Miracle-dz/UniFAR-FTUs huggingface dataset:
Spontaneous oscillations of cytoplasmic free calcium ion concentration in cultured smooth muscle cells from guinea pig ileum.

The cytoplasmic free calcium ion concentration ([Ca2+]i) of cultured guinea pig ileum longitudinal muscle cells loaded with a fluorescent [Ca2+]i indicator, fura-2, was measured by digital ratio imaging microscopy. Spontaneous [Ca2+]i oscillations were observed in 25% to 80% of the cells, which differed with the batches of the cultured cells after 5 to 8 days in culture. The frequency and amplitude of the [Ca2+]i oscillations in each individual cell were usually regular, but heterogeneity between neighboring cells was observed. The spontaneous [Ca2+]i oscillations were also observed even after incubation of the cells under a serum-free condition for 72 hr. Exchange of extracellular solution to Ca(2+)-free solution containing EGTA or BAPTA immediately stopped the [Ca2+]i oscillations. The ratio of the oscillating cells was dependent on the extracellular calcium ion concentration ([Ca2+]o); and heterogeneity in the range of the [Ca2+]o to generate the [Ca2+]i oscillations was observed. An inorganic Ca(2+)-antagonist, LaCl3, immediately suppressed the [Ca2+]i oscillations, but the treatment with verapamil or nicardipine, Ca(2+)-channel blockers, did not have any effect on the [Ca2+]i oscillations. An inhibitor of the intracellular Ca2+ pump, thapsigargin, induced a transient increase in [Ca2+]i and then inhibited the spontaneous [Ca2+]i oscillations. Neomycin, a compound known to inhibit phosphoinositide turnover, inhibited the [Ca2+]i oscillations. (ABSTRACT TRUNCATED AT 250 WORDS)
Towards a Framework for Self-Adaptive Reliable Network Services in Highly-Uncertain Environments

In future inhomogeneous, pervasive and highly dynamic networks, end-nodes may often only rely on unreliable and uncertain observations to diagnose hidden network states and decide upon possible remediation actions. Inherent challenges exists to identify good and timely decision strategies to improve resilience of end-node services. In this paper we present a framework, called ODDR (Observation, Diagnosis, Decision, Remediation), for improving resilience of network based services through integration of self-adaptive monitoring services, network diagnosis, decision actions, and finally execution (and monitoring) of remediation actions. We detail the motivations to the ODDR design, then we present its architecture, and finally we describe our current activities towards the realization and assessment of the framework services and the main results currently achieved.
Extending the class of order-k delineable problems for the gene expression messy genetic algorithm

This paper revisits the recently introduced gene expression messy genetic algorithm (GEMGA) and offers some modifications to the extend the class of order-k delineable problems (class of problems that can be solved using a bounded order of relations) in GEMGA. The fundamental components that control the delineability of relations are reviewed in the light of the recently proposed SEARCH framework. Modified class and relation comparison statistics of GEMGA are proposed. The sample complexity of this improved version of GEMGA is shown to be subquadratic. Theoretical conclusions are also substantiated by experimental results for large, multimodal order-k delineable problems with respect to class average comparison statistic. We also present results for the recently constructed Goldberg-Lewei test functions.
Addressing high frequency effects in VLSI interconnects with full wave model and CFH

In order to accurately characterize dispersive system of VLSI interconnects at higher frequencies, full wave analysis which takes into account all possible field components and satisfies all boundary conditions is required. However, conventional circuit simulation of interconnects with full wave models is extremely CPU expensive. This paper presents a new method to extend the moment matching technique, complex frequency hopping, to the case of interconnects modeled with full wave analysis. Formulation of circuit equations is modified to incorporate interconnect stencil from full wave analysis. A new algorithm for the moment generation for interconnect networks with full wave models has been developed. Full wave analysis has been carried out with the efficient 'spectral domain approach'. Results have shown that the proposed method is accurate while it yields a speed up of one to three orders of magnitude over conventional simulation techniques.
Performance Modeling of Anonymity Protocols

