gebhart/patrepeval huggingface dataset:
Interactive 3D modeling from multiple images using scene regularities (2002)

Due to the complexity of real scenes and the fragility of fully automated vision techniques, results from many automated modeling systems are disappointing. Automated techniques often require manual clean-up and postprocessing to segment the scene into coherent objects and surfaces, or to triangulate sparse point matches. They may also be required to enforce geometric constraints such as known orientations of surfaces. For instance, building interiors and exteriors provide vertical and horizontal lines and parallel and perpendicular planes. In this paper, we attack the 3D modeling problem from the other side: we specify some geometric knowledge ahead of time (e.g., known orientations of lines, co-planarity of points, initial scene segmentations), and use these constraints to guide our matching and reconstruction algorithms. We present two interactive (semi-automated) systems for recovering 3D models of large-scale environments from multiple images.
Diffraction phase microscopy: principles and applications in materials and life sciences (2014)

The main obstacle in retrieving quantitative phase with high sensitivity is posed by the phase noise due to mechanical vibrations and air fluctuations that typically affect any interferometric system. In this paper, we review diffraction phase microscopy (DPM), which is a common-path quantitative phase imaging (QPI) method that significantly alleviates the noise problem. DPM utilizes a compact Mach–Zehnder interferometer to combine several attributes of current QPI methods. This compact configuration inherently cancels out most mechanisms responsible for noise and is single-shot, meaning that the acquisition speed is limited only by the speed of the camera employed. This technique is also nondestructive and does not require staining or coating of the specimen. This unique collection of features enables the DPM system to accurately monitor the dynamics of various nanoscale phenomena in a wide variety of environments. The DPM system can operate in both transmission and reflection modes in order to accommodate both transparent and opaque samples, respectively. Thus, current applications of DPM include measuring the dynamics of biological samples, semiconductor wet etching and photochemical etching processes, surface wetting and evaporation of water droplets, self-assembly of nanotubes, expansion and deformation of materials, and semiconductor wafer defect detection. Finally, DPM with white light averages out much of the speckle background and also offers potential for spectroscopic measurements.
HIV Integrase Inhibitors with Nucleobase Scaffolds:  Discovery of a Highly Potent Anti-HIV Agent (2005)

HIV integrase is essential for HIV replication. However, there are currently no integrase inhibitors in clinical use for AIDS. We have discovered a conceptually new beta-diketo acid that is a powerful inhibitor of both the 3'-processing and strand transfer steps of HIV-1 integrase. The in vitro anti-HIV data of this inhibitor were remarkable as exemplified by its highly potent antiviral therapeutic efficacy against HIV(TEKI) and HIV-1(NL4)(-)(3) replication in PBMC (TI >4,000 and >10,000, respectively).
Towards eradication of inappropriate therapies for ICD lead failure by combining comprehensive remote monitoring and lead noise alerts (2018)

ICD remote monitoring with systematic review of all transmitted data is associated with a very low rate of inappropriate shocks related to lead failure. Dedicated noise alerts further reduce inappropriate detection of ventricular arrhythmias.
A Heterogeneous Von Neumann/Explicit Dataflow Processor (2016)

Decades-old explicit dataflow architectures eliminate many of the overheads of general-purpose processors but have not been successful because of their lack of sufficient control speculation and the latency overhead of explicit communication. This article observes a synergy between out-of-order (OoO) and explicit dataflow processors, in which dynamically switching between them according to program phases can greatly improve performance and energy efficiency.
Fault Ride Through of Inverter-Interfaced Renewable Energy Sources for Enhanced Resiliency and Grid Code Compliance (2022)

