gebhart/patrepeval huggingface dataset:
Prediction of lung cancer genotype noninvasively using droplet digital PCR (ddPCR) analysis of cell-free plasma DNA (cfDNA). (2014)

8059 Background: Noninvasive plasma genotyping has the potential to accelerate delivery of targeted therapies to genotype-defined cancer populations and obviate repeat biopsies, particularly following drug resistance. We recently reported on a new assay for plasma genotyping using ddPCR of cfDNA (Oxnard et al., Clinical Cancer Research, 2014). Here, we aimed to predict the genotype of tumor biopsies using plasma genotyping. Methods: We identified patients (pts) with advanced NSCLC and acquired resistance to erlotinib that underwent rebiopsy and plasma collection on three IRB-approved protocols. Rebiopsy specimens underwent clinical EGFR genotyping. Plasma was collected in EDTA tubes, cfDNA extracted, and EGFR genotype quantified using ddPCR assays for L858R, exon 19 del and T790M. Serial plasma genotyping on treatment was performed for a subset of pts. This assay was then piloted in pts with advanced NSCLC who had not yet undergone tumor genotyping. Results: A total of 32 pts undergoing rebiopsy had plasma available for analysis. Sensitivity of plasma genotyping for EGFR exon 19 del and L858R was 57%; sensitivity increased to 91% among 11 pts with symptomatic bone or visceral metastases. One additional pt with no tumor EGFR sensitizing mutation but response to erlotinib had high levels of plasma exon 19 del, suggesting that plasma genotyping may identify mutations missed by tumor genotyping. T790M was detected on rebiopsy in 16 pts (50%); plasma genotyping was concordant with rebiopsy T790M status in 27 of 32 pts (84%). Post-treatment plasma specimens were available for 12 pts; the 5 pts with a partial response on imaging had a significant decrease in plasma concentration compared to the 7 pts without a response (median 895 copies/mL decrease vs 2 copies/mL increase, p=0.01). In 17 NSCLC pts without a known genotype, we identified EGFR mutations in 3 pts with a median 3 day turnaround time, up to 19 days before tumor genotyping confirmed the result. Conclusions: Plasma genotyping of cfDNA with ddPCR can predict tumor genotype rapidly and quantitatively with a high degree of accuracy, potentially obviating the need for re-biopsy in some circumstances. Clinical development of this assay is ongoing.
Advances in domain independent linear text segmentation (2000)

This paper describes a method for linear text seg- mc. ntation which is twice as accurate and over seven times as fast as the state-of-the-art (Reynar, 1998). Inter-sentence similarity is replaced by rank in the local context. Boundary locations are discovered by divisive clustering.
Left-Right Asymmetry Determination in Vertebrates (2001)

▪ Abstract A distinctive and essential feature of the vertebrate body is a pronounced left-right asymmetry of internal organs and the central nervous system. Remarkably, the direction of left-right asymmetry is consistent among all normal individuals in a species and, for many organs, is also conserved across species, despite the normal health of individuals with mirror-image anatomy. The mechanisms that determine stereotypic left-right asymmetry have fascinated biologists for over a century. Only recently, however, has our understanding of the left-right patterning been pushed forward by links to specific genes and proteins. Here we examine the molecular biology of the three principal steps in left-right determination: breaking bilateral symmetry, propagation and reinforcement of pattern, and the translation of pattern into asymmetric organ morphogenesis.
A novel block cipher design paradigm for secured communication (2016)

Unmanned aerial vehicles (UAV) are commonly used to conduct tasks (e.g. monitor and surveillance) in various civilian applications from a remote location. Wireless communications (i.e. radio frequency) are often used to remotely pilot the UAV and stream data back to the operator. The characteristics of the wireless communication channel allows attackers to monitor and manipulate the operation of the UAV through passive and active attacks. Cryptography is selected as a countermeasure to mitigate these threats; however, a drawback of using cryptography is the impact on the real-time operation and performance of the UAV. This paper proposes the Permutation Substitution Network (PSN) design paradigm with an instance presented which is the Alternative Advanced Encryption Standard (AAES) and analysis of its performance against the standardised Substitution Permutation Network (SPN) design paradigm the Advanced Encryption Standard (AES). Results indicate that using the PSN paradigm is a feasible approach in comparison to the SPN design paradigm.
Encryption: Security Considerations for Portable Media Devices (2007)

