Miracle-dz/UniFAR-FTUs huggingface dataset:
Modulation of immune responses to bovine herpesvirus‐1 in cattle by immunization with a DNA vaccine encoding glycoprotein D as a fusion protein with bovine CD154

The objective of this study was to determine whether a DNA vaccine encoding bovine CD154 linked to a truncated version of bovine herpesvirus‐1 (BHV‐1) glycoprotein D (tgD‐CD154) induces enhanced tgD‐specific immune responses in cattle. In vitro characterization demonstrated that tgD and tgD‐CD154 both bind to cultured bovine B cells, whereas only tgD‐CD154 induces interleukin‐4‐dependent proliferation, suggesting that tgD‐CD154 specifically binds the CD40 receptor and induces receptor signalling. Calves were immunized with plasmid encoding either tgD or tgD‐CD154 by intradermal injection with a needle‐free device. After two immunizations, tgD‐specific immune responses were observed in both vaccinated groups and after challenge with BHV‐1 these responses further increased. Animals immunized with plasmid encoding tgD‐CD154 had significantly higher tgD‐specific serum titres of immunoglobulins G and A but significantly lower numbers of tgD‐specific interferon‐γ‐secreting cells than animals immunized with plasmid encoding tgD after BHV‐1 challenge. This suggests that the expression of an antigen as a chimeric protein with CD154 can qualitatively alter immune responses in cattle. Since we previously showed that plasmid encoding tgD‐CD154 induces significantly enhanced secondary tgD‐specific antibody responses in sheep, there appear to be interspecies differences in the immune responses induced by tgD‐CD154, which suggests that both proteins in the chimeric molecule may influence protein targeting and the induction of an immune response.
Progress toward a sea-floor observatory at a carbonate/hydrate mound in the northern Gulf of Mexico

The Gulf of Mexico hydrates research consortium has been designing a sea-floor observatory to monitor natural gas hydrates in the gulf of Mexico for almost ten years. The observatory will consist of seismo-acoustic receiving arrays, geochemical arrays in the lower water column and upper sediments as well as systems for observing microbial activity. Mississippi Canyon Lease Block 118 (MC118) in the northern part of the Gulf has been selected as the site of the observatory. A carbonate/hydrate mound approximately one kilometer in diameter occurs in the south-central portion of MC118 at a water depth of about 900 m. The surface morphology of the mound has been imaged by multi-beam bathymetric sonar from an autonomous underwater vehicle (AUV) operating 40 m above the sea floor, by video cameras deployed on and a few meters above the sea floor from surface vessels and by visual observations from manned submarines. Gravity and box cores have been collected for lithologic and bio-geochemical studies of the near-surface sediments on the mound. Microbial sulfate reduction, anaerobic methane oxidation, and methanogenesis are all important processes in the upper four meters of sediment. These microbial processes seem to control the diffusive flux of methane from the sediments into the overlying water column. The activity of microbes is also focused within patches or dasiahot spotspsila at the main, active mounds. This activity is primarily dependent upon an active fluid flux of hydrocarbon-rich fluids. The geochemical evidence suggests that the fluid flux waxes and wanes over time and that the microbial activity is sensitive to such change. The subsurface structure of the mound has been investigated by chirp-sonar profiles acquired by the AUV simultaneously with acquisition of the swath bathymetry data and by a psuedo-3D grid of high-resolution seismic profiles obtained using the surface-source/deep-receiver technique. Also, deep seismic 3D volumes obtained by the petroleum industry have been viewed. The surface of the mound is pocked by craters apparently formed during episodic fluid expulsion events. Gases venting from the mound, as well as those contained in outcropping hydrates, have been analyzed and found to be thermogenic, perhaps having migrated up faults from a deep, as yet undiscovered, petroleum reservoir. The deep seismic data show that the faults emanate from a salt diapir located some hundreds of meters below the mound. It was observed during a cruise in November, 2007, that craters and outcrops had changed significantly during the 14-month period since the previous cruise in September, 2006. The mound therefore has been shown to be sufficiently dynamic to warrant continuous monitoring over the five-to-ten years that the observatory is expected to be operational.
Isolation and identification of endophytic fungi from Avicennia marina in Ramanathapuram District, Karankadu, Tamilnadu, India

