Miracle-dz/UniFAR-FTUs huggingface dataset:
Sirex noctilio host choice and no-choice bioassays

Sirex noctilio F. , the European woodwasp, is an exotic invasive pest newly introduced to the northeastern U.S. This woodwasp kills trees in the Pinus genus and could potentially cause millions of dollars of damage in the southeastern U.S., where pine plantations are extensive. At present, little is known about the preferences of this wasp for southeastern pine species, and further, little methodology exists as related to conducting host choice or no-choice bioassays with this species. My thesis developed methodology to successfully perform S. noctilio host choice and no-choice bioassays (both colonization and emergence from bolts), examined S. noctilio behavioral and developmental responses to southeastern U.S. pine species using bolts, and investigated possible mechanisms to explain these behavioral responses. Results indicated larger bolts were preferred to smaller bolts by S. noctilio, and P. strobus and P. virginiana were preferred out of six southeastern species in host choice bioassays.
Biotic interactions and seed deposition rather than abiotic factors determine recruitment at elevational range limits of an alpine tree

Abiotic factors, biotic interactions and dispersal ability determine the spatial distribution of species. Theory predicts that abiotic constraints set range limits under harsh climatic conditions and biotic interactions set range limits under benign climatic conditions, whereas dispersal ability should limit both ends of the distribution. However, empirical studies exploring how these three components jointly affect species across environmental gradients are scarce. Here, we present a study that jointly examines these factors to investigate the constraints of the recruitment of Swiss stone pine (Pinus cembra) at and beyond its upper and lower elevational range limits in the Swiss Alps. We investigated the natural recruitment of pines and additionally conducted seed transplant experiments to test how much abiotic factors (mean summer and winter temperatures, soil moisture), biotic interactions (understorey vegetation cover, canopy cover, seed predation) and/or seed deposition by the spotted nutcracker (Nucifraga caryocatactes) affect pine establishment. We found significant effects of biotic interactions and seed deposition by spotted nutcrackers on the recruitment of Swiss stone pine at both the upper and lower elevational range, but could not detect significant effects of abiotic factors. Importantly, dispersal limitation rather than temperature and soil moisture restricted the recruitment of pines at the upper elevational range. Synthesis. Our study highlights the importance of biotic interactions and dispersal ability in setting the upper range limits of species that have been regarded as mainly controlled by climate. This suggests that potential range shifts of plants in response to climate warming may strongly depend on seed dispersal and biotic interactions and not only on climatic factors.
Characterizing the Intact Prophage of Mycobacterium chelonae Bergey

Mycobacteriophage (phage), are viruses that infect bacteria. All bacteria can be infected by phage, and each bacterial species has a unique set of phage that infect them, making phage prime candidates for studying viral diversity and evolution. Some phage integrate their genome into the host genome upon infection (prophage), where they may potentially remain indefinitely, coevolving with the host, and providing growth factors and other benefits to the host. The purpose of my research is to characterize a prophage within the genome of the bacterial host Mycobacterium chelonae Bergey to determine if it is still functional and potentially impacting the fitness of the host bacterium. Characterization of this prophage has revealed that multiple genes are conserved with regard to both the DNA and protein sequences. The integrase cassette is highly conserved, complete with integrase and two potential repressors, suggesting the phage may be capable of excising from the host genome. Multiple structural genes including capsid and tail proteins are also conserved, suggesting the prophage may be capable of producing intact virions. At least two prophage genes are transcriptionally active. These include a predicted repressor and transmembrane protein. Expression of these genes suggests that the prophage does indeed have some potential for affecting the biology of the host bacterium. Experiments are currently underway to determine if intact virion particles are being produced during bacterial growth.
Engineering Complex Microenvironments to Manipulate and Study Cellular Mechanobiology

