gebhart/patrepeval huggingface dataset:
Antegrade Side Branch Access in Branched Aortic Arch Endografts: A Porcine Feasibility Study (2013)

To describe the deployment technique for a single side branch arch endograft in a porcine model and prove the concept of transseptal or transapical antegrade access for catheterization and introduction of the mating stent-graft.Six domestic pigs were operated with retrograde delivery of a single side branch arch endograft and antegrade introduction of a mating stent-graft using transseptal access (n=3) and transapical access (n=3). Technical feasibility, operating time, radiation parameters, and hemodynamic changes were studied.Transseptal and transapical access techniques were feasible in all animals. Catheterization and introduction of the mating stent-graft was feasible in 2 of 3 animals in the transseptal group and all animals in the transapical group. Technical feasibility was better in the transapical group, with shorter operating and fluoroscopy times and less hemodynamic impact during endograft deployment. Hemodynamic changes were short and reversible in all animals in both groups.Antegrade transcardiac access to the aortic arch for implantation of mating stent-grafts in branched arch endografting is feasible in a porcine model with reversible impact on hemodynamic measures during deployment. Transapical access was technically easier, with shorter operating and fluoroscopy times.
Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forsythensis are Components of a Polymicrobial Intracellular Flora within Human Buccal Cells (2005)

Previously, we used in situ hybridization and confocal microscopy to detect the periodontal pathogens Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, and Tannerella forsythensis within buccal epithelial cells taken directly from the mouth. This study tested the hypothesis that the intracellular flora of buccal cells is polymicrobial. Mixtures containing a red fluorescent universal probe paired with green fluorescent versions of either A. actinomycetemcomitans-, P. gingivalis-, or T. forsythensis-specific probes were hybridized with buccal cells collected from each of 38 healthy humans. We verified co-localization of probe pairs within cells by generating three-dimensional reconstructions. Intracellular bacteria were detected in every subject. Each cell that was labeled with a species-specific probe also contained bacteria recognized only by the universal probe. Bacteria labeled with specific probes often occupied smaller regions within larger masses of bacteria. Those findings suggest that future studies of invasion by oral bacteria may need to include microbial consortia.
Innovative Applications of Artificial Intelligence 2014 (2015)

This issue features expanded versions of articles selected from the 2014 AAAI Conference on Innovative Applications of Artificial Intelligence (IAAI) held in Quebec City, Canada. We present a selection of four articles describing deployed applications plus two more articles that discuss work on emerging applications.
Impacts of acidic ISR on geochemistry and bacteria in Kazakhstan (2013)

In Kazakhstan, in-situ recovery (ISR) mining utilizes H2SO4 (pH &lt; 2) to mobilize uranium from naturally reducing conditions. ISR can be less environmentally impactful than physical mining techniques, but it risks groundwater (GW) contamination. Presented here is a geochemical and metagenomic analysis and comparison of pre-, mid-, and post-mining GW conditions. Biostimulation may limit the spread of U and decrease the time of exposure, compared to natural attenuation, by orders of magnitude
Dynamic Pooling Improves Nanopore Base Calling Accuracy (2021)

In nanopore sequencing, electrical signal is measured as DNA molecules pass through the sequencing pores. Translating these signals into DNA bases (base calling) is a highly non-trivial task, and its quality has a large impact on the sequencing accuracy. The most successful nanopore base callers to date use convolutional neural networks (CNN) to accomplish the task. Convolutional layers in CNNs are typically composed of filters with constant window size, performing best in analysis of signals with uniform speed. However, the speed of nanopore sequencing varies greatly both within reads and between sequencing runs. Here, we present dynamic pooling, a novel neural network component, which addresses this problem by adaptively adjusting the pooling ratio. To demonstrate the usefulness of dynamic pooling, we developed two base callers: Heron and Osprey. Heron improves the accuracy beyond the experimental high-accuracy base caller Bonito developed by Oxford Nanopore. Osprey is a fast base caller that can compete in accuracy with Guppy high-accuracy mode, but does not require GPU acceleration and achieves a near real-time speed on common desktop CPUs. Availability: https://github.com/fmfi-compbio/osprey, https://github.com/fmfi-compbio/heron.
Effect of Counterions on the Ribbonlike Supramolecular Assembly Formation of Dinuclear Metal Complexes in the Lyotropic Mesophase (2000)

