Miracle-dz/UniFAR-FTUs huggingface dataset:
Generation of dense statistical connectomes from sparse morphological data

Sensory-evoked signal flow, at cellular and network levels, is primarily determined by the synaptic wiring of the underlying neuronal circuitry. Measurements of synaptic innervation, connection probabilities and subcellular organization of synaptic inputs are thus among the most active fields of research in contemporary neuroscience. Methods to measure these quantities range from electrophysiological recordings over reconstructions of dendrite-axon overlap at light-microscopic levels to dense circuit reconstructions of small volumes at electron-microscopic resolution. However, quantitative and complete measurements at subcellular resolution and mesoscopic scales to obtain all local and long-range synaptic in/outputs for any neuron within an entire brain region are beyond present methodological limits. Here, we present a novel concept, implemented within an interactive software environment called NeuroNet, which allows (i) integration of sparsely sampled (sub)cellular morphological data into an accurate anatomical reference frame of the brain region(s) of interest, (ii) up-scaling to generate an average dense model of the neuronal circuitry within the respective brain region(s) and (iii) statistical measurements of synaptic innervation between all neurons within the model. We illustrate our approach by generating a dense average model of the entire rat vibrissal cortex, providing the required anatomical data, and illustrate how to measure synaptic innervation statistically. Comparing our results with data from paired recordings in vitro and in vivo, as well as with reconstructions of synaptic contact sites at light- and electron-microscopic levels, we find that our in silico measurements are in line with previous results.
Heterogeneity of Nicotinic Receptor Class and Subunit mRNA Expression among Individual Parasympathetic Neurons from Rat Intracardiac Ganglia

Neurons have the potential to form thousands of distinct neuronal nicotinic receptors from the eight α and three β subunits that currently are known. In an effort to determine how much of this potential complexity is realized among individual neurons, we examined the nicotinic pharmacological and biophysical properties and receptor subunit mRNA expression patterns in individual neurons cultured from rat epicardial ganglia. Analysis of the whole-cell pharmacology of these neurons showed a diversity of responses to the agonists acetylcholine, nicotine, cytisine, and 1,1-dimethyl-4-phenylpiperazinium, suggesting that a heterogeneous population of nicotinic receptor classes, or subtypes, is expressed by individual neurons. Single-channel analysis demonstrated three distinct conductances (18, 24, and 31 pS), with patches from different neurons containing different combinations of these channel classes. We used single-cell RT-PCR to examine nicotinic acetylcholine receptor (nAChR) subunit mRNA expression by individual neurons. Although mRNAs encoding all eight neuronal nAChR subunits for which we probed (α2–α5, α7, β2–β4) were present in multicellular cultures, we found that individual epicardial neurons express distinct subsets of these nAChR subunit mRNAs. These results suggest that individual epicardial neurons express distinct arrays of nAChR subunits and that these subunits may assemble into functional receptors with distinct and variable subunit composition. This variable receptor subunit expression provides an explanation for the diversity of pharmacological and single-channel responses we have observed in individual neurons.
Endocytosis of synaptic vesicle membrane at the frog neuromuscular junction

