gebhart/patrepeval huggingface dataset:
Impact of Electrostatic Coupling and Wafer-Bonding Defects on Delay Testing of Monolithic 3D Integrated Circuits (2017)

Monolithic three-dimensional (M3D) integration is gaining momentum, as it has the potential to achieve significantly higher device density compared to 3D integration based on through-silicon vias. M3D integration uses several techniques that are not used in the fabrication of conventional integrated circuits (ICs). Therefore, a detailed analysis of the M3D fabrication process is required to understand the impact of defects that are likely to occur during chip fabrication. In this article, we first analyze electrostatic coupling in M3D ICs, which arises due to the aggressive scaling of the interlayer dielectric (ILD) thickness. We then analyze defects that arise due to voids created during wafer bonding, a key step in most M3D fabrication processes. We quantify the impact of these defects on the threshold voltage of a top-layer transistor in an M3D IC. We also show that wafer-bonding defects can lead to a change in the resistance of interlayer vias (ILVs), and in some cases lead to an open in an ILV or a short between two ILVs. We then analyze the impact of these defects on path delays using HSpice simulations. We study their impact on the effectiveness of delay-test patterns for multiple instances of IWLS 2005 benchmarks in which these defects were randomly injected. Our results show that the timing characteristics of an M3D IC can be significantly altered due to coupling and wafer-bonding defects if the thickness of its ILD is less than 100nm. Therefore, for such M3D ICs, test-generation methods must be enhanced to take M3D fabrication defects into account.
Intravascular optical coherence tomography image analysis method (2015)

Intravascular optical coherence tomography (IVOCT) has the resolution and contrasts necessary to identify coronary artery plaques. Currently, segmentation of images and identification of plaque composition are typically done manually. We have created a method for automated plaque classification using tissue optical characteristics and textures. Altogether, we used over 13,500 images from both manually annotated clinical IVOCT data and ex-vivo IVOCT pullback data annotated accurately using a novel approach with 3D microscopic cryo-imaging. Using 5-fold stratified cross validation on user selected volumes of interest, accuracy was 92.5% with area under the curve of 0.98, 0.99, 0.99 for calcium, lipid and fibrous, respectively. With the classifier fixed, there was good agreement between pixel-based classification and annotated IVOCT ex vivo image data. Results encourage us to pursue fully automated processing of IVOCT.
Keratin–hydroxyapatite composites: Biocompatibility, osseointegration, and physical properties in an ovine model (2010)

Reconstituted keratin has shown promise as an orthopaedic biomaterial. This in vivo study investigates the biological response of composite materials prepared from reconstituted keratin containing a high content of hydroxyapatite (HA) (40 wt % HA), implanted for up to 18 weeks in the long bones of sheep. Keratin-HA composites were compared with a commercially available polylactic acid (PLA) HA composite (BIO RCI HA®, Smith and Nephew). Porous keratin-HA materials displayed excellent biocompatibility and osseointegration, with full integration into bone by 12 weeks. Dense keratin-HA materials also showed excellent biocompatibility, with a more limited osseointegration, involving the penetration of new bone into the periphery of the implant after eight weeks. In contrast, the PLA-HA implant did not integrate with surrounding tissue. Microindentation showed that porous keratin-HA implants were initially soft, but became stiffer as new bone penetrated the implant from four weeks onwards. In contrast, although the initial rigidity of dense keratin-HA composites was maintained for at least two weeks, the implant material weakened after four weeks. The PLA-HA implant maintained its physical properties throughout the course of the trial. This study demonstrates the increased osseointegration/osteoconduction capacity of keratin-HA composites and provides further evidence supporting the suitability of keratin-based materials, such as bone graft substitutes and soft tissue fixation devices.
Reduction of off-flavor in liquid foods with immobilized acetic acid bacteria. (1988)

