gebhart/patrepeval huggingface dataset:
Fifty years of brain tissue mechanical testing: From in vitro to in vivo investigations (2010)

Beginning in the 1960s many studies have been performed to investigate the mechanical properties of brain. In this paper we point out the difficulties linked with in vitro experimental protocols as well as the advantages of using recently developed non-invasive in vivo techniques, such as magnetic resonance elastography. Results of in vitro and in vivo work are compared, emphasizing the specificities and disparities of the in vitro as well as the in vivo results. In particular, a detailed discussion of the results obtained from dynamic shear experiments and magnetic resonance elastography is given before arriving at a tentative conclusion on the state of knowledge of the mechanical properties of brain.
Spectrally beam combined fiber lasers for high power, efficiency, and brightness (2013)

Spectral Beam Combining (SBC) of fiber lasers provides a simple, robust architecture for power scaling lasers to high power. With appropriate designs, power scaling beyond the single fiber limit can be achieved while maintaining near diffraction limited beam quality and high efficiency. We present experimental results where we achieved > 3 kW at an M<sup>2</sup> = 1.35 and > 39% E-O efficiency by combining 12 individual fiber lasers into a single high brightness beam.
Luteinizing Hormone Inhibits Potassium Outward Currents in Swine Granulosa Cells by Intracellular Calcium Mobilization* (1991)

Potassium currents of swine granulosa cells were studied using the patch clamp technique in the whole cell configuration. Granulosa cells stepped to positive potentials (+60 mV) from -40 mV holding potential exhibit a slowly activating, noninactivating outward potassium current. Tail current reverse potential (between -90 and -100 mV) and the current inhibition brought about by the replacement of KCl with CsCl in the pipette solution indicate that this current is carried by K ions. LH was found to significantly reduce the amplitude of this current. The effect was dose and time dependent. Similar inhibition (20-30% of the initial current) was reached with doses of 1-50 micrograms/ml, but in times proportionally shorter as the dose increased (50% inhibition was reached in 170-180 and 30-40 sec with 1 and 50 micrograms LH/ml, respectively). Much longer and variable times (3-10 min) were required with lower doses (0.2 microgram/ml). The effect of LH was independent of extracellular Ca, while preexposure of cells to TMB-8, an inhibitor of intracellular Ca mobilization, completely prevented the effect of LH. Outward currents after LH treatment could be completely restored by perfusing the cells with ionomycin in Ca-free medium to facilitate calcium efflux from the cells. The present studies indicate that LH modifies the bioelectrical properties of swine granulosa cells. This effect is mediated by an elevation of intracellular calcium, probably mobilized from intracellular stores. The induced changes in K conductance may play a specific role in the transduction mechanisms for LH.
Extraction and simulation of potential bridging faults and open defects affecting standard cell libraries (2008)

Shorts and opens are the most common type of defects in digital integrated circuits ICs. They can affect interconnect wires connecting gates or transistors inside. Tools targeting the extraction of these potential defects focus only on the inter-gate bridging faults in order to use this information in pattern generation, and no one presents a method to extract potential intra-grate bridging fault, or open and resistive-open defects. This paper presents a new approach to automate the extraction and simulation of potential intra-gate defect in standard cell library, based on the use of verification and simulation CAD tools. Experimental results show the efficiency of our approach to identify and simulate potential intra-gate defects in 65nm technology.
RPA, a Class II ARFGAP Protein, Activates ARF1 and U5 and Plays a Role in Root Hair Development in Arabidopsis (2006)

