Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic tags reveal the hidden lives of fishes

The past six decades have seen the emergence of new electronic tag technologies enabling scientists to remotely study the behavior of fishes in a wide variety of aquatic habitats. This revolution began in the 1950s and 1960s with the first studies utilizing acoustic and radio transmitters to actively track fish movements. Subsequent decades saw the development of passive monitoring systems enabling researchers to scale up the number of individuals followed, and the duration and spatial extent of tracking studies. Recent decades also have witnessed the increasingly-widespread use of sophisticated satellite transmitters to quantify fish movements in remote parts of the ocean beyond the range of fixed listening arrays. Most recently, high-frequency sampling devices incorporating accelerometers and other novel sensors have given us unparalleled new and detailed insights into fish behavior. All of these technologies have yielded important insights into fish spatial behaviors, and shown that many species are most active at night, or in deep waters, but we need better ground-truthing to reveal the full context and purpose of these spatial patterns. Recent advances in animal-mounted cameras have provided important ground-truthing breakthroughs, allowing us to see behavior and habitat use from the fishes' own perspective. However, current generations of animal-mounted cameras are reliant on natural light, or use artificial light overlapping the visual spectrum of most fishes. To see what fishes are doing at night, we need to develop new animal-mounted cameras using far red spectrum light, or high-frequency sound, to illuminate the view field without impacting natural behavior.
High density stress response in plants and the role of anthocyanin biosynthesis under adverse environmental conditions

High density stress response in plants and the role of anthocyanin under adverse environmental conditions Max Misyura Advisors: University of Guelph, 2013 Professor Joseph Colasanti Professor Steven Rothstein Plant stress significantly contributes to crop yield losses globally. Research on physiological responses of plants to stress provides potential targets for future crop improvement. The work presented here examines physiological changes of high density stress response and the role of the anthocyanin biosynthetic pathway in plant growth and development under nitrogen limitation and high light conditions. Physiological changes in response to high density stress in plants were examined using multiple approaches such as global transcriptome and metabolite analysis to identify potentially novel means by which the plants deal with high density stress. In addition, production of anthocyanin pigment and its flavonoid precursors were examined to identify crucial steps in the anthocyanin biosynthesis pathway for normal plant growth and development and their role in tolerance to high light and nitrogen stress. The work presented here demonstrates the involvement of ethylene production in high density stress response in rice, as well as highlights the importance of the first two biochemical steps of the flavonoid biosynthesis pathway in plant growth and development. Better understanding of plant stress response is not only fundamental to plant biology, but also has direct implications for agriculture. Hopefully, future studies will determine whether these findings can be applied in crop improvement to help with enhancing yields of staple crops.
Epstein-Barr Virus (EBV) Encoded Dutpase Exacerbates the Immune pathology of Lupus Nephritis In Vivo

Epstein-Barr virus (EBV) is an environmental factor with strong links to systemic lupus erythematous (SLE) pathogenesis; however, the mechanism(s) remains unclear. The goal of this study was to determine whether the EBV protein “deoxyuridine triphosphate nucleotidohydrolase (dUTPase)”, which can induce aberrant immune responses, contributes to the immunopathology of lupus nephritis (LN). Using the NZM2410/J SLE mouse model, we demonstrated that intramuscular injections of EBV-dUTPase protein (10 μg) significantly enhanced glomerulonephritis compared to PBSinjected controls. The inflammation was characterized by interstitial/ tubular cellular infiltrates, as well as increased IgG complex formation and C3 deposition in glomeruli. Additional immunohistochemical analyses revealed that EBV-dUTPase strongly induced IL-17 in glomeruli and tubules. More importantly, examination of kidney biopsies from class III/IV LN patients demonstrated the presence of EBVdUTPase in infiltrating plasma-cell aggregates near glomeruli, where neighboring cells with increased TLR-2 and IL-17 expression were observed, suggesting EBV-dUTPase may exacerbate the immunopathologies in some LN patients.
Cytotoxic Xanthones from the Leaves of Garcinia Urophylla