With the proliferation of removable media devices, such as iPods and USB drives, large amounts of an organization's sensitive data can easily be removed. The author explores the complexities of protecting networks against removable media, including guidelines for purchasing encryption software. This article examines how to develop portable and removable media security policies, as well as how encryption can assist in authenticating, authorizing, and auditing removable media devices.
Defective <i>FA2H</i> leads to a novel form of neurodegeneration with brain iron accumulation (NBIA) (2010)

These findings link white matter degeneration and NBIA for the first time and implicate new signaling pathways in the genesis of NBIA.
Host strategies against virus entry via the olfactory system (2011)

In mammals, odorants are inhaled through the nose and inside the nasal cavity they trigger olfactory sensory neurons (OSN) that are located within the olfactory epithelium. OSN project their axons into glomerular structures of the olfactory bulb. There they synapse with dendrites of second-order neurons that project their axons to the olfactory cortex. Thus, olfaction is based on direct interaction of environmental matters with OSN. This poses the question of how neurotropic viruses are prevented from infecting OSN and entering the central nervous system. Recent evidence indicates that upon instillation of neurotropic virus OSN are readily infected. By axonal transport virus reaches the glomerular layer of the olfactory bulb where it is efficiently curbed by a type I IFN dependent mechanism. In this review local mechanisms limiting virus entry via the olfactory system and virus spread within the CNS are recapitulated in the context of anatomical properties of the olfactory system.
Observation of quantized subband states and evidence for surface electron accumulation in CdO from angle-resolved photoemission spectroscopy (2008)

The electronic structure of well-ordered single-crystal thin films of CdO(100) has been studied using angle-resolved photoemission spectroscopy. Quantized electron subbands are observed above the valence-band maximum. The existence of these states provides evidence of an intrinsic electron accumulation space-charge layer near the CdO surface, an interpretation supported by coupled Poisson-Schr\"odinger calculations. The origin of the accumulation layer result is discussed in terms of the bulk band structure of CdO calculated using quasiparticle-corrected density-functional theory, which reveals that the conduction-band minimum at the Brillouin-zone center lies below the charge neutrality level.
Effects of phase-to-intensity noise conversion by multiple reflections on gigabit-per-second DFB laser transmission systems (1989)

Large power penalties and bit-error-rate floors have been observed in some Gb/s systems using distributed feedback (DFB) lasers, which could be attributed to interferometric conversion of laser phase noise to intensity noise by multiple reflections at connectors and splices. The authors calculated the power spectral density of the interferometric noise and its impact on system performance as a function of both the magnitude and number of reflections, and they compare the theoretical predictions with experimental results. Their studies indicate that connectors and splices with return losses of more than about 25 dB are required for the reliable operation of Gb/s fiber transmission systems, even if optical isolators are used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Magnetically Levitated Homopolar Hollow-Shaft Motor (2009)

This paper describes a novel and compact topology for contactless levitation and rotation of a wide annular rotor through the walls of a sealed process chamber. In the proposed setup, a homopolar magnetic bearing biased by permanent magnets is combined with a high-pole-number segment motor. The paper discusses the functional principle of the motor, and gives design and optimization guidelines for the bearing and the drive unit, respectively. An experimental system is presented along with a set of measurement results verifying the theoretical considerations.
Absolute frequency measurement of rubidium 5S–7S two-photon transitions with a femtosecond laser comb (2005)

