Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C.
Overview of the ImageCLEFmed 2006 Medical Retrieval and Annotation Tasks

This paper describes the medial image retrieval and the medical annotation tasks of ImageCLEF 2006. These tasks are described in a separate paper from the other task to reduce the size of the overview papaer.These two medical tasks are described separately with respect to the goals, databases used, topics created and distributed among participants, results and techniques used. The best performing techniques are described in more detail to provide better insights about successful strategies. Some ideas for future tasks are also presented. The ImageCLEFmed medical image retrieval task had 12 participating groups and received 100 submitted runs. Most runs were automatic, with only a few manual or interactive. Purely textual runs were in the majority compared to purely visual, runs but most runs were mixed, i.e., using visual and textual information. None of the manual or interactive techniques were significantly better than those used for the automatic runs. The best–performing systems used visual and textual techniques combined, but combinations of visual and textual features often did not improve a system’s performance. Purely visual systems only performed well on the visual topics. The medical automatic annotation used a larger database in 2006, with 10’000 training images and 116 classes, up from 57 in 2005. Twelve participating groups submitted 27 runs. Despite the much larger number of classes, results were almost as good as in 2005 and a clear improvement in performance could be shown. The best– performing system of 2005 would have only received a position in the upper middle part in 2006.
Sphagnum peatland distribution in North America and Eurasia during the past 21,000 years

The distribution and abundance of Sphagnum spores in North America and Eurasia are mapped for the past 21 ka. The present‐day distribution of abundant Sphagnum spores corresponds closely to areas with peatland development, with maximum Sphagnum abundance between 630 and 1300 mm annual precipitation and between −2° and 6°C mean annual air temperature. During the Wisconsin glaciation, there were apparently not large areas of peatland in North America, except in Alaska. High Sphagnum spore percentages were found in eastern North America during deglaciation. Major peatland development occurred in boreal North America after 9 ka and there was a southward movement of high Sphagnum spore abundance after 5 ka in the western Great Lakes region. Major peatland development began after 9 ka in Europe and Asia. On the basis of maps of the area supporting peatlands, carbon accumulation in peatlands is estimated to be low prior to 11 ka, increased slightly between 11 and 5 ka, and greatly increased during the past 5 ka.
Optimal trajectory planning for Omni-directional mobile robots using direct solution of optimal control problem

In this paper we address the problem of finding trajectory for Omni-directional mobile robots. The objective of the trajectory planning is moving the robot from its initial position to a final position in the presence of static obstacles while minimizing a quadratic index of performance. Along the trajectory, the robot requires to observe certain velocity and acceleration limitations. This problem can be formulated as a constraint nonlinear optimal control problem. To solve this problem, we employ direct method of numerical solution in which the trajectories are parameterized by parametric polynomial functions. By this transforming, the main optimal control problem converts to a nonlinear programming problem (NLP) by lower computational cost. To solve the NLP and obtaining the trajectories, we utilize a new approach with too small run time. The performance and effectiveness of the proposed method are tested in simulations.
The relationship between visuo-spatial attention and nonword reading in developmental dyslexia

Focused visuo-spatial attention was studied in 10 developmental dyslexic children with impaired nonword reading, 10 dyslexic children with intact nonword reading, and 12 normally reading children. Reaction times to lateralized visual stimuli in a cued detection task showed that attentional facilitation of the target at the cued location was symmetrical in the three groups. However, dyslexics with impaired nonword reading selectively showed a lack of attentional inhibition for targets at the uncued location in the right visual field. This result was replicated in a second group of 13 dyslexics with impaired nonword reading. Individual differences in the ability of right attentional inhibition across the entire sample of dyslexics accounted for 17% of unique variance in nonword reading accuracy after controlling for individual differences in age, IQ, and phonological skills. A possible explanation based on the role of spatial attention mechanisms in the graphemic parsing process is discussed. Our results suggest that focused visuo-spatial attention may be crucial for nonword decoding.
High-Performance Memory-based Face Recognition for Visitor Identification

