Miracle-dz/UniFAR-FTUs huggingface dataset:
PROTEIN SECONDARY STRUCTURE PREDICTION EVALUATION AND A NOVEL TRANSITION SITE MODEL WITH NEW ENCODING SCHEMES

Protein Secondary Structure Prediction Evaluation and a Novel Transition Site Model with New Encoding Schemes Masood Zamani University of Guelph, 2017 Advisor: Dr. Stefan C. Kremer Rapid progress in genomics has led to the discovery of millions of protein sequences while less than 0.2% of the sequenced proteins’ structures have been resolved by X-ray crystallography or NMR spectroscopy which are complex, time consuming, and expensive. Employing advanced computational techniques for protein structure prediction at secondary and tertiary levels provides alternative ways to accelerate the prediction process and overcome the extremely low percentage of protein structures that have been determined. State-of the art protein secondary structure (PSS) prediction methods employ machine learning (ML) techniques, compared to early approaches based on statistical information and sequence homology. In this research, we develop a two-stage PSS prediction model based on Artificial Neural Networks (ANNs) and Genetic Programming (GP) through a novel framework of PSS transition sites, and new amino acid encoding schemes derived from the genetic Codon mappings, Clustering and Information theory. PSS transition sites represent structural information of protein backbones, and reduce the input space and learning parameters in the PSS prediction model. PSS transition sites can be utilized in Homology Modeling (HM) to define the boundary of secondary structure elements. The prediction performance of the proposed method is evaluated by using Q3 and segment overlap (SOV) scores on two standard datasets, RS126 and CB513, and the latest protein dataset, PISCES, compiled with very strict homology measures by which each sequence pair has a similarity below the twilight zone or less than 25%. The experimental results and statistical analyses of the proposed PSS model indicate statistically significant improvements in PSS prediction accuracy compared to the state-of-the-art ML techniques which commonly employ cascaded ANNs and SVMs. The proposed encoding schemes show advantages in extracting sequence and profile information, reducing input parameters and training performances. A successful PSS prediction model can be utilized in homology detection tools for distant protein sequences and protein tertiary structure prediction methods to reduce the complexity of the protein structure prediction which has important applications in medicine, agriculture and the biological sciences.
Sex-Specific Among-Individual Covariation in Locomotor Activity and Resting Metabolic Rate in Drosophila melanogaster

A key endeavor in evolutionary physiology is to identify sources of among- and within-individual variation in resting metabolic rate (RMR). Although males and females often differ in whole-organism RMR due to sexual size dimorphism, sex differences in RMR sometimes persist after conditioning on body mass, suggesting phenotypic differences between males and females in energy-expensive activities contributing to RMR. One potential difference is locomotor activity, yet its relationship with RMR is unclear and different energy budget models predict different associations. We quantified locomotor activity (walking) over 24 h and RMR (overnight) in 232 male and 245 female Drosophila melanogaster that were either mated or maintained as virgins between two sets of measurements. Accounting for body mass, sex, and reproductive status, RMR and activity were significantly and moderately repeatable (RMR: R=0.33±0.06; activity: R=0.58±0.03). RMR and activity were positively correlated among (rind=0.26±0.09) but not within (re=0.05±0.06) individuals. Moreover, activity varied throughout the day and between the sexes. Partitioning our analysis by sex and activity by time of day revealed that all among-individual correlations were positive and significant in males but nonsignificant or even significantly negative in females. Such differences in the RMR-activity covariance suggest fundamental differences in how the sexes manage their energy budget.
Using Conditioned Food Aversion (CFA) to reduce Pied Crow (Corbus albus) predation of plover nests

5 Introduction . 7 Methods . 22 Results . 42 Discussion . 55 Literature cited . 67 Appendices . 78 Appendix A: Comparison of Kittlitz’s Plover eggs with Japanese quail eggs . 78 Appendix B: Pilot study to investigate effect of egg-covering on nest predation . 79 Appendix C: Camera trap images of predators at artificial plover nests . 84
Shigella sonnei infection of zebrafish reveals that O-antigen mediates neutrophil tolerance and dysentery incidence