Avicennia marina (Tamil : Alai : Alai atti) : Avicennia marina is the dominant mangrose species in Karankadu and accounts for about 95% of the vegetative cover plant in Indian Sub-continent was investigated for endophytic mycoflora as a possible source of bioactive secondary metabolites. Being salinity resistant, this species dominate most mangrove area of the country including karankadu. Four hundred seventy three segments from 7 plants of Avicennia marina collected from different locations of karankadu mangrose forest in 2010 to 2011, were processed for me presence of endophytic fungi. A total 10 fungal species viz. Aspergillus flavus, A.niger, Aspergillus sp. , Penicillium sublateritium, Phomo chrysanthemicola, P.hedericola, Phoma sp. and Candida albicans were isolated. Among the endophytic flora, phoma was the most prominent genus. Interestingly no endophytes was isolated from 110 leaves samples and overall colonization frequency from surface. Sterilized stem was 8.85%.
QASYO: A Question Answering System for YAGO Ontology

The tremendous development in information technology led to an explosion of data and motivated the need for powerful yet efficient strategies for data mining and knowledge discovery. Question Answering (QA) systems made it possible to ask questions and retrieve answers using natural language (NL) queries, rather than the keyword-based retrieval mechanisms used by current search engines. In Ontology-based QA system, the knowledge based data, where the answers are sought, has a structured organization. The question-answer retrieval of ontology knowledge base provides a convenient way to obtain knowledge for use, but the natural language need to be mapped to the query statement of ontology. QASYO is a sentence level question-answering system that integrates natural language processing, ontologies and information retrieval technologies in a unified framework. It accepts queries expressed in natural language and YAGO ontology as inputs and provides answers drawn from the available semantic markup. QASYO combines several powerful techniques in a novel way to make sense of NL queries and to map them to semantic markup. Semantic analysis of questions is performed in order to extract keywords used in the retrieval queries and to detect the expected answer type. In this paper we describe the current version of the system, in particular discussing its reasoning capabilities, and Performance.
A Novel Approach to Identification of Speakers from Their Hum

Automatic Speaker Recognition (ASR) deals with identification speakers with the help of machine from their voice. An ASR system will be efficient if the proper speaker-speci¿c features are extracted. Most of the state-of-the-art ASR systems use the natural speech signal (either read speech or spontaneous or contextual speech) from the subjects. In this paper, an attempt is made to identify speakers from their hum. The experiments are shown for Linear Prediction Coefficients (LPC), Linear Prediction Cepstral Coefficients (LPCC), and Mel Frequency Cepstral Coefficients (MFCC) as input feature vectors to the polynomial classi¿er of 2nd and 3rd order approximation. Results are found to be better for MFCC than LP-based features.
Intralenticular metallic foreign body.

BACKGROUND Intralenticular metallic foreign bodies may be well tolerated for many years. CASE REPORT A 24-year-old caucasian man was referred with an intralenticular metallic foreign body present in the left eye for five days. Following initial treatment with topical steroid and antibiotic, the lens remained clear and visual acuity normal. Two years later the left eye developed an anterior uveitis, with reduced vision. A left phacoemulsification lens extraction with removal of the intralenticular foreign body and insertion of a posterior chamber intraocular lens was performed. CONCLUSION Management of intralenticular metallic foreign bodies may be conservative till intraocular inflammation or cataract develops.
Texture classification using local discriminative features and Fisher encoding

In this paper we introduce a new image representation for texture classification. Our work is motivated by recent developments in the field of local patch based features, compressive sensing and descriptor encoding methods. Novel features called Compressed Random Pixel Difference (CRPD) are proposed. These features are low in dimensionality, highly discriminative, and easy to compute. Combined with an efficient encoding method, an expressive and robust image descriptor is obtained. Experiments conducted on widely used texture datasets (KTH-TIPS-2a and Brodatz) demonstrate an efficiency of the proposed approach. On KTH-TIPS-2a dataset we have achieved the highest recognition accuracy (to the best of our knowledge) and on Brodatz dataset achieved performance is comparable to the state-of-the-art methods.
Characterization of Leishmania chagasi DNA Topoisomerase II: a Potential Chemotherapeutic Target

