Miracle-dz/UniFAR-FTUs huggingface dataset:
CONTINUOUS TIME CORRELATION ANALYSIS TECHNIQUES FOR SPIKE TRAINS By IL PARK A THESIS PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF

of Thesis Presented to the Graduate School of the University of Florida in Partial Fulfillment of the Requirements for the Degree of Master of Science CONTINUOUS TIME CORRELATION ANALYSIS TECHNIQUES FOR SPIKE TRAINS By Il Park May 2007 Chair: Jóse Carlos Pŕıncipe Major: Electrical and Computer Engineering Correlation is the most basic analysis tool for time series. To apply correlation to train of action potentials generated by neurons, the conventional method is to discretize the time. However, time binning is not optimal: time resolution is sacrificed, and it introduces the notorious problem of bin size sensitivity. Since spike trains can be considered as a realization of a point process, the signal has no amplitude and all information is embedded in the times of occurrence. Instead of time binning, we propose a set of methods based on kernel smoothing to analyze the correlations. Smoothing is done in continuous time so we do not lose the exact time of spikes while enabling interaction between spikes at a distance. We present three techniques derived from correlation: (1) spike train similarity measure, (2) synchrony detection mechanism, and (3) continuous cross correlogram.
On the X-ray emission of z ∼2 radio galaxies : IC scattering of the CMB and no evidence for fully-formed potential wells

We present the results of 20 ks Chandra observations for each of 5 radio galaxies in the redshift range $2.0 -2 ) may be surrounding the nuclei. We detect X-ray emission coincident with the radio hotspots or lobes in 4 of the 5 targets. This extended emission can be explained by the Inverse-Compton (IC) scattering of photons that make up the cosmic microwave background (CMB). The magnetic field strengths of ${\sim}100{-}200$ μ G that we derive agree with the equipartition magnetic field strengths. The relative ease with which the lobe X-ray emission is detected is a consequence of the $(1+z)^4$ increase in the energy density of the CMB. For one of the lobes, the X-ray emission could also be produced by a reservoir of hot, shocked gas. An HST image of the region around this radio component shows bright optical emission reminiscent of a bow-shock. By co-adding the 5 fields we created a deep, 100 ks exposure to search for diffuse X-ray emission from thermal intra-cluster gas. We detect no diffuse emission and derive upper limits of ${\sim}10^{44}$ erg s -1 , thereby ruling out a virialized structure of cluster-size scale at $z\sim2$. The average number of soft X-ray sources in the field surrounding the radio sources is consistent with the number density of AGN in the Chandra Deep Fields, with only one of the fields showing a marginally statistically significant factor 2 excess of sources with $f_{0.5-2~\rm~keV}>3\times10^{-15}$ erg s -1 cm -2 . Analysis of the angular distribution of the field sources shows no evidence for large-scale structure associated with the radio galaxies, as was observed in the case of PKS 1138-262 by [CITE].
Content-based video similarity model

The most commonly used method for content-based video retrieval is query by example. But the definition of video similarity brings great obstacle to further research. This paper puts forward a new approach to solve the difficulty. Firstly, it advances centroid feature vector of shot in order to reduce the storage of video database. Secondly, considering all the factors existing in human vision perception, it introduces a new comparison algorithm based on multi-granularity of video structure, which has great flexibility. Thirdly, after getting the similar video set, we take a brand-new method of feedback to adjust weight based on video similarity model. In this way, retrieval result can be optimized greatly.
Scale-up graph processing in the cloud: challenges and solutions

Processing large graphs is an important part of the big-data problem. Recently a number of scale-up systems such as X-Stream, Graphchi and Turbograph have been proposed for processing large graphs using secondary storage on a single machine. The design and evaluation of these systems however have focused on physical machines. We expect that a natural evolution of such systems is to the cloud where a virtual machine would run the graph processing algorithm and access the graph from secondary storage remotely connected through the network. We evaluate a state of the art graph processing system called X-Stream in EC2 to identify challenges in this space. Our primary finding is that the network bandwidth between a virtual machine and remote storage becomes the limiter for performance. We show that this bottleneck can be somewhat alleviated through the use of VM local instance storage, network provisioning and compression.
The tail-module of yeast Mediator complex is required for telomere heterochromatin maintenance

