gebhart/patrepeval huggingface dataset:
Structural Characterization of Graphene Nanosheets for Miniaturization of Potentiometric Urea Lipid Film Based Biosensors (2012)

Abstract The present article describes a miniaturized potentiometric urea lipid film based biosensor on graphene nanosheets. Structural characterization of graphene nanosheets for miniaturization of potentiometric urea lipid film based biosensors have been studied through atomic force microscopy (AFM) and transmission electron microscopy (TEM) measurements. UV‐Vis and Fourrier transform IR (FTIR) spectroscopy have been utilized to study the pre‐ and postconjugated surfaces of graphene nanosheets. The presented potentiometric urea biosensor exhibits good reproducibility, reusability, selectivity, rapid response times (∼4 s), long shelf life and high sensitivity of ca. 70 mV/decade over the urea logarithmic concentration range from 1×10 −6 M to 1×10 −3 M.
The effects of bilateral striatal lesions on the acquisition of an operant test of short term memory (1995)

It has been previously shown that lesions of the dorsal striatum can disrupt performance on a variety of cognitive tasks related to frontal cortex function. In order to extend these studies, we have investigated the effects of bilateral striatal lesions on the acquisition of an operant test of short term memory in the delayed nonmatching to position paradigm. The animals received either ibotenic acid or saline control injections into the dorsal striatum prior to training on the non-matching task. Striatal lesions retarded acquisition of the task, although with further training the lesioned rats achieved a similar level of asymptotic performance to the control animals. The lesioned rats also exhibited marked nocturnal locomotor hyperactivity when tested under conditions of food deprivation, but not when tested satiated. The results indicate that bilateral striatal lesions induce mild deficits in the acquisition of the discrimination rules involved in performance of the delayed nonmatching to position task. The present study does not support a role for the neostriatum in the specific mediation of short term memory in an operant DNMTP test.
3D Neutron Transport and HPC: A PWR Full Core Calculation Using PENTRAN SN Code and IBM BLUEGENE/P Computers (2011)

When dealing with nuclear reactor calculation schemes, the need for 3D transport-based reference solutions is essential for validation and optimization purposes. As SN transport methods may be considered promising with respect to comprehensive parallel computations, a 3D full PWR core benchmark was proposed to challenge the capabilities of the PENTRAN parallel SN code utilizing an IBM-BG/P computer. After a brief description of the benchmark, a parallel performance analysis is carried out, and shows that the parallelizable (Amdahl) fraction of PENTRAN is comprised between 0.994 f 0.996 for a number of BG/P nodes ranging from 17 to 1,156. The associated speedup reaches a value greater than 200 with 1,156 nodes. Using a best estimate model, PENTRAN results are then compared to Monte Carlo results rendered using the MCNP5 code. Good consistency is observed between the two methods (SN and Monte Carlo), with discrepancies less than 65 pcm for the k eff , and less than 2.5% for the flux at the pincell level.
Advertising Segment Routing Policies in BGP (2017)

This document defines a new BGP SAFI with a new NLRI in order to
advertise a candidate path of a Segment Routing Policy (SR Policy). An
SR Policy is a set of candidate paths, each consisting of one or more
segment lists. The headend of an SR Policy may learn multiple
candidate paths for an SR Policy. Candidate paths may be learned via a
number of different mechanisms, e.g., CLI, NetConf, PCEP, or BGP. This
document specifies the way in which BGP may be used to distribute
candidate paths. New sub-TLVs for the Tunnel Encapsulation Attribute
are defined.
In vivo application of SLSC imaging in human liver (2011)

