Miracle-dz/UniFAR-FTUs huggingface dataset:
Stay Fit, Stay Young: Mitochondria in Movement: The Role of Exercise in the New Mitochondrial Paradigm

Skeletal muscles require the proper production and distribution of energy to sustain their work. To ensure this requirement is met, mitochondria form large networks within skeletal muscle cells, and during exercise, they can enhance their functions. In the present review, we discuss recent findings on exercise-induced mitochondrial adaptations. We emphasize the importance of mitochondrial biogenesis, morphological changes, and increases in respiratory supercomplex formation as mechanisms triggered by exercise that may increase the function of skeletal muscles. Finally, we highlight the possible effects of nutraceutical compounds on mitochondrial performance during exercise and outline the use of exercise as a therapeutic tool in noncommunicable disease prevention. The resulting picture shows that the modulation of mitochondrial activity by exercise is not only fundamental for physical performance but also a key point for whole-organism well-being.
Comparing Discretization of the LIBOR Market Model in the Spot Measure

Various drift approximations for the displaced-discussion LIBOR market model in the spot measure are compared. The advantages, disadvantages and implementation choices for each of predictor-corrector and the Glasserman-Zhao method are discussed. Numerical tests are carried out and we conclude that the predictor-corrector method is superior.
Development of Normalized Cdna Library from Fusarium Wilt Infected Roots of a Tolerant Banana Genotype 'Calcutta-4' Musa acuminata ssp. burmannicoides

Management of the most devasting disease, Fusarium wilt of banana, caused by the fungus Fusarium oxysporum f. sp. , cubense, is a challenge to the plant pathologist and the banana grower. Currently, genomics is providing the way for understanding plant defense mechanism, having acquired an important place in crop improvement. To identify the relevant genes and to understand the defense mechanism induced during Fusarium wilt infection, a normalized cDNA library was constructed from infected root samples of a tolerant banana genotype, Musa acuminata spp. burmannicoides 'Calcutta-4', by duplex specific nuclease (DSN) based normalization, using the SMART (switching mechanism at 5' end of RNA transcript) full-length cDNA construction method. Sequencing and analysis of 600 clones revealed 392 non-redundant clones. In all, of 88% of the sequences were annotated using Musa genome database, and the remaining 12% were identified as novel loci not annotated. We observed several resistance genes, ROS scavenging genes and genes involved in ubiquitin-proteosome pathway in this study. These genes may have a possible role against Foc infection. These sequences would enrich the EST data developed against specific stress, which is an indispensable tool for predicting functional genes and understanding the defense mechanism.
ICEPIC EMPHASIS and ITS Solution Verification Validation and Uncertainty Quantification for a series of gas cell experiments at NRL.

Summary form only given. A series of gas-cell experiments were performed at NRL to be able to validate dry air chemistry/collision models available in Particle-in-Cell (PIC) codes for cavity System Generated Electromagnetic Pulse (SGEMP). The experimental setup is a co-axial power feed which transitions to a disk-shaped cathode. The electron beam then passes through a thin anode foil and then a pressure foil, which separates the vacuum diode from the gas cell; scattering and propagation in the foils is energy and angle dependent. The peak electron energy entering the gas cell is about 90 keV and the pulse-duration is about 100ns. In addition to voltage and current measurements at various locations, a feature of these experiments is laser interferometry, which measures the line-integrated electron density at various locations in the gas cell for a gas pressures ranging from 50 mTorr to 300 Torr. This paper will analyze the numerical error as well as aleatory and epistemic uncertainty. PIC and Monte Carlo electron transport algorithms are inherently stochastic in nature; therefore, an extension to Richardson extrapolation is developed to obtain an error bound on the simulations. To account for aleatory and epistemic uncertainty we use second order probability, an inner aleatory loop sampling the approximate distribution of variation in parameters in the experiment with an outer epistemic loop varying the parameters of the distribution and model form. By including both aleatory and epistemic uncertainty and numerical error, the simulation can be compared with the NRL gas cell experiment.
Reprogramming of 24nt siRNAs in rice gametes

