Miracle-dz/UniFAR-FTUs huggingface dataset:
Real time all intra HEVC HD encoder on FPGA

Higher compression efficiency in HEVC encoders comes with increased computational complexity, making real time encoding of high resolution videos a challenging task. This challenge can be addressed by software, yet hardware solutions are more appealing due to their superior performance and low power consumption. This paper presents an FPGA based hardware implementation of an all intra HEVC encoder, which can encode 8 bits per sample, 1920×1080 resolution, 30 frames per second raw video, that is viable in real time even at low operating frequencies. A major obstacle to real time encoding in available architectures is the dependency created by reference generation. Moreover, each coding unit (CU) has to be processed in multiple configurations to determine the most efficient split and prediction mode representation, based on the bit stream generated. We propose a new three stage architecture to reduce these dependencies and increase parallelism. Feedback needed for CU split and prediction direction decision from binarization is avoided by a Hadamard based early decision method. Feedback constrained coefficient and reconstruction derivation module exploits several optimization techniques. All modules can operate at 200 MHz and the encoder can achieve real time encoding with a minimum operating frequency of 140 MHz. The design consumes 83K LUTs, 28K registers, and 34 DSPs when implemented on Xilinx Zynq ZC706.
Comparative analysis of coordination strategies for electric vehicles

This paper gives a structured literature overview of coordinated charging of electric vehicles (EVs). The optimization objective, scale and method of each coordination strategy are the three parameters used to characterize and compare different approaches. The correlation between the three parameters and the research category are investigated, resulting in a correlation mapping of the different approaches.
Role-playing, group work and other ambitious teaching methods in a large requirements engineering course

Requirements engineering is offered to students at the faculty of information technology in the University of Technology, Sydney. It is a core subject in the Graduate Certificate in Information Technology and Graduate Diploma. This paper outlines the subject's objectives, the topics discussed. Details of the lecturing methods used are also presented, namely: role-playing and peer-assessment within a group environment. The paper also describes the main features of the online support tool utilised in addition to summarising the lessons learnt. The main aim is to highlight both successful practices and those that can be improved further.
The rehabilitation of unilateral neglect: a review of the evidence

Unilateral spatial neglect is a disorder that has, for many years, intrigued and frustrated researchers and clinicians working in the area of stroke rehabilitation. A vast literature exists on the subject of neglect, much of it published by neuropsychologists and neurologists. Many of these papers aim to identify the underlying causal mechanisms, in terms of the neuroanatomical structures and cognitive processes involved. More recently, research has focused on evaluation of rehabilitation strategies to reduce the disabling effects of neglect. Various research designs have been used to examine whether a particular approach is effective or not. These range from single-case experimental designs (where the individual acts as their own control) through to randomized controlled trials (RCTs). In the latter, comparisons are made between (typically) two groups, one randomly assigned to receive the therapy approach under investigation and the other assigned to the control treatment.
Forces that structure plant communities: quantifying the importance of the mycorrhizal symbiosis.

John Klironomos, Martin Zobel, Mark Tibbett, William D. Stock, Matthias C. Rillig, Jeri L. Parrent, Mari Moora, Alexander M. Koch, Jose M. Facelli, Evelina Facelli, Ian A. Dickie and James D. Bever
Exon 5 Encoding the Transmembrane Region of HLA-A Contains a Transitional Region for the Induction of Nonsense-Mediated mRNA Decay1

HLA class I alleles containing premature termination codons (PTCs) are increasingly being found. To understand their effects on MHC class I expression, HLA-A*2402 mutants containing PTCs were transfected into class I-deficient cells, and expression of HLA-A mRNA and protein was determined. In exons 2, 3, and 4, and in the 5′ part of exon 5, PTCs reduced mRNA levels by up to 90%, whereas in the 3′ part of exon 5 and in exons 6 and 7 they had little effect. Transition in the extent of nonsense-mediated mRNA decay occurred within a 48-nt segment of exon 5, placed 58 nt upstream from the exon 5/exon 6 junction. This transition did not conform to the positional rule obeyed by other genes, which predicted it to be ∼50–55 nt upstream of the exon 7/exon 8 junction and thus placing it in exon 6. Mutants containing extra gene segments showed the difference is caused by the small size of exons 5 and 6, which renders them invisible to the surveillance machinery. For the protein, a transition from secretion to membrane association occurs within a 26-nt segment of exon 5, 17 nt upstream of the exon 5/exon 6 junction. Premature termination in exon 5 can produce secreted and membrane-associated HLA-A variants expressed at high levels.
Rule Learning by Searching on Adapted Nets

