gebhart/patrepeval huggingface dataset:
Abstract 1352: Cytoplasmic galectin-7 has an antiapoptotic function by decreasing p53 nuclear translocation in breast cancer cells (2014)

Abstract Resistance to apoptosis induced by anti-cancer drugs is a major obstacle for the treatment of aggressive forms of breast cancer. Galectin-7 was recently shown to be specifically expressed in basal-like and HER-2 positive but not in luminal subtypes of human breast cancer. Overexpression of galectin-7 in breast cancer cells also increases lung and bone metastases. However, the molecular mechanisms used by galectin-7 to increase the dissemination of breast cancer cells remain largely unknown. Although galectins are best known for their ability to bind cell surface receptors, there is increasing evidence that their intracellular forms have important functions in cancer cells. This is particularly true in the control of apoptosis. Up to now, regulation of apoptosis by intracellular galectins has been largely attributed to their ability to translocate to mitochondria, possibly following their interaction with bcl-2. Here, we report that a mutant of galectin-7 that is unable to translocate to mitochondria and nucleus induces resistance of human breast cancer cells to apoptosis induced by etoposide or by hypoxia-mimicking conditions. Surprisingly, this mutant and the wild-type form of galectin-7 bind equally well to bcl-2 in vitro and in vivo. Interestingly, both forms decreases the translocation of p53 to the nucleus and reduce the expression of p21 following treatment with doxorubicin. These results challenges the current paradigm that mitochondrial galectins are important for resistance to apoptosis and call for a greater focus on the role of cytosolic galectins in cancer cells. Our data also indicate that targeting cytosolic galectin-7 could improve the efficacy of anti-cancer drugs for the treatment of aggressive forms of breast cancer. Citation Format: Andrée-Anne Grosset, Donald Gagné, Marilyne Labrie, Maria Vladoiu, Louis Gaboury, Nicolas Doucet, Yves St-Pierre. Cytoplasmic galectin-7 has an antiapoptotic function by decreasing p53 nuclear translocation in breast cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1352. doi:10.1158/1538-7445.AM2014-1352
Mechanically robust microfluidics and bulk wave acoustics to sort microparticles (2016)

Sorting microparticles (or cells, or bacteria) is significant for scientific, medical and industrial purposes. Research groups have used lithium niobate SAW devices to produce standing waves, and then to align microparticles at the node lines in polydimethylsiloxane (PDMS, silicone) microfluidic channels. The “tilted angle” (skewed) configuration is a recent breakthrough producing particle trajectories that cross multiple node lines, making it practical to sort particles. However, lithium niobate wafers and PDMS microfluidic channels are not mechanically robust. We demonstrate “tilted angle” microparticle sorting in novel devices that are robust, rapidly prototyped, and manufacturable. We form our microfluidic system in a rigid polymethyl methacrylate (PMMA, acrylic) prism, sandwiched by lead-zirconium-titanate (PZT) wafers, operating in through-thickness mode with inertial backing, that produce standing bulk waves. The overall configuration is compact and mechanically robust, and actuating PZT wafers in through-thickness mode is highly efficient. Moving to this novel configuration introduced new acoustics questions involving internal reflections, but we show experimental images confirming the intended nodal geometry. Microparticles in “tilted angle” devices display undulating trajectories, where deviation from the straight path increases with particle diameter and with excitation voltage to create the mechanism by which particles are sorted. We show a simplified analytical model by which a “phase space” is constructed to characterize effective particle sorting, and we compare our experimental data to the predictions from that simplified model; precise correlation is not expected and is not observed, but the important physical trends from the model are paralleled in the measured particle trajectories.
Efficient off-resonance correction for spiral imaging (2001)

