unachievable target. 
In this thesis, two new clock distribution schemes based on resonating the clock capacitance with on-chip inductance are proposed and test chip measurement results from prototyped designs are presented. When compared to conventional clock distributions found on high-performance microprocessors today, the proposed schemes achieve measured clock arrival time uncertainty and power dissipation that are improved by almost an order of magnitude. 
The first resonant clocking scheme to be presented is a resonant-load global clock. The idea is to augment a traditional tree-driven grid global clock distribution with a set of on-chip spiral inductors. The resulting distribution delivers a uniform phase, uniform-amplitude resonant clock that allows straightforward scalability to different clock load capacitances and different operating frequencies. The second resonant clocking scheme to be presented is a distributed differential oscillator (DDO) global clock. Like the resonant-load clock, the DDO clock resonates the clock capacitance with on-chip spiral inductors. However, the DDO design improves on the resonant-load design by distributing the clock differentially, reducing PVT-induced timing uncertainty at the local clock buffers through differential detection. This is particularly important given the sinusoidal global clock (rather than square wave) that are characteristic of resonant distributions. The design also has improved immunity to PVT variation due to the phase averaging effect of the distributed oscillator topology.
A new on-chip ESD protection circuit with dual parasitic SCR structures for CMOS VLSI (1992)

A new CMOS on-chip electrostatic discharge (ESD) protection circuit which consists of dual parasitic SCR structures is proposed and investigated. Experimental results show that with a small layout area of 8800 mu /sup 2/, the protection circuit can successfully perform negative and positive ESD protection with failure thresholds greater than +or-1 and +or-10 kV in machine-mode (MM) and human-body-mode (HBM) testing, respectively. The low ESD trigger voltages in both SCRs can be readily achieved through proper circuit design and without involving device or junction breakdown. The input capacitance of the proposed protection circuit is very low and no diffusion resistor between I/O pad and internal circuits is required, so it is suitable for high-speed applications. Moreover, this ESD protection circuit is fully process compatible with CMOS technologies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Code Compliance Assessment as a Learning Problem (2022)

Manual code reviews and static code analyzers are the traditional mechanisms to verify if source code complies with coding policies. However, these mechanisms are hard to scale. We formulate code compliance assessment as a machine learning (ML) problem, to take as input a natural language policy and code, and generate a prediction on the code's compliance, non-compliance, or irrelevance. This can help scale compliance classification and search for policies not covered by traditional mechanisms. We explore key research questions on ML model formulation, training data, and evaluation setup. The core idea is to obtain a joint code-text embedding space which preserves compliance relationships via the vector distance of code and policy embeddings. As there is no task-specific data, we re-interpret and filter commonly available software datasets with additional pre-training and pre-finetuning tasks that reduce the semantic gap. We benchmarked our approach on two listings of coding policies (CWE and CBP). This is a zero-shot evaluation as none of the policies occur in the training set. On CWE and CBP respectively, our tool Policy2Code achieves classification accuracies of (59%, 71%) and search MRR of (0.05, 0.21) compared to CodeBERT with classification accuracies of (37%, 54%) and MRR of (0.02, 0.02). In a user study, 24% Policy2Code detections were accepted compared to 7% for CodeBERT.
Plasmonic terahertz modulator based on a grating-coupled two-dimensional electron system (2016)

Electrically driven broadband modulator with large modulation depth and high speed is in high demand to meet the technical advancing and applications in terahertz fields recently. So far, the single-particle non-resonant absorption mechanism described by the Drude conductivity has been utilized in most of the related researches but is still not efficient enough. Here we proposed and demonstrated a terahertz modulator based on the collective electron plasma excitations (plasmons) in a grating-coupled two-dimensional electron gas in GaN/AlGaN heterostructure. By switching between the resonant and non-resonant conditions of the 2D plasmon excitation enabled by applying proper gate biases, the transmission of terahertz electromagnetic waves can be efficiently manipulated. Taking advantage of its resonant characteristic combined with the strong electric field enhancement in the active region, we experimentally achieved a maximum intensity modulation depth of 93%, a 3 dB operation bandwidth of ∼400 kHz, and a small required driving voltage amplitude of 2 V at a cryogenic temperature of 8.7 K. Owing to its excellent performances, this active plasmon-based terahertz modulator may offer some promising solutions in several fields of terahertz technology in the future.
Rapid Preparation of Released <i>N</i>-Glycans for HILIC Analysis Using a Labeling Reagent that Facilitates Sensitive Fluorescence and ESI-MS Detection (2015)

