Miracle-dz/UniFAR-FTUs huggingface dataset:
Document Structure with IR Tools

The IRTools software toolkit was modified for 2003 to utilize a MySQL database for the inverted index. Indexing was for each occurrence of each term in the collection, with HTML structure, location offset, paragraph, and subdocument weight considered. This structure enables some more sophisticated queries than a “bag of words” approach. Post hoc results from the TREC 2002 Named Page Web task are presented, in which a staged fall through approach to topic processing yielded good results, with exact precision of 0.49. The paper also provides an overview of IRTools and its interactive interface, as well as an invitation for IR researchers to get involved with the GridIR standards formation process.
Temporal Dependence in Uncoupling of Blood Volume and Oxygenation during Interictal Epileptiform Events in Rat Neocortex

We investigated the dynamic spatiotemporal relationships of cerebral blood volume (CBV), deoxygenated hemoglobin (Hbr), and light scatter (LS) associated with interictal epileptiform events with multiwavelength optical recording of intrinsic signals and simultaneous field potential recording. Interictal spikes (IISs) were induced with iontophoresis of bicuculline methiodide in rat neocortex. Intrinsic signal changes appeared as early as 100 msec after the IIS at all wavelengths and could be appreciated after only a single IIS. Initially, the largest signal arose from a focal increase in deoxygenation, which lasted for ∼2 sec, consistent with an “initial dip. ” An equally early focal increase in CBV had a smaller amplitude than the Hbr signal until >2 sec after the IIS, when its amplitude surpassed that of the Hbr signal but also spread to a larger, less focal area. The most spatially restricted and smallest amplitude signal was produced by LS. A later hyperoxygenation, or increase in blood oxygenation level-dependent signal, was often seen in the draining veins but inconsistently seen in the IIS focus. An inverted optical signal was recorded at all wavelengths from multiple regions in the surrounding cortex within 100 msec of the IIS. We therefore conclude that the IIS induces a rapid increase in metabolic demand, which cannot be met by a rapid, initially focal but small increase in CBV that results in a prolonged increase in Hbr (epileptic dip in oxygenated hemoglobin). The inverted optical signal in the surround arises from a decrease in CBV and a decrease in Hbr, likely resulting from a combination of shunting of CBV to the focus and decreased metabolic demand resulting from decreased neuronal activity, consistent with “surround inhibition. ”
Oral Administration of Semicarbazide Limits Weight Gain together with Inhibition of Fat Deposition and of Primary Amine Oxidase Activity in Adipose Tissue

An enzyme hitherto named semicarbazide-sensitive amine oxidase (SSAO), involved in the oxidation of primary amines, is abundantly expressed in adipocytes. Although SSAO physiological functions remain unclear, several molecules inhibiting its activity have been described to limit fat accumulation in preadipocyte cultures or to reduce body weight gain in obese rodents. Here, we studied whether oral administration of semicarbazide, a prototypical SSAO inhibitor, limits fat deposition in mice. Prolonged treatment with semicarbazide at 0.125% in drinking water limited food and water consumption, hampered weight gain, and deeply impaired fat deposition. The adiposomatic index was reduced by 31%, while body mass was reduced by 15%. Such treatment completely inhibited SSAO, but did not alter MAO activity in white adipose tissue. Consequently, the insulin-like action of the SSAO substrate benzylamine on glucose transport was abolished in adipocytes from semicarbazide-drinking mice, while their insulin sensitivity was not altered. Although semicarbazide is currently considered as a food contaminant with deleterious effects, the SSAO inhibition it induces appears as a novel concept to modulate adipose tissue development, which is promising for antiobesity drug discovery.
Modular design of data-parallel graph algorithms

Amorphous Data Parallelism has proven to be a suitable vehicle for implementing concurrent graph algorithms effectively on multi-core architectures. In view of the growing complexity of graph algorithms for information analysis, there is a need to facilitate modular design techniques in the context of Amorphous Data Parallelism. In this paper, we investigate what it takes to formulate algorithms possessing Amorphous Data Parallelism in a modular fashion enabling a large degree of code re-use. Using the betweenness centrality algorithm, a widely popular algorithm in the analysis of social networks, we demonstrate that a single optimisation technique can suffice to enable a modular programming style without loosing the efficiency of a tailor-made monolithic implementation.
Short paper: a dangerous 'pyrotechnic composition': fireworks, embedded wireless and insecurity-by-design