Two new xanthones, 7-hydroxydesoxymorellin (1) and isocaledonixanthone D (2), and four known ones, gaudichaudione H, 1,7-dihydroxy-3-methoxy-2-(3-methyl-2-butenyl)xanthone, 1,5-dihydroxy-3-methoxy-2-(3-methyl-2-butenyl)xanthone, and 1,3,7-trihydroxy-2-(3-methyl-2-butenyl)xanthone, as well as lupeol were isolated from the leaves of Garcinia urophylla (Guttiferae). Their structures were determined using a combination of 1D (1H NMR, 13C NMR, DEPT) and 2D (COSY, gHSQC, gHMBC) NMR spectroscopic techniques. Among the isolates, 7-hydroxydesoxymorellin (1), gaudichaudione H, 1,5-dihydroxy-3-methoxy-2-(3-methyl-2-butenyl)xanthone, and 1,3,7-trihydroxy-2-(3-methyl-2-butenyl)xanthone demonstrated cytotoxic activities against breast (MCF-7), prostate (DU-145), and lung (NCI-H460) human cancer cell lines.
Genomic Signals of Adaptation in the Allotetraploid Weed Capsella bursa-pastois

Polyploids are often exceptionally evolutionarily successful, and increased adaptive potential may contribute to their prevalence. However, adaptation is not well characterized in polyploids, and the extent that it contributes to polyploid success is currently unclear. Here we investigate the genomic basis of adaptation in one of the world’s most successful weeds. We obtained genotype-by sequencing (GBS) sequences from 261 C. bursa-pastoris accessions and 24 whole genome sequences spanning Eurasia. We identified climate associations and found adaptive signatures consistent with contemporary adaptation in recently colonized Asia, and longer adaptive divergence in the ancestral European range. Signatures of adaptation through selective sweep scans suggest preadapted parental genomes may also contribute to local adaptation in similar habitats. However, native climate did not predict fitness in a common garden. Local environmental adaptation is then likely a subtle factor in C. bursa-pastoris’ success, although the features of its diploid progenitor genomes notably influenced its adaptation.
Glycopeptide Resistance in S. aureus

The glycopeptides (particularly vancomycin) have been the recommended therapy for serious methicillin‐resistant Staphylococcus aureus (MRSA) infections. The increased incidence of MRSA has led to the frequent use of vancomycin. Unfortunately, with the increased use of vancomycin, isolates of S. aureus have been discovered with reduced susceptibility to vancomycin. Several studies suggest that reduced vancomycin susceptibility is associated with vancomycin treatment failure. Various forms of glycopeptide resistance have appeared in MRSA strains, including high‐level resistance, homogeneous and heterogeneous intermediate resistance. While vancomycin‐resistant S. aureus (VRSA) strains are limited to a handful of reported cases and vancomycin‐ intermediate S. aureus (VISA) strains remain rare; heterogeneous VISA (hVISA) strains are more common. This article summarizes the current knowledge regarding the history, definition, mechanisms, detection methods, epidemiology and clinical significance of ‘glycopeptide resistance in S. aureus ’ and discusses therapeutic optıons for the treatment of hVISA/VISA infections.
The Diverse Impact of Bacteriophages on the Bacterial Host

The viruses that infect bacteria, bacteriophages (or phages) are the most abundant biological entities on the planet. Phages are constantly causing bacterial population turnover through infection and lysis, a process that results in the replication of phages and the death of the bacterium. Alternately, phages can integrate into the bacterial genome, at which point the phage is referred to as a prophage. Prophages are abundant in bacterial genomes and are not merely inert entities, as some genes are expressed from the prophage, which can increase host and prophage fitness. Clinical and environmental isolates of the opportunistic human pathogen, Pseudomonas aeruginosa were investigated and found to possess prophages in their genomes which were inducible. I identified many novel phenotypes emerging after prophage acquisition, particularly an array of superinfection exclusion traits that protect the lysogenic host from subsequent phage infection. These traits are likely beneficial in the environment, protecting the bacterium (and the resident prophage) from infection and lysis. In addition to prophages protecting the host from infection, bacteria encode many systems to protect themselves, including the adaptive immune system known as CRISPR-Cas. I demonstrated that the CRISPR-Cas system of P. aeruginosa strain PA14 is active and targets phages and plasmids for degradation. Interestingly, the phages are not passive bystanders in this
Production of biogas: relationship between methanogenic and sulfate-reducing microorganisms

