Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Biodiversity Inventory of the Ichthyofauna of the Czech Republic

V roce 2003 vznikl projekt na zmapovani a ochranu biodiverzity využivajici novou taxonomickou metodu „DNA barkoding“. Metoda založena na sekvenci mitochondrialniho markeru prvni podjednotky cytochrom c oxidazy (COI) prokazala vysokou užitecnost při inventarizaci biodiverzity sladkovodnich ryb CR. Take byl použit jaderný marker prvniho intronu S7 ribosomalniho proteinu (RP1), aby bylo možne identifikovat připadne hybridy. Bylo analyzovano 67 ze 72 druhů, tj. 93,1 % ceske ichtyofauny. Odběr vzorků byl proveden na 106 lokalitach na zakladě třistupňoveho systemu. Vysoka haplotypova variabilita byla odhalena pro druh Barbatula barbatula, 27 jedinců/13 haplotypů a Phoxinus phoxinus, 25 jedinců / 10 haplotypů. Pro P. phoxinus byly pozorovany dvě linie; jedna zahrnovala jedince z řek spadajicich do umoři Severniho a Cerneho moře, druha jedince z Becvy a řek umoři Baltu. V připadě Squalius cephalus byly mezi 27 jedinci pozorovany ctyři haplotypy a vnitrodruhovou variabilitou 5,25 %, což by mohlo znamenat existenci samostatneho druhu. Take byly odhaleny dva druhy uhořů, jeden původni druh a druhý přivlecený z Ameriky. Ziskane informace přispěji k lepsimu monitorovani systemu NATURA 2000 a jako soucast databaze Barcode of Life přispěji ke komplexnimu chapani a porozuměni celosvětove biodiverzity.
Fault Localization via Risk Modeling

Internet backbone networks are under constant flux in order to keep up with demand and offer new features. The pace of change in technology often outstrips the pace of introduction of associated fault monitoring capabilities that are built into today's IP protocols and routers. Moreover, some of these new technologies cross networking layers, raising the potential for unanticipated interactions and service disruptions, which the individual layers' built-in monitoring capabilities may not detect. In these instances, operators typically employ higher layer monitoring techniques such as end-to-end liveness probing to detect lower or cross-layer failures, but lack tools to precisely determine where a detected failure may have occurred. In this paper, we evaluate the effectiveness of using risk modeling to translate high-level failure notifications into lower layer root causes in two specific scenarios in a tier-1 ISP. We show that a simple greedy heuristic works with accuracy exceeding 80 percent for many failure scenarios in simulation, while delivering extremely high precision (greater than 80 percent). We report our operational experience using risk modeling to isolate optical component and MPLS control plane failures in an ISP backbone.
Weakly Non-Linear Gaussian Fluctuations and the Edgeworth Expansion

We calculate the cosmological evolution of the 1-point probability distribution function (PDF), using an analytic approximation that combines gravitational perturbation theory with the Edgeworth expansion of the PDF. Our method applies directly to a smoothed mass density field or to the divergence of a smoothed peculiar velocity field, provided that rms fluctuations are small compared to unity on the smoothing scale, and that the primordial fluctuations that seed the growth of structure are Gaussian. We use this `Edgeworth approximation' to compute the evolution of $ $ and $ $; these measures are similar to the skewness and kurtosis of the density field, but they are less sensitive to tails of the probability distribution, so they may be more accurately estimated from surveys of limited volume. We compare our analytic calculations to cosmological N-body simulations in order to assess their range of validity. When $\sigma \ll 1$, the numerical simulations and perturbation theory agree precisely, demonstrating that the N-body method can yield accurate results in the regime of weakly non-linear clustering. We show analytically that `biased' galaxy formation preserves the relation $ \propto ^2$ predicted by second-order perturbation theory, provided that the galaxy density is a local function of the underlying mass density.
A Metric for Secrecy-Energy Efficiency Tradeoff Evaluation in 3GPP Cellular Networks

