Miracle-dz/UniFAR-FTUs huggingface dataset:
Changes in microtubule polarity orientation during the development of hippocampal neurons in culture

Microtubules in the dendrites of cultured hippocampal neurons are of nonuniform polarity orientation. About half of the microtubules have their plus ends oriented distal to the cell body, and the other half have their minus ends distal; in contrast, microtubules in the axon are of uniform polarity orientation, all having their plus ends distal (Baas, P.W., J.S. Deitch, M. M. Black, and G. A. Banker. 1988. Proc. Natl. Acad. Sci. USA. 85:8335-8339). Here we describe the developmental changes that give rise to the distinct microtubule patterns of axons and dendrites. Cultured hippocampal neurons initially extend several short processes, any one of which can apparently become the axon (Dotti, C. G., and G. A. Banker. 1987. Nature [Lond.]. 330:477-479). A few days after the axon has begun its rapid growth, the remaining processes differentiate into dendrites (Dotti, C. G., C. A. Sullivan, and G. A. Banker. 1988. J. Neurosci. 8:1454-1468). The polarity orientation of the microtubules in all of the initial processes is uniform, with plus ends distal to the cell body, even through most of these processes will become dendrites. This uniform microtubule polarity orientation is maintained in the axon at all stages of its growth. The polarity orientation of the microtubules in the other processes remains uniform until they begin to grow and acquire the morphological characteristics of dendrites. It is during this period that microtubules with minus ends distal to the cell body first appear in these processes. The proportion of minus end-distal microtubules gradually increases until, by 7 d in culture, about equal numbers of dendritic microtubules are oriented in each direction. Thus, the establishment of regional differences in microtubule polarity orientation occurs after the initial polarization of the neuron and is temporally correlated with the differentiation of the dendrites.
Strategic reasoning about bundling in swarming systems

The objects of study of this paper are swarming systems, a special kind of peer-to-peer systems where users interested in the same content at the same time cooperate with each other. In particular, we consider the problem of how to combine files into bundles in such systems. First, we analyze the case of a monopoly where a single publisher decides how to aggregate its files so as to satisfy user demands while mitigating its serving costs. We establish conditions for the existence and uniqueness of an equilibrium and how the publisher's bundling strategy affects its profit. Then, we consider the competitive case where bundling decisions of one publisher affect the outcome of other publishers. Using normal form games we analyze the impact of different system parameters on the Nash equilibrium.
Ordering Gene Expression Data Using One-dimensional Self-Organizing Maps

The microarray technology allows researchers to simultaneously measure gene expression levels of thousands of genes. Analysis of data produced by such experiments provides knowledge about the gene function. An important step in the analysis of gene expression data is the detection of genes with similar expression patterns. Real-time computational tools for organization and visualization are crucial to understand and analyze the data. In this work, we make use of an algorithm based on self-organizing neural networks for organizing gene expression data in order to reveal trends in gene expression profiles under the biological viewpoint.
A model-based online mechanism with pre-commitment and its application to electric vehicle charging

We introduce a novel online mechanism that schedules the allocation of an expiring and continuously-produced resource to self-interested agents with private preferences. A key application of our mechanism is the charging of pure electric vehicles, where owners arrive dynamically over time, and each owner requires a minimum amount of charge by its departure to complete its next trip. To truthfully elicit the agents' preferences in this setting, we introduce the new concept of pre-commitment: Whenever an agent is selected, our mechanism pre-commits to charging the vehicle by its reported departure time, but maintains flexibility about when the charging takes place and at what rate. Furthermore, to make effective allocation decisions we use a model-based approach by modifying Consensus, a well-known online optimisation algorithm. We show that our pre-commitment mechanism with modified Consensus incentivises truthful reporting. Furthermore, through simulations based on real-world data, we show empirically that the average utility achieved by our mechanism is 93% or more of the offline optimal.
Finding Optimal Solutions to Cooperative Pathfinding Problems