Inverter-interfaced renewable energy sources (IIRESs) are typically controlled during fault conditions to meet fault ride-through (FRT) requirements, e.g., reactive current generation (RCG) requirements specified by grid codes (GCs). However, fault currents generated by inverters are different from the traditional sources, i.e., synchronous generators. Consequently, phase selection methods (PSMs) used by protection relays could suffer from erroneous fault type classification. This paper develops a dual current controller (DCC) that regulates the inverter's negative- and positive-sequence currents to simultaneously meet phase selection and RCG requirements. First, the negative-sequence-current angle is obtained based on the angles of both zero- and positive-sequence currents to enable a correct operation for phase selection. Then, the positive-sequence current angle is adjusted to reach a trade-off between RCG requirements and phase selection achieved by the negative-sequence current. Lastly, the reference currents of the IIRES are generated in the stationary frame without violating the inverter's current limits. The proposed DCC supports the grid voltage by meeting the RCG requirements and enhancing the grid reliability and resilience by enabling correct phase selection. Comprehensive time-domain and real-time simulation verify the precise operation of the proposed DCC under various fault conditions and GCs.
Broadly tunable room temperature terahertz quantum cascade laser sources (2013)

We present widely-tunable room-temperature electrically-pumped terahertz laser sources based on efficient intra-cavity frequency mixing in mid-infrared quantum cascade lasers. Devices demonstrate 1.7–5.7 THz tuning range with power output varying between 10 and 60 μW.
Genetic diversity of Mycobacterium avium subspecies paratuberculosis and the influence of strain type on infection and pathogenesis: a review (2015)

Mycobacterium avium subspecies paratuberculosis (Map) is an important pathogen that causes a chronic, progressive granulomatous enteritis known as Johne's disease or paratuberculosis. The disease is endemic in many parts of the world and responsible for considerable losses to the livestock and associated industries. Diagnosis and control are problematic, due mostly to the long incubation period of the disease when infected animals show no clinical signs and are difficult to detect, and the ability of the organism to survive and persist in the environment. The existence of phenotypically distinct strains of Map has been known since the 1930s but the genetic differentiation of Map strain types has been challenging and only recent technologies have proven sufficiently discriminative for strain comparisons, tracing the sources of infection and epidemiological studies. It is important to understand the differences that exist between Map strains and how they influence both development and transmission of disease. This information is required to develop improved diagnostics and effective vaccines for controlling Johne's disease. Here I review the current classification of Map strain types, the sources of the genetic variability within strains, growth characteristics and epidemiological traits associated with strain type and the influence of strain type on infection and pathogenicity.
Optical molecular fluorescence determination of ultra-trace beryllium in occupational and environmental samples using highly alkaline conditions (2017)

Exposures to beryllium (Be), even at extremely low levels, can cause severe health effects in a percentage of those exposed; consequently, occupational exposure limits (OELs) promulgated for this element are the lowest established for any element. This work describes the advantages of using highly alkaline dye solutions for determination of Be in occupational hygiene and environmental samples by means of an optical molecular fluorescence technique after sample extraction in 1-3% (w˖w<sup>-1</sup>) aqueous ammonium bifluoride (NH<sub>4</sub>HF<sub>2</sub>). Improved attributes include the ability to further enhance the detection limits of Be in extraction solutions of high acidity with minimal dilution, which is particularly beneficial when NH<sub>4</sub>HF<sub>2</sub> solutions of higher concentration are used for extraction of Be from soil samples. Significant improvements in Be method detection limits (MDLs) are obtained at levels many-fold below those reported previously for this methodology. Notably, MDLs for Be of <0.01 ng l<sup>-1</sup> / 0.1 ng per sample have been attained, which are superior to MDLs routinely reported for this element by means of the most widely used ultra-trace elemental measurement technique, inductively coupled plasma mass spectrometry (ICP-MS). Very low MDLs for Be are essential in consideration of reductions in OELs for this element in workplace air by health organizations and regulatory agencies in the USA and internationally. Applications of enhanced Be measurements to air filter samples, surface wipe samples, soils and newly-designed occupational air sampler inserts are illustrated.
Inhibitor mediated protein degradation (2012)