Eukaryotic chromosome ends have a DNA–protein complex structure termed telomere. Integrity of telomeres is essential for cell proliferation. Genome-wide screenings for telomere length maintenance genes identified several components of the transcriptional regulator, the Mediator complex. Our work provides evidence that Mediator is involved in telomere length regulation and telomere heterochromatin maintenance. Tail module of Mediator is required for telomere silencing by promoting or stabilizing Sir protein binding and spreading on telomeres. Mediator binds on telomere and may be a component of telomeric chromatin. Our study reveals a specific role of Mediator complex at the heterochromatic telomere and this function is specific to telomeres as it has no effect on the HMR locus.
Role of Nitric Oxide Synthase Family in Diabetic Neuropathy

Diabetes mellitus is one of the most common chronic diseases and a major health problem in nearly all countries. Its prevalence has risen sharply worldwide during the past few decades. The increase in its prevalence is largely due to an epidemic of type 2 diabetes (T2DM) but also the type 1 diabetes (T1DM) incidence is rising all over the world. The “classical” microvascular complications of both types of diabetes are represented by diabetic retinopathy, diabetic renal disease, and diabetic polyneuropathy (DPN). The latter has known to be heterogeneous regarding symptoms, pattern of neurologic involvement, and progression in time, pathologic alterations, and underlying mechanisms. DPN results from the direct damage of peripheral nerve components and of the associated vasa nervorum. The main contributor to the DPN development is the cumulative effect of chronic hyperglycemia - duration of diabetes and level of metabolic control. Apart the major role of hyperglycemia one of the most important factor is nitric oxide (NO) system. The NO production and local release are dramatically changed and contribute to the DPN development. The process takes place by the modulation of the nitric oxide synthase (NOS) enzymes responsible for NO synthesis by the diabetic milieu. While the decline in NO bioavailability is due to the decrease in neuronal (NOS1) and endothelial (NOS3) expression, the increase of local NO levels with the formation of peroxynitrites arises from the upregulation of inducible (NOS2) protein. Thus, NOS genes became natural candidates for the study of DPN genetics. In comparison with the other diabetes microvascular complications, data regarding the genetic background of DPN are rather scarce, particularly for NOS genes. The aim of this review is to present the pathogenesis of DPN in both type 1 and type 2 diabetes and the effect of the NOS genes-NOS enzymes-NO system.
Privacy and interaction in quantum communication complexity and a theorem about the relative entropy of quantum states

We prove a fundamental theorem about the relative entropy of quantum states, which roughly states that if the relative entropy, S(/spl rho//spl par//spl sigma/)/spl Delta/=Tr /spl rho/(log /spl rho/-log /spl sigma/), of two quantum states /spl rho/ and /spl sigma/ is at most c, then /spl rho//2/sup O(c)/ 'sits inside' /spl sigma/. Using this 'substate' theorem, we give tight lower bounds for the privacy loss of bounded error quantum communication protocols for the index function problem. We also use the 'substate' theorem to give tight lower bounds for the k-round bounded error quantum communication complexity of the pointer chasing problem, when the wrong player starts, and all the log n bits of the kth pointer are desired.
On a dynamic topology of covert groups

