Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of monocot and dicot plant development with constitutively active alleles of phytochrome B

Abstract The constitutively active missense allele of Arabidopsis phytochrome B, AtPHYBY276H or AtYHB, encodes a polypeptide that adopts a light‐insensitive, physiologically active conformation capable of sustaining photomorphogenesis in darkness. Here, we show that the orthologous OsYHB allele of rice phytochrome B (OsPHYBY283H) also encodes a dominant “constitutively active” photoreceptor through comparative phenotypic analyses of AtYHB and OsYHB transgenic lines of four eudicot species, Arabidopsis thaliana, Nicotiana tabacum (tobacco), Nicotiana sylvestris and Solanum lycopersicum cv. MicroTom (tomato), and of two monocot species, Oryza sativa ssp. japonica and Brachypodium distachyon. Reciprocal transformation experiments show that the gain‐of‐function constitutive photomorphogenic (cop) phenotypes by YHB expression are stronger in host plants within the same class than across classes. Our studies also reveal additional YHB‐dependent traits in adult plants, which include extreme shade tolerance, both early and late flowering behaviors, delayed leaf senescence, reduced tillering, and even viviparous seed germination. However, the strength of these gain‐of‐function phenotypes depends on the specific combination of YHB allele and species/cultivar transformed. Flowering and tillering of OsYHB‐ and OsPHYB‐expressing lines of rice Nipponbare and Kitaake cultivars were compared, also revealing differences in YHB/PHYB allele versus genotype interaction on the phenotypic behavior of the two rice cultivars. In view of recent evidence that the regulatory activity of AtYHB is not only light insensitive but also temperature insensitive, selective YHB expression is expected to yield improved agronomic performance of both dicot and monocot crop plant species not possible with wild‐type PHYB alleles.
Genotype x Environment interaction in Mungbean (Vigna radiata (L.) Wilczek) cultivars grown in different agro-climatic zones of Karnataka

Fourteen genotypes were tested at five locations in North-Karnataka in the kharif season-2008 to study their yield stability. Pooled analysis of variance and stability analysis were performed. The genotypic (G) x environment (E) interaction and both variance due to genotypes and environment were significant. The partioning of G x E interaction into linear and non-linear components indicated that both predictable and unpredictable components shared the interaction. On the basis of stability parameters, the top yielding genotypes such as DGGV-2 (964 Kg/ha) DLGG-22 (945 Kg/ha) and DGGS-16 (933 Kg/ha) exhibit the stable performance across the environments. The genotypes BGS-9 (933 Kg/ha), BPMR-1 (903 Kg/ha) and KGS-83 (908 Kg/ha) gave higher yield across the locations but their performance was unstable due to significant deviation from regression. On the basis of results, DGGV-2, DLGG-22 and DGGS-16 were the most suitable and desirable genotypes which showed higher stable grain yields at different agro-climatic regions.
A simple, non‐toxic method for separating seeds based on density, and its application in isolating Arabidopsis thaliana seed oil mutants

Premise Seed oil is an economically important trait in Brassica oilseed crops. A novel method was developed to isolate Arabidopsis thaliana seeds with altered oil content. Methods and Results In A. thaliana, seed oil content is correlated with seed density, with high‐oil seeds being less dense than wild type and tending to float in solution, and low‐oil seeds being denser and tending to sink. In contrast to previous methods, which used toxic chemicals and density gradient centrifugation, different concentrations of calcium chloride (CaCl2) were employed to separate seeds without the need for centrifugation. The method was validated using known seed oil mutants, and 120,822 T‐DNA mutagenized A. thaliana lines were then screened for novel seed density phenotypes. Conclusions A number of candidate mutants, as well as new alleles of two genes known to influence seed oil biosynthesis, were successfully isolated.
Implantation, orientation and validation of a commercially produced heart-rate logger for use in a perciform teleost fish

