Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of genetic determinants for growth and structure of Listeria monocytogenes biofilms / by Nicholas Choy.

CHARACTERIZATION OF GENETIC DETERMINANTS FOR GROWTH AND STRUCTURE OF Listeria monocytogenes BIOFILMS Nicholas Choy Advisor: Lakehead University, 2006 Dr. Heidi Schraft This thesis investigated wild-type Listeria monocytogenes EGD and five of its corresponding mutant strains (Ml, M4, M7, M il and M l4) for their ability to form biofilms on glass at 22°C and 37°C, with and without shear force. Cell counts of 24 h-old biofilms ranged from 10 ̂ to lO^cfu/cm^. For all strains investigated, biofilms grown without shear force at 22°C had higher mean biofilm cell counts than at 37°C (P<0.05). Biofilms of wild-type L. monocytogenes EGD and its mutant M il {clpB gene deleted) were further analyzed with scanning electron microscopy (SEM). SEM imaging of biofilms grown at 37°C without shear force showed that the wild-type strain EGD produced significantly more biofilm cells than its mutant M U. For biofilms grown at 22°C, both strains displayed characteristic three-dimensional biofilms with cells embedded in what is believed to be extracellular polymeric substances (EPS) when dehydrated with hexamethyldisilizane (HMDS). With the aid of confocal scanning laser microscopy (CSLM), biofilm structures of wild type Listeria monocytogenes EGD and its corresponding mutant strains were quantitatively described with PHLIP using the image analysis program. Strains were then characterized with a statistical method known as principal components analysis (PCA). Results from this analysis revealed three strains (M l4, M il and M7) having high thickness and surface-to-biovolume ratio when grown under three conditions (22°C with shear, 37°C with and without shear). A complementation in trans was then performed on mutant M il to ascertain that the phenomenon observed regarding biofilm production and stucture on glass, could be attributed to the absence of the clpB gene. Reproduced with permission of the copyright owner. Further reproduction prohibited without permission.
Diel variation of grazing of the dinoflagellate Lepidodinium sp. and ciliate Euplotes sp. on algal prey: the effect of prey cell properties

The effect on protist grazing of diel variation of carbon to nitrogen ratio (C:N) in algal prey was investigated using the dinoflagellate Lepidodinium sp. and the ciliate Euplotes sp. as predators and the green algae Dunaliella salina and Chlorella autotrophica as respective prey. Both predator and prey cultures were maintained in light:dark cycle, with an additional set of prey cultures in a reversed light:dark cycle to that of predator cultures. Grazing experiments were conducted near the end of light (light experiment) and dark (dark experiment) phase with the algal prey in the same and opposite phases provided as mono-diets. In all experiments, prey at the end of light phase (day prey) possessed higher C:N than prey at the end of dark phase (night prey). Grazing rates in the light experiments were higher than in the dark experiments for both predators. Grazing rates and C ingestion rates (IRs) on day prey were higher than that on night prey for both predators. However, similar N IRs on day and night prey were observed in Lepidodinium sp. , suggesting a compensatory feeding response of the predator by taking extra C for sufficient acquisition of N from the prey with relatively high C:N.
A comparative analysis of textile schools by journal publications listed in Web of ScienceTM

Abstract In this study, a comparative analysis of textile schools around the world based on research journal publications is made using the most popular bibliometric evaluation methodology. The study benchmarks bibliometric evaluation of professional research institutions related to textile, apparel, fashion and clothing in recent years from 2014 to 2019. Based on Web of ScienceTM , a total of 124,362 research publications (not counting conference papers) from 2014 to 2019 were found to be textile or fiber related. Out of more 1000 textile schools worldwide, 31 schools from 18 countries or territories were identified to be among the top 100 institutions contributing the textile or fiber related publications listed in Web of ScienceTM. These 31 textile schools are ranked in terms of productivity and citation impact, including total number of publications, publication per staff, h-index, total citations, average citations, and citation per staff. While these bibliometric measures provide some insights of the trends of the research activities and influences of textile schools in the world, they should be interpreted with caution as the quality of research contributions in terms of originality, scientific rigor and societal impact may not be reflected by the publication counts and the cites they receive.
Comprehensive Genomic Characterization and Expression Analysis of the Lipoxygenase Gene Family in Watermelon under Hormonal Treatments

