Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-Agent Simulation: New Approaches to Exploring . . .

As part of the long term quest to develop more disaggregate, temporally dynamic models of spatial behaviour, micro-simulation has evolved to the point where the actions of many individuals can be computed. These multi-agent systems/simulation (MAS) models are a consequence of much better micro data, more powerful and user-friendly computer environments often based on parallel processing, and the generally recognised need in spatial science for modelling temporal process. In this paper, we develop a series of multi-agent models which operate in cellular space. These demonstrate the well-known principle that local action can give rise to global pattern but also how such pattern emerges as the consequence of positive feedback and learned behaviour. We first summarise the way cellular representation is important in adding new process functionality to GIS, and the way this is effected through ideas from cellular automata (CA) modelling. We then outline the key ideas of multi-agent simulation and this sets the scene for three applications to problems involving the use of agents to explore geographic space. We first illustrate how agents can be programmed to search route networks, finding shortest routes in ad hoc as well as structured ways equivalent to the operation of the Bellman-Dijkstra algorithm. We then demonstrate how the agent-based approach can be used to simulate the dynamics of water flow, implying that such models can be used to effectively model the evolution of river systems. Finally we show how agents can detect the geometric properties of space, generating powerful results that are not possible using conventional geometry, and we illustrate these ideas by computing the visual fields or isovists associated with different viewpoints within the Tate Gallery. Our forays into MAS are all based on developing reactive agent models with minimal interaction and we conclude with suggestions for how these models might incorporate cognition, planning, and stronger positive feedbacks between agents.
The Prospects of Epigenetics in Neuroscience

One of the known features of neuroprogenitors at early embryonic stages is their ploripotent property in generating diverse cell types during the brain development. Although the Darwinian theory of evolution could explain the origin of the species diversity based on random genetic mutations and natural selection, but it could not explain the cellular diversity in a single organism. In fact, after the discovery of DNA structure it became clear that the genetic material of all cells is the same in any specific organism. Waddington in1939 suggested that the same genetic materials may have diverse phenotypic outcome in different environments. He proposed the theory of epigenetic (means at the top of genetic) to explain the origin of cellular differentiation and the establishment of structural and functional characters of different cells in every organism (Waddington 1939). After decades advanced molecular techniques such as DNA methylation, histone modification, RNA editing and RNA interference (e.g. Micro RNA) were discovered to explore the molecular mechanisms of epigenetic regulation (reviewed in Abdolmaleky et al., 2004, 2008 and 2011a).
Intraoperative Cerebral Autoregulation Assessment Using Ultrasound-Tagged Near-Infrared-Based Cerebral Blood Flow in Comparison to Transcranial Doppler Cerebral Flow Velocity: A Pilot Study.

OBJECTIVE This was a pilot study comparing the ability of a new ultrasound-tagged near-infrared (UT-NIR) device to detect cerebral autoregulation (CA) in comparison to transcranial Doppler (TCD). DESIGN An unblinded, prospective, clinical feasibility study. SETTING Tertiary-care university hospital cardiac surgical operating rooms. PARTICIPANTS Twenty adult patients undergoing cardiac surgery with cardiopulmonary bypass (CPB). INTERVENTIONS There were no clinical interventions based on study monitoring devices, but a continuous correlation analysis of digital data from transcranial Doppler (TCD) velocity was compared with a novel UT-NIR device and correlation analysis of change signals versus mean arterial pressure was performed in order to detect presence or absence of intact CA and for determination of the lower limit of cerebral autoregulation during CPB. MEASUREMENTS AND MAIN RESULTS Similar and highly significant concordance (κ = 1.00; p<0.001) was demonstrated between the 2 methodologies for determination of CA, indicating good correlation between the 2 methodologies. Intact CA was absent in 2 patients during CPB, and both devices were able to detect this. CONCLUSIONS To the authors' knowledge this is the first clinical report of a UT-NIR device that shows promise as a clinically useful modality for detection of CA and the lower limit of cerebral autoregulation. The utility of UT-NIR was demonstrated further during times at which extensive usage of electrocautery or functional absence of the transcranial window rendered TCD uninterpretable.
Promoting Optimal Physical Exercise for Life: An Exercise and Self-Management Program to Encourage Participation in Physical Activity after Discharge from Stroke Rehabilitation—A Feasibility Study

