gebhart/patrepeval huggingface dataset:
NuSeT: A Deep Learning Tool for Reliably Separating and Analyzing Crowded Cells (2019)

Abstract Segmenting cell nuclei within microscopy images is a ubiquitous task in biological research and clinical applications. Unfortunately, segmenting low-contrast overlapping objects that may be tightly packed is a major bottleneck in standard deep learning-based models. We report a Nu clear Se gmentation T ool (NuSeT) based on deep learning that accurately segments nuclei across multiple types of fluorescence imaging data. Using a hybrid network consisting of U-Net and Region Proposal Networks (RPN), followed by a watershed step, we have achieved superior performance in detecting and delineating nuclear boundaries in 2D and 3D images of varying complexities. By using foreground normalization and additional training on synthetic images containing non-cellular artifacts, NuSeT improves nuclear detection and reduces false positives. NuSeT addresses common challenges in nuclear segmentation such as variability in nuclear signal and shape, limited training sample size, and sample preparation artifacts. Compared to other segmentation models, NuSeT consistently fares better in generating accurate segmentation masks and assigning boundaries for touching nuclei.
Dynamic regulation of sarcoplasmic reticulum Ca<sup>2+</sup> stores by stromal interaction molecule 1 and sarcolipin during muscle differentiation (2012)

During muscle development, the sarco/endoplasmic reticulum (SR/ER) undergoes remodeling to establish a specialized internal Ca(2+) store for muscle contraction. We hypothesized that store operated Ca(2+) entry (SOCE) is required to fill Ca(2+) stores and is, therefore, critical to creating a mature SR/ER. Stromal interaction molecule 1 (STIM1) functions as a sensor of internal Ca(2+) store content and an activator of SOCE channels. Myocytes lacking STIM1 display reduced SR Ca(2+) content and altered expression of key SR proteins. Sarcolipin (SLN), an inhibitor of the SR calcium pump, was markedly increased in the muscle of mutant STIM1 mice. SLN opposes the actions of STIM1 by limiting SOCE, reducing SR Ca(2+) content and delaying muscle differentiation. During mouse muscle development SLN is highly expressed in embryonic muscle, while the expression of STIM1 is up-regulated postnatally. These results suggest that SOCE regulates SR/ER specialization and that SLN and STIM1 act in opposing fashions to govern SOCE during myogenesis.
Joint channel and source decoding for vector quantized images using turbo codes (2002)

This paper presents a novel joint decoding scheme for image transmission over noisy channels. The proposed decoding scheme includes two features of interaction between a turbo channel decoder and a vector quantization source decoder. First, the source decoder makes use of the channel soft outputs for better reconstruction; second, a feedback algorithm is designed for using source information to improve the error correction capability of the turbo decoder. Significant improvement in terms of the error correction capability and the quality of reconstructed images is achieved compared to a separately operating decoding system.
Primary cultures of rat hepatocytes as a model system of canalicular development, biliary secretion, and intrahepatic cholestasis. II. Taurolithocholate-induced alterations of canalicular morphology and of the distribution of filipin-cholesterol complexes. (1982)

Hepatocytes in primary monolayer culture treated with taurolithocholate showed distinct ultrastructural changes localized primarily to the bile canalicular membrane. These alterations comprised disturbance and proliferation of tight junctions, dilatation of the canaliculi, loss of microvilli, thickening of the pericanalicular ectoplasm, and bizarre lamellar transformations of canaliculi. In freeze-fracture replicas the lamellae projecting into the canalicular lumen were found to be devoid of intramembranous particles. Localization by the use of filipin of cholesterol in plasma membranes of taurolithocholate affected hepatocytes revealed an extensive accumulation of cholesterol in membranes of dilated canaliculi, and also in outpouchings of the contiguous membrane in the ultimate vicinity. Furthermore, a pronounced segregation of cholesterol-rich membrane material into the lumen of dilated canaliculi and into enlargements of the intercellular space could be observed in thin sections. In contrast, a total absence of cholesterol was noted in the lamellar projections of the bizarre transformed canaliculi. The reliability of these findings and their consequences for the mechanism of taurolithocholate-induced cholestasis are discussed and it is suggested that the incorporation of cholesterol into the canalicular membrane reflects only one aspect of the cholestatic effect of taurolithocholate. An additional aspect seems to comprise the dislocation of membrane bound proteins and perhaps other membrane components. This is probably caused by independent mechanisms.
Pulse Radiolysis of Pyrrolidine (1970)