A new spiral imaging technique incorporates the acquisition of a field map into imaging interleaves. Variable density spiral trajectories are designed to oversample the central region of k-space, and interleaves are acquired at two different echo times. A field map is extracted from this data and multifrequency reconstruction is used to form an off-resonance corrected image using the entire dataset. Simulation, phantom, and in vivo results indicate that this technique can be used to achieve higher image and/or field map spatial resolution compared to conventional techniques. Magn Reson Med 45:521-524, 2001.
An approach to design distributed CTI applications using Petri nets: an example of a call center (2002)

In this paper we apply a formal approach, based on Petri nets, to design a logical structure for call centers based on sophisticated computer telephony integration applications. A typical call center consists of a set of operators, called agents, who process inbound calls from clients. This call processing may involve the use of computer systems and other devices, such as faxes, as well as communication with other agents. The treatment of each call being processed is heavily regulated by a script, which is specially designed for specific kinds of calls by the experts in telemarketing. However, the design of such scripts can be problematic. In this paper, we stress the need for tools supporting a scripting process. We propose a formal model intended to serve as a basis for such tools. Specifically, we introduce formal models called script nets for formal representation of scripts and of the call center as a whole. We have also introduced various ways to structure script nets, using a transition hierarchy and macroplaces.
Capturing Three-Dimensional In Vivo Lumbar Intervertebral Joint Kinematics Using Dynamic Stereo-X-Ray Imaging (2013)

Availability of accurate three-dimensional (3D) kinematics of lumbar vertebrae is necessary to understand normal and pathological biomechanics of the lumbar spine. Due to the technical challenges of imaging the lumbar spine motion in vivo, it has been difficult to obtain comprehensive, 3D lumbar kinematics during dynamic functional tasks. The present study demonstrates a recently developed technique to acquire true 3D lumbar vertebral kinematics, in vivo, during a functional load-lifting task. The technique uses a high-speed dynamic stereo-radiography (DSX) system coupled with a volumetric model-based bone tracking procedure. Eight asymptomatic male participants performed weight-lifting tasks, while dynamic X-ray images of their lumbar spines were acquired at 30 fps. A custom-designed radiation attenuator reduced the radiation white-out effect and enhanced the image quality. High resolution CT scans of participants' lumbar spines were obtained to create 3D bone models, which were used to track the X-ray images via a volumetric bone tracking procedure. Continuous 3D intervertebral kinematics from the second lumbar vertebra (L2) to the sacrum (S1) were derived. Results revealed motions occurring simultaneously in all the segments. Differences in contributions to overall lumbar motion from individual segments, particularly L2-L3, L3-L4, and L4-L5, were not statistically significant. However, a reduced contribution from the L5-S1 segment was observed. Segmental extension was nominally linear in the middle range (20%-80%) of motion during the lifting task, but exhibited nonlinear behavior at the beginning and end of the motion. L5-S1 extension exhibited the greatest nonlinearity and variability across participants. Substantial AP translations occurred in all segments (5.0 ± 0.3 mm) and exhibited more scatter and deviation from a nominally linear path compared to segmental extension. Maximum out-of-plane rotations (<1.91 deg) and translations (<0.94 mm) were small compared to the dominant motion in the sagittal plane. The demonstrated success in capturing continuous 3D in vivo lumbar intervertebral kinematics during functional tasks affords the possibility to create a baseline data set for evaluating the lumbar spinal function. The technique can be used to address the gaps in knowledge of lumbar kinematics, to improve the accuracy of the kinematic input into biomechanical models, and to support development of new disk replacement designs more closely replicating the natural lumbar biomechanics.
Parallel Algorithm for Hardware Implementation of Inverse Halftoning (2005)

A parallel algorithm and its hardware implementation are proposed for an inverse halftone operation. The algorithm is based on lookup tables from which the inverse halftone value of a pixel is directly determined using a pattern of pixels. A method has been developed that allows accessing more than one value from the lookup table at any time. The lookup table is divided into smaller lookup tables, such that each pattern selected at any time goes to a separate smaller lookup table. The 15-pixel parallel version of the algorithm was tested on sample images and a simple and effective method has been used to overcome quality degradation due to pixel loss in the proposed algorithm. It can provide at least 4 times decrease in lookup table size when compared with a serial lookup table method implemented multiple times for the same number of pixels.
An integrated time-of-flight versus residual energy subsystem for a compact dual ion composition experiment for space plasmas (2015)