Frog nerve-muscle preparations were quick-frozen at various times after a single electrical stimulus in the presence of 4-aminopyridine (4-AP), after which motor nerve terminals were visualized by freeze-fracture. Previous studies have shown that such stimulation causes prompt discharge of 3,000-6,000 synaptic vesicles from each nerve terminal and, as a result, adds a large amount of synaptic vesicle membrane to its plasmalemma. In the current experiments, we sought to visualize the endocytic retrieval of this vesicle membrane back into the terminal, during the interval between 1 s and 2 min after stimulation. Two distinct types of endocytosis were observed. The first appeared to be rapid and nonselective. Within the first few seconds after stimulation, relatively large vacuoles (approximately 0.1 micron) pinched off from the plasma membrane, both near to and far away from the active zones. Previous thin-section studies have shown that such vacuoles are not coated with clathrin at any stage during their formation. The second endocytic process was slower and appeared to be selective, because it internalized large intramembrane particles. This process was manifest first by the formation of relatively small (approximately 0.05 micron) indentations in the plasma membrane, which occurred everywhere except at the active zones. These indentations first appeared at 1 s, reached a peak abundance of 5.5/micron2 by 30 s after the stimulus, and disappeared almost completely by 90 s. Previous thin-section studies indicate that these indentations correspond to clathrin-coated pits. Their total abundance is comparable with the number of vesicles that were discharged initially. These endocytic structures could be classified into four intermediate forms, whose relative abundance over time suggests that, at this type of nerve terminal, endocytosis of coated vesicles has the following characteristics: (a) the single endocytotic event is short lived relative to the time scale of two minutes; (b) earlier forms last longer than later forms; and (c) a single event spends a smaller portion of its lifetime in the flat configuration soon after the stimulus than it does later on.
Fast Parallel PageRank: A Linear System Approach

In this paper we investigate the convergence of iterative stationary and Krylov subspace methods for the PageRank linear system, including the convergence dependency on teleportation. We demonstrate that linear system iterations converge faster than the simple power method and are less sensitive to the changes in teleportation. In order to perform this study we developed a framework for parallel PageRank computing. We describe the details of the parallel implementation and provide experimental results obtained on a 70-node Beowulf cluster.
A word clustering approach for language model-based sentence retrieval in question answering systems

In this paper we propose a term clustering approach to improve the performance of sentence retrieval in Question Answering (QA) systems. As the search in question answering is conducted over smaller segments of data than in a document retrieval task, the problems of data sparsity and exact matching become more critical. In this paper we propose Language Modeling (LM) techniques to overcome such problems and improve the sentence retrieval performance. Our proposed methods include building class-based models by term clustering, and then employing higher order n-grams with the new class-based model. We report our experiments on the TREC 2007 questions from QA track. The results show that the methods investigated here enhanced the mean average precision of sentence retrieval from 23.62% to 29.91%.
Bmc Medical Informatics and Decision Making Online Detection and Quantification of Epidemics

Background: Time series data are increasingly available in health care, especially for the purpose of disease surveillance. The analysis of such data has long used periodic regression models to detect outbreaks and estimate epidemic burdens. However, implementation of the method may be difficult due to lack of statistical expertise. No dedicated tool is available to perform and guide analyses.
W&M ScholarWorks W&M ScholarWorks Reproduction and food habits of the lined seahorse, Reproduction and food habits of the lined seahorse, Hippocampus erectus (Teleostei: Syngnathidae) of Chesapeake Hippocampus erectus (Teleostei: Syngnathidae) of Chesapeake Bay, Virginia. Bay, Virginia.

The reproductive and feeding biology of the lined seahorse, Hippocampus erectus , was studied in Chesapeake Bay. Seahorses are monogamous, and males incubate the eggs received from females in a closed brood pouch (= marsupium). Females do not play any parental care after mating. Total sex ratio and the operational sex ratio was strongly skewed toward females. Males and females had similar number of eggs/embryos and hydrated oocytes, respectively. The number of eggs/embryos found in the male brood pouch varied from 97 to 1,552 (fish from 80 to 126 mm TL), whereas the number of hydrated oocytes in female varied from 90 to 1,313 (fish from 60 to 123 mm TL). Both, the number of eggs/embryos and hydrated oocytes were better linearly correlated to total weight than to total length. The small snout and mouth size limits the feeding of the lined seahorse to small prey size. Amphypods were the predominant food items found in the guts, especially Ampithoe longimana , Gammarus mucronatus, and Caprella penantis . The lined seahorse is not abundant in Chesapeake Bay, but keeps a breeding population which is probably brought inside the bay by currents on drifting vegetation. Chances to find a partner may be difficult because of its low abundance, due to turbid waters, and its sedentary behavior.
Random Walk and Graph Cut for Co-Segmentation of Lung Tumor on PET-CT Images