People with stroke do not achieve adequate levels of physical exercise following discharge from rehabilitation. We developed a group exercise and self-management program (PROPEL), delivered during stroke rehabilitation, to promote uptake of physical activity after discharge. This study aimed to establish the feasibility of a larger study to evaluate the effect of this program on participation in self-directed physical activity. Participants with subacute stroke were recruited at discharge from one of three rehabilitation hospitals; one hospital offered the PROPEL program whereas the other two did not (comparison group; COMP). A high proportion (11/16) of eligible PROPEL program participants consented to the study. Fifteen COMP participants were also recruited. Compliance with wearing an accelerometer for 6 weeks continuously and completing physical activity questionnaires was high (>80%), whereas only 34% of daily heart rate data were available. Individuals who completed the PROPEL program seemed to have higher outcome expectations for exercise, fewer barriers to physical activity, and higher participation in physical activity than COMP participants (Hedge's g ≥ 0.5). The PROPEL program delivered during stroke rehabilitation shows promise for reducing barriers to exercise and increasing participation in physical activity after discharge. This study supports feasibility of a larger randomized trial to evaluate this program.
Cloning, Purification, and Characterization of a Heat- and Alkaline-Stable Endoglucanase B from Aspergillus niger BCRC31494

Endoglucanase B (EGLB) derived from Aspergillus niger BCRC31494 has been used in the food fermentation industry because of its thermal and alkaline tolerance. It was cloned and expressed in Pichia pastoris. According to sequence analysis, the gene open reading frame comprises 1,217 bp with five introns (GenBank GQ292753). According to sequence and protein domain analyses, EGLB was assigned to glycosyl hydrolase family 5 of the cellulase superfamily. Several binding sites were found in the promoter region. The purified recombinant enzyme was induced by 0.5% methanol, and it exhibited optimal activity at 70 °C and pH 4. EGLB was stable for 3 h at temperatures below 60 °C, with more than 90% of its activity remaining. The enzyme was specific for substrates with β-1,3 and β-1,4 linkages. In Lineweaver-Burk plot analysis, the Km and Vmax values of EGLB for β-D-glucan were 134 mg/mL and 4.68 U/min/mg, respectively. The enzyme activity was increased by 1.86-fold by Co2+ and by 2-fold by Triton X-100 and Tween 80. These favorable properties make EGLB a potential candidate for use in laundry and textile industrial applications.
ECONOMETRICS AND THE THEORY OF ECONOMIC POLICY: THE TINBERGEN-THEIL CONTRIBUTIONS 40 YEARS ON

IN 1986 we celebrated the 50th anniversary not only of the publication of Keynes' "General Theory", but also of the world's first econometric model. Between them, these two developments have probably had a greater impact on the scope of economic analysis than any other innovation this century. Keynes' contribution was the start of modern macroeconomics and, despite a major challenge from neoclassical economics, it remains the dominant paradigm in macroeconomic thinking. Tinbergen's econometric models of the Dutch and the US economies (Tinbergen 1936, 1939),1 built up from his business cycle research, started a revolution by opening up the possibility of forecasting analysis and policy evaluation with empirical models. Now there is hardly a government or agency, investment bank or market analyst without access to such models. At the time Tinbergen was writing a few empirical studies of the demand for agricultural products had been constructed in the US (Schultz, 1938), but the ability to use their results for policy purposes still lay in the future (Waugh, 1944). Tinbergen's models were therefore the first of a whole economy and the first to be aimed specifically at policy analysis (see Klaassen et al., 1959). At that time many countries were faced with major problems of unemployment, inadequate demand and investment. Tinbergen introduced his models to help him formulate corrective policies that were consistent across sectors and expenditure groups. From all this activity emerged Tinbergen's theory of economic policy. Every student now knows that an equal number of instruments and targets is a necessary condition for the existence of policies capable of reaching specified targets. But more significantly, his theory obliges policy makers to make an efficient, and consistent, use of their policy instruments. The crucial question then was, how should those targets be chosen? To resolve that, Theil introduced the flexible target approach: first you decide where you would like to go, and then you pick policies to steer the economy as
Linear Basis Models for Prediction and Analysis of Musical Expression