We have developed a novel concept for a Compact Dual Ion Composition Experiment (CoDICE) that simultaneously provides high quality plasma and energetic ion composition measurements over 6 decades in ion energy in a wide variety of space plasma environments. CoDICE measures the two critical ion populations in space plasmas: (1) mass and ionic charge state composition and 3D velocity and angular distributions of ∼10 eV/q-40 keV/q plasma ions—CoDICE-Lo and (2) mass composition, energy spectra, and angular distributions of ∼30 keV-10 MeV energetic ions—CoDICE-Hi. CoDICE uses a common, integrated Time-of-Flight (TOF) versus residual energy (E) subsystem for measuring the two distinct ion populations. This paper describes the CoDICE design concept, and presents results of the laboratory tests of the TOF portion of the TOF vs. E subsystem, focusing specifically on (1) investigation of spill-over and contamination rates on the start and stop microchannel plate (MCP) anodes vs. secondary electron steering and focusing voltages, scanned around their corresponding model-optimized values, (2) TOF measurements and resolution and angular resolution, and (3) cross-contamination of the start and stop MCPs' singles rates from CoDICE-Lo and -Hi, and (4) energy resolution of avalanche photodiodes near the lower end of the CoDICE-Lo energy range. We also discuss physical effects that could impact the performance of the TOF vs. E subsystem in a flight instrument. Finally, we discuss advantages of the CoDICE design concept by comparing with capabilities and resources of existing flight instruments.
Presentation of structured documents without a style sheet (2007)

In order to present most XML documents for human consumption, formatting information must be introduced and applied. Formatting is typically done through a style sheet, however, it is conceivable that one could wish to view the document without having a style sheet (either because a style sheet does not exist, or is unavailable, or is inappropriate for the display device). This paper describes a method for formatting structured documents without a provided style sheet. The idea is to first analyze the document to determine structures and features that might be relevant to style decisions. A transformation can be constructed to convert the original document to a generic form that captures the semantics that will be expressed through formatting and style. In the second stage styling is applied to the structures and features that have been discovered by applying a pre-defined style sheet for the generic form. The document instance, and if available, the corresponding schema or DTD can be analyzed in order to construct the transformation. This paper will describe the generic form used for formatting and techniques for generating transformations to it.
Tuneable porous carbonaceous materials from renewable resources (2009)

Porous carbon materials are ubiquitous with a wide range of technologically important applications, including separation science, heterogeneous catalyst supports, water purification filters, stationary phase materials, as well as the developing future areas of energy generation and storage applications. Hard template routes to ordered mesoporous carbons are well established, but whilst offering different mesoscopic textural phases, the surface of the material is difficult to chemically post-modify and processing is energy, resource and step intensive. The production of carbon materials from biomass (i.e. sugars or polysaccharides) is a relatively new but rapidly expanding research area. In this tutorial review, we compare and contrast recently reported routes to the preparation of porous carbon materials derived from renewable resources, with examples of our previously reported mesoporous polysaccharide-derived "Starbon" carbonaceous material technology.
Wide Table Layout Optimization based on Column Ordering and Duplication (2017)