Accurate lung tumor delineation plays an important role in radiotherapy treatment planning. Since the lung tumor has poor boundary in positron emission tomography (PET) images and low contrast in computed tomography (CT) images, segmentation of tumor in the PET and CT images is a challenging task. In this paper, we effectively integrate the two modalities by making fully use of the superior contrast of PET images and superior spatial resolution of CT images. Random walk and graph cut method is integrated to solve the segmentation problem, in which random walk is utilized as an initialization tool to provide object seeds for graph cut segmentation on the PET and CT images. The co-segmentation problem is formulated as an energy minimization problem which is solved by max-flow/min-cut method. A graph, including two sub-graphs and a special link, is constructed, in which one sub-graph is for the PET and another is for CT, and the special link encodes a context term which penalizes the difference of the tumor segmentation on the two modalities. To fully utilize the characteristics of PET and CT images, a novel energy representation is devised. For the PET, a downhill cost and a 3D derivative cost are proposed. For the CT, a shape penalty cost is integrated into the energy function which helps to constrain the tumor region during the segmentation. We validate our algorithm on a data set which consists of 18 PET-CT images. The experimental results indicate that the proposed method is superior to the graph cut method solely using the PET or CT is more accurate compared with the random walk method, random walk co-segmentation method, and non-improved graph cut method.
An Estimator-Based Distributed Voltage-Predictive Control Strategy for AC Islanded Microgrids

This paper presents an estimator-based voltage-predictive control strategy for ac islanded microgrids, which is able to perform voltage control without any communication facilities. The proposed control strategy is composed of a network voltage estimator and a voltage-predictive controller for each distributed generator, where the voltage estimator serves as an essential tool to obtain network voltages response without using communication links, while the voltage-predictive controller is able to implement offset-free voltage control for a specified bus. The dynamic performance of the proposed voltage control strategy is analyzed through small-signal analysis method, from which the design guideline for the controller parameters is formulated. Furthermore, the robustness of the proposed voltage control strategy is investigated under a series of parameters uncertainties, including the line parameters perturbation, load parameters variation, different disturbance locations, LC filters perturbation, output impedances perturbation, and DG unit fault. The simulation and experimental results show that the proposed control approach is able to perform offset-free voltage control without any communication links and has a good capability to reject uncertain perturbations of islanded microgrids.
Vision-based drowsiness detector for real driving conditions

This paper presents a non-intrusive approach for drowsiness detection, based on computer vision. It is installed in a car and it is able to work under real operation conditions. An IR camera is placed in front of the driver, in the dashboard, in order to detect his face and obtain drowsiness clues from their eyes closure. It works in a robust and automatic way, without prior calibration. The presented system is composed of 3 stages. The first one is preprocessing, which includes face and eye detection and normalization. The second stage performs pupil position detection and characterization, combining it with an adaptive lighting filtering to make the system capable of dealing with outdoor illumination conditions. The final stage computes PERCLOS from eyes closure information. In order to evaluate this system, an outdoor database was generated, consisting of several experiments carried out during more than 25 driving hours. A study about the performance of this proposal, showing results from this testbench, is presented.
Towards an Intelligent Multilingual Keyboard System

This paper proposes a practical approach employing n-gram models and error-correction rules for Thai key prediction and Thai-English language identification. The paper also proposes rule-reduction algorithm applying mutual information to reduce the error-correction rules. Our algorithm reported more than 99% accuracy in both language identification and key prediction.
Strengthening Adaptation in Cyber-Physical Systems via Meta-Adaptation Strategies