Several drugs cause the degradation of their target proteins. The discovery of compounds with this property has been serendipitous. We have discovered that the tert‐butyl carbamate‐protected arginine (Boc 3 Arg) moiety is a degron that can be used to construct inhibitors that induce degradation of their target proteins. Boc 3 Arg‐linked ethacrynic acid and thiobenzofurazan cause the specific degradation of glutathione‐S‐transferase (GST) isozymes in lysates and whole cells. Similarly, the degradation of Escherichia coli dihydrofolate reductase (eDHFR) is induced when treated with trimethoprim (TMP)‐linked Boc 3 Arg. Importantly, TMP forms a noncovalent complex with eDHFR, so covalent attachment of the Boc 3 Arg degron is not required for degradation of the target protein. These Boc 3 Arg‐inhibitors induced degradation of 30–80% of their abundant target proteins within 2–5 hours. The proteasome is required for Boc 3 Arg‐mediated degradation but the ubiquitin pathways do not appear to be involved. These results demonstrate that the Boc 3 Arg moiety provides a general strategy for inducing protein degradation that should be useful in therapeutic and conditional protein knockdown applications. This work was supported by NIH GM54403 (LH) and AI075466 (LH).
A 2-to-48-MHz Phase-Locked Loop (2004)

A 2-to-48-MHz phase-locked loop (PLL), developed for the U.S. space program, meets or exceeds all space shuttle clock electrical interface requirements by taking as its reference a 2-to-48-MHz clock signal and outputting a phaselocked clock signal set at the same frequency as the reference clock with transistor- transistor logic (TTL) voltage levels. Because it is more adaptable than other PLLs, the new PLL can be used in industries that employ signaling devices and as a tool in future space missions. A conventional PLL consists of a phase/frequency detector, loop filter, and voltage-controlled oscillator in which each component exists individually and is integrated into a single device. PLL components phase-lock to a single frequency or to a narrow bandwidth of frequencies. It is this design, however, that prohibits them from maintaining phase lock to a dynamically changing reference clock when a large bandwidth is required a deficiency the new PLL overcomes. Since most PLL components require their voltage-controlled oscillators to operate at greater than 2-MHz frequencies, conventional PLLs often cannot achieve the low-frequency phase lock allowed by the new PLL. The 2-to-48-MHz PLL is built on a wire-wrap board with pins wired to three position jumpers; this makes changing configurations easy. It responds to variations in voltage-controlled oscillator (VCO) ranges, duty cycle, signal-to-noise ratio (SNR), amplitude, and jitter, exceeding design specifications. A consensus state machine, implemented in a VCO range detector which assures the PLL continues to operate in the correct range, is the primary control state machine for the 2-to-48-MHz PLL circuit. By using seven overlapping frequency ranges with hysteresis, the PLL output sets the resulting phase-locked clock signal at a frequency that agrees with the reference clock with TTL voltage levels. As a space-shuttle tool, the new PLL circuit takes the noisy, degraded reference clock signals as input and outputs phase-locked clock signals of the same frequency but with a corrected wave shape. Since its configuration circuit can be easily changed, the new PLL can do the following: readily respond to variations in VCO ranges, duty cycle, SNR, amplitude, and jitter; continuously operate in the correct VCO range because of its consensus state machine; and use its range detector implements to overlap seven frequency ranges with hysteresis, thus giving the current design a flexibility that exceeds anything available at the time of this development. These features will benefit any industry in which safe and timely clock signals are vital to operation.
Siliceous Mesocellular Foam‐Supported Aza(bisoxazoline)‐Copper Catalysts (2008)

Abstract Aza(bisoxazoline) was easily immobilized on siliceous mesocellular foam (MCF) in a systematic approach. It was found that silanol precapping, linker group flexibility, ligand loading, and silanol postcapping were important factors to consider in optimizing silica‐supported aza(bisoxazoline) catalysts. The optimized MCF‐supported aza(bisoxazoline)‐copper catalyst offered the same enantioselectivity as its homogeneous counterpart, and excellent recyclability. The heterogenized catalyst showed a much higher chemoselectivity in a short reaction time. The heterogenized aza(bisoxazoline)‐copper(I) catalyst was successfully applied to a circulating flow‐type packed bed reactor with excellent productivity and enantioselectivity. The circulating flow‐type reactor was found to be very useful for gas‐generating catalytic reactions such as cyclopropanation reaction.
Dimethyphenylpiperazinium, a nicotinic receptor agonist, downregulates inflammation in monocytes/macrophages through PI3K and PLC chronic activation (2006)

