Miracle-dz/UniFAR-FTUs huggingface dataset:
A Case Study of the Application of a Multilevel Growth Curve Model and the Prediction of Health Trajectories

This case study provides guidance on the application of a multilevel growth curve model and the prediction of health trajectories. Using our secondary data analysis as an example, we introduce definitions of the multilevel growth curve model, random intercept and slope, and the intraclass correlation coefficient. We discuss time centering and time metrics, marginal effects for drawing frailty trajectories, as well as multiple imputation for handling missing values.
Time-Varying Network Vector Autoregression Model

In this paper, we study the time-varying network vector auto-regressive model (TV-NVAR) with the networking effect. Constituting an ultra-high dimensional vector, nodes are assumed to be a linear combination of (a) their previous values, (b) their neighbours' previous values, (c) exogenous variables, and (d) independent noises. We adopt non-parametric methods to obtain time-varying and profile estimations, and present Monte Carlo simulations to validate these estimations. Moreover, we utilize our model to study the inter-city spillover effect on the productivity of 185 Chinese cities over years between 1995 and 2009.
Proving and Disproving Information Inequalities: Theory and Scalable Algorithms

Proving or disproving an information inequality is a crucial step in establishing the converse results in coding theorems. However, an information inequality involving more than a few random variables is difficult to be proved or disproved manually. In 1997, Yeung developed a framework that uses linear programming for verifying linear information inequalities. Under the framework, this paper considers a few other problems that can be solved by using Lagrange duality and convex approximation. We will demonstrate how linear programming can be used to find an analytic proof of an information inequality or an analytic counterexample to disprove it if the inequality is not true in general. The way to automatically find a shortest proof or a smallest counterexample is explored. When a given information inequality cannot be proved, the sufficient conditions for a counterexample to disprove the information inequality are found by linear programming. Lastly, we propose a scalable algorithmic framework based on the alternating direction method of multipliers to accelerate solving a multitude of user-specific problems whose overall computational cost can be amortized with the number of users, and present its publicly-available software implementation for large-scale problems.
Zinc as promoter of growth and biochemical activity in basil cultivars under in vitro conditions

In vitro cultivation of basil allows the manipulation of the concentration of certain micronutrients, commonly neglected by the micropropagation protocols. It is a plant of great economic importance for the cosmetic and pharmaceutical industry, due to the components present in its essential oil. In view of the above, the objective of this study was to evaluate zinc (Zn) concentrations in the micropropagation of basil, in addition to antioxidant activity and total phenolic compounds. Basil seeds, cultivars Manolo and Grecco Palla were oxygenated for 4 h, passed through asepsis and placed in test tubes with MS medium supplemented with 30 g L -1 sucrose and 6.5 g L -1 agar and pH adjusted to 5.8. The treatments were composed by the addition or not of 25 μM of zinc sulfate (ZnSO4) and arranged in a completely randomized design. The tubes containing the seeds and the culture medium were kept in a growth chamber for 90 days. The cultivar Manolo was more sensitive to the addition of ZnSO4 due to the increase in the number of leaves and in the antioxidant activity, however, the addition of this component in the culture medium did not influence the production of phenolic compounds or the activity of the antioxidant enzymes SOD, CAT and APX.
Cereal beta-amylases

Cereal beta-amylases are perhaps best known in terms of the vital role they play in releasing easily fermentable sugars from cereal grain starch to fuel the production of alcohol by yeast in brewing. The extent to which they have been investigated is indeed largely due to their significance in this economically important industry. However, cereal beta-amylases are also, or could be, employed in many other aspects of the food industry and the analysis of starch, and they constitute valuable markers in cereal assessment and breeding studies. Quite apart from their practical significance, they are rewarding objects of biochemical and physiological research. They are interesting models for the study of enzyme polymorphism, post-translational modification and the differential expression of isoenzymes. In spite of their often high activities in situ and all that is known about their generation, they are an enigma in that their physiological function, or even necessity, remains unclear. It has been recently recognised that there are two different categories of cereal beta-amylases which exhibit different tissue and taxonomic specificities and physiological developmental patterns. The classical' beta-amylases present at high activities in cereal seeds appear to be limited to the endosperm of the species of the Triticeae tribe of the Festucoideae subfamily of the Gramineae (wheat, barlcy and rye), whereas all cereals exhibit a different, tissue-ubiquitous' form of the enzyme which is present at much lower activity levels. The physiological phenomenology and the usage of cereal beta-amylases are discussed in relation to these two categories of enzyme.
Rising methane emissions from boreal lakes due to increasing ice-free days