Modern data analytical tasks often witness very wide tables, from a few hundred columns to a few thousand. While it is commonly agreed that column stores are an appropriate data format for wide tables and analytical workloads, the physical order of columns has not been investigated. Column ordering plays a critical role in I/O performance, because in wide tables accessing the columns in a single horizontal partition may involve multiple disk seeks. An optimal column ordering will incur minimal cumulative disk seek costs for the set of queries applied to the data. In this paper, we aim to find such an optimal column layout to maximize I/O performance. Specifically, we study two problems for column stores on HDFS: column ordering and column duplication. Column ordering seeks an approximately optimal order of columns; column duplication complements column ordering in that some columns may be duplicated multiple times to reduce contention among the queries' diverse requirements on the column order. We consider an actual fine-grained cost model for column accesses and propose algorithms that take a query workload as input and output a column ordering strategy with or without storage redundancy that significantly improves the overall I/O performance. Experimental results over real-life data and production query workloads confirm the effectiveness of the proposed algorithms in diverse settings.
Searching cell‐secreted proteomes for potential urinary bladder tumor markers (2006)

To search for biomarkers critical for bladder carcinoma diagnosis and prognosis, secreted proteomes of highly malignant U1 and pre-malignant U4 cell lines were initially analyzed. Proteins in the culture media of the U1 and U4 cell lines were systematically examined by SDS-PAGE combined with MALDI-TOF MS. Among them, expression of pro-u-plasminogen activator (pro-u-PA) was confirmed by Western blot analysis and further evaluated. In analyzing urine samples from bladder cancer patients and normal subjects, we established a statistically significant relationship between the low level and absence of pro-u-PA in urine with high stages and grades of the tumor samples. Constitutive expression of Ras dominant negative protein led to increased expression of pro-u-PA in culture media, indicating that the loss of pro-u-PA is associated with oncogenic transformation. Analysis of cancer-secreted proteomes can be a feasible, non-invasive and efficient strategy for searching potential bladder tumor biomarkers. Our work also has identified the loss of pro-u-PA in urine as potential marker of more advanced bladder carcinoma.
In vivo localization of human colon adenocarcinoma by monoclonal antibody binding to a highly expressed cell surface antigen. (1988)

We have produced a monoclonal antibody (SF-25) against a human hepatoma cell line (FOCUS) that strongly reacts with an antigen shared by all six colon adenocarcinoma cell lines. This cell surface antigen was uniformly expressed in all 17 human adenocarcinomas of the colon obtained at surgery but not on the normal adjacent mucosa counterpart. Other normal tissues were negative except for a population of cells in the distal tubule of the kidney as shown by immunoperoxidase staining and direct binding to membrane preparations. Binding of this Mr 125,000 antigen to antibody is disrupted by detergents, sodium dodecyl sulfate, and paraformaldehyde fixation but not by treatment of FOCUS cells with trypsin. The SF-25 antibody when labeled with 125I shows a striking capacity by both biodistribution and nuclear imaging studies to localize human colon adenocarcinoma grown as solid tumors in nude mice. SF-25 may be useful in distinguishing between normal colon and the transformed phenotype.
Effect of Methotrexate on an In Vitro Patient-Derived Model of Proliferative Vitreoretinopathy (2017)

PVR cells obtained from human membranes can be successfully isolated, cultured, and profiled in vitro. Using these primary cultures, we identified MTX as capable of significantly reducing growth and inducing cell death of PVR cells in vitro.
SUMOylation inhibitors synergize with FXR agonists in combating liver fibrosis (2020)

Farnesoid X receptor (FXR) is a promising target for nonalcoholic steatohepatitis (NASH) and fibrosis. Although various FXR agonists have shown anti-fibrotic effects in diverse preclinical animal models, the response rate and efficacies in clinical trials were not optimum. Here we report that prophylactic but not therapeutic administration of obeticholic acid (OCA) prevents hepatic stellate cell (HSC) activation and fibrogenesis. Activated HSCs show limited response to OCA and other FXR agonists due to enhanced FXR SUMOylation. SUMOylation inhibitors rescue FXR signaling and thereby increasing the efficacy of OCA against HSC activation and fibrosis. FXR upregulates Perilipin-1, a direct target gene of FXR, to stabilize lipid droplets and thereby prevent HSC activation. Therapeutic coadministration of OCA and SUMOylation inhibitors drastically impedes liver fibrosis induced by CCl<sub>4</sub>, bile duct ligation, and more importantly NASH. In conclusion, we propose a promising therapeutic approach by combining SUMOylation inhibitors and FXR agonists for liver fibrosis.
A MOF platform for incorporation of complementary organic motifs for CO<sub>2</sub> binding (2015)