(1) 極微量のA. aceti湿菌体を脱脂豆乳に添加した場合でも,良好な不快臭の低減効果が得られ,A. acetiはアルデヒドを酸化するのに非常に高い触媒能を持っていることが明らかになった. (2) k-カラギーナンに包括固定した固定化酢酸菌を脱脂豆乳に接触させると不快臭が低減し,固定化酢酸菌は未固定酢酸菌の場合と同様に不快臭を低減させるのに有効であることがわかった. (3) 固定化酢酸菌がn-ヘキサナール等のアルデヒドを酸化する場合,最大反応速度を与える作用温度は50°C付近に,また,作用pHは5付近にあった. (4) 5°Cで65日間保存しても,固定化酢酸菌のアルデヒド酸化活性はほとんど低下しなかった.脱脂豆乳を用いて固定化酢酸菌を繰り返し使用した場合,数10回繰り返し使用しても固定化酢酸菌の酸化活性および固定化菌体の外観は全く影響を受けなかった.
Intermediate-node initiated reservation (IIR): a new signaling scheme for wavelength-routed networks with sparse conversion (2004)

In this work, we propose a new distributed signaling scheme, within the GMPLS framework for establishing lightpaths in wavelength-routed networks with sparse wavelength conversion. Analytical models are developed to evaluate the performance of the proposed scheme. Theoretical and simulation results show that compared to the classic schemed designed primarily for networks with no wavelength conversion, the proposed signaling scheme can achieve much lower blocking probability.
Transport of Electronic Excitation Energy in Dye-Loaded Zeolite L (2005)

Zeolite L is an aluminosilicate with one-dimensional channels, having an opening diameter of 7.1 Å. This allows the incorporation of different, electronically non-interacting dye molecules to build an artificial photonic antenna system. The conditions within the channels are such that the dye molecules cannot glide past each other. Hence, a consecutive incorporation leads to crystals with different compartments, where the density of one kind of dye is dominant. The photophysical processes taking place on such dye-loaded zeolite L antenna systems can be studied either on single micrometer or submicrometer sized crystals, on crystals dispersed in a solvent, orcoated as thin layers on a support. The energy transfer process that occurs is of the Förster-type and its transfer rate can be tuned, e.g. by first incorporating the acceptor dyes, in a second step consecutively incorporating different amounts of spacer molecules and then in a third step adding the donor dyes. By selectively exciting the donor, energy transfer to the unexcited acceptor as a function of the amount of spacer molecules can be observed. To make a quantitative analysis, one has to take into consideration the situation at the phase boundaries of the particular compartments. This has been done by modeling the distribution of the dye molecules and empty sites within a zeolite crystal by means of a Monte Carlo simulation.
Ataxia-Telangiectasia Locus: Sequence Analysis of 184 kb of Human Genomic DNA Containing the Entire <i>ATM</i> Gene (1997)

Ataxia-telangiectasia (A-T) is an autosomal recessive disorder involving cerebellar degeneration, immunodeficiency, chromosomal instability, radiosensitivity, and cancer predisposition. The genomic organization of the A-T gene, designated ATM, was established recently. To date, more than 100 A-T-associated mutations have been reported in the ATM gene that do not support the existence of one or several mutational hotspots. To allow genotype/phenotype correlations it will be important to find additional ATM mutations. The nature and location of the mutations will also provide insights into the molecular processes that underly the disease. To facilitate the search for ATM mutations and to establish the basis for the identification of transcriptional regulatory elements, we have sequenced and report here 184,490 bp of genomic sequence from the human 11q22-23 chromosomal region containing the entire ATM gene, spanning 146 kb, and 10 kb of the 5'-region of an adjacent gene named E14/NPAT. The latter shares a bidirectional promoter with ATM and is transcribed in the opposite direction. The entire region is transcribed to approximately 85% and translated to 5%. Genome-wide repeats were found to constitute 37.2%, with LINE (17.1%) and Alu (14.6%) being the main repetitive elements. The high representation of LINE repeats is attributable to the presence of three full-length LINE-1s, inserted in the same orientation in introns 18 and 63 as well as downstream of the ATM gene. Homology searches suggest that ATM exon 2 could have derived from a mammalian interspersed repeat (MIR). Promoter recognition algorithms identified divergent promoter elements within the CpG island, which lies between the ATM and E14/NPAT genes, and provide evidence for a putative second ATM promoter located within intron 3, immediately upstream of the first coding exon. The low G+C level (38.1%) of the ATM locus is reflected in a strongly biased codon and amino acid usage of the gene.
Preparation and Biological Properties of Water-Soluble Adjuvant Fractions from Delipidated Cells of <i>Mycobacterium smegmatis</i> and <i>Nocardia opaca</i> (1973)

