Miracle-dz/UniFAR-FTUs huggingface dataset:
Multimodal Wireless Networks: Communication and Surveillance on the Same Infrastructure

In this paper, we propose a new family of wireless networks-the multimodal wireless networks. These networks offer multiple functionalities realized on the same infrastructure. A multimodal wireless network has two modes of operation: 1) the communication mode, when the network is used as a traditional wireless communication network, and 2) the surveillance mode, when the network is used as a distributed sensor network that can detect illegal intrusion. The surveillance functionality is realized by analyzing the properties of the received signals, and the change of the propagation environment caused by the intruder serves as the basis for intrusion detection. We derive maximum likelihood estimators and detectors based on the generalized likelihood ratio test that detects changes in the propagation environment: the single-cycle detector, which makes decisions at the end of each scanning cycle, and the multicycle detector, which combines information from multiple scanning cycles prior to detection. We also analyze the performance of these detectors by deriving the Cramer-Rao lower bound on the variance of the parameter estimators and determining the distribution of the log-likelihood ratio under both detection hypotheses. This will allow us to compare the theoretical performance of the single-cycle and the multicycle detectors and obtain analytical results to determine the decision threshold for a given probability of false alarm. To prevent performance degradation due to slowly drifting parameter values, we propose different strategies to track and update the parameter estimates. The experimental results obtained from an implemented prototype surveillance system show very promising detection capabilities. For example, the state of a door (open or closed) could be detected with a probability of 0.99 at a probability of false alarm 10-5.
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring

Diatoms are micro-algal indicators of freshwater pollution. Current standardized methodologies are based on microscopic determinations, which is time consuming and prone to identification uncertainties. The use of DNA-barcoding has been proposed as a way to avoid these flaws. Combining barcoding with next-generation sequencing enables collection of a large quantity of barcodes from natural samples. These barcodes are identified as certain diatom taxa by comparing the sequences to a reference barcoding library using algorithms. Proof of concept was recently demonstrated for synthetic and natural communities and underlined the importance of the quality of this reference library. We present an open-access and curated reference barcoding database for diatoms, called R-Syst::diatom, developed in the framework of R-Syst, the network of systematic supported by INRA (French National Institute for Agricultural Research), see http://www.rsyst. inra.fr/en. R-Syst::diatom links DNA-barcodes to their taxonomical identifications, and is dedicated to identify barcodes from natural samples. The data come from two sources, a culture collection of freshwater algae maintained in INRA in which new strains are regularly deposited and barcoded and from the NCBI (National Center for Biotechnology Information) nucleotide database. Two kinds of barcodes were chosen to support the database: 18S (18S ribosomal RNA) and rbcL (Ribulose-1,5-bisphosphate carboxylase/oxygenase), because of their efficiency. Data are curated using innovative (Declic) and classical bioinformatic tools (Blast, classical phylogenies) and up-to-date taxonomy (Catalogues and peer reviewed papers). Every 6 months R-Syst::diatom is updated. The database is available through the R-Syst microalgae website (http://www.rsyst.inra.fr/) and a platform dedicated to next-generation sequencing data analysis, virtual_BiodiversityL@b (https://galaxy-pgtp.pierroton.inra.fr/). We present here the content of the library regarding the number of barcodes and diatom taxa. In addition to these information, morphological features (e.g. biovolumes, chloroplasts…), life-forms (mobility, colony-type) or ecological features (taxa preferenda to pollution) are indicated in R-Syst::diatom. Database URL: http://www.rsyst. inra.fr/
Paternal care in the European starling,
 Sturnus vulgaris
 : incubation

In polygynous passerines, males of some species provide food for their nestlings, but male incubation seems to be rare. In the European starling both the mating system and the extent to which males help with incubation vary. This enabled the relationship between mating system and male incubation to be investigated. The extent to which males provided care to a particular nest depended on mating status: monogamous males incubated more than polygynous males did in any of their females' nests. On average, bigynous males incubated as much in their two nests as monogamous males did in their single nest, but polygynous males who invested in only one of their nests incubated less than monogamous males. Females partly compensated for the variation in male incubation, but still nests of polygynously mated females were attended less. Polygynous males invested more in the nests of the first females mated with (primary female) than in the nests of later settling females. Secondary females received less help the later they laid their eggs in relation to the mate's primary female. Bigynous males that incubated in both their nests invested more in the nests of their primary females the earlier these eggs were laid in relation to those of the secondary females. Male help with incubation may affect a female's fitness, both because increased attentiveness resulted in shorter incubation times and because females receiving less help may pay a higher cost in terms of energy expenditure. Hence, there will be a conflict between polygynously mated females over paternal incubation.
Permitted and Forbidden Sets in Symmetric Threshold-Linear Networks

