gebhart/patrepeval huggingface dataset:
Flow Cytometric DNA and Nuclear Antigen Content in Astrocytic Neoplasms (1988)

Simultaneous flow cytometric DNA content and proliferation-associated nuclear antigen (p105) quantitation was performed on 23 astrocytic tumors and the results correlated with histologic subtype. Three of nine anaplastic astrocytomas and one of ten glioblastomas had an identifiable aneuploid peak, while all four well differentiated astrocytomas were diploid. Cell cycle analysis of malignant gliomas revealed a higher mean percentage of S and G2M cells compared to well differentiated astrocytomas but there was considerable overlap between histologic subtypes. Nuclear antigen analysis of diploid tumors showed a higher mean p105 fluorescence of S + G2M cells than G0G1 cells from the same case but there were no apparent differences in p105 expression by histologic subtype. Aneuploid tumors showed enhanced expression of p105 relative to diploid cells. The findings suggest that the aggressive course of high grade glial tumors may be related to an abnormal DNA stemline or an increase in proliferative activity.
METHODOLOGY AND OPTIMIZING OF MULTIPLE FRAME FORMAT BUFFERING WITHIN FPGA H.264/AVC DECODER WITH FREXT (2008)

This work evaluated the role of designing the frame buffer of a hardware video decoder, with integrated support for the H.264/AVC codec and its Fidelity Range Extensions (FRExt) amendment. With focus on organizing external memory data access, the frame buffer was designed to provide intermediate data storage for the decoder, while using an efficient store and load scheme that takes into consideration each frame pixel format of the video data. VHDL was used to model the frame buffer. Exploitation of reconfigurability and post-synthesis FPGA simulations were used to evaluate behavior and scalability while providing an analysis of approaches to adding FRExt to the memory management.
Photochemistry of the cis- and trans-dibromobis(ethylenediamine)ruthenium(III) cations (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of the cis- and trans-dibromobis(ethylenediamine)ruthenium(III) cationsMark E. Rerek and Peter S. SheridanCite this: Inorg. Chem. 1984, 23, 14, 2198–2201Publication Date (Print):July 1, 1984Publication History Published online1 May 2002Published inissue 1 July 1984https://doi.org/10.1021/ic00182a043RIGHTS & PERMISSIONSArticle Views40Altmetric-Citations2LEARN 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 InReddit PDF (580 KB) Get e-Alerts Get e-Alerts
Physics of Pumping Methanol/Water Solutions for Fuel Cell Applications (2007)

Proton exchange membrane fuel cells are environmentally friendly energy conversion devices. A special class of PEMFCs, direct methanol fuel cells (DMFCs), oxidize liquid methanol solutions at the cell anode as opposed to hydrogen gas. The use of methanol as fuel makes DMFCs highly attractive for portable applications due to the high volumetric energy density of liquid methanol. Previous work has shown that electroosmotic (EO) pumps can be used to pump pure methanol to obtain relatively high flow rates per power in applications with minimal pressure loads. This study explores the unique aspects of pumping methanol/water solutions for fuel cell applications with non negligible pressure loads. We explore EO pump figures of merit pertinent to portable fuel cell applications including flow rate per power and the ratio of EO pump power to fuel cell power. Experimental studies reveal EO pump power to DMFC power ratios of 5% or less for borosilicate glass substrates. Further, we will discuss unique aspects of pumping low ion density methanol/water solutions that affect EO pump performance including solution conductivity and transient pH gradients. Ultimately this work provides a theoretical and experimental basis for a miniature DMFC system using an EO pump for fuel delivery.
Cell-type-specific population dynamics of diverse reward computations (2022)

