Miracle-dz/UniFAR-FTUs huggingface dataset:
Synaptic vesicle dynamics in living cultured hippocampal neurons visualized with CY3-conjugated antibodies directed against the lumenal domain of synaptotagmin

Antibodies directed against the lumenal domain of synaptotagmin I conjugated to CY3 (CY3-Syt1-Abs) and video microscopy were used to study the dynamics of synaptic vesicles in cultured hippocampal neurons. When applied to cultures after synapse formation, CY3-Syt1-Abs produced a strong labeling of presynaptic vesicle clusters which was markedly increased by membrane depolarization. The increase of the rate of CY3-Syt1-Ab uptake in a high K+ medium was maximal during the first few minutes but persisted for as long as 60 min. In axons developing in isolation, CY3-Syt1-Abs, in combination with electron microscopy immunocytochemistry, revealed the presence of synaptic vesicle clusters which move in bulk in anterograde and retrograde direction. Clusters are present both in the axon shaft and in filopodia but not in the filopodia of the growth cone. Both presynaptic vesicle clusters and clusters present in isolated axons were disrupted by okadaic acid as previously shown for synaptic vesicle clusters at the frog neuromuscular junction. These findings indicate that synaptic vesicle aggregation may occur independently of cell-cell interaction, but that, in the absence of a synaptic contact, vesicle clusters are not stably anchored to a given region of the cell surface. Labeling of synaptic vesicles in immature isolated neurons was found to be depolarization and Ca2+ dependent, demonstrating that Ca(2+)-regulated exocytosis is an intrinsic characteristic of synaptic vesicles irrespective of their localization at a synapse.
Joint Source, Channel and Space-time Coding of Progressive Sources in MIMO Systems

The optimization of joint source and channel coding for a sequence of numerous progressive packets is a challenging problem. Further, the problem becomes more complicated if the space-time coding is also involved with the optimization in a multiple-input multiple-output (MIMO) system. This is because the number of ways of jointly assigning channels codes and space-time codes to progressive packets is much larger than that of solely assigning channel codes to the packets. We are unaware of any feasible and complete solution for such optimization of joint source, channel, and space-time coding of progressive packets. This paper applies a parametric approach to address that complex joint optimization problem in a MIMO system. We use the parametric methodology to derive some useful theoretical results, and then exploit those results to propose an optimization method where the joint assignment of channel codes and space-time codes to the packets can be optimized in a packet-by-packet manner. As a result, the computational complexity of the optimization is exponentially reduced, compared to the conventional exhaustive search. The numerical results show that the proposed method significantly improves the peak-signal-to-noise ratio performance of the rate-based optimal solution in a MIMO system.
Comparison of different classifiers in movement recognition using WSN-based wrist-mounted sensors

The analysis of human movement is a widely studied field of health applications, such as telerehabilitation, analysis of daily activities, and emergency detection. In this paper, the comparison of different classifiers is presented for a new movement recognition system, which can be used for the detection of emergency situations. The system uses 9-degree-of-freedom (9DOF) sensor boards that are attached to wrist-mounted Wireless Sensor Network (WSN) motes. The 9DOF sensor boards are built up from a tri-axial accelerometer, a tri-axial gyroscope, and a tri-axial magnetometer. Measurement data for classification were collected from multiple subjects. Eleven movement classes were constructed in order to recognize specific arm movements in stationary positions and also during the movement of the body. Various time-domain features (TDF) were calculated in different processing window widths. Depending on the used window size, sensors and TDFs, 48 different data sets were constructed, which were used for training and for validating of the system. Different classifiers were tested and compared using the original and the dimensionally reduced data sets. The dimension reduction is performed using the Linear Discriminant Analysis (LDA) method. The tested classifiers were the minimum distance classifier, the MultiLayer Perceptron (MLP) network, the naive Bayes classifier and the Support Vector Machine (SVM).
A Logic Approach to Mine Syntactic Fragments of Mesh Keywords in Biomedical Literature