The polar growth of plant cells depends on the secretion of a large amount of membrane and cell wall materials at the growing tip to sustain rapid growth. Small GTP-binding proteins, such as Rho-related GTPases from plants and ADP-ribosylation factors (ARFs), have been shown to play important roles in polar growth via regulating intracellular membrane trafficking. To investigate the role of membrane trafficking in plant development, a Dissociation insertion line that disrupted a putative ARF GTPase-activating protein (ARFGAP) gene, AT2G35210, was identified in Arabidopsis (Arabidopsis thaliana). Phenotypic analysis showed that the mutant seedlings developed isotropically expanded, short, and branched root hairs. Pollen germination in vitro indicated that the pollen tube growth rate was slightly affected in the mutant. AT2G35210 is specifically expressed in roots, pollen grains, and pollen tubes; therefore, it is designated as ROOT AND POLLEN ARFGAP (RPA). RPA encodes a protein with an N-terminal ARFGAP domain. Subcellular localization experiments showed that RPA is localized at the Golgi complexes via its 79 C-terminal amino acids. We further showed that RPA possesses ARF GTPase-activating activity and specifically activates Arabidopsis ARF1 and ARF1-like protein U5 in vitro. Furthermore, RPA complemented Saccharomyces cerevisiae glo3Delta gcs1Delta double mutant, which suggested that RPA functions as an ARFGAP during vesicle transport between the Golgi and the endoplasmic reticulum. Together, we demonstrated that RPA plays a role in root hair and pollen tube growth, most likely through the regulation of Arabidopsis ARF1 and ARF1-like protein U5 activity.
Vorapaxar for reduction of thrombotic cardiovascular events in myocardial infarction and peripheral artery disease (2015)

Vorapaxar is a novel antiplatelet agent that has demonstrated efficacy in reducing atherosclerotic events in patients with a history of MI or PAD without a history of stroke, transient ischemic attack, or ICH when taken in combination with aspirin and clopidogrel.
Neural models of cursive script handwriting (1989)

The main characteristics of cursive script handwriting are reviewed, and a basic coding scheme is described. Two types of neural networks are described: (i) a self-organizing network, similar to that used by T. Kohonen for his phonetic typewriter (see IEEE Comput., p.11-22, 1988), which is able to discover Graphotopic Maps; (ii) a three-layer perceptron called NetWrite in analogy with the NeTalk architecture developed by C.R. Rosemberg and T. Sejnowksi (see Complex Syst., vol.1, p.145-68, 1987), that can recognize digraphs. Pros and cons are discussed, as well as an integration proposal.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The value of magnetic resonance imaging as a biomarker for amyotrophic lateral sclerosis: a systematic review (2016)

Despite the existing MRI biomarkers, there is a need for large cohorts with long term MRI and clinical follow-up. MRI assessment could be improved by standardized MRI protocols with multicentre studies.
Magneto-optical investigation of the shape anisotropy of individual micron-sized magnetic elements (2011)

In this work, the anisotropy of individual microstructured magnetic elements has been investigated. The investigated elements are of elliptical shape with different sizes and aspect ratios (AR), structured from a 5-nm-thick permalloy (Ni80Fe20) film. For the measurements, a new magneto-optical Kerr effect (MOKE) magnetometer was used. To allow for the investigation of individual microstructured elements, a micro-focused probing laser beam (spatial resolution ≈1μm) has been combined with a self-stabilizing positioning system of high accuracy, including a rotating unit. Hysteresis loops can be taken for varying orientation of the symmetry axes of the magnetic elements relative to the applied field. For the characterization of the anisotropy, the coercive field as a function of the magnetization direction is extracted from the corresponding hysteresis loops. These results make a quantitative and systematic study of the influence of the shape anisotropy on the magnetic behavior of microstructures possible. The experimental data has been compared to an extended Stoner-Wohlfarth model.
Jitter and clock recovery for periodic traffic in broadband packet networks (1994)

The transparent transport of real-time periodic traffic through a broadband packet network requires the recovery of source clock frequency at the destination. The arriving packet stream at the destination buffer contains the source clock frequency information, which can be recovered by monitoring the buffer level, and using it to adjust the destination clock frequency without buffer under- or overflow. However, the inherently stochastic nature of packet transport in a broadband packet network makes the recovery difficult. The authors illustrate the packet jitter phenomenon, and develop algorithms to construct the destination clock frequency such that it asymptotically follows the source clock frequency with minimal variation. They provide a systematic design procedure for the implementation of these algorithms, and apply them to a computer model of a single stage FCFS multiplexer to demonstrate their effectiveness and different design trade-offs. They also discuss the application of the algorithms to the audio and video services.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance (2016)