If the back propagation network can produce an inference structure with high and robust performance, then it is sensible to extract rules from it. The KT algonthm is a novel algonthm for generating rules from an adapted net efficiently. The algorithm is able to deal with both single-layer and multi-layer networks, and can learn both confirming and disconfirming rules. Empirically, the algorithm is demonstrated in the domain of wind shear detection by infrared sensors with success.
Plasticity in Repressor-DNA Interactions Neutralizes Loss of Symmetry in Bipartite Operators*

Transcription factor-DNA interactions are central to gene regulation. Many transcription factors regulate multiple target genes and can bind sequences that do not conform strictly to the consensus. To understand the structural mechanism utilized by the transcription regulators to bind diverse target sequences, we have employed the repressor AraR from Bacillus subtilis as a model system. AraR is known to bind to eight different operator sites in the bacterial genome. Although there are differences in the sequences of four of these operators, ORE1, ORX1, ORA1, and ORR3, the AraR-DNA binding domain (AraR-DBD) as well as full-length AraR unexpectedly binds to each of these sequences with similar affinities as measured by fluorescence anisotropy experiments. We have determined crystal structures of AraR-DBD in complex with two different natural operators ORE1 and ORX1 up to 2.07 and 1.97 Å resolution, respectively. These structures were compared with the previously reported structures of AraR-DBD bound to two other natural operators (ORA1 and ORR3). Interactions of two molecules of AraR-DBD with the symmetric operator, ORE1, are identical, but their interaction with the non-symmetric operator ORX1 results in breakdown of the symmetry in protein-DNA interactions. The novel interactions observed are accompanied by local conformational change in the DNA. ChIP-sequencing (ChIP-Seq) data on other transcription factors has shown that they can bind to diverse targets, and hence the plasticity exhibited by AraR may be a general phenomenon. The ability of transcription factors to form alternate interactions may be important for employment in new functions and evolution of novel regulatory circuits.
The form of sound through hybrid materials

We describe a digital design process that interfaces real-time data with 3D modeling and 3D printing techniques. Digital Impressionism (DI) is a platform that explores new material possibilities, by 3D modeling physical and digital objects, as affected by invisible forces that act upon them in real time. Using a 3D pointcloud as a medium, we describe an experimental project run with students in our programme, incorporating realtime audio data to manipulate 3D physical forms, resulting in new static and dynamic shapes with what we call a hybrid materiality. The modeling platform of DI treats materials as composites, through which substance becomes physical via the digital interference the environment applies to digital forms. We describe dynamic modeling processes through which data enables a new hybrid tectonic made of composite shapes and materials. This abstract introduces the project and describes our methodology and results so far.
An Analytical Approach to Space-Time Block Coding With Decision Feedback Channel Estimation

We consider a space-time block coded system having L time slots and using decision feedback channel estimation with a finite window size. The channel matrix estimate is updated every L time slots by: 1) a least-squares (LS) estimate and 2) a minimum mean-square error (MMSE) estimate. Using a Markov model of the decision process, we analyze the decoding error probability (DEP) of this scheme in Rayleigh fading. The transition probability matrix is obtained by simulation of the decision process for a system using the Alamouti code. From this matrix, the DEP can be computed for any time shift. We find from computations that the DEP increases with increase in the time shift but tends to saturate with time to a steady-state value. It is also observed that both the state and the transition probabilities tend to saturate with the increase in average signal-to-noise ratio per diversity branch
Mathematical modeling of the immune system response to pathogens

