Miracle-dz/UniFAR-FTUs huggingface dataset:
Predictive systems ecology

Human societies, and their well-being, depend to a significant extent on the state of the ecosystems that surround them. These ecosystems are changing rapidly usually in response to anthropogenic changes in the environment. To determine the likely impact of environmental change on ecosystems and the best ways to manage them, it would be desirable to be able to predict their future states. We present a proposal to develop the paradigm of predictive systems ecology, explicitly to understand and predict the properties and behaviour of ecological systems. We discuss the necessary and desirable features of predictive systems ecology models. There are places where predictive systems ecology is already being practised and we summarize a range of terrestrial and marine examples. Significant challenges remain but we suggest that ecology would benefit both as a scientific discipline and increase its impact in society if it were to embrace the need to become more predictive.
A high resolution bladder wall map: Feasibility study

The aim of this work is to provide the surgeon-urologist with a system for automatic 2D and 3D-reconstruction of the bladder wall to help him within the treatment of bladder cancer as well as planning and documentation of the interventions. Within this small pilot-framework a fast feasibility study was made to clear if it is generally possible to build a bladder wall model using a special endoscope with an embedded laser-based distance measurement, an optical navigation system and modern image stitching techniques. Some experiments with a realistic bladder phantom have shown that this initial concept is generally acceptable and can be used with some extensions to build a system which can provide an automatic bladder wall reconstruction in real time to be used within a surgical intervention.
Resource allocation for QOS-aware OFDMA cellular networks with cooperative relaying

This paper proposes a QoS-aware resource allocation scheme, called as cooperative resource allocation scheme (CoRA), for relay-based OFDMA systems with both QoS and Best-effort (BE) users. Using CoRA, cooperative transmission between the Base-station (BS) and the Relay-station (RS) is employed to fulfill the requirements of QoS users. Moreover, resource scheduling is allowed not only at the BS but also at each RS to fully exploit time-varying channel state and multiuser diversity, so as to achieve efficient radio resource utilization. The design of subchannel and power allocation in CoRA can be formulated as a non-linear combinatorial optimization problem, which aims at maximizing the system utility while satisfying the data rate requirements of QoS users and the separate transmission power constraints at both BS and RSs. To address the prohibitively high computational complexity in solving the optimization problem, we decompose the global optimization problem in CoRA into subchannel allocation and power control sub-problems as a suboptimal solution. Numerical results demonstrate that our proposed CoRA scheme is able to significantly improve the network performance in terms of power saving, user utilities, system throughput, as well as the number of admitted users.
SpyTag/SpyCatcher Cyclization Enhances the Thermostability of Firefly Luciferase

SpyTag can spontaneously form a covalent isopeptide bond with its protein partner SpyCatcher. Firefly luciferase from Photinus pyralis was cyclized in vivo by fusing SpyCatcher at the N terminus and SpyTag at the C terminus. Circular LUC was more thermostable and alkali-tolerant than the wild type, without compromising the specific activity. Structural analysis indicated that the cyclized LUC increased the thermodynamic stability of the structure and remained more properly folded at high temperatures when compared with the wild type. We also prepared an N-terminally and C-terminally shortened form of the SpyCatcher protein and cyclization using this truncated form led to even more thermostability than the original form. Our findings suggest that cyclization with SpyTag and SpyCatcher is a promising and effective strategy to enhance thermostability of enzymes.
On the Benefits of Random Linear Coding for Unicast Applications in Disruption Tolerant Networks