In cooperative pathfinding problems, non-interfering paths that bring each agent from its current state to its goal state must be planned for multiple agents. We present the first practical, admissible, and complete algorithm for solving problems of this kind. First, we propose a technique called operator decomposition, which can be used to reduce the branching factors of many search algorithms, including algorithms for cooperative pathfinding. We then show how a type of independence common in instances of cooperative pathfinding problems can be exploited. Next, we take the idea of exploiting independent subproblems further by adding improvements that allow the algorithm to recognize many more cases of such independence. Finally, we show empirically that these techniques drastically improve the performance of the standard admissible algorithm for the cooperative pathfinding problem, and that their combination results in a complete algorithm capable of optimally solving relatively large problems in milliseconds.
Depolarization of rat basophilic leukemia cells inhibits calcium uptake and exocytosis

We have investigated the unusual observation that depolarization of rat basophilic leukemia cells in high potassium not only fails to induce secretion, but also inhibits the secretion induced when receptors for IgE are aggregated by antigen. Antigen-stimulated 45Ca uptake and the rise in cytoplasmic free ionized calcium measured with the fluorescent indicator quin2 were both inhibited in depolarized cells. 45Ca efflux, on the other hand, was unaffected, which confirms that IgE receptor activation was not impaired in high potassium. Unlike the large increase in total cell calcium seen when cells in normal saline solution were stimulated with antigen, there was a decrease in total cell calcium when depolarized cells were stimulated. This is consistent with our finding that 45Ca uptake was inhibited while 45Ca efflux was unaffected. Inhibition of 45Ca uptake and secretion closely paralleled the decrease in membrane potential, and could be overcome by increasing the extracellular calcium concentration. We conclude that changes in the electrochemical gradient for calcium are important in determining calcium influx and the magnitude of antigen-stimulated secretion from rat basophilic leukemia cells, while the release of calcium from intracellular stores is unaffected.
A Pedestrian Detection Method Using Background Modeling and Object Proposal

As the technique of pedestrian detection has been used in a wide application, the methods of background modeling and object proposal become one of the popular research projects in the field of computer vision. In this article, we review some common methods of background modeling and object proposal, we also analyze basic targets in object proposal and clarify the strength and weakness of these methods. To avoid some disadvantages of common methods particularly low computational efficiency or poor localization quality, we put forward a method combined with Gaussian Mixture Model for background modeling and BING++ (Binarized Normed Gradients for Objectness Estimation) for object proposal for adaptive efficiency in more complex conditions. Finally, we evaluate our method by precision and recall for the localization, and make comparisons of results processed by BING and BING++. It is observed that the detection recall and mean average best overlap of the proposals processed by BING++ is higher than BING, and just with little more time as cost. In sum, BING++ can supple higher localization quality. Respectively, GMM can make detection more adaptive as well as flexible and BING++ can achieve comparable performance in the simulation of pedestrian detection.
Impact of an Intensivist-Led Multidisciplinary Extended Rapid Response Team on Hospital-Wide Cardiopulmonary Arrests and Mortality*