N-glycosylation of proteins is now routinely characterized and monitored because of its significance to the detection of disease states and the manufacturing of biopharmaceuticals. At the same time, hydrophilic interaction chromatography (HILIC) has emerged as a powerful technology for N-glycan profiling. Sample preparation techniques for N-glycan HILIC analyses have however tended to be laborious or require compromises in sensitivity. To address these shortcomings, we have developed an N-glycan labeling reagent that provides enhanced fluorescence response and MS sensitivity for glycan detection and have also simplified the process of preparing a sample for analysis. The developed labeling reagent rapidly reacts with glycosylamines upon their release from glycoproteins. Within a 5 min reaction, enzymatically released N-glycans are labeled with this reagent comprised of an NHS-carbamate reactive group, a quinoline fluorophore, and a tertiary amine for enhancing ESI+ MS ionization. To further expedite the released N-glycan sample preparation, rapid tagging has been integrated with a fast PNGase F deglycosylation procedure that achieves complete deglycosylation of a diverse set of glycoproteins in approximately 10 min. Moreover, a technique for HILIC-SPE of the labeled glycans has been developed to provide quantitative recovery and facilitate immediate HILIC analysis of the prepared samples. The described approach makes it possible to quickly prepare N-glycan samples and to incorporate the use of a fluorescence and MS sensitivity enhancing labeling reagent. In demonstration of these new capabilities, we have combined the developed sample preparation techniques with UHPLC HILIC chromatography and high sensitivity mass spectrometry to thoroughly detail the N-glycan profile of a monoclonal antibody.
Incorporating sparse representation phone identification features in automatic speech recognition using exponential families (2010)

Sparse representation phone identification features (SPIF) is a recently developed technique to obtain an estimate of phone posterior probabilities conditioned on an acoustic feature vector. In this paper, we explore incorporating SPIF phone posterior probability estimates in large vocabulary continuous speech recognition (LVCSR) task by including them as additional features of exponential densities that model the HMM state emission likelihoods. We compare our proposed approach to a number of other well known methods of combining feature streams or multiple LVCSR systems. Our experiments show that using exponential models to combine features results in a word error rate reduction of 0.5% absolute (18.7% down to 18.2%); this is comparable to best error rate reduction obtained from system combination methods, but without having to build multiple systems or tune the system combination weights.
Real-Time Human Tracking by Audio-Visual Integration for Humanoids-Integration of Active Audition and Face Recognition- (2003)

This paper describes a real-time human tracking system by audio-visual integrtation for the humanoid SIG. An essential idea for real-time and robust tracking is hierarchical integration of multi-modal information. The system creates three kinds of streams - auditory, visual and associated streams. An auditory stream with sound source direction is formed as temporal series of events from audition module which localizes multiple sound sources and cancels motor noise from a pair of microphones. A visual stream with a face ID and its 3D-position is formed as temporal series of events from vision module by combining face detection, face identification and face localization by stereo vision. Auditory and visual streams are associated into an associated stream, a higher level representation according to their proximity. Because the associated stream disambiguates parcially missing information in auditory or visual streams, “focus-of-attention” control of SIG works well enough to robust human tracking. These processes are executed in real-time with the delay of 200 msec using off-the-shelf PCs distributed via TCP/IP. As a result, robust human tracking is attained even when the person is visually occluded and simultaneous speeches occur.
Hybrid graphene electrode for the diagnosis and treatment of epilepsy in free-moving animal models (2023)

Abstract Various electrophysiological and imaging techniques have been studied for the diagnosis and treatment of epilepsy. In particular, electrocorticography (ECoG) provides valuable information that can guide clinical treatment of patients with epilepsy. Currently, it is necessary to define the clinical benefits of ECoG in free-moving animals for the treatment of epilepsy. Here, we present the results of simultaneous recordings of multiple cortical sites and responsive neurostimulations for epilepsy treatment carried out in free-moving rats. In this study, we developed a high-density, flexible electrode array comprising graphene/Au/graphene that stably wraps onto the cortex surface of a living rat brain, exhibiting a superior signal-to-noise ratio. The hybrid graphene multichannel electrode successfully detected brain signals with high-throughput spatiotemporal resolution and substantially suppressed pilocarpine-induced epileptic discharges and behavior. Simultaneous recording and neurostimulation in awake animals can lead to a fundamental change in the treatment of medically intractable epilepsy.
MEMS scanners and emerging 3D and interactive Augmented Reality display applications (2013)

