gebhart/patrepeval huggingface dataset:
Nondestructive evaluation of alternative substrate quality using glancing-incidence x-ray diffraction and Raman spectroscopy (2002)

Alternate substrate technology holds promise for the growth of high-quality lattice-mismatched epitaxial films. Unfortunately, the technology has been plagued by difficulties in reproducibility of results. Some of this problem resides in a lack of characterization of the thin, twist bonded layer used as the template for subsequent epitaxial growth. In this work, grazing-incidence diffraction (GID) and micro-Raman spectroscopy were used to characterize the alternative substrate prior to growth. The 14- and 50-nm-thin GaAs layers were bonded to (100) GaAs substrates and, subsequently, exposed by standard thinning and etching techniques. The crystalline quality of the thin bonded substrates was studied by GID. The full widths at half maximum (FWHM) of the 004 peaks were used to monitor the optimum bonding condition. The measured FWHM varied from 29 to 601 arc s with smooth surfaces exhibiting the lowest values. The effects of bond pressures on template layers were studied for a series of 50 nm alternative substrates prepared using pressures ranging from 75 to 25 psi with a constant bonding temperature of 450 °C. All transferred template layers prepared within this pressure range showed poor quality (FWHM ranged from 324 to 601 arc s) when compared to bulk GaAs of 15 arc s. Micro-Raman measurements were also carried out on these samples. A transverse optical (TO) phonon line is seen and the intensity ratios of the TO to longitudinal optical phonon were much higher than that of GaAs substrate, confirming that the bonding process is causing damage to the thin template layer.
Phonon propagation with isotope scattering and spontaneous anharmonic decay (1990)

Calculations of the propagation of high-energy phonons introduced into a crystal at T=0 K are presented. The phonons are assumed to undergo elastic scattering and anharmonic decay processes. We show that in addition to the ``quasidiffusion'' component to the phonon propagation (discussed previously by Levinson and co-workers) there is also a contribution that arrives at close to the time expected for ballistic propagation. This latter mode of propagation continues to be of substantial importance even when the elastic scattering is much stronger than the anharmonic processes.
Mutually orthogonal transceivers for blind uplink CDMA irrespective of multipath channel nulls (1999)

Suppression of multiuser interference (MUI) and mitigation of multipath effects constitute major challenges in the design of third-generation wireless mobile systems. Most wideband and multicarrier uplink CDMA schemes suppress MUI statistically in the presence of unknown multipath. For fading resistance, they all rely on transmit- or receive-diversity and multichannel equalization based on bandwidth-consuming training or blind techniques. Either way, they impose restrictive and difficult to check conditions on the FIR channel nulls. Relying on symbol blocking, we design a mutually-orthogonal usercode-receiver (AMOUR) system for quasi-synchronous blind CDMA that eliminates MUI deterministically and mitigates fading irrespective of the unknown multipath and the adopted signal constellation. Analytic evaluation and preliminary simulations reveal the generality, flexibility, and superior performance of AMOUR over competing alternatives.
Author response: Insights into the key determinants of membrane protein topology enable the identification of new monotopic folds (2018)

Key sequence motifs, defined using the first reported structure of a monotopic membrane protein with a reentrant helix, enable identification of new monotopic membrane protein families previously predicted as membrane spanning.
AECID Fingerprinting Positioning Performance (2009)

The paper presents results from a field trial of the adaptive enhanced cell ID (AECID) fingerprinting positioning method that has been implemented by Ericsson AB for the GSM cellular system. The algorithm exploits own and neighbor cell global identities (CGIs), measured timing advance (TA) and quantized signal strength measurements to derive the radio fingerprint. The algorithm operates by collection of A-GPS measurements of opportunity, followed by a tagging by the fingerprint. All A-GPS measurements with the same fingerprint are then stored in separate clusters. In this way a large number of clusters covering the cellular network are created. Finally, a polygon is computed to describe the boundary of each cluster. The field trial of the AECID algorithm was performed in Shanghai, PRC, covering 15 dense urban and 11 suburban cells. About 4600 A-GPS reference measurements were collected for clustering and for performance evaluation. The results show that the inaccuracy of the AECID method is less than 25% of the inaccuracy of the CGI-TA positioning method, measured in terms of the area of the reported geographical regions.
Observations on the 1149.x family of standards (2002)