The ability of an ultrasound system to differentiate signals in the presence of clutter is of key clinical importance. There are several sources of clutter but assessing their relative importance and developing methods of reducing them remain areas of active research. We have developed a novel method called short-lag-spatial-coherence (SLSC) imaging that is based purely on the spatial coherence of the backscattered echoes and has a potential to suppress clutter. We compare matched SLSC and B-mode images beamformed from the individual-channel data acquired on human liver in vivo. While all of the SLSC images have higher contrast and CNR then their B-mode counterparts highest improvements can be observed for poor quality fundamental B-mode images that are overwhelmed with acoustic noise.
Exploring how fishermen respond to the challenges facing the fishing industry: A study of diversification and multiple-job holding in the English Channel fishery (2013)

Twenty-five lymph nodes from patients with non-Hodgkin's lymohomas were evaluated by immunologic technics applied to cell suspensions and tissue sections. Malignant lymphomas with cytologic characteristics similar to those of neoplastic cells were found to be immunologically heterogeneous. The distribution as well as the number of neoplastic cells with distinctive immunologic surface markers could not be related to the cytologic type of malignant lymphomas. The number of malignant cells simultaneously expressing the T- and B-cell markers was increased in malignant lymphoma nodes. Cells positive for the triple markers (Ig+, EAC+, T+, where Ig = immunoglobulin, EAC = erythrocytes sensitized with antibody and complement, and T = T marker) represented the predominant population in these nodes, and the distributions of these cells were useful in diagnosis. Monoclonal immunoglobulins were detected in all lymphoma cells but not in the patients' sera. The tissue distribution of EAC-positive cells may have a prognostic significance. The paucity of cells with the Fc receptors was a characteristic feature of all lymphoma cells studied. Evaluations of immunologic markers on lymphoma cells in conjunction with the histologic characteristics may provide a sounder basis for diagnosis.
Convolutional neural network with structural input for visual object tracking (2019)

Numerous deep learning approaches have been applied to visual object tracking owing to their capabilities to leverage huge training data for performance improvement. Most of these approaches have limitations with regard to learning target specific information rich features and therefore observe reduced accuracy in the presence of different challenges such as occlusion, scale variations, rotation and clutter. We proposed a deep neural network that takes input in the form of two stacked patches and regresses both the similarity and the dis-similarity scores in single evaluation. Image patches are concatenated depth-wise and fed to a six channel input of the network. The proposed network is generic and exploits the structural differences between the two input patches to obtain more accurate similarity and dissimilarity scores. Online learning is enforced via short-term and long-term updates to improve the tracking performance. Extensive experimental evaluations have been performed on OTB2015 and TempleColor128 benchmark datasets. Comparisons with state-of-the-art methods indicate that the proposed framework has achieved better tracking performance. The proposed tracking framework has obtained improved accuracy in different challenges including occlusion, background clutter, in-plane rotation and scale variations.
Brain Invaders 2: an open source Plug & Play multi-user BCI videogame (2020)

International audience
A 0.5- mu m EEPROM cell using poly-Si TFT technology (1993)

A 0.5- mu m EEPROM (electrically erasable programmable read only memory) cell using poly-Si thin-film transistor (TFT) technology is reported. 10- mu s programming time and a good endurance over 10/sup 4/ program/erase cycles were obtained. These device characteristics are promising for low-cost and high-density EEPROMs.
Late Colon Involvement by Lobular Carcinoma of the Breast: A Diagnosis to Keep in Mind! (2019)

SCOPUS: ar.j
NMR propagator measurements on flow through a random pack of porous glass beads and how they are affected by dispersion, relaxation, and internal field inhomogeneities (2004)

We flow water through a pack of porous glass beads and employ NMR to measure molecular displacement distributions--the propagators--in the Stokes flow regime. Fluid is flowed over several evolution times to attain fixed mean displacements, and the time dependence of the resulting propagators is analyzed for the effects of diffusion, NMR relaxation, and signal loss due to internal fields. We delineate and illustrate the experimental regimes in which these different effects make their presence felt. Simulations on a simple model system reproduce the essential features of our experimental results and provide insight into the mechanisms shaping the propagators.
Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data (2012)