Abstract The production of high-quality methane depends on many factors, including temperature, pH, substrate, composition and relationship of the microorganisms. The qualitative and quantitative composition of methanogenic and sulfate-reducing microorganisms and their relationship in the experimental bioreactors has never been studied. The aim of this research was to characterize, for the first time, the diversity of the methanogenic microorganisms and sulfate-reducing bacteria, and study their relationship and biogas production in experimental bioreactors. Amplification of 16S rRNA gene fragments was carried out. Purified amplicons were paired-end sequenced on an Illumina Mi-Seq platform. The dominant morphotypes of these microorganisms in the bioreactor were homologous (99%) by the sequences of 16S rRNA gene to the Methanosarcina, Thermogymnomonas, Methanoculleus genera and Archaeon deposited in GenBank. Three dominant genera of sulfate-reducing bacteria, Desulfomicrobium, Desulfobulbus and Desulfovibrio, were detected in the bioreactor. The phylogenetic trees showing their genetic relationship were constructed. The diversity and number of the genera, production of methane, hydrogen sulfide and hydrogen in the bioreactor was investigated. This research is important for understanding the relationship between methanogenic microbial populations and other bacterial physiological groups, their substrate competition and, in turn, can be helpful for controlling methanogenesis in bioreactors.
Examining of multiple imputation method in two missing observation mechanisms.

This study contains an examination of the missing data structures, occurring in many fields, especially in livestock. It also examines the processes to obtain the solution for the missing data. For this purpose, linolenic acid measurements obtained from four different anatomic regions of two animal species were taken as dependent variables. For the dependent variable, the observations were deleted at the ratio of 10% and 20%, creating the missing structures of missing completely at random (MCAR) and missing at random (MAR). Subsequently, these data sets were completed using multiple imputation (MI) method. Generalized Estimating Equation (GEE) and mixed model methods were used in the missing data structures and for the purpose of evaluating the data completed with MI. The study were obtained almost same results obtained from GEE and mixed model in the missing data structures. At the same time, there was not found difference between the methods in completed data using MI method. As a result, it is stated that valid results obtained in missing data structures by used GEE and mixed model analysis. When these results are also compared, it can be concluded that multiple imputation (with these ratio of missing) is not necessary before GEE and mixed model.
The Impact of Protein Binding on Antibacterial Activities of Antibiotics is more than Predicted by Considering its Numerical Value Alone: Effects of Serum Proteins on Activities of Poorly Penetrating Agents and Inhibition of ß- Lactamase Activity-Part II

Objectives: Protein binding decreases antibacterial activities as the free fraction only crosses membranes thus reaching intracellular targets. However, serum components may increase antibacterial activities. Therefore, the effect of serum proteins on activities of s-lactams and macrolides was examined. Methods: Strains with defined resistance genotypes were selected; MRSA, ermB-, mefA-, gyrA Ser81-Phemutants of S. pneumoniae, and TEM-1 or TEM-3 s-lactamase producing E. coli were used. Ten antibiotics known to penetrate into bacteria either well or poorly and/or known to be labile or stable to inactivation by s-lactamases were used. Strains were incubated in Brain Heart Infusion Broth (BHI), BHI +50% heat inactivated human serum or active serum, or 45 g/L albumin. MICs were determined and Kill-kinetics was recorded following exposure to constant or fluctuating drug concentrations. Kill constants and areas under the bacterial kill curves were calculated. Results: Albumin and inactive serum increased MICs and reduced kill rates of the agents studied in conformity with their protein binding. However, active serum increased the activities of such agents known to penetrate poorly into strains with permeation barriers. In addition, active as well as inactive serum restored the activities of s-lactams against s-lactamase producing strains due to enzyme inhibition. Conclusions: Serum proteins permeabilized bacteria and inhibited s-lactamase activity. The impact of serum proteins on antibacterial activities against specific drug-bug associations is more than predicted by considering the numerical value of protein binding alone.
Report of papillorenal syndrome in a family and literature review

