gebhart/patrepeval huggingface dataset:
Extended cut-off wavelength nBn detector utilizing InAsSb/InSb digital alloy absorber (2017)

We investigated a novel approach to extend a cut-off wavelength of Sb-based nBn detectors. We incorporated a series of single InSb monolayer into InAsSb bulk that allowed to realize a digital alloy absorber with an extended cut-off wavelength of λ = 4.6 μm at <i>T</i> = 200 K. The cut-off wavelength extension to 4.6μm is technologically important for realization of detectors covering CO<sub>2</sub> absorption line at 4.26μm.
Monoclonal Antibody Against the Turn of the 42-Residue Amyloid β-Protein at Positions 22 and 23 (2010)

Aggregation of the 42-mer amyloid β-protein (Aβ42) plays a critical role in the pathogenesis of Alzheimer's disease (AD). We have proposed a toxic conformer with a turn at positions 22 and 23, as well as a nontoxic conformer with a turn at positions 25 and 26, in Aβ42 aggregates from systematic proline scanning and solid-state NMR studies. Although recent clinical trials of immunization targeting Aβ42 aggregates have proved useful, some adverse effects were reported. One of the reasons was hypothesized to be excessive immunoreactions derived from the unintended removal of nontoxic Aβ42, which plays an important role in the physiological function. To develop a monoclonal antibody for toxic Aβ42, E22P-Aβ10-35, a minimum moiety for neurotoxicity containing the turn at positions 22 and 23, was used for the generation of antibodies, following the selection of clones using Aβ42 mutants of E22P (turn-inducing) and E22V (turn-preventing). The obtained clone (11A1) showed a high binding affinity (K(D) = 10.3 nM) for Aβ42 using surface plasmon resonance. 11A1 also inhibited the neurotoxicity of Aβ42 in PC12 cells. Immunohistochemical studies showed that not only extracellular but intracellular amyloid was stained in human AD brains. In Western blotting analyses using human brains, low-molecular weight-oligomers rather than the monomer of Aβ were readily recognized by 11A1. These results imply that 11A1 could detect toxic Aβ42 oligomers with the turn at positions 22 and 23 and that 11A1 could be applicable for the therapeutic targeting of toxic Aβ42 in AD.
High Accuracy, High Temperature Pressure Probes for Aerodynamic Testing (2011)

This paper presents a ruggedized high accuracy, extremely miniature pressure transducer suitable for numerous applications where size, accuracy and environmental conditions are of critical importance. High transducer accuracy was achieved by using a highly sensitive piezoresistive pressure sensor in conjunction with high resolution digital electronics for sensor output amplification and correction. The paper presents various ways that this transducer can be packaged to make it suitable for flow measurements in both wind tunnels and real world application such as gas turbine engines testing. These methods include miniature differential transducers, miniature 5-hole probes, and pressure rakes. Data from these various configurations are presented showing excellent response over temperature and flow regimes. I. Introduction he technology developed and discussed in this paper was originally developed for Wind Tunnel Applications, where typical flight performance studies using hypervelocity wind tunnel test articles involve the measurement of very low pressures at elevated temperatures. These initial installations were used for static and quasi-static measurements only. After the success 8 of these initial measurements it was decided to extend the use of the sensing and amplifier technologies into the more demanding regime of flow measurements. There are many areas where accurate flow measurement is critical: wind tunnel, ground based engine testing, and flight test can all benefit from high accuracy miniature flow measurement techniques. Many of these applications require both high temperature and high accuracy in order to be useful to the design engineer. We present in this paper a miniature pressure transducer developed specifically to address these instrumentation challenges. Test results are presented and potential benefits, in terms of measurement accuracy and cost savings, are discussed.
MaPle: a fast algorithm for maximal pattern-based clustering (2004)