Activation of nicotinic acetylcholine receptors (nAChRs) on inflammatory cells induces anti-inflammatory effects. The intracellular mechanisms that regulate this effect are still poorly understood. In neuronal cells, nAChRs are associated with phosphatidylinositol 3-kinase (PI3K). This enzyme, which can activate phospholipase C (PLC), is also present in monocytes. The aim of this study was to assess the role of these proteins in the signaling pathways involved in the anti-inflammatory effect of dimethylphenylpiperazinium (DMPP), a synthetic nAChR agonist, on monocytes and macrophages. The results indicate that PI3K is associated with alpha3, -4, and -5 nAChR subunits in monocytes. The PI3K inhibitors wortmannin and LY294002 abrogated the inhibitory effect of DMPP on LPS-induced TNF release by monocytes. Treatment with DMPP for 24 and 48 h provoked a mild PLC phosphorylation, which was blocked by the nAChR antagonist mecamylamine and reversed by PI3K inhibitors. Treatment of monocytes and alveolar macrophages with DMPP reduced the inositol 1,4,5-trisphosphate (IP3)-dependent intracellular calcium mobilization induced by platelet-activating factor (PAF), an effect that was reversed by mecamylamine in alveolar macrophages. DMPP did not have any effect on PAF receptor expression. DMPP also inhibited the thapsigargin-provoked calcium release, indicating that the endoplasmic reticulum calcium stores might be depleted by treatment with the nAChR agonist. Taken together, these results suggest that PI3K and PLC activation is involved in the anti-inflammatory effect of DMPP. PLC limited, but constant activation could induce, the depletion of intracellular calcium stores, leading to the anti-inflammatory effect of DMPP.
Inside-Out Rotary Ramjet Turbogenerator (2006)

A method for implementing the Brayton cycle to provide a practical rotary ramjet engine/generator based on a fundamentally “inside-out” approach is presented. Such a rotary ramjet turbogenerator eliminates the need for the conventional bladed compressor and turbine used in traditional gas turbine engines. It replaces these with a single inside-out supersonic circumferential rotor having integrated varying-area shaped ceramic ramjet channels in its radially inward surface, in which compression, combustion and expansion occur. The inside-out design places all rotating parts under compressive centrifugal loading, allowing ceramic fabrication of the high-temperature ramjet channel sections to enable operation at increased combustor exit temperatures with substantially reduced cooling requirements. The increased combustor temperature leads to increased maximum power and increased thermal efficiency when operating at maximum power. Furthermore, in this inside-out approach the centripetal acceleration acting on the flow in the ramjet channels causes high-density reactants to be forced into the radially inward-facing combustor, and low-density combustion products to be forced out of the combustor. This greatly assists in mixing and flameholding without the need for vortex generators or similar devices. The advantages of the inside-out approach over previous rotary ramjet systems become increasingly important as the rotor radius is decreased, since the centripetal acceleration then becomes increasingly large.
Correction of Pathological Accumulation of Glycosaminoglycans in Central Nervous System and Peripheral Tissues of MPSIIIA Mice Through Systemic AAV9 Gene Transfer (2012)

Mucopolysaccharidosis type IIIA (MPSIIIA) is a rare lysosomal storage disorder caused by mutations in the sulfamidase gene. Accumulation of glycosaminoglycan (GAG) inside the lysosomes is associated with severe neurodegeneration as well as peripheral organ pathological changes leading to death of affected individuals during adolescence. There is no cure for MPSIIIA. Due to the limitation of the blood-brain barrier, enzyme replacement therapy and gene therapy strategies attempted thus far have not achieved whole-body correction of the disease. After the systemic administration of an adeno-associated virus 9 (AAV9) vector encoding for sulfamidase under the control of a ubiquitous promoter, we were able to obtain widespread expression of the therapeutic transgene in brain and in peripheral organs, and sulfamidase activity in serum of both male and female MPSIIIA mice. This was accompanied by the normalization of GAG storage levels in most peripheral organs. In brain, decrease in GAG tissue content following AAV9 gene transfer of sulfamidase was associated with the resolution of neuroinflammation. Finally, correction of disease phenotype resulted in a remarkable prolongation of survival of both male and female AAV-treated MPSIIIA mice. This proof-of-concept study will be relevant to the future development of therapies for MPSIIIA.
Neutron transmutation doping of polycrystalline silicon (1976)

