Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of Cyclic AMP Production by Signal Transduction Pathways in Preglomerular Microvessels and Microvascular Smooth Muscle Cells

Cyclic AMP affects microvascular smooth muscle contraction and growth. Therefore, it is important to elucidate mechanisms regulating cyclic AMP production in microvascular smooth muscle. In this study, we determined whether several signal transduction pathways regulate receptor-induced cyclic AMP in isolated preglomerular microvessels and microvascular smooth muscle cells. Preglomerular microvessels were incubated with isoproterenol (β-adrenoceptor agonist) and with and without U73122 (phospholipase C inhibitor), GF109203X (protein kinase C inhibitor), 1-butanol (phospholipase D inhibitor), CGP77675 (c-src inhibitor), HA1077 (Rho kinase inhibitor), Y27632 (Rho kinase inhibitor), LY294002 (phosphatidylinositol-3-kinase inhibitor), dipenyleneiodonium (NADPH oxidase inhibitor), or Tempol (superoxide dismutase mimetic). Cultured preglomerular microvascular smooth muscle cells were incubated with isoproterenol or forskolin (direct activator of adenylyl cyclase) and with or without U73122, C2-ceramide (phospholipase D inhibitor), or PP1 [src family inhibitor, 1-(1,1-dimethylethyl)-1-(4-methylphenyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine]. All studies were conducted with 3-isobutyl-1-methylxanthine (broad-spectrum phosphodiesterase inhibitor) to eliminate changes in cyclic AMP degradation. In microvessels isoproterenol-induced cyclic AMP was not affected by Y27632, HA1007, LY294002, dipenylene-iodonium, or Tempol; was increased by U73122 and GF109203X; and was decreased by 1-butanol and CGP77675. In cells, U73122 increased and C2-ceramide and PP1 decreased isoproterenol-induced cyclic AMP. Forskolin-induced cyclic AMP was not altered. These results indicate that receptor-mediated activation of adenylyl cyclase is 1) not modulated by Rho kinase, phosphatidylinositol-3-kinase, NADPH oxidase, or superoxide; 2) is attenuated by phospholipase C and protein kinase C; and 3) is augmented by phospholipase D and src. Phospholipase C, phospholipase D, and src modulate receptor-induced cyclic AMP by affecting β-adrenoreceptor/G protein/adenylyl cyclase coupling rather than by directly affecting adenylyl cyclase activity.
Decomposing Volume for VWAP Strategies

In this paper, we present a new methodology for modeling intraday volume which allows fora significant reduction in the Volume Weighted Average Price (VWAP) on orders risk. Theresults are obtained for the all stocks included in the CAC40 index at the beginning ofSeptember 2004. The idea of considered models is based on the decomposition of tradedvolume into two parts: one reflects volume changes due to market evolutions, the second onedescribes the stock specific volume pattern. The dynamics of the specific part of volume isdepicted by ARMA, and SETAR models.
Postselected versus nonpostselected quantum teleportation using parametric down-conversion

We study the experimental realisation of quantum teleportation as performed by Bouwmeester {\em et al}. [Nature {\bf 390}, 575 (1997)] and the adjustments to it suggested by Braunstein and Kimble [Nature {\bf 394}, 841 (1998)]. These suggestions include the employment of a detector cascade and a relative slow-down of one of the two down-converters. We show that coincidences between photon-pairs from parametric down-conversion automatically probe the non-Poissonian structure of these sources. Furthermore, we find that detector cascading is of limited use, and that modifying the relative strengths of the down-conversion efficiencies will increase the time of the experiment to the order of weeks. Our analysis therefore points to the benefits of single-photon detectors in non-post-selected type experiments, a technology currently requiring roughly $6^{\circ}$K operating conditions.
Title: Shifted Encoding Strategy in Retinal Luminance Adaptation: from Firing Rate to Neural Correlation Running Title: Information Encoding during Adaptation