The richness and complexity of recurrent cortical circuits is an inexhaustible source of inspiration for thinking about high-level biological computation. In past theoretical studies, constraints on the synaptic connection patterns of threshold-linear networks were found that guaranteed bounded network dynamics, convergence to attractive fixed points, and multistability, all fundamental aspects of cortical information processing. However, these conditions were only sufficient, and it remained unclear which were the minimal (necessary) conditions for convergence and multistability. We show that symmetric threshold-linear networks converge to a set of attractive fixed points if and only if the network matrix is copositive. Furthermore, the set of attractive fixed points is nonconnected (the network is multiattractive) if and only if the network matrix is not positive semidefinite. There are permitted sets of neurons that can be coactive at a stable steady state and forbidden sets that cannot. Permitted sets are clustered in the sense that subsets of permitted sets are permitted and supersets of forbidden sets are forbidden. By viewing permitted sets as memories stored in the synaptic connections, we provide a formulation of long-term memory that is more general than the traditional perspective of fixed-point attractor networks. There is a close correspondence between threshold-linear networks and networks defined by the generalized Lotka-Volterra equations.
Triangle inequality variations in the internet

Triangle inequality violations (TIVs) are important for latency sensitive distributed applications. On one hand, they can expose opportunities to improve network routing by finding shorter paths between nodes. On the other hand, TIVs can frustrate network embedding or positioning systems that treat the Internet as a metric space where the triangle inequality holds. Even though triangle inequality violations are both significant and curious, their study has been limited to aggregate data sets that combine measurements taken over long periods of time. The limitations of these data sets open crucial questions in the design of systems that exploit (or avoid) TIVs: are TIVs stable or transient? Or are they illusions caused by aggregating measurements taken at different times? We collect latency matrices at varying sizes and time granularities and study dynamic properties of triangle inequality violations in the Internet. We show that TIVs are not results of measurement error and that their number varies with time. We examine how latency aggregates of data measured over longer periods of time preserve TIVs. Using medians to compute violations eliminates most of the TIVs that appear sporadically during the measurement but it misses many of the ones that are present for more than five hours.
Sindbis virus ts103 has a mutation in glycoprotein E2 that leads to defective assembly of virions

Sindbis virus mutant ts103 is aberrant in the assembly of virus particles. During virus budding, proper nucleocapsid-glycoprotein interactions fail to occur such that particles containing many nucleocapsids are formed, and the final yield of virus is low. We have determined that a mutation in the external domain of glycoprotein E2, Ala-344----Val, is the change that leads to this phenotype. Mapping was done by making recombinant viruses between ts103 and a parental strain of the virus, using a full-length cDNA clone of Sindbis virus from which infectious RNA can be transcribed, together with sequence analysis of the region of the genome shown in this way to contain the ts103 lesion. A partial revertant of ts103, called ts103R, was also mapped and sequenced and found to be a second-site revertant in which a change in glycoprotein E1 from lysine to methionine at position 227 partially suppresses the phenotypic effects of the change at E2 position 344. An analysis of revertants from ts103 mutants in which the Ala----Val change had been transferred into a defined background showed that pseudorevertants were more likely to arise than were true revertants and that the ts103 change itself reverted very infrequently. The assembly defect in ts103 appeared to result from weakened interactions between the virus membrane glycoproteins or between these glycoproteins and the nucleocapsid during budding. Both the E2 mutation leading to the defect in virus assembly and the suppressor mutation in glycoprotein E1 are in the domains external to the lipid bilayer and thus in domains that cannot interact directly with the nucleocapsid. This suggests that in ts103, either the E1-E2 heterodimers or the trimeric spikes (consisting of three E1-E2 heterodimers) are unstable or have an aberrant configuration, and thus do not interact properly with the nucleocapsid, or cannot assembly correctly to form the proper icosahedral array on the surface of the virus.
Object oriented approach to combined learning of decision tree and ADF GP

There are many learning methods for classification systems. Genetic programming (one of the methods) can change trees dynamically, but its learning speed is slow. Decision tree methods using C4.5 construct trees quickly, but the network may not classify correctly when the training data contains noise. For such problems, we proposed an object oriented approach, and a learning method that combines decision tree making method (C4.5) and genetic programming. To verify the validity of the proposed method we developed two different medical diagnostic systems. One is a medical diagnostic system for the occurrence of hypertension the other is for the meningoencephalitis. We compared the results of proposed method with prior ones.
The Phosphate Starvation Stimulon of Corynebacterium glutamicum Determined by DNA Microarray Analyses