Five years of experience with the IEEE 1149.1 standard are discussed. It has been widely accepted across the electronics industry. It has made major contributions to board level testability. However, the advancement of the 1149.1 standard has not been as rapid as one might have imagined and there are some outstanding problems that it does not well address. As a member of the 1149.1 and P1149.4 working groups, as well as a developer of software for ATE systems, the author is interested in what one can learn from the 1149 and discusses his experiences in this field.
Sialylated core 1 based O-linked glycans enhance the growth rate of mammary carcinoma cells in MUC1 transgenic mice. (2004)

The MUC1 mucin, found on the luminal surface of simple epithelial cells is upregulated and aberrantly glycosylated in many carcinomas particularly breast and ovarian. MUC1 expressed by normal mammary epithelial cells, carries core 2 glycans but in breast carcinomas the simple core 1 based glycans are added. The binding of the monoclonal antibody SM3 to its peptide epitope in the tandem repeat of MUC1 is blocked by the branched core 2 glycans found on MUC1 expressed by normal cells. Thus SM3 does not bind to MUC1 expressed by normal mammary epithelial cells but reacts with more than 90% of breast carcinomas, suggesting that the loss of at least some core 2 glycans is a very common event in breast carcinogenesis. To determine if the change in glycosylation observed in breast carcinomas confers an advantage to cancer cells, murine mammary carcinoma cell lines were developed that express MUC1 carrying core 2 or core 1 linked glycans. The in vivo growth rate in wild-type and nude mice were identical regardless of the O-glycosylation patterns. However, the tumors that grew out of wild-type mice lost most of their MUC1 expression. In contrast, in MUC1 transgenic mice, where expression of MUC1 was retained by the tumor, a striking difference in growth rate was observed. In these mice, cells expressing core 1 glycans grew significantly faster than cells expressing core 2 glycans. These data suggest that MUC1 transgenic mice are more tolerant to core 1 expressing tumors than to tumors expressing core 2.
Supplementary Figure Legends 1-4, Methods from Temporal Dissection of Tumorigenesis in Primary Cancers (2023)

Supplementary Figure Legends 1-4, Methods from Temporal Dissection of Tumorigenesis in Primary Cancers
Hardware-Accelerated Regular Expression Matching with Overlap Handling on IBM PowerEN Processor (2013)

Programmable hardware accelerators for regular expression (regex) matching are evolving into increasingly complex stream processors, which involve multiple state machines that operate in parallel, and specialized post-processors that can process instructions dispatched by the state machines. To improve the speed and the storage-efficiency, complex regexs are decomposed into simpler subexpressions, where each subexpression can fire one or more instructions. Although the impact of regex decompositions on the storage efficiency is well-known, little has been done to address the correctness and completeness. We show that regex decompositions can result in false positives if overlaps between subexpressions are not taken into account. We describe formal methods to recognize various types of subexpression overlaps that can arise in regex decompositions. We also describe efficient post-processing techniques to eliminate the associated false positives. To enable efficient mapping of the decomposed regexs to the postprocessors, we propose integer programming based register allocation methods. Our methods pack narrow variables to reduce the register and instruction usage, and take advantage of multi-register reset instructions to reduce the number of instructions that must be executed in parallel. Experiments on regex sets obtained from open-source and proprietary network intrusion detection systems demonstrate orders of magnitude improvement in the storage efficiency over state-of-the-art.
Successful Intercalation into Multiwall Carbon Nanotubes without Breaking Tubular Structure (1998)

Abstract Though the presence of nanotubes in a carbon sample may be clearly detected by electron microscopy, yet it has been difficult to determine if the nanotubes in question belong to a Russian doll or scroll type. This work shows how a chemical reaction with ferric chloride or with potassium metal reveals the differences between the two types of intratube shell arrangement. Scroll nanotubes are intercalated by alien molecules which penetrate from the side of the scroll and fill the intershell spaces. The corresponding intershell spaces expansion was directly observed in this work by TEM. Russian doll nanotubes do not enter the reaction and stay intact. The reaction with scroll nanotubes is accompanied with a remarkable tube swelling which is easily observed by scanning electron microscopy. The presence of intercalated nanotubes may also be detected by X-ray diffraction and Raman spectroscopy. Key Words: carbonnanotubesintercalationelectron microscopy
Practical energy efficient link adaptation for MIMO-OFDM systems (2012)