The effect of counterions on the formation of the ribbonlike supramolecular assembly of a dinuclear metal complex in the lyotropic mesophase has been examined by optical microscopy, cryo-transmission electron microscopy, atomic force microscopy, and X-ray diffraction. Potassium and ammonium salts of [Cr2(l-tart2H)(phen)2]- (tart = tartrate(IV−), phen = 1,10-phenanthroline) in water display liquid crystals, where ribbonlike assemblies are formed like that of the sodium salt. Sheetlike assemblies are found in dilute solutions of sodium, potassium, and ammonium salts. On the other hand, aqueous solutions of [Co(en)3]3+ (en = ethylenediamine) salts do not display liquid crystals because of the nonrigid character of the ribbons. The [Co(en)3]3+ salts form sheets and ribbonlike assemblies in the same solution. The ribbons gather like strings or roll spirally. The characteristic assembly formation of [Co(en)3]3+ salts may originate in the bulky structure of [Co(en)3]3+.
Placing search in context (2002)

Keyword-based search engines are in widespread use today as a popular means for Web-based information retrieval. Although such systems seem deceptively simple, a considerable amount of skill is required in order to satisfy non-trivial information needs. This paper presents a new conceptual paradigm for performing search in context, that largely automates the search process, providing even non-professional users with highly relevant results. This paradigm is implemented in practice in the IntelliZap system, where search is initiated from a text query marked by the user in a document she views, and is guided by the text surrounding the marked query in that document ("the context"). The context-driven information retrieval process involves semantic keyword extraction and clustering to automatically generate new, augmented queries. The latter are submitted to a host of general and domain-specific search engines. Search results are then semantically reranked, using context. Experimental results testify that using context to guide search, effectively offers even inexperienced users an advanced search tool on the Web.
Measuring anisotropic thermal conduction in polyisobutylene following step shear strains (2000)

Abstract The connection between polymer chain orientation and several macroscopic properties in a polymer melt was studied using mechanical and optical techniques. Anisotropic thermal conductivity following shear deformation was measured using forced Rayleigh light scattering, the refractive index tensor is followed using birefringence measurements, and the stress was measured mechanically in a parallel‐plate rheometer. The thermal diffusivity measured in the flow and neutral directions increased and decreased, respectively, immediately following the deformation. These quantities then relaxed to the equilibrium value on the time‐scale of the stress‐relaxation memory. Comparison of the difference between measured flow and neutral direction thermal diffusivities with the analogous flow‐induced birefringence in the same deformation provided indirect evidence for a linear relation between stress and thermal diffusivity at two different values of strain. Mechanical measurements were used to characterize the memory of the fluid.
Scalable and Efficient Flow-Based Community Detection for Large-Scale Graph Analysis (2017)

Community detection is an increasingly popular approach to uncover important structures in large networks. Flow-based community detection methods rely on communication patterns of the network rather than structural properties to determine communities. The Infomap algorithm in particular optimizes a novel objective function called the map equation and has been shown to outperform other approaches in third-party benchmarks. However, Infomap and its variants are inherently sequential, limiting their use for large-scale graphs. In this article, we propose a novel algorithm to optimize the map equation called RelaxMap. RelaxMap provides two important improvements over Infomap: parallelization, so that the map equation can be optimized over much larger graphs, and prioritization, so that the most important work occurs first, iterations take less time, and the algorithm converges faster. We implement these techniques using OpenMP on shared-memory multicore systems, and evaluate our approach on a variety of graphs from standard graph clustering benchmarks as well as real graph datasets. Our evaluation shows that both techniques are effective: RelaxMap achieves 70% parallel efficiency on eight cores, and prioritization improves algorithm performance by an additional 20--50% on average, depending on the graph properties. Additionally, RelaxMap converges in the similar number of iterations and provides solutions of equivalent quality as the serial Infomap implementation.
SURVEY AND SUMMARY A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation (2010)

In many eukaryotic mRNAs one or more short ‘upstream’ open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and to amplify the signals likely explains their occurrence in most polyamine pathway mRNAs. The uORFmediated polyamine responsive autoregulatory circuits found in polyamine pathway mRNAs exemplify the translationally regulated dynamic interface between components of the proteome and metabolism.
Wireless system for structural health monitoring based on Lamb waves (2012)

Structural health monitoring systems are increasingly used for comprehensive fatigue tests and surveillance of large scale structures. In this paper we describe the development and validation of a wireless system for SHM application based on Lamb-waves. The system is based on a wireless sensor network and focuses especially on low power measurement, signal processing and communication. The sensor nodes were realized by compact, sensor near signal processing structures containing components for analog preprocessing of acoustic signals, their digitization and network communication. The core component is a digital microprocessor ARM Cortex-M3 von STMicroelectronics, which performs the basic algorithms necessary for data acquisition synchronization and filtering. The system provides network discovery and multi-hop and self-healing mechanisms. If the distance between two communicating devices is too big for direct radio transmission, packets are routed over intermediate devices automatically. The system represents a low-power and low-cost active structural health monitoring solution. As a first application, the system was installed on a CFRP structure.
Ocular Wavefront Transformation (2009)