Gametes constitute a critical stage of the plant life cycle, during which the genome undergoes reprogramming in preparation for embryogenesis. Here we characterized the small RNA transcriptomes of egg cells and sperm cells from rice to elucidate genome-wide distributions of 24nt siRNAs, which are a hallmark of RNA-directed DNA methylation (RdDM) in plants and are typically concentrated at boundaries of heterochromatin. We found that 24nt siRNAs were depleted from heterochromatin boundaries in both gametes, reminiscent of siRNA patterns in DDM1-type nucleosome remodeler mutants. In sperm, 24nt siRNAs were spread across broad heterochromatic regions, while in eggs, 24nt siRNAs were concentrated at a smaller number of heterochromatic loci throughout the genome, which were shared with vegetative tissues and sperm. In both gametes, patterns of CHH methylation, typically a strong indicator of RdDM, were similar to vegetative tissues, although lower in magnitude. These findings indicate that the small RNA transcriptome undergoes large-scale re-programming in both male and female gametes, which is not correlated with recruitment of DNA methyltransferases in gametes and suggestive of unexplored regulatory activities of gamete small RNAs in seeds after fertilization.
Automatic Functionality Assignment to AUTOSAR Multicore Distributed Architectures

The automotive electronic architectures have moved from federated architectures, where one function is implemented in one ECU (Electronic Control Unit), to distributed architectures, where several functions may share resources on an ECU. In addition, multicore ECUs are being adopted because of better performance, cost, size, fault-tolerance and power consumption. In this paper we present an approach for the automatic software functionality assignment to multicore distributed architectures. We consider that the systems use the AUTomotive Open System ARchitecture (AUTOSAR). The functionality is modeled as a set of software components composed of subtasks, called runnables, in AUTOSAR terminology. We have proposed a Simulated Annealing metaheuristic optimization that decides: the (i) mapping of software components to multicore ECUs, (ii) the assignment of runnables to the ECU cores, (iii) the clustering of runnables into tasks and (iv) the mapping of tasks to “OS-Applications” (used to isolate mixed safety-criticality functions). We are interested to determine an implementation such that (1) the mapping constraints are satisfied, (2) the runnables are schedulable and (3) they are spatially and temporally isolated if they have different safety-criticality levels, (4) the overall communication bandwidth is minimized and (5) the utilization of the cores and ECUs is balanced. The proposed approach was evaluated on three realistic case studies.
A live-cell screen for altered Erk dynamics reveals principles of proliferative control

Complex, time-varying responses have been observed widely in cell signaling, but how specific dynamics are generated or regulated is largely unknown. One major obstacle has been that high-throughput screens for identifying pathway components are typically incompatible with the live-cell assays used to monitor dynamics. Here, we address this challenge by performing a drug screen for altered Erk signaling dynamics in primary mouse keratinocytes. We screened a library of 429 kinase inhibitors, monitoring Erk activity over 5 h in more than 80,000 single live cells. The screen revealed both known and uncharacterized modulators of Erk dynamics, including inhibitors of non-EGFR receptor tyrosine kinases (RTKs) that increased Erk pulse frequency and overall activity. Using drug treatment and direct optogenetic control, we demonstrate that drug-induced changes to Erk dynamics alter the conditions under which cells proliferate. Our work opens the door to high-throughput screens using live-cell biosensors and reveals that cell proliferation integrates information from Erk dynamics as well as additional permissive cues.
Crossing the Theshold Paradox: Modelling Creative Cognition in the Global Workspace

I present a hypothetical global model of everyday creative cognition located within Baars’ Global Workspace Theory, based on theories of predictive cognition and specific work on statistical modelling of music perception. The key idea is a proposal for regulating access to the Global Workspace, overcoming what Baars calls the Threshold Paradox. This idea is motivated as a general mechanism for managing the world, and an argument is given as to its evolutionary value. I then show how this general mechanism produces effects which are indistinguishable from spontaneous creative inspiration, best illustrated by Wallas’ (1926) “Aha! ” moment. I argue that W. A. Mozart’s introspective account of compositional experience closely matches the proposed process, and refer to a computational system which will form the basis of an implementation of the ideas, for musical composition.
Auto Default Gateway Settings for Virtual Machines in Servers using Default Gateway Weight Settings Protocol (DGW)

Availability is one of the most important concerns in the networking world. For any high available network, we need to maintain 99.99999% availability. That is why it is one of the most important factors to find out the single point of failure in the network architecture and eliminate that single point of failure (SPOF) from physical network and logical network. SPOF in our server infrastructure has been analysed in terms of communicating with the router for forwarding traffic with multiple routers. We have developed an algorithm that will automatically select default gateway into the network interface card of virtual machines. The proposed algorithm will automatically enable Default Gateway Weight settings (DGW) protocol among routers by configuring Network interface card with default gateway of all routers. The proposed protocol works based on weight settings for the multiple default gateway configuration in the host. There will be heartbeat communication and re-convergence will be performed within the shortest possible time. Lowest weight setting will select the path for packet forwarding through specified routers related with the default gateway from the virtual machine.
Estimating conservation effectiveness across protected areas in Limpopo Province, South Africa

