Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular and Phenotypic Characterization of Infectious Bursal Disease Virus Isolates

Abstract Two infectious bursal disease viruses (IBDVs 1174 and V1) were isolated from IBDV-vaccinated broiler flocks in California and Georgia. These flocks had a history of subclinical immunosuppression. These isolates are commonly used in IBDV progeny challenge studies at Auburn, AL, as well as vaccine manufacturer's vaccine efficacy studies, because they come from populated poultry-producing states, and are requested by poultry veterinarians from those states. Nested polymerase chain reaction (PCR) generated viral genome products for sequencing. A 491-bp segment from the VP2 gene, covering the hypervariable region, from each isolate was analyzed and compared with previously sequenced isolates. Sequence analysis showed that they were more closely related to the Delaware (Del) E antigenic variant than they are to the Animal Health Plant Inspection Service (APHIS) standard, both at the nucleotide level (96%, 97%) and at the amino acid level (94%, 97%). Both isolates had the glutamine to lysine shift in amino acid 249 which has been reported to be critical in binding the virus neutralizing Mab B69. Phenotypic studies showed that both isolates produced rapid atrophy of the bursae and weight loss, without the edematous bursal phase, in 2-wk-old commercial broilers having antibody against IBDV. A progeny challenge study showed both isolates produced more atrophy of the bursae (less percentage of protection) than the Del E isolate. Molecular and phenotypic data of these important IBDV isolates help in the improved detection and control of this continually changing and important viral pathogen of chickens.
Photoisomerization of Stilbene Dendrimers: The Need for a Volume-conserving Isomerization Mechanism¶

Abstract Highly branched stilbene dendrimers were synthesized and their photochemical behavior was studied. Even the stilbene dendrimer with molecular weight over 6500 underwent trans–cis isomerization in the excited singlet state within the lifetime of 10 ns. The photoisomerization of C=C double bond of stilbene dendrimers in the excited state may proceed by a volume-conserving novel mechanism such as hula-twist rather than conventional 180° rotation around the C=C double bond based on fluorescence and isomerization experiments.
THE MYCOPLASMA GALLISEPTICUM 16S–23S RRNA INTERGENIC SPACER REGION SEQUENCE AS A NOVEL TOOL FOR EPIZOOTIOLOGICAL STUDIES

Mycoplasma gallisepticum (MG) is the most pathogenic and economically significant mycoplasma pathogen of poultry. Economic losses from condemnation or downgrading of carcasses, reduced feed and egg production efficiency, and increased medication costs are additional factors that make this one of the costliest disease problems confronting commercial poultry production worldwide. It has become increasingly important to develop methods to characterize and identify MG strains and strain variability. Reliable methods for the differentiation of MG strains play a pivotal role in understanding the epizootiology and spread of the disease because they generate the information necessary to identify and track new outbreaks.
About the Authors

Hadassa Guttman is a 2014 graduate of Stevenson University with a bachelor of science in biotechnology. While at Stevenson she was a member of TriBeta, Sigma Xi, Alpha Chi, and Treasurer of Gamma Sigma Epsilon. She completed her Masters of Applied Molecular Biology at the University of Maryland Baltimore County in 2015 and currently works as at PapGene, Inc., an early cancer diagnostics company in Baltimore, Maryland. This paper is based on a thesis written during her senior year as part of an extra project to receive honors in biology.
Providing Confidential Policy Conjecture To Images Uploaded By Users On Social Sites

Today users sharing large volume of images through social sites inadvertently become a major problem of maintaining confidentiality. To help the users to control access to their shared content needs some tools. An Adaptive Privacy Policy Prediction (A3P) used in this paper to address the confidentiality problem.A3P system helps the user to compose confidentiality setting of their images by examine the role of social context, image content and metadata these act as a possible indicators of users privacy preferences.A3P system uses the two-level framework according to users available history on the site to determines the best available privacy policy for users images being uploaded. The solution relies on an image classification framework for image categories which may be associated with similar policies, and on an algorithm which predict the policy to automatically generate a policy for each newly uploaded image, also according to user's social
HETEROSIS IN AN ISOLATED, EFFECTIVELY SMALL, AND SELF-FERTILIZING POPULATION OF THE FLOWERING PLANT LEAVENWORTHIA ALABAMICA