Pattern-based clustering is important in many applications, such as DNA micro-array data analysis, automatic recommendation systems and target marketing systems. However, pattern-based clustering in large databases is challenging. On the one hand, there can be a huge number of clusters and many of them can be redundant and thus make the pattern-based clustering ineffective. On the other hand, the previous proposed methods may not be efficient or scalable in mining large databases. We study the problem of maximal pattern-based clustering. Redundant clusters are avoided completely by mining only the maximal pattern-based clusters. MaPle, an efficient and scalable mining algorithm is developed. It conducts a depth-first, divide-and-conquer search and prunes unnecessary branches smartly. Our extensive performance study on both synthetic data sets and real data sets shows that maximal pattern-based clustering is effective. It reduces the number of clusters substantially. Moreover, MaPle is more efficient and scalable than the previously proposed pattern-based clustering methods in mining large databases.
Multiscale Sampling for Wide Dynamic Range Electro-optic Receivers (2009)

We experimentally demonstrate a novel multiscale sampling technique for extending the dynamic range of a phase-modulated analog optical system employing passband signals by 20dB. Envelope distortion is compensated using digital post-processing.
Disubstituted Indazoles as Potent Antagonists of the Integrin α<sub>v</sub>β<sub>3</sub> (1999)

A new series of indazole-containing alpha(v)beta(3) integrin antagonists is described. Starting with lead compound 18a, variations in a number of structural features were explored with respect to inhibition of the binding of beta(3)-transfected 293 cells to fibrinogen and to selectivity for alpha(v)beta(3) over GPIIbIIIa, another RGD-binding integrin. Indazoles attached to a 2-aminopyridine or 2-aminoimidazole by a propylene linker at the indazole 1-position and to a diaminopropionate derivative via a 5-carboxylate amide provided the best potency with moderate selectivity. Several differences in the SAR of the diaminopropionate moiety were observed between this series and a series of isoxazoline-based selective GPIIbIIIa antagonists. Compound 34a (SM256) was a potent antagonist of alpha(v)beta(3) (IC(50) 2.3 nM) with 9-fold selectivity over GPIIbIIIa.
A graph-convolutional neural network model for the prediction of chemical reactivity (2018)

We present a supervised learning approach to predict the products of organic reactions given their reactants, reagents, and solvent(s). The prediction task is factored into two stages comparable to manual expert approaches: considering possible sites of reactivity and evaluating their relative likelihoods. By training on hundreds of thousands of reaction precedents covering a broad range of reaction types from the patent literature, the neural model makes informed predictions of chemical reactivity. The model predicts the major product correctly over 85% of the time requiring around 100 ms per example, a significantly higher accuracy than achieved by previous machine learning approaches, and performs on par with expert chemists with years of formal training. We gain additional insight into predictions <i>via</i> the design of the neural model, revealing an understanding of chemistry qualitatively consistent with manual approaches.
Single-carrier frequency-domain equalization for space-time-coded transmissions over broadband wireless channels (2002)

We propose a scheme like that of S. Alamouti (see IEEE Journal on Selected Areas in Communications, p.1451-8, 1998) for combining space-time block-coding with single-carrier frequency-domain equalization. With 2 transmit antennas, the scheme is shown to achieve significant diversity gains at low complexity over frequency-selective fading channels.
High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast (2012)

DNA replication origins are necessary for the duplication of genomes. In addition, plasmid-based expression systems require DNA replication origins to maintain plasmids efficiently. The yeast autonomously replicating sequence (ARS) assay has been a valuable tool in dissecting replication origin structure and function. However, the dearth of information on origins in diverse yeasts limits the availability of efficient replication origin modules to only a handful of species and restricts our understanding of origin function and evolution. To enable rapid study of origins, we have developed a sequencing-based suite of methods for comprehensively mapping and characterizing ARSs within a yeast genome. Our approach finely maps genomic inserts capable of supporting plasmid replication and uses massively parallel deep mutational scanning to define molecular determinants of ARS function with single-nucleotide resolution. In addition to providing unprecedented detail into origin structure, our data have allowed us to design short, synthetic DNA sequences that retain maximal ARS function. These methods can be readily applied to understand and modulate ARS function in diverse systems.
Surface-energy-induced selective growth of (001) grains in magnetostrictive ternary Fe–Ga-based alloys (2012)