Lipoxygenases (LOXs) are non-haem iron-containing dioxygenases and play vital roles in a variety of plant biological processes. Here, we first carried out the genome-wide identification of LOX genes in watermelon. A total of 16 LOX genes were identified, which could be classified into two categories according to phylogenetic analysis: the 9-LOXs (ClLOX1–4, 12, and 15) and 13-LOXs (ClLOX5–11, 13, 14, and 16). Furthermore, the protein structures, intrachromosomal distributions, and gene structures were thoroughly analyzed. Cis-element analysis of the promoter regions indicated that the expression of ClLOX genes may be influenced by stress and plant hormones. Bioinformatic and expression analyses revealed that the expression of ClLOX genes is tissue-specific and hormone-responsive. The detected LOX genes exhibited distinctive expression patterns in various tissues. Different ClLOX genes showed different responses to methyl jasmonate (MeJA), salicylic acid (SA), and ethylene (ET) treatments, particularly ClLOX7, which exhibited the most active response to the above treatments. This study provides valuable information for a better understanding of the functions of LOX genes and further exploration of the LOX gene family in watermelon.
Antiviral activity of macrophage‐activating Chinese mixed herb hot water extract

Macrophage‐activating Chinese mixed herb (MACH) extract, a hot‐water decoction of Cucurbita moschata (pumpkin seed), Carthamus tinctorius (safflower flower), P. asiatica (psyllium seed), and L. japonica (Japanese honeysuckle flower), is able to induce the production of interferon and interleukin, and hence reduce viral load in patients with hepatitis C virus (HCV) infection. The aim of this study was therefore to analyze the antiviral activity in the available models and identify the mechanism of alleviation of HCV infection.
Transfer Pricing, Thin Capitalization, Financial Distress, Earning Management, dan Capital Intensity Terhadap Tax Avoidance Dimoderasi oleh Sales Growth

This study aims to examine the effect of transfer pricing, thin capitalization, financial distress, earnings management, and capital intensity on tax avoidance with sales growth as moderating. This study uses a sample of manufacturing companies in the basic industrial sector and chemical goods, the consumer goods industry sector, and other goods industry sectors listed on the Indonesia Stock Exchange during the 2016-2018 period as many as 32 companies. Data collection techniques using purposive sampling method and analyze using panel data multiple regression method. The results showed that transfer pricing, financial distress, earnings management, and sales growth have a negative effect on tax avoidance. Thin capitalization has a positive effect on tax avoidance , while capital intensity has no effect on tax avoidance. Sales growth as a moderator is able to strengthen the negative influence of transfer pricing and financial distress and the positive influence of thin capitalization and capital intensity on tax avoidance. Sales growth weakens the negative effect of earnings management on tax avoidance
Genetic Signatures of the Retina in Health and Disease

1 CHAPTER 1: THE GENOTYPE TO PHENOTYPE QUESTION UNDERLYING VISION.2 1.1 The eye 1.1.1 Features of the eye across species.3 1.1.2 The retinal layer and the role of rod and cone photoreceptors.5 1.1.3 The importance of cone cells in the context of retinal disease.6 1.2 Cone phototransduction signaling 1.2. 1 The first steps in visual response by cones.7 1.2. 2 Structural dynamics of cone opsins during phototransduction.9 1.3 Evolutionary dynamics of the eye 1.3. 1 Evolution of retinal circuitry.12 1.3. 2 Evolution of cone photoreceptors.13 1.4 Structural features of cone photoreceptors 1.4. 1 Cone disc renewal.16 1.4. 2 Cone disc morphogenesis.19 1.5 Mammalian models to better elucidate cone cell structure and function
Analysis of High-Frequency Measurement of Transistors Along With Electromagnetic and SPICE Cosimulation