Physical-layer security is now being considered for information protection in future wireless communications. However, a better understanding of the inherent secrecy of wireless systems under more realistic conditions, with a specific attention to the relative energy consumption costs, has to be pursued. This paper aims at proposing new analysis tools and investigating the relation between secrecy capacity and energy consumption in a 3rd Generation Partnership Project (3GPP) cellular network , by focusing on secure and energy efficient communications. New metrics that bind together the secure area in the Base Station (BS) sectors, the afforded date-rate and the power spent by the BS to obtain it, are proposed that permit evaluation of the tradeoff between these aspects. The results show that these metrics are useful in identifying the optimum transmit power level for the BS, so that the maximum secure area can be obtained while minimizing the energy consumption.
Non-uniform sampling of plenoptic signal based on the scene complexity variations for a free viewpoint video system

Acquisition of a free viewpoint video (FVV) system is theoretically considered as a problem of plenoptic signal sampling. It is typically performed by using a regular camera grid. While a regular acquisition itself results in non-uniform sampling density, this non-uniformity does not match the scene complexity and frequency variations. This paper proposes an irregular acquisition method for optimum non-uniform plenoptic sampling corresponding to the variations of the scene complexity. Specifically, scene complexity is measured through analyzing DCT coefficients of reference images of the scene, describing the frequency behavior of the plenoptic signal over the scene space. An optimization model is formulated to calculate the optimum configurations of the acquisition cameras including positions and orientations. The theoretical analysis and numerical simulations demonstrate that the rendered video quality can be significantly improved (around 40% in mean PSNR) by employing the proposed irregular acquisition compared with the regular camera grid.
Netzwerk: migration of a packet-switching network simulation environment from MS Windows PC to Linux PC and to HPC

We develop a simulation model of the OSI network layer of packet-switching networks. We present the scope of our research and the need for simulation tools. We discuss the migration from an MS Windows interactive, real-time, GUI-based tool to two packages that can run under Linux. We describe aspects common to all serial execution versions that have been extensively used in a serial execution under the SHARCNET environment. Then, we focus on the porting to a parallel implementation. We examine and discuss alternate candidate solutions and their trade-offs while converting the serial code to the parallel code. We discuss the parallelization of the code using pthread POSIX threading. Current work is targeted to design a model with a parallel architecture in mind from the outset.
A Process Algebra for Supervisory Coordination

A supervisory controller controls and coordinates the behavior of different components of a complex machine by observing their discrete behaviour. Supervisory control theory studies automated synthesis of controller models, known as supervisors, based on formal models of the machine components and a formalization of the requirements. Subsequently, code generation can be used to implement this supervisor in software, on a PLC, or embedded microprocessor. In this article, we take a closer look at the control loop that couples the supervisory controller and the machine. We model both event-based and state-based observations using process algebra and bisimulation-based semantics. The main application area of supervisory control that we consider is coordination, referred to as supervisory coordination, and we give an academic and an industrial example, discussing the process-theoretic concepts employed.
Machine Learning for Helicopter Dynamics Models

Machine Learning for Helicopter Dynamics Models by Ali Punjani Master of Science in Computer Science University of California, Berkeley Professor Pieter Abbeel, Chair We consider the problem of system identification of helicopter dynamics. Helicopters are complex systems, coupling rigid body dynamics with aerodynamics, engine dynamics, vibration, and other phenomena. Resultantly, they pose a challenging system identification problem, especially when considering non-stationary flight regimes. We pose the dynamics modeling problem as direct high-dimensional regression, and take inspiration from recent results in Deep Learning to represent the helicopter dynamics with a Rectified Linear Unit (ReLU) Network Model, a hierarchical neural network model. We provide a simple method for initializing the parameters of the model, and optimization details for training. We describe three baseline models and show that they are significantly outperformed by the ReLU Network Model in experiments on real data, indicating the power of the model to capture useful structure in system dynamics across a rich array of aerobatic maneuvers. Specifically, the ReLU Network Model improves 58% overall in RMS acceleration prediction over state-of-the-art methods. Predicting acceleration along the helicopter’s up-down axis is empirically found to be the most difficult, and the ReLU Network Model improves by 60% over the prior state-ofthe-art. We discuss explanations of these performance gains, and also investigate the impact of hyperparameters in the novel model.
A Sufficient Condition for Parameters Estimation in Dynamic Random Testing