DNA topoisomerase II (topo II), an enzyme essential for cellular replication, is an eminent target for antimicrobial therapy against Leishmania chagasi, the major cause of visceral leishmaniasis in Latin America. The complete L. chagasi (Lch) TOP2 gene, encoding L. chagasi topo II, was isolated from genomic DNA using the polymerase chain reaction. The LchTOP2 gene revealed an open reading frame (ORF) of 3,711 base pairs predicting a protein with 1,236 amino acids and an estimated molecular weight of 140 kDA. The L. chagasi topo II sequence had high identity with the L. donovani topo II (98.8%) and L. infantum topo II (98.7%), followed by Crithidia fasciculata topo II (84.4%), Trypanosoma cruzi topo II (67.6%) and Trypanosoma brucei topo II (66.6%). Lch topo II had low identity with the human homologs htopo II α (26.3%) and htopo II β (26.4%). Differences between L. chagasi TOP2 and human TOP2 genes suggest that leishmanial topo II is a potential target for the development of new antileishmanial agents.
Trajectory tracking algorithm for autonomous vehicles using adaptive reinforcement learning

The off-shore industry requires periodic monitoring of underwater infrastructure for preventive maintenance and security reasons. The tasks in hostile environments can be achieved automatically through autonomous robots like UUV, AUV and ASV. When the robot controllers are based on prespecified conditions they could not function properly in these hostile changing environments. It is beneficial to count with adaptive control strategies that are capable to readapt the control policies when deviations, from the desired behavior, are detected. In this paper, we present an online selective reinforcement learning approach for learning reference tracking control policies given no prior knowledge of the dynamical system. The proposed approach enables real-time adaptation of the control policies, executed by the adaptive controller, based on ongoing interactions with the non-stationary environments. Applications on surface vehicles under nonstationary and perturbed environments are simulated. The presented simulation results demonstrate the performance of this novel algorithm to find optimal control policies that solve the trajectory tracking control task in unmanned vehicles.
Implementation of the Spherical Coordinate Representation of Protein 3D Structures and its Applications Using FORTRAN 77/90 Language

We previously described the representation of protein 3D structures in spherical coordinates (rho, phi, theta) and two of its applications: separation of the outer layer (OL) from the inner core (IC) of proteins, and assessment of protein surface protrusions and invaginations (Reyes, V.M., 2011& 2009). Here we present results demonstrating the performance success of the FORTRAN 77 and 90 programs used in the implementation of the two said applications, and how to implement both applications. In particular, we show here data that demonstrate the success of our OL-IC separation procedure using a subset of the Laskowski et al. (1996) dataset. Using a theoretical model protein in the form of a scalene ellipsoid grid of points with and without an artificially constructed protrusion or invagination, we also show results demonstrating that protrusions and invaginations on the protein surface maybe predicted. The nine programs we present here and their respective functions are: find_molec_centr. f: finds the x-, y- and z-coordinates of the protein molecular geometric centroid, cart2sphere_degrees. f90: converts PDB protein coordinates to spherical, with phi and theta in degrees, cart2sphere_radians. f90: does the same thing as the second program, but with phi and theta in radians, spher2cart_degrees. f90: converts the coordinates from spherical back to PDB, where input phi and theta are in degrees, spher2cart_radians. f90: does the same thing as the fourth program, but with phi and theta in radians, find_rho_cutoff. f: determines the rho cut-off for finding the boundary between OL and IC, phi6_theta8_binning. f90: performs the binning of phi in six- and theta in eight-degree increments, phi10_theta10_binning. f90: performs the binning of phi and theta both in ten-degree increments, and bin_rho. f90: performs the binning of rho values for plotting the frequency distribution of maximum rho values.
3D 모바일에서의 현실감