Abstract Quantifying how the heart rate of ectothermic organisms responds to environmental conditions (e.g. water temperature) is important information to quantify their sensitivity to environmental change. Heart rate studies have typically been conducted in lab environments where fish are confined. However, commercially available implantable heart rate biologgers provide the opportunity to study free-swimming fish. Our study aimed to determine the applicability of an implantable device, typically used on fusiform-shaped fish (e.g. salmonids), for a perciform fish where morphology and anatomy prevent ventral incisions normally used on fusiform-shaped fish. We found that ventrolateral incisions allowed placement near the heart, but efficacy of the loggers was sensitive to their orientation and the positioning of the electrodes. Electrocardiogram detection, signal strength and subsequent heart rate readings were strongly influenced by logger orientation with a significant effect on the quality and quantity of heart rate recordings. We provide details on the surgical procedures and orientation to guide future heart rate biologger studies on perciform-shaped fish.
les staphylocoques à coagulase négative dans l'écosystème des salaisons

Certaines especes de Staphylocoques a Coagulase Negative (SCN) sont naturellement presentes ou employees comme ferments de salaison. La diversite de cette flore au niveau des ateliers de salaisons reste mal connue en raison notamment de la difficulte a identifier les especes de SCN. Nous avons developpe une PCR specifique pour identifier Staphylococcus xylosus, principale espece presente dans les produits carnes fermentes. Une PCR multiplex ciblant S. xylosus et trois especes de staphylocoques pathogenes opportunistes a ete developpee permettant l'identification de ces especes et du genre Staphylococcus. Ces methodes et des methodes complementaires basees sur la caracterisation des souches par analyse en PFGE apres restriction de l'ADN, par sequencage du gene sodA et par hybridation avec des sondes specifiques ont permis l'etude de la diversite des SCN d'ateliers de salaisons traditionnelles, artisanales ou industrielles. Nous avons pu montrer que, dans un atelier traditionnel n'utilisant aucun ferment, S. equorum et S. succinus ont colonise majoritairement les produits et l'environnement alors que les especes S. xylosus et S. carnosus habituellement utilisees comme ferments sont minoritaires et n'ont pas ete retrouvees au niveau des produits finis. Le suivi de S. carnosus et S. xylosus, utilises comme ferments dans un atelier artisanal et un industriel, a revele qu'ils ne colonisent pas l'environnement et que S. xylosus devient dominant dans les produits. Il pourrait etre interessant de developper de nouveaux ferments appartenant aux especes S. equorum ou S. succinus qui semblent adaptees a l'environnement carne.
Effects of Population Weighting on PM10 Concentration Estimation

Particulate matter with an aerodynamic diameter of 10 μm or less (PM10) pollution poses a considerable threat to human health, and the first step in quantifying health impacts of human exposure to PM10 pollution is exposure assessment. Population-weighted exposure level (PWEL) estimation is one of the methods that provide a more refined exposure assessment as it includes the spatiotemporal distribution of the population into the pollution concentration estimation. This study assessed the population weighting effects on the estimated PM10 concentrations in Malaysia for years 2000, 2008, and 2013. Estimated PM10 annual mean concentrations with a spatial resolution of 5 kilometres retrieved from satellite data and population count obtained from the Gridded Population of the World version 4 (GPWv4) from the Centre for International Earth Science Information Network (CIESIN) were overlaid to generate the PWEL of PM10 for each state. The calculated PWEL of PM10 concentrations were then classified based on the World Health Organization (WHO) and the national Air Quality Guidelines (AQG) and interim targets (IT) for comparison. Results revealed that the annual mean PM10 concentrations in Malaysia ranged from 31 to 73 µg/m3 but became generally lower, ranging from 20 to 72 µg/m3 after population weighting, suggesting that the PM10 population exposure in Malaysia might have been overestimated. PWEL of PM10 distribution showed that the majority of the population lived in areas that complied with the national AQG, but were vulnerable to exposure level 3 according to the WHO AQG and IT, indicating that the population was nevertheless potentially exposed to significant health effects from long-term exposure to PM10 pollution.
Changes in the Rhythm of Speech Difference between People with Nondegenerative Mild Cognitive Impairment and with Preclinical Dementia

