gebhart/patrepeval huggingface dataset:
Thermodynamically stable Metal/III-V compound-semiconductor interfaces (1986)

Chemical reactions that occur at a metal/III-V compound-semiconductor interface should be minimized if the change in Gibbs free energy of the bulk materials with respect to any possible reaction products is positive. However, the large positive change in entropy caused by vaporization of the highly volatile group V elements is a very important contribution to the Gibbs free energy of these systems, especially at higher temperatures. Thus, a particular metal/III-V compound-semiconductor interface may be thermodynamically stable at one temperature, but unstable with respect to sublimation of elemental group V species at a higher temperature if the enthalpy change for the reaction is positive. Examination of bulk phase diagrams makes it possible to rationalize the reaction products observed and to predict which will be the most stable interface for any particular metal/III-V system.
Volume grating recording in fluorinated silicate glasses (1997)

Sodium-zinc-aluminum-silicate glasses doped with silver, cerium, fluorine, and bromine were melted in 100 cc fused silica crucibles in an electrical furnace. The polished glass plates were exposed to UV radiation of a He-Cd laser at 325 nm. Spatial frequencies of the interference patterns written ranged from 500 to 700 l/mm. Exposed samples under went heat treatment at temperatures from 500 to 520 °C to produce photoinduced crystallization. The thickness of gratings formed were from 1 mm to 10 mm. High diffraction efficiencies up to 75% and losses less than 10% have been obtained in these glasses for exposure doses of 100 mJ/cm 2 . The dependence of the grating properties on glass composition and thermodevelopment schedule is studied.
A xyloglucan-specific endo- -1,4-glucanase from Aspergillus aculeatus: expression cloning in yeast, purification and characterization of the recombinant enzyme (1999)

A full-length c-DNA encoding a xyloglucan-specific endo -beta-1, 4-glucanase (XEG) has been isolated from the filamentous fungus Aspergillus aculeatus by expression cloning in yeast. The colonies expressing functional XEG were identified on agar plates containing azurine-dyed cross-linked xyloglucan. The cDNA encoding XEG was isolated, sequenced, cloned into an Aspergillus expression vector, and transformed into Aspergillus oryzae for heterologous expression. The recombinant enzyme was purified to apparent homogeneity by anion-exchange and gel permeation chromatography. The recombinant XEG has a molecular mass of 23,600, an isoelectric point of 3.4, and is optimally stable at a pH of 3.4 and temperature below 30 degreesC. The enzyme hydrolyzes structurally diverse xyloglucans from various sources, but hydrolyzes no other cell wall component and can therefore be considered a xyloglucan-specific endo -beta-1, 4-glucanohydrolase. XEG hydrolyzes its substrates with retention of the anomeric configuration. The Kmof the recombinant enzyme is 3.6 mg/ml, and its specific activity is 260 micromol/min per mg protein. The enzyme was tested for its ability to solubilize xyloglucan oligosaccharides from plant cell walls. It was shown that treatment of plant cell walls with XEG yields only xyloglucan oligosaccharides, indicating that this enzyme can be a powerful tool in the structural elucidation of xyloglucans.
A nonvolatile memory based on reversible phase changes between fcc and hcp (2005)

A nonvolatile memory technology utilizing reversible changes between fcc and hcp crystalline phases is proposed. In this new type of phase-change memory, data are stored in different forms of crystalline phases of (Ge/sub 1/Sb/sub 2/Te/sub 4/)/sub 0.8/(Sn/sub 1/Bi/sub 2/Te/sub 4/)/sub 0.2/ chalcogenide alloy. RESET operation produces the less conductive metastable fcc phase via melt-quenching from the more conductive stable hcp phase and SET operation involves a phase change from fcc directly to hcp. Both RESET and SET operations can be completed as fast as 70 ns with large changes in cell resistance.
COMPUTER ASSISTED NEGOTIATION OF MULTIOBJECTIVE WATER RESOURCES CONFLICTS<sup>1</sup> (1992)