The formation, decay, and absorption spectra of transients formed from pyrrolidine in aqueous solutions were studied. The solvated electron ( ${\rm e}_{{\rm aq}}^{-}$) reacts with the protonated and the nonprotonated pyrrolidine forming the ${\rm C}_{4}{\rm H}_{8}{\rm N}$· radical. The rate constants are: $k({\rm e}_{{\rm aq}}^{-}+{\rm C}_{4}{\rm H}_{8}{\rm NH}_{2}{}^{+})=(7.5\pm 1.5)\times 10^{6} M^{-1} \text{second}^{-1}$ and $k({\rm e}_{{\rm aq}}^{-}+{\rm C}_{4}{\rm H}_{8}{\rm NH})=(1.1\pm 0.5)\times 10^{6} M^{-1} \text{second}^{-1}$. The ${\rm C}_{4}{\rm H}_{8}{\rm N}$· radical has an absorption maximum at 3200 A, $\epsilon =510 M^{-1} {\rm cm}^{-1}$, and disappears in a second-order reaction, $k=3.1\times 10^{9} M^{-1} \text{second}^{-1}$. The rate constants for the reaction of aqueous pyrrolidine with OH radicals, $k=9.6\times 10^{9} M^{-1} \text{second}^{-1}$ for pH 2 and $k=1.45\times 10^{10} M^{-1} \text{second}^{-1}$ for pH 8, were also determined. The pyrrolidine transients formed b...
A survey on multiple object tracking algorithm (2016)

Visual Multiple Object Tracking (VMOT) is an important computer vision task which has gained increasing attention due to its academic and commercial potential. There are many different approaches have been proposed to solve the problem. Compared with single object tracking which focuses on appearance model, motion model and other factors, multiple object tracking shares these common challenges, and has some more challenging tasks to be tackled, such as identifying among multiple objects, frequent occlusion due to the crowd, initializing and terminating of the object tracking, et al, which making it difficult to get a comprehensive understanding of this problem. In this paper, we try to make systematic review on VMOT. We review the recent advances in various aspects and introduce the classification of each aspect in detail. The main aspects include observation model and tracking algorithm. In each aspect, the existing methods are classified into different groups, and each group is discussed in details for their principles, advantages and drawbacks. This review work can provide researchers, especially new comers to the topic of VMOT, a general understanding of the state-of-the-arts, and help them to comprehend the aspects of a VMOT system and the inter-connection of these aspects.
Symmetry Aspects of H<sub>2</sub> Splitting by Five-Coordinate d<sup>6</sup> Ruthenium Amides, and Calculations on Acetophenone Hydrogenation, Ruthenium Alkoxide Formation, and Subsequent Hydrogenolysis in a Model <i>trans</i>-Ru(H)<sub>2</sub>(diamine)(diphosphine) System (2012)

The potential energy surface (PES) of H(2) addition to the Ru═N bond of a model five-coordinate ruthenium amide (Ru═N), leading to an octahedral trans-Ru(H)(2)(diamine)(diphosphine) (HRu-NH) and subsequent acetophenone hydrogenation, is studied using M06 density functional theory methods. A qualitative molecular orbital analysis reveals that H(2) addition to the ground state of Ru═N (which has a distorted trigonal-bipyramidal geometry) fits the criterion of a symmetry-forbidden reaction. A transition state (TS) for H(2) heterolytic splitting by Ru═N corresponds to the reaction taking place on an excited state of the Ru═N having a square-pyramidal geometry and gives ΔG°(⧧) = 19.5 kcal/mol. The reaction between HRu-NH and acetophenone proceeds by a localized hydride-transfer TS with ΔG°(⧧) = 11.5 kcal/mol. This TS leads to an ion pair between a square-pyramidal d(6) ruthenium amino cation and the alkoxide and is uphill from the separated reactants by 3.5 kcal/mol. Subsequent abstraction of the amino proton by the alkoxide within the ion pair is barrierless, but it also lacks any thermodynamic driving force. In contrast, reorientation of the alkoxide within the ion pair to form an octahedral ruthenium alkoxide is calculated to be exoergic by 7.1 kcal/mol. These features of the PES suggest that the known rapid production of ruthenium alkoxides when stoichiometric amounts of acetophenone and HRu-NH are reacted at low temperatures proceeds by a simple direct route following hydride transfer. For the simplified model complex, ruthenium alkoxide is calculated to be the thermodynamic product of the hydrogenation reaction (exoergic by 3.6 kcal/mol). A TS for H(2) heterolytic splitting across the Ru-alkoxide bond is calculated to have ΔG°(⧧) (16.0 kcal/mol), slightly smaller than that of H(2) addition to the five-coordinate Ru═N.
Anion-Mediated Architecture and Photochromism of Rigid Bipyridinium-Based Coordination Polymers (2016)