This study explores several speech parameters related to mild cognitive impairment, as well as those that might be flagging the presence of an underlying neurodegenerative process. Speech is an excellent biomarker because it is not invasive and, what is more, its analysis is rapid and economical. Our aim has been to ascertain whether the typical speech patterns of people with Alzheimer's disease are also present during the disorder's preclinical stages. To do so, we shall be using a task that involves reading out aloud. This is followed by an analysis of the recordings, looking for the possible parameters differentiating between those older people with MCI and a high probability of developing dementia and those with MCI that will not do so. We found that the disease's most differentiating parameters prior to its onset involve changes in speech duration and an alteration in rhythm rate and intensity. These parameters seem to be related to the first difficulties in lexical access among older people with AD.
Delimitation difficulties in species splits: a morphometric case study on the Euxoa tritici complex (Lepidoptera, Noctuidae)

Abstract. Genital characteristics tend to vary greatly between Lepidoptera species, providing helpful features for species delimitation. The differences between species are usually remarkable and suspicions about species identity never arise. However, fairly often, and possibly increasingly, taxa are elevated to species rank on the basis of very slight morphological differences, often without quantitative support. Euxoa tritici (Linnaeus) is a typical example of a variable species split into several morphologically similar species. The present study tested whether the diagnostic genital characters of the current classification, based on nonquantitative methodology, provide safe identification of species. Both traditional distance morphometrics as well as modern geometric morphometrics, which also enables quantitative shape exploration, were used. Moreover, whether the study specimens can be unambiguously categorized into several species with visual comparisons was tested independently using four specialist entomologists. Genital types of several named species as well as considerable variation in genitalia were found, but no support was found for the presence of several morphologically distinguishable species with quantitative morphometric analyses. Neither were study specimens categorized unambiguously by specialists. The results suggest that pure visual comparisons may lead to unsound taxonomic conclusions and that a quantitative approach in critical cases should be used more frequently.
Nonlinear Distribution of Adiponectin in Patients With Nonalcoholic Fatty Liver Disease Limits Its Use in Linear Regression Analysis

REFERENCES 1. Bell CM, Redelmeier DA. Mortality among patients admitted to hospitals on weekends as compared with weekdays. N Engl J Med. 2001;345:663–668. 2. Shaheen AA, Kaplan GG, Myers RP. Weekend versus weekday admission and mortality from gastrointestinal hemorrhage caused by peptic ulcer disease. Clin Gastroenterol Hepatol. 2009;7:303–310. 3. Ananthakrishnan AN, McGinley EL, Saeian K, et al. Outcomes of weekend admissions for upper gastrointestinal hemorrhage: a nationwide analysis. Clin Gastroenerol Hepatol. 2009;7:296–302. 4. Nahon S, Pariente A, Latrive JP; for a group of investigators of the ANGH (Association Nationale des Gastroentrologues des Hpitaux Gnraux). Weekend admission does not influence the mortality of upper GI bleeding caused by peptic ulcers: results of a French prospective study of the ANGH group. Clin Gastroenterol Hepatol. 2009;7:911. 5. Nahon S, Nouel O, Hagge H, et al; Groupe des Hmorragies Digestives Hautes de l’Association Nationale des Hpatogastroentrologues des hpitaux Gnraux. Favorable prognosis of upper-gastrointestinal bleeding in 1041 older patients: results of a prospective multicenter study. Clin Gastroenterol Hepatol. 2008;6:886–892. 6. Cals P, Masliah C, Bernard B, et al. French Club for the Study of Portal Hypertension. Early administration of vapreotide for variceal bleeding in patients with cirrhosis. N Engl J Med. 2001;344:23–28. 7. Levacher S, Letoumelin P, Pateron D, et al. Early administration of terlipressin plus glyceryl trinitrate to control active upper gastrointestinal bleeding in cirrhotic patients. Lancet. 1995;346:865–868.
Receptor Affect Agonist-Promoted Trafficking