The dynamic nature of complex Cyber-Physical Systems puts extra requirements on their functionalities: they not only need to be dependable, but also able to adapt to changing situations in their environment. When developing such systems, however, it is often impossible to explicitly design for all potential situations up front and provide corresponding strategies. Situations that come out of this “envelope of adaptability” can lead to problems that end up by applying an emergency fail-safe strategy to avoid complete system failure. The existing approaches to self-adaptation cannot typically cope with such situations better—while they are adaptive (and can apply learning) in choosing a strategy, they still rely on a pre-defined set of strategies not flexible enough to deal with those situations adequately. To alleviate this problem, we propose the concept of meta-adaptation strategies, which extends the limits of adaptability of a system by constructing new strategies at runtime to reflect the changes in the environment. Though the approach is generally applicable to most approaches to self-adaptation, we demonstrate our approach on IRM-SA—a design method and associated runtime model for self-adaptive distributed systems based on component ensembles. We exemplify the meta-adaptation strategies concept by providing three concrete meta-adaptation strategies and show its feasibility on an emergency coordination case study.
High‐sensitivity TFA‐free LC‐MS for profiling histones

The analysis of proteins by RPLC commonly involves the use of TFA as an ion‐pairing agent, even though it forms adducts and suppresses sensitivity. The presence of adducts can complicate protein molecular weight assignment especially when protein isoforms coelute as in the case of histones. To mitigate the complicating effects of TFA adducts in protein LC‐MS, we have optimized TFA‐free methods for protein separation. Protein standards and histones were used to evaluate TFA‐free separations using capillary (0.3 mm id) and nanoscale (0.1 mm id) C8 columns with the ion‐pairing agents, formic acid or acetic acid. The optimized method was then used to examine the applicability of the approach for histone characterization in human cancer cell lines and primary tumor cells from chronic lymphocytic leukemia patients.
Extractors and pseudorandom generators

We introduce a new approach to constructing extractors. Extractors are algorithms that transform a &quote;weakly random&quote; distribution into an almost uniform distribution. Explicit constructions of extractors have a variety of important applications, and tend to be very difficult to obtain.We demonstrate an unsuspected connection between extractors and pseudorandom generators. In fact, we show that every pseudorandom generator of a certain kind is an extractor.A pseudorandom generator construction due to Impagliazzo and Wigderson, once reinterpreted via our connection, is already an extractor that beats most known constructions and solves an important open question. We also show that, using the simpler Nisan--Wigderson generator and standard error-correcting codes, one can build even better extractors with the additional advantage that both the construction and the analysis are simple and admit a short self-contained description.
Computational Characteristics of Production Seismic Migration and its Performance on Novel Processor Architectures

We describe the computational characteristics of the Kirchhoff prestack seismic migration currently used in daily production runs at Petrobras and its port to novel architectures. Fully developed in house, this portable and fault tolerant application has high sequential and parallel efficiency, with parallel scalability tested up to 8192 processors on the IBM Blue Gene without exhausting parallelism. Production load comprises thousands of jobs per year, consuming the installed park of a few thousand x86 CPU cores, with top production runs continuously using up to 1000 dedicated processors during 20 days. A built in mechanism automatically produces, collects and stores job performance data, allowing single job performance analysis and multi job performance statistics. Its port to quad-core x86 and Sony PlayStation 3 achieved very high price/performance and performance/watt gains over single core x86 machines. Port to the PS3 is described in detail. Experimental performance data on a modest PS3 cluster is also presented.
Characterization and modeling of thermal dynamic behavior of AlGaAs/GaAs HBTs

This study presents a systematic investigation for the first time on the dynamic thermal impedance of AlGaAs/GaAs HBTs. A simple small-signal measurement technique is developed to measure the frequency domain relationship between the dissipation power and the HBT junction temperature. The technique provides a unique measurement tool to analyse device thermal structure, such as die attachment and heat-sink. A multi-section RC circuit is proposed in the paper to describe the thermal impedance. The agreements between measurement and simulation results are excellent. This investigation is useful in terms of modeling the HBT self-heating effect and its impact on HBT linearity or other temperature-sensitive performance.
Sequencing and the Success of Gradualism: Empirical Evidence from China's Agricultural Reform