ABSTRACT: Since the early 1970s, a large volume of literature has accumulated related to multiobjective water resources management problems. A relatively small portion of this specifically addresses the negotiation process required when there are multiple decision makers with conflicting objectives. This paper focuses on that process and describes a computer program designed to assist such negotiation processes. This interactive computer assisted negotiation support system is called ICANS. ICANS is designed for dynamic, multi‐issue, multi‐party negotiation problems. Based on information provided in confidence by each party via an interactive graphical interface, the program can help determine if there exist any possible alternatives that are equivalent or even preferred to each party's decision in the absence of a negotiated agreement. If such alternatives exist, through a series of iterations in which each party's input data, assumptions, and preferences may change, ICANS can assist the parties in their search for a mutually acceptable and preferred agreement. A simple example illustrates the data requirements and the use of ICANS in negotiation experiments.
Palladium- and Copper-Catalyzed Arylation of Carbon−Hydrogen Bonds (2009)

The transition-metal-catalyzed functionalization of C-H bonds is a powerful method for generating carbon-carbon bonds. Although significant advances to this field have been reported during the past decade, many challenges remain. First, most of the methods are substrate-specific and thus cannot be generalized. Second, conversions of unactivated (i.e., not benzylic or alpha to heteroatom) sp(3) C-H bonds to C-C bonds are rare, with most examples limited to t-butyl groups, a conversion that is inherently simple because there are no beta-hydrogens that can be eliminated. Finally, the palladium, rhodium, and ruthenium catalysts routinely used for the conversion of C-H bonds to C-C bonds are expensive. Catalytically active metals that are cheaper and less exotic (e.g., copper, iron, and manganese) are rarely used. This Account describes our attempts to provide solutions to these three problems. We have developed a general method for directing-group-containing arene arylation by aryl iodides. Using palladium acetate as the catalyst, we arylated anilides, benzamides, benzoic acids, benzylamines, and 2-substituted pyridine derivatives under nearly identical conditions. We have also developed a method for the palladium-catalyzed auxiliary-assisted arylation of unactivated sp(3) C-H bonds. This procedure allows for the beta-arylation of carboxylic acid derivatives and the gamma-arylation of amine derivatives. Furthermore, copper catalysis can be used to mediate the arylation of acidic arene C-H bonds (i.e., those with pK(a) values <35 in DMSO). Using a copper iodide catalyst in combination with a base and a phenanthroline ligand, we successfully arylated electron-rich and electron-deficient heterocycles and electron-poor arenes possessing at least two electron-withdrawing groups. The reaction exhibits unusual regioselectivity: arylation occurs at the most hindered position. This copper-catalyzed method supplements the well-known C-H activation/borylation methodology, in which functionalization usually occurs at the least hindered position. We also describe preliminary investigations to determine the mechanisms of these transformations. We anticipate that other transition metals, including iron, nickel, cobalt, and silver, will also be able to facilitate deprotonation/arylation reaction sequences.
Recent Advances in Shape Memory Soft Materials for Biomedical Applications (2016)

Shape memory polymers (SMPs) are smart and adaptive materials able to recover their shape through an external stimulus. This functionality, combined with the good biocompatibility of polymers, has garnered much interest for biomedical applications. In this review, we discuss the design considerations critical to the successful integration of SMPs for use in vivo. We also highlight recent work on three classes of SMPs: shape memory polymers and blends, shape memory polymer composites, and shape memory hydrogels. These developments open the possibility of incorporating SMPs into device design, which can lead to vast technological improvements in the biomedical field.
Uses of Hyperspectral and Multispectral Laser Induced Fluorescence Imaging Techniques for Food Safety Inspection (2004)

Spectral imaging including machine vision and multispectral imaging can provide a rapid, nondestructive means to assess agricultural commodities for their quality and safety for human consumption. These nondestructive techniques generally rely on reflectance measurements; the most commonly used spectral regions range through the visible (Vis) to the near infrared (NIR). Another optical sensing technique is based on fluorescence that is generally regarded as more sensitive optical sensing tools compared to reflectance techniques. Recently, we developed two imaging systems for food safety research; a laboratory-based hyperspectral imaging system capable of both reflectance and fluorescence measurements and a multispectral laser induced fluorescence imaging system. Because many contiguous spectral bands are acquired with each hyperspectral image pixel, the resulting data quantity makes uses of hyperspectral imaging spectrometer for on-line food safety inspection impractical. Instead, the spectral and spatial information is used to determine several optimal wavebands that can be implemented to a multispectral imaging system. We present a systematic method for using hyperspectral image data to identify few wavebands to be used in multispectral detection systems. Also presented is a two-band ratio as a multispectral fusion method along with automated detection for animal feces contamination on apples. The fluorescence imaging techniques demonstrated that even minute animal feces, not clearly visible to human eye, could be detected. Practical considerations for development of multispectral fluorescence imaging systems for on-line uses are also discussed.
The Retinoblastoma Protein Region Required for Interaction with the E2F Transcription Factor Includes the T/E1A Binding and Carboxy-Terminal Sequences (1992)

