gebhart/patrepeval huggingface dataset:
A Deep Learning Algorithm for Piecewise Linear Interface Construction (PLIC). (2021)

Piecewise Linear Interface Construction (PLIC) is frequently used to geometrically reconstruct fluid interfaces in Computational Fluid Dynamics (CFD) modeling of two-phase flows. PLIC reconstructs interfaces from a scalar field that represents the volume fraction of each phase in each computational cell. Given the volume fraction and interface normal, the location of a linear interface is uniquely defined. For a cubic computational cell (3D), the position of the planar interface is determined by intersecting the cube with a plane, such that the volume of the resulting truncated polyhedron cell is equal to the volume fraction. Yet it is geometrically complex to find the exact position of the plane, and it involves calculations that can be a computational bottleneck of many CFD models. However, while the forward problem of 3D PLIC is challenging, the inverse problem, of finding the volume of the truncated polyhedron cell given a defined plane, is simple. In this work, we propose a deep learning model for the solution to the forward problem of PLIC by only making use of its inverse problem. The proposed model is up to several orders of magnitude faster than traditional schemes, which significantly reduces the computational bottleneck of PLIC in CFD simulations.
The herpes simplex virus type 1 origin-binding protein interacts specifically with the viral UL8 protein (1994)

The products of herpes simplex virus type 1 (HSV-1) genes UL5, UL8 and UL52 form a complex in virus-infected cells that exhibits both DNA helicase and DNA primase activities. UL8 protein was purified from insect cells infected with a recombinant baculovirus and used to generate monoclonal antibodies (MAbs). MAb 0811 was shown to recognize the UL8 protein in both Western blots and immunoprecipitation assays and to co-precipitate the other two proteins in the complex from insect cells triply infected with recombinants expressing the UL5, UL8 and UL52 polypeptides. Experiments performed using extracts from doubly infected cells indicated that UL8 could interact separately with both the UL5 and UL52 proteins. Similar experiments using a recombinant virus that expressed the HSV-1 origin-binding protein (OBP), UL9, demonstrated a direct physical interaction between the helicase-primase complex and OBP which involved the UL8 subunit. The C-terminal DNA-binding domain of OBP is dispensable for this interaction, as evidenced by the ability of MAb 0811 to co-precipitate a truncated UL9 protein, containing only the N-terminal 535 amino acids, with UL8.
Biological and Conformational Evaluation of Bifunctional Compounds for Opioid Receptor Agonists and Neurokinin 1 Receptor Antagonists Possessing Two Penicillamines (2010)

Neuropathic pain states and tolerance to opioids can result from system changes in the CNS, such as up-regulation of the NK1 receptor and substance P, lead to antiopioid effects in ascending or descending pain-signaling pathways. Bifunctional compounds, possessing both the NK1 antagonist pharmacophore and the opioid agonist pharmacophore with delta-selectivity, could counteract these system changes to have significant analgesic efficacy without undesirable side effects. As a result of the introduction of cyclic and topological constraints with penicillamines, 2 (Tyr-cyclo[d-Pen-Gly-Phe-Pen]-Pro-Leu-Trp-NH-[3',5'-(CF(3))(2)-Bzl]) was found as the best bifunctional compound with effective NK1 antagonist and potent opioid agonist activities, and 1400-fold delta-selectivity over the mu-receptor. The NMR structural analysis of 2 revealed that the relative positioning of the two connected pharmacophores as well as its cyclic and topological constraints might be responsible for its excellent bifunctional activities as well as its significant delta-opioid selectivity. Together with the observed high metabolic stability, 2 could be considered as a valuable research tool and possibly a promising candidate for a novel analgesic drug.
Infertility and Testicular Defects in Hormone-Sensitive Lipase-Deficient Mice (2001)