Anonymous network communication protocols provide privacy for Internetbased communication. In this paper, we focus on the performance and scalability of anonymity protocols. In particular, we develop performance models for two anonymity protocols from the prior literature (Buses and Taxis), as well as our own newly proposed protocol (Motorcycles). Using a combination of experimental implementation, simulation, and analysis, we show that: (1) the message latency of the Buses protocol is O(N), scaling quadratically with the number of participants; (2) the message latency of the Taxis protocol is O(N), scaling linearly with the number of participants; and (3) the message latency of the Motorcycles protocol is O(log N), scaling logarithmically with the number of participants. Motorcycles can provide scalable anonymous network communication, without compromising the strength of anonymity provided by Buses or Taxis.
Delay optimization using SOP balancing

Reducing delay of a digital circuit is an important topic in logic synthesis for standard cells and LUT-based FPGAs. This paper presents a simple, fast, and very efficient synthesis algorithm to improve the delay after technology mapping. The algorithm scales to large designs and is implemented in a publicly-available technology mapper. The code is available online. Experimental results on industrial designs show that the method can improve delay after standard cell mapping by 30% with the increase in area 2.4%, or by 41% with the increase in area by 3.9%, on top of a high-effort synthesis and mapping flow. In a separate experiment, the algorithm was used as part of a complete industrial standard cell design flow, leading to improvements in area and delay after place-and-route. In yet another experiment, the algorithm was applied before FPGA mapping into 4-LUTs, resulting in 16% logic level reduction at the cost of 9% area increase on top of a high-effort mapping.
Reversible coagulation–fragmentation processes and random combinatorial structures: Asymptotics for the number of groups

The equilibrium distribution of a reversible coagulation‐fragmentation process (CFP) and the joint distribution of components of a random combinatorial structure (RCS) are given by the same probability measure on the set of partitions. We establish a central limit theorem for the number of groups (= components) in the case a(k) = qkp−1, k ≥ 1, q, p > 0, where a(k), k ≥ 1, is the parameter function that induces the invariant measure. The result obtained is compared with the ones for logarithmic RCS's and for RCS's, corresponding to the case p < 0. © 2004 Wiley Periodicals, Inc. Random Struct. Alg. 2004
Evaluation and comparison of natural language and graphical user interfaces in "query-by-impressions" scenes

Impression-based retrieval of multimedia content is the best way of finding items that suit the preferences, feelings, or mental states of users. This kind of system presents a relatively short set of words that denotes impressions and users estimate one or more words from this with a graphical user interface (GUI) to input into the system. With this approach, an increased number of words presented leads to increased costs for the user, in terms of the time and labor required to enter impressions. Conversely, a set of words that is too limited will often leave users unable to accurately represent their target impressions. We therefore compare the accuracy of retrieval and convenience of using an NLI (natural language interface) and GUI, which we introduced into an impression-based music-retrieval system. The results reveal their respective advantages and disadvantages, and suggest guidelines on the design of a better NLI.
A Runtime Framework for Adaptive Compositional Modeling

The rapid emergence of embedded devices and sensor networks that frequently exchange object-level images foretells an increasing reliance on object-level systems. Additionally, nearly all computing systems, including control systems, enterprise applications, scientific codes and dynamic libraries operate eventually at the object code level. Studying adaptivity and runtime composition issues in such systems is becoming an important focus of systems research. In this thesis, we describe an object-level framework that will manipulate an object module to instrument control functionality and adaptivity in order to realize complex compositional scenarios. Using function and parameter remapping capabilities, our framework transcends programming language and design boundaries, and enables applications to adapt dynamically during runtime. We introduce the capability to “restart” an application automatically, a feature we utilize to support adaptivity not only spatially, over the algorithm domain, but temporally as well. A high-level adaptive control language based on XML is presented that allows complex adaptive scenarios to be expressed concisely. Additionally, the construction of several adaptive scenarios using our framework is illustrated, along with several experiments in “learning adaptivity“ using reinforcement learning techniques.
Comparison of abstract decision encoding in the monkey 3 prefrontal cortex , the presupplementary and cingulate 4 motor areas 5 6 7 8

