gebhart/patrepeval huggingface dataset:
Mucosal vaccines (WS-049) (2010)

We evaluated the immunogenicity of the RTS,S antigen when combined with MSP1 42 and with AMA1, antigens derived from the asexual blood stage.The objectives of this study were (i) to determine whether MSP1 42 and AMA1 vaccines formulated with the AS02 A Adjuvant System were safe and immunogenic in the rhesus monkey model; (ii) to investigate whether MSP1 42 or AMA1 induced immune interference to each other, or to RTS,S, when added singly or in combinations at a single injection site; (iii) in the event of immune interference, to determine if this could be reduced when antigens were administered at separate sites.We found that MSP1 42 and AMA1 were safe and immunogenic.When malaria antigens were delivered together in one formulation, MSP1 42 and RTS,S reduced AMA1-specific antibody responses as measured by ELISA however, only MSP1 42 lowered parasite growth inhibitory activity of anti-AMA1 antibodies as measured by growth inhibition assay.Unlike RTS,S, MSP1 42 significantly reduced AMA1 IFN-g and IL-5 responses.MSP1 42 suppression of AMA1 IFN-g responses was not seen in animals receiving RTS,S+AMA1+MSP1 42 suggesting that RTS,S restored IFN-g responses.Conversely, AMA1 had no effect on MSP1 42 antibody and IFN-g and IL-5 responses.Neither AMA1 alone or combined with MSP1 42 affected RTS,S antibody or IFN-g and IL-5 responses.Immune interference by MSP1 42 on AMA1 antibody responses was also evident when AMA1, MSP1 42 and RTS,S were administered concurrently at separate sites.These results suggest that immune interference may be complex and should be considered for the design of multi-antigen vaccines against malaria.
Radioimmunotherapy of experimental head and neck squamous cell carcinoma (HNSCC) with E6-specific antibody using a novel HPV-16 positive HNSCC cell line (2011)

We describe a proof-of-principle RIT study targeting HPV16 E6 oncoprotein with radiolabeled mAb to E6 in a stably transformed HPV16+ HNSCC cell line and tumor model in nude mice, and demonstrate potential utility of RIT as a novel molecular targeted therapy for HNSCC.
Non-Linear Domain Adaptation with Boosting (2013)

A common assumption in machine vision is that the training and test samples are drawn from the same distribution. However, there are many problems when this assumption is grossly violated, as in bio-medical applications where differ-ent acquisitions can generate drastic variations in the appearance of the data due to changing experimental conditions. This problem is accentuated with 3D data, for which annotation is very time-consuming, limiting the amount of data that can be labeled in new acquisitions for training. In this paper we present a multi-task learning algorithm for domain adaptation based on boosting. Unlike previous approaches that learn task-specific decision boundaries, our method learns a sin-gle decision boundary in a shared feature space, common to all tasks. We use the boosting-trick to learn a non-linear mapping of the observations in each task, with no need for specific a-priori knowledge of its global analytical form. This yields a more parameter-free domain adaptation approach that successfully lever-ages learning on new tasks where labeled data is scarce. We evaluate our approach on two challenging bio-medical datasets and achieve a significant improvement over the state of the art. 1
A Mott Insulator-Based Oscillator Circuit for Reservoir Computing (2020)

In this work, we use a Cr-doped V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> based Mott oscillator circuit to build a reservoir computing system that has much smaller model size than an equivalent LSTM. In contrast to an LSTM, our reservoir computing system can be trained very efficiently and on-line, with very low latency. We demonstrate close to state-of-the-art performance with three benchmark tasks: speech recognition, handwritten digit recognition, and HDD channel decoding. We show that our Mott circuit-based reservoir computing system brings significant reduction in power consumption and inference speed compared to CPU, GPU, or FPGA based systems.
Nanoparticle formation from material sputtering and liquid precursors (2015)

Dust particles can be produced in low-pressure plasmas using different methods. The most well-known technique consists in injecting a reactive gas in addition to the buffer gas. Volume reactions create the molecular precursors at the origin of nanoparticle nucleation and growth. The precursors can also be injected in the gas phase by material sputtering. A material exposed to the plasma will be sputtered by plasma ions and will release molecular precursors. Another possibility is to use a liquid precursor and to evaporate it for injection in the plasma.