In this paper, we investigate the benefits of using a form of network coding known as Random Linear Coding (RLC) for unicast communications in a mobile Disruption Tolerant Network (DTN) under epidemic routing. Under RLC, DTN nodes store and then forward random linear combinations of packets as they encounter other DTN nodes. We first consider the case where there is a single block of packets propagating in the network and then consider the case where blocks of K packets arrive according to a Poisson arrival process. Our performance metric of interest is the delay until the last packet in a block is delivered. We show that for the single block case, when bandwidth is constrained, applying RLC over packets destined to the same node achieves (with high probability) the minimum delay needed to deliver the block of data. We find through simulation that RLC achieves smaller block delivery delay than non-network-coded packet forwarding under bandwidth constraint, and the relative benefit increases further when buffer space within DTN nodes is limited. For the case of multiple blocks, our simulations show that RLC offers only slight improvement over the non-coded scenario when only bandwidth is constrained, but more significant improvement when both bandwidth and buffers are constrained. We remark that when the network is relatively loaded, RLC achieves improvements over non-coding scheme only if the spreading of the information is appropriately controlled.
Interaction of Nuclease Colicins with Membranes: Insertion Depth Correlates with Bilayer Perturbation

Background Protein transport across cellular membranes is an important aspect of toxin biology. Escherichia coli cell killing by nuclease colicins occurs through DNA (DNases) or RNA (RNases) hydrolysis and to this end their cytotoxic domains require transportation across two sets of membranes. In order to begin to unravel the molecular mechanisms underlying the membrane translocation of colicin nuclease domains, we have analysed the membrane association of four DNase domains (E9, a charge reduction E9 mutant, E8, and E7) and one ribosomal RNase domain (E3) using a biomembrane model system. Principal Results We demonstrate, through the use of large unilamellar vesicles composed of synthetic and E. coli lipids and a membrane surface potential sensor, that the colicin nuclease domains bind anionic membranes only, with micromolar affinity and via a cooperative binding mechanism. The evaluation of the nuclease bilayer insertion depth, through a fluorescence quenching analysis using brominated lipids, indicates that the nucleases locate to differential regions in the bilayer. Colicin DNases target the interfacial region of the lipid bilayer, with the DNase E7 showing the deepest insertion, whereas the ribosomal RNase E3 penetrates into the hydrophobic core region of the bilayer. Furthermore, the membrane association of the DNase E7 and the ribosomal RNase E3 induces vesicle aggregation, lipid mixing and content leakage to a much larger extent than that of the other DNases analysed. Conclusions/Significance Our results show, for the first time, that after the initial electrostatically driven membrane association, the pleiotropic membrane effects induced by colicin nuclease domains relate to their bilayer insertion depth and may be linked to their in vivo membrane translocation.
Remote control of a robotic platform based on hand gesture recognition

Computer vision based detection can be used to identify hand gestures and movement and use these commands in order to implement a control system for a robotic platform. This paper presents the technical implementation of a hand movement and gesture detection system based on two VGA USB cameras and the control of a customizable robotic platform using the commands transmitted from a computer after image processing. Hand gestures are identified using an adaptive binarization method based on histogram analysis and hand contour with peak value detection for identifying the fingertips.
Memory-guided exploration in reinforcement learning

We focus on the task transfer in reinforcement learning and specifically in Q-learning. There are three main model free methods for performing task transfer in Q-learning: direct transfer, soft transfer and memory-guided exploration. In direct transfer, the Q-values from a previous task are used to initialize the Q-values of the next task. The soft transfer initializes the Q-values of the new task with a weighted average of the standard initialization value and the Q-values of the previous task. In memory-guided exploration the Q-values of previous tasks are used as a guide in the initial exploration of the agent. The weight that the agent gives to its past experience decreases over time. We explore stability issues related to the off-policy nature of memory-guided exploration and compare memory-guided exploration to soft transfer and direct transfer in three different environments.
Critical Race Theory: An Introduction

This best-selling primer explains the movement's organizational history, major themes, central figures, and likely future. The second edition contains material on new developments that have taken place since the first edition, including the rapid growth in the Latino population, nativism against that group, the election of the nation's first black president, and the advent of right-wing populism.
CONFIRMATORY FACTOR ANALYSIS OF THE MAIN MODELS PROPOSED FOR THE PURPOSE-IN-LIFE TEST IN A SAMPLE OF SPANISH UNDERGRADUATES

