gebhart/patrepeval huggingface dataset:
ISA - an inverse surface-based approach for cortical fMRI data projection (2017)

Surface-based approaches have proven particularly relevant and reliable to study cortical functional magnetic resonance imaging (fMRI) data. However projecting fMRI volumes onto the cortical surface remains a challenging problem. Very few methods have been proposed to solve it and most of them rely on a simple interpolation. We propose here an original surface-based method based on a model representing the relationship between cortical activity and fMRI images, and a resolution through an inverse problem. This approach shows interesting perspectives for fMRI data processing as it is highly robust to noise and offers a good accuracy in terms of activations localization.
Novel algorithm for real-time adaptive signal detection and identification (1998)

This paper describes a novel digital signal processing algorithm for adaptively detecting and identifying signals buried in noise. The algorithm continually computes and updates the long-term statistics and spectral characteristics of the background noise. Using this noise model, a set of adaptive thresholds and matched digital filters are implemented to enhance and detect signals that are buried in the noise. The algorithm furthermore automatically suppresses coherent noise sources and adapts to time-varying signal conditions. Signal detection is performed in both the time- domain and the frequency-domain, thereby permitting the detection of both broad-band transients and narrow-band signals. The detection algorithm also provides for the computation of important signal features such as amplitude, timing, and phase information. Signal identification is achieved through a combination of frequency-domain template matching and spectral peak picking. The algorithm described herein is well suited for real-time implementation on digital signal processing hardware. This paper presents the theory of the adaptive algorithm, provides an algorithmic block diagram, and demonstrate its implementation and performance with real- world data. The computational efficiency of the algorithm is demonstrated through benchmarks on specific DSP hardware. The applications for this algorithm, which range from vibration analysis to real-time image processing, are also discussed.
In vivo antitumor activity of 4-amino 4-methyl 2-pentyne 1-al, an inhibitor of aldehyde dehydrogenase. (1992)

4-amino-4-methyl-2-pentyne-1-al (AMPAL), a new irreversible inhibitor of aldehyde dehydrogenase (ALDH) has been assayed for its in vitro and in vivo antitumor activity. In vitro, AMPAL inhibits the proliferation and the ALDH activity of L1210 and RBL5 cell lines. In vivo, AMPAL significantly increases the mean survival time of mice i.p. grafted with leukemia (L1210, P815, MBL2, EL4, RBL5 cell lines) or carcinoma cells (Krebs cell line), without haematopoetic toxicity. No carcinostatic effect was observed against the P388 leukemia and the 3LL Lewis lung carcinoma. A possible relationship between the ALDH isoenzyme activity of the tumor and its sensitivity to AMPAL is discussed in the light of previous reports concerning the role of aldehydes in cell growth control.
Solid-Phase Preparation of Hydantoins through a New Cyclization/Cleavage Step (2001)

An efficient process for the solid-phase synthesis of hydantoins has been developed. The amino acid starting material is anchored to the resin from its carboxylic acid end through formation of a very stable amide bond. After introduction of different functional groups, the cleavage/cyclization step can be performed in acidic or basic conditions.
Solidification of Colloidal Crystals of Silica (1995)

Photopolymerization of methyl acrylate, methyl methacrylate, and a mixture of methyl methacrylate and 2-hydroxyethyl methacrylate, each containing ordered 3-(trimethoxysilyl)propyl-coated monodisperse 152 nm diameter silica particles, produces polymer composites in which the ordering of the particles is maintained. The silica particles formed face centered cubic colloidal crystals in both the monomers and the polymers with (111) lattice planes parallel to the film plane. Both the monomer and the polymer dispersions are selective optical filters of a narrow bandwidth of visible light by Bragg diffraction.
High-frequency nano-motion imaging of artificial nanostructures (2020)

There is growing interest and technological opportunity in nanomechanics and the fundamentals of nano- to pico-scale dynamics, which derive from the fact that electromagnetic and quantum forces become stronger as the dimensions of objects decrease, competing with elastic forces at sub-micron scales; while movements become faster as mass decreases, achieving Gigahertz bandwidth at the nanoscale.&lt;br/&gt;&lt;br/&gt;We report on a novel approach to the visualization of such movements that is based on the detection of secondary electrons and photons emerging from the interaction of a focused electron beam with moving components of nano-objects. The technique extends the static (zero-frequency) imaging capabilities of a conventional scanning electron microscope to enable hyperspectral spatial mapping of fast (MHz-GHz) thermal and externally-driven nano- to pico-scale motion in nanostructures.
Spatiotemporal mode-locking: new route to high-power fiber lasers (Conference Presentation) (2018)