We present a practical link adaptation algorithm for MIMO-OFDM systems. The proposed solution is based on sounding the channel periodically and choosing the optimal mode that will maximize the throughput or energy efficiency while satisfying the application's quality of service (QoS) requirements. In addition, we address practical problems such as computational complexity of the algorithm and determination of sounding period, by novel closed form formulations and iterative algorithms.
Achievable secrecy in arbitrary erasure networks with feedback (2014)

We present achievability schemes for secure message transmission in the presence of a passive eavesdropper, over arbitrary networks, where each edge corresponds to an independent erasure channel and we have available public channel state feedback. Our schemes are efficiently described through linear programming formulations, that generalize the information flow linear programs to networks with security constraints; different sources of secrecy show up as parameters in our linear programs, and solving the optimization problem enables to select the optimal (in terms of rate) scheme that integrates them. As far as we know, these are the first linear programming formulations for secret message transmission over arbitrary networks with erasures and channel state feedback.
Analytical electron microscopy and Raman spectroscopy studies of carbon nitride thin films (1993)

Deposition of carbon nitride thin films on Si(100) and polycrystalline Zr substrates was performed by dc magnetron sputtering of a graphite target under a pure nitrogen ambient. The resulting carbon nitride films (CNx) are primarily amorphous with a small volume fraction of nanocrystallites. Both energy-dispersive x-ray analysis and electron energy loss spectroscopy measurements showed that the amorphous matrix has uniform nitrogen-to-carbon ratios ∼0.4–0.8 depending on deposition conditions. Carbon and nitrogen K edge structures obtained from electron energy loss spectroscopy studies suggest that the amorphous carbon nitride matrix is primarily sp2 bonded. Apart from the carbon–nitrogen stretching vibration, Raman spectra of CNx films closely resemble those of diamondlike carbon films. Intensity and peak width changes of Raman features in the 1300–1600 cm−1 range due to inorganic carbon (D and G peak) under different deposition conditions are explained in terms of the extent of structural disorder in these films.
Cyclic and Acyclic Defensins Inhibit Human Immunodeficiency Virus Type-1 Replication by Different Mechanisms (2010)

Defensins are antimicrobial peptides expressed by plants and animals. In mammals there are three subfamilies of defensins, distinguished by structural features: alpha, beta and theta. Alpha and beta-defensins are linear peptides with broad anti-microbial activity that are expressed by many mammals including humans. In contrast, theta-defensins are cyclic anti-microbial peptides made by several non-human primates but not humans. All three defensin types have anti-HIV-1 activity, but their mechanisms of action differ. We studied the anti-HIV-1 activity of one defensin from each group, HNP-1 (alpha), HBD-2 (beta) and RTD-1 (theta). We examined how each defensin affected HIV-1 infection and demonstrated that the cyclic defensin RTD-1 inhibited HIV-1 entry, while acyclic HNP-1 and HBD-2 inhibited HIV-1 replication even when added 12 hours post-infection and blocked viral replication after HIV-1 cDNA formation. We further found that all three defensins downmodulated CXCR4. Moreover, RTD-1 inactivated X4 HIV-1, while HNP-1 and HBD-2 inactivated both X4 and R5 HIV-1. The data presented here show that acyclic and cyclic defensins block HIV-1 replication by shared and diverse mechanisms. Moreover, we found that HNP-1 and RTD-1 directly inhibited firefly luciferase enzymatic activity, which may affect the interpretation of previously published data.
Structure‐Based Evaluation of C5 Derivatives in the Catechol Diether Series TargetingHIV‐1 Reverse Transcriptase (2013)