In recent years several papers have examined the structure of the Purpose-In-Life Test, which measures the achievement of meaning in life from the approach of logotherapy, having found heterogeneous results. The aim of this study was to test different models proposed in previous literature with a sample of 766 Spanish undergraduates (220 males, 546 females) from two universities of the Valencia Community (Spain), aged between 18 and 36 (M = 21.96; SD = 3.56). Confirmatory factor analysis of these models was conducted. The adjustment values and the factorial structures obtained were compared, finding empirical support for three bi-factorial models.
The response of trypanosomes and other eukaryotes to ER stress and the spliced leader RNA silencing (SLS) pathway in Trypanosoma brucei

Abstract The unfolded protein response (UPR) is induced when the quality control machinery of the cell is overloaded with unfolded proteins or when one of the functions of the endoplasmic reticulum (ER) is perturbed. Here, I describe UPR in yeast and mammals, and compare it to what we know about pathogenic fungi and the parasitic protozoans from the order kinetoplastida, focusing on the novel pathway the spliced leader silencing (SLS) in Trypanosoma brucei. Trypanosomes lack conventional transcription regulation, and thus, lack most of the UPR machinery present in other eukaryotes. Trypanosome genes are transcribed in polycistronic units that are processed by trans-splicing and polyadenylation. In trans-splicing, which is essential for processing of each mRNA, an exon known as the spliced leader (SL) is added to all mRNAs from a small RNA, the SL RNA. Under severe ER stress, T. brucei elicits the SLS pathway. In SLS, the transcription of the SL RNA gene is extinguished, and the entire transcription complex dissociates from the SL RNA promoter. Induction of SLS is mediated by an ER-associated kinase (PK3) that migrates to the nucleus, where it phosphorylates the TATA-binding protein (TRF4), leading shut-off of SL RNA transcription. As a result, trans-splicing is inhibited and the parasites activate a programmed cell death (PCD) pathway. Despite the ability to sense the ER stress, the different eukaryotes, especially unicellular parasites and pathogenic fungi, developed a variety of unique and different ways to sense and adjust to this stress in a manner different from their host.
Pauvreté monétaire, pauvreté non monétaire : une analyse des interactions appliquée à la Guinée

Depuis la fin du XIXeme siecle, les preoccupations concernant la definition de la pauvrete ne cessent de croitre dans les milieux universitaires et politiques. Les implications sur les programmes de lutte contre la pauvrete dependent en grande partie de la definition que l'on retient de la notion meme de pauvrete. Cette these a pour ambition de questionner les rapports parfois ambigus entre trois grandes familles informationnelles. L'utilitarisme qui constitue, aujourd'hui encore, grâce a de nombreuses extensions theoriques, le paradigme dominant dans les analyses relatives a la pauvrete, definit cette notion comme un etat de denuement monetaire ne permettant pas de subvenir aux besoins des personnes concernees. L'attention exclusive portee aux ressources monetaires ne permet cependant pas d'apprehender la pauvrete dans sa totalite. C'est la raison pour laquelle deux approches – concernant les besoins essentiels et les capabilites – permettent d'enrichir la definition de la pauvrete d'informations plurielles comme les besoins de base ou les libertes. Si elles semblent s'opposer de prime abord, la presente recherche montre que les trois approches retenues sont beaucoup plus convergentes. Apres avoir presente les domaines de substitution et de complementarite theoriques, nous avons mobilise les donnees issues de l'Observatoire de la Guinee maritime pour les confronter a la realite. Les resultats empiriques corroborent les conclusions theoriques : les approches monetaires et multidimensionnelles tendent a fournir une information complementaire quant a la realite du phenomene de pauvrete sur notre echantillon. Si l'identification monetaire des menages pauvres ne permet pas d'en saisir la multidimensionnalite, il n'en reste pas moins que le revenu reste important dans la probabilite qu'un menage soit victime de pauvrete multidimensionnelle.
Rate and timing precision of motor coordination in Developmental Dyslexia.