Lakes account for about 10% of the boreal landscape and are responsible for approximately 30% of biogenic methane emissions that have been found to increase under changing climate. However, the quantification of this climate-sensitive methane source is fraught with large uncertainty under warming climate conditions. Only a few studies have addressed the mechanism of climate impact on the increase of northern lake methane emissions. This study uses a large observational dataset of lake methane concentrations in Finland to constrain methane emissions with an extant process-based lake biogeochemical model. We found that the total current diffusive emission from Finnish lakes is 0.12 ± 0.03 Tg CH4 yr−1 and will increase by 26%–59% by the end of this century depending on different warming scenarios. We discover that while warming lake water and sediment temperature plays an important role, the climate impact on ice-on periods is a key indicator of future emissions. We conclude that these boreal lakes remain a significant methane source under the warming climate within this century.
Pengaturan Kecepatan Motor Brushless DC(Direct Current) Menggunakan Cuk Converter

Keuntungan seperti efisiensi tinggi, rasio inersia/torsi tinggi, jangkauan pengaturan kecepatan yang besar dan rendahnya electro magnetic interference (EMI) menjadi alasan motor brushless Direct Current (BLDC) menjadi pilihan yang tepat dalam banyak aplikasi di kehidupan sehari-hari. Motor BLDC terdiri dari belitan 3 fasa pada stator dan magnet permanen pada rotornya. Dalam operasi BLDC memerlukan gelombang untuk bekerja, maka penggunaan inverter diperlukan. Inverter juga digunakan untuk tujuan kontrol kecepatan dikontrol kecepatan BLDC konvensional. Pada makalah ini dilakukan penelitian mengenai pengaruh penggunaan cuk converter untuk mengatur kecepatan pada motor BLDC. Cuk converter sendiri memiliki sifat tegangan keluaran yang dihasilkan dapat diatur menjadi lebih tinggi atau lebih rendah dari tegangan masukan, Cuk converter dipilih karena dapat dioperasikan dalam berbagai jangkauan kontrol kecepatan. Kata Kunci— Kontrol Kecepatan, Motor Brushless DC (BLDC), Cuk Converter
Development of an endogenous androgen receptor-mediated luciferase expression assay (AR-LUX) for interactive androgenic action