Transcript quantification is a long-standing problem in genomics and estimating the relative abundance of alternatively-spliced isoforms from the same transcript is an important special case. Both problems have recently been illuminated by high-throughput RNA sequencing experiments which are quickly generating large amounts of data. However, much of the signal present in this data is corrupted or obscured by biases resulting in non-uniform and non-proportional representation of sequences from different transcripts. Many existing analyses attempt to deal with these and other biases with various task-specific approaches, which makes direct comparison between them difficult. However, two popular tools for isoform quantification, MISO and Cufflinks, have adopted a general probabilistic framework to model and mitigate these biases in a more general fashion. These advances motivate the need to investigate the effects of RNA-seq biases on the accuracy of different approaches for isoform quantification. We conduct the investigation by building models of increasing sophistication to account for noise introduced by the biases and compare their accuracy to the established approaches. We focus on methods that estimate the expression of alternatively-spliced isoforms with the percent-spliced-in (PSI) metric for each exon skipping event. To improve their estimates, many methods use evidence from RNA-seq reads that align to exon bodies. However, the methods we propose focus on reads that span only exon-exon junctions. As a result, our approaches are simpler and less sensitive to exon definitions than existing methods, which enables us to distinguish their strengths and weaknesses more easily. We present several probabilistic models of of position-specific read counts with increasing complexity and compare them to each other and to the current state-of-the-art methods in isoform quantification, MISO and Cufflinks. On a validation set with RT-PCR measurements for 26 cassette events, some of our methods are more accurate and some are significantly more consistent than these two popular tools. This comparison demonstrates the challenges in estimating the percent inclusion of alternatively spliced junctions and illuminates the tradeoffs between different approaches.
Glutamate‐induced activation of nitric oxide synthase is impaired in cerebral cortexin vivoin rats with chronic liver failure (2007)

It has been proposed that impairment of the glutamate-nitric oxide-cyclic guanosine monophosphate (cGMP) pathway in brain contributes to cognitive impairment in hepatic encephalopathy. The aims of this work were to assess whether the function of this pathway and of nitric oxide synthase (NOS) are altered in cerebral cortex in vivo in rats with chronic liver failure due to portacaval shunt (PCS) and whether these alterations are due to hyperammonemia. The glutamate-nitric oxide-cGMP pathway function and NOS activation by NMDA was analysed by in vivo microdialysis in cerebral cortex of PCS and control rats and in rats with hyperammonemia without liver failure. Similar studies were done in cortical slices from these rats and in cultured cortical neurons exposed to ammonia. Basal NOS activity, nitrites and cGMP are increased in cortex of rats with hyperammonemia or liver failure. These increases seem due to increased inducible nitric oxide synthase expression. NOS activation by NMDA is impaired in cerebral cortex in both animal models and in neurons exposed to ammonia. Chronic liver failure increases basal NOS activity, nitric oxide and cGMP but reduces activation of NOS induced by NMDA receptors activation. Hyperammonemia is responsible for both effects which will lead, independently, to alterations contributing to neurological alterations in hepatic encephalopathy.
A nano-stepping robotic instrumentation platform (2013)

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2013.
Behaviour of oxygen-related thermal donors in Ge crystals Czochralski-grown from the melt covered fully by B2O3 (2011)

Oxygen-related thermal donors (OTDs) in oxygen-enriched Czochralski Ge crystals grown from a melt fully covered by B2O3 liquid were investigated by infrared spectroscopy. Interstitially dissolved oxygen concentrations [Oi] and thermal donor concentrations NTD in Ge specimens annealed at 350°C for 64h and at 550°C for 1h, followed by subsequent fast cooling to room temperature, were measured in comparison with those in as-grown Ge. By annealing at 350°C, an absorption peak developed at 780 cm−1 and the peak height at 855 cm−1 related to [Oi], decreased. The absorption coefficient at 780 cm−1 showed the same correlation to the difference between the total concentration of oxygen atoms and the dissolved oxygen concentration in the annealed specimens. It was found that the number of oxygen atoms forming the OTD increases with increasing annealing time at 350°C.
A web service for automatic word class acquisition (2009)