Learning to read builds on the speech processes of the child at many levels (Denckla, 1979; Mann, 1986), and language impairment is one of the most common behavioral correlates of developmental dyslexia (Doehring, Trites, Patel, & Fiedorowicz, 1981; Jorm, 1979; Vellutino, 1978). Current dyslexia research therefore has emphasized the linguistic analysis of language deficits and has brought converging evidence to the effect that phonological processing deficits, for example, play a critical role in reading impairment (Mann, 1986; Wagner & Torgensen, 1987).
Improvement of xylanase production by Aspergillus niger XY-1 using response surface methodology for optimizing the medium composition

ObjectiveTo study the optimal medium composition for xylanase production by Aspergillus niger XY-1 in solid-state fermentation (SSF). MethodsStatistical methodology including the Plackett-Burman design (PBD) and the central composite design (CCD) was employed to investigate the individual crucial component of the medium that significantly affected the enzyme yield.ResultsFirstly, NaNO3, yeast extract, urea, Na2CO3, MgSO4, peptone and (NH4)2SO4 were screened as the significant facotrs positively affecting the xylanase production by PBD. Secondly, by valuating the nitrogen sources effect, urea was proved to be the most effective and economic nitrogen source for xylanase production and used for further optimization. Finally, the CCD and response surface methodology (RSM) were applied to determine the optimal concentration of each significant variable, which included urea, Na2CO3 and MgSO4. Subsequently a second-order polynomial was determined by multiple regression analysis. The optimum values of the critical components for maximum xylanase production were obtained as follows: x1 (urea)=0.163 (41.63 g/L), x2 (Na2CO3)=−1.68 (2.64 g/L), x3 (MgSO4)=1.338 (10.68 g/L) and the predicted xylanase value was 14374.6 U/g dry substrate. Using the optimized condition, xylanase production by Aspergillus niger XY-1 after 48 h fermentation reached 14637 U/g dry substrate with wheat bran in the shake flask.ConclusionBy using PBD and CCD, we obtained the optimal composition for xylanase production by Aspergillus niger XY-1 in SSF, and the results of no additional expensive medium and shortened fermentation time for higher xylanase production show the potential for industrial utilization.
I-Vector estimation as auxiliary task for Multi-Task Learning based acoustic modeling for automatic speech recognition

I-Vectors have been successfully applied in the speaker identification community in order to characterize the speaker and its acoustic environment. Recently, i-vectors have also shown their usefulness in automatic speech recognition, when concatenated to standard acoustic features. Instead of directly feeding the acoustic model with i-vectors, we here investigate a Multi-Task Learning approach, where a neural network is trained to simultaneously recognize the phone-state posterior probabilities and extract i-vectors, using the standard acoustic features. Multi-Task Learning is a regularization method which aims at improving the network's generalization ability, by training a unique network to solve several different, but related tasks. The core idea of using i-vector extraction as an auxiliary task is to give the network an additional inter-speaker awareness, and thus, reduce overfitting. Overfitting is a commonly met issue in speech recognition and is especially impacting when the amount of training data is limited. The proposed setup is trained and tested on the TIMIT database, while the acoustic modeling is performed using a Recurrent Neural Network with Long Short-Term Memory cells.
Simultaneous measurement of intracellular Ca(2+) and nitric oxide: a new method.