Recent experiments in understanding the mechanism of the retinoblastoma protein (RB) function have revealed the existence of several cellular proteins that are complexed with RB. One of these cellular proteins is the E2F transcription factor, which was originally identified due to its inducibility by E1A during an adenovirus infection. The E2F recognition sequence is found in the promoters of several cellular genes involved in growth control, including several oncogenes. In this report, we provide evidence that the interaction of E2F and RB is mediated through a region on RB where viral oncogenes such as SV40 T antigen and adenovirus E1A bind and where tumorigenic mutations also cluster. Additional carboxy-terminal sequences are also required for the interaction with E2F. These observations provide evidence for a direct connection between tumor suppressor function and the gene expression program leading to cellular growth regulation.
Heterogeneous Network Motifs (2019)

Many real-world applications give rise to large heterogeneous networks where nodes and edges can be of any arbitrary type (e.g., user, web page, location). Special cases of such heterogeneous graphs include homogeneous graphs, bipartite, k-partite, signed, labeled graphs, among many others. In this work, we generalize the notion of network motifs to heterogeneous networks. In particular, small induced typed subgraphs called typed graphlets (heterogeneous network motifs) are introduced and shown to be the fundamental building blocks of complex heterogeneous networks. Typed graphlets are a powerful generalization of the notion of graphlet (network motif) to heterogeneous networks as they capture both the induced subgraph of interest and the types associated with the nodes in the induced subgraph. To address this problem, we propose a fast, parallel, and space-efficient framework for counting typed graphlets in large networks. We discover the existence of non-trivial combinatorial relationships between lower-order ($k-1$)-node typed graphlets and leverage them for deriving many of the $k$-node typed graphlets in $o(1)$ constant time. Thus, we avoid explicit enumeration of those typed graphlets. Notably, the time complexity matches the best untyped graphlet counting algorithm. The experiments demonstrate the effectiveness of the proposed framework in terms of runtime, space-efficiency, parallel speedup, and scalability as it is able to handle large-scale networks.
Microwave-Frequency, Negative-Index Metamaterial Designs Based on Degenerate Dielectric Resonators (2012)

In this letter, three different negative-index metamaterial designs based on single-particle degenerate dielectric resonators are presented. The resonator designs are realized by introducing high-contrast perturbations to the cavity geometry so as to bring the lowest-order electric and magnetic cavity resonances into frequency alignment. Since negative-index behavior can be demonstrated with only a single-type resonator (as opposed to dual-particle), these types of degenerate dielectric resonators potentially offer a size advantage so that the structure is less apt to fall outside the effective-medium region.
Three‐dimensional quadrature array coil elements for improved parallel magnetic resonance imaging performance at 1.5 Tesla (2011)

Abstract In this study, a special concept of 3D quadrature array coil elements is presented. It allows for doubling the number of phased‐array coil elements over a localized region of interest (ROI) without the necessity of reducing the sizes of the elements below optimal dimensions and thus losing performance due to domination of the noise of the elements. In this study, a 3D quadrature array coil element is formed of a planar coil element in combination with a perpendicular orientated, geometrically decoupled, second coil element. Simulation results of such a perpendicular arrangement of single coil elements are presented demonstrating the improvement in spatial sensitivity distribution and signal‐to‐noise ratio (SNR) over the localized ROI. In addition, an eight‐channel prototype array coil was built out of 3D quadrature array elements approving the advantageous encoding capabilities and SNR performance of the presented concept by in vivo T 2 ‐weighted spin‐echo imaging studies on the thoracic human spinal cord. © 2011 Wiley Periodicals, Inc. Concepts Magn Reson Part A 38A: 61–73, 2011.
Purification and characterization of a thermostable xylanase from a thermophilic fungus <i>Thermoascus aurantiacus</i> (1987)