Four metal–organic coordination compounds Zn2(bcbp)Cl4 (1), Zn(bcbp)(PO3F) (2), [CdCl(Hbcbp)(bcbp)]·(ClO4)2 (3), and [Cd2(bcbp)4]·(ClO4)·F3 (4) (H2bcbp·2PF6 = 1,1′-bis(4-carboxyphenyl)-(4,4′-bipyridinium) hexafluorophosphate) have been synthesized via a solvothermal method and structurally characterized. Compound 1 is a 1D coordination polymer, while compound 2 shows a 2D + 2D → 3D inclined polycatenation structure. In the case of compound 3, due to the capped chlorine atoms and uncoordinated carboxyl of bcbp ligand, it exhibits a 1D T-shaped coordination configuration. Compound 4 is an unprecedented 13-fold interpenetrating structure with huge diamondoid frameworks. Because of the presence of electron-deficient bipyridinium moieties, the photochromic behaviors of these compounds have also been studied. Interestingly, only compounds 1–3 exhibit color changes under light irradiation. The impact of these anions on the photochromic process is discussed.
A multiscale model of thrombus development (2007)

A two-dimensional multiscale model is introduced for studying formation of a thrombus (clot) in a blood vessel. It involves components for modelling viscous, incompressible blood plasma; non-activated and activated platelets; blood cells; activating chemicals; fibrinogen; and vessel walls and their interactions. The macroscale dynamics of the blood flow is described by the continuum Navier-Stokes equations. The microscale interactions between the activated platelets, the platelets and fibrinogen and the platelets and vessel wall are described through an extended stochastic discrete cellular Potts model. The model is tested for robustness with respect to fluctuations of basic parameters. Simulation results demonstrate the development of an inhomogeneous internal structure of the thrombus, which is confirmed by the preliminary experimental data. We also make predictions about different stages in thrombus development, which can be tested experimentally and suggest specific experiments. Lastly, we demonstrate that the dependence of the thrombus size on the blood flow rate in simulations is close to the one observed experimentally.
Somatomedin Activity in Sera of Genetically Small Mice (1980)

Somatomedin activity as determined by the stimulation of [3H]thymidine incorporation into chick embryo fibroblast DNA, was measured in extracts of sera from genetically small mice. Somatomedin activity was low in the sera from growth hormone deficient mice [Snell (dw/dw), Ames (df/df), and little (lit/lit)] whereas somatomedin activity was normal in serum from the pygmy (pg/pg)) mouse, a mutant proposed as a model for growth hormone resistance. GH treatment of the Snell mouse resulted in an increase in somatomedin activity to normal levels.
P2P resource pool and its application to optimize wide-area application level multicasting (2004)

The concept of resource pool has a very long history. Propelled by the need to share CPU cycles of supercomputers for highthroughput computing jobs from the scientific community, the vision is most recently explored by the advocates of Grid. On the other hand, the advent of P2P researches has demonstrated the feasibility of integrating potentially unlimited amount of less powerful machines around the world. Organizing a P2P resource pool thus becomes an interesting research topic. This paper attempts to address two problems. The first is how to organize a P2P resource pool, and our answer is to combine the self-organizing strength of P2P DHT with an in-system, selfscaling monitoring infrastructure that is layered on top of DHT. The second question is the utility of the P2P resource pool for interesting applications. And we choose to showcase its power by optimizing wide-area application level multicasting (ALM), a problem far more challenging and interesting than conventional tasks such as massively parallel computation. We show that utilizing spare resources in the pool results in significant savings for single ALM session. Furthermore, we adopt a purely market-driven approach to optimize multiple concurrent sessions. As expected, sessions of higher priority are given higher share of resources.
La utilización del ordenador como ayuda para la enseñanza y aprendizaje de la escritura : estudio de caso (1995)