Objective:The effectiveness of rapid response teams remains controversial. However, many studied rapid response teams were not intensivist-led, had limited involvement beyond the initial activations, and did not provide post-ICU follow-up. The objective of this study was to examine the impact of implementing an intensivist-led multidisciplinary extended rapid response team on hospital-wide cardiopulmonary arrests and mortality. Design:This was a pre-post rapid response team implementation study. Setting:Tertiary care academic center in Saudi Arabia. Patients:A total of 98,391 patients in the 2-yr pre-rapid response team and 157,804 patients in the 3-yr post-rapid response team implementation were evaluated. Intervention:The rapid response team was activated by any health care provider based on pre-defined criteria and a four-member intensivist-led multidisciplinary rapid response team responded to provide the necessary management and disposition. The rapid response team function was extended to provide follow-up until clinical stabilization. In addition, the rapid response team provided a mandatory post-ICU follow-up for a minimum of 48 hrs. Measurements and Main Results:The primary outcomes were cardiopulmonary arrests and mortality. After rapid response team implementation, non-ICU cardiopulmonary arrests decreased from 1.4 to 0.9 per 1,000 hospital admissions (relative risk, 0.68; 95% confidence interval, 0.53–0.86; p = 0.001) and total hospital mortality decreased from 22.5 to 20.2 per 1,000 hospital admissions (relative risk, 0.90; 95% confidence interval, 0.85–0.95; p < 0.0001). For patients who required admission to the ICU, there was a significant reduction in the Acute Physiology and Chronic Health Evaluation II scores after rapid response team implementation from 29.3 ± 9.3 to 26.9 ± 8.5 (p < 0.0001), with reduction in hospital mortality from 57.4% to 48.7% (relative risk, 0.85; 95% confidence interval, 0.78–0.92; p < 0.0001). Do-not-resuscitate orders for ward referrals increased from 0.7 to 1.7 per 1,000 hospital admissions (relative risk, 2.58; 95% confidence interval, 1.95–3.42; p < 0.0001) and decreased for patients admitted to ICU from the wards from 30.5% to 26.1% (relative risk, 0.86; 95% confidence interval, 0.74–0.99; p = 0.03). Additionally, ICU readmission rate decreased from 18.6 to 14.3 per 100 ICU alive discharges (relative risk, 0.77; 95% confidence interval, 0.66–0.89; p < 0.0001) and post-ICU hospital mortality from 18.2% to 14.8% (relative risk, 0.85; 95% confidence interval, 0.72–0.99; p = 0.04). Conclusion:The implementation of rapid response team was effective in reducing cardiopulmonary arrests and total hospital mortality for ward patients, improving the outcomes of patients who needed ICU admission and reduced readmissions and mortality of patients who were discharged from the ICU.
UMD-TTIC-UW at SemEval-2016 Task 1: Attention-Based Multi-Perspective Convolutional Neural Networks for Textual Similarity Measurement

We describe an attention-based convolutional neural network for the English semantic textual similarity (STS) task in the SemEval2016 competition (Agirre et al., 2016). We develop an attention-based input interaction layer and incorporate it into our multiperspective convolutional neural network (He et al., 2015), using the PARAGRAM-PHRASE word embeddings (Wieting et al., 2016) trained on paraphrase pairs. Without using any sparse features, our final model outperforms the winning entry in STS2015 when evaluated on the STS2015 data.
The ecological validity of the Rey–Osterrieth Complex Figure: Predicting everyday problems in children with neuropsychological disorders

Despite its extensive use, the validity of the Rey Complex Figure in predicting everyday behavioral executive dysfunction displayed by children with various neuropsychological disorders is unknown. The copied figures of 263 children aged 6 to 17 years were rescored using an accuracy approach that measured visuospatial ability and three process approaches developed to measure executive functioning. Controlling for age and IQ, partial correlations between scores derived by all scoring methods and the parent ratings on an executive function inventory were zero. In contrast, all four scoring approaches were associated with parent ratings on questionnaires that indexed children's academic achievement, developmental status, and adaptive ability. The findings suggest that the ecological validity of the Rey Complex Figure for children with various central nervous system disorders is more associated with visual-motor integration skills than executive functioning.
The RING Finger Domain of Varicella-Zoster Virus ORF61p Has E3 Ubiquitin Ligase Activity That Is Essential for Efficient Autoubiquitination and Dispersion of Sp100-Containing Nuclear Bodies

ABSTRACT Varicella zoster virus encodes an immediate-early (IE) protein termed ORF61p that is orthologous to the herpes simplex virus IE protein ICP0. Although these proteins share several functional properties, ORF61p does not fully substitute for ICP0. The greatest region of similarity between these proteins is a RING finger domain. We demonstrate that disruption of the ORF61p RING finger domain by amino acid substitution (Cys19Gly) alters ORF61p intranuclear distribution and abolishes ORF61p-mediated dispersion of Sp100-containing nuclear bodies. In addition, we demonstrate that an intact ORF61p RING finger domain is necessary for E3 ubiquitin ligase activity and is required for autoubiquitination and regulation of protein stability.
WHICH TYPES OF PUBLIC SCHOOL SPENDING ARE MOST EFFECTIVE? NEW EVIDENCE ON THE SCHOOL QUALITY DEBATE