It was hypothesized that mobile 3D provide the sense of presence in different quantity and quality aspects in virtual reality. And it was supposed that the construction of presence involves various levels and dimensions. The factors of mobile 3D game are divided into 4 super-factors; condition factor, interface factor, attention factor, feedback factor that resulted into 20 sub-factors resulted from the factor analysis. Our primary goal is the development of valid Mobile 3D presence scale, and to find out the factor structure of the scale.
Self-Reconfigurable Modular Robots Adaptively Transforming a Mechanical Structure: Algorithm for Adaptive Transformation to Load Condition

Self-reconfigurable modular robots are composed of modules which are able to autonomously change the way they are connected. An appropriate control algorithm enables the modular robots to change their shape in order to adapt to their immediate environment. In this paper, we propose an algorithm for adaptive transformation to load condition of the modular robots. The algorithm is based on a simple idea that modules have tendency to gather around stress-concentrated parts and reinforce the parts. As a result of the self-reconfiguration rule, the modular robots form an appropriate structure to stand for the load condition. Applying the algorithm to our modular robot named “CHOBIE II,” we show by computer simulation that the modules are able to construct a cantilever structure with avoiding overstressed states.
Prevalence and genetic location of non-transferable trimethoprim resistant dihydrofolate reductase genes in South African commensal faecal isolates

Summary In a recent survey of trimethoprim resistance. 357 Gram-negative aerobic organisms were isolated from healthy volunteers from rural and urban populations in South Africa. Trimethoprim resistance did not transfer to an Escherichia coli J62–2 recipient strain by conjugation in a liquid mating in 161 (45·1%) of the isolates. These isolates which did not transfer their resistance were probed with intragenic oligonucleotide probes for the types Ia. Ib. IIIa. V. VI. VII. VIII. IX. X and XII dihydrofolate reductase genes. Contrary to all previous data, the most prevalent dihydrofolate reductase gene in this group of non-transferable isolates which hybridized, was the type VII (38%) followed by the type Ia (25%). Ib (12%). V (1·7%) and VIII (1·2%). None of the strains hybridized to the types IIIa. VI. XI. X and the XII dihydrofolate reductase probes. Southern blots of plasmid and chromosomal DNA from selective isolates revealed that the type VII dihydrofolate reductase genes were located on the chromosome and were associated with the integrase gene of Tn21. However, the type Ib and V dihydrofolate reductase genes were all found on plasmids which could not be mobilized. The type Ia dihydrofolate reductase genes were found on both non-transferable plasmids and on the chromosome. The nature of the genetic structures associated with a dihydrofolate reductase gene strongly affects the means of spread of the gene in a population.
Analysis of the Interaction of the Novel RNA Polymerase II (pol II) Subunit hsRPB4 with Its Partner hsRPB7 and with pol II

ABSTRACT Under conditions of environmental stress, prokaryotes and lower eukaryotes such as the yeast Saccharomyces cerevisiaeselectively utilize particular subunits of RNA polymerase II (pol II) to alter transcription to patterns favoring survival. In S. cerevisiae, a complex of two such subunits, RPB4 and RPB7, preferentially associates with pol II during stationary phase; of these two subunits, RPB4 is specifically required for survival under nonoptimal growth conditions. Previously, we have shown that RPB7 possesses an evolutionarily conserved human homolog, hsRPB7, which was capable of partially interacting with RPB4 and the yeast transcriptional apparatus. Using this as a probe in a two-hybrid screen, we have now established that hsRPB4 is also conserved in higher eukaryotes. In contrast to hsRPB7, hsRPB4 has diverged so that it no longer interacts with yeast RPB7, although it partially complements rpb4− phenotypes in yeast. However, hsRPB4 associates strongly and specifically with hsRPB7 when expressed in yeast or in mammalian cells and copurifies with intact pol II. hsRPB4 expression in humans parallels that of hsRPB7, supporting the idea that the two proteins may possess associated functions. Structure-function studies of hsRPB4-hsRPB7 are used to establish the interaction interface between the two proteins. This identification completes the set of human homologs for RNA pol II subunits defined in yeast and should provide the basis for subsequent structural and functional characterization of the pol II holoenzyme.
Developmental complexity of the stimuli included in mispronunciation detection tasks.