Our improved understanding of cell mechano-sensing has been enabled by developments in biomaterials platforms and in vitro culture systems. These emerging systems model key aspects of the cellular niche in a controlled fashion, enabling one to ask and answer questions that could not be addressed in vivo due to the complex interactions of these multiple discrete signals. These emerging materials include key features of the native microenvironment, including complex mechanical properties, degradable domains, and native-scale feature sizes. In this thesis work, we designed a 2D methacrylated hyaluronic acid hydrogel (MeHA) system to recapitulate the multiple adhesive interactions normally present in the developing mesenchymal progenitor cell niche, including an RGD adhesive motif (from fibronectin) and the HAVDI adhesive motif (from NCadherin). This system allowed for the decoupled presentation of cell-ECM interactions and cell-cell interactions while simultaneously modulating other variables present in the microenvironment, such as changes in substrate stiffness. Using this system, we elucidated a new signaling pathway through which HAVDI ligation altered MSC mechanosensing of ECM stiffness, which culminated in downstream differences in cellular proliferation and differentiation. Our findings suggest that HAVDI presentation may be harnessed towards novel biomaterial design to direct cellular behavior and allow for tuning of response to substrate stiffness in regenerative medicine applications. Building from this platform, we further investigated nuclear morphology of MSCs on these 2D MeHA substrates and in native tissue, and showed that nuclear morphology and mechanotransduction were markedly different on planar substrates compared to within the native tissue niche. These findings suggested that dimensionality and the manner by which nuclear pre-stress is established in 3D regulates strain transmission to the nucleus. To better recapitulate these interactions, we cultured cells in 3D MMP-degradable HA hydrogels, and showed that these remodelable systems more accurately recapitulated the in vivo cellular response in vitro. Moving forward, work with these defined synthetic 3D niches will play a critical role in understanding of complex processes governing stem cell development and differentiation, as well as disease pathologies that arise when these processes become disrupted. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Bioengineering First Advisor Robert L. Mauck
Protease-Based Magnetic Sensor for Rapid Detection of Candidemia

We are developing a rapid, point-of-care (POC) test for detection of Candidemia using giant magnetoresistive (GMR) biosensors. Candidemia is a fungal infection caused by the overgrowth of a yeast called Candida albicans. It is the 4th leading cause of bloodstream infections in hospitalized patients in the U.S. and severely affects immunocompromised individuals. Candidemia can be fatal if not treated rapidly and is often only detected post-mortem. The current gold standard for its detection is a blood culture, which typically takes 3-5 days, wasting precious treatment time. Therefore rapid, unambiguous diagnosis is required to improve prognosis. This technology aims to detect a unique enzyme that is secreted by C. albicans during infection. This enzyme, Sap6, is a protease that can degrade a synthetic peptide. The POC test works by immobilizing magnetic nanoparticles onto the GMR biosensor via the peptide. Once peptide cleavage by Sap6 occurs, the magnetic nanoparticle is released away from the sensor surface. This change in the magnetic field of the GMR sensors is detected in real-time. We have demonstrated this proof-of-concept in a 96-well plate format using a fluorescent sensor. This assay immobilizes approximately 1.8 g of peptide per well which can then be released by 13.34 g of protease in 10 minutes at room temperature. We have translated the assay to the GMR biosensors and detected up to 60% reduction in signal within 60 minutes. We hope to optimize this technology by reducing the detection time and expand it further to test other diseases like cystic fibrosis.
Application of activity sensors for estimating behavioral patterns