As we enter what many scientists call the Earth’s six mass extinction (McCallum 2015; Pimm et al. 2014; Thomas et al. 2004), the importance of biodiversity conservation is more apparent than ever. Declines in biodiversity are associated with changes that are reducing or homogenising biological diversity at many levels, from genes to habitats and ecosystems (Gaston & Spicer 2004). Probably the most efficient and widespread tool developed in response to the biodiversity crisis is the establishment of protected areas (PAs). Today, there are 202 467 designated terrestrial and inland water PAs, covering 14.7% of the land surface (UNEP-WCMC & IUCN 2016). However, despite the increased number and extent of the protected area (PA) portfolio over recent decades (Chape et al. 2005), biodiversity loss continues (Bertzky et al. 2012) and, in some cases, even within PAs (Craigie et al. 2010; Françoso et al. 2015; Laurance et al. 2012). This has led to the growing recognition that effective management of PAs is at least as important as their size, number and physical characteristics (IUCN-WCPA 2009; Leverington et al. 2010).
Functional Genomics for Improving Gene Function Assessment in Bacteria

Author(s): Shao, Wenjun | Advisor(s): Arkin, Adam P; Savage, David F | Abstract: Functional genomics uses system-wide approaches to generate genome-scale data and to describe gene functions. Recent genome-wide transcriptome studies have observed a great number of unexpected transcripts internal or antisense to known genes in bacteria and archaea, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected transcriptional start sites (TSSs). In the first part of this thesis, we present the methodology to generate a set of high-confidence TSSs. Using high-resolution tiling microarrays and 5’-end RNA sequencing, combined with a semi-supervised machine learning approach, we identified 2,531 TSSs in S. oneidensis MR-1. We then classified them based on their relative positive compared with the current gene model. 18% of the identified TSSs were located inside coding sequences (CDSs). In the second part of this thesis, we present the conservation study of the high-confidence TSSs identified in MR-1. Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved. 30% of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated. Combining with the genome-wide mutagenesis data, we show that having internal promoters significantly eliminate polar effects which are expected if the internal promoters are not functional.In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) were significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.In the last part of the thesis, I present the development of a high-throughput assay, bacterial two-hybrid sequencing (B2H-seq), to construct protein interactome in bacteria. This technique, if successful, will complement the existing large-scale mutant fitness profiling method in Arkin lab, and improve the gene function annotation.
Diversity and Life-cycle Analysis of Pacific Ocean Zooplankton by Videomicroscopy and DNA Barcoding. I. Cnidaria

Most, but not all cnidarian species in the classes Hydrozoa, Scyphozoa and Anthozoa have a life cycle in which a colonial, asexually reproducing hydroid phase alternates with a free-swimming, sexually reproducing medusa phase that, in the hydrozoans, is usually microscopic. Hydrozoan medusae were collected by zooplankton tows in Newport Bay and the Pacific Ocean near Newport Beach, California, and hydroid colonies were collected from solid substrates in the same areas. Specimens were documented by videomicroscopy, preserved in ethanol, and sent to the Canadian Centre for DNA Barcoding at the University of Guelph, Ontario, Canada for DNA barcoding. Among the order Anthomedusae (athecate hydroids), DNA barcoding allowed for the discrimination between the medusae of eight putative species of Bougainvillia, and the hydroid stages were documented for two of these. The medusae of three putative species of Amphinema were identified, and the hydroid stages were identified for two of them. DNA barcodes were obtained from medusae of one species of Cladonema, one adult of the By-the wind Sailor, Velella Velella, five putative species of Corymorpha with the matching hydroid phase for one; and Coryne eximia, Turritopsis dohrnii and Turritopsis nutricula with the corresponding hydroid phases. The actinula larvae and hydroid for the pink-hearted hydroid Ectopleura crocea were identified and linked by DNA barcoding. Among the order Leptomedusae (thecate hydroids) medusae were identified for Clytia elsaeoswaldae, Clytia gracilis and Clytia sp. 701 AC and matched with the hydroid phases for the latter two species. Medusae were matched with the hydroid phases for two species of Obelia (including O. dichotoma) and Eucheilota bakeri. Obelia geniculata was collected as a single hydroid. DNA barcodes were obtained for hydroids of Orthopyxis everta and three other species of Orthopyxis. The medusa of one member of the family Solmarisidae, representing the order Narcomedusae, and one member (Liriope tetraphylla) of the order Trachymedusae were recognized as medusae. In the Scyphozoa, DNA barcoding confirmed the planktonic larval stage (ephyra) of the Moon Jelly, Aurelia aurita, the adult medusa of which is occasionally common in and around Newport Bay. In the Anthozoa, antipathula larvae were identified from the Onion Anemone, Paranthus rapiformis and a cerinula larva was identified from the Tube-dwelling Anemone, Isarachnanthus nocturnus. We have yet to find the adults of these species locally.
Construction of Distributed Sensors Network Based on DTP/DIA