Using a computationally driven approach, a class of inhibitors with picomolar potency known as the catechol diethers were developed targeting the non-nucleoside-binding pocket of HIV-1 reverse transcriptase. Computational studies suggested that halogen-bonding interactions between the C5 substituent of the inhibitor and backbone carbonyl of conserved residue Pro95 might be important. While the recently reported crystal structures of the reverse transcriptase complexes confirmed the interactions with the non-nucleoside-binding pocket, they revealed the lack of a halogen-bonding interaction with Pro95. To understand the effects of substituents at the C5 position, we determined additional crystal structures with 5-Br and 5-H derivatives. Using comparative structural analysis, we identified several conformations of the ethoxy uracil dependent on the strength of a van der Waals interaction with the Cγ of Pro95 and the C5 substitution. The 5-Cl and 5-F derivatives position the ethoxy uracil to make more hydrogen bonds, whereas the larger 5-Br and smaller 5-H position the ethoxy uracil to make fewer hydrogen bonds. EC50 values correlate with the trends observed in the crystal structures. The influence of C5 substitutions on the ethoxy uracil conformation may have strategic value, as future derivatives can possibly be modulated to gain additional hydrogen-bonding interactions with resistant variants of reverse transcriptase.
Visual Analytics Framework for the Assessment of Temporal Hypergraph Prediction Models (2019)

Members of communities often share topics of interest. However, usually not all members are interested in all topics, and participation in topics changes over time. Prediction models based on temporal hypergraphs that—in contrast to state-of-the-art models—exploit group structures in the communication network can be used to anticipate changes of interests. In practice, there is a need to assess these models in detail. While loss functions used in the training process can provide initial cues on the model’s global quality, local quality can be investigated with visual analytics. In this paper, we present a visual analytics framework for the assessment of temporal hypergraph prediction models. We introduce its core components: a sliding window approach to prediction and an interactive visualization for partially fuzzy temporal hypergraphs.
Abrasive Wear Behavior of Heat‐Treated ABC‐Silicon Carbide (2003)

Hot‐pressed silicon carbide, containing aluminum, boron, and carbon additives (ABC‐SiC), was subjected to three‐body and two‐body wear testing using diamond abrasives over a range of sizes. In general, the wear resistance of ABC‐SiC, with suitable heat treatment, was superior to that of commercial SiC. When the fine‐scale (3 μm) diamond abrasives were used, it was found that thermal annealing at 1300°C increased the resistance to three‐body wear by a factor of almost three, and two‐body wear by a factor of almost two, compared with as‐hot‐pressed samples. Higher annealing temperatures, however, led to a decline in wear resistance from its highest value. Similar behavior was seen for 1300°C‐annealed samples subjected to 15 μm diamond abrasive, although higher‐temperature annealing at 1500°–1600°C enhanced the wear resistance again. When coarse abrasives (72 μm) were used, the wear resistance progressively increased with increased annealing temperature from ∼1000° to 1600°C. Corresponding transmission and scanning electron microscopy studies indicated that, whereas transgranular, conchoidal cracking was dominant in the mild abrasive wear with fine‐scale (3 μm) abrasives, intergranular cracking and subsequent grain pullout was far more predominant in the more severe abrasive wear with coarse abrasives. Because the hardness and indentation toughness were barely altered during thermal treatment, the observed wear behavior was attributed mainly to the thermally induced microstructural changes, including the crystallization of glassy grain‐boundary films, the possible strengthening of the boundaries due to the enhancement of the aluminum, and the formation of aluminum‐rich, coherent nanoscale precipitates in the matrix grains above 1300°C.
Relative Expression of Proinflammatory and Antiinflammatory Genes Reveals Differences between Healing and Nonhealing Human Chronic Diabetic Foot Ulcers (2010)

driven neoplasms (Reifenberger et al., 2004; Palomba et al., 2012). Our identification of somatic RAS mutations in vascular tumors has clinical relevance. Current therapies against these lesions are limited to steroids and β-blockers, which achieve mixed results, often limited to tumor size reduction without resolution (Wine Lee et al., 2014). Some infantile vascular tumors, such as VASC101, are unresponsive to such interventions (Wine Lee et al., 2014). These cases may harbor RAS mutations, and might respond to farnesyl transferase inhibitors or Raf/Mek/Erk inhibitors, which block signaling upstream or downstream of RAS. The finding that RAS mutation drives vascular tumors provides potential opportunities to develop targeted therapies for current drug-resistant lesions.
Release 0.3.0 (2014)