We show that a simple, memory-based technique for view-based face recognition, motivated by the real-world task of visitor identification, can outperform more sophisticated algorithms that use Principal Components Analysis (PCA) and neural networks. This technique is closely related to correlation templates; however, we show that the use of novel similarity measures greatly improves performance. We also show that augmenting the memory base with additional, synthetic face images results in further improvements in performance. Results of extensive empirical testing on two standard face recognition datasets are presented, and direct comparisons with published work show that our algorithm achieves comparable (or superior) results. This paper further demonstrates that our algorithm has desirable asymptotic computational and storage behavior, and is ideal for incremental training. Our system is incorporated into an automated visitor identification system that has been operating successfully in an outdoor environment for several months.
Construction of a word similarity dataset and evaluation of word similarity techniques for Vietnamese

Measuring word similarity is a core issue because it has many applications in natural language processing. Although many studies have been reported and the techniques have been developed for addressing this issue for English, however, the study dealing with the applications, analyses and evaluation word similarity techniques to Vietnamese still has not reported yet. Especially, there is still lack of the benchmark Vietnamese dataset for evaluating these techniques. In this paper, we report three main topics including: firstly, construct a benchmark dataset for evaluation of similar techniques to the Vietnamese language; secondly, experiment with some similarity techniques based on WordNet and word embeddings; and finally, propose an extension for Lesk algorithm in order to improving the efficiency of similar measuring with Vietnamese language.
Changes in GABAB Modulation During a Theta Cycle May Be Analogous to the Fall of Temperature During Annealing

Changes in GABAB modulation may underlie experimentally observed changes in the strength of synaptic transmission at different phases of the theta rhythm (Wyble, Linster, & Hasselmo, 1997). Analysis demonstrates that these changes improve sequence disambiguation by a neural network model of CA3. We show that in the framework of Hopfield and Tank (1985), changes in GABAB suppression correspond to changes in the effective temperature and the relative energy of data terms and constraints of an analog network. These results suggest that phasic changes in the activity of inhibitory interneurons during a theta cycle may produce dynamics that resemble annealing. These dynamics may underlie a role for the theta cycle in improving sequence retrieval for spatial navigation.
Finite-time stabilization of Port-Controlled Hamiltonian systems with application to nonlinear affine systems

The finite-time stabilization of nonlinear Port-Controlled Hamiltonian (PCH) systems is investigated in this paper, and a number of approaches to the finite-time control design are proposed. Based on a finite-time stability criterion and the so-called "energy shaping plus damping injection" technique, the continuous finite-time stabilization problem is studied for the PCH systems, and several global stabilization results are obtained. Via Hamiltonian realization, the results obtained for the Hamiltonian systems are applied to investigate continuous finite-time stabilization of nonlinear affine systems, and several global control design results are presented. Study on several examples shows that the control design approaches developed in this paper work very well.
Facilitating interpersonal interaction and learning online: Linking theory and practice

Introduction: An earlier study of physicians' perceptions of interactive online learning showed that these were shaped both by program design and quality and the quality and quantity of interpersonal interaction. We explore instructor roles in enhancing online learning through interpersonal interaction and the learning theories that inform these. Methods: This was a qualitative study using focus groups and interviews. Using purposive sampling, 50 physicians were recruited based on their experience with interactive online CME and face‐to‐face CME. Qualitative thematic and interpretive analysis was used. Results: Two facilitation roles appeared key: creating a comfortable learning environment and enhancing the educational value of electronic discussions. Comfort developed gradually, and specific interventions like facilitating introductions and sharing experiences in a friendly, informative manner were helpful. As in facilitating effective small‐group learning, instructors' thoughtful use of techniques that facilitated constructive interaction based on learner's needs and practice demands contributed to the educational value of interpersonal interactions. Discussion: Facilitators require enhanced skills to engage learners in meaningful interaction and to overcome the transactional distance of online learning. The use of learning theories, including behavioral, cognitive, social, humanistic, and constructivist, can strengthen the educational design and facilitation of online programs. Preparation for online facilitation should include instruction in the roles and techniques required and the theories that inform them.
Greenhouse gas emissions from shifting cultivation in the tropics, including uncertainty and sensitivity analysis