Dynamic Random Testing (DRT) is a testing strategy to improve traditional random testing and random-partition testing strategies. The essential idea of DRT is that the testing profile, based on which test classes are chosen to select next test case, should be dynamically adjusted according to the testing history. DRT can have various forms depending on parameters settings, application scenarios and test suite partitioning schemes. This paper discusses the theoretical boundary of the parameters in DRT and their impact on the actual effectiveness in practice. A sufficient condition for the parameters estimation in DRT is proposed and further examined through experiments on three subject programs. Data indicates that the proposed sufficient condition provides a reasonable guideline for choosing parameters when applying the DRT strategy.
After-Ripening Induced Transcriptional Changes of Hormonal Genes in Wheat Seeds: The Cases of Brassinosteroids, Ethylene, Cytokinin and Salicylic Acid

Maintenance and release of seed dormancy is regulated by plant hormones; their levels and seed sensitivity being the critical factors. This study reports transcriptional regulation of brassinosteroids (BR), ethylene (ET), cytokinin (CK) and salicylic acid (SA) related wheat genes by after-ripening, a period of dry storage that decays dormancy. Changes in the expression of hormonal genes due to seed after-ripening did not occur in the anhydrobiotic state but rather in the hydrated state. After-ripening induced dormancy decay appears to be associated with imbibition mediated increase in the synthesis and signalling of BR, via transcriptional activation of de-etiolated2, dwarf4 and brassinosteroid signaling kinase, and repression of brassinosteroid insensitive 2. Our analysis is also suggestive of the significance of increased ET production, as reflected by enhanced transcription of 1-aminocyclopropane-1-carboxylic acid oxidase in after-ripened seeds, and tight regulation of seed response to ET in regulating dormancy decay. Differential transcriptions of lonely guy, zeatin O-glucosyltransferases and cytokinin oxidases, and pseudo-response regulator between dormant and after-ripened seeds implicate CK in the regulation of seed dormancy in wheat. Our analysis also reflects the association of dormancy decay in wheat with seed SA level and NPR independent SA signaling that appear to be regulated transcriptionally by phenylalanine ammonia lyase, and whirly and suppressor of npr1 inducible1 genes, respectively. Co-expression clustering of the hormonal genes implies the significance of synergistic and antagonistic interaction between the different plant hormones in regulating wheat seed dormancy. These results contribute to further our understanding of the molecular features controlling seed dormancy in wheat.
Regulation of sterol carrier protein gene expression by the Forkhead transcription factor FOXO3a Published, JLR Papers in Press, October 16, 2003. DOI 10.1194/jlr.M300111-JLR200

The SCP gene encodes two proteins, sterol carrier protein X (SCPx) and SCP2, that are independently regulated by separate promoters. SCPx has been shown to be the thiolase involved in the breakdown of branched-chain fatty acids and in the biosynthesis of bile acids. The in vivo function of SCP2 however remains to be established. The transcriptional regulation of SCPx and SCP2 is unclear, but their promoter regions contain several putative regulatory domains. We show here that both SCPx and SCP2 are upregulated by the daf-16-like Forkhead transcription factor FOXO3a (also known as FKHRL1) on the level of promoter activity. It was recently described that Forkheads regulate protection against (oxidative) stress in both Caenorhabditis elegans and mammalian cells. We looked into a role for SCP2 in the cellular defense against oxidative damage and found that a fluorescent fatty acid analog bound to SCP2 is protected against H2O2/Cu2+-induced oxidative damage. We propose a model for the way in which SCP2 could protect fatty acids from peroxidation.
Minimum-Decoding-Complexity, Maximum-rate Space-Time Block Codes from Clifford Algebras

