Miracle-dz/UniFAR-FTUs huggingface dataset:
Features of alpha-synuclein that could explain the progression and irreversibility of Parkinson's disease

Alpha-synuclein is a presynaptic protein expressed throughout the central nervous system, and it is the main component of Lewy bodies, one of the histopathological features of Parkinson's disease (PD) which is a progressive and irreversible neurodegenerative disorder. The conformational flexibility of α-synuclein allows it to adopt different conformations, i.e., bound to membranes or form aggregates, the oligomers are believed to be the more toxic species. In this review, we will focus on two major features of α-synuclein, transmission and toxicity, that could help to understand the pathological characteristics of PD. One important feature of α-synuclein is its ability to be transmitted from neuron to neuron using mechanisms such as endocytosis, plasma membrane penetration or through exosomes, thus propagating the Lewy body pathology to different brain regions thereby contributing to the progressiveness of PD. The second feature of α-synuclein is that it confers cytotoxicity to recipient cells, principally when it is in an oligomeric state. This form causes mitochondrial dysfunction, endoplasmic reticulum stress, oxidative stress, proteasome impairment, disruption of plasma membrane and pore formation that lead to apoptosis pathway activation and consequent cell death. The complexity of α-synuclein oligomerization and formation of toxic species could be a major factor for the irreversibility of PD and could also explain the lack of successful therapies to halt the disease.
Heterocercal tail function in leopard sharks: a three-dimensional kinematic analysis of two models

Two different models have been proposed to explain the function of the heterocercal tail in shark locomotion. The classical model proposes that, as a result of lift generated by the tail as it beats, the net force acting on the tail is directed dorsally and anteriorly. In contrast, Thomson's model suggests that the tail generates a net force directed through the shark's center of gravity, i.e. ventrally and anteriorly. In this study, we evaluate these two models by describing the three-dimensional kinematics of the heterocercal tail in the leopard shark Triakis semifasciata during swimming. Lateral and posterior views of the tail were examined from four individuals swimming in a flow tank at 1.2 L s-1 (where L is total length) using two high-speed video cameras filming simultaneously at 250 fields s-1. These two simultaneous views allowed eight landmarks on the tail to be followed in three dimensions through time. These landmarks allowed the tail to be divided into separate surfaces whose orientation over time was calculated. Points located anteriorly on the tail go through significantly smaller excursions and reach their maximum lateral excursion significantly earlier in the beat cycle than points on the trailing edge of the tail. Three-dimensional angle calculations show that the terminal lobe leads the ventral lobe through a beat, as predicted by the classical model. Dye-stream visualizations confirmed that this pattern of movement deflects water ventrally and posteriorly to the moving tail, providing strong support for the classical model. Additionally, our results show that a three-dimensional analysis is critical to understanding the function of the heterocercal tail.
Quantitative Modeling of Currents from a Voltage Gated Ion Channel Undergoing Fast Inactivation

Ion channels play a central role in setting gradients of ion concentration and electrostatic potentials, which in turn regulate sensory systems and other functions. Based on the structure of the open configuration of the Kv1.2 channel and the suggestion that the two ends of the N-terminal inactivating peptide form a bivalent complex that simultaneously blocks the channel pore and binds to the cytoplasmic T1 domain, we propose a six state kinetic model that for the first time reproduces the kinetics of recovery of the Drosophila Shaker over the full range of time scales and hyperpolarization potentials, including tail currents. The model is motivated by a normal mode analysis of the inactivated channel that suggests that a displacement consistent with models of the closed state propagates to the T1 domain via the S1-T1 linker. This motion stretches the bound (inactivating) peptide, hastening the unblocking of the pore. This pulling force is incorporated into the rates of the open to blocked states, capturing the fast recovery phase of the current for repolarization events shorter than 1 ms. If the membrane potential is hyperpolarized, essential dynamics further suggests that the T1 domain returns to a configuration where the peptide is unstretched and the S1-T1 linker is extended. Coupling this novel hyperpolarized substate to the closed, open and blocked pore states is enough to quantitatively estimate the number of open channels as a function of time and membrane potential. A straightforward prediction of the model is that a slow ramping of the potential leads to very small currents.
The Significance of Religious Education in Local Primary Schools (Specific Reference to Christianity)