Surface-energy-induced selective grain growth has been used to increase the presence of preferred planes in polycrystalline ternary Fe–Ga based alloys and thereby maximize the magnetostrictive performance of these alloys. In this study, alloys were either doped with elemental sulfur or annealed under sulfur atmospheres to control the sulfur concentration on the surface of samples during annealing. We show that the segregation of sulfur, which is known to play an important role in controlling surface energy, can be correlated to the selective growth of {001} grains and an increase in the saturation magnetostriction of the samples. The results show that sulfur atoms are adsorbed (diffused) from the sulfur atmosphere (bulk interior) and segregate on the sample surface. The correlation between surface chemistry, texture development and magnetostriction is presented. The formation of {001} grains occurred under slight surface segregation of sulfur, i.e. at levels of concentration of surface sulfur between 0.5 and 1.35 at.%, for alloys of (Fe0.813Ga0.187)99B1 and (Fe0.813Ga0.187)99.5B0.5 doped with 50 ppm S. In the case of (Fe0.81Ga0.19)99(NbC)1 alloy annealed under a H2S atmosphere, abnormal growth of (001) grains resulted in 88.3% of the sample area being covered with a (001) grain.
Introduction and characterization of a functionally linked metal ion binding site at the exposed heme edge of myoglobin (2003)

A binding site for metal ions has been created on the surface of horse heart myoglobin (Mb) near the heme 6-propionate group by replacing K45 and K63 with glutamyl residues. One-dimensional (1)H NMR spectroscopy indicates that Mn(2+) binds in the vicinity of the heme 6-propionate as anticipated, and potentiometric titrations establish that the affinity of the new site for Mn(2+) is 1.28(4) x 10(4) M(-1) (pH 6.96, ionic strength I = 17.2 microM, 25 degrees C). In addition, these substitutions lower the reduction potential of the protein and increase the pK(a) for the water molecule coordinated to the heme iron of metmyoglobin. The peroxidase [2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonic acid), ABTS, as substrate] and the Mn(2+)-peroxidase activity of the variant are both increased approximately 3-fold. In contrast to wild-type Mb, both the affinity for azide and the midpoint potential of the variant are significantly influenced by the addition of Mn(2+). The structure of the variant has been determined by x-ray crystallography to define the coordination environment of bound Mn(2+) and Cd(2+). Although slight differences are observed between the geometry of the binding of the two metal ions, both are hexacoordinate, and neither involves coordination by E63.
Pulse-actuated fuel-injection spark plug. [Patent application] (1976)

A replacement spark plug for reciprocating internal combustion engines that functions as a fuel injector and as a spark plug to provide a ''stratified-charge'' effect is described. The conventional carburetor is retained to supply the main fuel-air mixture which may be very lean because of the stratified charge. The replacement plug includes a cylindrical piezoelectric ceramic which contracts to act as a pump whenever an ignition pulse is applied to a central rod through the ceramic. The rod is hollow at its upper end for receiving fuel, it is tapered along its lower length to act as a pump, and it is flattened at its lower end to act as a valve for fuel injection from the pump into the cylinder. The rod also acts as the center electrode of the plug, with the spark jumping from the plug base to the lower end of the rod to thereby provide spark ignition that has inherent proper timing with the fuel injection.
Novel View Synthesis of Dynamic Scenes with Globally Coherent Depths\n from a Monocular Camera (2020)

This paper presents a new method to synthesize an image from arbitrary views\nand times given a collection of images of a dynamic scene. A key challenge for\nthe novel view synthesis arises from dynamic scene reconstruction where\nepipolar geometry does not apply to the local motion of dynamic contents. To\naddress this challenge, we propose to combine the depth from single view (DSV)\nand the depth from multi-view stereo (DMV), where DSV is complete, i.e., a\ndepth is assigned to every pixel, yet view-variant in its scale, while DMV is\nview-invariant yet incomplete. Our insight is that although its scale and\nquality are inconsistent with other views, the depth estimation from a single\nview can be used to reason about the globally coherent geometry of dynamic\ncontents. We cast this problem as learning to correct the scale of DSV, and to\nrefine each depth with locally consistent motions between views to form a\ncoherent depth estimation. We integrate these tasks into a depth fusion network\nin a self-supervised fashion. Given the fused depth maps, we synthesize a\nphotorealistic virtual view in a specific location and time with our deep\nblending network that completes the scene and renders the virtual view. We\nevaluate our method of depth estimation and view synthesis on diverse\nreal-world dynamic scenes and show the outstanding performance over existing\nmethods.\n
Characterization of Scattering From Nanoparticles Using Far-Field Interferometric Microscopy (2008)