In the first part of this presentation, we will present some surprising phenomena observed in a dusty plasma produced by material sputtering. Particularly, the appearance of a wide variety of instabilities will be characterized. One type of instability is relatively original as it appears as bright plasma spots (plasmoids) moving rapidly in the plasma. High-speed imaging provides very interesting results concerning their behavior and interactions. Indeed, plasmoids interact with each other and phenomena like splitting or merging are observed.

The second aspect will concern the nanoparticle growth from a liquid precursor. This work has just started recently and very preliminary results will be presented. It concerns the growth of soot analogs in a plasma. The general context of this study is the formation of soot particles in the road transportation sector where biofuels are more and more used. The objective of this collaborative project is to form soot analogs in well-controlled conditions in order to study precisely their formation, composition and structure. This understanding will help to develop methods for minimizing their production and noxious effects.
Leveraging the power for genomics for immuno-oncology (2021)

<div class="authors authors-lg"><div class="author"><div class="author-img"><img src="https://cdn.insights.bio/uploads/Golub headshot sq.jpg" data-image="1"></div><div class="author-det"> <!--StartFragment--><b>Todd Golub</b> is a founding core member of the Broad Institute and serves as the institute’s chief scientific officer and director of its Cancer Program. He is also the director of the Gerstner Center for Cancer Diagnostics at the Broad Institute. Dr Golub is a world leader in understanding the basis of cancer, by creating and applying tools of genomics. He has made fundamental discoveries in the molecular basis of childhood leukemia, and laid the foundation for the diagnosis and classification of human cancers using gene expression analysis. He also pioneered the development of chemical screening approaches based on gene expression. He joined the faculty of the Dana-Farber Cancer Institute and Harvard Medical School in 1997. At the same time he served as the leader of cancer genomics at the Whitehead Institute/MIT Center for Genome Research, which evolved into the Cancer Program at the Broad Institute. Dr Golub has directed that program since 2004, and is also currently the Charles A. Dana Investigator in Human Cancer Genetics at the Dana-Farber Cancer Institute and professor of pediatrics at Harvard Medical School. He is the recipient of multiple awards, including the Erasmus Hematology Award; the Richard and Hinda Rosenthal Memorial Award and the Outstanding Achievement Award from the American Association for Cancer Research; the Paul Marks Prize for Cancer Research; the E. Mead Johnson Award from the Society for Pediatric Research; and the Judson Daland Prize for Outstanding Achievement in Clinical Investigation from the American Philosophical Society. In 2014, he was elected as a member to the National Academy of Medicine (formerly the Institute of Medicine). Dr Golub has served on the scientific advisory boards of numerous organizations including serving as chair of St. Jude Children’s Research Hospital and the Board of Scientific Advisors of the National Cancer Institute. Golub received his B.A. from Carleton College and his M.D. from the University of Chicago Pritzker School of Medicine. He completed his internship, residency, and fellowship training at Boston Children’s Hospital and the Dana-Farber Cancer Institute.<!--EndFragment--> </div></div></div>
Isomeric Poly(benzophenone)s: Synthesis of Highly Crystalline Poly(4,4'-benzophenone) and Amorphous Poly(2,5-benzophenone), a Soluble Poly(p-phenylene) Derivative. [Erratum to document cited in CA120:271297] (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleIsomeric Poly(benzophenone)s: Synthesis of Highly Crystalline Poly(4,4'-benzophenone) and Amorphous Poly(2,5-benzophenone), a Soluble Poly(p-phenylene) Derivative. [Erratum to document cited in CA120:271297]R. W. Phillips, V. V. Sheares, E. T. Samulski, and J. M. DeSimoneCite this: Macromolecules 1995, 28, 8, 3012Publication Date (Print):April 1, 1995Publication History Published online1 May 2002Published inissue 1 April 1995https://pubs.acs.org/doi/10.1021/ma00112a062https://doi.org/10.1021/ma00112a062research-articleACS PublicationsRequest reuse permissionsArticle Views95Altmetric-Citations1LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Assessment of stereopsis in human infants. (1980)