The problem of detecting hidden communities in large-scale networks has a long history in traffic analysis from secret societies evading detection to spy agencies datamining call record information looking for criminals. Graph theoretic partitioning is a well studied topic in both computer science and sociology. However, these methods are based on discovering communities by the narrow intuition of minimal edge cut-sets additionally we found these methods to have poor tolerance to random addition and removal of vertices and edges from the graph with an exponential rise in community mis-detection error. Recent work on partitioning techniques in the complex networks literature offer better tools to the covert community hunter. Based on a broader intuition of maximizing modularity, these methods can accurately delineate community boundaries, while tolerating random errors fairly well. While much attention has been paid to their role in increasing our knowledge about network structure and dynamics, lesser attention has been paid to the privacy and anonymity aspects of revealing social structure in large technological networks. We make a start on this problem, by analyzing the ability of simple community hiding strategies to withstand a community detection attack by a well organized globally knowledgeable adversary, in a theoretical Erdos-Renyi network as well as a real world email communication network. We find that asking members of a secret group, to randomly initiate contact with members of the network does not help. Pure strategies connecting highly central elements in the covert group to other central elements does not help either. However, when members resort to hybrid strategies of topology manipulation, we find a striking result: the introduction of contact between the most central covert elements and random members of the network, allows up to 92% of the covert group to remain hidden from the detection algorithm. Even more importantly, locally computable centrality measures work equally well as those calculated with global topology knowledge. Our findings as much relevance to sybil attacks in sensor networks, as to dissident groups secret societies that wish to protect themselves against a repressive regime.
Modeling the M(t)=M=s(t) Queue with an Exhaustive Discipline

The M=M=s queueing model assumes arrival rates, service rates, and number of servers to be constant in time. It is straightforward to extend the model to allow a time-varying arrival rate and a time-varying service rate, and the resulting models can be solved numerically using standard solvers for ordinary difierential equations. The extension to a time-varying number of servers requires consideration of the behavior of a server that is providing service when scheduled to leave. Past work has (implicitly or explicitly) assumed a pre-emptive discipline, where the customer rejoins the queue. We demonstrate how to model an exhaustive discipline that is often more realistic, where servers complete their current service before leaving. We discuss how to compute the virtual waiting time distribution for this model and outline its extension to incorporate customer abandonments.
Gene Network Biological Validity Based on Gene-Gene Interaction Relevance

In recent years, gene networks have become one of the most useful tools for modeling biological processes. Many inference gene network algorithms have been developed as techniques for extracting knowledge from gene expression data. Ensuring the reliability of the inferred gene relationships is a crucial task in any study in order to prove that the algorithms used are precise. Usually, this validation process can be carried out using prior biological knowledge. The metabolic pathways stored in KEGG are one of the most widely used knowledgeable sources for analyzing relationships between genes. This paper introduces a new methodology, GeneNetVal, to assess the biological validity of gene networks based on the relevance of the gene-gene interactions stored in KEGG metabolic pathways. Hence, a complete KEGG pathway conversion into a gene association network and a new matching distance based on gene-gene interaction relevance are proposed. The performance of GeneNetVal was established with three different experiments. Firstly, our proposal is tested in a comparative ROC analysis. Secondly, a randomness study is presented to show the behavior of GeneNetVal when the noise is increased in the input network. Finally, the ability of GeneNetVal to detect biological functionality of the network is shown.
Sequential decision making with vector outcomes

We study a multi-round optimization setting in which in each round a player may select one of several actions, and each action produces an outcome vector, not observable to the player until the round ends. The final payoff for the player is computed by applying some known function f to the sum of all outcome vectors (e.g., the minimum of all coordinates of the sum). We show that standard notions of performance measure (such as comparison to the best single action) used in related expert and bandit settings (in which the payoff in each round is scalar) are not useful in our vector setting. Instead, we propose a different performance measure, and design algorithms that have vanishing regret with respect to our new measure.
A Framework for Managing and Analyzing Changes of Security Policies

Modern enterprise systems need to comply to complex security policies. Due to legal regulations such as Basel II or \acs{hipaa}, the enforcement of these security policies needs to be carefully monitored and analyzed. The monitoring of complex and often dynamic access control requirements results in a vast amount of information that needs to be analyzed both in case of incidents and during regular audits. We present an extensible framework for managing and analyzing security policies during their whole life cycle. Our framework integrates versioning of policies and log files with policy animation, static analysis, and debugging techniques. For example, this combination allows for comparing different versions of security policies or the replaying and animation of system traces based on log files.
The actin-binding protein comitin (p24) is a component of the Golgi apparatus