Present paper describes one of the systems with distributed data acquisition. The presented online sensors network covers the North-west region of Russia. Sensors measure atmospheric parameters: temperature, humidity and pressure. Measured data are transferred through Internet channels to database server every 5 minutes and may be also stored locally on the side of data source. All the acquired information is represented on the web-server http://thermo.karelia. ru/eng/. The sensors net is functioning on Data Transfer Protocol for Distributed Information Acquisition (DTP/DIA), which was designed especially for these purposes. The main features of DTP/DIA are simple implementation, reliability, ability to resolve various sources of information, support of up to 16 millions unique devices. In this net DTP/DIA uses TCP/IP packet as envelope.
Alkyl gallates display elicitor activities in tobacco plants

Alkyl gallates showed elicitor activities on tobacco in both whole plants and cell suspensions. Methyl gallate (MG), ethyl gallate (EG) and n-propyl gallate (PG) infiltration into tobacco leaves induced hypersensitive reaction-like lesions and topical production of autofluorescent compounds revealed under UV light. When sprayed on tobacco plants at 5 mM, EG promoted upregulation of defence-related genes such as the antimicrobial PR1, β-1,3-glucanase PR2, chitinase PR3 and osmotin PR5 target genes. Tobacco BY-2 cells challenged with EG underwent cell death in 48 h, significantly reduced in the presence of the protease inhibitor aprotinin. The three alkyl gallates all caused alkalinisation of the BY-2 extracellular medium, whereas gallic acid did not trigger any pH variation. Using EGTA or LaCl3, we showed that Ca2+ mobilisation occurred in BY-2 cells elicited with EG. Overall, our findings are the first evidence of alkyl gallate elicitor properties with early perception events on plasma membrane, potential hypersensitive reactions and PR-related downstream defence responses in tobacco. Highlights – Alkyl gallates elicited defence reactions in tobacco – Alkyl gallates induced local biochemical changes in tobacco leaves – Alkyl gallates caused modification of plasma membrane properties – Ethyl gallate led to defence transcript accumulation and dose-dependent cell death associated with hypersensitive response – Alkyl gallates are novel elicitor agents well-suited to crop protection schemes.
An automatic approach for building secure systems

Building a secure system is one of the most complex and error-prone processes in computing. Unfortunately, the current design and development process is primarily manual, ad hoc, and far from satisfactory. In this thesis, I propose a new automatic approach for building secure systems. With this approach, users only need to specify desired security and system requirements. Such an automatic system can then explore the possible design space, generate design candidates, evaluate those candidates to find the most efficient correct design, and finally generate source code implementing the optimal design. Compared to the manual design and development process, this automatic approach is faster, more economical, yields protocols and implementations of higher security and efficiency. To demonstrate this automatic approach for building secure systems, we have focused on one of the most important aspects, designing and developing security protocols. In particular, I have designed and developed an automatic toolbox, called Athena, for automatic protocol generation, verification and implementation. The system contains three components: the automatic protocol generator (APG), the automatic protocol verifier (APV), and the automatic code generator (ACG). APV proposes a new automatic approach for security protocol analysis. Given a security protocol and desired security requirements, APV analyzes the protocol automatically. When APV terminates, it can either generate a proof of correctness, if the protocol satisfies the given requirements, or generate a counterexample, if the protocol is flawed. APV is the first automatic approach that has both the capability of providing a proof of correctness when the protocol is correct and the capability of generating a counterexample when the protocol is flawed. Athena runs efficiently and this high efficiency enables the approach of automatic protocol generation. APG uses powerful pruning techniques to drastically reduce the protocol search space. It is the first approach for automatic generation of security protocols. In our experiments, APG has generated new protocols that are more efficient than previous protocols proposed in the literature for different system settings. The composition of APG, APV and ACG forms an end-to-end system, Athena, which is the first system able to automatically generate, verify, and implement security protocols.
A look at textures analysis for remote sensing

The authors look at texture analysis as an activity which simultaneously considers (i) a texture measure, (ii) a texture algorithm and finally (iii) misclassification properties. Because the structural characteristics of textural fields are difficult to define, an immediate consequence is the numerous number of texture measures required. Several segmentation algorithms are also required. The authors report some experiments in which examples from (i) and (ii) are simultaneously studied on a "Malaysian" data-set. In particular they use the entropy (E) anti contrast (C) from the co-occurrence matrix as texture measures, and simultaneously employ the idea of region growing and thresholding as a package in texture analysis. <<ETX>>