Terahertz (THz) silicon-based electronics is undergoing rapid developments. In order to keep this momentum high, an accurate and optimized on-wafer characterization procedure needs to be developed. While evaluating passive elements, the measured s-parameter data can be verified by a direct use of EM simulation tools. However, this verification requires to precisely introduce part of the measurement environment such as the probes, pads, and access lines to accurately predict the impact of calibration and layout for on-wafer measurements. Unfortunately, this procedure is limited to passive elements. Hence, in this work, we propose a new procedure to emulate the measurement of active devices using an electromagnetic SPICE cosimulation. By this method, one can clearly highlight that a measurement artifact that was observed for the transistor measurement can be reproduced. One of the most representative examples of measurement artifact involves the measurement and estimation of ${f}_{\text {MAX}}$ which is not constant over all frequency bands. Also, the measurement is difficult to perform above 40 GHz. This typical problem is now undoubtedly attributed to the probe-to-substrate coupling and probe-to-probe coupling which are strongly dependent on the probe geometry. Finally, this cosimulation procedure evidently underlines the need for an optimized deembedding procedure above 200 GHz.
“His inner-self must be good”: An ethnographic-vignette study of social interactions between children with autism spectrum disorder and typically developing peers

Children with autism spectrum disorder (ASD) can benefit from greater social integration through positive peer relationships. The study aimed to understand children’s views toward autism as well as experiences of interactions between children with ASD and typically developing (TD) peers. After ethnographic observations in a mainstream primary school educating diverse students, interviews were conducted with 10 students with ASD and ten of their TD peers using open-ended and vignette questions about three hypothetical scenarios set in varied contexts: a classroom, a birthday party, and a public setting. Narrative analysis focused on how the children constructed their experiences in response to these vignettes. Children with ASD frequently experienced isolation in peer interactions. While their TD peers favored interactions with those with ASD, believing that their behaviors of concern are extrinsic and their intentions must be good, their lack of understanding of ASD and of social skills that could be used to facilitate more positive interactions could result in unintended harm and exclusion. Early school-based intervention would assist in increasing the acceptance of neurodevelopmental differences and diversity.
Climatic and land‐use drivers along a latitudinal gradient: species diversity in temperate grasslands on agricultural soils

Questions Do remaining mesophytic grasslands on soils with agricultural potential respond to a latitudinal gradient? Are climatic or land use factors the principal drivers of regional and local diversity of these grasslands? Location The mesophytic grasslands of the Argentine Pampas, between 32°S and 38°S, along 600km within the Mesopotamic, Rolling and Flooding Pampas of the Rio de la Plata grasslands. Methods The species presence and cover was recorded in each of 96 remnant grasslands on soils suitable for cropping, grouped in five sampling locations. In each region, confidence intervals for gamma diversity and for the slope of species/area curves were estimated. Unconstrained ordination was applied to detect the principal gradients in floristic composition and correlation analysis to identify their main drivers. Mantel test was used to evaluate the correlation between floristic similarity and geographical distance, and with Euclidean distance in fragmentation and climatic variables. To rank the climatic and land use factors that account for local species richness and percent number of exotics, we applied correlation analysis and regression models. Results Community composition (73% native species) was mainly related to climatic variables determined by latitude, with a slight influence of fragmentation variables. Regional species richness responded to latitude: gamma diversity decreased linearly with increasing distance from the Equator, and so did the rate of species accumulation with expanding area. Alpha diversity did not vary in a systematic way with latitude, being associated with landscape fragmentation and mean annual precipitation. Relative importance of C4 grasses and mean percent exotics showed opposite latitudinal tendencies, the former decreasing and the latter increasing towards the South. Conclusions Latitude was a strong determinant of regional diversity and community composition, but a partial driver for local species richness mainly influenced by landscape fragmentation. While climatic and geographical drivers determined gradual latitudinal turnover in regional species pools, within regions land-use history, stochastic processes and biotic interactions were also important. All these patterns need to be considered together when delimiting grassland nature reserves for conservation of the most diverse ecosystems of this region, threatened by agricultural expansion and intensification. This article is protected by copyright. All rights reserved.
Identification of candidate genes for resistance to Soybean mosaic virus strain SC3 by using fine mapping and transcriptome analyses