A thermostable endo-β-D-xylanase (1,4-β-D-xylan xylanohydrolase, EC 3.2.1.8) was purified from the culture filtrate of a thermophilic fungus Thermoascus aurantiacus C436, using a single chromatographic step on SP-Sephadex C50. The purified preparation was homogeneous based on denaturing polyacrylamide and isoelectric focusing gels. The xylanase had a subunit molecular mass of 32 000 daltons, isoelectric point at pH 7.1, apparent K m and V max of 0.17% (w/v) xylan and 61.3IU/mg protein, respectively, at 50 °C. The pH and temperature optima for xylan hydrolysis were pH 5.1 and 80 °C, respectively. The xylanase retained full activity following incubation at 60 °C for 97 h or 70 °C for 24 h. At 80 °C, the half-life of the enzyme was 54 min. The xylanase was not affected by copper sulfate, zinc sulfate, calcium chloride, cobalt chloride, barium chloride, magnesium sulfate, and EDTA at concentrations of 2 mM. Mercury chloride at 2 mM concentration abolished all xylanase activity, while lead acetate at the same concentration reduced xylanase activity by approximately 25%. From the initial hydrolysis products of xylan, the xylanase was deduced to hydrolyse xylan through an endo-acting mechanism.
New mid-IR nonlinear optical crystal: CdSiP<inf>2</inf> (2008)

We report for the first time the phase matching properties of a new negative uniaxial crystal, CdSiP <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> , which can be pumped at 1 or 1.5 microns to generate mid-IR output in the 2–9μm spectral range.
Relevance of plasma biomarkers to imaging biomarkers (2023)

Abstract Background Recent advances in blood‐based biomarkers have shown promising abilities to estimate brain pathological statuses related to amyloid‐β (Aβ) deposition, phosphorylated tau deposition, and neurodegeneration using minimally invasive methods. The objective of this study was to evaluate the potential of blood‐based ATN classification, by analyzing relevance of plasma biomarkers to imaging biomarkers. Method There were 161 subjects, consisting of 62 cognitively normal (CN), 13 MCI, 40 Alzheimer’s dementia (AD) and 46 non‐Alzheimer’s dementia (non‐AD) individuals. Plasma Aβ composite biomarker was measured using immunoprecipitation‐mass spectrometry assay by combining plasma ratios of APP 669‐711 /Aβ 1‐42 and Aβ 1‐40 /Aβ 1‐42 . Plasma levels of p‐tau 181, glial fibrillary acidic protein (GFAP) and neurofilament light (NfL) were measured using the Simoa Ⓡ platform. PiB‐PET, THK5351‐PET, FDG‐PET and structural MRI images, and their representative semiquantitative values; PiB‐SUVR, THK‐SUVR, FDG‐PET scores (representing the degree of AD‐like glucose hypometabolism), and VSRAD ® scores (representing the degree of medial temporal atrophy), respectively, were used to analyze the relationships with the plasma biomarkers. Result The ROC analyses showed that AUCs of plasma Aβ composite, p‐tau 181, GFAP and NfL to discriminate Aβ status (PiB‐positive vs. negative) were 0.934, 0.835, 0.720 and 0.583, respectively. Whereas AUCs of those to discriminate clinical status (CN/MCI vs. dementia) were 0.649, 0.655, 0.800 and 0.803, respectively. Correlations to PiB‐SUVR were stronger in Aβ composite (r = 0.657) and p‐tau 181 (r = 0.551). Both p‐tau and GFAP showed higher correlations to THK‐SUVR (r = 0.444 and 0.416, respectively), and to FDG‐PET scores (r = 0.533 and 0.541, respectively) compared with other biomarkers. Correlations to VSRAD scores were only significant in NfL (r = 0.319). NfL also showed the highest correlation to MMSE scores (r = ‐0.583) (all the above r values were p < 0.001). These results were supported by multiple regression analyses between each imaging data and each plasma biomarker values using SPM8 adjusting for age and sex. Conclusion The results demonstrated reasonable relationships between the plasma biomarkers and imaging biomarkers, suggesting clinical utility of blood‐based ATN classification. GFAP and NfL are expected to reflect different aspects of neurodegeneration like FDG‐PET and structural MRI.
Fast Semi-automatic Target Initialization based on Visual Saliency for Airborne Thermal Imagery (2014)