[1] Annual emissions of CO2, CH4, CO, N2O, and NOx from biomass burning in shifting cultivation systems in tropical Asia, Africa, and America were estimated at national and continental levels as the product of area burned, aboveground biomass, combustion completeness, and emission factor. The total area of shifting cultivation in each country was derived from the Global Land Cover 2000 map, while the area cleared and burned annually was obtained by multiplying the total area by the rotation cycle of shifting cultivation, calculated using cropping and fallow lengths reported in the literature. Aboveground biomass accumulation was estimated as a function of the duration and mean temperature of the growing season, soil texture type, and length of the fallow period. The uncertainty associated with each model variable was estimated, and an uncertainty and sensitivity analysis of greenhouse gas estimates was performed with Monte Carlo and variance decomposition techniques. Our results reveal large uncertainty in emission estimates for all five gases. In the case of CO2, mean (standard deviation) emissions from shifting cultivation in Asia, Africa, and America were estimated at 241 (132), 205 (139), and 295 (197) Tg yr−1, respectively. Combustion completeness and emission factors were the model inputs that contributed the most to the uncertainty of estimates. Our mean estimates are lower than the literature values for atmospheric emission from biomass burning in shifting cultivation systems. Only mean values could be compared since other studies do not provide any measure of uncertainty.
Reliable Train Network with Active Supervisor

In this paper, a new reliable hierarchical model is suggested for a two-wagon train Networked Control System. Each wagon has a Controller that carries the control load and an Entertainment server that handles the entertainment. A supervisory controller runs on top of the two controllers and the two entertainment servers. Contrary to a similar model in the literature, the Supervisory node replaces a Controller as soon as it fails (Active Supervisor). All system states are analyzed and simulated using OPNET. It is shown that, for all states, this architecture has zero control packets dropped and the end-to-end delay is below the maximum target delay. A comparison between this Active model and the other model in the literature is presented. It is found that the entertainment in this new architecture is kept available for the passengers in more of the system states when compared to the architecture previously presented in the literature.
Aperture controlled grouting – benefits of the discrete fracture network approach

Fractured rocks, specifically sedimentary sequences, present a particular challenge for grouting, as major connected fractures that must be sealed will rarely be intersected by vertical groutholes. The aperture controlled grouting (ACG) method can be readily applied using discrete fracture network (DFN) analysis approaches to understand the pattern of fractures that need to be grouted. Aperture controlled grouting then utilises a combination of the principles of fracture grouting and grouting intensity number (GIN) grouting for practical and cost-effective grouting of tunnel, dam, shaft, or environmental restoration projects. This paper illustrates the application of DFN techniques for fracture assessment for grouting design and then compares the ACG approach to more conventional grouting approaches based on recent grouting experience.
SRTM DEM accuracy assessment over vegetated areas in Norway

Results from the Shuttle Radar Topography Mission (SRTM) are presented. The SRTM C‐band and X‐band digital elevation models (DEMs) are evaluated with regard to elevation accuracies over agricultural fields, forest areas and man‐made features in Norway. High‐resolution digital maps and satellite images are used as background data. In general, many terrain details can be observed in the SRTM elevation datasets. The elevation accuracy (90% confidence level) of the two SRTM systems is estimated to less than 6.5 m for open agricultural fields and less than 11 m considering all land surface covers. This is better than specifications. Analysis of dense Norwegian forest stands shows that the SRTM system will produce elevation data that are as much as 15 m higher than the ground surface. The SRTM DEM products will therefore partly indicate canopy elevations in forested areas. We also show that SRTM data can be used to update older DEMs obtained from other sources, as well as estimating the volume of rock removed from large man‐made gravel pits.
Quaternary coastal lithofacies, sequence development and stratigraphy in a passive margin setting, North Carolina and Virginia, USA