Abstract The quest for understanding how pianists interpret notated music to turn it into a lively musical experience, has led to numerous models of musical expression. Several models exist that explain expressive variations over the course of a performance, for example in terms of phrase structure, or musical accent. Often however expressive markings are written explicitly in the score to guide performers. We present a modelling framework for musical expression that is especially suited to model the influence of such markings, along with any other information from the musical score. In two separate experiments, we demonstrate the modelling framework for both predictive and explanatory modelling. Together with the results of these experiments, we discuss our perspective on computational modelling of musical expression in relation to musical creativity.
D04.05 - Feasibility mock-ups of feedback schedulers

Control and computation co-design deals with the interaction between feedback control laws design and their implementation on a real execution resource. Control design is often carried out in the framework of continuous time, or under the assumption of ideal sampling with equidistant intervals and known delays. Implementation on a real-time execution platform introduces many timing uncertainties and distortions to the ideal timing scheme, e.g. due to variable computation durations, complex preemption patterns between concurrent activities, uncertain network induced communication delays or occasional data loss. Analyzing, prototyping, simulating and guaranteeing the safety of complex control systems are very challenging topics. Models are needed for the mechatronic continuous system, for the discrete controllers and diagnosers, and for network behavior. Real-time properties (task response times) and the network Quality of Service (QoS) influence the controlled system properties (Quality of Control, QoC). To reach effective and safe systems it is not enough to provide theoretic control laws and leave programmers and real-time systems engineers just do their best to implement the controllers. This report first describes, through the detailed design of a quadrotor drone controller, the main features of {\sc Orccad}, an integrated development environment aimed to bridge the gap between advanced control design and real-time implementation. Besides control design and implementation, a real-time (hardware-in-the-loop) simulation has been designed to assess the control design with a simulated target rather than with the real plant. Using this HIL structure, several experiments using flexible real-time control features are reported, namely Kalman filters subject to data loss, control under (m,k)-firm constraints, control with varying sampling rates and feedback scheduling using the MPC approach.
A patch-clamp study of histamine-secreting cells

The ionic conductances in rat basophilic leukemia cells (RBL-2H3) and rat peritoneal mast cells were investigated using the patch-clamp technique. These two cell types were found to have different electrophysiological properties in the resting state. The only significant conductance of RBL-2H3 cells was a K+-selective inward rectifier. The single channel conductance at room temperature increased from 2-3 pS at 2.8 mM external K+ to 26 pS at 130 mM K+. This conductance, which appeared to determine the resting potential, could be blocked by Na+ and Ba2+ in a voltage-dependent manner. Rat peritoneal mast cells had a whole-cell conductance of only 10-30 pS, and the resting potential was close to zero. Sometimes discrete openings of channels were observed in the whole-cell configuration. When the Ca2+ concentration on the cytoplasmic side of the membrane was elevated, two types of channels with poor ion specificity appeared. A cation channel, observed at a Ca2+ concentration of approximately 1 microM, had a unit conductance of 30 pS. The other channel, activated at several hundred micromolar Ca2+, was anion selective and had a unit conductance of approximately 380 pS in normal Ringer solution and a bell-shaped voltage dependence. Antigenic stimulation did not cause significant changes in the ionic conductances in either cell type, which suggests that these cells use a mechanism different from ionic currents in stimulus-secretion coupling.
A fast image detection method using variance and variance covariance matrix