This paper provides evidence regarding gains to agricultural market liberalization in China. We empirically identify the different effects that incentive reforms and gradual market liberalization have on China's agricultural economy during its transition period. We find that average gains within the agricultural sector to incentive reform exceed gains to market liberalization by a factor of ten. Our method of analyzing the effects of transition policies on economic performance can be generalized to other reform paths in other transition economies.
Automatic detection of defects in riveted lapjoints using Eddy current

A method for detection and classiication of defects originating from rivet holes in a riveted lap-joint using eddy current (EC) inspection is presented in this paper. The EC-signals were acquired from a number of lap-joints using a tailor-made deep penetrating probe, and a digital single frequency EC-instrument. A number of rivets in the lap-joints had defects located in the second layer of the lap-joint. The problem consisted in detecting and classifying defect signals in presence of strong interference due to rivet responses. The preprocessing before detection consisted of median ltering, rotation and de-biasing of the eddy current pattern. The rotation was performed so that the signal energy from the rivet responses was maximized along the quadrature direction, and the defect response energy was maximized in the in-phase direction of the EC-signal. Feature extraction was then performed using wavelets, PCA and block-mean values of the defect signal. The classiication was performed using a standard multi-layer perceptron neural network.
The GREYC machine translation system for the IWSLT 2008 evaluation campaign.

This year's GREYC machine translation (MT) system presents three major changes relative to the system presented during the previous campaign, while, of course, remaining a pure example-based MT system that exploits proportional analogies. Firstly, the analogy solver has been replaced with a truly non-deterministic one. Secondly, the engine has been re-engineered and a better control has been introduced. Thirdly, the data used for translation were the data provided by the organizers plus alignments obtained using a new alignment method. This year we chose to have the engine run with the word as the processing unit on the contrary to previous years where the processing unit used to be the character. The tracks the system participated in are all classic BTEC tracks (Arabic-English, Chinese-English and Chinese-Spanish) plus the so-called PIVOT task, where the test set had to be translated from Chinese into Spanish by way of English.
α-Synuclein (αSyn) Preformed Fibrils Induce Endogenous αSyn Aggregation, Compromise Synaptic Activity and Enhance Synapse Loss in Cultured Excitatory Hippocampal Neurons

Synucleinopathies are characterized by the accumulation of insoluble α-synuclein (αSyn). To test whether αSyn aggregates modulate synaptic activity, we used a recently developed model in primary neurons for inducing αSyn pathology. We demonstrated that preformed fibrils (PFFs) generated with recombinant human αSyn compromised synaptic activity in a time- and dose-dependent manner and that the magnitude of these deficits correlated with the formation of αSyn pathology in cultured excitatory hippocampal neurons from both sexes of mice. Remarkably, acute passive infusion of αSyn PFFs from whole-cell patch-clamp pipette decreased mEPSC frequency within 10 min followed by induction of αSyn pathology within 1 d. Moreover, by direct addition of αSyn PFFs into culture medium, the formation of misfolded αSyn inclusions dramatically compromised the colocalization of synaptic markers and altered dynamic changes of dendritic spines, but the viability of neurons was not affected up to 7 d post-treatment with αSyn PFFs. Our data indicate that intraneuronal αSyn fibrils impaired the initiation of synaptogenesis and their physiological functions, thereby suggesting that targeting synaptic dysfunction in synucleinopathies may provide a promising therapeutic direction. SIGNIFICANCE STATEMENT Under pathological conditions, the presynaptic protein α-synuclein (αSyn) aggregates to form intraneuronal inclusions. To understand how and to what extent αSyn aggregates modulate synaptic activity before neuron loss, we demonstrate that αSyn preformed fibrils (PFFs) reduced synaptic activity in a dose- and time-dependent manner. The magnitude of these deficits correlated with the deposition of αSyn pathology, which dramatically compromised the colocalization of synaptic markers and altered the dendritic spine dynamics. The present work further highlights the impact of αSyn PFFs on synaptogenesis and physiological function, which may be applicable to other types of synucleinopathies.