The 84-kDa hormone-sensitive lipase (gene designation Lipe; EC 3.1.1.3) is a cholesterol esterase and triglyceride hydrolase that functions in the release of fatty acids from adipocytes. The role of hormone-sensitive lipase in other tissues such as the testis, where a specific 120-kDa testis-specific isoform is expressed, is unknown. To study this, we examined the fertility and testicular histology of gene-targeted hormone-sensitive lipase-deficient mice. Homozygous hormone-sensitive lipase-deficient male mice are infertile and have decreased testis weights; female homozygotes are fertile. Testicular abnormalities, detected at the light and electron microscopic levels, included the presence of multinucleated round and elongating spermatids, vacuolization of the seminiferous epithelium, asynchronization of the spermatogenic cycle, sloughing of postmeiotic germ cells from the seminiferous epithelium into the lumen, and a marked reduction in the numbers of late spermatids. Extensive nuclear head deformation was noted in late spermatids as well as the sharing of a common acrosome in multinucleated cells. In some multinucleated cells, nuclei were separated from their acrosomes, with the acrosomes remaining attached to areas of ectoplasmic specializations, suggesting defects in intercellular cytoplasmic bridge integrity. Although the lumen of the epididymis was essentially devoid of spermatozoa and filled instead with spherical degenerating cells, the epididymal epithelial cells appeared normal. The few late spermatids present in the epididymis were abnormal. There was no morphological evidence, as judged by the absence of lipid droplets of triacylglycerol or cholesteryl ester accumulation in the testis. Together, the data suggest that hormone-sensitive lipase deficiency results in abnormalities in spermiogenesis that are incompatible with normal fertility. We speculate that a metabolite downstream from the hormone-sensitive lipase reaction may be essential for membrane stabilization and integrity in the seminiferous epithelium and, in particular, may play an important role in the maintenance of intercellular cytoplasmic bridges between postmeiotic germ cells.
Iron Carbonyl-Promoted Isomerization of Olefin Esters to Their α,β-Unsaturated Esters:  Methyl Oleate and Other Examples (1996)

Ultraviolet photolysis of stoichiometric amounts of methyl oleate and Fe(CO)(5) in hexanes solvent at 0 degrees C gives Fe(CO)(3)(eta(4)-alpha,beta-ester) in which the alpha,beta-unsaturated ester isomer of methyl oleate is stabilized by eta(4)-oxadiene pi coordination of the olefin and ester carbonyl groups to the Fe(CO)(3) unit. Treatment of the Fe(CO)(3)(eta(4)-alpha,beta-ester) with pyridine or CO liberates the free alpha,beta-ester, methyl octadec-trans-2-enoate, in 70% yield. The Fe(CO)(3) unit both catalyzes the olefin isomerization and stabilizes the alpha,beta-unsaturated ester, which results in the formation of the alpha,beta-ester in a yield far above that (3.5%) observed for simple catalyzed methyl oleate isomerization. The much smaller olefin esters, methyl 3-butenoate and ethyl 4-methyl-4-pentenoate, are isomerized under the same conditions to their alpha,beta-unsaturated esters in 94 and 90% yields, respectively. The effects of reaction conditions on the yield, the use of Fe(CO)(3)(cis-cyclooctene)(2) as a nonphotolytic catalyst, and the mechanism of this useful synthetic process are discussed.
A stabilization technique for phase-locked frequency synthesizers (2002)

A stabilization technique is presented that relaxes the tradeoff between the settling speed and the magnitude of output sidebands in phase-locked frequency synthesizers. The method introduces a zero in the open-loop transfer function through the use of a discrete-time delay cell, obviating the need for resistors in the loop filter. A 2.4-GHz CMOS frequency synthesizer employing the technique settles in approximately 60 /spl mu/s with 1-MHz channel spacing while exhibiting a sideband magnitude of -58.7 dBc. Designed for Bluetooth applications and fabricated in a 0.25-/spl mu/m digital CMOS technology, the synthesizer achieves a phase noise of -112 dBc/Hz at 1-MHz offset and consumes 20 mW from a 2.5-V supply.
Applications of ultrasound image reconstruction using deep learning (2022)