The detection and elimination of pathogens in an organism are the main tasks of its immune system. The most important cells involved in these processes are neutrophils and macrophages. These processes might have two resolutions: The first is the possibility of pathogen elimination, and the other the possibility of the inflammation resolution. In this work, we present several mathematical models involving immune cell densities and inflammation levels. Our general goal is to exhibit the possible pathogen eradication or the inflammation resolution. We use bifurcation techniques in order to analyze how parameter variations may change the system evolution. Our results indicate that the elimination of apoptotic neutrophils by macrophages has a dichotomy effect: It contributes to the decrease of the inflammation level, but it may hinder the pathogen elimination. Also, an increment of the average neutrophil life can improve healthy outcomes. Moreover, we find scenarios when pathogens cannot be eliminated, as well as conditions for their successful eradication.
Atomic background and EXAFS of gaseous hydrides of Ge, As, Se and Br.

K edge absorption spectra of elements from Ge to Br in gaseous hydrides were measured at the BM 29 station of ESRF with noise level as low as 2x10(-5), so far achievable only on noble gases. The dominant feature of the spectra is the atomic background similar to that of Kr and comparable to it in the quality of detail. Onto the background, a smooth weak EXAFS signal due to the hydrogen neighbors is superposed. For the very simple molecules such as these, its contribution can be calculated ab initio, with exact treatment of the effect of molecular vibrations, so that no best-fit adjustment to the experimental data is necessary. In comparison to the main constituent of the atomic background, i.e. the shake-up absorption edges, the EXAFS signal is of minor importance in HBr with a single H neighbor, but of the same order of magnitude in GeH4.
Reductive Dehalogenation and Conversion of 2-Chlorophenol to 3-Chlorobenzoate in a Methanogenic Sediment Community: Implications for Predicting the Environmental Fate of Chlorinated Pollutants

ABSTRACT Biotransformation of 2-chlorophenol by a methanogenic sediment community resulted in the transient accumulation of phenol and benzoate. 3-Chlorobenzoate was a more persistent product of 2-chlorophenol metabolism. The anaerobic biotransformation of phenol to benzoate presumably occurred via para-carboxylation and dehydroxylation reactions, which may also explain the observed conversion of 2-chlorophenol to 3-chlorobenzoate.
TATTCGGGAATAACAACATGGATATGTGG TTT EVS 113 ATGTGATATGATCTATCATGAAAGGACTTA JB 1 GCGCTTCGAACTCTGAGGAAGAATTGTG JB 2 GCGCCCTAGGTTAGTTAGTTAACCCTTTT GCCAGA RTKnF TGATGCGCTGGCAGTGTT RTKnP TGCGCCGGTTGCATTCGATTCCTGT RTKnR CTCGCATCAACCAAACCGTTA

Most Vibrio Wscheri strains isolated from the Euprymna scolopes light organ carry plasmids, often including both a large (>40 kb) plasmid, and one or more small (<12 kb) plasmids. The large plasmids share homology with pES100, which is the lone plasmid in V. Wscheri type strain ES114. pES100 appears to encode a conjugative system similar to that on plasmid R721. The small plasmids lack extensive similarity to pES100, but they almost always occur in cells that also harbor a large plasmid resembling pES100. We found that many or all of these small plasmids share homology with pES213, a plasmid in strain ES213. We determined the 5501-bp pES213 sequence and generated selectable antibiotic resistance encoding pES213 derivatives, which enabled us to examine replication, retention, and transfer in V. Wscheri. An 863-bp fragment of pES213 with features characteristic of -type replicons conferred replication without requiring any pES213 open reading frame (ORF). We estimated that pES213 derivatives were maintained at 9.4 copies per genome, which corresponds well with a model of random plasmid segregation to daughter cells and the »10¡4 per generation frequency of plasmid loss. pES213 derivatives mobilized between V. Wscheri strains at frequencies up to »10¡4 in culture and in the host, apparently by employing the pES100 conjugative apparatus. pES213 carries two homologs of the putative pES100 origin of transfer (oriT), and V. Wscheri strains lacking the pES100 conjugative relaxase, including a relaxase mutant, failed to serve as donors for transmission of pES213 derivatives. In other systems, genes directing conjugative transfer can function in trans to oriT, so it was noteworthy that ORFs adjacent to oriT, VFB51 in pES100 and traYZ in pES213, enhanced transfer 100to 1000-fold when provided in cis. We also identiWed and disrupted the V. Wscheri recA gene. RecA was not required for stable pES213 replication but surprisingly was required in donors for eYcient transfer of pES213 derivatives. These studies provide an explanation for the prevalence and co-occurrence of pES100and pES213-type plasmids, illuminate novel elements of pES213 mobilization, and provide the foundation for new genetic tools in V. Wscheri.  2005 Elsevier Inc. All rights reserved. 0147-619X/$ see front matter  2005 Elsevier Inc. All rights reserved. doi:10.1016/j.plasmid. 2005.01. 003 ¤ Corresponding author. Fax: +1 706 542 2674. E-mail address: estabb@uga.edu (E.V. Stabb). A.K. Dunn et al. / Plasmid 54 (2005) 114–134 115
SOD 1 targeted to the mitochondrial intermembrane space prevents motor neuropathy in the Sod 1 knockout mouse