Shigella flexneri is historically regarded as the primary agent of bacillary dysentery, yet the closely-related Shigella sonnei is replacing S. flexneri, especially in developing countries. The underlying reasons for this dramatic shift are mostly unknown. Using a zebrafish (Danio rerio) model of Shigella infection, we discover that S. sonnei is more virulent than S. flexneri in vivo. Whole animal dual-RNAseq and testing of bacterial mutants suggest that S. sonnei virulence depends on its O-antigen oligosaccharide (which is unique among Shigella species). We show in vivo using zebrafish and ex vivo using human neutrophils that S. sonnei O-antigen can mediate neutrophil tolerance. Consistent with this, we demonstrate that O-antigen enables S. sonnei to resist phagolysosome acidification and promotes neutrophil cell death. Chemical inhibition or promotion of phagolysosome maturation respectively decreases and increases neutrophil control of S. sonnei and zebrafish survival. Strikingly, larvae primed with a sublethal dose of S. sonnei are protected against a secondary lethal dose of S. sonnei in an O-antigen-dependent manner, indicating that exposure to O-antigen can train the innate immune system against S. sonnei. Collectively, these findings reveal O-antigen as an important therapeutic target against bacillary dysentery, and may explain the rapidly increasing S. sonnei burden in developing countries. Author Summary Shigella sonnei is predominantly responsible for dysentery in developed countries, and is replacing Shigella flexneri in areas undergoing economic development and improvements in water quality. Using Shigella infection of zebrafish (in vivo) and human neutrophils (in vitro), we discover that S. sonnei is more virulent than S. flexneri because of neutrophil tolerance mediated by its O-antigen oligosaccharide acquired from the environmental bacteria Plesiomonas shigelloides. To inspire new approaches for S. sonnei control, we show that increased phagolysosomal acidification or innate immune training can promote S. sonnei clearance by neutrophils in vivo. These findings have major implications for our evolutionary understanding of Shigella, and may explain why exposure to P. shigelloides in low and middle-income countries (LMICs) can protect against dysentery incidence.
Five Decades of Wetland Soil Development of a Constructed Tidal Salt Marsh, North Carolina, USA

We periodically measured soil properties (bulk density, organic carbon, total nitrogen, and total phosphorus) in a tidal salt marsh constructed in 1970 over the past five decades (1984, 1995, 1998, 2017) to identify trajectories of soil formation over time. Bulk density was greater in surface (0–10 cm) than subsurface (10–30 cm) soils and decreased with time at a similar rate in both depths. Percent organic carbon (C), nitrogen (N), and total phosphorus (P) increased with time, with concentrations in surface soils increasing three times faster than subsurface soils. Surface C and N pools (g/m2, 0–10 cm) exhibited asymptotic trajectories with time, with rapid accumulation in the first two decades that began to equilibrate after 25 years, while subsurface pools of C and N continued to increase in a linear manner. Soil P pools did not exhibit a significant trend related to marsh age. Soil N:P increased in both depths over time, suggesting gradual relaxation of N-limitation of these systems. Our findings can help restoration ecologists identify soil properties, including bulk density, C, N, and C:N suitable for gauging restoration success and better estimate the time frame necessary for recovery of soil-based ecosystem services.
The Effects of Genotype × Phenotype Interactions on Silver Nanoparticle Toxicity in Organotypic Cultures of Murine Tracheal Epithelial Cells

Silver nanoparticles (AgNP) are used in multiple applications but primarily in the manufacturing of antimicrobial products. Previous studies have identified AgNP toxicity in airway epithelial cells, but no in vitro studies to date have used organotypic cultures as a high-content in vitro model of the conducting airway to characterize the effects of interactions between host genetic and acquired factors, or gene × phenotype interactions (G×P), on AgNP toxicity. In the present study, we derived organotypic cultures from primary murine tracheal epithelial cells (MTEC) to characterize nominal and dosimetric dose-response relationships for AgNP-induced barrier dysfunction, glutathione (GSH) depletion, reactive oxygen species (ROS) production, lipid peroxidation, and cytotoxicity across two genotypes (A/J and C57BL/6J mice), two phenotypes (“Normal” and “Type 2 [T2]-Skewed”), and two exposures (an acute exposure of 24 h and a subacute exposure of 4 hours, every other day, over 5 days [5×4 h]). We characterized the “T2-Skewed” phenotype as an in vitro model of chronic respiratory diseases, which was marked by increased sensitivity to AgNP-induced barrier dysfunction, GSH depletion, ROS production, lipid peroxidation, and cytotoxicity, suggesting that asthmatics are a sensitive population to AgNP exposures in occupational settings. This also suggests that exposure limits, which should be based upon the most sensitive population, should be derived using in vitro and in vivo models of chronic respiratory diseases. This study highlights the importance of considering dosimetry as well as G×P effects when screening and prioritizing potential respiratory toxicants. Such in vitro studies can be used to inform regulatory policy aimed at special protections for all populations.
POSSIBILITY OF BROILER PRODUCTION ON REUSED LITTER