The increasing use of Global Positioning System (GPS) collars in habitat selection studies provides large numbers of precise location data points with reduced field effort. However, inclusion of activity sensors in many GPS collars also grants the potential to remotely estimate behavioral state. Thus, only using GPS collars to collect location data belies their full capabilities. Coupling behavioral state with location data would allow researchers and managers to refine habitat selection models by using diel behavioral state changes to partition fine-scale temporal shifts in habitat selection. We tested the capability of relatively unsophisticated GPS-collar activity sensors to estimate behavior throughout diel periods using free-ranging female elk (Cervus canadensis) in the Jemez Mountains of north-central New Mexico, USA, 2013–2014. Collars recorded cumulative number of movements (hits) per 15-min recording period immediately preceding GPS fixes at 0000, 0600, 1200, and 1800 hr. We measured diel behavioral patterns of focal elk, categorizing active (i.e., foraging, traveling, vigilant, grooming) and inactive (i.e., resting) states. Active behaviors (foraging, traveling) produced more average hits (0.87 ± 0.69 hits/min, 4.0 ± 2.2 hits/min, respectively; 95% CI) and inactive (resting) behavior fewer hits (−1.1 ± 0.61 95% CI). We differentiated active and inactive behavioral states with a bootstrapped threshold of 5.9 ± 3.9 hits/15-min recording period. Mean cumulative activity-sensor hits corresponded with observed diel behavioral patterns: hits increased during crepuscular (0600, 1800 hr) observations when elk were most active (0000–0600 hr: d = 0.19; 1200–1800 hr: d = 0.64) and decreased during midday and night (0000 hr, 1200 hr) when elk were least active (1800–0000 hr: d = −0.39; 0600–1200 hr: d = −0.43). Even using relatively unsophisticated GPS-collar activity sensors, managers can remotely estimate behavioral states, approximate diel behavioral patterns, and potentially complement location data in developing habitat selection models. © 2016 The Wildlife Society.
A Survey Of K-Means And GA-KM The Hybrid Clustering Algorithm

: In this paper we present application of hybrid clustering algorithm that combines partitioning clustering algorithm and heuristic search algorithm. Our method uses portioning method with Genetic algorithm . First we cluster the data using K-Means clustering algorithm with the value of K no. of clusters then we calculate the centroid of K cluster obtain from the previous step. Than we apply Genetic algorithm for centroids for the given value K clusters (GAKM). After applying the GAKM we compare the result of simple K-Means and GAKM algorithm . our experimental results shows that the cluster obtained from GAKM are provides more optimal result in comparison of simple K-Means algorithm cluster result .
Pretreatment of citrus by-products affects polyphenol recovery: a review

ABSTRACT A large amount of citrus waste is generated annually. This waste is of great economic worth, since it contains high levels of polyphenols, which have attracted scientific interest due to their potent antimicrobial and antiradical activities. Pretreatment is a crucial step that precedes the extraction process and influences the yields and quality of polyphenols. This review emphasizes the effect of different drying processes, such as freeze drying, hot-air drying, vacuum drying, microwave drying, infrared drying, and high-speed drying, on the polyphenol retention in citrus by-products. Further treatments of the dried citrus by-products for assisting the liberation of bound polyphenols are also provided and comprehensively discussed.
Consideraciones taxonómicas sobre Barbus moulouyensis Pellegrin, 1924 (Actinopterygii, Cyprinidae) con la descripción de una especie nueva de Luciobarbus Heckel, 1843 de Marruecos

The taxonomy of Barbus Cuvier and Cloquet, 1816 has been reviewed in the last years and as consequence some species traditionally included in genus Barbus sensu lato have been assigned to different genera. In North Africa the species of the former genus Barbus have been included in the genera Luciobarbus Heckel, 1843, Carasobarbus Karaman, 1971 and Enteromius Cope, 1867. We studied populations of the former genus Barbus of the Moulouya river basin in Morocco through molecular, morphometric, and osteological data. Our data clearly showed that populations from Moulouya river basin described originally as Barbus moulouyensis Pellegrin, 1924 belong to the genus Carasobarbus and not to Luciobarbus . Moreover, populations of the genus Luciobarbus exist in the Moulouya river basin and could not be assigned to any previously described species. Consequently, we describe a new Luciobarbus species from the Moulouya river basin.
Complementary studies of lipid membrane dynamics using iSCAT and STED microscopy