Deep learning has gained tremendous popularity as a tool for ultrasound beamforming and image reconstruction. In previous work, we trained deep neural networks (DNNs) to estimate the echogenicity of a medium, to improve acoustical and electronic signal-to-noise ratio (SNR) in channel data, and to detect targeted microbubbles nondestructively for real-time ultrasound molecular imaging. Here, we present several advancements to each application. First, we compare the speckle- and noise-reducing performance of DNNs trained with simple linear Field II simulations of photographic images versus that of DNNs trained with full wave finite-difference time domain numerical simulations containing realistic abdominal walls and the resulting image degradation artifacts. We further extend our nondestructive molecular imaging DNN to incorporate spatiotemporal information using an extended simulation study to increase specificity for stationary bound microbubbles and further improve nondestructive molecular imaging.
Semi-analytical modeling of microring resonators with distributed Bragg reflectors (2009)

A semi-analytical method for fast simulation of microring resonators with distributed Bragg reflectors (DBR-MRR) is presented. Under the low loss condition, the structure exhibits a spectral response similar to that of a sampled-grating distributed Bragg reflector (SGDBR). However, the DBR-MRR can achieve higher reflectivity with significantly fewer gratings due to multiple reflection encounters with the same DBR gratings.
A Signaling Complex of Ca <sup>2+</sup> -Calmodulin-Dependent Protein Kinase IV and Protein Phosphatase 2A (1998)

Stimulation of T lymphocytes results in a rapid increase in intracellular calcium concentration ([Ca 2+ ] i ) that parallels the activation of Ca 2+ -calmodulin–dependent protein kinase IV (CaMKIV), a nuclear enzyme that can phosphorylate and activate the cyclic adenosine monophosphate (cAMP) response element–binding protein (CREB). However, inactivation of CaMKIV occurs despite the sustained increase in [Ca 2+ ] i that is required for T cell activation. A stable and stoichiometric complex of CaMKIV with protein serine-threonine phosphatase 2A (PP2A) was identified in which PP2A dephosphorylates CaMKIV and functions as a negative regulator of CaMKIV signaling. In Jurkat T cells, inhibition of PP2A activity by small t antigen enhanced activation of CREB-mediated transcription by CaMKIV. These findings reveal an intracellular signaling mechanism whereby a protein serine-threonine kinase (CaMKIV) is regulated by a tightly associated protein serine-threonine phosphatase (PP2A).
Alpha detection for characterization of D&D sites (1994)

Characterization of radioactive contaminants is required during D&D operations at any facility where radioactivity is suspected or known to exist. Alpha radiation is an excellent indicator of the presence of many isotopes (such as Pu{sup 239}) which are otherwise difficult to observe. However, traditional fieldable alpha detectors have been hampered by the short range of alpha particles in air and in detector windows. We have developed an alpha detection technology that avoids the problems mentioned above. In a monitor using the long-range alpha detector (LRAD) technology, we detect the ion pairs produced by an alpha particle`s interaction with air rather than the particles themselves. In this paper, we discuss several applications to air and soil monitoring as well as potentially contaminated building surfaces and process equipment.
Delta-Aminolevulinic Acid Dehydratase Polymorphism: Influence on Lead Levels and Kidney Function in Humans (1997)

Delta-aminolevulinic acid dehydratase (ALAD) polymorphism has been reported to modify lead pharmacokinetics (i.e., individuals who express the ALAD2 allele [ALAD2 subjects] have higher blood lead levels than homozygotes for the ALAD1 allele [ALAD1 subjects]). In our study of 89 lead-exposed workers (7 ALAD2 homozygotes or heterozygotes) and 34 unexposed workers (10 ALAD2 heterozygotes), concentrations of urinary calcium and creatinine were lower in ALAD2 subjects than in ALAD1 subjects (respective medians: calcium--78 mg/l versus 185 mg/l, p = .003; creatinine--11.2 mmol/l versus 14.9 mmol/l, p = .008). No association was found between ALAD genotype and blood lead levels or bone lead levels. However, expression of the ALAD2 allele occurred less frequently among lead-exposed workers than in unexposed controls. The results indicated the presence of ALAD allele-specific differences in kidney function, as well as a possible genetic healthy-worker selection.
Low complexity image registration techniques based on integral projections (2016)

A low complexity image registration based on integral projections is proposed. The scaling factor estimation involves resampling operations on one image integral projection vector. The rotation estimation use only convolutions with a variable length vector. It is shown that the proposed approach provides a promising alternative to more complex registration methods.
Theoretical Investigation and Structural Optimization of Single‐Electrode Triboelectric Nanogenerators (2014)