Analysis and simulations show that coherent confocal microscopy techniques, such as Optical Coherence Microscopy, can be used to estimate the polarizability tensor of an imaged nanoparticle. The estimation process is robust to noise and defocus.
3D nonlinear PET-CT image registration algorithm with constrained Free-Form Deformations (2008)

This paper presents a 3D nonlinear PET-CT image registration method guided by a B-Spline Free-Form Deformations (FFD) model, dedicated to thoracic and abdominal regions. It is divided into two stages: one FFD-based registration of structures that can be identified in both images; and a whole-image intensity registration step constrained by the FFD computed during the first step. Different similarity criteria have been adopted for both stages: Root Mean Square (RMS) to register recognized structures and Normalized Mutual Information (NMI) for optimizing the whole-image intensity stage. Structure segmentation is performed according to a hierarchical procedure, where the extraction of a given structure is driven by information derived from a simpler one. This information is composed of spatial constraints and expressed by the means of regions of interest, in which a 3D simplex mesh deformable model based method is applied. The results have been very positively evaluated by three medical experts. 1.
The ENHANCER OF SHOOT REGENERATION 2 gene in Arabidopsis Regulates CUP-SHAPED COTYLEDON 1 at the Transcriptional Level and Controls Cotyledon Development (2006)

Cytokinins stimulate shoot regeneration in tissue culture but the genes required for this developmental process are not well understood. Here we show that the Arabidopsis gene, ENHANCER OF SHOOT REGENERATION 2 (ESR2), encoding an AP2-domain transcriptional factor, functions in the regeneration of shoots in tissue culture. ESR2 overexpression conferred cytokinin-independent shoot regeneration from cre1/ahk4 mutant explants, suggesting that CRE1 is not required for ESR2-mediated shoot regeneration. ESR2 directly targeted CYCLIN D1;1, ARABIDOPSIS PHOSPHOTRANSMITTER 6 (AHP6) and CUP-SHAPED COTYLEDON 1 (CUC1) in assays involving the translocation of ESR2-ER (estradiol receptor) fusions to the nucleus. Knock-down of ESR2 expression by RNA interference (RNAi) reduced CUC1 expression and resulted in altered cotyledon phenotypes at a low frequency, including partially fused cotyledons and triple cotyledons. Phenotypes of induced ESR2 expression in a cuc1-1 mutant background were suppressed. Our results suggest that ESR2 plays a role in shoot regeneration through transcriptional regulation of CUC1.
ANAEROBIC DIGESTION OF WASTEWATER WITH HIGH SULFATE CONCENTRATION USING MICRO-AERATION AND NATURAL ZEOLITES (2016)

The behavior of anaerobic digestion in batch and UASB reactors using a microaerobic process and natural zeolites was studied. Laboratory assays were carried out across 4 sets of variables: different COD/SO42- ratios, different airflow levels, with and without natural zeolites and room and mesophilic controlled temperatures. The microaerobic process demonstrated hydrogen sulfide removal levels exceeding 90% in most cases, while maintaining the flammable condition of the generated biogas. The level of COD removal exceeded 75% in UASB reactors despite their operation under very low hydraulic retention times (2.8-4.8 hours). The effectiveness of natural zeolites in accelerating UASB reactor startup was demonstrated. Results showing the positive influence of zeolites on the granulation process in UASB reactors were also achieved.
The core-assisted mesh protocol (1999)

The core-assisted mesh protocol (CAMP) is introduced for multicast routing in ad hoc networks. CAMP generalizes the notion of core-based trees introduced for internet multicasting into multicast meshes that have much richer connectivity than trees. A shared multicast mesh is defined for each multicast group; the main goal of using such meshes is to maintain the connectivity of multicast groups even while network routers move frequently, CAMP consists of the maintenance of multicast meshes and loop-free packet forwarding over such meshes. Within the multicast mesh of a group, packets from any source in the group are forwarded along the reverse shortest path to the source, just as in traditional multicast protocols based on source-based trees. CAMP guarantees that within a finite time, every receiver of a multicast group has a reverse shortest path to each source of the multicast group. Multicast packets for a group are forwarded along the shortest paths front sources to receivers defined within the group's mesh. CAMP uses cores only to limit the traffic needed for a router to join a multicast group; the failure of cores does not stop packet forwarding or the process of maintaining the multicast meshes.
Phenotyping tumor infiltrating lymphocytes (PhenoTIL) on H&E tissue images: predicting recurrence in lung cancer (2019)