The absolute frequencies of rubidium 5S-7S two-photon transitions at 760 nm are measured to an accuracy of 20 kHz with an optical frequency comb based on a mode-locked femtosecond Ti:sapphire laser. The rubidium 5S-7S two-photon transitions are potential candidates for frequency standards and serve as important optical frequency standards for telecommunication applications. The accuracy of the hyperfine constant of the 7S1/2 state is improved by a factor of 5 in comparison with previous results.
Shear wave polarization anisotropy in the upper mantle beneath Honshu, Japan (1983)

Shear wave polarization anisotropy in the wedge portion of the upper mantle between a subducting plate and the earth's surface is investigated using three‐component seismograms of intermediate depth and deep earthquakes recorded at 14 local stations in Honshu, Japan. Eighty nine high‐quality seismograms were selected from a period of 3 years. The data used in this study are restricted such that incidence angles are smaller than the critical angle of 30° to the earth's surface in order to avoid phase shifts in the shear wave train. To find directions of the maximum and minimum velocities in split shear waves, where shear waves are resolved into two phases with the maximum time separation, each set of the two horizontal component seismograms is rotated in the horizontal plane. The split shear waves thus obtained are again recombined after the correction of anisotropy, and the anisotropy‐corrected particle motion is compared with the focal mechanism for a cross‐check of the observed anisotropy. Directions of the maximum axes are plotted on azimuthincidence angle stereograms at each station. The stereograms and the cross sections of seismic ray paths show that (1) the anisotropic material is distributed at intermediate location between earthquake sources and receiving stations, and (2) the anisotropic region is separated into two parts: one in the north of the present study area with the polarization of the maximum velocity shear wave trending 0° to 30° from the north (north anisotropy) and the other in the south with it trending 90° to 120° (south anisotropy). The maximum time delays between the two shear waves along a vertical seismic ray is about l s for both the anisotropic regions. The horizontal extent of the anisotropic area in the north is 50 km at depths of 50 to 150 km. perhaps prevalent in west Honshu. However, the depth of anisotropic material is not well constrained because of insufficient coverage of seismic ray paths and angles. If we assume the vertical extent of the anisotropic material to be 100 km, the maximum velocity contrast would be 4%. If we adopt a crack alignment model, for the observed anisotropy, cracks are inferred to be distributed vertically trending 0° to 30° in the north and 90° to 120° in the south. If we assume an olivine alignment model, olivine crystals are inferred to be aligned in the north with the a axis of the slip direction trending 0° to 30° and the slip plane normal to the b axis being vertical and in the south anisotropy with the axis trending 90° to 120° and the slip plane being horizontal.
Activity Recognition using Actigraph Sensor (2010)

Numerous accelerometers are being extensively used in the recognition of simple ambulatory activities. Using wearable sensors for activity recognition is the latest topic of interest in smart home research. We use an Actigraph watch with an embedded accelerometer sensor to recognize real-life activities done in a home. Real-life activities include the set of Activities of Daily Living (ADL). ADLs are the crucial activities we perform everyday in our homes. Actigraph watches have been profusely used in sleep studies to determine the sleep/wake cycles and also the quality of sleep. In this paper, we investigate the possibility of using Actigraph watches to recognize activities. The data collected from an Actigraph watch was analyzed to predict ADLs (Activities of Daily Living). We apply machine learning algorithms to the Actigraph data to predict the ADLs. Also, a comparative study of activity prediction accuracy obtained from four machine learning algorithms is discussed.
The productivity paradox of information technology (1993)

article Free Access Share on The productivity paradox of information technology Author: Erik Brynjolfsson View Profile Authors Info & Claims Communications of the ACMVolume 36Issue 12Dec. 1993pp 66–77https://doi.org/10.1145/163298.163309Published:01 December 1993Publication History 215citation25,352DownloadsMetricsTotal Citations215Total Downloads25,352Last 12 Months2,602Last 6 weeks235 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
The spider mite family Tetranychidae in New Zealand. L. The genus Bryobia (1967)