Single‐electrode triboelectric nanogenerators (SETENGs) significantly expand the application of triboelectric nanogenerators in various circumstances, such as touch‐pad technologies. In this work, a theoretical model of SETENGs is presented with in‐depth interpretation and analysis of their working principle. Electrostatic shield effect from the primary electrode is the main consideration in the design of such SETENGs. On the basis of this analysis, the impacts of two important structural parameters, that is, the electrode gap distance and the area size, on the output performance are theoretically investigated. An optimized electrode gap distance and an optimized area size are observed to provide a maximum transit output power. Parallel connection of multiple SETENGs with micro‐scale size and relatively larger spacing should be utilized as the scaling‐up strategy. The discussion of the basic working principle and the influence of structural parameters on the whole performance of the device can serve as an important guidance for rational design of the device structure towards the optimum output in specific applications.
Current Status Of The NAVSEA Backscatter Absorption Gas Imaging (BAGI) Development Project (1989)

During the last five years, work has been underway at the Lawrence Livermore National Laboratory (LLNL) to develop a method for imaging gas clouds that are normally invisible to the human eye. The effort was initiated to provide an effective means of locating leaks of hazardous vapors. Although conventional point or line-of-sight detectors are well suited to the measurement of gas concentrations, their utility in identifying the origin and direction of travel of gas plumes is limited. To obtain spatial information from sensors that provide only zero- or one-dimensional readings, either sequential readings at many different locations from a single device, or multiplexed simultaneous measurements from a sensor array must be taken. The former approach is time consuming and, therefore, impractical in emergency situations where rapid action is required. The latter is useful only in cases where the probability of a hazardous release is high enough to warrant the prior installation of a sensor network. Either method demands high measuremental precision and sufficient discrimination against both interfering gases and interfering sources of the target gas. Backscatter Absorption Gas Imaging (BAGI) is a new technique that makes gas clouds and their surroundings "visible" in a real-time video image. It is superior to conventional sensors in characterizing the spatial properties of gas clouds because it provides data that are inherently two-dimensional. Less measuremental precision is required by the BAGI technique because it conveys information as contrasts between different areas in an image rather than as absolute concentration values. Furthermore, the pictorial display of this information allows it to be rapidly assimilated by emergency-response teams. The size and orientation of the plume are evident through comparison with familiar objects that also appear in the image. Subtler evaluations can be made as well, such as the distinction between innocous and hazardous sources of the target gas. For example, in using a conventional sensor to search for the source of a gas that is also present at low levels in automobile exhaust, one might be led astray near a highway. Gas imaging allows the searcher to recognize that the cars are producing the gas, and that they are not the objective of the search.
Conductive and Stretchable Silver-Polymer Blend for Electronic Applications (2016)

Stretchable and flexible electronic devices have gained significant attention in recent years, as they can be integrated into many systems such as medical sensors, displays, and robots. One of the primary areas of research is designing stretchable interconnects which provide adequate conductivity and mechanical robustness. Metal-based interconnects have been reported to have the highest conductivity, but are not stretchable enough, while elastomer interconnects are not conductive enough. In this paper we report a silver polymer blend composite that provides excellent conductivity, stretchability and flexibility for use as a stretchable interconnect. The composite was prepared by dispersing silver flakes in a Polyvinyl alcohol (PVA), Phosphoric acid (H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> PO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> ) and poly(3,4-ethyl-ene-dioxythiophene) (PEDOT): Poly(styrene sulfonic acid) (PSS) polymer mixture. Silver was chosen as it has the highest conductivity of all metals, while the PEDOT:PSS/PVA-H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> PO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sub> blend was chosen as the blend offers a practical trade-off between conductivity and stretchability for the composite matrix. The polymer blend provides conductive pathways between the silver flakes, leading to the blend's superior electrical properties, even at large deformations. The synthesis process of the composite material, along with the observed electrical and mechanical properties of the composite will be presented in detail.
A D<sup>V</sup>‐like phenotype is obliteratedby A226P in the partial D DBS (2001)