This study examined the possibility of raising broiler chicks on partially or totally used litter and its effect on broiler performance, economic efficiency, carcass traits, litter characteristics, FPD score and welfare. At 7 day old, 360 Cobb broiler chicks were randomly allocated in 12 pens till 6 weeks of age, with 3 replicates of 4 experimental treatments contained 30 birds per pen. The treatments included; T1: new litter (NL), T2: mixed litter (NU), T3: 100% used litter (UL) and T4: 100% used litter treated with alum (UT). The results indicated that differences in most traits; LBW, FC, FCR, livability %, EPEI, economic feasibility, carcass traits and behavior patterns were insignificant (P<0.05) between different litter type groups. Except that, litter characteristics, FPD and FS grades were significant (P<0.05) between all types of litter where FP and FS scores were higher on used litter. Overall data trended to be numerically higher in NL group and always followed by UT group. In conclusion, results suggesting that recycling litter had no adverse effect on broiler performance, survival %, carcass traits, economic consideration and broiler welfare. Beside of that, alum amendment to composted reused litter offered an additional improvement on productive performance, litter quality and welfare. Our results provided evidence that, broiler chicks raised on reused treated litter can grow, perform and have welfare equal to that of birds reared on new litter. But, complementary studies measuring the impact on immune response, antioxidant enzymatic activity as well as a bacterial count, would be useful and necessary.
Microbial Degradation of Plastic in Aqueous Solutions Demonstrated by CO2 Evolution and Quantification

The environmental accumulation of plastics worldwide is a consequence of the durability of the material. Alternative polymers, marketed as biodegradable, present a potential solution to mitigate their ecological damage. However, understanding of biodegradability has been hindered by a lack of reproducible testing methods. Here, we present a new approach to assess biodegradability by monitoring bacterial respiration, in an aqueous media supplemented with a polymer as a single carbon source. Rhodococcus rhodochrous and Alcanivorax borkumensis are good model organisms for soil and marine systems respectively, allowing simulations of plastic biodegradation in these key environments. We demonstrate that polymer molecular weight reduction is the critical factor in the biodegradability of low-density polyethylene. Additionally, we tested a wide variety of plastics, including environmentally weathered and laboratory aged samples, using the same method allowing direct comparisons of the relative biodegradability of various polymers.
Similar categorical representation from sound and sight in the occipito-temporal cortex of sighted and blind

The Ventral Occipito-Temporal Cortex (VOTC) shows reliable category selective response to visual information. Do the development, topography and information content of this categorical organization depend on visual input or even visual experience? To further address this question, we used fMRI to characterize the brain responses to eight categories (4 living, 4 non-living) presented acoustically in sighted and early blind individuals, and visually in a separate sighted group. Using a combination of decoding and representational similarity analyses, we observed that VOTC reliably encodes sounds categories in the sighted and blind groups, using a representational structure strikingly similar to the one found in vision. Moreover, we found that the representational connectivity between VOTC and large-scale brain networks was substantially similar across modalities and groups. Blind people however showed higher decoding accuracies and higher inter-subject consistency for the representation of sounds in VOTC, and the correlation between the representational structure of visual and auditory categories was almost double in the blind when compared to the sighted group. Crucially, we also demonstrate that VOTC represents the categorical membership of sounds rather that their acoustic features in both groups. Our results suggest that early visual deprivation triggers an extension of the intrinsic categorical organization of VOTC that is at least partially independent from vision.
Forage quality and quantity affect red mason bees and honeybees differently in flowers of strawberry varieties

Nectar is a vital source of energy for bees and other pollinators and pollen represents the only source of protein in the diet of bees. Nectar and pollen quality and quantity can therefore affect foraging choices. Strawberry, Fragaria × ananassa (Rosaceae), is a flowering crop that requires insect pollination for the berries to develop optimally. The solitary red mason bee, Osmia bicornis L. (Hymenoptera: Megachilidae), occurs naturally but like the eusocial western honeybee, Apis mellifera mellifera L. (Hymenoptera: Apidae), it is also a commercially reared pollinator used in strawberry production. We hypothesized that strawberry nectar and pollen quality would affect the foraging choice of these two types of bees. In this study nectar and pollen quality is represented by various levels of sugar and protein content, respectively, as well as the number of open strawberry flowers in the experimental field, would affect the foraging choice of these two types of bees. Consistent with previous studies, we found significant and major differences between strawberry varieties in proportions of sucrose in the nectar sugar and in pollen viability – a proxy for pollen protein content. All measured parameters had a significant effect on red mason bee visitation frequency. Contrary to expectations, honeybee foraging behavior was only affected by the number of open flowers and not by any of the quality parameters measured. Our findings indicate that red mason bees were capable of assessing nectar and pollen quality and prioritize accordingly. The pattern observed indicates that individual red mason bees changed foraging focus between strawberry varieties depending on whether nectar or pollen was collected. Our results suggest that targeted breeding of varieties toward high levels of nectar sugar and sucrose concentrations and high pollen protein content may increase pollination success from red mason bees and possibly other solitary bees.
Role of Arbuscular Mycorrhizal Fungi in Plant Growth Regulation: Implications in Abiotic Stress Tolerance