ABSTRACT The phosphate (Pi) starvation stimulon of Corynebacterium glutamicum was characterized by global gene expression analysis by using DNA microarrays. Hierarchical cluster analysis of the genes showing altered expression 10 to 180 min after a shift from Pi-sufficient to Pi-limiting conditions led to identification of five groups comprising 92 genes. Four of these groups included genes which are not directly involved in P metabolism and changed expression presumably due to the reduced growth rate observed after the shift or to the exchange of medium. One group, however, comprised 25 genes, most of which are obviously related to phosphorus (P) uptake and metabolism and exhibited 4- to >30-fold-greater expression after the shift to Pi limitation. Among these genes, the RNA levels of the pstSCAB (ABC-type Pi uptake system), glpQ (glycerophosphoryldiester phosphodiesterase), ugpAEBC (ABC-type sn-glycerol 3-phosphate uptake system), phoH (unknown function), nucH (extracellular nuclease), and Cgl0328 (5′-nucleotidase or related esterase) genes were increased, and pstSCAB exhibited a faster response than the other genes. Transcriptional fusion analyses revealed that elevated expression of pstSCAB and ugpAEBC was primarily due to transcriptional regulation. Several genes also involved in P uptake and metabolism were not affected by Pi starvation; these included the genes encoding a PitA-like Pi uptake system and a putative Na+-dependent Pi transporter and the genes involved in the metabolism of pyrophosphate and polyphosphate. In summary, a global, time-resolved picture of the response of C. glutamicum to Pi starvation was obtained.
The thermal denaturation of partly purified bacterial deoxyribonucleic acid and its taxonomic applications.

1 Partly purified DNA and the corresponding highly purified DNA was obtained from 25 strains of Gram negative, rod-shaped bacteria. 2 The DNAs were examined by the thermal denaturation method and the melting temperatures of both partly and highly purified DNA samples from the same strain were in close agreement. 3 For all strains, the mean difference in G+C contents estimated from the melting temperatures of each partly and highly purified DNA was 0.4% G+C. 4 The presence of residual RNA and protein in the partly purified DNA samples contributed to variations in the total hyperchromism but did not significantly affect the accuracy of the melting temperature determination.
Data centric research at the University of Queensland

The University of Queensland (UQ) is in the top 100 universities worldwide measured through a number of major rankings. In 2012, the University had more than 46,000 students including 11,000 international students from 134 nations. It has one of Australia’s largest PhD enrolments, with more than 12,600 postgraduate students. The University’s outstanding 200,000-plus alumni include a Nobel laureate, the CEO of a Fortune 500 company, an Academy Award winner, and leaders in government, law, science, public service and the arts. UQ hosts a cross-disciplinary group of researchers working on data centric approaches, spanning the engineering, business and science faculties. The group’s strength lies in its diversity and ability to cater for the entire data pipeline. Members of the group have, and continue to contribute to all aspects of data-centric research including data modelling, indexing, querying, cleansing, analyzing, visualizing, as well as use and adoption over a number of application areas. Currently the group has 26 full time staff and over 50 PhD students. The group was awarded the highest ranking under the Australian Research Council (ARC) Excellence of Research in Australia scheme in 2012 (www.arc.gov.au/era/). From 2005-2010, we managed the ARC Research Network in Enterprise Information Infrastructure (eii.edu.au). The aims of EII were to provide focus for research exchange via networking and collaboration and to improve the quality, impact and visibility of Australian ICT research. This was a unique initiative of the ARC, funded by the ARC in conjunction with financial support provided by 21 Australian and international institutions. Over the course of 5 years, and led by Xiaofang Zhou as convenor of the network, EII made a profound impact on the Australian research community, University sector and IT industry in terms of research collaboration, research training (especially through the annual PhD school), and research quality. Over the years, we have also organized, or contributed to the organization of a number of major conferences in Brisbane including VLDB 1990, WWW 1998, WISE 2004, BPM 2007, DASFAA 2009, ACIS 2010 and ICDE 2013. ACM Multimedia will also be hosted by us in 2015. In this article we first present a short chronology outlining the major topics and achievements of the group in the last three decades. We then present details on a selected number of current topics that we would like to share our viewpoint on, in terms of our focus, contributions and way forward.
Text Alignment in a Tool for Translating Revised Documents