Chemical vapor deposition (CVD) of doped silane has been used by others to deposit a polycrytalline silicon film (polysil) on metal or graphite substrates, but dopant migration to grain boundaries during deposition apparently prohibits attaining a uniform or desired dopant concentration. In contrast, we have used neutron transmutation doping to introduce a uniform phosphorus dopant concentration in commercially available undoped CVD polysil at doping concentrations greater than or equal to 2 x 10/sup 15/ cm/sup -3/. Radiation damage annealing to 800/sup 0/C did not indicate dopant migration. Carrier mobility increased with doping concentration and the minority carrier lifetime (MCL) appears to be comparable to that of neutron transmutation doped (NTD) single crystal Si. Application of this technique to photovoltaic solar cell fabrication is discussed.
Virtual Floating-Point Units for Low-Power Embedded Processors (2012)

Floating-point (FP) arithmetic is becoming increasingly common in many embedded applications. Typically these applications execute in battery-powered, energy-constrained environments. Due to their tight area and power constraints, however, embedded processors often do not incorporate dedicated FP hardware. Instead, they only support fixed-point (FxP) arithmetic at the expense of considerably increased programming complexity and longer runtimes. In this paper, we propose low-overhead approaches to support FP arithmetic (addition, subtraction, multiplication, fused multiply-add) without incurring the high area and power penalties of dedicated FP hardware. Our approaches utilize the existing FxP execution resources in processors plus a small amount of additional hardware to support FP operations. Compared to a baseline processor with dedicated FP hardware, a processor with our approaches can reduce the area and power consumption by 24% and 31%, respectively. We also demonstrate that a processor using our approaches improves energy efficiency and performance by nearly 30%.
Mutation of the ATP Cassette Binding Transporter A1 (ABCA1) C-Terminus Disrupts HIV-1 Nef Binding but Does Not Block the Nef Enhancement of ABCA1 Protein Degradation (2010)

HIV-1 infection and antiretroviral therapy are associated with a dyslipidemia marked by low levels of high-density lipoprotein and increased cardiovascular disease, but it is unclear whether virion replication plays a causative role in these changes. The HIV-1 Nef protein can impair ATP cassette binding transporter A1 (ABCA1) cholesterol efflux from macrophages, a potentially pro-atherosclerotic effect. This viral inhibition of efflux was correlated with a direct interaction between ABCA1 and Nef. Here, we defined the ABCA1 domain required for the Nef-ABCA1 protein-protein interaction and determined whether this interaction mediates the ability of Nef to downregulate ABCA1. Nef expressed in HEK 293 cells strongly inhibited ABCA1 efflux and protein levels but did not alter levels of cMIR, another transmembrane protein. Analysis of a panel of ABCA1 C-terminal mutants showed Nef binding required the ABCA1 C-terminal amino acids between positions 2225 and 2231. However, the binding of Nef to ABCA1 was not required for inhibition because the C-terminal ABCA1 mutants that did not bind Nef were still downregulated by Nef. Given this discordance, the mechanism of downregulation was investigated and was found to involve the acceleration of ABCA1 protein degradation but did not to depend upon the ABCA1 PEST sequence, which mediates the calpain proteolysis of ABCA1. Furthermore, it did not associate with a Nef-dependent induction of signaling through the unfolded protein response but was significantly dependent upon proteasomal function and could act on an ABCA1 mutant that fails to exit the endoplasmic reticulum. In summary, we show that Nef downregulates ABCA1 function by a post-translational mechanism that stimulates ABCA1 degradation but does not require the ability of Nef to bind ABCA1.