Motor axon degeneration is a critical but poorly understood event leading to weakness and muscle atrophy in motor neuron diseases. Here, we investigated oxidative stress-mediated axonal degeneration in mice lacking the antioxidant enzyme, Cu,Zn superoxide dismutase (SOD1). We demonstrate a progressive motor axonopathy in these mice and show that Sod1 / primary motor neurons extend short axons in vitro with reduced mitochondrial density. Sod1 / neurons also show oxidation of mitochondrial—but not cytosolic—thioredoxin, suggesting that loss of SOD1 causes preferential oxidative stress in mitochondria, a primary source of superoxide in cells. SOD1 is widely regarded as the cytosolic isoform of superoxide dismutase, but is also found in the mitochondrial intermembrane space. The functional significance of SOD1 in the intermembrane space is unknown. We used a transgenic approach to express SOD1 exclusively in the intermembrane space and found that mitochondrial SOD1 is sufficient to prevent biochemical and morphological defects in the Sod1 / model, and to rescue the motor phenotype of these mice when followed to 12 months of age. These results suggest that SOD1 in the mitochondrial intermembrane space is fundamental for motor axon maintenance, and implicate oxidative damage initiated at mitochondrial sites in the pathogenesis of motor axon degeneration.
MS5 Mediates Early Meiotic Progression and Its Natural Variants May Have Applications for Hybrid Production in Brassica napus

MS5, a novel gene, determines the proper progression of early meiosis, and its different alleles provide a promising pollination-control system for heterosis breeding in Brassica napus. During meiotic prophase I, chromatin undergoes dynamic changes to establish a structural basis for essential meiotic events. However, the mechanism that coordinates chromosome structure and meiotic progression remains poorly understood in plants. Here, we characterized a spontaneous sterile mutant MS5bMS5b in oilseed rape (Brassica napus) and found its meiotic chromosomes were arrested at leptotene. MS5 is preferentially expressed in reproductive organs and encodes a Brassica-specific protein carrying conserved coiled-coil and DUF626 domains with unknown function. MS5 is essential for pairing of homologs in meiosis, but not necessary for the initiation of DNA double-strand breaks. The distribution of the axis element-associated protein ASY1 occurs independently of MS5, but localization of the meiotic cohesion subunit SYN1 requires functional MS5. Furthermore, both the central element of the synaptonemal complex and the recombination element do not properly form in MS5bMS5b mutants. Our results demonstrate that MS5 participates in progression of meiosis during early prophase I and its allelic variants lead to differences in fertility, which may provide a promising strategy for pollination control for heterosis breeding.
Utilization of Spatial Coherence in Functional Neuroimage-Based Classification