In this paper we present a Web service for building NLP resources to construct semantic word classes in Japanese. The system takes a few seed words belonging to the target class as input and uses automatic class expansion to suggest semantically similar training samples for the user to label. The system automatically generates random negative training samples as well, and then trains a supervised classifier on this labeled data to generate the target word class from 107 candidate words extracted from a corpus of of 108 Web documents. This system eliminates the need for expert machine learning knowledge in creating semantic word classes, and we experimentally show that it significantly reduces the human effort required to build them.
Topology-controlled volume rendering (2006)

Topology provides a foundation for the development of mathematically sound tools for processing and exploration of scalar fields. Existing topology-based methods can be used to identify interesting features in volumetric data sets, to find seed sets for accelerated isosurface extraction, or to treat individual connected components as distinct entities for isosurfacing or interval volume rendering. We describe a framework for direct volume rendering based on segmenting a volume into regions of equivalent contour topology and applying separate transfer functions to each region. Each region corresponds to a branch of a hierarchical contour tree decomposition, and a separate transfer function can be defined for it. The novel contributions of our work are 1) a volume rendering framework and interface where a unique transfer function can be assigned to each subvolume corresponding to a branch of the contour tree, 2) a runtime method for adjusting data values to reflect contour tree simplifications, 3) an efficient way of mapping a spatial location into the contour tree to determine the applicable transfer function, and 4) an algorithm for hardware-accelerated direct volume rendering that visualizes the contour tree-based segmentation at interactive frame rates using graphics processing units (GPUs) that support loops and conditional branches in fragment programs.
Birth cohort relative to an influenza A virus’s antigenic cluster introduction drives patterns of children’s antibody titers (2022)

An individual's antibody titers to influenza A strains are a result of the complicated interplay between infection history, cross-reactivity, immune waning, and other factors. It has been challenging to disentangle how population-level patterns of humoral immunity change as a function of age, calendar year, and birth cohort from cross-sectional data alone. We analyzed 1,589 longitudinal sera samples from 260 children across three studies in Nicaragua, 2006-16. Hemagglutination inhibition (HAI) titers were determined against four H3N2 strains, one H1N1 strain, and two H1N1pdm strains. We assessed temporal patterns of HAI titers using an age-period-cohort modeling framework. We found that titers against a given virus depended on calendar year of serum collection and birth cohort but not on age. Titer cohort patterns were better described by participants' ages relative to year of likely introduction of the virus's antigenic cluster than by age relative to year of strain introduction or by year of birth. These cohort effects may be driven by a decreasing likelihood of early-life infection after cluster introduction and by more broadly reactive antibodies at a young age. H3N2 and H1N1 viruses had qualitatively distinct cohort patterns, with cohort patterns of titers to specific H3N2 strains reaching their peak in children born 3 years prior to that virus's antigenic cluster introduction and with titers to H1N1 and H1N1pdm strains peaking for children born 1-2 years prior to cluster introduction but not being dramatically lower for older children. Ultimately, specific patterns of strain circulation and antigenic cluster introduction may drive population-level antibody titer patterns in children.
Surface-plasmon mediated total absorption of light into silicon (2011)

We report surface-plasmon mediated total absorption of light into a silicon substrate. For an Au grating on Si, we experimentally show that a surface-plasmon polariton (SPP) excited on the air/Au interface leads to total absorption with a rate nearly 10 times larger than the ohmic damping rate of collectively oscillating free electrons in the Au film. Rigorous numerical simulations show that the SPP resonantly enhances forward diffraction of light to multiple orders of lossy waves in the Si substrate with reflection and ohmic absorption in the Au film being negligible. The measured reflection and phase spectra reveal a quantitative relation between the peak absorbance and the associated reflection phase change, implying a resonant interference contribution to this effect. An analytic model of a dissipative quasi-bound resonator provides a general formula for the resonant absorbance-phase relation in excellent agreement with the experimental results.
Cholinergic agonists regulate JAK2/STAT3 signaling to suppress endothelial cell activation (2009)