Fireworks are used around the world to salute popular events such as festivals, weddings, and public or private celebrations. Besides their entertaining effects fireworks are essentially colored explosives which are sometimes directly used as weapons. Modern fireworks systems heavily rely on `wireless pyrotechnic firing systems'. Those `embedded cyber-physical systems' (ECPS) are able to remotely control pyrotechnic composition ignition. The failure to properly secure these computer sub-systems may have disastrous, if not deadly, consequences. They rely on standardized wireless communications, off the shelf embedded hardware and custom firmware. In this short paper, we describe our experience in discovering and exploiting a wireless firing system in a short amount of time without any prior knowledge of such systems. In summary, we demonstrate our methodology starting from analysis of firmware, the discovery of vulnerabilities and finally by demonstrating a real world attack. Finally, we stress that the security of pyrotechnic firing systems should be considered seriously, which could be achieved through improved safety compliance requirements and control.
2 Supersymmetric Yang-Mills and the Quantum Hall Effect

It is argued that there are strong similarities between the infra-red physics of N=2 supersymmetric Yang-Mills and that of the quantum Hall effect, both systems exhibit a hierarchy of vacua with a sub-group of the modular group mapping between them. The coupling flow for pure SU(2) N = 2 supersymmetric Yang-Mills in 4-dimensions is reexamined and an earlier suggestion in the literature, that was singular at strong coupling, is modified to a form that is well behaved at both weak and strong coupling and describes the crossover in an analytic fashion. Similarities between the phase diagram and the flow of SUSY Yang-Mills and that of the quantum Hall effect are then described, with the Hall conductivity in the latter playing the role of the θparameter in the former. Hall plateaux, with odd denominator filling fractions, are analogous to fixed points at strong coupling in N=2 SUSY Yang-Mills, where the massless degrees of freedom carry an odd monopole charge. PACS Nos. 11.10. Hi, 11.30. Pb, 12.60. Jv, 73.40. Hm
Design & Analysis of BWCM Model for Wireless Ad hoc Networks

Quality of Service (QoS) support in Mobile Ad-hoc NETworks (MANETs) is a challenging task. The major challenge in ad hoc networks lies in adapting multicast communication to environments, where mobility is unlimited and failures are frequent. Such problems increase the delays and decrease the throughput. To meet these challenges, to provide QoS, and hence to improve the performance, Bandwidth Control Management BWCM model can be used. In this paper, to provide the BWCM model that decrease MAC delay for real and non-real time application in wireless ad hoc network. In order to enhance the control of congestion, a BWCM model has been proposed for bandwidth management in mobile ad hoc networks that has a significant influence on the performance on network in term of delay. The proposed model achieves a reduction in terms of average delay by about 60-70% in comparison to the original model at a cost of about 15% decrease in throughput. The average delay obtained is quite stable and low under different channel conditions, mobility scenarios, and traffic scalability. The performance of this model is studied using NS2 simulator under different load and speed condition and DSDV as a routing protocol has been used. The proposed model to be an efficient tool for reducing the delay of real and non-real time application in MANET. Index Terms—NS2, DSDV, BWCM, MANET
M-MRAC backstepping for systems with unknown virtual control coefficients

The paper presents an over-parametrization free certainty equivalence state feedback backstepping adaptive control design method for systems of any relative degree with unmatched uncertainties and unknown virtual control coefficients. It uses a fast prediction model to estimate the unknown parameters, which is independent of the control design. It is shown that the system's input and output tracking errors can be systematically decreased by the proper choice of the design parameters. The benefits of the approach is demonstrated in numerical simulations.
Minimal realization of the dynamical structure function and its application to network reconstruction

Network reconstruction, i.e., obtaining network structure from data, is a central theme in systems biology, economics and engineering. In some previous work, we introduced dynamical structure functions as a tool for posing and solving the problem of network reconstruction between measured states. While recovering the network structure between hidden states is not possible since they are not measured, in many situations it is important to estimate the minimal number of hidden states in order to understand the complexity of the network under investigation and help identify potential targets for measurements. Estimating the minimal number of hidden states is also crucial to obtain the simplest state-space model that captures the network structure and is coherent with the measured data. This paper characterizes minimal order state-space realizations that are consistent with a given dynamical structure function by exploring properties of dynamical structure functions and developing an algorithm to explicitly obtain such a minimal realization.
Experimental Investigation of the Link between Eyebrow Movements and Turn-Taking

Following our work on the relationship between eyebrow movements and the fundamental frequency of the voice, this article presents the results of a study on the temporal location of rapid eyebrow movements with respect to speaking turns during dialogue. We used an automatic movement-acquisition system coupled with the simultaneous, synchronized recording of the vocal production. This procedure permits an objective analysis of eyebrow movements in relation to the vocal production. The data obtained show that the speakers' rapid eyebrow movements were associated with turn-taking (occurring on or before speaking turn onset). These findings suggest that rapid eyebrow movements are mainly linked to motivation and the intention to communicate.
Implied Volatility Spreads and Expected Market Returns