A new method for testing stereopsis in infants is described for use in the early assessment of binocular function. Four 6- and 12-month-old infants were presented with a dynamic random-element stereogram generated on a color television monitor. A stereoscopic form was moved laterally, either left or right, to elicit the visual attention of the infant. An observer, unaware of the direction of form movement, made a forced-choice judgment of the direction of form displacement based on information gleaned from observations of the infant's behavior. The observer's performance for all three age groups exceeded chance levels of responding (p < 0.001). Individual infants within each age group also provided strong evidence of stereopsis. The applicability of the method for the screening of binocular anomalies is discussed.
Control of spatial excitation patterns in two-level systems by use of time-domain fields (1994)

Spatial structures created by pulsed field interactions with surface-bound two-level systems are considered. Superresolved pattern formation is possible by the use of extra degrees of freedom programmed in the time-domain field.
On the Write Schemes and Efficiency of FeFET 1T NOR Array for Embedded Nonvolatile Memory and Beyond (2022)

Ferroelectric field-effect-transistor (FeFET) 1T NOR Array is promising for multiple applications yet not well studied on its write mechanism and schemes. In this work, we demonstrate: i) A comprehensive model which reflects two FeFET write mechanisms – one to ground Source (S), Drain (D) & Body (B) nodes and use Gate (G) to write, and the other to float S/D and use G & B to write; ii) 3 write schemes for conventional FeFET 1T NOR arrays and another one for the diagonal array, the latter of which shows the advantages of low write energy and high write efficiency but with the penalty area cost; iii) A study of parasitic parameters, particularly gate resistance (R <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</inf> ), gate capacitance (C <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</inf> ) and word line resistance (R <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">WL</inf> ), in FeFET 1T NOR array, which is critical for further prospective 1T NOR array design; iv) An implementation of FeFET 1T NOR array in the Ising machine system to evaluate the feasibility of our write scheme and array structure for embedded nonvolatile memory (NVM) applications.
Bisim: a simulator for custom ECL circuits (2003)

Bisim is an event-driven, transistor-level, logic simulator that models both the logical and timing characteristics of custom emitter-coupled-logic/current-mode-logic circuits. Node voltages are represented by piecewise-linear waveforms, transistor currents are represented by piecewise-constant waveforms, and transistors are modeled as voltage-controlled current switches. Bisim's realistic circuit models enable it to simulate correctly a wide variety of circuit topologies while retaining much of the speed of higher level simulators.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Wound Assay vehicle from HDAC6 Plays a Noncanonical Role in the Regulation of Antitumor Immune Responses, Dissemination, and Invasiveness of Breast Cancer (2023)

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Structure Evolution during Cyclic Deformation of an Elastic Propylene-Based Ethylene−Propylene Copolymer (2006)

In-situ structural evolution during uniaxial extension and subsequent retraction of a thermoplastic elastomer (TPE) based on propylene-dominant ethylene−propylene (EP) copolymer was studied. Combined measurements of time-resolved wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS) as well as stress−strain curves revealed molecular mechanism responsible for the elastic behavior. During the first cycle of deformation, a fraction of the crystals was destroyed, while the rest was reoriented. At strains larger than 1.0, strain-induced α-crystals in the lamellar form took place, resulting in the creation of a network with well-oriented lamellae having their normals parallel to the stretching direction. With the increase of strain, more crystals were induced, forming an enhanced network with strain-hardening behavior. During retraction and even after complete relaxation to zero stress, the majority of the strain-induced crystalline network remains in tact as being “permanent set”, where lamellar stacks act as the network points. This strain-induced crystalline network structure is thermally stable at room temperature and is responsible for the elastic behavior during subsequent cyclic deformation, similar to a vulcanized rubber.
Interferon-γ Induces X-linked Inhibitor of Apoptosis-associated Factor-1 and Noxa Expression and Potentiates Human Vascular Smooth Muscle Cell Apoptosis by STAT3 Activation (2008)