Observation techniques with high spatial and temporal resolution, such as single-particle tracking (SPT) based on interferometric Scattering (iSCAT) microscopy, and fluorescence correlation spectroscopy applied on a super-resolution STED microscope (STED-FCS), have revealed new insights of the molecular organization of membranes. While delivering complementary information, there are still distinct differences between these techniques, most prominently the use of fluorescent dye-tagged probes for STED-FCS and a need for larger scattering gold nanoparticle tags for iSCAT. Using lipid analogues tagged with a hybrid fluorescent tag – gold nanoparticle construct, in this work we directly compare results from STED-FCS and iSCAT measurements of phospholipid diffusion in a supported lipid bilayer. Compared to dye-tagged lipid analogues, gold nanoparticle tagging introduced a 50-fold reduction in the diffusion coefficient. Nevertheless, the mode of diffusion remained free, at least on the spatial scales probed (>40nm). These FCS measurements of hybrid fluorescent tag – gold nanoparticle labeled lipids also revealed that commercially supplied streptavidin-coated gold nanoparticles contain large quantities of free streptavidin. A direct comparison of STED-FCS and iSCAT revealed a 2-3-fold difference in diffusion coefficients between both approaches, but the relative differences in mobility between different lipid analogues were identical for both. In conclusion, our experiments reveal that large scattering tags introduce a significant slow-down in diffusion but no additional bias, and our labeling approach creates a new way of exploiting complementary information from STED-FCS and iSCAT measurements.
Finding turning‐points in ultra‐high‐resolution animal movement data

Recent advances in biologging have resulted in animal location data at unprecedentedly high temporal resolutions, sometimes many times per second. However, many current methods for analysing animal movement (e.g. step selection analysis or state‐space modelling) were developed with lower‐resolution data in mind. To make such methods usable with high‐resolution data, we require techniques to identify features within the trajectory where movement deviates from a straight line. We propose that the intricacies of movement paths, and particularly turns, reflect decisions made by animals so that turn points are particularly relevant to behavioural ecologists. As such, we introduce a fast, accurate algorithm for inferring turning‐points in high‐resolution data. For analysing big data, speed and scalability are vitally important. We test our algorithm on simulated data, where varying amounts of noise were added to paths of straight‐line segments interspersed with turns. We also demonstrate our algorithm on data of free‐ranging oryx Oryx leucoryx. We compare our algorithm to existing statistical techniques for break‐point inference. The algorithm scales linearly and can analyse several hundred‐thousand data points in a few seconds on a mid‐range desktop computer. It identified turnpoints in simulated data with complete accuracy when the noise in the headings had a standard deviation of ±8∘, well within the tolerance of many modern biologgers. It has comparable accuracy to the existing algorithms tested, and is up to three orders of magnitude faster. Our algorithm, freely available in R and Python, serves as an initial step in processing ultra high‐resolution animal movement data, resulting in a rarefied path that can be used as an input into many existing step‐and‐turn methods of analysis. The resulting path consists of points where the animal makes a clear turn, and thereby provides valuable data on decisions underlying movement patterns. As such, it provides an important breakthrough required as a starting point for analysing subsecond resolution data.
Oligomeric Composition of Polyols From Fatty Acid Methyl Ester: The Effect of Ring‐Opening Reactants of Epoxide Groups

Commercial availability of fatty acid methyl ester (FAME) from palm oil targeted for biodiesel offers a good feedstock for the production of structurally well‐defined polyols for polyurethane applications. The effect of molecular weight (MW), odd and even carbon numbers, and the linear and branched structure reactants used in the ring‐opening reaction of epoxidized fatty acid methyl ester (E‐FAME) on the properties of polyols was investigated. Conversions of E‐FAME to PolyFAME polyols were confirmed by Fourier transform infrared analysis, oxirane oxygen content, and hydroxyl number. Gel permeation chromatography (GPC) calibrated against polyether polyols as a standard and vapor pressure osmometry were used for MW determination. GPC chromatograms of PolyFAME polyols clearly demonstrated the formation of oligomers during ring‐opening reactions. MW, and odd and even carbon numbers in a structure of linear diols and branched diol used in the syntheses of PolyFAME polyols did not have an effect on crystallinity, glass transition, or melt temperatures measured using Differential scanning calorimetry (DSC). PolyFAME polyols ring‐opened with water, methanol, and 1,2‐propanediol contained secondary hydroxyl groups, whereas PolyFAME polyols ring‐opened with linear diols contained a mixture of primary and secondary hydroxyl groups. It was found that the concentration of primary hydroxyl groups increased significantly by increasing the number of carbons from C2 to C3 in the linear diols. The viscosity of PolyFAME polyols also increased with the MW of linear diols used in the E‐FAME ring‐opening reaction. These findings would be beneficial for formulators in choosing the most cost effective polyols for polyurethane formulations.
A meta-analysis of seed protein concentration QTL in soybean