The discovery of new and potentially meaningful dependencies between biomedical keywords in literature can take great advantage from the application of a logic approach to text mining. This is motivated by the peculiarity of logic approaches to be able to express and manipulate relations between objects. We investigate the application of a logic approach to the task of frequent pattern discovery in Medline abstracts. Frequent patterns represent frequent syntactic fragments ofs. Frequent patterns represent frequent syntactic fragments of MeSH keywords. Preliminary experiments with a collection of abstracts obtained by querying Medline on a specific disease are reported.
An Efficient Load Balancing Algorithm for P2P Systems

Peer-to-Peer (P2P) networks are considered to be the most important development for content distribution and sharing infrastructures. The quality of services provided by the majority of the P2P systems is questioned. Load balancing among peers is critical and a key challenge. This paper proposes a load balancing algorithm based on stochastic analysis. It addresses the out-of-date problem as a result of node’s state changes during loads movement among nodes.
Mortality differences by APOE genotype estimated from demographic synthesis

The 4 allele of apolipoprotein E (APOE) is associated with increased risk of two major causes of death in low‐mortality populations: ischemic heart disease and Alzheimer’s disease. It is less common among centenarians than at younger ages. Therefore, it is likely that it is associated with excess risk of death. This article extends demographic models that estimate relative mortality risks from changes in gene frequencies with age. The resulting demographic synthesis combines gene frequencies with data on mortality by genotype from cohort studies. The model was applied to data from Denmark, Finland, France, Italy, Sweden, and the United States. Near age 50, the 3/4 genotype is associated with a risk of death of 1.34 times that of the 3/3 (95% CI 1.18–1.67). The relative risk for 4/4 is the square of the relative risk for 3/4, 1.81. The 2/3 genotype is protective with a relative risk of 0.84 (0.68–0.93) near age 50. These relative risks move toward 1.0 at the oldest ages and APOE genotype is associated with little variation in mortality over age 100. There are no significant differences in the relative risks by sex. There is little evidence of differences within Europe in the effects of APOE. This approach can be generalized to combine data on genetic risk factors for disease from a wide variety of study designs and sample characteristics. Genet. Epidemiol. 22:146–155, 2002. © 2002 Wiley‐Liss, Inc.
Efficient concept detection by fusing simple visual features

Concept detection is one of the important tasks in video indexing due to its importance to bridging the semantic gap in multimedia retrieval. Many methods have been proposed for this task, however finding a method which can generalize well for a large number of concepts and is scalable for processing huge video databases is still challenging. In this paper, we introduce a general framework for efficient and scalable concept detection by fusing SVM classifiers trained by only simple visual features such as color moments, edge orientation histogram and local binary patterns. We evaluate the proposed framework for detecting a large number of concepts on various TRECVID datasets with hundreds of hours of video. Experimental results show that the proposed framework achieves good performance with a small computational cost.
OASIS at NTCIR-6: On-line Query Translation for Chinese-Japanese Cross-Lingual Information Retrieval

This paper reports results of Chinese – Japanese CLIR experiments using on-line query translation techniques. Approaches to employ English as a pilot language and to utilize several on-line translation systems are introduced. They were tested on NTCIR – 3, 4, 5, and 6 collections. Proposed procedures can be helpful under certain circumstances.
A Compressed Sensing Approach for Biological Microscopy Image Denoising

Compressed Sensing (CS) provides a new framework for signal sampling, exploiting redundancy and sparsity in incoherent bases. For images with homogeneous objects and background, CS provides an optimal reconstruction framework from a set of random projections in the Fourier domain, while constraining bounded variations in the spatial domain. In this paper, we propose a CS-based method to simultaneously acquire and denoise data based on statistical properties of the CS optimality, signal modeling and characteristics of noise reconstruction. Our approach has several advantages over traditional denoising methods, since it can under-sample, recover and denoise images simultaneously. We demonstrate with simulated and practical experiments on fluorescence images that we obtain images with similar or increased SNR even with reduced exposure times. Such results open the gate to new mathematical imaging protocols, offering the opportunity to reduce exposure time along with photo-toxicity and photo-bleaching and assist biological applications relying on fluorescence microscopy.
Mining Maximal Frequent Patterns in Molecular Data with Lookahead Pruning