decision encoding. Two types of measurements were used for this evaluation. 439 First, we compared the decision SLR coefficients of decision neurons across the three 440 areas (ad, Figure 7A). Moreover, we related the strength of the decision processing of 441 these brain areas to their encoding strength of stimulus intensity, by intensity selective 442 neurons (aint, Figure 7B). We calculated a three-way ANOVA for the absolute values 443 of the SLR coefficients with the following factors: neuron type (intensityor decision444 coding), analysis phase (stimulus or delay phase), and recording area (PFC, preSMA, 445 CMAr). This analysis showed a significant effect of recording area (PFC: ad = 0.22; 446 preSMA ad = 0.27; CMAr ad = 0.24; p < 0.05, ANOVA). Post-hoc tests revealed that 447 preSMA showed significantly higher decision encoding strength than PFC (p < 0.01, 448 Wilcoxon test, Bonferroni corrected). No differences of decision encoding strength 449 were found between the analysis phases (p > 0.05, ANOVA). In all three areas the 450 encoding strength of the abstract decision (ad = 0.24) was significantly larger 451 compared to the encoding strength of stimulus intensity (aint = 0.04; p < 0.05, 452 ANOVA). 453 454 As a second measurement of the encoding strength, we used the choice probability 455 indices (sc) derived from salient and threshold trials for all recording areas during the 456 stimulus and delay phase, respectively. For a comparison of absolute differences of 457 choice probability indices, a chance discrimination level 0.5 was used (sc = | choice 458 probability – 0.5 | ). A three-way ANOVA with factors trial type (salient/threshold) × 459 trial phase (stimulus/delay phase) × recording area (preSMA, CMAr, PFC) showed a 460 significant effect of the recording area (Figure 13C, PFC: sc = 0.11; preSMA 461
Weighted frequency warping for voice conversion

This paper presents a new voice conversion method called Weighted Frequency Warping (WFW), which combines the well known GMM approach and the frequency warping approach. The harmonic plus stochastic model has been used to analyze, modify and synthesize the speech signal. Special phase manipulation procedures have been designed to allow the system to work in pitch-asynchronous mode. The experiments show that the proposed technique reaches a high degree of similarity between the converted and target speakers, and the naturalness and quality of the resynthesized speech is much higher than those of classical GMM-based systems.
Single Stock Circuit Breakers – Issues in Fragmented Markets 1

Since the May 6 , 2010 flash crash in the U.S., appropriate measure s ensuring safe, fair and reliable markets become more relevant from the pers pective of investors and regulators. Circuit breakers in various forms are already imple mented for individual markets to ensure price continuity and prevent potential market failu re and crash scenarios. However, coordinated inter-market safeguards have hardly bee n adopted, but are essential in a fragmented environment to prevent situations, where main markets halt trading but stock prices continue to decline as traders eventually mi grate to alternative markets. The objective of this paper is to provide insight into recent cir cu t breaker implementations, their individual specifications and potential coordination between v ues. Further, we empirically study the impact of circuit breakers in a single market and a fragmented market context. We find a decline in market volatility after the circuit brea ker, but at the cost of higher implicit trading costs. Moreover, by analyzing trading at the satell ite market during the home markets CB, we find market quality and price discovery to be sorel y afflicted as traders systematically retreat from trading. Only with the home market reentering trading, the satellite market restores pre circuit breaker market conditions.
The Impact of Body Mass Index on Short- and Long-Term Outcomes in Patients Undergoing Coronary Artery Graft Bypass