Digestion by lysozyme of delipidated cells of Mycobacterium smegmatis liberates a water-soluble immunoadjuvant fraction which is chemically very similar to the water-soluble adjuvant (WSA) obtained previously from purified cell walls, but which contains somewhat more non-peptidoglycan amino acids. The yield of peptidoglycan-arabinogalactan complex is about 10 times greater starting from whole cells than from cell walls. The main biological properties of this "neo-WSA" are described: it increases circulating antibodies to ovalbumin in guinea pigs, it does not produce polyarthritis in rats or induce hypersensitivity to tuberculin, it does not increase susceptibility to histamine or hyperreactivity to endotoxin, and does not produce spleen and liver hypertrophy. Analogous immunostimulant fractions have also been obtained from delipidated cells of Nocardia opaca by lysozyme treatment.
Simulation and Experiment of Fourier Transform Digital Holographic Adaptive Optics (2013)

Fourier transform digital holographic adaptive optics imaging system is described. The results from the simulation and experiment are reported that demonstrate the feasibility of this adaptive optics system.
Altered expression of the alpha7beta1 integrin in human and murine muscular dystrophies. (1997)

The alpha7beta1 integrin is the primary laminin receptor on skeletal myoblasts and adult myofibers. It has distinct functions during muscle development and contributes to muscle structural integrity. We have studied this integrin in cases where expression of dystrophin or laminin are compromised. Immunofluorescence demonstrates an increase in alpha7beta1 in patients with Duchenne muscular dystrophy and in mdx mice that lack dystrophin. Analysis of RNA from mdx mice and from patients with Duchenne and Becker muscular dystrophies indicates that the increase in the alpha7beta1 integrin is regulated at the level of alpha7 gene transcription. In contrast, the levels of alpha7beta1 integrin are severely diminished in patients with laminin alpha2 chain congenital dystrophy muscular dystrophy and in dy/dy mice that also do not make the alpha2 laminin chain. Analysis of RNA from the hindlimbs of dy/dy mice demonstrated that in the absence of laminin alpha7 gene transcription is inhibited and limited to specific alternatively spliced isoforms. We suggest that the increased expression of alpha7beta1 integrin in the absence of dystrophin compensates for the reduced dystrophin-mediated linkage of fibers with the basal lamina and modulates the development of pathology associated with these diseases. The decrease in alpha7beta1 integrin and its transcripts in the absence of laminin likely contributes to the severe myopathy that results from laminin alpha2 chain deficiency and suggests that laminin-2 regulates expression of the alpha7 integrin gene. The role of the alpha7beta1 integrin in muscle integrity also suggests that compromised expression of this receptor may underlie as yet undefined myopathies.
Mechanical properties of DNA origami nanoassemblies are determined by Holliday junction mechanophores (2016)

DNA nanoassemblies have demonstrated wide applications in various fields including nanomaterials, drug delivery and biosensing. In DNA origami, single-stranded DNA template is shaped into desired nanostructure by DNA staples that form Holliday junctions with the template. Limited by current methodologies, however, mechanical properties of DNA origami structures have not been adequately characterized, which hinders further applications of these materials. Using laser tweezers, here, we have described two mechanical properties of DNA nanoassemblies represented by DNA nanotubes, DNA nanopyramids and DNA nanotiles. First, mechanical stability of DNA origami structures is determined by the effective density of Holliday junctions along a particular stress direction. Second, mechanical isomerization observed between two conformations of DNA nanotubes at 10-35 pN has been ascribed to the collective actions of individual Holliday junctions, which are only possible in DNA origami with rotational symmetric arrangements of Holliday junctions, such as those in DNA nanotubes. Our results indicate that Holliday junctions control mechanical behaviors of DNA nanoassemblies. Therefore, they can be considered as 'mechanophores' that sustain mechanical properties of origami nanoassemblies. The mechanical properties observed here provide insights for designing better DNA nanostructures. In addition, the unprecedented mechanical isomerization process brings new strategies for the development of nano-sensors and actuators.
A new enzymatic method of acrylamide production. (1982)