Mining maximal frequent patterns in large database is now a well attended problem in data mining field. In this paper we present an algorithm which mines maximal frequent substructures in a molecular data. The algorithm uses bottom-up depth first search approach to scan data and find maximal frequent substructures. Algorithm works on the concept of look-ahead pruning to restrict the candidate generation and unnecessary scans of database. This algorithm also uses the concepts of dynamic reordering of candidates and support lower bound to efficiently find even the long patterns in molecular data. Initial results on anti HIV-1 data show that this algorithm works better than the simple Apriori algorithm in finding long frequent patterns.
Increasing sybil attack detection probability in open-access distributed systems

Sybil attack is the most prominent and challenging attack in open-access distributed systems like peer-to-peer systems. In sybil attack, a malicious user creates multiple fake identities called sybil identities leading to most of the honest nodes in the network to be controlled by them. Many centralized approaches being available, the proposed protocol uses a decentralized approach to defend against sybil attack. The proposed protocol, Extended SybilLimit is an extension of the SybilLimit protocol which leverages social network as a defense against sybil attack. SybilLimit aims at reducing the number of sybil nodes accepted but does not focus in the malicious or false updations that occur during routing. The Extended SybilLimit focuses more on false updation detection thereby increasing the attack detection probability by 5% and also reduces the number of sybil nodes in the system. The Malicious Updation Detection (MUD) algorithm is used to detect the fake updations and it augments to the verification of the suspects in Extended SybilLimit protocol.
A novel model of piezoelectric ceramic hysteretic

Piezoelectric actuators are widely applied as actuators in micro/nano-positioning systems, due to its characteristic of infinitely small displacement resolution. While the tracking control accuracy of the piezoelectric actuator is limited due to their inherent hysteretic nonlinearity. This paper describes a mathematical model which could compensate the hysteresis of piezoelectric actuator based on an inverse control in open-loop operation. The basis of the inverse control is formed by a hysteresis mathematical model, which can describe precisely phenomena. The mathematical modeling framework could precisely predict a hysteresis path for arbitrarily assigned input profiles. The new hysteretic model makes use of polar coordinate which has the advantage that the proposed model simplifies the identification procedure of its inverse model. The model can accurately predict the response of hysteretic nonlinearity in piezoelectric ceramic actuators; utilizing a piezoelectric-driven actuator, it is experimentally demonstrated that if the memory units is sufficiently recorded, model response in the prediction of a hysteresis track is significantly improved.
A spatial time series framework for modeling daily precipitation at regional scales