EL OBJETIVO DE ESTA TESIS ES EL ESTUDIO DESCRIPTIVO-ANALITICO DE LA UTILIZACION QUE SE HIZO DEL ORDENADOR COMO AYUDA PARA LA ENSENANZA Y APRENDIZAJE DE LA ESCRITURA EN UN AULA DE EDUCACION INFANTIL CON NINOS DE CINCO ANOS. PARA ELLO SE ESTUDIA EL CONTEXTO DEL AULA, PRESTANDO ESPECIAL ATENCION A LA ORGANIZACION DEL AULA, DE LAS TAREAS, ASI COMO A LA FORMA DE ABORDAR LA ENSENANZA DE LA ESCRITURA POR PARTE DE LA MAESTRA. SE HACE UN ANALISIS DETALLADO DE LA ESCRITURA DE LOS NINOS EN EL ORDENADOR, Y SE MUESTRA SU DESARROLLO EN EL TIEMPO. LOS PROGRAMAS QUE SE UTILIZARON FUERON SERIES DE COLORES Y ESCRIBO, DISTRIBUIDOS POR EL PROYECTO ATENEA. EN LAS CONCLUSIONES SE ESPECIFICAN LAS PRINCIPALES APORTACIONES DEL ORDENADOR PARA LA ESCRITURA, ASI COMO LAS APORTACIONES DE UNA METODOLOGIA DE INVESTIGACION -ESTUDIO DE CASO- QUE SE LLEVO A CABO DE FORMA COLABORATIVA.
TREC-3 Ad-Hoc, Routing Retrieval and Thresholding Experiments using PIRCS. (1994)

The PIRCS retrieval system has been upgraded in TREC-3 to handle the full English collections of 2 GB in an efficient manner. For ad-hoc retrieval, we use recurrent spreading of activation in our network to implement query learning and expansion based on the best-ranked subdocuments of an initial retrieval. We also augment our standard retrieval algorithm with a soft-Boolean component. For routing, we use learning from signal-rich short documents or subdocument segments. For the optional thresholding experiment, we tried two approaches to transforming retrieval status values (RSV&apos;s) so that they could be used to partition documents into retrieved and nonretrieved sets. The first method normalizes RSV&apos;s using a query self-retrieval score. The second, which requires training data, uses logistic regression to convert RSV&apos;s into estimates of probability of relevance. Overall, our results are highly competitive with those of other participants. 1. INTRODUCTION PIRCS is an experimental info...
Flexible fiber/wire-shaped solar cells in progress: properties, materials, and designs (2015)

Development of various fiber/wire-shaped solar cells, conventional materials, device properties, innovative designs, and integrated power systems is reviewed.
Outbreak Management and Implications of a Nosocomial Norovirus Outbreak (2007)

The significant disruption of patient care and cost of this single nosocomial outbreak support aggressive efforts to prevent transmission of noroviruses in health care settings.
HEAD GESTURES, GAZE AND THE PRINCIPLES OF CONVERSATIONAL STRUCTURE (2006)

Much of the work on embodied conversational agents is concerned with building computational models of nonverbal behaviors that can generate the right behavior in the appropriate context. In this paper, we discuss, from a linguistic and a conversation theoretic point of view, how nonverbal behaviors in conversations work. We look particularly at gaze and head movements. These play a variety of functions in face-to-face interactions. We show how these functions are structured by general principles governing cooperative actions and symbolic communication.
A low power, low noise, 1.8 GHz voltage-controlled oscillator (1997)

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1997.
Characterization of a glycoprotein alpha-galactosidase from lentil seeds (Lens culinaris). (1983)

alpha-Galactosidase (alpha-D-galactoside galactohydrolase, EC 3.2.1.22), an enzyme responsible for mobilizing the raffinose family of oligosaccharides in legume seeds, has been isolated from lentils (Lens culinaris) and purified about 4,000-fold. The Sephadex gel filtration profile showed the presence of two forms of the enzyme, alpha-galactosidase I with an apparent Mr = 160,000 and alpha-galactosidase II of Mr = 40,000. Enzyme II readily aggregates to form I when any attempt is made to concentrate the solution. Thus, only enzyme I was purified and its properties studied. The multistep purification procedure included affinity binding of the enzyme to concanavalin A-Sepharose, indicating its glycoprotein nature with glucose/mannose termini of the carbohydrate moieties. The amino acid and carbohydrate compositions of the native enzyme and that of the glycopeptide obtained from pronase-digested, denatured enzyme have been determined. Asparagine seems to be involved in forming the linkage with the carbohydrate moiety. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of enzyme I shows a single protein band with Mr = 40,000 which also stains with periodic acid-Schiff reagent. Thus, the enzyme consists of four identical glycoprotein subunits. The isoelectric point of the enzyme is 8.0. The pH optima of enzyme I and II are 6.1 and 4.7, respectively. The substrate specificity and the mode of substrate inhibition of enzyme I is discussed. The effect of temperature on Vmax and Km of the enzyme is presented; at pH 6.1 the energy of activation is 62.1 kJ/mol and the delta H value is -34.3 kJ/mol in the temperature range 20-50 degrees C. Preliminary studies show that enzyme I possesses hemagglutinating properties with glucose/mannose specificity.
Early Mitochondrial Dysfunction in Long-lived Mclk1+/- Mice (2008)