CO2 capture is essential for reducing the carbon footprint of coal-fired power plants. Here we show, both experimentally and computationally, a new design strategy for capturing CO2 in nanoporous adsorbents. The approach involves 'complementary organic motifs' (COMs), which have a precise alignment of charge densities that is complementary to the CO2 quadrupole. Two promising COMs were post-synthetically incorporated into a robust metal-organic framework (MOF) material using solvent-assisted ligand incorporation (SALI). We demonstrate that these COM-functionalized MOFs exhibit high capacity and selectivity for CO2 relative to other reported motifs.
Magic finger (2012)

We present Magic Finger, a small device worn on the fingertip, which supports always-available input. Magic Finger inverts the typical relationship between the finger and an interactive surface: with Magic Finger, we instrument the user's finger itself, rather than the surface it is touching. Magic Finger senses touch through an optical mouse sensor, enabling any surface to act as a touch screen. Magic Finger also senses texture through a micro RGB camera, allowing contextual actions to be carried out based on the particular surface being touched. A technical evaluation shows that Magic Finger can accurately sense 22 textures with an accuracy of 98.9%. We explore the interaction design space enabled by Magic Finger, and implement a number of novel interaction techniques that leverage its unique capabilities.
Vinylamycin, a New Depsipeptide Antibiotic, from Streptomyces sp. (1999)

A new depsipeptide antibiotic, vinylamycin, was isolated from the culture broth of an actinomycete strain. The producing organism, designated MI982-63F1, was identified as a member of Streptomyces. Vinylamycin was isolated from the culture broth by extraction with EtOAc and purified by crystallization from EtOAc. The structure of vinylamycin was determined by spectroscopic analysis and degradation studies. Vinylamycin showed antimicrobial activities against Gram-positive bacteria including MRSA.
Nonlinear Dynamics of Cantilever-Sample Interactions in Atomic Force Microscopy (2010)

The interaction of the cantilever tip of an atomic force microscope (AFM) with the sample surface is obtained by treating the cantilever and sample as independent systems coupled by a nonlinear force acting between the cantilever tip and a volume element of the sample surface. The volume element is subjected to a restoring force from the remainder of the sample that provides dynamical equilibrium for the combined systems. The model accounts for the positions on the cantilever of the cantilever tip, laser probe, and excitation force (if any) via a basis set of set of orthogonal functions that may be generalized to account for arbitrary cantilever shapes. The basis set is extended to include nonlinear cantilever modes. The model leads to a pair of coupled nonlinear differential equations that are solved analytically using a matrix iteration procedure. The effects of oscillatory excitation forces applied either to the cantilever or to the sample surface (or to both) are obtained from the solution set and applied to the to the assessment of phase and amplitude signals generated by various acoustic-atomic force microscope (A-AFM) modalities. The influence of bistable cantilever modes of on AFM signal generation is discussed. The effects on the cantilever-sample surface dynamics of subsurface features embedded in the sample that are perturbed by surface-generated oscillatory excitation forces and carried to the cantilever via wave propagation are accounted by the Bolef-Miller propagating wave model. Expressions pertaining to signal generation and image contrast in A-AFM are obtained and applied to amplitude modulation (intermittent contact) atomic force microscopy and resonant difference-frequency atomic force ultrasonic microscopy (RDF-AFUM). The influence of phase accumulation in A-AFM on image contrast is discussed, as is the effect of hard contact and maximum nonlinearity regimes of A-AFM operation.
Synthesis of Benzimidazole Based Analogues of Sphingosine‐1‐phosphate: Discovery of Potent, Subtype‐Selective S1P<sub>4</sub> Receptor Agonists. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.