Abstract. This study is a continuation of our earlier reports on the identification and mapping of the Soybean mosaic virus (SMV) strain SC3 resistance gene present on chromosome 13 (LG F) of soybean (Glycine max (L.) Merr. ). We used a combination of fine mapping and transcriptome sequencing to discover the candidate genes for SMV resistance in Qihuang-1. To fine-map the resistance gene, near-isogenic lines (NILs) from a cross between Qihuang-1 (resistant) and Nannong 1138-2 (susceptible) were genotyped with simple sequence repeats (SSR) and insertion and deletion (indel) markers to identify recombination events. Analysis of plants carrying key recombination events placed the resistance gene to a 180-kb region of the ‘Williams 82’ genome sequence with 17 annotated genes. Transcriptome and quantitative real-time PCR (qRT-PCR) analyses revealed that SMV resistance in Qihuang-1 was probably attributable to the four candidate genes (Glyma13g25920, Glyma13g25950, Glyma13g25970 and Glyma13g26000). The four candidate genes identified in this study can be used in further studies to investigate the role of resistance genes in conferring SC3 resistance in Qihuang-1.
Genetic Analysis of Effect of Heat Stress on Genomic DNA from Cowpea (Vigna unguiculata (L) Walp.)

Aims: Genetic analysis was used to study the effect of heat st ress on young seedlings of cowpea ( Vigna unguiculata (L) Walp. ). Study Design: Four different colors of cowpea seeds (white, dirty w hite, deep brown and light brown) were obtained from GeneBank of International Institute of Tropical Agriculture (IITA) Ibadan, Nigeria. Seeds from each of the cowpea four colors we re first pre-germinated and young seedlings subjected to DNA extraction. Extracted DNA subjected to different temperature treatments at 75°C and 100°C for one hour and control not heated. Place and Duration of Study: Department of Chemical Sciences Afe Babalola University Ado Ekiti, Nigeria between January 2015 and June 2015. Methodology: UV wavelength absorption spectrum analysis (A 200 – A 960 ) was carried out on control DNA and DNA heated at 75°C and 100°C respectively. Cl uster analysis of optical density (OD) data was carried out to establish the relationship between co ntrol DNA and heat treated DNA (75°C and 100°C). Results: DNA concentrations of Vigna unguiculata (L) Walp. were between 0.40 to 1.15 mg/ml, 0.33 to 0.84 mg/ml, and 0.26 to 0.89 mg/ml for control a nd heat treatments of 75°C and 100°C respectively. DNA UV absorption spectra of control and heat treatments of 75°C and 100°C were generally different due to differential UV wavelengt h absorption. Cluster analysis revealed three different clusters (cluster 1, cluster 2 and cluster 3) among control DNA and heat treated DNA. Cluster 1 comprised of V1-control, V1-75°C and V1-10 0°C, with V1-75°C and V1-100°C having similar characters. Cluster 2 was made up of V4-control, V4-75°C and V4-100°C, with V4-75°C and V4-100°C having the same characters. Cluster 3 was largel y characterized by dissimilar DNA extracts of V3-75°C, V2-control, V3-100°C, V2-100°C, V 3-control and V2-75°C. Conclusion: Genetic diversity among individual Vigna unguiculata (L) Walp. accession DNA as obtained in this study could possibly be as a result of variations in heat tolerance among dissimilar cowpea genomic compositions
Attachment and sleep: A dyadic intensive longitudinal actigraphy study

Attachment and sleep are linked across the lifespan, but attachment regulation of sleep among couples is understudied. This study aimed to replicate and extend prior research by testing whether romantic partners’ attachment orientations interacted to predict sleep, assessed via self-report and actigraphy over 14 days. Participants (N = 208 couples) completed measures of attachment anxiety and avoidance and the Pittsburgh Sleep Quality Index. They also wore actigraphy monitors to assess nightly sleep quality and duration. Anxious people self-reported worse sleep quality, replicating two prior studies. In contrast to previous studies, anxious and low-avoidant people slept significantly worse with avoidant partners, while avoidant people slept somewhat better with avoidant partners. Results indicted dyadic regulation of several sleep outcomes and provided new insights regarding how partner avoidance can exacerbate or buffer sleep quality.
Modelling non‐stationary water ages in a tropical rainforest: A preliminary spatially distributed assessment