Mildly deleterious mutations are thought to play a major role in the extinction of natural populations, especially those that are small, isolated, or inbred. Self-fertilization should reduce the effective size of populations and simultaneously reduce migration between populations. A history of self-fertilization should therefore cause a population to harbor a substantial ‘‘local drift load’’ caused by the fixation of mildly deleterious mutations. This hypothesis was tested in Leavenworthia alabamica, which contains large, self-incompatible populations and smaller self-compatible populations with adaptations for self-fertilization. The fitness of offspring from withinand between-population crosses was compared to quantify heterosis caused by the masking of deleterious alleles in the heterozygous state. Little heterosis was observed in crosses between five large, self-incompatible populations and two of the three small, self-fertilizing populations of L. alabamica. However, the most geographically isolated and genetically divergent self-fertilizing population (Tuscumbia) exhibited a 110.2% increase in germination and a 73.6% increase in fitness, which is consistent with a sizeable local drift load. The finding of substantial heterosis for fitness supports the idea that small effective size, reproductive isolation, and self-fertilization can make populations particularly vulnerable to mutation accumulation.
Natural History and Conservation of Island Boas (Boa constrictor) in Belize

Abstract Boa constrictors inhabiting islands off the coast of Belize have been historically collected for the pet trade, and enthusiasts have described these as a dwarfed race. Additionally, it has been suggested that these boas feed on birds, yet no dietary data are available. I initiated a mark-recapture study of five Belizean island populations and have accumulated data on mainland individuals to describe the natural history and population biology of boas in this region. Results indicate that adult island boas from West Snake Cay eat small passerine birds (gray-breasted martins, Progne chalybea) that average 7% of the snake's mass. Fecal samples from boas on other islands contained bird feathers and, although these feathers were unidentifiable, this indicates that other island boa populations also consume birds. Compared to mainland boas, island boas have significantly smaller litters of smaller neonates (lighter and shorter) and have extraordinarily small population sizes (range 8–88 total individuals). According to IUCN criteria, island boas can be classified as Endangered based solely on total population and subpopulation sizes. Collection data, gathered from the literature and unpublished sources, revealed a decline in one island population (Crawl Cay) that is currently estimated to consist of eight free-ranging individuals. Island populations of Belizean boas warrant immediate conservation priority due to their low reproductive output, small population sizes, and continued demand in the pet trade.
Group grey target decision making based on prospect theory

Considering the impact on group decision making from that every decision maker has grey targets about attributes, a method of group grey target decision making is proposed on the prospect theory. A prospect value function is defined by using the expected grey target as reference point. A linear operator with the features of the "rewarding good and punishing bad" is used to standardize the prospect values. The positive or negative sign of the standardized values can reflect adequately that the attributes' values hit the bull's eye or not. Then, the weight model of decision maker is proposed based on group's consistency and influence of the maximum and minimum evaluation on the deviation of decision. And the project hits bull's eye or not is judged according to the positive or negative sign of comprehensive prospect values. Finally, the emergency plan selection shows the feasibility and effectiveness of the proposed model.
Pattern analysis in successional communities – An approach for studying shifts in ecological interactions

Abstract Many ecological studies have addressed issues of vegetation spatial patterns in attempts to understand the processes generating them. We investigated changes in ecological processes during succession via the analysis of shrubs' spatial patterns in a system of linear sand dunes, an arid ecosystem located in the Negev Desert in Israel during three consecutive years. We hypothesized that spatial patterns change from clustered to regular as succession progresses due to changes in the relative importance of facilitation and competition in this environment. In this ecosystem communities of early successional stages are frequently disturbed by high rates of sand movement, whereas in later successional stages sand stability is high. We mapped in the field individual shrubs on high-resolution aerial photographs, and converted the digital images to a GIS data set. Using Ripley's K-function we analysed spatial patterns at three levels: the single-species level, among species and at the individual level, in three communities characterizing different successional stages. In the early successional communities we found clustered spatial patterns, in comparison with stable habitats where spatial patterns tended to be regular. We argue that these shifts in spatial patterns are indicative of the assumption that in this sand-dune system ecological interactions change from facilitation to competition as succession progresses. Further, we argue that these interactions operate in different spatial scales at the different successional stages, and that the study of these processes should be conducted at the spatial scales specific to each community. Nomenclature: Feinbrun-Dothan & Danin (1991).
COMPARING G MATRICES: A MANOVA APPROACH

Abstract There is considerable interest in comparing genetic variance-covariances matrices (G matrix). However, present methods are difficult to implement and cannot readily be extended to incorporate effects of other variables such as habitat, sex, or location. In this paper I present a method based on MANOVA that can be done using only standard statistical packages (coding for the method using SPLUS is available from the author). The crux of the approach is to use the jackknife method to estimate the pseudovalues of the estimates; these estimates can then be used as datapoints in a MANOVA. I illustrate the method using two published datasets: (1) variation in G matrices resulting from differences in rearing condition, species, and sex in the crickets Gryllus firmus and G. pennsylvanicus; and (2) variation in G matrices associated with habitat and history in the amphipod Gammarus minus.
Two-dimensional Gap Analysis: A Tool for Efficient Conservation Planning and Biodiversity Policy Implementation