This article investigates the intertemporal relation between volatility spreads and expected returns on the aggregate stock market. We provide evidence for a significantly negative link between volatility spreads and expected returns at the daily and weekly frequencies. We argue that this link is driven by the information flow from option markets to stock markets. The documented relation is significantly stronger for the periods during which (i) S&P 500 constituent firms announce their earnings; (ii) cash flow and discount rate news are large in magnitude; and (iii) consumer sentiment index takes extreme values. The intertemporal relation remains strongly negative after controlling for conditional volatility, variance risk premium, and macroeconomic variables. Moreover, a trading strategy based on the intertemporal relation with volatility spreads has higher portfolio returns compared to a passive strategy of investing in the S&P 500 index, after transaction costs are taken into account.
AID-Targeting and Hypermutation of Non-Immunoglobulin Genes Does Not Correlate with Proximity to Immunoglobulin Genes in Germinal Center B Cells

Upon activation, B cells divide, form a germinal center, and express the activation induced deaminase (AID), an enzyme that triggers somatic hypermutation of the variable regions of immunoglobulin (Ig) loci. Recent evidence indicates that at least 25% of expressed genes in germinal center B cells are mutated or deaminated by AID. One of the most deaminated genes, c-Myc, frequently appears as a translocation partner with the Ig heavy chain gene (Igh) in mouse plasmacytomas and human Burkitt's lymphomas. This indicates that the two genes or their double-strand break ends come into close proximity at a biologically relevant frequency. However, the proximity of c-Myc and Igh has never been measured in germinal center B cells, where many such translocations are thought to occur. We hypothesized that in germinal center B cells, not only is c-Myc near Igh, but other mutating non-Ig genes are deaminated by AID because they are near Ig genes, the primary targets of AID. We tested this “collateral damage” model using 3D-fluorescence in situ hybridization (3D-FISH) to measure the distance from non-Ig genes to Ig genes in germinal center B cells. We also made mice transgenic for human MYC and measured expression and mutation of the transgenes. We found that there is no correlation between proximity to Ig genes and levels of AID targeting or gene mutation, and that c-Myc was not closer to Igh than were other non-Ig genes. In addition, the human MYC transgenes did not accumulate mutations and were not deaminated by AID. We conclude that proximity to Ig loci is unlikely to be a major determinant of AID targeting or mutation of non-Ig genes, and that the MYC transgenes are either missing important regulatory elements that allow mutation or are unable to mutate because their new nuclear position is not conducive to AID deamination.
Fundamentals of reperfusion injury for the clinical cardiologist.

Case presentation: S.B. is a 48-year-old man who suffered an acute anterior myocardial infarction and received fibrinolytic therapy. The patient died ≈12 hours after reperfusion. K.R. is a 68-year-old diabetic woman who underwent conventional coronary artery bypass graft surgery and developed low output syndrome after reperfusion postoperatively. V.A. is a 55-year-old man who developed a stunned myocardium after percutaneous coronary reperfusion. What is reperfusion injury, and why is it important? Reperfusion of coronary flow is necessary to resuscitate the ischemic or hypoxic myocardium. Timely reperfusion facilitates cardiomyocyte salvage and decreases cardiac morbidity and mortality. Reperfusion of an ischemic area may result, however, in paradoxical cardiomyocyte dysfunction, a phenomenon termed “reperfusion injury. ” Modalities for reperfusion include not only thrombolysis, but also percutaneous coronary intervention (PCI), coronary artery bypass grafting (CABG), and cardiac transplantation. Reperfusion injury has been observed in each of these situations. We discuss here the fundamental principles of reperfusion injury from a mechanistic and pharmacological standpoint. ### What is reperfusion injury, and why is it important? The myocardium can tolerate brief periods (up to 15 minutes) of severe and even total myocardial ischemia without resultant cardiomyocyte death. Although the cardiomyocytes suffer ischemic injury, the damage is reversible with prompt arterial reperfusion. Indeed, such transient periods of ischemia are encountered in the clinical situations of angina, coronary vasospasm, and balloon angioplasty, and are not associated with concomitant myocyte cell death.1,2⇓ With increasing duration and severity of ischemia, however, greater cardiomyocyte damage can develop, with a predisposition to a spectrum of reperfusion-associated pathologies, collectively called reperfusion injury.3 Reperfusion injury results in myocyte damage through myocardial stunning, microvascular and endothelial injury, and irreversible cell damage or necrosis (termed lethal reperfusion injury; Figure 1). 3,4⇓ Figure 1. Mechanisms and mediators of reperfusion injury. Reperfusion strategies are required to resuscitate the ischemic myocardium. In the clinical realm, these include …
Learning Markov Decision Processes for Model Checking