Mode-locking of lasers has led to breakthroughs in numerous scientific fields and applications.Today, all mode-locked lasers are based on resonators that support a single transverse spatial mode. In the early days of laser development, locking of a few transverse and longitudinal modes of a laser was considered. In the intervening 50 years, almost no attention has been paid to locking of multiple transverse modes. In the past year, theoretical and experimental observations of locking of multiple transverse and longitudinal modes of a fiber laser have been reported. Strong spatial and spectral filtering in the laser underlie the formation of multimode ultrashort wave packets in the laser. Understanding of spatiotemporal mode-locking requires generalizing concepts from conventional 1-D mode-locking into higher dimensions: spatiotemporal dispersions (chromatic and modal dispersion) and saturable absorption, nonlinear coupling between spatiotemporal (3+1-D) modes, and spatiospectral filtering. Interactions between modes through linear and nonlinear coupling lead to shifts of the resonances, to yield states with long-range order. In the time domain, these mode-locked states correspond to coherent, spatiotemporal pulse trains. Several qualitatively-new types of mode-locking have been identified. Investigations of new 3D lasing states should be a fertile scientific direction. In addition, the peak power of spatiotemporally-mode-locked lasers scales by more than the mode area, which should lead to unprecedented performance from fiber lasers.
O1‐01‐02: TAU PHOSPHORYLATION RATES CHANGE FROM BRAIN TO CEREBROSPINAL FLUID AND ARE DIFFERENTIALLY AFFECTED BY ALZHEIMER DISEASE (2019)

Abnormally phosphorylated tau aggregates are a core pathology of Alzheimer disease (AD) rising together with clinical symptoms. Elevated phosphorylated tau (p-tau) in AD cerebrospinal fluid (CSF) has been attributed to a passive released of hyperphosphorylated tau occurring during AD neurons death. However, recent studies suggest CSF tau is actively released from cells under physiological and pathological conditions. We hypothesized active release could also affect the pattern of tau phosphorylation. The purpose of this study is to compare tau phosphorylation abundance in soluble brain extracts vs CSF, and in normal vs AD CSF to evidence potential changes occurring during tau active secretion from neurons. We developed highly sensitive and specific mass spectrometry method using parallel reaction monitoring (PRM) to identify p-tau sites. This method enabled site-specific p-tau/tau rates measurements independent from absolute tau concentrations. Measurements were performed on sarkosyl-soluble tau from human brain lysates and CSF pools from participants with (n=5) and without AD (n=7) according to amyloid status. We detected more than 30 distinct phosphorylated tau sites in sarkosyl-soluble human brain lysate and 12 sites on truncated tau in CSF. Phosphorylation comparison evidenced pT205 and pS208, that are recognized by AT8 antibody and define Braak stages of brain tau aggregation, were not detected in brain soluble tau but were found in both normal and AD CSF. Phosphorylation rates comparison evidenced that active release of tau from soluble brain fraction to CSF modified the phosphorylation abundance in a site-specific manner. CSF tau from non-AD participants were significantly hyperphosphorylated at T111, T205, S208, T217 and T231. In AD CSF, hyperphosphorylation on these sites was exacerbated and phosphorylation on T153 and T175 were specifically detected. Inversely, we found S199 and S202 were hypophosphorylated in normal CSF compared to brain, and not hyperphosphorylated in AD CSF.
Risk Factors Affecting Return to Sports and Patient-Reported Outcomes After Opening-Wedge High Tibial Osteotomy in Active Patients (2022)

Higher postoperative MPTA was associated with the worsening of patient-reported outcomes among those patients who did return to their preoperative sports after OWHTO. Also, participation in high-activity sports was confirmed to be a significant risk factor for a decreased rate of return to preoperative sports. These findings can support preoperative planning and intraoperative decision making, particularly for active patients.
Medicinal Chemistry Optimization of a Diaminopurine Chemotype: Toward a Lead for Trypanosoma brucei Inhibitors (2020)