To produce acrylamide from acrylonitrile by use of a new enzyme, nitrile hydratase, a number of nitrile-utilizing microorganisms were screened for the enzyme activity by an intact cell system. An isobutyronitrile-utilizing bacterium, strain B23, showed the best productivity among 1 86 strains tested. The strain was identified taxonomically as Pseudomonas chlororaphis. The culture and reaction conditions for the production were studied for the strain. Under the optimum conditions, 400 grams/liter of acrylamide was produced in 7.5hr. The yield was nearly 100% with a trace amount of acrylic acid. The cell-free extract of the strain showed strong activity of nitrile hydratase toward acrylonitrile and extremely low activity of amidase toward acrylamide.
Long-amplicon TCRβ repertoire sequencing to reveal human T-cell receptor variable gene polymorphism: Implications for the prediction and interpretation of immunotherapy outcome. (2018)

129 Background: Human T cell antigen receptors play a critical role in protective immune responses but are also implicated in autoimmune disease and immune-mediated adverse events during immunotherapy. The antigen specificity of the T cell receptor is determined in part by the sequence of the CDR and Framework regions encoded by the TCRB variable gene. Previous studies of population sequencing data indicate that current antigen receptor allele databases, such as IMGT, fail to capture a significant portion of human variation. Here we use long-amplicon multiplex sequencing of rearranged TCRB receptors to validate putative novel human variable gene alleles previously recovered from 1000 genomes data. Methods: TCRB rearrangements were amplified from cDNA from 85 Caucasians undergoing treatment for melanoma using AmpliSeq-based multiplex Framework 1 and Constant gene primers to produce ~330bp amplicons. Samples were sequenced using the Ion Torrent S5 530 chip to produce ~1.5M raw reads per sample. Ion Reporter was used for clonotyping and identification of variable gene sequences absent from the IMGT database. Putatively novel sequences were compared to those reported in the Lym1k database of alleles recovered from 1000 genomes data. Results: We identified 15 novel variable gene alleles that are absent from the IMGT database and result in amino acid changes to the CDR or Framework regions of the TCR. Typically, a single individual was found to be heterozygous for a novel variant, though we note two instances where multiple individuals possessed a novel variant. We also identified novel variable gene alleles that are absent from the Lym1k database, potentially due to challenges in inferring receptor alleles from short-read population sequencing studies. Conclusions: We find evidence for significant human diversity in TCRB variable gene alleles beyond what is currently represented in the IMGT database. TCRB sequencing using multiplex Framework 1 and Constant gene targeting primers is ideally suited for studying the role of TCRB polymorphism in autoimmune disease and immune-mediated adverse events during immunotherapy.
Thermal barrier coatings for heat engine components (1980)

A comprehensive NASA-Lewis program of coating development for aircraft gas turbine blades and vanes is presented. Improved ceramic layer compositions are investigated, along the MCrAlY bond films and the methods of uniform deposition of the coatings; the thermomechanical and fuel impurity tolerance limits of the coatings are being studied. Materials include the ZrO2-Y2O3/NiCrAlY system; the effects of the bond coat and zirconia composition on coating life and Mach 1 burner rig test results are discussed. It is concluded that Diesel engines can also utilize thermal barrier coatings; they have been used successfully on piston crowns and exhaust valves of shipboard engines to combat lower grade fuel combustion corrosion.
<i>In vitro</i>evolution of a T cell receptor with high affinity for peptide/MHC (2000)

T cell receptors (TCRs) exhibit genetic and structural diversity similar to antibodies, but they have binding affinities that are several orders of magnitude lower. It has been suggested that TCRs undergo selection in vivo to maintain lower affinities. Here, we show that there is not an inherent genetic or structural limitation on higher affinity. Higher-affinity TCR variants were generated in the absence of in vivo selective pressures by using yeast display and selection from a library of Valpha CDR3 mutants. Selected mutants had greater than 100-fold higher affinity (K(D) approximately 9 nM) for the peptide/MHC ligand while retaining a high degree of peptide specificity. Among the high-affinity TCR mutants, a strong preference was found for CDR3alpha that contained Pro or Gly residues. Finally, unlike the wild-type TCR, a soluble monomeric form of a high-affinity TCR was capable of directly detecting peptide/MHC complexes on antigen-presenting cells. These findings prove that affinity maturation of TCRs is possible and suggest a strategy for engineering TCRs that can be used in targeting specific peptide/MHC complexes for diagnostic and therapeutic purposes.
Fatigue Strength Improvement of Box Welds by Using Low Transformation Temperature Welding Material. Tripled Fatigue Strength by Postweld Heat Treatment. (2001)