Knowledge of the distribution and diversity of RNA viruses is still limited in spite of their possible environmental and epidemiological impacts because RNA virus-specific metagenomic methods have not yet been developed. We herein constructed an effective metagenomic method for RNA viruses by targeting long double-stranded (ds)RNA in cellular organisms, which is a hallmark of infection, or the replication of dsRNA and single-stranded (ss)RNA viruses, except for retroviruses. This novel dsRNA targeting metagenomic method is characterized by an extremely high recovery rate of viral RNA sequences, the retrieval of terminal sequences, and uniform read coverage, which has not previously been reported in other metagenomic methods targeting RNA viruses. This method revealed a previously unidentified viral RNA diversity of more than 20 complete RNA viral genomes including dsRNA and ssRNA viruses associated with an environmental diatom colony. Our approach will be a powerful tool for cataloging RNA viruses associated with organisms of interest.
Clonal descent and microevolution of <i>Neisseria meningitidis</i> during 30 years of epidemic spread (1997)

Serogroup A meningococci of subgroups III, IV-1 and IV-2 are probably descended from a common ancestor that existed in the nineteenth century. The 10.5kb sequences spanning five distinct chromosomal loci, encoding cell-surface antigens, a secreted protease or housekeeping genes and intergenic regions, were almost identical in strains of those subgroups isolated in 1966, 1966 and 1917 respectively. During the subsequent two to three decades, all of these loci varied as a result of mutation, translocation or import of DNA from unrelated neisseriae. Thus, microevolution occurs frequently in naturally transformable bacteria. Many variants were isolated only once or within a single geographical location and disappeared thereafter. Other variants achieved genetic fixation within months or a few years. The speed with which sequence variation is either eliminated or fixed may reflect sequential bottlenecks associated with epidemic spread and contrasts with the results of phylogenetic analyses from bacteria that do not cause epidemics.
AZO-CROWN ETHERS. THE DYES WITH AZO GROUP DIRECTLY INVOLVED IN THE CROWN ETHER SKELETON (1980)

Abstract Crown-type polyether azo dyes 1∼3 were synthesized, and the ion-pair extraction of sodium and potassium ion was studied. The extraction behavior resembles those of benzo-type crown ethers, but changes on light illumination due to trans–cis isomerization of the dyes. The cis-form lacks the affinity to metal ions.
Expression of FACT in mammalian tissues suggests its role in maintaining of undifferentiated state of cells (2011)

The Facilitates Chromatin Transcription (FACT) chromatin remodeling complex, comprised of two subunits, SSRP1 and SPT16, is involved in transcription, replication and DNA repair. We recently showed that curaxins, small molecules with anti-cancer activity, target FACT and kill tumor cells in a FACT-dependent manner. We also found that FACT is overexpressed in human and mouse tumors and that tumor cells are sensitive to FACT downregulation. To clarify the clinical potential of FACT inhibition, we were interested in physiological role(s) of FACT in multicellular organisms. We analyzed SSRP1 and SPT16 expression in different cells, tissues and conditions using Immunohistochemical (IHC) staining of mouse and human tissues and analysis of publically available high-content gene expression datasets. Both approaches demonstrated coordinated expression of the two FACT subunits, which was primarily associated with the stage of cellular differentiation. Most cells of adult tissues do not have detectable protein level of FACT. High FACT expression was associated with stem or less-differentiated cells, while low FACT levels were seen in more differentiated cells. Experimental manipulation of cell differentiation and proliferation in vitro, as well as tissue staining for the Ki67 proliferation marker, showed that FACT expression is related more to differentiation than to proliferation. Thus, FACT may be part of a stem cell-like gene expression signature and play a role in maintaining cells in an undifferentiated state, which is consistent with its potential role as an anti-cancer target.
NVSim-CAM (2016)