In the contemporary context of studying religious education in a secular society, the process such as individualization makes it harder for children to get the opportunity to learn from religion in an organized way. At school young students can learn in an orderly and beneficial way from religion. However, we hardly know how they are making progress on this subject and what the significance of their participation in this subject really is. Currently, religious education at primary schools in Western Europe has evolved into a subject that seeks to support students to develop their religious identity. From a socio-cultural perspective, religious education aims to support students to develop their religious identity by giving them the opportunity to participate at religious practices. Religious tradition such as Christianity involve religious practices such as praying, gathering, taking care of the fellow men, dealing with life and death, or the interpretation of religious stories. In these practices the reality that surrounds us is related to the transcendent reality of God the only reliable tool that is use in their study is the bible. Here religious people use concepts like God, creation, nature, redemption, or eternity, and strategies as interpretation, symbolization or imagination. From this perspective, progress in religious education refers to participation at religious practices in a more expert way. The aim of this research is to get a clear view on the significance of studying Christian Religious Education (CRE) in primary school by gathering all the available evidence and the influences this education has had on the way they live their lives, communicate with the secular world and to bring to light factors that help to explain this significance. Is there any benefit of religious education in schools? And how does it affect the child? Are the implications positive or negative? What is the progress of these students? To be more precise, what are the learning effects in Christian religious education of these students at the various levels of the primary school regarding their understanding of religion? And secondly, which factors are enhancing and which are diminishing this progress? Contents
Terminal decline in well-being differs between residents in East Germany and West Germany

Lifespan research has long been interested in how contexts shape individual development. Using the separation and later reunification of Germany as a kind of natural experiment we examine whether and how living and dying in the former East or West German context has differentially shaped late-life development of well-being. We apply multi-level growth models to annual reports of life satisfaction collected over 20+ years since German reunification from 4,159 deceased participants in the Socio-Economic Panel (NWest= 3,079, Mage at death = 73.90, 47% women; NEast= 1,080, Mage at death = 72.23, 48% women). We examine differences between East and West Germany in levels, rates of change, and onset of terminal decline in well-being and the role of age at death, gender, education, disability and time spent in reunification. Analyses revealed that West Germans reported higher life satisfaction than East Germans, and that these differences get smaller both with passing time since reunification and in late life. The gap between East and West Germany diminishes over the last 10 years of life by more than 25%. Taking into account key individual characteristics only slightly attenuated this pattern, with education and age at death moderating late-life well-being level and decline in East Germany. Our results are consistent with long-standing notions that contextual factors shape individual development and illustrate the plasticity of human development. After having experienced disadvantages in life circumstances for up to 40 years through living in East Germany, effects of this natural experiment diminish considerably with passing time since reunification.
Political Uncertainty and Risk Premia

We develop a general equilibrium model of government policy choice in which stock prices respond to political news. The model implies that political uncertainty commands a risk premium whose magnitude is larger in weaker economic conditions. Political uncertainty reduces the value of the implicit put protection that the government provides to the market. It also makes stocks more volatile and more correlated, especially when the economy is weak. We find empirical evidence consistent with these predictions.
TOP-SIFT: A New Method for SIFT Descriptor Selection

The large amount of SIFT descriptors in an image and the high dimensionality of SIFT descriptor has made problems for large-scale image dataset in terms of speed and scalability. In this paper, we propose a descriptor selection algorithm via dictionary learning and only a small set of features are reserved, which we refer to as TOP-SIFT. We discover the inner relativity between the problem of descriptor selection and dictionary learning for sparse representation, and then turn our problem into dictionary learning. Compared with the earlier methods, our method is neither relying on the dataset nor losing important information, and the experiments have shown that our algorithm can save memory space and increase the retrieval speed efficiently while maintain the recognition performance as well.
eXtreme Programming and SCRUM : A Comparative Analysis of Agile Methods

—Agile methods are playing an increasingly important role in the realm of software development. In an attempt to develop improved methods to designing and implementing software systems, several pioneering efforts have been suggested. This paper examines two such agile methods, eXtreme Programming (XP) and SCRUM. The values and principles of the eXtreme Programming movement are described, including commentary on the effectiveness of XP in practice. The SCRUM development process is described in detail, followed by a brief look at the advantages and disadvantages SCRUM provides. XP and SCRUM are compared in full, focusing on the crucial differences between the two agile methods. Finally, the way in which XP and SCRUM can be used together to obtain maximum benefits is suggested.
Online walking motion and foothold optimization for quadruped locomotion

We present an algorithm that generates walking motions for quadruped robots without the use of an explicit footstep planner by simultaneously optimizing over both the Center of Mass (CoM) trajectory and the footholds. Feasibility is achieved by imposing stability constraints on the CoM related to the Zero Moment Point and explicitly enforcing kinematic constraints between the footholds and the CoM position. Given a desired goal state, the problem is solved online by a Nonlinear Programming solver to generate the walking motion. Experimental trials show that the algorithm is able to generate walking gaits for multiple steps in milliseconds that can be executed on a real quadruped robot.
Optimal Precoder for Rate⩽1 Space-Time Block Codes