The cholinergic anti-inflammatory pathway is a physiological mechanism that inhibits cytokine production and minimizes tissue injury during inflammation. Previous investigations revealed that cholinergic stimulation (via cholinergic agonists and vagus nerve stimulation) suppresses endothelial cell activation and leukocyte recruitment. The purpose of this study was to investigate the mechanisms by which cholinergic agonists (e.g., nicotine and GTS-21) regulate endothelial cell activation. Specifically, we examined the effects of cholinergic agonists on IL-6-mediated endothelial cell activation through the JAK2/STAT3 signaling pathway. Treatment of macrovascular human umbilical vein endothelial cells (HUVECs) and microvascular endothelial cells (MVECs) with the cholinergic agonists nicotine and GTS-21 significantly reduced IL-6-mediated monocyte chemoattractant protein-1 (MCP-1) production and ICAM-1 expression which are regulated through the JAK2/STAT3 pathway. We found that treatment of endothelial cells with cholinergic agonists significantly reduced STAT3 activation by phosphorylation and DNA binding. The inhibition of STAT3 phosphorylation was reversed by sodium orthovanadate, an inhibitor of tyrosine phosphatases, as well as by NSC-87877 suggesting a SHP1/2-dependent mechanism. Further investigations showed that cholinergic agonists reduced the phosphorylation of JAK2, an upstream component of the JAK2/STAT3 pathway. Finally, we observed that nicotine and GTS-21 treatment decreased levels of SOCS3 (suppressor of cytokine signaling; a regulator of the inflammatory activity of IL-6) in activated endothelial cells. These data demonstrate that cholinergic agonists suppress IL-6-mediated endothelial cell activation through the JAK2/STAT3 pathway. Our results have significant implications for better understanding the therapeutic potential of cholinergic agonists for treating IL-6 mediated inflammatory conditions.
Glycoprotein CD44 expression and its association with survival in breast cancer. (1993)

To investigate the clinical significance of CD44 expression (lymphocyte-homing receptor) in adenocarcinoma, deparaffinized sections from 198 female breast carcinomas were stained with Hermes-3 MoAb for CD44 glycoprotein. In 16% of the cancers most (> or = 90%) of the cancer cells stained positively for CD44, whereas the rest of the cancers were either heterogenous (46%) or negative (38%) in CD44 staining. Cancers with > 50% CD44 positive cells were more often poorly differentiated (grade 3) than those with < or = 50% positive cells (38 vs. 19%, P = 0.006), they had higher mitotic counts (P = 0.04), and were more often estrogen receptor negative (52 vs. 31%, P = 0.01). Among ductal not otherwise specified cancers and node-positive cancers strong CD44 expression was associated with poor outcome (P = 0.05 and 0.02, respectively). However, CD44 expression was not an independent prognostic factor in these subgroups in a multivariate analysis. Unlike in lymphomas the unfavorable prognosis associated with CD44 expression may not be explained by the greater metastatic potential of CD44-positive cells, because the difference in mortality between the groups appeared to diminish with time, and CD44 positivity was associated with aggressive histological features.
Near-Infrared Compositional Analysis of Gas and Condensate Reservoir Fluids at Elevated Pressures and Temperatures (2002)

The near-infrared spectroscopic (NIR) analysis of several fluid mixtures approximating natural gases or condensates is reported. Spectra were measured under wide variations of pressure and temperature in accord with conditions found in various gas or condensate reservoirs. Some restrictions simulating currently feasible hardware specifications were placed on spectral data before they were used for analysis. We employed principal components regression (PCR) on inverted Beer's Law for compositional analysis. The result shows that it is feasible to conduct an in situ compositional analysis in the reservoir environment. In fact, this algorithm is currently being utilized successfully with an optical spectrometer operating down-hole in oil wells.