Objective This study was designed to investigate the impact of body mass index (BMI) on short- and long-term outcomes after initial revascularization with coronary artery bypass graft (CABG) surgery. Methods 4916 Chinese who consecutively underwent isolated, primary CABG at the Cardiovascular Institute of Fuwai Hospital from January 1, 1999 to December 31, 2005 were included in this study. They were classified based on BMI as follows: underweight: <18.5 kg/m2, normal weight: 18.5 to 23.9 kg/m2, overweight: 24 to 27.9 kg/m2, obesity: 28 to 32 kg/m2, and severe obesity: >32 kg/m2. Short (in-hospital) and long-term (5-years) major post-operative complications and mortalities were compared among various BMI groups after initial revascularization. Results Multiple regression analysis of five years follow-up of clinical end points indicated that various BMI groups were not associated with significant differences in 5 years mortality and MACCE, however, old age, smoking, hypertension, myocardial infarction and heart failure were the risk factor for the mortality. Conclusions In this large-scale study with long term follow-up after primary CABG in an exclusively ethnic Chinese population, we found that different BMI groups were not significantly associated with 5-years mortality and MACCE, however, old age, smoking, hypertension, myocardial infarction and heart failure were the risk factors of post-operative mortality, and old age, hypertension and heart failure increased the rate of MACCE.
Complete Description of Polarization Effects in Top Quark Decays Including Higher Order QCD Corrections

The complete set of matrix elements for all polarization configurations in top quark decays is presented including higher order QCD corrections. The analysis is done in the framework of the helicity formalism. The results can be used in a variety of circumstances, e.g. in the experimental analysis of top quark production and decay at Tevatron, LHC and NLC. Relations to LEP1 and LEP2 physics are pointed out.
Full-Exon Resequencing Reveals Toll-Like Receptor Variants Contribute to Human Susceptibility to Tuberculosis Disease

Tuberculosis (TB) is the leading cause of death worldwide due to an infectious agent. Data have accumulated over decades suggesting that variability in human susceptibility to TB disease has a genetic component. Toll-like receptors (TLRs) play a critical role in initiating the innate immune response to many pathogens in mouse models, but little is known about their role in human infections. Human TLRs have been reported to recognize mycobacterial antigens and initiate an immune response. We tested the hypothesis that amino acid-altering polymorphisms in five TLRs were associated with susceptibility to TB disease using a population-based case-control study with 1,312 adult TB patients and controls. Full-coding region sequencing of the five TLR genes in all 1,312 subjects yielded a data set in excess of 16 Mb. Rare nonsynonymous polymorphisms in TLR6-TLR1-TLR10 were significantly overrepresented among African-American TB cases compared with ethnically-matched control subjects. Common nonsynonymous polymorphisms in TLR6-TLR1-TLR10 also were significantly associated with TB disease in certain ethnic groups. Among African Americans, homozygotes for the common-variant haplotype TLR1-248S, TLR1-602I, and TLR6-249S had a significantly increased TB disease risk. A transmission/disequilibrium test on an independent sample found that the TLR1-248S variant was preferentially transmitted to diseased children, thereby confirming disease association. These results are consistent with recent reports implicating TLR1 variants, including TLR1-602, in significantly altered innate immune responses. Also consistent with disease association, rare TLR6 variants were defective in their ability to mediate NF-κB signal transduction in transfected human cells. Taken together, the data suggest that variant TLRs contribute to human susceptibility to TB disease. Extensive full-exon resequencing was critical for revealing new information about the role of TLRs in human-pathogen interactions and the genetic basis of innate immune function.
The Emerging Field of Human Social Genomics

Although we generally experience our bodies as being biologically stable across time and situations, an emerging field of research is demonstrating that external social conditions, especially our subjective perceptions of those conditions, can influence our most basic internal biological processes—namely, the expression of our genes. This research on human social genomics has begun to identify the types of genes that are subject to social-environmental regulation, the neural and molecular mechanisms that mediate the effects of social processes on gene expression, and the genetic polymorphisms that moderate individual differences in genomic sensitivity to social context. The molecular models resulting from this research provide new opportunities for understanding how social and genetic factors interact to shape complex behavioral phenotypes and susceptibility to disease. This research also sheds new light on the evolution of the human genome and challenges the fundamental belief that our molecular makeup is relatively stable and impermeable to social-environmental influence.
Improving the Performance of Overlapped Transmission with TCP in Multihop Ad Hoc Networks