Comitin (p24) was first identified in Dictyostelium discoideum as a membrane-associated protein which binds in gel overlay assays to G and F actin. To analyze its actin-binding properties we used purified, bacterially expressed comitin and found that it binds to F actin in spin down experiments and increases the viscosity of F actin solutions even under high-salt conditions. Immunofluorescence studies, cell fractionation experiments and EM studies of vesicles precipitated with comitin-specific monoclonal antibodies showed that comitin was present in D. discoideum on: (a) a perinuclear structure with tubular or fibrillary extensions; and (b) on vesicles distributed throughout the cell. In immunofluorescence experiments using comitin antibodies NIH 3T3 fibroblasts showed a similar staining pattern as D. discoideum cells. Using bona fide Golgi markers the perinuclear structure was identified as the Golgi apparatus. The results were supported by an electron microscopic study using cryosections. Based on these data we propose that also in Dictyostelium the stained perinuclear structure is the Golgi apparatus. In vivo the perinuclear structure was found to be attached to the actin and the microtubule network. Alteration of the actin network or depolymerization of the microtubules led to its dispersal into vesicles distributed throughout the cell. These results suggest that the Golgi apparatus in D. discoideum is connected to the actin network by comitin. This protein seems also to be present in mammalian cells.
Random Access in DVB-RCS2: Design and Dynamic Control for Congestion Avoidance

In the current DVB generation, satellite terminals are expected to be interactive and capable of transmission in the return channel with satisfying quality. Considering the bursty nature of their traffic and the long propagation delay, the use of a random access technique is a viable solution for such a Medium Access Control (MAC) scenario. In this paper, random access communication design in DVB-RCS2 is considered with particular regard to the recently introduced Contention Resolution Diversity Slotted Aloha (CRDSA) technique. This paper presents a model for design and tackles some issues on performance evaluation of the system by giving intuitive and effective tools. Moreover, dynamic control procedures that are able to avoid congestion at the gateway are introduced. Results show the advantages brought by CRDSA to DVB-RCS2 with regard to the previous state of the art.
Characterization of Genetic Structure and Genealogies Using RAPD-PCR Markers: A Random Primer for the Novice and Nervous

CONTENTS SYNOPSIS INTRODUCTION WHAT ARE RAPDs Introduction Scoring RAPD Polymorphisms Sources of Polymorphism and Amplification Artifacts Population Genetic, Genealogical, and Phylogenetic Implications of Dominance and Cryptic Variation: A Preliminary Overview PROBLEMS WITH RAPD-PCR AND SOME REMEDIES Repeatability of Banding Patterns Within and Among Individuals Background Some Remedies Comigration of Bands Background Some Remedies
Imaging calcium dynamics in living plants using semi-synthetic recombinant aequorins