Interferon (IFN)-gamma actions on the vessel wall play an important role in the pathogenesis of arteriosclerosis, yet the contribution of different IFN-gamma signaling pathways to the phenotypic modulation of vascular smooth muscle cells (VSMCs) are poorly understood. We investigated the effects of IFN-gamma on VSMCs and arteries through interactions involving signal transducer and activator of transcription (STAT) proteins. In addition to STAT1 activation, IFN-gamma consistently phosphorylated STAT3 in human VSMCs but weakly or not at all in human endothelial cells or mouse VSMCs. STAT3 activation resulted in nuclear translocation of this transcription factor. By selectively inhibiting STAT3 and not STAT1 signaling, we identified a number of candidate IFN-gamma-inducible, STAT3-dependent gene products by microarray analysis. Results for selected genes, including the pro-apoptotic molecules X-linked inhibitor of apoptosis associated factor-1 (XAF1) and Noxa, were verified by real time quantitative reverse transcription-PCR and immunoblot analyses. IFN-gamma-induced STAT3 and STAT1 signaling in VSMCs demonstrated reciprocal inhibition. STAT3 activation by IFN-gamma sensitized VSMCs to apoptosis triggered by both death receptor- and mitochondrial-mediated pathways. Knock down of XAF1 and Noxa expression inhibited the priming of VSMCs to apoptotic stimuli by IFN-gamma. Finally, we confirmed the in vivo relevance of our observations using a chimeric animal model of immunodeficient mice bearing human coronary artery grafts in which the expression of XAF1 and Noxa as well as the pro-apoptotic effects induced by IFN-gamma were dependent on STAT3. The data suggest STAT1-independent signaling by IFN-gamma via STAT3 that promotes the death of human VSMCs.
A Large Field of View Coincidence Imaging System Based on One-Dimensional Sharing Block Detectors (2009)

For such as breast cancer imaging, dedicated coincidence imaging detector will be promising for new instrumentation of nuclear medicine. For this purpose, a large field of view (FOV) coincidence imaging system was developed and tested. The imaging system consists of four sets of one-dimensional sharing block detectors and a single gamma probe and measures coincidence between these two detectors. The one-dimensional sharing detector uses 5 GSO blocks optically coupled to 6 dual photomultiplier tubes (PMT). The size of a single GSO is 2.9 mm times 2.9 mm times 15 mm. The signals from four one-dimensional sharing detectors are fed to weighted summing circuits. They are digitized by 100 MHz free running analog to digital (A-D) converters and are used to calculate the position of gamma interaction. Coincidence was measured between this gamma imaging detector (panel detector) and a hand-held single gamma probe. Acquired data was transferred to a personal computer and displayed. Most spots corresponding to GSO crystals were resolved in the position histogram. Spatial resolution was around 4 to 6 mm FWHM when the detector is greater than 25 mm. The sensitivity was 0.1-0.2% when the single probe was 25 mm away from the imager surface. Images of phantoms were successfully obtained. We conclude developed coincidence imaging system has large FOV and easy to handle, reasonable spatial resolution and may have potential to be a new instrument for nuclear medicine.
The Superstable 25 kDa Monolayer Protected Silver Nanoparticle: Measurements and Interpretation as an Icosahedral (2012)