The research described in this thesis was aimed at developing an in vitro cell-based reporter gene system applicable to the detection of the illegal use of androgenic growth promoters in cattle, and the presence of potential endocrine disrupters present in surface waters and interfering with androgenic action. The system is based on a luciferase reporter gene placed under transcriptional control of an authenticated androgen-responsive element (ARE) and an endogenously expressed androgen receptor. This system allows for the integration of the effects of certain modulators of androgenic signal transduction. A second important goal of the research was to gain insight into the mechanisms underlying enhanced growth promotion by mixtures of androgenic and estrogenic compounds. The use of such mixtures, which results in activation and subsequent interaction of multiple steroid receptors, is occasionally observed in illegal hormonal treatments of cattle. When applied to the screening of calf urine samples for anabolic androgens, the developed AR-LUX assay was able to identify androgen-treated animals with similar results as obtained by standard GC-MS analysis. However, both techniques should be regarded as complementary rather than interchangeable screening tools. Liquid samples confiscated at cattle farms outside the Netherlands were found to generate a very strong response in the AR-LUX assay despite the fact that GC-MS analysis did not detect the presence of any anabolic compounds. Possibly, the samples contained a mixture of conventional androgenic compounds, each at undetectably low amounts and/or (novel) unknown compounds not tested for by GC-MS. These results emphasize the additional value of the developed AR-LUX assay. Also, the AR-LUX assay was used to determine the androgenic activity of a number of aquatic environmental samples. A number of these samples were found to contain androgenic activity at varying concentrations. Interestingly, in 2 samples containing androgens, enhancing interactive mixture effects were observed, which were probably due to interactions by estrogenic compounds and estrogen receptor activation. Our research furthermore indicates that certain established progestagens are able to activate ARE-mediated luciferase expression via progesterone receptors; we hypothesise preferentially through the progesterone receptor-α isoform. This indicates that androgen reporter assays based on the activation of the androgen receptor alone rather than on activation of a response element might produce results quite different from those observed in assay systems featuring multiple steroid receptors. This further emphasizes the notion that the AR-LUX assay is not merely detecting activation of the androgen receptor by androgens, but also allows for the detection of other androgenic substances that regulate gene expression via alternative pathways leading to activation of an established androgen response element.
A Fast, Non-invasive Method of Measuring Growth in Tadpoles Using Image Analysis

Measuring the performance of anuran tadpoles under a varietyof conditions is a common research theme in herpetology. Thereare a number of variations in how performance is measured in-cluding assessing tadpole survival (e.g., Brown et al. 2006; Loman2004) or time to metamorphosis (e.g., Holbrook and Petranka2004). The most often-used variable is the growth rate of tadpoles,measured either as the size of the animals at the end of the experi-ment (e.g., Pahkala et al. 2003) or by subtracting initial mass fromfinal (e.g., Relyea 2004; Relyea and Hoverman 2003; Rosenbergand Pierce 1995). Rarely though, do researchers measure tadpolemass at multiple times throughout the duration of the experiment,likely due to the time required to perform the measurements or thestress induced upon the tadpoles. Indeed, to do this tadpoles mustbe weighed by removing them from water and blotting them dry,which if not done quickly, can result in mortality.In this paper, we describe a novel measure for assessing anurantadpole growth that is simple, inexpensive, requires minimal re-moval from water, and is nearly directly correlated with tadpolemass. This measure is therefore useful for obtaining repeated mea-sures throughout experiments without harming individuals. Fur-thermore, this measure allows for bulk assessments of growth onmultiple tadpoles at once if time is limited, or if large numbers ofindividuals are involved.Our method involves the use of image analysis, whereby digitalphotographs of specimens are taken and computer software usedto measure features of the specimens (Davis et al. 2004; Davis etal. 2007; Davis and Grayson 2007; Davis and Maerz 2007). Varia-tions of this technique are already frequently employed by herpe-tological researchers interested in tadpole shape (Relyea 2004,2005; Relyea and Hoverman 2003; Van Buskirk 2002; Wilson etal. 2005), though to our knowledge, this technique has not beenused to assess growth rates or directly compared to other mea-sured of size. We therefore set out here to determine if this tech-nique could be used to assess tadpole size and if this measure ofsize was related to traditional mass measurements. There weretwo components to this research. First, we examined a set of lab-reared tadpoles that varied in size, using traditional (tadpole mass)and the image analysis size measures. Second, we employed thistechnique to measure tadpoles that were being raised in an ongo-ing, unrelated experiment to evaluate its utility in the field.For our first component, we obtained egg masses of
Development and validation of the DIabetes Severity SCOre (DISSCO) in 139 626 individuals with type 2 diabetes: a retrospective cohort study