Reduced activity of CLK-1/MCLK1 (also known as COQ7), a mitochondrial enzyme that is necessary for ubiquinone biosynthesis, prolongs the lifespan of nematodes and mice by a mechanism that is distinct from that of the insulin signaling pathway. Here we show that 2-fold reduction of MCLK1 expression in mice reveals an additional function for the protein, as this level of reduction does not affect ubiquinone levels yet affects mitochondrial function substantially. Indeed, we observe that the phenotype of young Mclk1(+/-) mutants includes a severe reduction of mitochondrial electron transport, ATP synthesis, and total nicotinamide adenine dinucleotide (NAD(tot)) pool size as well as an alteration in the activity of key enzymes of the tricarboxylic acid cycle. Surprisingly, we also find that Mclk1 heterozygosity leads to a dramatic increase in mitochondrial oxidative stress by a variety of measures. Furthermore, we find that the mitochondrial dysfunction is accompanied by a decrease in oxidative damage to cytosolic proteins as well as by a decrease in plasma isoprostanes, a systemic biomarker of oxidative stress and aging. We propose a mechanism for the conjunction of low ATP levels, high mitochondrial oxidative stress, and low non-mitochondrial oxidative damage in a long-lived mutant. Our model helps to clarify the relationship between energy metabolism and the aging process and suggests the need for a reformulation of the mitochondrial oxidative stress theory of aging.
Toxicity of Topical Antifungal Agents to Stratified Human Cultivated Corneal Epithelial Sheets (2014)

Topical micafungin and voriconazole appeared to be the least toxic to the corneal epithelium. Drug prescription should consider not only fungal species and susceptibility but also ocular toxicity and stage of treatment.
Network Synchrony in the Nucleus Accumbens<i>In Vivo</i> (2001)

Nucleus accumbens neurons show membrane potential fluctuations between a very negative resting membrane potential and periodical plateau depolarizations. Because action potential firing occurs only during the depolarized state, the control of transitions between states is important for information processing within this region, with an impact on accumbens-related behaviors. It has been proposed that ensembles of active neurons in the nucleus accumbens could be based on a population of cells depolarizing simultaneously into the UP state. In this study, in vivo intracellular recordings from accumbens neurons were performed simultaneously with local field potential recordings to examine whether the nucleus accumbens can exhibit synchronization of membrane potential states in a population of neurons. These simultaneous recordings indicated that local field potential shifts occurred synchronously with transitions to the UP state. Furthermore, manipulations that evoked prolonged plateau depolarizations also evoked field potentials of similar duration. Such signals likely occurred because of simultaneous membrane potential changes in a population of neurons. Together with our previous studies, these results suggest that membrane potential states in the nucleus accumbens can be synchronized by synaptic inputs from the hippocampus.
Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes (2013)

Genome-wide gene-expression studies have shown that hundreds of yeast genes are induced or repressed transiently by changes in temperature; many are annotated to stress response on this basis. To obtain a genome-scale assessment of which genes are functionally important for innate and/or acquired thermotolerance, we combined the use of a barcoded pool of ~4,800 nonessential, prototrophic Saccharomyces cerevisiae deletion strains with Illumina-based deep-sequencing technology. As reported in other recent studies that have used deletion mutants to study stress responses, we observed that gene deletions resulting in the highest thermosensitivity generally are not the same as those transcriptionally induced in response to heat stress. Functional analysis of identified genes revealed that metabolism, cellular signaling, and chromatin regulation play roles in regulating thermotolerance and in acquired thermotolerance. However, for most of the genes identified, the molecular mechanism behind this action remains unclear. In fact, a large fraction of identified genes are annotated as having unknown functions, further underscoring our incomplete understanding of the response to heat shock. We suggest that survival after heat shock depends on a small number of genes that function in assessing the metabolic health of the cell and/or regulate its growth in a changing environment.