A number of papers have established that a high density of tumor-infiltrating lymphocytes (TILs) is highly correlated with a better prognosis for many different cancer types. More recently, some studies have shown that the spatial interplay between different subtypes of TILs (e.g. CD3, CD4, CD8) is more prognostic of disease outcome compared to just metrics related to TIL density. A challenge with TIL subtyping is that it relies on quantitative immunofluoresence or immunohistochemistry, complex and tissue-destructive technologies. In this paper we present a new approach called PhenoTIL to identify TIL sub-populations and quantify the interplay between these sub-populations and show the association of these interplay features with recurrence in early stage lung cancer. The approach comprises a Dirichlet Process Gaussian Mixture Model that clusters lymphocytes on H&E images. The approach was evaluated on a cohort of N=178 early stage non-small cell lung cancer patients, N=100 being used for model training and N=78 being used for independent validation. A Linear Discriminant Analysis classifier was trained in conjunction with 186 PhenoTIL features to predict the likelihood of recurrence in the test set. The PhenoTIL features yielded an AUC=0.84 compared to an approach involving just TIL density alone (AUC=0.58). In addition, a Kaplan-Meier analysis showed that the PhenoTIL features were able to statistically significantly distinguish early from late recurrence (p = 4 ∗ 10 −5 ).
Multi-path Label Switched Paths Signaled Using RSVP-TE (2015)

This document describes extensions to Resource ReSerVation Protocol -
Traffic Engineering for the set up of multi-path Traffic Engineered
Label Switched Paths (LSPs) in Multi Protocol Label Switching (MPLS)
and Generalized MPLS networks, i.e., LSPs that conform to traffic
engineering constraints, but follow multiple independent paths from
source to destination.
BRoCoM: A Bayesian Framework for Robust Computing on Memristor Crossbar (2022)

Memristor crossbar arrays are considered to be a promising platform for neuromorphic computing. To deploy a trained neural network (NN) model on memristor crossbars, memristors need to be programmed to the corresponding weight values. In fact, due to device-based process variation and noise, deviations of the stored weights from the trained weights are inevitable, thereby causing the degradation of the actual inference performance. This article proposes a unified Bayesian inference-based framework, BRoCoM, which connects device nonidealities and algorithmic training together for robust computing on memristor crossbars. BRoCoM is able to incorporate different levels of nonidealities into prior weight distribution, and transform robustness optimization to Bayesian NN (BNN) training, the weights of NNs are optimized to accommodate uncertainties and minimize inference degradation. Experimental results confirm the capability of the proposed BRoCoM to achieve stable inference performance while tolerating the nonideal effects of process variation and noise.
Methods for fabrication of flexible hybrid electronics (2017)

Printed and flexible hybrid electronics is an emerging technology with potential applications in smart labels, wearable electronics, soft robotics, and prosthetics. Printed solution-based materials are compatible with plastic film substrates that are flexible, soft, and stretchable, thus enabling conformal integration with non-planar objects. In addition, manufacturing by printing is scalable to large areas and is amenable to low-cost sheet-fed and roll-to-roll processes. FHE includes display and sensory components to interface with users and environments. On the system level, devices also require electronic circuits for power, memory, signal conditioning, and communications. Those electronic components can be integrated onto a flexible substrate by either assembly or printing. PARC has developed systems and processes for realizing both approaches. This talk presents fabrication methods with an emphasis on techniques recently developed for the assembly of off-the-shelf chips. A few examples of systems fabricated with this approach are also described.
Mercury Detoxification by Bacteria: Simulations of Transcription Activation and MercuryCarbon Bond Cleavage (2011)

This chapter contains sections titled: Introduction Transcription Activation of MerOP by MerR upon Hg(II)-Binding HgC Bond Cleavage Catalyzed by the MerB Summary and Conclusions References