Ternary Content-Addressable Memory (TCAM) is widely used in networking routers, fully associative caches, search engines, etc. While the conventional SRAM-based TCAM suffers from the poor scalability, the emerging nonvolatile memories (NVM, i.e., MRAM, PCM, and ReRAM) bring evolution for the TCAM design. It effectively reduces the cell size, and makes significant energy reduction and scalability improvement. New applications such as associative processors/accelerators are facilitated by the emergence of the nonvolatile TCAM (nvTCAM). However, nvTCAM design is challenging. In addition to the emerging device's uncertainty, the nvTCAM cell structure is so diverse that it results in a design space too large to explore manually. To tackle these challenges, we propose a circuit-level model and develop a simulation tool, NVSim-CAM, which helps researchers to make early design decisions, and to evaluate device/circuit innovations. The tool is validated by HSPICE simulations and data from fabricated chips. We also present a case study to illustrate how NVSim-CAM benefits the nvTCAM design. In the case study, we propose a novel 3D vertical ReRAM based TCAM cell, the 3DvTCAM. We project the advantages/disadvantages and explore the design space for the proposed cell with NVSim-CAM.
Indirect Controlled Phased Source (2006)

We propose here a novel phase controllable oscillator to realize phase shift for the phased array. The phase of the oscillator is controlled by the phase of reference frequency of a phase locked loop. Since the reference frequency is usually lower than 100MHz, the phase shifting can be much easier, have a lower cost, and be more accurate than that in microwave phase shifters. A four-element scanning array antenna using this novel phase control technique is demonstrated with a scanning range of plusmn40deg in this letter
Hadoop GIS (2013)

Support of high performance queries on large volumes of spatial data becomes increasingly important in many application domains, including geospatial problems in numerous fields, location based services, and emerging scientific applications that are increasingly data- and compute-intensive. The emergence of massive scale spatial data is due to the proliferation of cost effective and ubiquitous positioning technologies, development of high resolution imaging technologies, and contribution from a large number of community users. There are two major challenges for managing and querying massive spatial data to support spatial queries: the explosion of spatial data, and the high computational complexity of spatial queries. In this paper, we present <i>Hadoop-GIS</i> - a scalable and high performance spatial data warehousing system for running large scale spatial queries on Hadoop. Hadoop-GIS supports multiple types of spatial queries on MapReduce through spatial partitioning, customizable spatial query engine RESQUE, implicit parallel spatial query execution on MapReduce, and effective methods for amending query results through handling boundary objects. Hadoop-GIS utilizes global partition indexing and customizable on demand local spatial indexing to achieve efficient query processing. Hadoop-GIS is integrated into Hive to support declarative spatial queries with an integrated architecture. Our experiments have demonstrated the high efficiency of Hadoop-GIS on query response and high scalability to run on commodity clusters. Our comparative experiments have showed that performance of Hadoop-GIS is on par with parallel SDBMS and outperforms SDBMS for compute-intensive queries. Hadoop-GIS is available as a set of library for processing spatial queries, and as an integrated software package in Hive.
Quantification of renal pathology by image analysis (Methods in Renal Research) (2007)

Recent advances in computer image analysis techniques allow more accurate quantification of kidney pathological lesions, which are identified by histological staining or immunohistochemistry. This article provides a detailed description of the basic techniques for quantifying these lesions in digital images of light microscopy using Image J software, which is freely available over the Internet. The methods discussed include calibrating measurements, applying scales to images, assessment of object size and thickness, cell counting and point counting, and analysis of area stained. Our explanations indicate how these methods can be used to evaluate glomerular hypertrophy, tubular and vascular injury, accumulation of inflammatory cells and myofibroblasts, deposition of extracellular matrix, and the development of renal scarring.
The Optimal Condition for the Production and Extraction of Monacolin K from Red-Koji (2003)