A morphological study of the genus Bryobia (Acarina: Tetranychidae) in New Zealand has revealed the presence of six species and one sub species. They are: -B. cristata (Duges), B. repensi n. sp., B. rubrioculus (Scheuten), B. rubrioculus f. prunicola Mathys, B. watersi n. sp., B. variabilis n. sp., B. annatensis n. sp. Detailed descriptions and illustrations of each species are provided.
Analysis of Genome Plasticity in Pathogenic and Commensal <i>Escherichia coli</i> Isolates by Use of DNA Arrays (2003)

Genomes of prokaryotes differ significantly in size and DNA composition. Escherichia coli is considered a model organism to analyze the processes involved in bacterial genome evolution, as the species comprises numerous pathogenic and commensal variants. Pathogenic and nonpathogenic E. coli strains differ in the presence and absence of additional DNA elements contributing to specific virulence traits and also in the presence and absence of additional genetic information. To analyze the genetic diversity of pathogenic and commensal E. coli isolates, a whole-genome approach was applied. Using DNA arrays, the presence of all translatable open reading frames (ORFs) of nonpathogenic E. coli K-12 strain MG1655 was investigated in 26 E. coli isolates, including various extraintestinal and intestinal pathogenic E. coli isolates, 3 pathogenicity island deletion mutants, and commensal and laboratory strains. Additionally, the presence of virulence-associated genes of E. coli was determined using a DNA "pathoarray" developed in our laboratory. The frequency and distributional pattern of genomic variations vary widely in different E. coli strains. Up to 10% of the E. coli K-12-specific ORFs were not detectable in the genomes of the different strains. DNA sequences described for extraintestinal or intestinal pathogenic E. coli are more frequently detectable in isolates of the same origin than in other pathotypes. Several genes coding for virulence or fitness factors are also present in commensal E. coli isolates. Based on these results, the conserved E. coli core genome is estimated to consist of at least 3,100 translatable ORFs. The absence of K-12-specific ORFs was detectable in all chromosomal regions. These data demonstrate the great genome heterogeneity and genetic diversity among E. coli strains and underline the fact that both the acquisition and deletion of DNA elements are important processes involved in the evolution of prokaryotes.
Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells (2008)

Degradation of mRNA is one of the key processes that control the steady-state level of gene expression. However, the rate of mRNA decay for the majority of genes is not known. We successfully obtained the rate of mRNA decay for 19 977 non-redundant genes by microarray analysis of RNA samples obtained from mouse embryonic stem (ES) cells. Median estimated half-life was 7.1 h and only <100 genes, including Prdm1, Myc, Gadd45 g, Foxa2, Hes5 and Trib1, showed half-life less than 1 h. In general, mRNA species with short half-life were enriched among genes with regulatory functions (transcription factors), whereas mRNA species with long half-life were enriched among genes related to metabolism and structure (extracellular matrix, cytoskeleton). The stability of mRNAs correlated more significantly with the structural features of genes than the function of genes: mRNA stability showed the most significant positive correlation with the number of exon junctions per open reading frame length, and negative correlation with the presence of PUF-binding motifs and AU-rich elements in 3'-untranslated region (UTR) and CpG di-nucleotides in the 5'-UTR. The mRNA decay rates presented in this report are the largest data set for mammals and the first for ES cells.
<title>Sensitive sub-Doppler multiwave-mixing spectroscopy for flame and graphite furnace atomizers</title> (1995)

Resonant degenerate four-wave mixing is presented as an unusually sensitive nonlinear laser method that yields Doppler-free spectral resolution at trace-concentration levels even when using low laser power levels. Using a non-planar four-wave mixing optical setup, one can extract the signal beam from the input beams more easily, and hence, suppress the background noise more effectively and improve signal-to- noise ratios. Optical alignment is simple and convenient for this multiphoton setup. Sub-Doppler spectral resolution allows reliable measurement of many isotope and hyperfine lines using room-pressure flame atomizers, low-pressure discharge atomizers or room-pressure graphite furnace atomizers. While maintaining sub-Doppler spectral resolution, four-wave mixing still yields parts-per-trillion level detection sensitivity using these popular analytical atomizers. While flame atomizers offer convenient and fast sample introduction, low- pressure discharge atomizers offer better spectral resolution (i.e., sub-Doppler plus sub-Lorentzian), and graphite furnace atomizers yield lower atomizer background noise. Since laser power requirements are low (e.g., mW for CW lasers and nJ for pulsed lasers), many compact lasers (e.g., solid-state lasers) could be used in this simple yet sensitive nonlinear laser method.
Fairness and mutual profitability in collective behavior of automata (1983)