Constructing an accurate system model for formal model verification can be both resource demanding and time-consuming. To alleviate this shortcoming, algorithms have been proposed for automatically learning system models based on observed system behaviors. In this paper we extend the algorithm on learning probabilistic automata to reactive systems, where the observed system behavior is in the form of alternating sequences of inputs and outputs. We propose an algorithm for automatically learning a deterministic labeled Markov decision process model from the observed behavior of a reactive system. The proposed learning algorithm is adapted from algorithms for learning deterministic probabilistic finite automata, and extended to include both probabilistic and nondeterministic transitions. The algorithm is empirically analyzed and evaluated by learning system models of slot machines. The evaluation is performed by analyzing the probabilistic linear temporal logic properties of the system as well as by analyzing the schedulers, in particular the optimal schedulers, induced by the learned models.
Propensity Score Techniques to Evaluate Returns of College Education

This paper surveys the empirical evidence on causal effects of college education on earnings for China and compares alternative studies in the light of their underlying identifying assumptions. Recent data from a national survey, the Chinese Health and Family Life Survey (CHFLS), provide the empirical basis for the application of mathematical models for the return to college education. In the empirical analysis we assess the earning differential of college graduates versus high school graduates. Probit estimates show that parental kind of job, gender and urban influence positively the probability of obtaining a university degree. Then a matching method is used to estimate the effect of college achievement on earnings. Results suggest that eliminating selection bias college education has a significant positive impact on earnings. This conclusion leads to important policy implications both for the financing of college education and on individual decisions.
Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences

The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.
Live imaging of bidirectional traffic from the ERGIC

The endoplasmic reticulum-Golgi intermediate compartment (ERGIC) defined by the cycling lectin ERGIC-53 consists of tubulovesicular clusters, but it is unknown if these membranes are transport vehicles or stationary entities. Here, we show by live imaging that GFP-ERGIC-53 mainly localizes to long-lived stationary and some short-lived highly mobile elements. Unlike the anterograde marker VSV-G-GFP, GFP-ERGIC-53 does not vectorially move to the Golgi upon exit from the ERGIC, as assessed by a novel quantitative vector field method. Dual-color imaging of GFP-ERGIC-53 and a secretory protein (signal-sequence-tagged dsRed) reveals that the stationary elements are sites of repeated sorting of retrograde and anterograde cargo, and are interconnected by highly mobile elements. These results suggest that the ERGIC is stationary and not simply a collection of mobile carriers that mediate protein traffic from endoplasmic reticulum to Golgi.
Quantitative analysis of nucleic acid three-dimensional structures.

A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. The input of MC-Annotate is a PDB formatted DNA or RNA three-dimensional structure. The output of MC-Annotate is composed of a structural graph that contains the annotations, and a series of HTML documents, one for each nucleotide conformation and base-base interaction present in the input structure. The atomic coordinates of all nucleotides and the homogeneous transformation matrices of all base-base interactions are stored in the structural graph. Symbolic classifications of nucleotide conformations, using sugar puckering modes and nitrogen base orientations around the glycosyl bond, and base-base interactions, using stacking and hydrogen bonding information, are introduced. Peculiarity factors of nucleotide conformations and base-base interactions are defined to indicate their marginalities with all other examples. The peculiarity factors allow us to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization. The annotations attached to each nucleotide conformation include its class, its torsion angles, a distribution of the root-mean-square deviations with examples of the same class, the list of examples of the same class, and its peculiarity value. The annotations attached to each base-base interaction include its class, a distribution of distances with examples of the same class, the list of examples of the same class, and its peculiarity value. The distance between two homogeneous transformation matrices is evaluated using a new metric that distinguishes between the rotation and the translation of a transformation matrix in the context of nitrogen bases. MC-Annotate was used to build databases of nucleotide conformations and base-base interactions. It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base interactions in the regions where the RNA contacts the protein. The question of whether the current database of RNA three-dimensional structures is complete is addressed.
Validation challenges in model composition: The case of adaptive systems

Model Driven Engineering helps dealing with complexity by promoting models as abstraction units. Aspect Oriented Modeling helps separating concerns that crosscut across different models. MDE and AOM have well identified challenges that need to be addressed. However, there are new challenges that appear when combining both techniques. In this paper we present the challenges that appear when validating the model composition in the context of MDE and AOM applied to adaptive systems.