Human African trypanosomiasis (HAT), or sleeping sickness, is caused by the protozoan parasite <i>Trypanosoma brucei</i> and transmitted through the bite of infected tsetse flies. The disease is considered fatal if left untreated. To identify new chemotypes against <i>Trypanosoma brucei</i>, previously we identified 797 potent kinase-targeting inhibitors grouped into 59 clusters plus 53 singleton compounds with at least 100-fold selectivity over HepG2 cells. From this set of hits, a cluster of diaminopurine-derived compounds was identified. Herein, we report our medicinal chemistry investigation involving the exploration of structure-activity and structure-property relationships around one of the high-throughput screening (HTS) hits, <i>N</i><sup>2</sup>-(thiophen-3-yl)-<i>N</i><sup>6</sup>-(2,2,2-trifluoroethyl)-9<i>H</i>-purine-2,6-diamine (<b>1</b>, NEU-1106). This work led to the identification of a potent lead compound (<b>4aa</b>, NEU-4854) with improved in vitro absorption, distribution, metabolism, and excretion (ADME) properties, which was progressed into proof-of-concept translation of in vitro antiparasitic activity to <i>in vivo</i> efficacy.
Interval Velocity Analysis in Complex Areas – Azimuth Considerations (2009)

Through analysis of simple examples, we demonstrate how parameterization of the CIGs according to the acquisition azimuth of the migrated traces, may lead to a wrong velocity model. We then present a method for defining an azimuth CIG in a way that will
Canola productivity and carbon footprint under different cropping systems in eastern Canada (2023)

Abstract Diversified crop rotation with an appropriate sequence may be a promising strategy for increasing crop productivity while reducing greenhouse gas emissions (GHGs) and lowering carbon (C) footprint for more sustainable agricultural systems. The objectives of this study were to (i) assess the agronomic performance and C footprint of canola ( Brassica napus L.) production in different cropping systems, and (ii) better understand how canola could be adapted to existing cropping systems in eastern Canada. A four-year canola-based phase rotation study, including maize ( Zea mays L.), wheat ( Triticum aestivum L.), and soybean ( Glycine max L.), started in 2011 and continued for two cycles in Ottawa, ON; Montreal, QC; and Canning, NS. It was found that, compared to continuous monoculture (canola, maize or wheat), diversified cropping systems increased crop yields by an average of 32% and reduced the C footprint of all rotations by 33%, except under severe heat and drought conditions. The effect of rotation on yield and C footprint of canola production varied significantly among site-years. At Ottawa, the canola following soybean (SC) had 12% higher canola yield than monoculture canola (CC), 5 and 8% higher canola yield than canola following wheat (WC) or maize (MC). At Montreal, canola yield ranked as MC &gt; SC &gt; WC &gt; CC. At Canning, the highest canola yield was in WC (21%) and SC (13%). Overall, most SC rotations had the lowest C footprint, and CC cropping had the highest C footprint, with only a few exceptions. Regardless of the cropping system, canola required more N input and was high in oil and protein in the harvested product, and produced the highest C footprint, while soybean had the lowest C footprint at all three sites. Our findings indicate that a diversified cropping system with canola production following soybean significantly improved canola yield while lowering the C footprint. However, profitable and sustainable canola production in eastern Canada is threatened by climate change-induced drought and heat stress.
Methods for pre‐basic seed production of herbage cultivars (1986)

Abstract The methods for pre‐basic seed production of herbage cultivars outlined in the paper result from the experience of multiplying 23 species comprising 37 ‘Grasslands’ cultivars and selections. Factors discussed include paddock history, isolation, sowing methods, row spacing, seeding rates, management, roguing, pollination, harvesting, post‐harvest management of the crop, hygiene, seed processing and cleaning, seed storage, postharvest quality control, equipment, manpower required, and multiplication rates.
Absorption and emission of radiation by plasmons in two-dimensional electron-gas disks (1986)

The theoretical formalism of Ritchie et al. is used to characterize the electromagnetic properties of plasma oscillations in two-dimensional electron-gas disks, such as those produced lithographically in the GaAs-${\mathrm{Al}}_{\mathrm{x}}$${\mathrm{Ga}}_{1\mathrm{\ensuremath{-}}\mathrm{x}}$As semiconductor heterojunction system. The disks are treated as very thin, oblate spheroids of free-electron gas on the surface of a high-dielectric-constant substrate, and the resonant frequencies are obtained for modes symmetric about the plane of the disk, particularly the lowest-order (dipole) mode. The plasmon fields in this quasi-two-dimensional system are quantized in order to calculate the interaction between the plasmons and the photon field. Closed-form expressions are obtained for the photon absorption cross section and the radiative contribution to the decay width, and the results are compared with those from recent relevant experimental work.
The Enabling Power of Mobile Devices (2019)