A SPATIAL TIME SERIES FRAMEWORK FOR MODELING DAILY PRECIPITATION AT REGIONAL SCALES Phaedon C. Kyriakidis * Norman L. Miller Jinwon Kim university of California Santa Barbara, Santa Barbara, CA Lawrence Berkeley National Laboratory, Berkeley, CA University of California Los Angeles, Los Angeles, CA INTRODUCTION Estimates of precipitation at regional scales constitute one of the most important input parameters for hydrologic impact assessment studies. A t these scales, Limited Area Models (LAMs) provide an emerging means for enhancing the accuracy of precipitation predictions (Giorgi and Mearns, 1991; K i m and Soong, 1996; Miller and Kim, 1996; K i m et al., 1998). Dynamical downscaling using L A M s yield precipitation predictions which are physically and dynamically consistent with other atmospheric variables produced in the downscaling procedure. Dynamical downscaling, however, is computationally expensive and not error-free due to limited spatial resolution and model parameterizations. Stochastic characterization of rainfall fields based on rain gauge data and ancillary information, e.g., terrain elevation, still provides one of the basic tools for constructing rainfall maps at regional scales (Bras and Rodriguez-Iturbe, 1985; Seo et al., 2000; Kyriakidis et al., 2001b), even though the physical and dynamic consistency of such maps is not guaranteed. Time domain approaches for modeling daily precipitation typically involve vectors of time series, e.g., multivariate autoregressive (AR) models. Such models exploit the typically better informed time domain, but are limited to predictions only at rain gauge locations (Wilks, 1998; von Storch and Zwiers, 1999). This limitation hinders the all important task of spatiotemporal mapping. More recently, time series approaches have been generalized to a continuous spatial domain and maps of precipitation levels are constructed at any arbitrary location via interpolation of time series model parameters (Johnson et al., 2000). In this paper, a framework for stochastic spatiotemporal modeling of daily precipitation in a hindcast mode is presented. Observed precipitation levels in space and time are modeled as a joint realization of a collection of space-indexed time series, one for each spatial location. Time series model parameters are spatially varying, thus capturing space-time interactions. Stochastic simulation, i.e., the procedure of generating alternative precipitation realizations (synthetic fields) over the space-time domain of interest (Deutsch and Journel, 1998), is employed for ensemble pre- diction. The simulated daily precipitation fields reproduce a data-based histogram and spatiotem- * Corresponding author address: Phaedon C. Kyriakidis, University of California Santa Barbara, Dept. of Geogra- phy, Ellison Hall 5710, CA 93117; e-mail: phaedon@geog.ucsb. edu
Alternative splicing during Arabidopsis flower development results in constitutive and stage-regulated isoforms

Alternative splicing (AS) is a process in eukaryotic gene expression, in which the primary transcript of a multi-exon gene is spliced into two or more different mature transcripts, thereby increasing proteome diversity. AS is often regulated differentially between different tissues or developmental stages. Recent studies suggested that up to 60% of intron-containing genes in Arabidopsis thaliana undergo AS. Yet little is known about this complicated and important process during floral development. To investigate the preferential expression of different isoforms of individual alternatively spliced genes, we used high throughput RNA-Seq technology to explore the transcriptomes of three floral development stages of Arabidopsis thaliana and obtained information of various AS events. We identified approximately 24,000 genes that were expressed at one or more of these stages, and found that nearly 25% of multi-exon genes had two or more spliced variants. This is less frequent than the previously reported 40–60% for multiple organs and stages of A. thaliana, indicating that many genes expressed in floral development function with a single predominant isoform. On the other hand, 1716 isoforms were differentially expressed between the three stages, suggesting that AS might still play important roles in stage transition during floral development. Moreover, 337 novel transcribed regions were identified and most of them have a single exon. Taken together, our analyses provide a comprehensive survey of AS in floral development and facilitate further genomic and genetic studies.
Patient preference compared with random allocation in short-term psychodynamic supportive psychotherapy with indicated addition of pharmacotherapy for depression

Abstract Depressed patients randomized to psychotherapy were compared with those who had been chosen for psychotherapy in a treatment algorithm, including addition of an antidepressant in case of early nonresponse. There were no differences between randomized and by-preference patients at baseline in adherence and outcome. About half of the early nonresponders refused the additional medication. However, no clear effect of medication addition on ultimate outcome could be demonstrated. In total, 37% of the patients achieved remission. The study suggested that randomization of patients does not induce a great influence on outcome. It might be warranted to continue an initially ineffective psychotherapy for depression, because a considerable number of patients do have a pattern of delayed response.
Red Sea Suberea mollis Sponge Extract Protects against CCl4-Induced Acute Liver Injury in Rats via an Antioxidant Mechanism