Ocular wavefront transformation is perhaps the most widely used theory in wavefront optics for vision correction because the pupil size of a human eye changes due to accommodation or the change of illumination, and because the pupil constriction is most likely not concentric.[1, 2, 3] For example, in laser vision correction, the pupil size of an eye is relatively large when an ocular wavefront is captured under an aberrometer. To obtain the entire ocular wavefront, it is recommended that the ambient light is kept low to dilate the pupil size during the wavefront exam so the surgeon can use either a large or a small treatment zone. However, if a smaller wavefront map is captured, it is impossible to devise an accurate treatment over a larger zone because the wavefront information over the captured zone is unknown. When the patient is under the laser, the pupil size changes because the ambient light changes. Furthermore, the cyclorotation of the eye due to the change from a sitting position to a lying position moves the pupil center between the wavefront capture and the laser ablation. [4] Theoretically, it was shown that correction of the error due to rotation and translation of the pupil gives significant benefits in vision correction. [5, 6] Iris registration [7] was designed to correct the error from the misalignment between the pupil in front of the aberrometer and the pupil under the laser. Because the iris features are not affected by the change of pupil size, they can be used as reliable references to establish the relative geometrical displacement between two image frames. [8] A common coordinate system is thus established to facilitate the full correction of ocular aberrations. For practical applications, however, a full correction is not possible partly because of the fluctuation of the high-order aberrations and partly because of the instrument error. Therefore, it is desirable to have a theoretical tool for the error analysis of an imperfect correction for the misalignment of the eye between the pupil in front of the aberrometer and the pupil under the laser. Moreover, for a majority of the data analysis for ocular aberrations, it is a common practice that the pupil sizes of different wavefront exams are standardized to a given size. Therefore, the pupil resizing of a known wavefront is also a subject of discussion. In addition, the constriction and decentration of the pupil makes wavefront refraction change when high-order aberrations are present. This becomes a useful tool for the design of the optical surfaces for the correction of presbyopia. [9]
The effects of genetic and pharmacological blockade of the CB1 cannabinoid receptor on anxiety (2002)

The aim of this study was to compare the effects of the genetic and pharmacological disruption of CB1 cannabinoid receptors on the elevated plus-maze test of anxiety. In the first experiment, the behaviour of CB1-knockout mice and wild-type mice was compared. In the second experiment, the cannabinoid antagonist SR141716A (0, 1, and 3 mg/kg) was administered to both CB1-knockout and wild type mice. Untreated CB1-knockout mice showed a reduced exploration of the open arms of the plus-maze apparatus, thus appearing more anxious than the wild-type animals, however no changes in locomotion were noticed. The vehicle-injected CB1-knockout mice from the second experiment also showed increased anxiety as compared with wild types. Surprisingly, the cannabinoid antagonist SR141716A reduced anxiety in both wild type and CB1 knockout mice. Locomotor behaviour was only marginally affected. Recent evidence suggests the existence of a novel cannabinoid receptor in the brain. It has also been shown that SR141716A binds to both the CB1 and the putative novel receptor. The data presented here supports these findings, as the cannabinoid receptor antagonist affected anxiety in both wild type and CB1-knockout mice. Tentatively, it may be suggested that the discrepancy between the effects of the genetic and pharmacological blockade of the CB1 receptor suggests that the novel receptor plays a role in anxiety.
On the Usefulness of the Mechanical Index Displayed on Clinical Ultrasound Scanners for Predicting Contrast Microbubble Destruction (2005)

The MI displayed on clinical ultrasound scanners does not predict the degree of microbubble destruction and should not be used by itself to define exposure conditions for destruction of microbubble contrast agents.
Circulatory shear stress induces molecular changes and side population enrichment in primary tumor-derived lung cancer cells with higher metastatic potential (2021)

Cancer is a leading cause of death and disease worldwide. However, while the survival for patients with primary cancers is improving, the ability to prevent metastatic cancer has not. Once patients develop metastases, their prognosis is dismal. A critical step in metastasis is the transit of cancer cells in the circulatory system. In this hostile microenvironment, variations in pressure and flow can change cellular behavior. However, the effects that circulation has on cancer cells and the metastatic process remain unclear. To further understand this process, we engineered a closed-loop fluidic system to analyze molecular changes induced by variations in flow rate and pressure on primary tumor-derived lung adenocarcinoma cells. We found that cancer cells overexpress epithelial-to-mesenchymal transition markers TWIST1 and SNAI2, as well as stem-like marker CD44 (but not CD133, SOX2 and/or NANOG). Moreover, these cells display a fourfold increased percentage of side population cells and have an increased propensity for migration. In vivo, surviving circulatory cells lead to decreased survival in rodents. These results suggest that cancer cells that express a specific circulatory transition phenotype and are enriched in side population cells are able to survive prolonged circulatory stress and lead to increased metastatic disease and shorter survival.
Demonstration of 10.9 nm table-top soft x-ray laser at 1 Hz repetition rate (2010)