The optimal condition for the production and extraction of monacolin K was reported. HPLC was used to determine monacolin K a kind of metabolite of Monascus from red-koji made of Monascus purpureus CBS 281.34. After culturing Monascus in solid and liquid media at for 10 days, each of these were inoculated with soybean, wheat, barley, waxy rice, and rice and cultivated at for 11 days. The production of monacolin K was the highest(0.35g/100g) when cultured with rice. The yield of monacolin K in red-koji increased with drying temperature and time according to the removal of water. Considering monacolin K content and the degree of death of Monascus, red-koji was dried at for 60 min. Although monacolin K in red-koji was mostly extracted by 80% ethanol, there was no difference in monacolin K between shaking for 1 min and extraction for hr after sonication for 7 min. The extracted yield of monacolin K was the highest when the ratio of red-koji and 80% ethanol was 1:9. Moreover, the production of monacolin K appeared to be parallel with that of the pigment.
Context Is (Almost) Everything: Academic Historians and Digital Archival Collections (2021)

Access to online archival materials has become vital for many academic historians and other researchers. The COVID-19 global pandemic has aimed the spotlight on the digital archival collections hosted by archives institutions and available through the web. In light of this increased role of digital archival collections, it is imperative for archivists to gain a better understanding of academic historians’ perceptions of these materials. The study reported in this article builds on previous work in the archives, history, and library and information studies disciplines to assess current perceptions that academic historians have toward digital archival collections. The article concludes that these virtual materials have created a paradoxical situation, whereby the ease of access potentially shapes historical understanding and interpretation in ways that are difficult (if not impossible) to anticipate and not always desirable. Archivists must pay careful attention to the presentation of what content is placed online and how users interact with it is important for the design of digital archival collections.
Interventional endoscopy for the treatment of pancreatic pseudocyst and walled‐off necrosis (with videos) (2014)

Pancreatic pseudocysts and walled-off necrosis are typical late complications of acute pancreatitis, and they require drainage in symptomatic cases presenting with infection. Transgastrointestinal endoscopic treatment with endoscopic ultrasound-guided drainage has become common and yields a good treatment outcome for pancreatic pseudocyst. Walled-off necrosis, however, contains necrotic tissue, and thus many cases additionally require an invasive treatment that includes endoscopic necrosectomy. Methods that involve a procedure-specific large-diameter metal stent, additional endoscopic drainage techniques, and the hybrid approach method of adding percutaneous drainage have been described, and considerable advances in these methods have now made it possible to cure almost all cases of walled-off necrosis with endoscopic treatment alone. However, without being restricted to endoscopic treatments, a wide range of options including surgery should be considered as treatments for walled-off necrosis.
A strong hybrid promoter for quasi-constitutive expression of heterologous proteins in Yarrowia lipolytica (1997)

International audience
Binaural and transaural spatialization techniques in multichannel 5.1 production (Anwendung binauraler und transauraler Wiedergabetechnik in der 5.1 Musikproduktion) (2012)

The work presented here aims at overcoming some of the weaknesses of the 5.1 standard in terms of stability and precision of lateral sources. In addition to traditional surround panning (which relies on constant-power panning and/or multichannel microphone recordings) an extra spatialization layer based on binaural/transaural processing is introduced. This article discusses the audio signal processing and panning methods, and shows different applications scenarios and use cases.
Tools for design, interactive simulation and visualization for dynamic analysis of mechanical models (2000)

Mathematical models used in scientific computing are becoming large and complex. In order to handle the size and complexity, the models should be better structured (using object-orientation) and visualized (using advanced user interfaces). Visualization is a difficult task, requiring a great deal of effort from scientific computing specialists. Currently, the visualization of a model is tightly coupled with the structure of the model itself. This has the effect that any changes to the model require that the visualization be redesigned as well. Our vision is to automate the generation of visualizations from mathematical models. In other words, every time the model changes, its visualization is automatically updated without any programming efforts. The innovation of this thesis is demonstrating this approach in a number of different situations, e.g. for input and output data, and for two- and three-dimensional visualizations. We show that this approach works best for object-oriented languages (ObjectMath, C++, and Modelica).