A cluster obtained in high yield from the reduction of a silver-thiolate precursor, Ag-SCH2CH2Ph, exhibited a single sharp peak near 25 kDa in the matrix-assisted laser desorption mass spectrum (MALDI MS) and a well- defined metal core of ∼2 nm measured with transmission electron microscopy (TEM). The cluster yields a single fraction in high-performance liquid chromatography (HPLC). Increased laser fluence fragments the cluster until a new peak near 19 kDa predominates, suggesting that the parent cluster Ag152(SCH2CH2Ph)60evolves into a stable inorganic core Ag152S60. Exploiting combined insights from investigations of clusters and surface science, a core−shell structure model was developed, with a 92-atom silver core having icosahedral- dodecahedral symmetry and an encapsulating protective shell containing 60 Ag atoms and 60 thiolates arranged in a network of six-membered rings resembling the geometry found in self-assembled monolayers on Ag(111). The structure is in agreement with small-angle X-ray scattering (SAXS) data. The protective layer encapsulating this silver cluster may be the smallest known three-dimensional self-assembled monolayer. First-principles electronic structure calculations show, for the geometry-optimized structure, the development of a ∼0.4 eV energy gap between the highest-occupied and lowest-unoccupied states, originating from a superatom 90-electron shell-closure and conferring stability to the cluster. The optical absorption spectrum of the cluster resembles that of plasmonic silver nanoparticles with a broad single feature peaking at 460 nm, but the luminescence spectrum shows two maxima with one attributed to the ligated shell and the other to the core.
Analysis of the Non-Linear Behavior of ECLIPSE Actuators (2005)

This work discusses the development and characterization of rectangular shaped Epoxy Composite Laminated Piezoelectric Stress-Enhanced actuators (ECLIPSE). ECLIPSE actuators are unimorph type d31 actuators that are manufactured with a lead zirconate titanate (PZT) plate sandwiched between unidirectional Kevlar 49/epoxy composite layers with dissimilar coefficients of thermal expansion in orthogonal directions. Cooling the actuator from an elevated curing temperature resulted in a residual stress gradient through the actuator, a compressive stress on the brittle piezoelectric plate, and a large out-of-plane deformation. Extended classical lamination theory (ECLT) is used to model the residual stress state and curvature of the actuator. The model results are compared to the classical lamination theory. The ECLT was developed by Hyer to explain the non-linear behavior of unsymmetric cross-ply laminates [1-3]. Three actuator layups were fabricated and characterized: [90/PZT/90/0], [90/90/PZT/90/0/0], and [90/90/90/PZT/90/0/0/0]. It is shown that geometric non-linearity is important to consider when modeling ECLIPSE actuators.
Toward Automated N-Glycopeptide Identification in Glycoproteomics (2016)

Advances in software-driven glycopeptide identification have facilitated N-glycoproteomics studies reporting thousands of intact N-glycopeptides, i.e., N-glycan-conjugated peptides, but the automated identification process remains to be scrutinized. Herein, we compare the site-specific glycoprofiling efficiency of the PTM-centric search engine Byonic relative to manual expert annotation utilizing typical glycoproteomics acquisition and data analysis strategies but with a single glycoprotein, the uncharacterized multiple N-glycosylated human basigin. Detailed site-specific reference glycoprofiles of purified basigin were manually established using ion-trap CID-MS/MS and high-resolution Q-Exactive Orbitrap HCD-MS/MS of tryptic N-glycopeptides and released N-glycans. The micro- and macroheterogeneous basigin N-glycosylation was site-specifically glycoprofiled using Byonic with or without a background of complex peptides using Q-Exactive Orbitrap HCD-MS/MS. The automated glycoprofiling efficiencies were assessed against the site-specific reference glycoprofiles and target/decoy proteome databases. Within the limits of this single glycoprotein analysis, the search criteria and confidence thresholds (Byonic scores) recommended by the vendor provided high glycoprofiling accuracy and coverage (both >80%) and low peptide FDRs (<1%). The data complexity, search parameters including search space (proteome/glycome size), mass tolerance and peptide modifications, and confidence thresholds affected the automated glycoprofiling efficiency and analysis time. Correct identification of ambiguous peptide modifications (methionine oxidation/carbamidomethylation) whose mass differences coincide with several monosaccharide mass differences (Fuc/Hex/HexNAc) and of ambiguous isobaric (Hex<sub>1</sub>NeuAc<sub>1</sub>-R/Fuc<sub>1</sub>NeuGc<sub>1</sub>-R) or near-isobaric (NeuAc<sub>1</sub>-R/Fuc<sub>2</sub>-R) monosaccharide subcompositions remains challenging in automated glycoprofiling, arguing particular attention paid to N-glycopeptides displaying such "difficult-to-identify" features. This study provides valuable insights into the automated glycopeptide identification process, stimulating further developments in FDR-based glycoproteomics.