Title: Shifted encoding strategy in retinal luminance adaptation: from firing rate 1 to neural correlation 2 Running title: Information encoding during adaptation 3 Authors: Lei Xiao, Mingsha Zhang, Dajun Xing, Pei-Ji Liang and Si Wu 4 Affiliations: 5 Department of Biomedical Engineering, Shanghai Jiao Tong University, 800 6 Dong Chuan Road, Shanghai 200240, China. 7 Institute of Neuroscience, Chinese Academy of Science, 320 Yue Yang Road, 8 Shanghai 200031, China. 9 Center for Neural Science, New York University, New York 10003,USA 10 State Key Laboratory of Cognitive Neuroscience and Learning & 11 IDG/McGovern Institute for Brain Research, Beijing Normal University, Beijing 12 100875, China. 13 Correspondence: 14 Si Wu, Dr. 15 State Key Laboratory of Cognitive Neuroscience & Learning 16 Beijing Normal University 17 19 Xinjiekouwai Street, Beijing 100875, China 18 Phone: +86-010-58804004 19 Email: wusi@bnu.edu. cn 20 21 22 Articles in PresS. J Neurophysiol (July 17, 2013). doi:10.1152/jn.00221. 2013
Increase in plasma β endorphins precedes vasodepressor syncope

SIR,-Galatius-Jensen and colleagues' chose to monitor the arterial saturation and the electrocardiogram on days two to six after acute myocardial infarction (AMI). It is not clear why they did not study changes in the first 24 hours. We have communicated with all coronary care units in the UK and found that few prescribe oxygen in the first 24 hours and none routinely measures oxygen saturation. In a pilot study we also have found a high incidence of hypoxaemia in these patients (83% of those who did not receive oxygen) but we studied this in the initial 24 hours after admission with AMI.2 We have subsequently repeated our study with synchronous measurement of the ST segment and arrhythmia analysis using 24 hour Holter monitoring during the first 24 hours after admission. After studying 50 patients (25 received supplemental oxygen and 25 did not) we found hypoxaemia (Spo2 < 90%) in 43% of all patients-in 18% of those who received oxygen supplementation and in 68% of those who did not. There was severe hypoxaemia (Spo2 < 80%) in 16% of patients and 86% of these were in the group that did not receive supplemental oxygen. Because in an earlier study there was a good correlation between the incidence of hypoxaemia and opiates and because hypoxaemia was reversed with oxygen3 we attribute the high incidence of hypoxaemia to the use of opiates for analgesia immediately after AMI. Unlike Galatius-Jensen and colleagues we found no association between arrhythmia and the timing, incidence, or degree of hypoxaemia. Like them we did find a patient whose ST segment changes exactly corresponded with reciprocal changes in oxygen saturation and therefore we conclude that hypoxaemia may influence the degree of ischaemia. As in our original pilot study we again conclude that all patients who have had an AMI should be monitored with a pulse oximeter and that hypoxaemia should be treated appropriately. A T WILSON K S CHANNER Cardiology Department, Royal Hallamshire Hospital, Sheffield
Should Central Banks Really Be Flexible?

In this paper I show that central bank flexibility may not be desirable when it encourages trade unions to behave more aggressively. The argument is based on a model where risk averse trade unions interact with a central bank. A flexible central bank stabilizes economic shocks and reduces output volatility. This enables trade unions to realize higher real wages without risking the unemployment of some insider workers. Risk averse insiders demand higher real wages, generate more inflation and more unemployment. The overall e ect on welfare may be negative. A conservative central bank instead increases output and employment on average but raises output volatility. The argument also sheds new light on the issue of optimum currency areas. Wage claims are lower and employment is higher in a currency union if national trade unions expect the central bank to do less to secure employment of insider workers in their country. JEL Classification: E52, E58
Zero-gradient-sum algorithms for distributed convex optimization: The continuous-time case