BACKGROUND Phonological representations are important for speech and literacy development. Mispronunciation detection tasks have been proposed as an appropriate measure of phonological representations for children with speech disorder. There has been limited analysis, however, of the developmental complexity of task stimuli. Further, the tasks have not been used widely with typical populations. AIMS The study aimed to examine the developmental progression of children's performance on a mispronunciation detection task, to evaluate the complexity of the task's stimuli, and to analyse the association between task performance and other skills important for literacy success. METHODS & PROCEDURES A cross-sectional design was used to compare the mispronunciation detection performance of monolingual children within mainstream classrooms aged 4;0-4;5 (n = 26), 4;6-5;0 (n = 49), and 5;1-5;6 (n = 64). Comparison of the complexity of vowel mismatches, single consonant mismatches, consonant deletion mismatches, and consonant transposition mismatches was conducted. OUTCOMES & RESULTS Children in the youngest age group were outperformed by the older age groups in the phonological representation task. Fine-grained mismatches were more difficult to detect than coarse-grained mismatches. There was a trend for vowel substitutions to be the most difficult mismatch to detect. Performance in the mispronunciation detection task was moderately correlated with the children's receptive vocabulary, speech, phonological awareness, and letter knowledge skills. CONCLUSIONS & IMPLICATIONS Mismatch type must be taken into account when designing mispronunciation detection tasks. Access to segmental phonological representations is related to speech, language, and letter knowledge in children from mainstream classrooms.
Paratuberculosis recognized as a problem at last: A review

Summary This article attempts to review briefly current opinions on Johne's disease, or paratuberculosis, in ruminants caused by Mycobacterium avium subsp. paratuberculosis. Paratuberculosis has been known to be prevalent in domestic livestock, such as cattle, goats, and sheep, for more than a century. Despite this knowledge only minor efforts have been made to control the disease and, with the attention being focussed on the eradication of other diseases, the problem of paratuberculosis has been neglected in most countries in the past decades. However, recent epidemiological surveys performed in Europe showed a high prevalence of paratuberculosis in cattle and sheep, indicating that the situation has become quite alarming. In addition, the possible role of M. avium subsp. Paratuberculosis in the aetiology of Crohn's disease in humans is still debated, as discussed in this article. Therefore, there is suddenly renewed interest in paratuberculosis, and the disease is recognized as a significant problem. As a consequence, there is a need for reliable diagnostic tools for large‐scale use to allow the introduction of programmes to control and eventually eradicate the disease. The current status and the possibilities for such programmes are discussed.
A multiple active contour model for cardiac boundary detection on echocardiographic sequences

Tracing of left-ventricular epicardial and endocardial borders on echocardiographic sequences is essential for quantification of cardiac function. The authors designed a method based on an extension of active contour models to detect both epicardial and endocardial borders on short-axis cardiac sequences spanning the entire cardiac cycle. They validated the results by comparing the computer-generated boundaries to the boundaries manually outlined by four expert observers on 44 clinical data sets. The mean boundary distance between the computer-generated boundaries and the manually outlined boundaries was 2.80 mm (sigma=1.28 mm) for the epicardium and 3.61 (sigma=1.68 mm) for the endocardium. These distances were comparable to interobserver distances, which had a mean of 3.79 mm (sigma=1.53 mm) for epicardial borders and 2.67 mm (sigma=0.88 mm) for endocardial borders. The correlation coefficient between the areas enclosed by the computer-generated boundaries and the average manually outlined boundaries was 0.95 for epicardium and 0.91 for endocardium. The algorithm is fairly insensitive to the choice of the initial curve. Thus, the authors have developed an effective and robust algorithm to extract left-ventricular boundaries from echocardiographic sequences.