The paper examines students' achievement in standardized math and science tests using the Longitudinal Study of American Youth. Most standard measures of school inputs, such as class size and teacher experience, bear no relation to student achievement. However, computer resources specifically devoted to the given subject are strongly related to student performance. Second, the teacher's field of study in some cases significantly affects outcomes. The hypothesis that public school expenditures are efficiently allocated across types of inputs is rejected. A cost-benefit analysis reveals that too much is being spent on reducing class size relative to spending on classroom computers. JEL Classification Numbers: H52, I21
Element Partition Trees For H-Refined Meshes to Optimize Direct Solver Performance. Part I: Dynamic Programming

Abstract We consider a class of two- and three-dimensional h-refined meshes generated by an adaptive finite element method. We introduce an element partition tree, which controls the execution of the multi-frontal solver algorithm over these refined grids. We propose and study algorithms with polynomial computational cost for the optimization of these element partition trees. The trees provide an ordering for the elimination of unknowns. The algorithms automatically optimize the element partition trees using extensions of dynamic programming. The construction of the trees by the dynamic programming approach is expensive. These generated trees cannot be used in practice, but rather utilized as a learning tool to propose fast heuristic algorithms. In this first part of our paper we focus on the dynamic programming approach, and draw a sketch of the heuristic algorithm. The second part will be devoted to a more detailed analysis of the heuristic algorithm extended for the case of hp-adaptive grids.
Research on visible and near infrared spectral-polarimetric properties of soil polluted by crude oil

Hydrocarbon contaminated soil can impose detrimental effects on forest health and quality of agricultural products. To manage such consequences, oil leak indicators should be detected quickly by monitoring systems. Remote sensing is one of the most suitable techniques for monitoring systems, especially for areas which are uninhabitable and difficulty to access. The most available physical quantities in optical remote sensing domain are the intensity and spectral information obtained by visible or infrared sensors. However, besides the intensity and wavelength, polarization is another primary physical quantity associated with an optical field. During the course of reflecting light-wave, the surface of soil polluted by crude oil will cause polarimetric properties which are related to the nature of itself. Thus, detection of the spectralpolarimetric properties for soil polluted by crude oil has become a new remote sensing monitoring method. In this paper, the multi-angle spectral-polarimetric instrument was used to obtain multi-angle visible and near infrared spectralpolarimetric characteristic data of soil polluted by crude oil. And then, the change rule between polarimetric properties with different affecting factors, such as viewing zenith angle, incidence zenith angle of the light source, relative azimuth angle, waveband of the detector as well as different grain size of soil were discussed, so as to provide a scientific basis for the research on polarization remote sensing for soil polluted by crude oil.
Architecture for a Low Complexity Rate-Adaptive Reed-Solomon Encoder

Multiple error-correcting Reed-Solomon (RS) codes have many practical applications. The complexity of an RS encoder depends on multiplications in the finite field over which the code is defined. We consider a triangular basis for representing the field elements, and present an architecture for a rate-adaptive RS encoder using a triangular basis multiplication algorithm. The architecture supports pipeline and bit-serial operations, and has a low circuit complexity. >
The Role of Abiotic Soil Parameters as a Factor in the Success of Invasive Plant Species