This paper presents a family of continuous-time distributed algorithms called Zero-Gradient-Sum (ZGS) algorithms, which solve unconstrained, separable, convex optimization problems over undirected networks with fixed topologies. The ZGS algorithms are derived using a Lyapunov function candidate that exploits convexity, and get their name from the fact that they yield nonlinear networked dynamical systems whose states slide along an invariant, zero-gradient-sum manifold and converge asymptotically to the unknown minimizer. We also present a systematic way to construct ZGS algorithms, show that a subset of them converge exponentially, and obtain lower bounds on their convergence rates in terms of the convexity characteristics of the problem and the network topology, including its algebraic connectivity. Finally, we show that some of the well-studied continuous-time distributed consensus algorithms are special cases of ZGS algorithms and discuss the ramifications.
Epistemological and theoretical challenges for studying power and politics in information systems

Abstract. The study of the role of power in managing information systems (IS) still offers a major epistemological challenge to researchers in the field. Although significant work has been done, there is yet to emerge a research approach that permits a penetrating study of the phenomenon of power by virtue of adopting a Machiavellian stance. This paper proposes such an approach in the form of an interpretivist position combined with a theoretical framework whose origin lies in political science and the sociology of technology. In developing its philosophical argument, the paper compares three meta‐theories that have been applied to study IS: Phenomenology, Critical Theory and Structuration Theory. All three are compared in terms of their epistemological position regarding the relationship between power and IS. We argue that, although enlightening, those meta‐theories fail to unravel the hidden and strategic nature of power. The paper concludes by proposing a particular theoretical formulation that, rather than censoring power and politics, will provide the epistemological means for unravelling them.
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia

MOTIVATION DNA microarrays are routinely applied to study diseased or drug-treated cell populations. A critical challenge is distinguishing the genes directly affected by these perturbations from the hundreds of genes that are indirectly affected. Here, we developed a sparse simultaneous equation model (SSEM) of mRNA expression data and applied Lasso regression to estimate the model parameters, thus constructing a network model of gene interaction effects. This inferred network model was then used to filter data from a given experimental condition of interest and predict the genes directly targeted by that perturbation. RESULTS Our proposed SSEM-Lasso method demonstrated substantial improvement in sensitivity compared with other tested methods for predicting the targets of perturbations in both simulated datasets and microarray compendia. In simulated data, for two different network types, and over a wide range of signal-to-noise ratios, our algorithm demonstrated a 167% increase in sensitivity on average for the top 100 ranked genes, compared with the next best method. Our method also performed well in identifying targets of genetic perturbations in microarray compendia, with up to a 24% improvement in sensitivity on average for the top 100 ranked genes. The overall performance of our network-filtering method shows promise for identifying the direct targets of genetic dysregulation in cancer and disease from expression profiles. AVAILABILITY Microarray data are available at the Many Microbe Microarrays Database (M3D, http://m3d.bu.edu). Algorithm scripts are available at the Gardner Lab website (http://gardnerlab.bu.edu/SSEMLasso).
Narrations and Storytelling as Methodological Key Elements for Studying User Experience

INTRODUCTION User Experience (UX) is a topic that overcomes barriers between various research domains in its quest to define what constitutes a positive experience. The field of Human Computer Interaction is deeply multidisciplinary; the concept of UX tends to even increase this already fuzzy domain of HCI and bringing even more approaches together. This also had the consequence that people from as many backgrounds as the domain itself tried and try to understand and explain the concept of UX, resulting in a variety of interpretations, expressions and frameworks that focus on specific parts of the user experience.
Enhanced alcohol self-administration and reinstatement in a highly impulsive, inattentive recombinant inbred mouse strain