Objective To investigate the clinical manifestations and genetic features of children with papillorenal syndrome caused by PAX2 gene mutation. Methods Clinical manifestations, imaging changes and sequencing data were collected and analyzed from a family with papillorenal syndrome who were diagnosed in Wuhan Children's Hospital in February 2018. "PAX2", "papillorenal syndrome" and "renal coloboma syndrome" were used as key words to search in China National Knowledge Infrastructure, Wangfang Data Knowledge Service Platform, PubMed and Human Gene Mutation Database up to April 2018. Results A ten years old girl was admitted due to "edema and urine output decreased for one week". Lab showed BUN 25.30 mmol/L, Scr 766.5 μmol/L, Urine protein 3.6 g/24 h. Imaging examination showed bilateral vesical and ureter reflux combined with left duplex kidney and duplication of ureter. Developmental dysplasia of the left hip was also found. The father of the patient had been diagnosed with chronic kidney disease for 10 years and on hemodialysis for 6 years. Next generation sequencing revealed that both the father and daughter carried a heterozygous nonsense mutation in the exon3 c.219C>G(p.Y73X) of PAX2. No Chinese literature ever was reported about papillorenal syndrome. Ninety-four articles in English were retrieved and 177 patients with papillorenal syndrome were confirmed by gene analysis with a total of 92 PAX2 variants. Ten nonsense mutations had been reported. Developmental dysplasia of the hip (DDH) never be reported before. Conclusion Papillorenal syndrome caused by PAX2 mutation can mainly manifest as abnormal development of both kidney and optic nerve, which may be accompanied by other systemic abnormalities, it is rarely reported in China. DDH may be a new phenotype of papillorenal syndrome. Key words: Urogenital abnormalities; Mutation; PAX2 transcription factor; Phenotype; Papillorenal syndrome
Changes in the Quality of Black Mulberry and Blueberry Sherbets During Storage

This study was evaluated the quality properties of traditional drink sherbets that are prepared from black mulberry and blueberry fruits. After production sherbets were investigated to determine their pH, acidity, °brix and colour values, total sugar, phenolic, anthocyanin and antioxidant contents. Moreover the sherbets stored at 4°C during 2 months and the changes in these quality properties were examined per month. As a result statistically significant changes were observed in the quality properties of these sherbets of black mulberry and blueberry fruits which are known with their rich content of phytochemical compounds. The results show that in blueberry sherbet the degradation of phenolics was faster than black mulberry sherbet. Anthocyanins that are higher in black mulberry sherbets after production were preserved better in blueberry sherbets at the end of 2nd month. L*and a* values decreased for blackberry and blueberry sherbets during storage. b* value decreased from 5.59 to 4.92 for blackberry sherbet while it increased from 0.62 to 0.79 for blueberry sherbet at the end of the storage time.
The functional morphology of the intermandibulo-cervical envelope of the American alligator (Alligator mississippiensis)

x CHAPTER 1: INTRODUCTION: REPTILE SKIN.1 1.1. General Morphology and Histology of the Reptilian Integument.2 1.1.1. Epidermis.2 1.1.2. Dermis.6 1.2. References.8 CHAPTER 2: THE INTERMANDIBULO-CERVICAL INTEGUMENT OF THE AMERICAN ALLIGATOR (ALLIGATOR MISSISSIPPIENSIS). 13 2.
PHYTOSOCIOLOGICAL EXAMINATION OF IHLARA SPECIAL ENVIRONMENTAL CONSERVATION ZONE

The aim of this study was to detect the syntaxa in the Ihlara valley vegetation which have not been previously phytosociologically assessed. Ihlara Valley is geographically located in Central Anatolia and in the Irano-Turanian phytogeographical regions. The study area is located within the B5 square based on the Grid System (Davis et al. 1965-1985). According to the Braun-Blanquet (1932) method, there are three plant associations belonging to three different vegetation types in the region; Pistacio terebinthi – Celtidetum tournefortii (shrub vegetation), Astragaletum karamasici – microcephali (tragacanth steppe vegetation), and Rubo sancti Salicetum albae (riparian vegetation). These three syntaxa are all new to the world of science.
Étude des propriétés de surface du bactériophage MS2 et du norovirus murin au cours de différents traitements d’inactivation