Recently, new techniques have been proposed to allow multiple transmissions to occur in the same geographical area by using the communicators’ knowledge of some of the interfering packets to recover the desired information. Overlapped carrier-sense multiple-access (OCSMA), physical-layer network coding, analog network coding, and COPE are examples of this technique, for which we have coined the term overlapped transmission. Much of the previous research on overlapped transmission focuses on the physical-layer techniques; i.e., how the overlapped transmissions should be allowed to occur, how the signals should be designed and detected, and the error probabilities under different conditions. These works tend to make optimistic assumptions about the availability of packets to perform overlapped transmission: often performance is evaluated for a simple three-node network under the assumption that traffic is always available at each of the edge nodes. In this paper, we explain why these protocols may suffer under realworld traffic conditions because of directional traffic flows and congestion control at the transport layer. We then investigate how transmission control affects the performance of the OCSMA protocol. We propose modifications to the TCP parameters and the OCSMA protocol to improve the performance. We also show that OCSMA offers better fairness over the IEEE 802.11 MAC protocol in several scenarios.
Multivariate analysis and reverse engineering of signal transduction pathways

This thesis presents mathematical and computational approaches to studying signal transduction pathways. The biology of cellular signalling is introduced, highlighting the importance of signalling pathways in regulating the processes of cell division and proliferation. A brief history of mathematical approaches to such systems is presented. Two multivariate analysis methods, principal component analysis and clustering, are introduced and applied to both gene expression and simulated protein concentration data. Several recent reverse engineering methods that have been used to study genetic networks are introduced. Finally, a reverse engineering method intended to elucidate the structure of genetic networks is adapted to the study of signal transduction systems.
Multimatch D7.1 Evaluation Methodology Del 7.1 Evaluation Methodology Page 2 Di 18 Del 7.1 Evaluation Methodology Executive Summary Del 7.1 Evaluation Methodology

The aim of the MultiMatch evaluation activity will be to ensure that the individual components and the complete system prototypes are tested and that their development is assessed during the project life-cycle with respect to performance and usability (i.e. laboratory-based and user-centred evaluation). Component and system development will be monitored to ensure that the functional specifications defined in WP 1 are respected and performance evaluation will comprehend internal project assessment plus evaluation against external benchmarks. The usability testing will involve the MultiMatch user groups and a set of field trials will be organised. This first deliverable of Workpackage 7 describes the approaches that will be used in order to evaluate the MultiMatch system. It focuses in particular on the definition of the methodology to be used for Prototype 1 both with respect to the laboratory-based and the user-centred evaluation; an update will be released at 24 months providing final details on the evaluation processes decided for Prototype 2. Deliverables 7.2 and 7.3, to be consigned at 18 and 29 months respectively, will describe the results of the evaluation of Prototypes 1 and 2 at component and overall system level. Deliverable 7.4, to be consigned at 30 months, will describe the results of the field trials with the operational system. We adopt both laboratory-based and user-centred evaluation strategies in order to be able to assess as many aspects as possible of the system. The former will allow us to evaluate component and overall system performance mainly from the perspective of retrieval accuracy. For the first prototype we will build a set of test collections to enable us to perform some project internal evaluation of the different system components, comparing results obtained using with various settings and configurations in order to be able to tune and improve performance. We will also duplicate some of the past experiments of CLEF-the Cross-Language Evaluation Forum 1-so that we can compare performance against known benchmarks (as far as the availability of relevant data allows us). Our aim is to establish base-lines for the different components of the first prototype so that we can measure improvements achieved with the second prototype. However, measures of retrieval accuracy do not always correlate well with user satisfaction and overall system performance. The user-centred evaluations will thus aim at measuring the level of user satisfaction with the system and will focus on assessing the various user interfaces and the overall system …