Plant species dispersal has been strongly enhanced by human activities. Introduced species have to cope with indigenous species and local conditions. They may avoid indigenous species by occupying new (abiotic) territory. Once a species is established it may become a pest, and may seriously threaten other species and ecosystems.In this paper we focus on invasive plant species of the Dutch flora. We make two comparisons: (1) Dutch neophytes (i.e. arrived in The Netherlands after 1825) vs. indigenous Dutch flora; and (2) species of the Dutch flora that have become invasive outside Europe vs. non-invasive species of the Dutch flora. We hypothesize that at least part of the success of the invasive or neophyte species is due to their ability to grow under a wider range of abiotic soil circumstances than other species. We regard an invasive species as successful if it is able to disperse from the introduction site(s) and remain present in the invaded vegetation.For ten out of the sixteen abiotic factors there is a wider range for the neophytes: chlorine, potassium, mean highest and lowest groundwater level, phosphorus (and total content) and pH H2O.We hypothesized that part of the success of invasive species may be the adaptation to a variety of abiotic soil parameters. This is indeed the case for a number of the examined parameters, mostly related to nutrient availability and soil pH. This indicates that the success of invasive species is at least partly caused by their ability to grow under a wide range of nutrient availability and soil pH. Their success may therefore be stimulated by the increasing pollution of natural areas by excessive nitrogen.
Neurons and cardiomyocytes derived from induced pluripotent stem cells as a model for mitochondrial defects in Friedreich’s ataxia

SUMMARY Friedreich’s ataxia (FRDA) is a recessive neurodegenerative disorder commonly associated with hypertrophic cardiomyopathy. FRDA is due to expanded GAA repeats within the first intron of the gene encoding frataxin, a conserved mitochondrial protein involved in iron-sulphur cluster biosynthesis. This mutation leads to partial gene silencing and substantial reduction of the frataxin level. To overcome limitations of current cellular models of FRDA, we derived induced pluripotent stem cells (iPSCs) from two FRDA patients and successfully differentiated them into neurons and cardiomyocytes, two affected cell types in FRDA. All FRDA iPSC lines displayed expanded GAA alleles prone to high instability and decreased levels of frataxin, but no biochemical phenotype was observed. Interestingly, both FRDA iPSC-derived neurons and cardiomyocytes exhibited signs of impaired mitochondrial function, with decreased mitochondrial membrane potential and progressive mitochondrial degeneration, respectively. Our data show for the first time that FRDA iPSCs and their neuronal and cardiac derivatives represent promising models for the study of mitochondrial damage and GAA expansion instability in FRDA.
Acknowledging the Effect of the Depreciation of Tangible and Intangible Benefits upon the Evaluation of E-Gov Projects

In the complex world we live in government has become one of the most important players in the data processing market. Not only does it collect a considerable amount of data from various sources, but it is also responsible for transforming this data into information and feeding it back into society. In order to reduce running costs and improve efficiency much of the governmental data collection and transformation activity is made by automated and semi-automated means. Therefore, not surprisingly, government is also one of the biggest users of information and communication technology (ICT). All of this has made the analysis of public sector investments in ICT (or e-gov projects) a subject of interest for officials in decision-making positions. This paper presents a method for the evaluation of these investments. The method gives a way to evaluate the tangible and intangible benefits yielded by e-gov projects. Also, it takes into account that the value yielded by both tangibles and intangibles may change during the course of time, and that these changes may affect the value of e-gov projects.
The Leabra Cognitive Architecture: How to Play 20 Principles with Nature and Win!

This chapter provides a synthetic review of a long-term effort to produce an internally consistent theory of the neural basis of human cognition, the Leabra cognitive architecture, which explains a great deal of brain and behavioral data. In a highly influential commentary, Allen Newell (1973) first issued a call for a more comprehensive, principled approach to studying cognition. “You can’t play 20 questions with nature, and win,” he said, alluding to the old parlor guessing game involving 20 yes or no questions. His point was that cognition, and the brain that gives rise to it, is just too complex and multidimensional a system to ever hope that a series of narrowly framed experiments and/or models would ever be able to characterize it. Instead, a single cognitive architecture should be used to simulate a wide range of data at many levels in a cumulative manner. However, these cognitive architectures tend to be complex and difficult to fully comprehend. In an attempt to most clearly and simply present the Leabra biologicallybased cognitive architecture, we articulate 20 principles that motivate its design, at multiple levels of analysis.