In this paper a new simple efficient algorithm for image descriptor using variance covariance matrix and variance calculations is presented. Also an approach to use this descriptor for image recognition is described. The recognition proceeds by matching individual features to a database of features from known images using a fast nearest-neighbor algorithm. We apply the full search algorithm to detect the matched image from a database which consists of 300 images. To reduce the search space, we use the variance constraint in our search. Feature matching is a simple nearest neighbor search under the distance metric and performs extremely rapidly using the variance and variance covariance matrix. The algorithm allows significant acceleration in the matching process. Experimental results are presented on image database. These results confirm the effectiveness of the proposed algorithm.
Prolonged Classical NF-κB Activation Prevents Autophagy upon E. coli Stimulation In Vitro: A Potential Resolving Mechanism of Inflammation

Activation of NF-κB is known to prevent apoptosis but may also act as proapoptotic factor in order to eliminate inflammatory cells. Here, we show that classical NF-κB activation in RAW 264.7 and bone marrow-derived macrophages upon short E. coli coculture is necessary to promote cell death at late time points. At 48 hours subsequent to short-term, E. coli challenge increased survival of NF-κB-suppressed macrophages was associated with pattern of autophagy whereas macrophages with normal NF-κB signalling die. Cell death of normal macrophages was indicated by preceding downregulation of autophagy associated genes atg5 and beclin1. Restimulation of macrophages with LPS at 48 hours after E. coli treatment results in augmented proinflammatory cytokine production in NF-κB-suppressed macrophages compared to control cells. We thus demonstrate that classical NF-κB activation inhibits autophagy and promotes delayed programmed cell death. This mechanism is likely to prevent the recovery of inflammatory cells and thus contributes to the resolution of inflammation.
Colon cancer survival rates with the new American Joint Committee on Cancer sixth edition staging.

BACKGROUND The recently revised American Joint Committee on Cancer (AJCC) sixth edition cancer staging system increased the stratification within colon cancer stages II and III defined by the AJCC fifth edition system. Using nationally representative Surveillance, Epidemiology, and End Results (SEER) data, we compared survival rates associated with colon cancer stages defined according to both AJCC systems. METHODS Using SEER data (from January 1, 1991, through December 31, 2000), we identified 119,363 patients with colon adenocarcinoma and included all patients in two analyses by stages defined by AJCC fifth and sixth edition systems. Tumors were stratified by SEER's "extent of disease" and "number of positive [lymph] nodes" coding schemes. Kaplan-Meier analyses were used to compare overall and stage-specific 5-year survival. All statistical tests were two-sided. RESULTS Overall 5-year survival was 65.2%. According to stages defined by the AJCC fifth edition system, 5-year stage-specific survivals were 93.2% for stage I, 82.5% for stage II, 59.5% for stage III, and 8.1% for stage IV. According to stages defined by the AJCC sixth edition system, 5-year stage-specific survivals were 93.2% for stage I, 84.7% for stage IIa, 72.2% for stage IIb, 83.4% for stage IIIa, 64.1% for stage IIIb, 44.3% for stage IIIc, and 8.1% for stage IV. Under the sixth edition system, 5-year survival was statistically significantly better for patients with stage IIIa colon cancer (83.4%) than for patients with stage IIb disease (72.2%) (P<.001). CONCLUSIONS The AJCC sixth edition system for colon cancer stratifies survival more distinctly than the fifth edition system by providing more substages. The association of stage IIIa colon cancer with statistically significantly better survival than stage IIb in the new system may reflect current clinical practice, in which stage III patients receive chemotherapy but stage II patients generally do not.
Functional cortical cartography

My research has focused on understanding the relationship between structure and function in the human brain. Just like fingerprints, each person has a unique folding pattern in their brain. This convoluted folding pattern is surely part of what makes us individuals, but also introduces some difficulties into the field of neuroimaging. First among these difficulties is the challenge of ensuring you can compare the same brain area across a population of subjects. By using advanced analysis techniques I was able to create probabilistic maps of function brain areas, allowing one to predict the function of a particular brain area, only by knowing its anatomical location. Furthermore, I developed new analysis techniques to improve the effectiveness of group brain imaging studies. Finally, I used these new techniques to track the development of the brain’s auditory system, in structure and function, through childhood, adolescence and into adulthood.
FCC: Three Approaches for Semantic Textual Similarity