Lithofacies analysis is fundamental to unravelling the succession of depositional environments associated with sea‐level fluctuations. These successions and their timing are often poorly understood. This report defines lithofacies encountered within the north‐eastern North Carolina and south‐eastern Virginia Quaternary section, interprets their depositional environments, presents a model for coastal depositional sequence development in a passive margin setting and uses this understanding to develop the stratigraphy and Quaternary evolutionary history of the region. Data were obtained from numerous drill cores and outcrops. Chronology was based on age estimates acquired using optically stimulated luminescence, amino acid racemization, Uranium series and radiocarbon dating techniques. Geomorphic patterns were identified and interpreted using light detection and ranging imagery. Since lithofacies occurrence, distribution and stratigraphic patterns are different on interfluves than in palaeo‐valleys, this study focused on interfluves to obtain a record of highstand sea‐level cycles with minimal alteration by fluvial processes during subsequent lowstands. Nine primary lithofacies and four diagenetic facies were identified in outcrops and cores. The uppermost depositional sequence on interfluves exhibits an upward succession from shelly marine lithofacies to tidal estuarine lithofacies and is bounded below by a marine ravinement surface and above by the modern land surface. Older depositional sequences in the subsurface are typically bounded above and below by marine ravinement surfaces. Portions of seven depositional sequences were recognized and interpreted to represent deposition from late middle Pleistocene to present. Erosional processes associated with each successive depositional sequence removed portions of older depositional sequences. The stratigraphic record of the most recent sea‐level highstands (Marine Isotope Stage 5a and Marine Isotope Stage 3) is best preserved. Glacio‐isostatic adjustment has influenced depositional patterns so that deposits associated with late Quaternary sea‐level highstands (Marine Isotope Stages 5c, 5a and 3), which did not reach as high as present sea‐level according to equatorial eustatic records, are uplifted and emergent within the study area.
PAH and Mid-Infrared Luminosities as Measures of Star Formation Rate in Spitzer First Look Survey Galaxies

We present evidence that the 8 μm (dust) and 24 μm luminosities of star-forming galaxies are both strongly correlated with their 1.4 GHz and Hα luminosities over a range in luminosity of 2-3 orders of magnitude. At the bright end, the correlations are found to be essentially linear over a luminosity range of about 2 orders of magnitude (corresponding to star formation rates of several tenths to several tens of solar masses per year). However, at the faint end there appears to be a slope change for dwarf galaxies, possibly due to the lower dust-to-gas ratios and lower metallicities of the dwarfs. The correlations suggest that PAH features and mid-IR continuum emissions are good measures of the star formation rates of galaxies, and we present calibrations of star formation rates based on existing radio and Hα relations. Our findings are based on a sample of star-forming galaxies selected from the main field of the Spitzer First Look Survey with the aid of spectroscopic data from the Sloan Digital Sky Survey and VLA 1.4 GHz data.
Computed Tomography in the Evaluation of Carcinoma of the Ovary

Over a 26 month period, 34 patients with histologically proven ovarian malignancy were studied by computed tomography (CT). In nine patients, CT was obtained for evaluation of a pelvic or abdominal mass. Computed tomography was diagnostic of ovarian malignancy in seven and indeterminate regarding the origin of the tumor in two patients. Ten patients were evaluated by CT in order to rule out recurrent ovarian neoplasm. Disease free intervals prior to CT ranged from 6 to 36 months with an average of 18 months. In eight surgically proven cases, CT was true positive for recurrent tumor in six patients, true negative in one, and false positive in one. In 20 patients, serial CT examinations were valuable in the objective assessment of measurable tumor response following chemotherapy and radiation therapy. A major limitation of CT was its inability to detect peritoneal and liver surface implants smaller than 2 cm in size.
An atlas of the primary visual projections in the brain of the chick Gallus gallus

The localisation of the primary visual centres in the chick mesencephalon and diencephalon was determined by autoradiographic anterograde transport and degeneration techniques. Strong visual projections were found in the tectum, lateral anterior thalamic nucleus, lateroventral geniculate nucleus, superficial synencephalic nucleus, external nucleus, ectomammillary nucleus, tectal grey, dorsolateral anterior thalamus, rostrolateral part, and the pretectal optic area. Weaker retinal projections were found in the ventrolateral thalamus, two subregions of the dorsolateral anterior thalamus, lateral part, diffuse pretectal nucleus, dorsolateral anterior thalamus, magnocellular part, and the hypothalamus. An atlas of the retinal projections was constructed from sections.
How was Mulka’s Cave, an Aboriginal rock art site near Hyden, in south-central Western Australia, used by the people who decorated its walls, when the present entrance was much smaller.

Analysis of old photographs and survev data shows that nearly one metre of the sediment in Mulka's Cave, a profusely decorated Aboriginal rock art site in south-western Australia, has disappeared in the last 50 years. This evidence for erosion prompted us to reassess the results of previous research at the site. Our reconstruction of the floor level in 1950 affects light levels within the cave and the visibility of the artwork, causing us to reconsider how the cave was used when the artwork was made and to suggest that the present entrance may not then have been in use. Investigation of the deposits immediately outside the cave suggests, furthermore, that that area may not have been a major focus of camping. F~ather, camping occurred near a series of gnammas 500 m north of the cave.