The fatigue strength of box welds was tripled by using low transformation temperature welding wire and postweld heat treatment (PWHT). The improved fatigue strength was obtained due to the stress ratio effect resulting from compressive residual stress. The low transformation temperature welding material which contains 10 mass % Cr and 10 mass % Ni expands during the final cooling process of welding. This expansion of weld metal induced the compressive residual stress around the welded part. The PWHT at 720°C for 1 hour and subsequent cooling in air induced the transformation from austenite to martensite at the same time for three passes. That is, the volume expansion on three passes by PWHT became large compare with that on final pass in as-welded condition, and the compressive residual stress could be induced efficiently.
Beam‐type collisional activation of polypeptide cations that survive ion/ion electron transfer (2007)

Doubly protonated peptides that undergo an electron transfer reaction without dissociation in a linear ion trap can be subjected to beam-type collisional activation upon transfer from the linear ion trap into an adjacent mass analyzer, as demonstrated here with a hybrid triple quadrupole/linear ion trap system. The activation can be promoted by use of a DC offset difference between the ion trap used for reaction and the ion trap into which the products are injected of 12-16 V, which gives rise to energetic collisions between the transferred ions and the collision/bath gas employed in the linear ion trap used for ion/ion reactions. Such a process can be executed routinely on hybrid linear ion trap/triple quadrupole tandem mass spectrometers and is demonstrated here with several model peptides as well as a few dozen tryptic peptides. Collisional activation of the peptide precursor ions that survive electron transfer frequently provides structural information that is absent from the precursor ions that fragment spontaneously upon electron transfer. The degree to which additional structural information is obtained by collisional activation of the surviving singly charged peptide ions depends upon peptide size. Little or no additional structural information is obtained from small peptides (<8 residues) due to the high electron transfer dissociation (ETD) efficiencies noted for these peptides as well as the extensive sequence information that tends to be forthcoming from ETD of such species. Collisional activation of the surviving electron transfer products provided greatest benefit for peptides of 8-15 residues.
Identification of immunogenic and antibody-binding membrane proteins of pathogenic Trichomonas vaginalis (1983)

Characterization of immunogenic Trichomonas vaginalis membrane proteins was accomplished by using extrinsically and intrinsically labeled organisms and a highly sensitive and specific radioimmunoprecipitation procedure. Intact motile trichomonads were compared with detergent extracts as a source of antigen in radioimmunoprecipitation experiments. Approximately 20 proteins accessible to antibody were identified and ranged in molecular weight from 200,000 to 20,000. Localization on the parasite surface of the highly immunogenic membrane proteins was attempted by using, as the indicator system, formaldehyde-fixed protein A-bearing Staphylococcus aureus pretreated with the various antiserum reagents and incubated with live, motile parasites. Also, indirect immunofluorescence with fluorescein isothiocyanate--anti-rabbit immunoglobulin was also employed after incubation of organisms with either control serum or antiserum from immunized rabbits or after treatment of trichomonads with the immunoglobulin G fraction from each respective serum. No immunoglobulin G antibody appeared to be directed at the anterior trichomonal flagella or the posterior axostyle, whereas strong fluorescence was detected throughout the rest of the T. vaginalis surface. The biological significance of these data is discussed.
Extract knowledge from semi-structured websites for search task simplification (2011)

Simplifying the key tasks of search engine users by directly retrieving to them structured knowledge according to their queries is attracting much attention from both industry and academia. A bottleneck of this challenging problem is how to extract the structured knowledge from the noisy and complex Web scale websites automatically. In this paper, we propose an unsupervised automatic wrapper induction algorithm, named as Scalable Knowledge Extractor from webSites (SKES). SKES induces the wrapper in a divide and conquer mode, i.e., it divides the general wrapper into several sub-wrappers to learn from the data independently. Moreover, through employing techniques such as tag path representation of Web pages, SKES is verified to be efficient and noise-tolerant by the experimental results. Furthermore, based on our automatically extracted knowledge, we also built a prototype to serve structured knowledge to end users for simplifying their key search tasks. Very positive feedbacks were received on the prototype.