In this paper we describe the three approaches we submitted to the Semantic Textual Similarity task of SemEval 2012. The first approach considers to calculate the semantic similarity by using the Jaccard coefficient with term expansion using synonyms. The second approach uses the semantic similarity reported by Mihalcea in (Mihalcea et al., 2006). The third approach employs Random Indexing and Bag of Concepts based on context vectors. We consider that the first and third approaches obtained a comparable performance, meanwhile the second approach got a very poor behavior. The best ALL result was obtained with the third approach, with a Pearson correlation equal to 0.663.
Ordering the Preference Hierarchies for Internal Finance, Bank Loans, Bond and Share Issues

We estimate the incremental financing decision for a sample of some 150Dutch companies for the years 1984 through 1997, thereby distinguishinginternal finance and three types of external finance: bank borrowing, bondissues and share issues. First, we estimate a multinomial logit model whichconfirms several predictions of both the static trade-off theory and thepecking-order theory as to the determinants of financing choices. Next, weuse ordered probit models to determine which financing hierarchy fits thedata best. The results suggest that Dutch firms have a most-preferredfinancing hierarchy: (i) internal finance, (ii) bank loans, (iii) shareissues, (iv) bonds issues.
Reconciling Bilateral Trade Data for Use in GTAP

Bilateral trade flows are reported by both importers and exporters. Large discrepancies in reported import/export trade flows can be found when these two reports are compared. The GTAP database requires consistency between the export flow and its corresponding import flow for all partner pairs. Therefore, bilateral trade data in its reported form cannot be directly used for GTAP. Various methods can be used to produce a consistent set of bilateral trade flows. However, achieving consistency alone does not necessarily provide credible trade flows. Matrix balancing using trade totals published by international agencies is not appropriate since these totals are not reconciled but are simply totals from country-reported flows. A method is developed with the aim of extracting the most reliable reported trade flows from reported import and export flows. Specific examples are used to illustrate how discrepancies can result from reporting errors and transport margins. Evidence is shown indicating that discrepancies often arise from erroneous reporting by one of the partners. Systematic reporting errors associated with a reporter can be measured by the share of consistent transactions with partners. The most reliable reported flows are selected based on credibility of reporters. The source of international bilateral trade for GTAP is United Nations COMTRADE database. It contains the complete set of countries in the world and the set of commodities covering total merchandise trade. Since errors in reporting are country-commodity specific, data is processed at the individual country and SITC 4-digit level before aggregating to the 30-region 31- merchandise trade commodity database in version 3 of the GTAP data base.
PROPOSAL FOR SEQUENCING FURTHER ECHINODERM GENOMES FOR THE PURPOSES OF GLOBAL GENE REGULATORY NETWORK ANALYSIS

Gene regulatory networks (GRNs), when solved, provide immediate and predictive access to the specific functional termini at which genomic sequence determines the logic of the organismal regulatory system. GRN topology explains the fundamental processes of development (1), including dynamics (2), major evolutionary transitions (3), many aspects of physiological function, and normal and diseased regulatory states; and GRN structure also provides the only kind of blueprint on which to base rational strategies for re-engineering of developmental process (4,5). Thus in the next period of bioscience the elucidation of GRNs must become a major, targeted objective.
Encapsulation Methods for Transport of Asynchronous Transfer Mode (ATM) over MPLS Networks

An Asynchronous Transfer Mode (ATM) Pseudowire (PW) is used to carry ATM cells over an MPLS network. This enables service providers to offer "emulated" ATM services over existing MPLS networks. This document specifies methods for the encapsulation of ATM cells within a pseudowire. It also specifies the procedures for using a PW to provide an ATM service. [STANDARDS-TRACK]