Computational analysis of cellular activity has developed largely independently of modern transcriptomic cell typology, but integrating these approaches may be essential for full insight into cellular-level mechanisms underlying brain function and dysfunction. Applying this approach to the habenula (a structure with diverse, intermingled molecular, anatomical, and computational features), we identified encoding of reward-predictive cues and reward outcomes in distinct genetically defined neural populations, including TH<sup>+</sup> cells and Tac1<sup>+</sup> cells. Data from genetically targeted recordings were used to train an optimized nonlinear dynamical systems model and revealed activity dynamics consistent with a line attractor. High-density, cell-type-specific electrophysiological recordings and optogenetic perturbation provided supporting evidence for this model. Reverse-engineering predicted how Tac1<sup>+</sup> cells might integrate reward history, which was complemented by in vivo experimentation. This integrated approach describes a process by which data-driven computational models of population activity can generate and frame actionable hypotheses for cell-type-specific investigation in biological systems.
Site Specific TEM Specimen Preparation using an FIB/TEM System (2000)

Abstract The focused ion beam(FIB) technique, developed for the microelectronics industry has become a major method for site specific transmission electron microscopy(TEM) specimen preparation in a wide range of materials[l]. The FIB lift-out technique has improved the specimen preparation procedures by removing complicated initial fabrication required prior to the FIB milling[2]. However, conventional FIB techniques are still having increased difficulty in meeting failure analysis needs from high technology industries such as microelectronics. We have developed a site specific TEM specimen preparation method using a combination of an FIB instrument and an intermediate voltage TEM equipped with a scanning attachment [3]. In this method, the specimen is mounted on an FIB-TEM compatible specimen holder, so that localization of the specific site can be carried out in the FIB and TEM using the same holder. The scanning electron imaging mode may be used to observe surface structures of the milled area, and the scanning transmission electron microscopy(STEM) mode may be used to observe structures inside of the milled surface.
On collaborative content distribution using multi-message gossip (2006)

We study epidemic schemes in the context of collaborative data delivery. In this context, multiple chunks of data reside at different nodes, and the challenge is to simultaneously deliver all chunks to all nodes. Here we explore the inter-operation between the gossip of multiple, simultaneous message-chunks. In this setting, interacting nodes must select which chunk, among many, to exchange in every communication round. We provide an efficient solution that possesses the inherent robustness and scalability of gossip. Our approach maintains the simplicity of gossip, and has low message, connections and computation overhead. Because our approach differs from solutions proposed by network coding, we are able to provide insight into the tradeoffs and analysis of the problem of collaborative content distribution. We formally analyze the performance of the algorithm, demonstrating its efficiency with high probability.
Effect of metal coordination on the interaction of substituted phenanthroline and pyridine ligands with quadruplex DNA (2009)

A series of new mono-carboxamido phenanthrolines and bis-carboxamido pyridines have been prepared and their coordination chemistry to platinum(II) and palladium(II) investigated. Both the ligands and metal complexes have been designed with the appropriate geometric requirements to favour pi-pi interactions with guanine quartets, which are the core motif in quadruplex structures formed by folding single-stranded telomeric DNA. The interactions of these compounds with quadruplex-DNA have been investigated. The results show that some of these compounds induce the stabilisation of quadruplex-DNA (e.g. DeltaTm at 1 microM of 20 degrees C for one of the platinum(II) complexes) while there is no measurable interaction with duplex DNA at similar concentrations. In addition, the important role played by the metal centre in increasing the interaction of these planar molecules with quadruplex-DNA is highlighted.
Evaluation of Cellular Determinants Required for In Vitro Xenotropic Murine Leukemia Virus-Related Virus Entry into Human Prostate Cancer and Noncancerous Cells (2010)