We are pleased to present the 0.3.0 final release. See NEWS.md for the release notes, and http://julialang.org/downloads/ for binaries. For source builds in restricted environments (e.g. no network access) use the tarball attached below (julia-0.3.0_021d87dc72.tar.gz) as it already contains all dependencies pre-downloaded.
Total Synthesis of Indole and Dihydroindole Alkaloids. XVIII. Isomers and analogues of vinblastine (1980)

Abstract The synthesis and conformational analysis of (3′ R )‐3‐hydroxyleurosidine ( 5 ), (3′ S )‐3‐hydroxyleurosidine ( 10 ), (3′ S )‐3‐acetoxy‐4′‐deoxyleurosidine ( 15 ), (3′ R )‐3‐acetoxy‐4′‐deoxyleurosidine ( 23 ), (3′ R )‐3‐acetoxy‐4′‐deoxyvinblastine ( 16 ), (3′ S )‐3‐acetoxy‐4′‐deoxyleurosidine ( 28 ) is discussed.
Pt(II) Metal Complexes Tailored with a Newly Designed Spiro-Arranged Tetradentate Ligand; Harnessing of Charge-Transfer Phosphorescence and Fabrication of Sky Blue and White OLEDs (2015)

Tetradentate bis(pyridyl azolate) chelates are assembled by connecting two bidentate 3-trifluoromethyl-5-(2-pyridyl)azoles at the six position of pyridyl fragment with the tailored spiro-arranged fluorene and/or acridine functionalities. These new chelates were then utilized in synthesizing a series of Pt(II) metal complexes [Pt(Ln)], n = 1-5, from respective chelates L1-L5 and [PtCl2(DMSO)2] in 1,2-dimethoxyethane. The single-crystal X-ray structural analyses were executed on 1, 3, and 5 to reveal the generalized structures and packing arrangement in crystal lattices. Their photophysical properties were measured in both solution and solid state and are discussed in the context of computational analysis. These L1-L5 coordinated Pt(II) species exhibit intense emission, among which complex 5 shows remarkable solvatochromic phosphorescence due to the dominant intraligand charge transfer transition induced by the new bis(pyridyl azolate) chelates. Moreover, because of the higher-lying highest occupied molecular orbital of acridine, complex 5 can be considered as a novel bipolar phosphor. Successful fabrication of blue and white organic light-emitting diodes (OLEDs) using Pt(II) complexes 3 and 5 as the phosphorescent dopants are reported. In particular, blue OLEDs with 5 demonstrated peak efficiencies of 15.3% (36.3 cd/A, 38.0 lm/W), and CIE values of (0.190, 0.342) in a double-emitting layer structure. Furthermore, a red-emitting Os(II) complex and 5 were used to fabricate warm-white OLEDs to achieve peak external quantum efficiency, luminance efficiency, and power efficiency values as high as 12.7%, 22.5 cd/A, and 22.1 lm/W, respectively.
Experimental investigation in nodal aberration theory (NAT) with a customized Ritchey-Chrétien system: third-order coma (2018)

Nodal aberration theory (NAT) describes the aberration properties of optical systems without symmetry. NAT was fully described mathematically and investigated through real-ray tracing software, but an experimental investigation is yet to be realized. In this study, a two-mirror Ritchey-Chrétien telescope was designed and built, including testing of the mirrors in null configurations, for experimental investigation of NAT. A feature of this custom telescope is a high-precision hexapod that controls the secondary mirror of the telescope to purposely introduce system misalignments and quantify the introduced aberrations interferometrically. A method was developed to capture interferograms for multiple points across the field of view without moving the interferometer. A simulation result of Fringe Zernike coma was generated and analyzed to provide a direct comparison with the experimental results. A statistical analysis of the measurements was conducted to assess residual differences between simulations and experimental results. The interferograms were consistent with the simulations, thus experimentally validating NAT for third-order coma.