Despite primary space-time coding where the channel state information (CSI) is available at the receiver only, the capacity and performance of multiple-input multiple-output (MIMO) systems can be increased significantly when a complete or partial CSI is available at the transmitter. Recently, limited feedback methods including antenna subset selection and unitary preceding have been proposed for orthogonal space-time codes where a partial knowledge of the channel is available at the transmitter via an error-free, zero-delay feedback channel. In this paper, we propose a general structure matrix rather than a unitary one for precoding. By maximizing the signal-to-noise ratio (SNR) per received symbol, we find the optimal precoder for general space-time codes with rate⩽1 symbol per channel use. The performance of the optimal scheme is analytically evaluated. Next, we extend the result for limited feedback systems. Simulation results show that the proposed precoder outperforms the previous work.
Data recovery from corrupted observations via l1 minimization

This paper studies the problem of recovering a signal vector and the corrupted noise vector from a collection of corrupted linear measurements through the solution of a l1 minimization, where the sensing matrix is a partial Fourier matrix whose rows are selected randomly and uniformly from rows of a full Fourier matrix. After choosing the parameter in the l1 minimization appropriately, we show that the recovery can be successful even when a constant fraction of the measurements are arbitrarily corrupted, moreover, the proportion of corrupted measurement can grows arbitrarily close to 1, provided that the signal vector is sparse enough. The upper-bound on the sparsity of the signal vector required in this paper is asymptotically optimal and is better than those achieved by recent literatures [1, 2] by a ln(n) factor. Furthermore, the assumptions we impose on the signal vector and the corrupted noise vector are loosest comparing to the existing literatures [1-3], which lenders our recovery guarantees are more applicable. Extensive numerical experiments based on synthesis as well as real world data are presented to verify the conclusion of the proposed theorem and to demonstrate the potential of the l1 minimization framework.
Guillotine Subdivisions Approximate Polygonal Subdivisions: A Simple Polynomial-Time Approximation Scheme for Geometric TSP, k-MST, and Related Problems

We show that any polygonal subdivision in the plane can be converted into an "m-guillotine" subdivision whose length is at most $(1+{c\over m})$ times that of the original subdivision, for a small constant c. "m-Guillotine" subdivisions have a simple recursive structure that allows one to search for the shortest of such subdivisions in polynomial time, using dynamic programming. In particular, a consequence of our main theorem is a simple polynomial-time approximation scheme for geometric instances of several network optimization problems, including the Steiner minimum spanning tree, the traveling salesperson problem (TSP), and the k-MST problem.
Acute mast cell‐dependent neutrophil recruitment in the skin is mediated by KC and LFA‐1: inhibitory mechanisms of dexamethasone

This study examined adhesive and signaling pathways and anti‐inflammatory mechanisms of dexamethasone in acute mast cell‐dependent neutrophil recruitment in the skin in mice. Mast cell activation dose‐ and time‐dependently triggered influx of predominately neutrophils and secretion of cytokine‐induced neutrophil chemoattractant (KC). Neutralization of KC attenuated neutrophil recruitment upon mast cell activation. Mast cell activation‐ and KC‐induced neutrophil responses were significantly decreased in lymphocyte function‐associated antigen‐1 (LFA‐1)‐deficient mice. Dexamethasone inhibited neutrophil accumulation elicited by mast cell activation. It is interesting that dexamethasone significantly reduced the mast cell‐dependent secretion of KC, whereas neutrophil recruitment induced by exogenous KC was insensitive to dexamethasone treatment. Thus, KC is a fundamental mediator of neutrophil recruitment in acute mast cell‐dependent skin inflammation, and mast cell activation‐ and KC‐induced neutrophil responses are LFA‐1‐dependent. Moreover, dexamethasone inhibits mast cell‐regulated skin infiltration of neutrophils mainly by attenuating KC secretion. Thus, this study elucidates important interactions between chemokines and adhesion molecules in mast cell‐dependent neutrophil recruitment and provides new insight into mechanisms of dexamethasone in skin inflammation.
DZNep is a global histone methylation inhibitor that reactivates developmental genes not silenced by DNA methylation