The phenotypes of RHD alleles with gene conversions limited to exon 5 depended critically on the amino acid at position 226. If alanine was present at this position, gene conversions involving E233Q led to a D(Va)-like phenotype. If proline was present, many additional epitopes were lost, and the phenotype became reminiscent of DFR. The 5' breakpoint region is shared by 10 alleles and may represent the most active "hot spot" for gene conversions known in RH.
POP/FED: progressive query optimization for federated queries in DB2 (2006)

Federated queries are regular relational queries accessing data on one or more remote relational or non-relational data sources, possibly combining them with tables stored in the federated DBMS server. Their execution is typically divided between the federated server and the remote data sources. Outdated and incomplete statistics have a bigger impact on federated DBMS than on regular DBMS, as maintenance of federated statistics is unequally more complicated and expensive than the maintenance of the local statistics; consequently bad performance commonly occurs for federated queries due to the selection of a suboptimal query plan. To solve this problem we propose a progressive optimization technique for federated queries called POP/FED by extending the state of the art for progressive reoptimization for local source queries, POP [4]. POP/FED uses (a) an opportunistic, but risk controlled reoptimization technique for federated DBMS, (b) a technique for multiple reoptimizations during federated query processing with a strategy to discover redundant and eliminate partial results, and (c) a mechanism to eagerly procure statistics in a federated environment. In this demonstration we showcase POP/FED implemented in a prototype version of WebSphere Information Integrator for DB2 using the TPC-H benchmark database and its workload. For selected queries of the workload we show unique features including multi-round reoptimizations using both a new graphical reoptimization progress monitor POPMonitor and the DB2 graphical plan explain tool.
Neural Interface Biomaterials: Multifunctional Nanobiomaterials for Neural Interfaces (Adv. Funct. Mater. 4/2009) (2009)

Neural electrodes are designed to interface with the nervous system and provide control signals for neural prostheses. However, robust and reliable chronic recording and stimulation remains a challenge for neural electrodes. On page 573, Mohammad Reza Abidian and David Martin report a novel method for the fabrication of soft, low impedance, high charge density, and controlled releasing nanobiomaterials that can be applied for neural interfaces using drug loaded nanofibers, 3D conducting polymer nanostructures (PEDOT), and alginate hydrogel.
Vagal nerve stimulation effects on cerebellar tremor in multiple sclerosis (2005)

Although vagal nerve stimulation (VNS) is a common alternative\nadd-on treatment for epilepsy, the effects of the possible combination\nof VNS programmable options other than those established in\nantiepileptic protocols (e.g., current intensity, on-off operating\ntime) have not been fully investigated. This study reports the\neffect of low-intensity, low cycling VNS on a subject with persistent\ncerebellar tremor due to multiple sclerosis (MS).
Full Field Spectral Domain Optical Coherence Tomography With Improved Extended Depth of Focus (2010)

In Full field Optical Coherence Tomography (FFOCT) lateral resolution is achieved by high NA lenses. However, it decreases depth of focus (DOF). We incorporate interfering phase mask allowing to extend the DOF of a FFOCT
ACCESS: Smart scheduling for asymmetric cache CMPs (2011)

In current Chip-multiprocessors (CMPs), a significant portion of the die is consumed by the last-level cache. Until recently, the balance of cache and core space has been primarily guided by the needs of single applications. However, as multiple applications or virtual machines (VMs) are consolidated on such a platform, researchers have observed that not all VMs or applications require significant amount of cache space. In order to take advantage of this phenomenon, we explore the use of asymmetric last-level caches in a CMP platform. While asymmetric cache CMPs provide the benefit of reduced power and area, it is important to build in hardware/software support to appropriately schedule applications on to cores with suitable cache capacity. In this paper, we address this problem with our ACCESS architecture comprising of: (a) asymmetric caches across a group of cores, (b) hardware support that enables prediction of cache performance on the different sized caches and (c) OS scheduler support to make use of the prediction capability and appropriately schedule applications on to core with suitable cache capacity. Measurements on a working prototype using SPEC2006 benchmarks show that our ACCESS architecture can effectively schedule jobs in an asymmetric cache CMP and provide 23% performance improvement compared to a naive scheduler, and is 97% close to an oracle scheduler in making schedules.