Qi, Z. -m. , Sun Y. -n. , Wu, Q. , Liu, C. -y. , Hu, G. -h. and Chen, Q. -s. 2011. A meta-analysis of seed protein concentration QTL in soybean. Can. J. Plant Sci. 91: 221-230. An integrated map of QTLs related to seed protein concentration in soybean has been constructed, based on the public genetic map, soymap2 as a reference map, along with a set of 107 QTLs reported in the literature over the past 20 yr. Each of these QTLs was projected onto the soymap2 by software package BioMercator v2.1. Twenty-three consensus QTLs were detected. The confidence interval at all sites ranged from 1.52 to 14.31cM, and the proportion of the phenotypic variance associated with each of them from 1.5 to 20.8%. Major chromosomal sites were identified on LG I (Gm20), four important sites were identified, involving LG A1 (Gm05), B2 (Gm14), E (Gm07) and M (Gm15). A meta-analysis approach was used to improve the precision of the location of these sites. These results facilitate gene mining and molecular assist-selection in soybean.
Molecular Characterization of H9N2 Avian Influenza Viruses Isolated from Commercial Broiler Chickens in Egypt during 2014-2015

Avian influenza virus H9N2 is a panzootic pathogen that affects poultry causing mild to moderate respiratory distress but has been associated with high morbidity and considerable mortality. In this study, one hundred and twenty coloacal and tracheal swabs and organs (trachea, lung and spleen) were collected from broiler chicken flocks in 8 Egyptian governorates from summer 2014 to spring 2015. Results of RT-PCR revealed that 36 flocks were positive out of 120 flocks for H9N2 (30%) with seasonal distribution as follow: 0.8% in summer of 2014, 5.8% in Autumn of 2014, 19.2% in winter of 2014 and 4.1% in Spring of 2015. Sequencing of HA gene and phylogenetic analysis of 7 selected H9N2 isolates representative of different governorates indicated that all isolates belong to G1-like lineage and are closely related to other Middle East H9N2 isolates.
Invasive Russian Knapweed (Acroptilon repens) Creates Large Patches Almost Entirely by Rhizomic Growth

Russian knapweed is an outcrossing perennial invasive weed in North America that can spread by both seed and horizontal rhizomic growth leading to new shoots. The predominant mode of spread at the local scale and dispersal at the long-distance scale informs control but has not been quantitatively researched. We used amplified fragment-length polymorphisms (AFLPs) of DNA collected from 174 shoots in two discrete patches of Russian knapweed at each of three locations in Montana. Out of the 174 shoots collected, we found nine AFLP genotypes. Three out of the six patches were monotypic; the other three patches each had one rare genotype. No genotypes were shared between patches. The maximum diameter of a genet (a genetic individual) was 56.5 m. These results indicate that patch expansion at the local scale is almost entirely by rhizomes that spread and develop new shoots. At the long-distance scale, dispersal is by seed. Controlling seed development through biological control and herbicide use may be effective at stopping long-distance dispersal but may not affect expansion of existing patches. Nomenclature: Russian knapweed, Acroptilon repens (L.) DC, Rhaponticum repens (L.) Hidalgo, Centaurea repens L.