Recent studies have demonstrated that marine sponges and their active constituents exhibited several potential medical applications. This study aimed to evaluate the possible hepatoprotective role as well as the antioxidant effect of the Red Sea Suberea mollis sponge extract (SMSE) on carbon tetrachloride- (CCl4-) induced acute liver injury in rats. In vitro antioxidant activity of SMSE was evaluated by 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH) assay. Rats were orally administered three different concentrations (100, 200, and 400 mg/kg) of SMSE and silymarin (100 mg/kg) along with CCl4 (1 mL/kg, i.p., every 72 hr) for 14 days. Plasma aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), and total bilirubin were measured. Hepatic malondialdehyde (MDA), reduced glutathione (GSH), nitric oxide (NO), superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT) were also measured. Liver specimens were histopathologically examined. SMSE showed strong scavenging activity against free radicals in DPPH assay. SMSE significantly reduced liver enzyme activities. Moreover, SMSE significantly reduced hepatic MDA formation. In addition, SMSE restored GSH, NO, SOD, GPx, and CAT. The histopathological results confirmed these findings. The results of this study suggested a potent protective effect of the SMSE against CCl4-induced hepatic injury. This may be due to its antioxidant and radical scavenging activity.
Auto-Calibration of Pan-Tilt-Zoom Cameras: Estimating Intrinsic and Radial Distortion Parameters

In this paper we propose a method for PTZ camera auto-calibration over the camera’s zoom range. The method is based on the minimization of re-projection errors of feature points detected in images captured by the camera at different orientations and zoom levels. Experiments conducted on both synthetic and real data show the method achieves good results compared to methods that require higher computational costs or access to the camera.
KCTD10 Is Involved in the Cardiovascular System and Notch Signaling during Early Embryonic Development

As a member of the polymerase delta-interacting protein 1 (PDIP1) gene family, potassium channel tetramerisation domain-containing 10 (KCTD10) interacts with proliferating cell nuclear antigen (PCNA) and polymerase δ, participates in DNA repair, DNA replication and cell-cycle control. In order to further investigate the physiological functions of KCTD10, we generated the KCTD10 knockout mice. The heterozygous KCTD10+/− mice were viable and fertile, while the homozygous KCTD10−/− mice showed delayed growth from E9.0, and died at approximately E10.5, which displayed severe defects in angiogenesis and heart development. Further study showed that VEGF induced the expression of KCTD10 in a time- and dose-dependent manner. Quantitative real-time PCR and western blotting results revealed that several key members in Notch signaling were up-regulated either in KCTD10-deficient embryos or in KCTD10-silenced HUVECs. Meanwhile, the endogenous immunoprecipitation (IP) analysis showed that KCTD10 interacted with Cullin3 and Notch1 simultaneously, by which mediating Notch1 proteolytic degradation. Our studies suggest that KCTD10 plays crucial roles in embryonic angiogenesis and heart development in mammalians by negatively regulating the Notch signaling pathway.
Application of verification techniques to inverse monoids

The word problem for inverse monoids generated by a set $Gamma$ subject to relations of the form $e=f$, where $e$ and $f$ are both idempotents in the free inverse monoid generated by $Gamma$, is investigated. It is shown that for every fixed monoid of this form the word problem can be solved in polynomial time which solves an open problem of Margolis and Meakin. For the uniform word problem, where the presentation is part of the input, EXPTIME-completeness is shown. For the Cayley-graphs of these monoids, it is shown that the first-order theory with regular path predicates is decidable. Regular path predicates allow to state that there is a path from a node $x$ to a node $y$ that is labeled with a word from some regular language. As a corollary, the decidability of the generalized word problem is deduced. Finally, some results on free partially commutative inverse monoids are presented.
Introduction to the quagga routing suite

Off-the-shelf routing products are often constrained by being designed to meet specific needs, in terms of both software and hardware. Networking professionals may face problems that require customization of software, or additional processing facilities or data storage, which are not provided for by those products. The Quagga Routing Suite provides implementations of several common routing protocols, distributed over multiple processes communicating via IPC, and support for their development, with source code provided under a modification-friendly license. Quagga can help networking professionals build such custom solutions, in combination with other open source software packages. Quagga also provides a path for network researchers to increase the visibility of their work, making it available to a wider community for potential testing and use, increasing the impact of that research.