We report a 10.9nm gain-saturated table-top soft x-ray laser operating at 1 Hz repetition rate. With average power of 1 microwatt and pulse energy up to ~ 2 microjoules this laser extends the ability to conduct table-top laser experiments to a shorter wavelength.
Study of the desorption/ionization mechanism in electrospray droplet impact secondary ion mass spectrometry (2011)

Electrospray droplet impact (EDI) secondary ion mass spectrometry (SIMS) is a desorption/ionization technique for mass spectrometry in which highly charged water clusters produced from an atmospheric-pressure electrospray are accelerated in vacuum by several kV and impact on the sample deposited on the metal substrate. The abundances of the secondary ions for C(60) and amino acids are measured as a function of the acceleration voltage of the primary charged water droplets. Two desorption/ionization mechanisms are suggested in the EDI ionization processes: low-energy and high-energy regimes. In the low-energy regime, the excess charges in the primary droplets play a role in the formation of secondary ions. In the high-energy regime, samples are ionized by the supersonic collision of the primary droplets with the sample. The yield of secondary ions increases by about three orders of magnitude with increase in the acceleration voltage of the primary droplets from 1.75 kV to 10 kV.
What Is Inflammatory Breast Cancer? Revisiting the Case Definition (2010)

The case definition for inflammatory breast cancer (IBC) is controversial. The American Joint Committee on Cancer defines IBC as redness, warmth and edema involving at least half the breast. The SEER program relies on a pathologic finding of dermal lymphatic invasion and recently added those with clinical involvement of more than 3/4 of the breast. We established a registry to collect information and specimens from IBC patients to clarify the epidemiology and biology of these tumors. The goals of this report are to suggest improvements regarding case definitions and provide data on the variety of presentations relevant to early diagnosis.
Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection (2015)

The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.
Precocious induction of oocyte maturation and ovulation in rainbow trout (Salmo gairdneri) : problems when using 17 α-hydroxy-20 β-dihydroprogesterone (1978)

The efficiency of 17 a-hydroxy-20 (3-dihydroprogesterone (17 a-20 p P) administered alone or after pituitary priming, was investigated in vivo before peripheral migration of the germinal vesicle 4 to 8 weeks prior to natural ovulation. Treatmert with 17 K -20 (3 P alone (2 injections of 3 mg/kg at a 2-day interval) induced oocyte maturation in 94 p. 100 of the fish, but only 25 p. 100 ovulated. Treatment with 17 a-20 p P (3 mg/kg once) 2 days after pituitary priming (1 ml/kg of trout pituitary extract, TPE, containing 3.25 x 10-3 mg/ml of trout gonadotropin, t-GTH) induced maturation in all fish, 59 p. 100 of which ovulated. In both cases, fish in which ovulation did not follow oocyte maturation were killed 15 days after the first injection ; ovarian follicles were either dissected by hand to remove mature oocytes, or incubated in vitro with prostaglandin F 2 &oelig; which induced successful ovulation. In all cases, oocytes obtained from in vivo ovulation, in vitro ovulation by PGF 2 &oelig; ' or manual dissection were fertilized to some extent.
N-degree ROADM Architecture Comparison: Broadcastand-Select versus Route-and-Select in 120 Gb/s DP-QPSK Transmission Systems (2014)

ROADM systems utilizing 4- and 9-degree broadcast-and-select or route-and-select architectures are studied experimentally with 120 Gb/s DP-QPSK transmission. Effects arising from passband narrowing and crosstalk accumulation due to non-ideal WSS filtering are considered concurrently.
Dlx1/2 and Otp coordinate the production of hypothalamic GHRH- and AgRP-neurons (2018)

Despite critical roles of the hypothalamic arcuate neurons in controlling the growth and energy homeostasis, the gene regulatory network directing their development remains unclear. Here we report that the transcription factors Dlx1/2 and Otp coordinate the balanced generation of the two functionally related neurons in the hypothalamic arcuate nucleus, GHRH-neurons promoting the growth and AgRP-neurons controlling the feeding and energy expenditure. Dlx1/2-deficient mice show a loss-of-GHRH-neurons and an increase of AgRP-neurons, and consistently develop dwarfism and consume less energy. These results indicate that Dlx1/2 are crucial for specifying the GHRH-neuronal identity and, simultaneously, for suppressing AgRP-neuronal fate. We further show that Otp is required for the generation of AgRP-neurons and that Dlx1/2 repress the expression of Otp by directly binding the Otp gene. Together, our study demonstrates that the identity of GHRH- and AgRP-neurons is synchronously specified and segregated by the Dlx1/2-Otp gene regulatory axis.