Mobile devices have been helping to empower underserved communities around the world. From bringing information on health and farming to substituting expensive devices, cellular phones and apps have proved to be powerful tools in poverty alleviation and disaster relief. The Mobile Lab at Santa Clara University focuses on developing mobile solutions for social benefit. We partner with organizations that operate in the field to develop appropriate solutions to solve specific problems. In this short paper, we illustrate the enabling power of mobile technology by describing some projects designed to empower people and their communities in a variety of ways.
Genome-Wide DNA Profiling of HIV-Related B-Cell Lymphomas (2013)

Non-Hodgkin lymphomas represent a frequent complication of human immunodeficiency virus (HIV) infection, occurring at higher frequency than in immunocompetent individuals, and causing morbidity and mortality. Here, we present the method we have followed to analyze the genomic lesions in HIV-related and in other immunodeficiency-related lymphomas, as well in diffuse large B-cell lymphoma (DLBCL) samples derived from immunocompetent hosts. The technology we have used is represented by the GeneChip Human Mapping 250K NspI arrays (Affymetrix, Santa Clara, CA, USA), arrays based on 25mer oligonucleotides initially designed for large-scale genotyping, that is, the detection of thousands of single-nucleotide polymorphisms (SNPs), then shown to be applicable for the detection of cancer alterations. The protocol is shown in all its steps with suggestions and tips. Applications of the technology and obtained results are also briefly summarized.
THE POTENTIAL ROLE OF EARLY-PHASE GRAFT INJURY IN INDUCTION OF LATE-PHASE CHEMORESISTANCE AFTER LIVER TRANSPLANTATION (2010)

Geng, W.1; Man, K.2; Cheng, Q.3; Ng, K. T.P.3; Liu, X. B.3; Liu, Y.3; Poon, R. T.P.3; Fan, S. T.2; Lo, C. M.3 Author Information
McGill Reddogs (2002)

For the Robocup 2001 competition, theMcGill Reddogs team moved from a monolithic architecture to a distributed one and created a flexible motion module. The Monte Carlo localization and custom script interpreter for behaviors were also replaced by simpler algorithms.
Magic-Angle-Spinning NMR Magnet Development: Field Analysis and Prototypes (2013)

We are currently working on a program to complete a 1.5 T/75 mm RT bore magic-angle-spinning nuclear magnetic resonance magnet. The magic-angle-spinning magnet comprises a <i>z</i>-axis 0.866-T solenoid and an <i>x</i>-axis 1.225-T dipole, each to be wound with NbTi wire and operated at 4.2 K in persistent mode. A combination of the fields creates a 1.5-T field pointed at 54.74 degrees (magic angle) from the rotation (<i>z</i>) axis. In the first year of this 3-year program, we have completed magnetic analysis and design of both coils. Also, using a winding machine of our own design and fabrication, we have wound several prototype dipole coils with NbTi wire. As part of this development, we have repeatedly made successful persistent NbTi-NbTi joints with this multifilamentary NbTi wire.
Synthesis of allylazo compounds by reactions of aryldiazonium salts with allylsilanes (1992)

Aryldiazonium tetrafluoroborates react with allylsilanes to yield allylazo compounds.If the allylic carbon attached to the azo group carries hydrogen, tautomerization with formation of hydrazones takes place.
Concise Total Synthesis of the Frog Alkaloid (−)‐205 B (2011)

Hoch stereokontrolliert verlief die Totalsynthese der Titelverbindung, in der eine Reaktion mit einem chiralen N-Acylpyridinium-Salz, eine neuartige, durch Trifluoressigsäureanhydrid vermittelte Addition eines Allylstannans an ein vinyloges Amid sowie eine allylische Tsuji-Trost-Aminierung und eine Ringschlussmetathese für den Aufbau des zentralen Gerüsts genutzt wurden. TIPS = Triisopropylsilyl. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Activated granulocytes oxidize the endogenous stem cell inhibitory peptide pGlu-Glu-Asp-Cys-Lys (pEEDCK) to the stimulatory dimer: a redox-mediated mechanism for demand-induced hematopoietic regulation. (1998)