It is well known that Alamouti code and, in general, space-time block codes (STBCs) from complex orthogonal designs (CODs) are single-symbol decodable/symbol-by-symbol decodable (SSD) and are obtainable from unitary matrix representations of Clifford algebras. However, SSD codes are obtainable from designs that are not CODs. Recently, two such classes of SSD codes have been studied: (i) coordinate interleaved orthogonal designs (CIODs) and (ii) minimum-decoding-complexity (MDC) STBCs from quasi-ODs (QODs). In this paper, we obtain SSD codes with unitary weight matrices (but not CODs) from matrix representations of Clifford algebras. Moreover, we derive an upper bound on the rate of SSD codes with unitary weight matrices and show that our codes meet this bound. Also, we present conditions on the signal sets which ensure full-diversity and give expressions for the coding gain
Three Generalizations of Fedosov Quantization

Fedosov’s simple geometrical construction for deformation quantization of symplectic manifolds is generalized in three ways without introducing new variables: (1) The base manifold is allowed to be a supermanifold. (2) The star product does not have to be of Weyl/symmetric or Wick/normal type. (3) The initial geometric structures are allowed to depend on Planck’s constant. MCS number(s): 53D05; 53D55; 58A15; 58A50; 58C50; 58Z05.
The reliability of an adolescent dietary pattern identified using reduced-rank regression: comparison of a FFQ and 3 d food record

Despite the increasing use of dietary patterns (DP) to study diet and health outcomes, relatively few studies have examined the reliability of DP using different dietary assessment methods. Reduced-rank regression (RRR) is an emerging statistical method that incorporates a priori information to characterise DP related to specific outcomes of interest. The aim of the present study was to compare DP identified using the RRR method in a FFQ with those in a 3 d food record (FR). Participants were 783 adolescents from the Western Australian Pregnancy (Raine) Cohort Study who completed both a FFQ and FR at 14 years of age. A similar ‘energy-dense, high-fat and low-fibre’ DP was identified in the FFQ and FR that was characterised by high intakes of processed meat and sugar-sweetened beverages, and low intakes of vegetables and fresh fruit. Nutrient profiles for this DP were consistent in the FFQ and FR. Pearson's correlation coefficient between participants' z-scores for the DP identified in the FFQ and FR was 0·35 for girls and 0·49 for boys (P< 0·05). The mean difference between DP z-scores derived from the FFQ and FR was − 0·08 (95 % CI − 0·21, 0·04) for girls and − 0·05 (95 % CI − 0·17, 0·07) for boys. The 95 % limits of agreement were − 2·55 to 2·39 for girls and − 2·52 to 2·41 for boys. These findings suggest that very similar DP may be identified and their z-scores show modest agreement when applying the RRR method to dietary intake data collected from adolescents using a FFQ or FR.
Parallel Binary Approach for Frequent Itemsets Mining

—The technique of association rules discovering is one of the most known and the most explored techniques of data mining. This technique has two main phases: the first is to extract all the frequent itemsets and the second is to generate association rules from these frequent itemsets. The first phase is the most expensive given the large number of accesses to transactions database and the large number of candidate itemsets. As databases are generally very large, a solution to avoid the repetitive and costly accesses is to represent them by compact structures. In this paper, we propose a parallel binary approach for frequent itemsets extracting, to deal with the great number of candidates and to take advantage of multicore architectures. This approach is implemented using a compact data structure based on signatures tree for the representation of the database to access it only once.
Zinc Transporter ZIP14 Functions in Hepatic Zinc, Iron and Glucose Homeostasis during the Innate Immune Response (Endotoxemia)