In this study, a semi-automatic target initialization algorithm is introduced based on a recently proposed visual saliency approach. First, a center-surround difference based initial window selection is utilized around the input point coordinate provided by the user, in order to select the window which is most likely to contain the actual target and background satisfying piecewise connectivity. Then, a recently proposed visual saliency algorithm is exploited in order to detect the bounding box encapsulating the most salient part of the object. The experiments support that the saliency based tracking window initialization is capable of handling marking errors, i.e. erroneous user inputs, and boosts the performance of several tracking algorithms in terms of the number of frames in which successful tracking is achieved, when compared with several fixed window size initializations.
Linearly-Coupled Fountain Codes (2014)

Network-coded multiple access (NCMA) is a communication scheme for wireless multiple-access networks where physical-layer network coding (PNC) is employed. In NCMA, a user encodes and spreads its message into multiple packets. Time is slotted and multiple users transmit packets (one packet each) simultaneously in each timeslot. A sink node aims to decode the messages of all the users from the sequence of receptions over successive timeslots. For each timeslot, the NCMA receiver recovers multiple linear combinations of the packets transmitted in that timeslot, forming a system of linear equations. Different systems of linear equations are recovered in different timeslots. A message decoder then recovers the original messages of all the users by jointly solving multiple systems of linear equations obtained over different timeslots. We propose a low-complexity digital fountain approach for this coding problem, where each source node encodes its message into a sequence of packets using a fountain code. The aforementioned systems of linear equations recovered by the NCMA receiver effectively couple these fountain codes together. We refer to the coupling of the fountain codes as a linearly-coupled (LC) fountain code. The ordinary belief propagation (BP) decoding algorithm for conventional fountain codes is not optimal for LC fountain codes. We propose a batched BP decoding algorithm and analyze the convergence of the algorithm for general LC fountain codes. We demonstrate how to optimize the degree distributions and show by numerical results that the achievable rate region is nearly optimal. Our approach significantly reduces the decoding complexity compared with the previous NCMA schemes based on Reed-Solomon codes and random linear codes, and hence has the potential to increase throughput and decrease delay in computation-limited NCMA systems.
Evaluation of a lung cancer RNA expression subtyping panel and comparison with histologic diagnosis in lung tumor samples from multiple data sets including The Cancer Genome Atlas (TCGA). (2014)

7566 Background: Lung cancer subtypes are described by morphological and molecular characteristics. Differentiation between various subtypes is important for guiding patient management. Variability in morphology, limited tissue, and the need for performing a growing number of genomic tests pose challenges to the current diagnostic standard. Methods: The Lung Subtype Panel (LSP), a previously published 57 gene expression panel for prediction of lung tumor morphologic class (Wilkerson et al.JMD 2013), was investigated using 2,168 lung cancer samples from multiple publically available data sets (TCGA, NCI, UNC, Duke, Expo, Seoul, Tokyo, and France). Data sets with both gene expression data and morphologic classification were selected. Three platforms for gene expression were represented: Affymetrix U133+2 (n=883), Agilent 44K (n=334), and Illumina RNA-seq (n=951). A centroid predictor was used to assign an expression-defined histologic class. Predicted results were compared with tumor morphologic classification and percent agreement was calculated. Results: Ten lung tumor RNA expression datasets were combined into three platform specific data sets comprised of a diverse patient population, including smokers and nonsmokers with Stage I – Stage IV disease. Using the centroid predictor for two classes only (adenocarcinoma or squamous cell carcinoma), the agreement of the predictor with morphologic classification ranged from 79%-94% across the 3 data sets. Analysis of the 4-class predictor is underway and will be reported. To estimate an error rate in morphologic classification, a subset of tumors were reviewed by multiple pathologists, which showed an agreement rate of 65% (CI 49%-73%). Conclusions: In multiple datasets with over two thousand lung cancer samples, molecular profiling using the Lung Subtype Panel compared favorably to light microscopic derived diagnoses, and showed a higher level of agreement than seen by reassessment by multiple pathologists. RNA-based tumor subtyping can provide valuable information, especially when tissue is limiting and the overall morphologic diagnosis remains unclear.