The genetic transformation of the higher plant Nicotiana plumbaginifolia to express the protein apoaequorin has recently been used as a method to measure cytosolic free calcium ([Ca2+]i) changes within intact living plants (Knight, M. R., A. K. Campbell, S. M. Smith, and A. J. Trewavas. 1991. Nature (Lond.). 352:524-526; Knight, M. R. , S. M. Smith, and A. J. Trewavas. 1992. Proc. Natl. Acad. Sci. USA. 89:4967-4971). After treatment with the luminophore coelenterazine the calcium-activated photoprotein aequorin is formed within the cytosol of the cells of the transformed plants. Aequorin emits blue light in a dose-dependent manner upon binding free calcium (Ca2+). Thus the quantification of light emission from coelenterazine-treated transgenic plant cells provides a direct measurement of [Ca2+]i. In this paper, by using a highly sensitive photon-counting camera connected to a light microscope, we have for the first time imaged changes in [Ca2+]i in response to cold-shock, touch and wounding in different tissues of transgenic Nicotiana plants. Using this approach we have been able to observe tissue-specific [Ca2+]i responses. We also demonstrate how this method can be tailored by the use of different coelenterazine analogues which endow the resultant aequorin (termed semi-synthetic recombinant aeqorin) with different properties. By using h-coelenterazine, which renders the recombinant aequorin reporter more sensitive to Ca2+, we have been able to image relatively small changes in [Ca2+]i in response to touch and wounding: changes not detectable when standard coelenterazine is used. Reconstitution of recombinant aequorin with another coelenterazine analogue (e-coelenterazine) produces a semi-synthetic recombinant aequorin with a bimodal spectrum of luminescence emission. The ratio of luminescence at two wavelengths (421 and 477 nm) provides a simpler method for quantification of [Ca2+]i in vivo than was previously available. This approach has the benefit that no information is needed on the amount of expression, reconstitution or consumption of aequorin which is normally required for calibration with aequorin.
La pauvreté persistante : un phénomène de classe, de cumul de désavantages ou d'individualisation?

The article evaluates the predictive value of three approaches towards poverty: social class, cumulative disadvantage and individualization. Data from the Swiss Household Panel are used. Consistent poverty is defined by low income and deprived living conditions, persistent poverty as being poor at three out of five points of measurement between 1999 and 2003. The individualization approach predicts persistent poverty better than the cumulative disadvantage approach, but is less predictive than social class. In contrast to social class that captures the stable nature of poverty over time, the individualization approach gives an account of its transitory nature. The results suggest that the three approaches do not apply with the same accuracy to gender specific situations.
Federal Reserve Bank of New York Staff Reports Interpreting the Great Moderation: Changes in the Volatility of Economic Activity at the Macro and Micro Levels

This paper presents preliminary findings and is being distributed to economists and other interested readers solely to stimulate discussion and elicit comments. The views expressed in the paper are those of the authors and are not necessarily reflective of views at the Federal Reserve Bank of New York or the Federal Reserve System. Any errors or omissions are the responsibility of the authors.
Transcriptome-wide studies of merkel cell carcinoma and validation of intratumoral CD8+ lymphocyte invasion as an independent predictor of survival.

PURPOSE Merkel cell carcinoma (MCC) is a polyomavirus-associated skin cancer that is frequently lethal and lacks established prognostic biomarkers. This study sought to identify biomarkers that improve prognostic accuracy and provide insight into MCC biology. PATIENTS AND METHODS Gene expression profiles of 35 MCC tumors were clustered based on prognosis. The cluster of genes overexpressed in good-prognosis tumors was tested for biologic process enrichment. Relevant mRNA expression differences were confirmed by quantitative polymerase chain reaction and immunohistochemistry. An independent set of 146 nonoverlapping MCC tumors (median follow-up, 25 months among 116 living patients) was employed for biomarker validation. Univariate and multivariate Cox regression analyses were performed. RESULTS Immune response gene signatures were prominent in patients with good prognoses. In particular, genes associated with cytotoxic CD8+ lymphocytes were overexpressed in tumors from patients with favorable prognoses. In the independent validation set, cases with robust intratumoral CD8+ lymphocyte infiltration had improved outcomes (100% MCC-specific survival, n = 26) compared with instances characterized by sparse infiltration (60% survival, n = 120). Only stage and intratumoral CD8 infiltration (but not age, sex, or CD8+ lymphocytes localized to the tumor-stroma interface) were significant in both univariate and multivariate Cox regression analyses. Notably, traditional histologic identification of tumor-infiltrating lymphocytes was not a significant independent predictor of survival. CONCLUSION Intratumoral CD8+ lymphocyte infiltration can be readily assessed on paraffin-embedded tissue, is independently associated with improved MCC-specific survival, and therefore, may provide prognostic information that enhances established MCC staging protocols.