The newly identified retrovirus-the xenotropic murine leukemia virus-related virus (XMRV)-has recently been shown to be strongly associated with familial prostate cancer in humans (A. Urisman et al., PLoS Pathog. 2:e25, 2006). While that study showed evidence of XMRV infection exclusively in the prostatic stromal fibroblasts, a recent study found XMRV protein antigens mainly in malignant prostate epithelial cells (R. Schlaberg et al., Proc. Natl. Acad. Sci. U. S. A. 106:16351-16356, 2009). To help elucidate the mechanisms behind XMRV infection, we show that prostatic fibroblast cells express Xpr1, a known receptor of XMRV, but its expression is absent in other cell lines of the prostate (i.e., epithelial and stromal smooth muscle cells). We also show that certain amino acid residues located within the predicted extracellular loop (ECL3 and ECL4) sequences of Xpr1 are required for efficient XMRV entry. Although we found strong evidence to support XMRV infection of prostatic fibroblast cell lines via Xpr1, we learned that XMRV was indeed capable of infecting cells that did not necessarily express Xpr1, such as those of the prostatic epithelial and smooth muscle origins. Further studies suggest that the expression of Xpr1 and certain genotypes of the RNASEL gene, which could restrict XMRV infection, may play important roles in defining XMRV tropisms in certain cell types. Collectively, our data reveal important cellular determinants required for XMRV entry into different human prostate cells in vitro, which may provide important insights into the possible role of XMRV as an etiologic agent in human prostate cancer.
CES-KD: Curriculum-based Expert Selection for Guided Knowledge Distillation (2022)

Knowledge distillation (KD) is an effective tool for compressing deep classification models for edge devices. However, the performance of KD is affected by the large capacity gap between the teacher and student networks. Recent methods have resorted to a multiple teacher assistant (TA) setting for KD, which sequentially decreases the size of the teacher model to relatively bridge the size gap between these models. This paper proposes a new technique called Curriculum Expert Selection for Knowledge Distillation (CES-KD) to efficiently enhance the learning of a compact student under the capacity gap problem. This technique is built upon the hypothesis that a student network should be guided gradually using stratified teaching curriculum as it learns easy (hard) data samples better and faster from a lower (higher) capacity teacher network. Specifically, our method is a gradual TA-based KD technique that selects a single teacher per input image based on a curriculum driven by the difficulty in classifying the image. In this work, we empirically verify our hypothesis and rigorously experiment with CIFAR-10, CIFAR-100, CINIC-10, and ImageNet datasets and show improved accuracy on VGG-like models, ResNets, and WideResNets architectures.
AI3SD Video: The "almost druggable" genome (2021)

This talk will briefly introduce the "Illuminating the Druggable Genome" knowledge management center, with focus on its protein-centric data aggregator, Pharos (https://pharos.nih.gov/), and the DrugCentral online pharmaceutical compendium (https://drugcentral.org/). Using Pharos/DrugCentral data, we then examine the question, "what proteins that could potentially be ligandable, are currently not?", in a disease context. To do this, we examine proteins available in the RSCB PDB (https://www.rcsb.org/) â the "PDB-ome" =&gt; 347 proteins that lack known ligands; Proteins for which chemical matter is known, N=2644 - the "SAR-ome" => of these, 115 proteins meet the "ligandable" criteria; the "Pocket-ome", i.e., proteins that have a close - by sequence identity - homologue with known 3D structure, which leads to ~700 ligandable proteins with PDB structures; 180 that have close homologues but lack 3D structures; and N=2623 proteins that could be modeled with reasonable confidence; last but not least, the "Phen-ome", which looks at this entire list (N = 6742) from the perspective of rare and common diseases, GWAS and mouse phenotype data, etc, and narrows down the previous lists. The "almost druggable genome" contains 715 ligandable (3D exists) proteins, 180 proteins for which chemical matter is likely to be found, and at least 100 proteins that could be subject to chemical probe optimization.
<title>Refractive index-based detection of biomolecular interactions</title> (2001)