Abiotic stresses hamper plant growth and productivity. Climate change and agricultural malpractices like excessive use of fertilizers and pesticides have aggravated the effects of abiotic stresses on crop productivity and degraded the ecosystem. There is an urgent need for environment-friendly management techniques such as the use of arbuscular mycorrhizal fungi (AMF) for enhancing crop productivity. AMF are commonly known as bio-fertilizers. Moreover, it is widely believed that the inoculation of AMF provides tolerance to host plants against various stressful situations like heat, salinity, drought, metals, and extreme temperatures. AMF may both assist host plants in the up-regulation of tolerance mechanisms and prevent the down-regulation of key metabolic pathways. AMF, being natural root symbionts, provide essential plant inorganic nutrients to host plants, thereby improving growth and yield under unstressed and stressed regimes. The role of AMF as a bio-fertilizer can potentially strengthen plants’ adaptability to changing environment. Thus, further research focusing on the AMF-mediated promotion of crop quality and productivity is needed. The present review provides a comprehensive up-to-date knowledge on AMF and their influence on host plants at various growth stages, their advantages and applications, and consequently the importance of the relationships of different plant nutrients with AMF.
Questioning Seeding Rates and its Influence on Phenotypic Expression of Wheat Populations for Participatory Plant Breeding—First Findings from Field Research across Organic Farms in Belgium and the Netherlands

In Belgium and The Netherlands, bread wheat ( Triticum aestivum L.) is getting attention within a growing movement looking for more sustainability of wheat cropping and breadmaking. The few varieties available are pure lines that do not match the wide range of environments and organic farming practices, so that yields and milling quality are often disappointing. Composite Cross Populations (CCP) have been created with the idea of evolutionary plant breeding through on-farm mass selection and seed saving. In 2015–2016, one such CCP of winter wheat was cropped side by side with a pure line variety in four organic farms with different wheat cropping practices, as a first step to answer some of the concerns arising from farmers’ networks we work with. Seeding rates ranged from the standard high to the very low ones practiced under the System of Wheat Intensification (SWI). Multivariate data analysis confirmed greater differentiation of the CCP both compared with pure line varieties and within populations on farms where inter-plant competition was less intense. Low seeding rates thus seem to enhance the phenotypic expression potential of a CCP, yet this is a neglected fact among participatory plant breeders. Since both CCP and SWI have great potential for ecological intensification within organic farming, we argue that more work is needed on finding new ways of combining innovation in farming practices and on-farm plant breeding, which also implies new ways of organising research.
Field evaluation of a quantitative, and rapid malaria diagnostic system using a fluorescent Blue-ray optical device

We improved a previously developed quantitative malaria diagnostic system based on fluorescent Blue-ray optical device. Here, we first improved the diagnostic system to enable fully automated operation and the field application was evaluated in Kenya. We detected Plasmodium falciparum in blood samples collected from 288 individuals aged 1-16 years using nested polymerase chain reaction (nPCR), rapid diagnostic test (RDT), and automated system. Compared to RDT, the automated system exhibited a higher sensitivity (100%; 95% confidence interval [CI], 93.3–100%) and specificity (92.8%; 95%CI, 88.5–95.8%). The limit of detection was 0.0061%. Linear regression analysis revealed a correlation between the automated system and microscopic examination for detecting parasitemia (adjusted R2 value=0.63, P=1.13×10−12). The automated system exhibited a stable quantification of parasitemia and a higher diagnostic accuracy for parasitemia than RDT. This indicates the potential of this system as a valid alternative to conventional methods used at local health facilities, which lack basic infrastructure.
Review of recent trends in charging infrastructure planning for electric vehicles

The exhaustive nature of fossil fuels and environmental concerns associated with greenhouse gases are the major causes of the paradigm shift from conventional vehicles to electric vehicles (EVs). The electrification of the transportation sector and the increasing popularity of the EVs have driven scientists and researchers to delve into charging stations. Underdeveloped charging infrastructure, optimal placement of charging stations, and charge scheduling in the charging stations are the major concerns for the large‐scale deployment of EVs. Even few questions related to EVs, such as the vehicle price and driving range, can be partially solved with a well‐developed charging infrastructure. Existing old infrastructure may bring severe limitations in the realization of the optimal placement of charging stations as EVs have not existed when the road and grid infrastructure have been developed. For the past few years, the studies associated with the optimal placement and sizing of EV charging stations have drawn the consideration of the researchers. The researchers have used different approaches, objective functions, and applied different optimization algorithms while dealing with the problem of charging station placement. The complex and dynamic nature of the problem has led researchers to apply different optimization algorithms for the solution of the problem. In this particular review study, the research works bearing on the charging infrastructure planning for the EVs are considered. Thus, this review work will endow the research community with the latest developments and research findings in the paradigm of charging infrastructure planning for EVs.