We have previously shown that the pentapeptide pGlu-Glu-Asp-Cys-Lys (pEEDCK), which is associated with mature leukocytes, maintains pluripotent hematopoietic stem cells (colony-forming units-spleen [CFU-S]) in a quiescent state under physiological conditions. It is also known that its oxidation product, the disulfide-bonded homodimer (pEEDCK)2, is a growth factor for CFU-S in vivo. In this paper we report on the combined actions of the monomer and dimer in inducing rapid changes in stem cell proliferation in vivo. A single injection of 20 microg/kg synthetic dimer into mice stimulated CFU-S proliferation (60% in S-phase after 9-11 hours) and population expansion. Stimulated CFU-S traversed one cell cycle, with an estimated S-phase time of 5.5 hours, and then become quiescent again. Proliferation of CFU-S in response to dimer showed no sensitivity to the inhibitory effects of monomeric pEEDCK, whereas CFU-S proliferation did display sensitivity to inhibition after injection of cytosine arabinoside or doxorubicin. Products of mature granulocytes undergoing an oxidative burst reaction rapidly oxidized monomeric pEEDCK to the dimer. The suppressive effect of endogenous pEEDCK monomer on stem cell proliferation was thus converted within minutes to a stimulatory signal (dimer). Because many in vivo situations (e.g., infection) requiring increased hematopoiesis involve granulocyte and macrophage activation, the formation of dimer from endogenous pEEDCK monomer may provide an almost instantaneous demand-induced emergency signal for increasing stem cell proliferation and blood cell production.
Correction: Copper(ii) gluconate (a non-toxic food supplement/dietary aid) as a precursor catalyst for effective photo-induced living radical polymerisation of acrylates (2017)

Correction for ‘Copper(<sc>ii</sc>) gluconate (a non-toxic food supplement/dietary aid) as a precursor catalyst for effective photo-induced living radical polymerisation of acrylates’ by Vasiliki Nikolaou <italic>et al.</italic>, <italic>Polym. Chem.</italic>, 2015, <bold>6</bold>, 3581–3585.
Amplification of hsa-miR-191/425 locus promotes breast cancer proliferation and metastasis by targeting DICER1 (2018)

The dysregulation of micro RNAs (miRNAs) is a crucial characteristic of human cancers. Herein, we observed frequent amplification of the MIR191/425 locus in breast cancer, which is correlated with poor survival outcome. We demonstrated that the miR-191/425 cluster binds the 3' untranslated region of the DICER1 transcript and posttranscriptionally represses DICER1 expression, thereby impairing global miRNAs biogenesis. Functionally, the forced expression of miR-191 or miR-425 stimulated the proliferation, survival, migration and invasion of breast cancer cells, whereas the inhibition of miR-191 or miR-425 suppressed these oncogenic behaviors of breast cancer cells, in a manner dependent on miR-191/425-mediated downregulation of DICER1. Furthermore, the miR-191/425 cluster promoted breast tumor growth, invasion and metastasis in vivo. The let-7 family of miRNAs was downregulated upon forced expression of miR-191 or miR-425, with a corresponding increase in the levels of let-7 target, high-mobility group AT-hook 2 (HMGA2). The forced expression of let-7 partially abrogated the miR-191/425-mediated oncogenic effects in breast cancer cells, suggestive of let-7 as a downstream effector of the miR-191/425-DICER1 axis. Collectively, we proposed that the inhibition of global miRNA processing, through miR-191/425-mediated downregulation of DICER1, promotes breast cancer progression.
Fibrinogen induces neural stem cell differentiation into astrocytes in the subventricular zone via BMP signaling (2020)

Neural stem/progenitor cells (NSPCs) originating from the subventricular zone (SVZ) contribute to brain repair during CNS disease. The microenvironment within the SVZ stem cell niche controls NSPC fate. However, extracellular factors within the niche that trigger astrogliogenesis over neurogenesis during CNS disease are unclear. Here, we show that blood-derived fibrinogen is enriched in the SVZ niche following distant cortical brain injury in mice. Fibrinogen inhibited neuronal differentiation in SVZ and hippocampal NSPCs while promoting astrogenesis via activation of the BMP receptor signaling pathway. Genetic and pharmacologic depletion of fibrinogen reduced astrocyte formation within the SVZ after cortical injury, reducing the contribution of SVZ-derived reactive astrocytes to lesion scar formation. We propose that fibrinogen is a regulator of NSPC-derived astrogenesis from the SVZ niche via BMP receptor signaling pathway following injury.