A biosensor was constructed by modifying the optics of a critical angle refractometer to enable it to measure changes in surface plasmon resonance. Initially, the utility of the critical angle refractometry to measure biomolecular interactions was examined using the Leica Automatic Critical Angle Refractometer 600 (AR600). While initial results suggested that the biomolecular interactions could be measured by critical angle refractometry, these proved to be an artifact of protein buildup on the surface. At lower concentrations of target protein, no change in the refractive index was observed. The AR600 was reconfigured from a critical angle refractometer to surface plasmon resonance technology to study molecular interactions between biomolecules. The performance of the SPR biosensor was demonstrated by measuring protein-protein interactions; specifically, avidin:anti-avidin interactions and streptavidin:anti-streptavidin interactions. Equilibrium dissociation constants were obtained by data analysis according to pseudo-first order binding kinetics. Polyclonal anti-streptavidin and monoclonal antiavidin demonstrated affinity constants of 9.7 x 10-5 M-1 and 4.3 x 10-5 M-1 for their respective ligands.
ChemInform Abstract: ORGANIC REACTIONS AT ALUMINA SURFACES. CHEMOSPECIFIC OXIDATION OF β‐HYDROXY SULFIDES AND SELENIDES INTO THE CORRESPONDING β‐KETO SULFIDES AND SELENIDES USING CHLORAL ON ACTIVATED ALUMINA (1977)

Abstract Aus den Epoxiden (I) entstehen mit Mercaptanen und Selenolen die Spaltprodukte (III), die an Aluminiumoxid mit Chloral zu den Ketonen (IV) oxidiert werden.
Macrophage Interleukin 1 Response to Injected Silicone in a Rat Model (1992)

Observations of silicone granuloma formation and migration of silicone to regional lymph nodes have indicated a need for more research into the possible immunological responses to silicone. The present study was undertaken to assess the effect of injected silicone particles on the ability of splenic macrophages to produce interleukin 1 (IL-1) and to determine the relative quantities produced. Lewis rats were divided into 4 groups: Group 1 animals (n = 3) were injected subcutaneously with sterile saline (2.5 ml) and served as control animals; Group 2 animals (n = 3) also served as control subjects, but macrophages isolated from these animals were exposed to lipopolysaccharide (LPS); Group 3 animals (n = 3) were injected subcutaneously with Freund's complete adjuvant (FCA) (2.5 ml) to serve as FCA control animals; and Group 4 animals (n = 3) received a subcutaneous injection of a sonicated slurry of equal parts FCA and silicone (2.5 ml each). IL-1 production was not significantly increased in splenic macrophages from animals exposed to the silicone slurry (p > 0.20) 8 months after injection as compared with control animals or animals given FCA alone. Macrophages exposed to LPS, a known mitogen, had significantly elevated IL-1 production. Subcutaneously injected silicone particles did not elicit an increase in IL-1 production in rat macrophages.
ChemInform Abstract: CYCLODEHYDRATION OF O‐VINYL ANILIDES. A GENERAL SYNTHESIS OF SUBSTITUTED QUINOLINES (1984)

Abstract Beim Versuch der sauren Verseifung des aus (1) und (II) zugänglichen Formamids (IIIa) entsteht neben dem Amin (IIIb) das Chinolin‐Derivat (IV).
Crystal engineering rescues a solution organic synthesis in a cocrystallization that confirms the configuration of a molecular ladder (2011)

Treatment of an achiral molecular ladder of C(2h) symmetry composed of five edge-sharing cyclobutane rings, or a [5]-ladderane, with acid results in cis- to trans-isomerization of end pyridyl groups. Solution NMR spectroscopy and quantum chemical calculations support the isomerization to generate two diastereomers. The NMR data, however, could not lead to unambiguous configurational assignments of the two isomers. Single-crystal X-ray diffraction was employed to determine each configuration. One isomer readily crystallized as a pure form and X-ray diffraction revealed the molecule as being achiral based on C(i) symmetry. The second isomer resisted crystallization under a variety of conditions. Consequently, a strategy based on a cocrystallization was developed to generate single crystals of the second isomer. Cocrystallization of the isomer with a carboxylic acid readily afforded single crystals that confirmed a chiral ladderane based on C(2) symmetry. The chiral ladderane and acid self-assembled to generate a five-component hydrogen-bonded complex that packs to form large solvent-filled homochiral channels of nanometer-scale dimensions. Whereas cocrystallizations are frequently applied to structure determinations of proteins, our study represents the first application of a cocrystallization to confirm the relative configuration of a small-molecule diastereomer generated in a solution-phase organic synthesis.
ReLaText: Exploiting Visual Relationships for Arbitrary-Shaped Scene Text Detection with Graph Convolutional Networks (2020)