MEMS scanners have advanced rapidly during the last 20 years thanks to the excellent mechanical and optical properties offered by silicon. They have been used in various display and imaging products. The performance of high resolution and high frequency MEMS laser scanners is close to meeting the demands of full HD displays (−120 million pixels per second). Important performance metrics and the performance of various electromagnetic, electrostatic, and piezoelectric actuated MEMS scanners developed in our group are reviewed and recent improvements in the piezoelectric actuated resonant MEMS scanner is presented. Second part of the paper is about some of the emerging 3D and interactive Augmented-Reality display applications enabled by pico-projectors using MEMS scanners. Those technologies are expected to play an important role in the future of human-computer interface.
Implementation trade-offs for a short-headway vehicle-follower automated transit system (1979)

An important aspect in the design of automated guideway transit (AGT) systems is the communication requirements for the longitudinal control of vehicles, that is, the requirements to measure vehicle states, transmit this information between vehicles, and subsequently control the individual vehicles. This paper examines the trade-offs in the data rates, word lengths, and allowable transmission time lags needed to maintain an acceptable level of vehicle performance, and how these requirements relate to the allocation of control computation between vehicle- and wayside-based computers. A nonlinear control law designed for short-headway vehicle-follower systems provides a baseline to examine these trade-offs. The specification of the parmeters entering the problem is approached through analytically derived results, using simplified linear models with verification and expansion of these results through a detailed simulation.
Heterozygous deficiency of hypoxia-inducible factor–2α protects mice against pulmonary hypertension and right ventricular dysfunction during prolonged hypoxia (2003)

Chronic hypoxia induces pulmonary vascular remodeling, leading to pulmonary hypertension, right ventricular hypertrophy, and heart failure. Heterozygous deficiency of hypoxia-inducible factor-1alpha (HIF-1alpha), which mediates the cellular response to hypoxia by increasing expression of genes involved in erythropoiesis and angiogenesis, has been previously shown to delay hypoxia-induced pulmonary hypertension. HIF-2alpha is a homologue of HIF-1alpha and is abundantly expressed in the lung, but its role in pulmonary hypertension remains unknown. Therefore, we analyzed the pulmonary response of WT and viable heterozygous HIF-2alpha-deficient (Hif2alpha(+/-)) mice after exposure to 10% O(2) for 4 weeks. In contrast to WT mice, Hif2alpha(+/-) mice were fully protected against pulmonary hypertension and right ventricular hypertrophy, unveiling a critical role of HIF-2alpha in hypoxia-induced pulmonary vascular remodeling. Pulmonary expression levels of endothelin-1 and plasma catecholamine levels were increased threefold and 12-fold respectively in WT but not in Hif2alpha(+/-) mice after hypoxia, suggesting that HIF-2alpha-mediated upregulation of these vasoconstrictors contributes to the development of hypoxic pulmonary vascular remodeling.
Preparation of barium titanate-potassium niobate ceramics using interface engineering and their piezoelectric properties (2010)

Barium titanate (BaTiO3, BT)–potassium niobate (KNbO3, KN) solid solution system (0.5BT–0.5KN) ceramics with various microstructures were prepared by two-step sintering method, and their piezoelectric properties were investigated. For 0.5BT–0.5KN ceramics, two phases, ferroelectric tetragonal and ferroelectric orthorhombic, coexisted in different grains at room temperature, owing to the limited solid solution system. The volume fraction of interface region between BT-rich tetragonal and KN-rich orthorhombic grains was controlled by sintering temperatures, and increased with decreasing sintering temperatures. Apparent piezoelectric constant d33* was measured using slope of strain vs. electric field curves. As the results, the d33* increased with decreasing sintering temperatures, which revealed that interface region between tetragonal and orthorhombic grains could contribute to enhancement of piezoelectric properties.
Characteristics performance of production-worthy multiple e-beam maskless lithography (2010)