Deficits in executive control have frequently been associated with alcohol use disorder. Here we investigated to what extent pre-existing genetically encoded levels of impulsive/inattentive behavior associate with motivation to take alcohol and vulnerability to cue-induced reinstatement of alcohol seeking in an operant self-administration paradigm. We took advantage of BXD16, a recombinant inbred strain previously shown to have enhanced impulsivity and poor attentional control. We compared BXD16 with C57BL/6J mice in a simple choice reaction time task (SCRTT) and confirmed its impulsive/inattentive phenotype. BXD16 mice were less active in a novel open field (OF), and were equally active in an automated home cage environment, showing that increased impulsive responding of BXD16 mice could not be explained by enhanced general activity compared to C57BL/6J mice. After training in a sucrose/alcohol fading self-administration procedure, BXD16 showed increased motivation to earn 10% alcohol solution, both under fixed ratio (FR1) and progressive ratio (PR2) schedules of reinforcement. Responding on the active lever readily decreased during extinction training with no apparent differences between strains. However, upon re-exposure to alcohol-associated cues, alcohol seeking was reinstated to a larger extent in BXD16 than in C57BL/6J mice. Although further studies are needed to determine whether impulsivity/inattention and alcohol seeking depend on common or separate genetic loci, these data show that in mice enhanced impulsivity coincides with increased motivation to take alcohol, as well as relapse vulnerability.
A Novel Framework for Nominal Entity Recognition

The re-ranking algorithm is a common method to use the results of subsequent stages, such as coreference resolution, to improve entity recognition. The nature of re-ranking is to select the most possible candidate from the entire candidate set. But if all of the candidates are incorrect, this method still can not give a right result. We propose a two-layer model to utilize the results of subsequent stages. This novel framework is able to overcome the disadvantage of re-ranking method, and correct the errors introduced by the first tagging. The experiments on the ACE2004 Chinese corpus show that the proposed framework are more effective than re-ranking method.
Cutsets in Infinite Graphs

We answer three questions posed in a paper by Babson and Benjamini. They introduced a parameter $C_G$ for Cayley graphs $G$ that has significant application to percolation. For a minimal cutset of $G$ and a partition of this cutset into two classes, take the minimal distance between the two classes. The supremum of this number over all minimal cutsets and all partitions is $C_G$. We show that if it is finite for some Cayley graph of the group then it is finite for any (finitely generated) Cayley graph. Having an exponential bound for the number of minimal cutsets of size $n$ separating $o$ from infinity also turns out to be independent of the Cayley graph chosen. We show a 1-ended example (the lamplighter group), where $C_G$ is infinite. Finally, we give a new proof for a question of de la Harpe, proving that the number of $n$-element cutsets separating $o$ from infinity is finite unless $G$ is a finite extension of $\mathbb{Z}$.
The Dynamics of Homologous Pairing during Mating Type Interconversion in Budding Yeast

Cells repair most double-strand breaks (DSBs) that arise during replication or by environmental insults through homologous recombination, a high-fidelity process critical for maintenance of genomic integrity. However, neither the detailed mechanism of homologous recombination nor the specific roles of critical components of the recombination machinery—such as Bloom and Werner syndrome proteins—have been resolved. We have taken a novel approach to examining the mechanism of homologous recombination by tracking both a DSB and the template from which it is repaired during the repair process in individual yeast cells. The two loci were labeled with arrays of DNA binding sites and visualized in live cells expressing green fluorescent protein–DNA binding protein chimeras. Following induction of an endonuclease that introduces a DSB next to one of the marked loci, live cells were imaged repeatedly to determine the relative positions of the DSB and the template locus. We found a significant increase in persistent associations between donor and recipient loci following formation of the DSB, demonstrating DSB-induced pairing between donor and template. However, such associations were transient and occurred repeatedly in every cell, a result not predicted from previous studies on populations of cells. Moreover, these associations were absent in sgs1 or srs2 mutants, yeast homologs of the Bloom and Werner syndrome genes, but were enhanced in a rad54 mutant, whose protein product promotes efficient strand exchange in vitro. Our results indicate that a DSB makes multiple and reversible contacts with a template during the repair process, suggesting that repair could involve interactions with multiple templates, potentially creating novel combinations of sequences at the repair site. Our results further suggest that both Sgs1 and Srs2 are required for efficient completion of recombination and that Rad54 may serve to dissociate such interactions. Finally, these results demonstrate that mechanistic insights into recombination not accessible from studies of populations of cells emerge from observations of individual cells.
Learning Word Importance with the Neural Bag-of-Words Model