Meme si les traitements thermiques ou la desinfection par les oxydants ont demontre leur efficacite virucide, les mecanismes lies a la perte du caractere infectieux ne sont pas connus. Ceci pose un reel probleme d’interpretation de la presence de genome viral en matiere de risque infectieux dans les aliments. Ce travail de these a pour objectif d’etudier l’evolution des proprietes de surface (charge et hydrophobie) de virus modeles, bacteriophage MS2 et norovirus murin, au cours de l’inactivation par la chaleur, l’hypochlorite de sodium et l’ozone. Pour nos deux virus, nous demontrons l’existence d’une temperature critique au-dela de laquelle la particule virale se destructure en liberant son genome. Un simple traitement a la RNase permettrait alors de ne detecter que des virus infectieux par biologie moleculaire. Le traitement thermique implique aussi une augmentation de l’hydrophobie soulignant des modifications conformationnelles de la capside. L’hypochlorite de sodium ne modifie que peu les proprietes de surface mais des phenomenes d’oxydation ont lieu au niveau de la capside puisque la charge du bacteriophage MS2 est legerement modifiee. Ces modifications diminuent la resistance thermique du virus. Nous demontrons un effet synergique de l’hypochlorite de sodium et la chaleur sur le bacteriophage MS2 (inactivation, RNase et hydrophobie). Quant a l’ozone gazeux, nous soulignons son interet pour le traitement virucide des aliments fragiles. Ainsi, ce travail precise les mecanismes d’inactivation des virus et ouvre de nouvelles perspectives tant pour discriminer les virus infectieux et non-infectieux que pour proposer l’exploration de nouveaux traitements technologiques
MELOCHIA CORCHORIFOLIA, A NEW HOST OF 16SRI-B PHYTOPLASMA IN CHINA

Melochia corchorifolia L. is a herb and weed commonly found in China. In August 2015, three M. corchorifolia plants displaying symptoms of phytoplasma infection such as witches’-broom, virescence and phyllody were found in two wastelands in Haikou, Hainan province, China. All symptomatic and three asymptomatic plants were collected for phytoplasma detection and classification (Dickinson and Hodgetts, 2013). Phytoplasma diagnosis was performed by nested PCR using phytoplasma universal primers P1/P7 and R16F2n/R16R2. Fragments ca. 1.8 (P1/P7) and 1.2 kb (R16F2n/R16R2) in size were only observed in symptomatic samples. For phytoplasma classification, gene fragments were amplified using R16F2n/R16R2 primers for 16S rRNA, rp(I)F1A/rp(I)R1A for rp, and fTufu/rTufu (Schneider et al., 1997) for tuf genes, respectively; three clones of each were sequenced. The consensus sequences were submitted to GenBank with the accession numbers KX150461 (16Sr RNA), KX158198 (rp) and KX158199 (tuf). A phylogenetic tree based on the partial 16Sr RNA gene sequences (1246 nt) from M. corchorifolia phytoplasma (Mcp) and other phytoplasma group representatives was built by MEGA 5.0 using neighbor-joining method. It showed that Mcp clustered with 'Candidatus Phytoplasma asteris' (16SrI group) phytoplasmas. Furthermore, virtual RFLP analyses were performed by iPhyClassifier and Vector NTI. 16Sr RNA, rp and tuf gene RFLP profiles of Mcp were consistent with the RFLP profiles of 16SrI-B, rpI-B and tuf-B subgroup phytoplasmas. To our knowledge, this is the first report on M. corchorifolia phytoplasma worldwide.
Los jagüeyes de los Montes de María en Sucre, Colombia: transformación alternativa y tradicional para acceso productivo y sobrevivencia

The present study through the use of geographical information system, determines the cattle ponds presence in the municipal territories of Chalan, Coloso and Toluviejo, department of Sucre, Colombia. The study area formed part of Montes de Maria formation, identified as an area of tropical dry forest of the Colombian Caribbean. Were determined in total 500 units, of which the water mirror for municipality was: Chalan 0.129%, Coloso 0.143% and Toluviejo 0.42%, with a minimum range of area for unit between 0.1125 and 0.445 ha. The high dependence that the human populations have to satisfy the necessities of domestic water is demonstrated and it is compared with social variables such as: concentration of land tenure and poverty. To conclude, that the cattle ponds represents an important access system to the water of great value and importance for the study area.