E-beam direct write (EBDW) is one of the potential solutions for technology nodes of 28-nm half-pitch (HP) and beyond. Throughput limitation confined its development mostly to small-volume prototyping. Recently, proposals have been made to achieve throughput greater than 10 wafers per hour (WPH) on a single column with >10,000 beams writing in parallel (MEBDW), or even greater than 100 WPH by further clustering multiple columns within a typical production-tool footprint. The MAPPER concept contains a CMOS-MEMS blanker array driven by high-speed optical data path architecture to simultaneously control >10,000 beams, switching them on and off independently. The MAPPER Pre-Alpha Tool with a 110-beam, 5-keV column and a 300-mm wafer stage has been installed in a semiconductor manufacturing cleanroom environment and is ready for imaging test. In this paper, the resist imaging results of 110-beam parallel raster-scan writing for 30-nm half-pitch (HP) dense hole on 300-mm wafer is shown. The challenges of implementing multiple e-beam maskless lithography (MEBML2) in mass production environment, including resolution, local variation, focusing, energy latitude, proximity effect correction and electron scattering model fitting of hole patterning are discussed. Similar to mask-error-enhanced-factor (MEEF), the new writing-error-enhanced-factor (WEEF) to describe the impact of writing error, is introduced.
Diffractive optical neural networks (2021)

We introduce a diffractive optical neural network architecture that can all-optically implement various functions, following the deep learning-based design of passive layers that work collectively. We created 3D-printed diffractive networks that implement all-optical classification of images of handwritten digits and fashion products as well as the function of an imaging lens, spectral filters, wavelength demultiplexers and ultra-short pulse shapers at terahertz part of the spectrum. This passive diffractive network framework is broadly applicable to different parts of the electromagnetic spectrum, including the visible wavelengths, and can perform at the speed of light various complex functions that computer-based neural networks can implement, and will find applications in all-optical image analysis, feature detection and object classification, also enabling new camera designs and optical components that perform unique tasks using diffractive networks designed by deep learning.
IFN- <i>α</i> 5 Mediates Stronger Tyk2-Stat-Dependent Activation and Higher Expression of 2′,5′-Oligoadenylate Synthetase Than IFN- <i>α</i> 2 in Liver Cells (2004)

Interferon-alpha5 (IFN-alpha5) is the main IFN-alpha subtype expressed in the liver. Hepatitis C virus (HCV) infection is associated with low IFN-alpha5 mRNA levels, possibly reflecting an escape mechanism of the virus. In this work, we sought to compare IFN-alpha2 and IFN-alpha5 with respect to activation of early cell signaling cascades and induction of antiviral genes in the human hepatoma HepG2 and Huh7 cell lines. We found that the Tyr701 phosphorylation kinetics of Stat1 mediated by IFN stimulation was higher when cells were incubated with IFN-alpha5 than when using IFN-alpha2. Similarly, Tyr(1054/1055) phosphorylation kinetics of Tyk2 were more intense after exposure to IFN-alpha5 than when using IFN-alpha2. Concomitantly, Tyr705 phosphorylation of Stat3 was higher after stimulation with IFN-alpha5 than with IFN-alpha2. In parallel to these findings, the mRNA levels of the antiviral IFN-inducible gene 2',5'-oligoadenylate synthetase were higher in cell samples treated with IFN-alpha5 than with IFN-alpha2. These findings suggest that interaction of IFN-alpha5 and IFN-alpha2 subtypes with IFN type I receptor occurs differently, and this affects the intensity of expression of antiviral genes. In conclusion, our data show that in hepatocytic cells, IFN-alpha5 induces stronger signaling and higher expression of antiviral genes than IFN-alpha2. These data warrant clinical trials to evaluate the efficacy of IFN-alpha5 in chronic viral hepatitis.
Design, Synthesis, and Biological Evaluation of Novel, Highly Active Soft ROCK Inhibitors (2015)

ROCK1 and ROCK2 play important roles in numerous cellular functions, including smooth muscle cell contraction, cell proliferation, adhesion, and migration. Consequently, ROCK inhibitors are of interest for treating multiple indications including cardiovascular diseases, inflammatory and autoimmune diseases, lung diseases, and eye diseases. However, systemic inhibition of ROCK is expected to result in significant side effects. Strategies allowing reduced systemic exposure are therefore of interest. In a continuing effort toward identification of ROCK inhibitors, we here report the design, synthesis, and evaluation of novel soft ROCK inhibitors displaying an ester function allowing their rapid inactivation in the systemic circulation. Those compounds display subnanomolar activity against ROCK and strong differences of functional activity between parent compounds and expected metabolites. The binding mode of a representative compound was determined experimentally in a single-crystal X-ray diffraction study. Enzymes responsible for inactivation of these compounds once they enter systemic circulation are also discussed.