Functional magnetic resonance imaging provides a non-invasive mechanism for monitoring brain activity of subjects during performance of a task. While this approach has been used extensively for human brain mapping activities, automated classification of subjects based on neural activation patterns is also of interest. However, due to the high dimensionality of the image data, classification accuracy is highly dependent upon the adequacy of the features used in the models. In this work 1 , we present a new feature refinement strategy that uses spatial coherence information to eliminate irrelevant features from consideration. For a neurobehavioral disinhibition dataset, we show that this new approach for feature selection using spatially coherent voxels (SCV) outperforms conventional methods.
Variance in response of pole-size trees and seedlings of Douglas-fir and western hemlock to nitrogen and phosphorus fertilizers

Three experiments were conducted to determine effects of N and P fertilizers on growth and levels of plant-tissue nutrients of Douglas-fir (Pseudotsugamenziesii (Mirb.) Franco) and western hemlock (Tsugaheterophylla (Raf.) Sarg. ). Both pole-size trees in closed-canopy stands and potted seedlings were used. Soil series were Bunker for Douglas-fir and Klone for western hemlock in experiments 1 and 3, and Vesta in experiment 2. For each species in experiments 1 and 2, P and N fertilizers were tested in six or eight treatments using factorial design. In experiment 3, N and P fertilizers were individually tested on seedlings, at one rate of application each. Nitrogen fertilizers used were urea in experiment 1 and ammonium nitrate in the other two experiments; P was applied as triple superphosphate in all three experiments. In general, fertilization changed levels of some plant-tissue nutrients of the pole-size trees and potted seedlings. Neither height nor basal-area growth of the trees was significantly affec.
Counterexample Generation in Stochastic Model Checking Based on PSO Algorithm with Heuristic

Providing counterexample for the refutation of a property is an essential feature of model checking, if it is not the most important. However, generating counterexample in stochastic model checking needs a dedicated algorithm. It usually costs too much time and memory, and sometimes it cannot find the counterexample. What is worse, generating smallest counterexample in stochastic model checking has been proved to be NP-complete, and it is unlikely to be efficiently approximable. Although there are a few heuristic methods that are applied to the construction of the counterexample, it is usually difficult to determine the heuristic function which is critical for counterexample generating. In this paper, we present a particle swarm optimization (PSO)-based approach to generating counterexample for stochastic model checking. We define the diagnostic sub-graph as counterexample, and extend PSO algorithm with heuristic (HPSO) to generate counterexample. It adopts indirect path coding scheme to expand the scope of the search space, and employs heuristic operator to generate more effective path. The validity of our approach is illustrated by some case studies in a prototype tool. The experiments show that HPSO algorithm can significantly outperform the present algorithm for counterexample generation in stochastic model checking.
Optimized Technique for Dna Structural Properties Discovering

An automated algorithm is presented to determine the DNA molecule intrinsic curvature profiles and the molecular spatial orientations in Atomic Force Microscope images. The curvature is composed by static and dynamic contributions. The former is the intrinsic curvature, a function of the DNA nucleotide sequence, while the latter is due to thermal fluctuations. This algorithm allows to reconstruct the intrinsic curvature profile excluding the thermal contribution. The DNA intrinsic curvature profile is computed in consequence of the detection of the correct spatial orientation of the molecules on the AFM substrate following the DNA deposition process. To discover the correct molecular orientations, we propose a fast heuristic orientation finding algorithm, that modifies one DNA molecular orientation at a time with linear-time heuristic transitions.
Model-based reliability analysis

Modeling, in conjunction with testing, is a rich source of insight. Model parameters are easily controlled and monitoring can be done unobtrusively. The ability to inject faults without otherwise affecting performance is particularly critical. Many iterations can be done quickly with a model while varying parameters and conditions based on a small number of validation tests. The objective of model-based reliability analysis (MBRA) is to identify ways to capitalize on the insights gained from modeling to make both qualitative and quantitative statements about product reliability. MBRA is developed and exercised in the realm of weapon system development and maintenance, where the challenges of severe environmental requirements, limited production quantities, and use of oneshot devices can make testing prohibitively expensive. However, the general principles are also applicable to other product types.