Different methods to measure the unstable radical nitric oxide (NO) have been established. We are going to present a new method to measure intracellular calcium and NO simultaneously in endothelial cells. A new fluorescent dye (DAF-2) has been developed recently which binds NO resulting in an enhanced fluorescence. We loaded porcine aortic endothelial cells with Fura-2, a fluorescent dye commonly used to measure intracellular calcium, and DAF-2 simultaneously (cell permeable dyes). Using excitation wavelengths of lambda 340 nm (Fura-2) and lambda 485 nm (DAF-2) we could show that thrombin induces an intracellular calcium increase and simultaneously a NO formation in endothelial cells which could be blocked by a NO synthase inhibitor. This new method of a simultaneous measurement of intracellular calcium and NO provides the possibility to follow intracellular calcium and NO distributions online, and is sensitive enough to monitor changes of NO formed by the constitutive endothelial NO-synthase.
Four metaphors of architecture in software organizations: finding out the meaning of architecture in practice

Current literature, research, and practice provide ambiguous meanings for the concept of architecture in the context of software and systems development. This qualitative and grounded theory based study delves into the practice of architecture design and description in three software-producing organizations. Nineteen architects, designers, and managers are interviewed and the general meanings of architecture in practical real-life situations are distilled and analyzed The ambiguity of the concept of architecture receives its explanation. Architecture emerges as a plastic concept including diverging and simultaneous connotations for different stakeholders. The research process produces four general metaphors for architecture, "architecture as blueprint", "architecture as literature", "architecture as language", and "architecture as decision". These metaphors and the research process are presented and discussed in detail.
TERRITORIAL AND TOPOLOGICAL LEVELS IN WORLDWIDE AIR TRANSPORT NETWORK ( 2000-2004 ) 15 TH European Colloquium on Theoretical and Quantitative Geography September 7-11 , 2007 , Montreux , Switzerland

The aim of this study is to characterize territorial and topological levels in the structure and evolution of the global air transportation network. Using data from the ITA database for both 2000 and 2004, we analyze the topology of these networks with a new approach based on weighted graphs from a small world perspective (Watts, 1999 ; Barabasi, 2002 ; Barat et al.2005). A first step is performed through graph clustering algorithms unfolding the different “small worlds” together making up the whole network. The clusters are seen as communities and are captured with the use of edge metrics conveying topological properties of the underlying communities. The metric we use is that from Auber, Chiricota et al. 2003 (see also (Amiel, Melançon et al. 2005)) which compares to Burt’s network constraint [(Burt 2000); see also (Burt 2005)]. The outcome of the clustering procedure provides a multilevel presentation of the most interconnected airports in the world. In a second stage, we identify the position of each city in the network (satellite, hub or bridge? ) and their cohesive role at every level of the hierarchical clusters. The confrontation of several metrics such as weighted degree or betweeness centrality of each city, and at various levels, help us qualify cities as hubs or bridges. A multilevel statistics on graph elaborated on the basis of Guimera et al.’s work (2005) can be used to measure each city’s contributions at different levels in the network. In a third stage, we attempt to detect the impact of territorial rules on the formation the clusters by systematically comparing clusters of cities and their territorial membership. Finally, we compare the two networks, from 2000 and 2004, in order to detect trends of territorial effects in level formation and changes in the individual position of major hubs.
Approaching the Symbol Grounding Problem with Probabilistic Graphical Models

n order for robots to engage in dialog with human teammates, they must have the ability to map between words in the language and aspects of the external world. A solution to this symbol grounding problem (Harnad, 1990) would enable a robot to interpret commands such as “Drive over to receiving and pick up the tire pallet. ” In this article we describe several of our results that use probabilistic inference to address the symbol grounding problem. Our speciﬁc approach is to develop models that factor according to the linguistic structure of a command. We ﬁrst describe an early result, a generative model that factors according to the sequential structure of language, and then discuss our new framework, generalized grounding graphs (G3). The G3 framework dynamically instantiates a probabilistic graphical model for a natural language input, enabling a mapping between words in language and concrete objects, places, paths and events in the external world. We report on corpus-based experiments where the robot is able to learn and use word meanings in three real-world tasks: indoor navigation, spatial language video retrieval, and mobile manipulation.