The signaling impact of a human 1-adrenergic receptor ( 1AR) polymorphism at residue 49 of the aminoterminus (Ser-to-Gly substitution) was studied by recombinantly expressing each receptor. The two receptors displayed identical agonist and antagonist binding affinities. Furthermore, basal and agonist-stimulated adenylyl cyclase activities were the same for these receptors as assessed in both cell types. Although short-term agonist exposure resulted in similar degrees of receptor internalization, long-term agonist-promoted downregulation was greater for Gly49 compared with Ser49. The Gly49 receptor underwent a 24 ± 3% loss of receptor density after exposure to isoproterenol for 18 h, whereas Ser49 underwent no such loss. In studies in which receptor synthesis was inhibited, agonist-promoted downregulation for Gly49 was 55 ± 3% compared with 36 ± 5% for Ser49. In the absence of agonist, degradative turnover of each receptor was the same. Immunoblotting revealed that some of the Ser49 receptor exists as a highly N-glycosylated form (≈105-kD molecular mass), which is not present with Gly49. Thus the phenotype of the Gly49 polymorphic receptor is that of wild-type coupling with enhanced agonist-promoted downregulation, which is associated with altered N-glycosylation. Based on this cellular phenotype, the 1AR Gly49 polymorphism may impart a beneficial effect in chronic heart failure.
Overexpression of thermoalkalophilic lipase from Bacillus stearothermophilus L1 in Saccharomyces cerevisiae

An expression vector system was developed for the secretory production of recombinant Bacillus stearothermophiluis L1 lipase in Saccharomyces cerevisiae. The mature L1 lipase gene was fused to α-amylase signal sequence from Aspergillus oryzae for the effective secretion into the culture broth and the expression was controlled under GAL10 (the gene coding UDP-galactose epimerase of S. cerevisiae) promoter. S. cerevisiae harboring the resulting plasmid successfully secreted L1 lipase into the culture broth. To examine an optimum condition for L1 lipase expression in the fed-batch culture, L1 lipase expression was induced at three different growth phases (early, mid, and late-exponential growth phases). Maximum production of L1 lipase (1,254,001) U/1, corresponding to 0.65 /1) was found when the culture was induced at an early growth phase. Secreted recombinant L1 lipase was purified only through CM-Sepharose chromatography, and the purified enzyme showed 1,963 U/mg of specific activity and thermoalkalophilic properties similar to those reported for the enzyme expressed in Escherichia coli.
Characterization and control of laser induced modification inside silicon

Internal modification of silicon is important for wafer stealth dicing. In this paper, the authors report experimental and simulation results of three-dimensional modification inside silicon wafers using laser pulses with 1.55 μm wavelength and 3.5 ns pulse duration. Permanent modification is generated inside silicon by tightly focusing and continuously scanning the laser beam inside samples, without damaging the front and back surface. Cross sections of these modifications are observed after cleaving the samples and are further analyzed after mechanical polishing followed by chemical etching. The shape of the modification is found to depend on the input beam shape, laser power, and scanning speed. With proper conditions, a nearly circular modification is obtained, which has potential application for waveguide writing inside silicon.Internal modification of silicon is important for wafer stealth dicing. In this paper, the authors report experimental and simulation results of three-dimensional modification inside silicon wafers using laser pulses with 1.55 μm wavelength and 3.5 ns pulse duration. Permanent modification is generated inside silicon by tightly focusing and continuously scanning the laser beam inside samples, without damaging the front and back surface. Cross sections of these modifications are observed after cleaving the samples and are further analyzed after mechanical polishing followed by chemical etching. The shape of the modification is found to depend on the input beam shape, laser power, and scanning speed. With proper conditions, a nearly circular modification is obtained, which has potential application for waveguide writing inside silicon.
Assays for Detecting Chromosomal Aberrations

This unit describes the techniques used to investigate chromosome structure to detect changes induced by toxicant exposure. Protocols are included for detecting microcucleus (MN) formation, changes in banding patterns by Giemsa banding or fluorescence in situ hybridization (FISH) using chromosome‐specific probes, and sister chromatid exchange (SCE) in cultures of established cell lines.
The Use of a Modified System Development Life Cycle (MSDLC) in a Sociological Environment to Improve Solution Validation