The Neural Bag-of-Words (NBOW) model performs classification with an average of the input word vectors and achieves an impressive performance. While the NBOW model learns word vectors targeted for the classification task it does not explicitly model which words are important for given task. In this paper we propose an improved NBOW model with this ability to learn task specific word importance weights. The word importance weights are learned by introducing a new weighted sum composition of the word vectors. With experiments on standard topic and sentiment classification tasks, we show that (a) our proposed model learns meaningful word importance for a given task (b) our model gives best accuracies among the BOW approaches. We also show that the learned word importance weights are comparable to tf-idf based word weights when used as features in a BOWSVM classifier.
1 / 1 A probabilistic method for identifying sex-linked genes using RNA-seq-derived genotyping data

workflow. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was. doi: bioRxiv preprint first posted online Jul. 27, 2015;. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was. doi: bioRxiv preprint first posted online Jul. 27, 2015;. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was. doi: bioRxiv preprint first posted online Jul. 27, 2015;. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was. doi: bioRxiv preprint first posted online Jul. 27, 2015;. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was. doi: bioRxiv preprint first posted online Jul. 27, 2015;. CC-BY-NC-ND 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was. Abstract The genetic basis of sex determination remains unknown for the vast majority of organisms with separate sexes. A key question is whether a species has sex chromosomes (SC). SC presence indicates genetic sex determination, and their sequencing may help identifying the sex-determining genes and understanding the molecular mechanisms of sex determination. Identifying SC, especially homomorphic SC, can be difficult. Sequencing SC is also very challenging, in particular the repeat-rich non-recombining regions. A novel approach for identifying sex-linked genes and SC consisting of using RNA-seq to genotype male and female individuals and study sex-linkage has recently been proposed. This approach entails a modest sequencing effort and does not require prior genomic or genetic resources, and is thus particularly suited to study non-model organisms. Applying this approach to many organisms is, however, difficult due to the lack of an appropriate statistically-grounded pipeline to analyse the data. Here we propose a model-based method to infer sex-linkage using a maximum likelihood framework and genotyping data from a full-sib family, which can be obtained for most organisms that can be grown in the lab and for economically important animals/plants. Our method works on any type of SC (XY, ZW, UV) and has been embedded in a pipeline that includes a genotyper specifically developed for RNA-seq data. Validation on empirical and …
Improving Image-Based Visual Servoing with Three-Dimensional Features

Neither of the classical visual servoing approaches, position-based and image-based, are completely satisfactory. In position-based visual servoing the trajectory of the robot is well stated, but the approach suffers mainly from the image features going out of the visual field of the cameras. On the other hand, image-based visual servoing has been found generally satisfactory and robust in the presence of camera and hand-eye calibration errors. However, in some cases, singularities and local minima may arise, and the robot can go further from its joint limits. This paper is a step towards the synthesis of both approaches with their particular advantages, i.e., the trajectory of the camera motion is predictable and the image features remain in the field of view of the camera. The basis is the introduction of three-dimensional information in the feature vector. Point depth and object pose produce useful behavior in the control of the camera. Using the task-function approach, we demonstrate the relationship between the velocity screw of the camera and the current and desired poses of the object in the camera frame. Camera calibration is assumed, at least coarsely. Experimental results on real robotic platforms illustrate the presented approach.
Novel dual-pulse actuation voltage for longer MEMS switch lifetime

A novel dual-pulse actuation voltage has been proposed to reduce dielectric charging in micro-electromechanical system (MEMS) switch, leading to a longer switch lifetime. Mathematical and transient circuit models have been utilized to simulate dielectric charging in the RF MEMS switch, enabling the analysis of charge built-up at the switch dielectric and substrate brought about by the actuation voltage curve used. The proposed dual pulse actuation signal has shown to improve the lifetime of the RF MEMS switch as it minimizes the charge built-up.