A certain class of noncooperative games is considered with two pure strategies for each of the automata players. The nature of the game is such that the pay-off of each player increases if any other participant in the game chooses the same pure strategy as that player, and decreases otherwise. The pay-off from a joint strategy is generally different for each automaton so that a joint strategy which is mutually profitable is not generally a fair play. A learning automaton model is proposed so that, without any prior agreement, as time unfolds a group of automata achieve a situation in mixed strategies which yields a pay-off for each automaton that is a trade-off between `fairness' and `profitability'. A formal mathematical proof of convergence of the collective situation in mixed strategies is given. An example is given to demonstrate the theoretical results.
Monocrystalline aluminium ohmic contact to <i>n</i>-GaAs by H2S adsorption (1981)

700-K H2S adsorption in the monolayer range onto the GaAs (100) surface induces profound modifications of surface properties. Al in situ epitaxially deposited near room temperature by molecular beam epitaxy (MBE) on a H2S adsorbed semiconductor surface exhibits low-effective Schottky-barrier height. It is shown that this Schottky-barrier lowering can be used to obtain monocrystalline nonalloyed ohmic contacts with low specific-contact resistances.
Characterization and Validation of the Slim-Form Open-Ended Coaxial Probe for the Dielectric Characterization of Biological Tissues at Millimeter-Wave Frequencies (2017)

This letter provides the calibration and optimization steps required for obtaining wideband millimeter-wave dielectric characteristics of human biological tissues using the commercially available slim-form open-ended coaxial probe. At the first stage, the reflection coefficients measured at the probe's calibration plane are transformed to the reflection coefficients of a desired aperture plane. Then, a rational optimization problem is solved to convert the aperture-plane reflection coefficients to dielectric permittivities. The measurement protocol is verified using three reference liquids and a test liquid representing dielectric characteristics of biological tissues.
Potential energy surfaces of fluorobenzene radical anions (2002)

Abstract Ab initio ROHF/6‐31+G* and MP2/6‐31+G*//ROHF/6‐31+G* calculations were used to consider fluorination's effect on potential energy surfaces (PESs) of benzene radical anion's (RAs). The Hartree–Fock PESs of symmetrically fluorinated radical anions were found to be pseudorotation surfaces. Unlike the benzene anion PES, pseudorotation surfaces include nonplanar structures. A Möbius band may represent the pseudorotation scheme of C 6 H stationary structures. Cutting the band out, we may obtain a pseudorotation scheme peculiar to C 6 F . This way of PES scheme building is also applicable to partially fluorinated RAs. A complicated structure of fluorinated anions' PES results from the avoided crossing of π states closed in energy together with the presence of a low‐lying vibronically active excited σ state. The number of stationary structures involved in pseudorotation varies in the series of anions, and may be changed at a higher level of calculations. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002
5G wireless backhaul networks: challenges and research advances (2014)

5G networks are expected to achieve gigabit-level throughput in future cellular networks. However, it is a great challenge to treat 5G wireless backhaul traffic in an effective way. In this article, we analyze the wireless backhaul traffic in two typical network architectures adopting small cell and millimeter wave communication technologies. Furthermore, the energy efficiency of wireless backhaul networks is compared for different network architectures and frequency bands. Numerical comparison results provide some guidelines for deploying future 5G wireless backhaul networks in economical and highly energy-efficient ways.