ZIP14 (slc39A14) is a zinc transporter induced in response to pro-inflammatory stimuli. ZIP14 induction accompanies the reduction in serum zinc (hypozincemia) of acute inflammation. ZIP14 can transport Zn2+ and non-transferrin-bound Fe2+ in vitro. Using a Zip14−/− mouse model we demonstrated that ZIP14 was essential for control of phosphatase PTP1B activity and phosphorylation of c-Met during liver regeneration. In the current studies, a global screening of ZIP transporter gene expression in response to LPS-induced endotoxemia was conducted. Following LPS, Zip14 was the most highly up-regulated Zip transcript in liver, but also in white adipose tissue and muscle. Using ZIP14−/− mice we show that ZIP14 contributes to zinc absorption from the gastrointestinal tract directly or indirectly as zinc absorption was decreased in the KOs. In contrast, Zip14−/− mice absorbed more iron. The Zip14 KO mice did not exhibit hypozincemia following LPS, but do have hypoferremia. Livers of Zip14−/− mice had increased transcript abundance for hepcidin, divalent metal transporter-1, ferritin and transferrin receptor-1 and greater accumulation of iron. The Zip14−/− phenotype included greater body fat, hypoglycemia and higher insulin levels, as well as increased liver glucose and greater phosphorylation of the insulin receptor and increased GLUT2, SREBP-1c and FASN expression. The Zip14 KO mice exhibited decreased circulating IL-6 with increased hepatic SOCS-3 following LPS, suggesting SOCS-3 inhibited insulin signaling which produced the hypoglycemia in this genotype. The results are consistent with ZIP14 ablation yielding abnormal labile zinc pools which lead to increased SOCS-3 production through G-coupled receptor activation and increased cAMP production as well as signaled by increased pSTAT3 via the IL-6 receptor, which inhibits IRS 1/2 phosphorylation. Our data show the role of ZIP14 in the hepatocyte is multi-functional since zinc and iron trafficking are altered in the Zip14−/− mice and their phenotype shows defects in glucose homeostasis.
Comparative performance analysis of eight blind source separation methods on radiocommunications signals

For about two decades, many second order (SO) and fourth order (FO) blind methods have been developed to separate overdetermined mixtures of statistically independent narrowband (NB) sources. Besides, mainly to overcome some limitations of these methods, sixth order methods have been developed. Nevertheless, despite of this great number of methods, the performance of the latter for arbitrary electromagnetic sources are still almost unknown, which limits their use in operational contexts. The purpose of this paper is to fill the gap previously mentioned by presenting a comparative performance analysis of eight blind source separation (BSS) methods for arbitrary overdetermined mixtures of sources borrowed from the radiocommunications context, and to show off both the advantages and the drawbacks of these methods.
A review on methods, issues and challenges in neuromorphic engineering

Biological systems have many key answers for our current limitations in scaling. Miniaturization and more speed were the driving forces for VLSI technology in past few decades. As we are reaching the dead end of Moore's law, now the paradigm has shifted towards intelligent machines. Many efforts are made to mimic the commonsense observed in animals. Automation and smart devices have taken a great momentum in recent years, but to imitate human intelligence in machines with existing hardware is not viable. By only developing complex algorithms and implementing software, intelligence is not accomplishable. This paper brings out the very basic differences between brain and computers. The complexity of human brain and flaws of current computing architecture is discussed. Neuromorphic Engineering emerges as a realistic solution whose architecture and circuit components resemble to their biological counterparts. This paper acts as a primer for Neuromorphic engineering. Brain functionality being analogous, the limitation of only digital systems is addressed by the mixed mode operation of ICs. Modelling of Neuron, various software and hardware available to realize these morphed architectures are studied. The gap between the software simulation and Hardware emulation, FPGA and VLSI implementation is debated. To reach to a larger audience the paper exposes many limitations of Neuromorphic engineering and come out with many open research issues.