Abstract The maintenance of biodiversity by securing representative and well-connected habitat networks in managed landscapes requires a wise combination of protection, management, and restoration of habitats at several scales. We suggest that the integration of natural and social sciences in the form of “Two-dimensional gap analysis” is an efficient tool for the implementation of biodiversity policies. The tool links biologically relevant “horizontal” ecological issues with “vertical” issues related to institutions and other societal issues. Using forest biodiversity as an example, we illustrate how one can combine ecological and institutional aspects of biodiversity conservation, thus facilitating environmentally sustainable regional development. In particular, we use regional gap analysis for identification of focal forest types, habitat modelling for ascertaining the functional connectivity of “green infrastructures”, as tools for the horizontal gap analysis. For the vertical dimension we suggest how the social sciences can be used for assessing the success in the implementation of biodiversity policies in real landscapes by identifying institutional obstacles while implementing policies. We argue that this interdisciplinary approach could be applied in a whole range of other environments including other terrestrial biota and aquatic ecosystems where functional habitat connectivity, nonlinear response to habitat loss and a multitude of economic and social interests co-occur in the same landscape.
Modified H5 Real-Time Reverse Transcriptase–PCR Oligonucleotides for Detection of Divergent Avian Influenza H5N1 Viruses in Egypt

Important Findings This study describes the results of real-time reverse transcriptase– PCR (RRT-PCR), modified from an existing protocol with regard to the detection of the partial H5 gene segment of the Egyptian H5N1 divergent viruses and applied to nationwide surveillance. The modified RRT-PCR assay was more sensitive than the original one in the detection of Egyptian isolates, with 104% amplification efficiency. Sixty-one field samples were found to be positive in our assay, but only 51 samples tested positive by the original protocol and were more sensitive than matrix gene RRT-PCR detection assay. A detection limit of 10 embryo infective doses (EID)50 with the updated oligonucleotides primers and probe set was found.
Proving SBAS Integrity Through Fault Tree-Based Systems Engineering

Proving system integrity of a Satellite-Based Augmentation System (SBAS) requires a comprehensive systems engineering approach with integrated safety assurance objectives to ensure all significant integrity threats are identified and mitigations for them are implemented to effectively reduce any residual safety risk to an acceptable level. Integrity is the assurance that the system will not only behave as intended (i.e., as described in the system requirements), but it also means that the SBAS will take the appropriate actions necessary to ensure overall system integrity when an unexpected error or failure condition is detected. Proving integrity involves significant challenges and is high dependant on accurately characterizing system integrity threats and rigorously verifying the effectiveness of threat mitigations in order to provide adequate assurance that the risk of errors and failure conditions contributing to an integrity failure (i.e., a hazard occurrence) is acceptably small. One of the most widely used techniques for identifying and assessing hazards in general and determining the effectiveness of proposed and implemented mitigations is Fault Tree Analysis (FTA). This technique uses Boolean logic to describe the combination of individual faults that can constitute a hazardous event, which in the case of an SBAS is failure of the system to provide a timely warning to users when individual corrections or satellites should not be used for navigation. Although the FTA cannot by itself prove system integrity, it is an excellent means of aggregating the causes of hazards with their mitigations to verify that the integrity threats have been identified, that their effect on the system is accurately characterized, and that the implemented mitigation effectively mitigates the safety risk to an acceptable level. This paper describes the critical role of the FTA in a proactive System/Safety Engineering environment in proving system integrity of an SBAS.
Effects of Litter Quality (Moisture, Ammonia, Uric Acid) on Development and Severity of Foot Pad Dermatitis in Growing Turkeys

Important Findings High dietary protein is thought to increase the incidence of foot pad dermatitis (FPD) as a result of increased uric acid and secondary ammonia production in the excreta or litter. This study was conducted on female turkeys over a period of 3 wk to test the effects of water alone, and also of these end products of protein metabolism, independent of the presence of excreta, on the development and severity of FPD. The results indicate that high litter moisture is the most likely factor causing FPD in turkeys. A focus on nitrogenous irritants in the litter was not substantiated. Exposure of birds to wet litter (in the absence of excreta) for only 8 hr/ day was sufficient to develop foot pad lesions.
Vegetation change in a man‐made salt marsh affected by a reduction in both grazing and drainage