Making use of previously translated texts is a very appealing idea that can be of considerable practical and economical benefit as a translation aid. There are different ways to exploit the potential of "re-translation" with different degrees of generality, complication and ambition. Example-based machine translation is probably the most ambitious end of the spectrum but there can be other points along it. In this paper I describe a simple tool which deals with a particular special case of the "re-translation" problem. It occurs when a new version of a previously translated document needs to be translated. The tool identifies the changes between the two versions of the source language (SL) text and retrieves appropriate sentences from the target language (TL) text. With that, it creates a bilingual draft which consists of sections in the TL text from the existing translation and update materials from the SL text, thereby reducing the effort required from the translator. This tool could substantially increase the productivity of translators which deal with technical documents of frequently modified products (software-based products are the best example of that). If this is true, it suggests that simple solutions can be very effective in addressing "real-life" translation problems. The paper is structured as follows. The first section discusses some relevant properties of typical texts which are likely to be (re-)translated with this tool. The second section is about the alignment process I will present a new length-based alignment algorithm, designed for dealing with texts that include additions and deletions. In the following section I will propose a quick procedure to find the differences between two versions of the same document. Then, I will show how the bilingual draft is constructed. The last section will discuss possible continuations of this research which will extend the applicability of the tool to more general translation situations.
Combined active damping with adaptive current control for converters with LCL filters

This paper proposes a grid side current control technique for Pulse Width Modulated converters connected to the grid through LCL filters. The system is modeled in order to allow the implementation of a multi-loop control strategy. The inner loop is designed for active damping using the classical approach of feeding back the capacitor voltage or current to implement a Proportional plus Derivative or a Proportional controller, respectively. The outer loop is designed for the compensation of parametric uncertainties and disturbances by means of a Model Reference Adaptive Controller. The adaptive behavior allows to easily design the outer controller despite de presence of the inner one.
Highlighting the impact of aging on type I collagen: label-free investigation using confocal reflectance microscopy and diffuse reflectance spectroscopy in 3D matrix model

During aging, alterations of extracellular matrix proteins contribute to various pathological phenotypes. Among these alterations, type I collagen cross-linking and associated glycation products accumulation over time detrimentally affects its physico-chemical properties, leading to alterations of tissue biomechanical stability. Here, different-age collagen 3D matrices using non-destructive and label-free biophotonic techniques were analysed to highlight the impact of collagen I aging on 3D constructs, at macroscopic and microscopic levels. Matrices were prepared with collagens extracted from tail tendons of rats (newborns, young and old adults) to be within the physiological aging process. The data of diffuse reflectance spectroscopy reveal that aging leads to an inhibition of fibril assembly and a resulting decrease of gel density. Investigations by confocal reflectance microscopy highlight poor-fibrillar structures in oldest collagen networks most likely related to the glycation products accumulation. Complementarily, an infrared analysis brings out marked spectral variations in the Amide I profile, specific of the peptidic bond conformation and for carbohydrates vibrations as function of collagen-age. Interestingly, we also highlight an unexpected behavior for newborn collagen, exhibiting poorly-organized networks and microscopic features close to the oldest collagen. These results demonstrate that changes in collagen optical properties are relevant for investigating the incidence of aging in 3D matrix models.
The Apolipoprotein ε4 Allele Confers Additional Risk in Children with Familial Hypercholesterolemia

Children with familial hypercholesterolemia (FH) exhibit substantial variance of LDL cholesterol. In previous studies, family members of children with FH were included, which may have influenced results. To avoid such bias, we studied phenotype in 450 unrelated children with FH and in 154 affected sib-pairs. In known families with classical FH, diagnosis was based on plasma LDL cholesterol above the age- and gender-specific 95th percentile. Girls had 0.47 ± 0.15 mmol/L higher LDL cholesterol, compared with boys (p = 0.002). Also in girls, HDL cholesterol increased by 0.07 ± 0.03 mmol/L per 5 y (pfor trend = 0.005); this age effect was not observed in boys. The distribution of apolipoprotein (apo) E genotypes was not significantly different between probands, their paired affected siblings, or a Dutch control population. Carriers with or without one ε4 allele had similar LDL and HDL cholesterol levels. Within the affected sib-pairs, the ε4 allele explained 72.4% of the variance of HDL cholesterol levels (−0.15 mmol/L, 95% confidence interval −0.24 to −0.05, p = 0.003). The effect of apoE4 on HDL cholesterol differed with an analysis based on probands or on affected sib-pairs. The affected sib-pair model used adjustment for shared environment, type of LDL receptor gene mutation, and a proportion of additional genetic factors and may, therefore, be more accurate in estimating effects of risk factors on complex traits. We conclude that the ε4 allele was associated with lower HDL cholesterol levels in an affected sib-pair analysis, which strongly suggests that apoE4 influences HDL cholesterol levels in FH children. Moreover, the strong association suggests that apoE4 carries an additional disadvantage for FH children.