DNA methylation, histone modifications, and nucleosomal occupancy collaborate to cause silencing of tumor-related genes in cancer. The development of drugs that target these processes is therefore important for cancer therapy. Inhibitors of DNA methylation and histone deacetylation have been approved by the Food and Drug Administration for treatment of hematologic malignancies. However, drugs that target other mechanisms still need to be developed. Recently, 3-deazaneplanocin A (DZNep) was reported to selectively inhibit trimethylation of lysine 27 on histone H3 (H3K27me3) and lysine 20 on histone H4 (H4K20me3) as well as reactivate silenced genes in cancer cells. This finding opens the door to the pharmacologic inhibition of histone methylation. We therefore wanted to further study the mechanism of action of DZNep in cancer cells. Western blot analysis shows that DZNep globally inhibits histone methylation and is not selective. Two other drugs, sinefungin and adenosine dialdehyde, have similar effects as DZNep on H3K27me3. Intriguingly, chromatin immunoprecipitation of various histone modifications and microarray analysis show that DZNep acts through a different pathway than 5-aza-2′-deoxycytidine, a DNA methyltransferase inhibitor. These observations give us interesting insight into how chromatin structure affects gene expression. We also determined the kinetics of gene activation to understand if the induced changes were somatically heritable. We found that upon removal of DZNep, gene expression is reduced to its original state. This suggests that there is a homeostatic mechanism that returns the histone modifications to their “ground state” after DZNep treatment. Our data show the strong need for further development of histone methylation inhibitors. [Mol Cancer Ther 2009;8(6):1579–88]
Using attribute grammars for the genetic selection of back-propagation networks for character recognition

Determining exactly which neural network architecture, with which parameters, will provide the best solution to a classification task is often based upon the intuitions and experience of the implementers of neural network solutions. The research presented in this paper is centered on the development of automated methods for the selection of appropriate networks, as applied to character recognition. The Network Generating Attribute Grammar Encoding system is a compact and general method for the specification of commonly accepted network architectures that can be easily expanded to include novel architectures, or that can be easily restricted to a small subset of some known architecture. Within this system, the context-free component of the attribute grammar specifies a class of basic architectures by using the non-terminals to represent network, layers and component structures. The inherited and synthesized attributes indicate the connections necessary to develop a functioning network from any parse tree that is generated from the grammar. The attribute grammar encoding is particularly conducive to the use of genetic algorithms as a strategy for searching the space of possible networks. The resultant parse trees are used as the genetic code, permitting a variety of different genetic manipulations. We apply this approach in the generation of backpropagation networks for recognition of characters from a set consisting of 20,000 examples of 26 letters.
Improving Ontology Service-Driven Entity Disambiguation

One of the long-standing challenges in natural language processing is uniquely identifying entities in text, which when performed accurately and with formal ontologies, supports efforts such as semantic search and question-answering. With the recent proliferation of comprehensive, formalized sources of knowledge (e.g., DBpedia, Freebase, OBO Foundry ontologies) and advancements in supportive Semantic Web technologies and services, leveraging such resources to address the entity disambiguation problem in the industry setting as “off the shelf” within natural language processing pipelines becomes a more viable proposition. In this paper, we evaluate this viability by building and evaluating an entity disambiguation pipeline founded on publicly available ontology services, namely those provided by the NCBO BioPortal. We chose BioPortal due to its current use as an ontology repository and provider of ontological services for the biomedical informatics community. To consider its usage outside the biomedical domain, and given our immediate project goal for facilitating semantic search over Earth science datasets for the DataONE project, we focus on the disambiguation of geographic entities. For this work, we leverage NCBO’s Term service in conjunction with NCBO’s entity disambiguation service, the Annotator, to demonstrate an enhancement of the Annotator service, through application of a vector space model representation of ontological entities and relationships to drive scoring improvements. This work ultimately provides a methodology and pipeline for improving publicly available ontology service-based entity disambiguation, demonstrated through an enhanced version of the NCBO Annotator service for geographic named entity disambiguation.
Detection of binary Markov sources over channels with additive Markov noise

We consider maximum a posteriori (MAP) detection of a binary asymmetric Markov source transmitted over a binary Markov channel. The MAP detector observes a long (but finite) sequence of channel outputs and determines the most probable source sequence. In some cases, the MAP detector can be implemented by simple rules such as the "believe what you see" rule or the "guess zero (or one) regardless of what you see" rule. We provide necessary and sufficient conditions under which this is true. When these conditions are satisfied, the exact bit error probability of the sequence MAP detector can be determined. We examine in detail two special cases of the above source: (i) binary independent and identically distributed (i.i.d.) source and (ii) binary symmetric Markov source. In case (i), our simulations show that the performance of the MAP detector improves as the channel noise becomes more correlated. Furthermore, a comparison of the proposed system with a (substantially more complex) traditional tandem source-channel coding scheme portrays superior performance for the proposed scheme at relatively high channel bit error rates. In case (ii), analytical as well as simulation results show the existence of a "mismatch" between the source and the channel (the performance degrades as the channel noise becomes more correlated). This mismatch is reduced by the use of a simple rate-one convolutional encoder.