Pristine tropical forests play a critical role in regional and global climate systems. For a better understanding of the eco‐hydrology of tropical “evergreen” vegetation, it is essential to know the partitioning of water into transpiration and evaporation, runoff and associated water ages. For this purpose, we evaluated how topography and vegetation influence water flux and age dynamics at high temporal (hourly) and spatial (10 m) resolution using the Spatially Distributed Tracer‐Aided Rainfall‐Runoff model for the tropics (STARRtropics). The model was applied in a tropical rainforest catchment (3.2 km2) where data were collected biweekly to monthly and during intensive monitoring campaigns from January 2013 to July 2018. The STARRtropics model was further developed, incorporating an isotope mass balance for evapotranspiration partitioning into transpiration and evaporation. Results exhibited a rapid streamflow response to rainfall inputs (water and isotopes) with limited mixing and a largely time‐invariant baseflow isotope composition. Simulated soil water storage showed a transient response to rainfall inputs with a seasonal component directly resembling the streamflow dynamics which was independently evaluated using soil water content measurements. High transpiration fluxes (max 7 mm/day) were linked to lower slope gradients, deeper soils and greater leaf area index. Overall water partitioning resulted in 65% of the actual evapotranspiration being driven by vegetation with high transpiration rates over the drier months compared to the wet season. Time scales of water age were highly variable, ranging from hours to a few years. Stream water ages were conceptualized as a mixture of younger soil water and slightly older, deeper soil water and shallow groundwater with a maximum age of roughly 2 years during drought conditions (722 days). The simulated soil water ages ranged from hours to 162 days and for shallow groundwater up to 1,200 days. Despite the model assumptions, experimental challenges and data limitation, this preliminary spatially distributed model study enhances knowledge about the water ages and overall young water dominance in a tropical rainforest with little influence of deeper and older groundwater.
Available phosphorus reduction in weaned piglets’ diets containing phytase combined with butyric and benzoic acids

This study aimed to evaluate the reduction of available phosphorus (Pa) in the diet of weaned piglets using phytase combined with butyric and benzoic acids. A total of 120 piglets with initial weight of 6.7 ± 0.02 kg were used in a randomized block design with six treatments: control; reduction of 0.15% Pa (Pa red); Phytase + Pa red; Phytase + butyric acid + Pa red; Phytase + benzoic acid + Pa red; Phytase + butyric acid + benzoic acid + Pa red; five replicates, with four animals each. The experimental diets had no influence on the fecal scores, Escherichia coli count, or the pH of the digestive tract. An improved villus:crypt ratio was found when the combination of phytase with butyric and benzoic acids was used. The histomorphometry of the jejunum and of the ileum showed no differences with respect to villus height, crypt depth, and villus:crypt ratio. The bones of the piglets fed with a diet containing reduced levels of available phosphorus showed less resistance to fracture. The levels of calcium in the raw bones were lower in the piglets that received a diet containing phytase and butyric acid. Reduced phosphorus deposition was observed in the bones of animals that received the diet containing phytase, butyric acid, and benzoic acid. It is concluded that the inclusion of phytase and butyric and benzoic acids, and their combination, in the diet of weaned piglets does not affect the pH of the stomach, duodenum, jejunum, ileum, cecum, and colon, and does not change the frequency of diarrhea or the E. Coli count. The association of butyric and benzoic acids with phytase in the diet of piglets after weaning improves the villus:crypt ratio of the duodenum. The use of phytase (1000 UF/kg) allows the formulation of diets for weaned piglets with a 0.15% reduction in the level of available phosphorus without damaging the concentration of calcium and phosphorus in the bones and without altering bone resistance.