In order to restore natural salt marsh in a 460-ha nature reserve established in man-made salt marsh in the Dollard estuary, The Netherlands, the artificial drainage system was neglected and cattle grazing reduced. Vegetation changes were traced through two vegetation surveys and monitoring of permanent plots over 15 yr after the management had been changed. Exclosure experiments were started to distinguish grazing effects from effects of increased soil waterlogging caused by the neglect of the drainage system. Both vegetation surveys and permanent plots demonstrated a dichotomy in vegetation succession. The incidence of secondary pioneer vegetation dominated by Salicornia spp. and Suaeda maritima increased from 0 to 20%, whereas the latesuccessional (Phragmites australis) vegetation from 10 to 15%. Grazing intensity decreased towards the sea. The grazed area contracted landward, which allowed vegetation dominated by tall species to increase seaward. Grazing and increased waterlogging interacted in several ways. The impact of trampling increased, and in the intensively grazed parts soil salinity increased. This can probably be explained by low vegetation cover in spring. Framework Ordination, an indirect-gradient-analysis technique, was used to infer the importance of environmental factors in influencing changes in species composition. Many changes were positively or negatively correlated with soil aeration and soil salinity, whereas elevation was of minor importance. Grazing accounted for only a few changes in species frequency. Changes in permanent plots were greater during the first than during the second half of the study period. In exclosures that were installed halfway through the study period, there was a relatively rapid recovery of previously dominant species that had decreased during the first half of the study period. Species richness per unit area in the reserve increased. At the seaward side of the marsh, the altered management allowed succession to proceed leading to establishment of stands of Phragmites australis, whereas on the landward side, the combination of moderate grazing with neglect of the drainage system appeared an effective measure in maintaining habitats for a wider range of halophytic species.
A LEG MOTION MODELING METHOD BASED ON NURBS FREE-FORM DEFORMATION

Human body modeling is an important research work in the fields of biomedicine andcomputer engineering. On the basis of NURBS FFD (free-form deformation), a motion modelingmethod is discussed to simulate the bend of human leg and corresponding de formations of muscles. Generally, FFD uses a trivariate tensor product spline to transmit deformations, and it is feasible to choose only two-order B-spline basis function in this case. According to the anatomic structure of joints, the simulation formulas are presented, and they coincide with the motion characteristics of knee joint and muscles. In the final experiment, a proper selected lattice space and these formulas yield a good visual effect of simulation. Compared with the method of curved patches, this method is simple and efficient. The formulas can be easily applied to simulate the motion of other joints.
The History of the UV Radiation Climate of the Earth—Theoretical and Space-based Observations¶

Abstract In the Archean era (3.8–2.5 Ga ago) the Earth probably lacked a protective ozone column. Using data obtained in the Earth's orbit on the inactivation of Bacillus subtilis spores we quantitatively estimate the potential biological effects of such an environment. We combine this practical data with theoretical calculations to propose a history of the potential UV stress on the surface of the Earth over time. The data suggest that an effective ozone column was established at a pO2 of ∼5 × 10−3 present atmospheric level. The improvement in the UV environment on the early Proterozoic Earth might have been a much more rapid event than has previously been supposed, with DNA damage rates dropping by two orders of magnitude in the space of just a few tens of millions of years. We postulate that a coupling between reduced UV stress and increased pO2 production could have contributed toward a positive feedback in the production of ozone in the early Proterozoic atmosphere. This would contribute to the apparent rapidity of the oxidation event. The data provide an evolutionary perspective on present-day Antarctic ozone depletion.
Analysis on the Architecture of Satellite Navigation Simulator

The satellite navigation signal simulator, as a high-precise standard signal source, can generate such satellite navigation signals as GPS, GLONASS and galileo and provide a simulation environment for the development and test of navigation receiver. This paper presents an overview of the main satellite navigation signal simulators in the world and analyzes their architectures.
Video Compression Encoding and Decoding Mechanism of H.264 Based on FPGA

In distributed-type video encoding, temporal correlation between key frames is not utilized. Based on this, selection method of encoding mode of key frames is put forward, which is based on band allocation. First, divide coefficient tape gained by key frames after FPGA conversion into low-frequency band and high-frequency band. Part of low-frequency band adopts H.264 encoding and decoding. Then make further selection to encoding mode of high-frequency band. H.264 encoding and decoding and traditional intra-frame encoding and decoding are carried out respectively. Finish selection of encoding mode at decoding end. At last transmit selection of encoding mode to encoding end through feedback channel. Simulation result shows that under the circumstance that complexity at encoding end is not added, method put forward has improved quality of video after decoding, enhancing peak signal to noise ratio (PSNR) of system by about 1-5bB.
Design of a thumb exoskeleton for hand rehabilitation

Exoskeletons for hand rehabilitation typically focus on finger flexion-extension and do not support thumb-finger opposition, a crucial function for object grasping. This work presents the mechanical design, implementation and preliminary evaluation of a novel portable thumb exoskeleton to assist thumb opposition movements in the context of activities of daily living. A usability study with 12 healthy subjects demonstrated that the exoskeleton was comfortable, easy to don and provided a natural opposition motion while generating forces of up to 10 N at the tip of the thumb and weighing less than 150 g. This proof of concept is a first step towards the development of portable hand rehabilitation systems to be used for home-based therapy and assistance.