Title of Dissertation: THE USE OF A MODIFIED SYSTEM DEVELOPMENT LIFE CYCLE (MSDLC) IN A SOCIOLOGICAL ENVIRONMENT TO IMPROVE SOLUTION VALIDATION Shanelle M. Harris, Doctor of Engineering, May 2019 Dissertation Chair: LeeRoy Bronner, Ph.D., P.E. Industrial and Systems Engineering Department This research is investigating the improvements to the current System Development Life Cycle (SDLC). The SDLC has been used since the 1970s with improvements through prototyping and iterations in the system develop phase, however the least expensive phase, system analysis, has not been utilized for improvement. The SDLC lacks the ability to be changing requirements, is not flexible, and lacks user involvement leading to less than complete solutions. With the speed of technology and increase complication of problems facing the world, there is a need to get solutions faster and more accurate. This research will examine the advantages and disadvantages of the SDLC methodologies and provide a validated model and analysis procedure to provide solutions with fewer inaccuracies through an extension of the analysis phase implementing Joint Application Development (JAD) sessions, continuous user involvement, and intermediate artifacts of analysis. The extended analysis phase integrates object–oriented analysis (OOA), Z notation, and Alloy modeling and execution to validate complex solutions. A cardiovascular disease public health case study based in Baltimore City will be used to demonstration the Modified System Development Life Cycle. THE USE OF A MODIFIED SYSTEM DEVELOPMENT LIFE CYCLE (MSDLC) IN A SOCIOLOGICAL ENVIRONMENT TO IMPROVE SOLUTION VALIDATION
Incorporating glucose oxidase activity into amyloid fibrils

vi 1. Chapter One – Introduction . 1 1.1 Context . 1 1.2 Introduction to amyloid fibrils . 2 1.3 Amyloid fibril structure . 5 1.4 Characterisation and purification of amyloid fibrils . 6 1.5 Amyloid fibrils in bionanotechnology . 7 1.6 Bovine insulin amyloid fibrils . 7 1.7 Bovine crystallin amyloid fibrils . 8 1.8 Glucose oxidase . 9 1.9 GOD assay methods . 14 1.10 GOD immobilisation . 14 1.11 Fibril cross-linking . 16 1.12 Poly(vinyl alcohol) film . 17 1.13 Antimicrobial applications . 19 1.14 Conclusion . 21 1.15 Thesis outline . 21 1.16 References . 22 2. Chapter Two – Methods . 29 2.1 General materials and methods . 29 2.2 Amyloid fibril formation . 30 2.2.1 Formation of amyloid fibrils by bovine insulin . 30 2.2.2 Crude crystallin extraction from bovine lenses . 30
RELATIONSHIPS AMONG DIET, GROWTH RATE, AND FOOD AVAILABILITY FOR THE SOUTH AFRICAN ROCK LOBSTER, JASUS LALANDII (DECAPODA, PALINURIDEA)

The diet (prey species composition and gut fullness) of adult male rock lobsters, Jasus lalandii, was determined from eight sites of contrasting growth rate on the West Coast of South Africa. The proportion of rock lobsters with full stomachs did not differ significantly between fast (FG) and slow growth (SG) sites, while gut fullness was slightly higher at the SG than the FG sites. Bray-Curtis similarity and multidimensional scaling plots showed that rock-lobster diets were not distinguishable at all eight sites studied, and that diets at FG and SG sites were not separated, implying that growth rate is independent of diet. The benthic communities at two sites, Dassen Island (FG) and Olifantsbos (SG) were compared using a video camera. Despite vast differences in the benthos, the diets of adult rock lobsters from these two sites of contrasting growth rates were similar. This leads to the conclusion that rock lobsters are highly selective foragers; a conclusion supported by statistical comparisons between diet and food availability. An analysis conducted on immature male rock lobsters (32-51 mm CL) collected from the Cape Town harbour wall (SG) and Mouille Point (FG) yielded the same results. It was concluded that growth rate is not related to diet per se, but rather to the availability of preferred prey in the benthos.