We introduce a new arbitrary-shaped text detection approach named ReLaText by formulating text detection as a visual relationship detection problem. To demonstrate the effectiveness of this new formulation, we start from using a "link" relationship to address the challenging text-line grouping problem firstly. The key idea is to decompose text detection into two subproblems, namely detection of text primitives and prediction of link relationships between nearby text primitive pairs. Specifically, an anchor-free region proposal network based text detector is first used to detect text primitives of different scales from different feature maps of a feature pyramid network, from which a text primitive graph is constructed by linking each pair of nearby text primitives detected from a same feature map with an edge. Then, a Graph Convolutional Network (GCN) based link relationship prediction module is used to prune wrongly-linked edges in the text primitive graph to generate a number of disjoint subgraphs, each representing a detected text instance. As GCN can effectively leverage context information to improve link prediction accuracy, our GCN based text-line grouping approach can achieve better text detection accuracy than previous text-line grouping methods, especially when dealing with text instances with large inter-character or very small inter-line spacings. Consequently, the proposed ReLaText achieves state-of-the-art performance on five public text detection benchmarks, namely RCTW-17, MSRA-TD500, Total-Text, CTW1500 and DAST1500.
Toward ubiquitous environments for mobile users (1998)

A computational paradigm that lets processes migrate with users would support truly ubiquitous computing environments. The article investigates the technical problems that must be solved to accommodate this model and examines some systems that are addressing the problems now. The review of current systems addressing these issues reveals that it is now possible to engineer a system in which the user's entire environment is available wherever and whenever it is required. However, the provision of such an environment represents a considerable engineering effort and many significant choices. At the University of Stirling, we are currently investigating these choices in the construction of a ubiquitous environment based on Java.
Optimization strategies of PEM electrolyser as part of solar PV system (2016)

Solar and wind power have intermittent nature. In order to guarantee continuous power supply, they need to be accompanied with energy storage systems or bridges between different energy sectors. Hydrogen is a potential candidate for both applications (an energy storage system and bridging technology). Hence, it is interesting to study the practical dynamic properties and limitations of electrolysers in the viewpoint of renewable energy production. This paper studies optimization strategies of a proton exchange membrane (PEM) electrolyser together with a solar photovoltaic (PV) system.
Execution Time and Code Size Optimization using Multidimensional Retiming and Loop Striping (2013)

International audience
The Polymorphism of a Cytosine Anion Studied by Electron Paramagnetic Resonance Spectroscopy (1991)

Electron addition to the nucleic acid base cytosine and several derivatives was studied in frozen aqueous solution and in aqueous glasses containing 10 M glucose, 7 M BeF2, 10 M LiCl and 8 N NaOH. Electron paramagnetic resonance spectroscopy revealed that three major types of spectra are obtained which can be classified into a group D giving a doublet (ca. 1.6 mT) and a group of triplet patterns T and T1 (ca. 3.0 mT total spread) which differ slightly in coupling values but which are both distinct from D by showing the loss of one sizeable proton coupling (ca. 1.0 mT) in deuterated solvents. Varying the type of glasses and other parameters such as pH, together with modification of the cytosine exocyclic groups, indicated that the triplet patterns represent electron adducts protonated at the amino group, whereas the doublets D should probably involve N3-protonated species. The equilibrium between doublets and triplets was found to depend strongly on the presence of Li+ and Be2+ and less strongly on pH or the presence of Na+, the former group of ions inducing the triplets. It is suggested that the influence of the ions derives mostly from their strength in stabilizing the amino-protonated tautomer of the electron adducts.