Objective Clinically applicable diabetes severity measures are lacking, with no previous studies comparing their predictive value with glycated hemoglobin (HbA1c). We developed and validated a type 2 diabetes severity score (the DIabetes Severity SCOre, DISSCO) and evaluated its association with risks of hospitalization and mortality, assessing its additional risk information to sociodemographic factors and HbA1c. Research design and methods We used UK primary and secondary care data for 139 626 individuals with type 2 diabetes between 2007 and 2017, aged ≥35 years, and registered in general practices in England. The study cohort was randomly divided into a training cohort (n=111 748, 80%) to develop the severity tool and a validation cohort (n=27 878). We developed baseline and longitudinal severity scores using 34 diabetes-related domains. Cox regression models (adjusted for age, gender, ethnicity, deprivation, and HbA1c) were used for primary (all-cause mortality) and secondary (hospitalization due to any cause, diabetes, hypoglycemia, or cardiovascular disease or procedures) outcomes. Likelihood ratio (LR) tests were fitted to assess the significance of adding DISSCO to the sociodemographics and HbA1c models. Results A total of 139 626 patients registered in 400 general practices, aged 63±12 years were included, 45% of whom were women, 83% were White, and 18% were from deprived areas. The mean baseline severity score was 1.3±2.0. Overall, 27 362 (20%) people died and 99 951 (72%) had ≥1 hospitalization. In the training cohort, a one-unit increase in baseline DISSCO was associated with higher hazard of mortality (HR: 1.14, 95% CI 1.13 to 1.15, area under the receiver operating characteristics curve (AUROC)=0.76) and cardiovascular hospitalization (HR: 1.45, 95% CI 1.43 to 1.46, AUROC=0.73). The LR tests showed that adding DISSCO to sociodemographic variables significantly improved the predictive value of survival models, outperforming the added value of HbA1c for all outcomes. Findings were consistent in the validation cohort. Conclusions Higher levels of DISSCO are associated with higher risks for hospital admissions and mortality. The new severity score had higher predictive value than the proxy used in clinical practice, HbA1c. This reproducible algorithm can help practitioners stratify clinical care of patients with type 2 diabetes.
Multispectral Fusion of RGB and NIR Images Using Weighted Least Squares and Alternating Guidance

In low light condition, color (RGB) images captured by camera contain much noise and loss of details and color. However, near infrared (NIR) images are robust to noise and have clear textures without color. In this paper, we propose multi-spectral fusion of RGB and NIR images using weighted least squares (WLS) and alternating guidance. Low light RGB images provide coarse image structure and color, while NIR images offer clear textures in a short distance. Since they are complementary, we adopt alternating guidance for fusion of RGB and NIR images based on WLS. First, we perform the first guidance for denoising on noisy RGB image to get base layer. Then, we conduct the second guidance for texture transfer on NIR image to get detail layer. Finally, we combine base and detail layers to produce a fusion result. We maximize the advantage of multispectral input (RGB and NIR) for fusion based on alternating guidance. Experimental results demonstrate that the proposed method achieves good performance in noise reduction, detail preservation and color reproduction as well as outperforms state-of-the-art ones in terms of quantitative measurement and computational efficiency.
Contribution of Horizontal Gene Transfer to Virulence and Antibiotic Resistance to Pathogens Transmitted in Healthcare Facilities

Pathogenicity islands (PAIs) are a specific group of genomic islands that contribute to genomic variability and virulence of bacterial pathogens. Using a strainspecific comparative genomic hybridization array, we report the identification of a 94kb PAI, designated ICEPm1, common to Proteus mirabilis, Providencia stuartii and Morganella morganii. These organisms are highly prevalent etiologic agents of catheter-associated urinary tract infections (caUTI), the most common hospital acquired infection. ICEPm1 carries virulence factors that are important for colonization of the urinary tract, including a known toxin (Proteus toxic agglutinin) and the High Pathogenicity Island (HPI) of Yersinia spp. Additionally, this PAI shares homology and gene organization similar to PAIs of other bacterial pathogens, several of which have been classified as mobile integrative and conjugative elements. Isolates from this study were cultured from patients with caUTI and show identical sequence similarity at three loci within ICEPm1 suggesting its transfer between bacterial genera. Screening for the 1 This study has been published with the following citation: Flannery EL, Mody L, Mobley HL. Identification of a Modular Pathogenicity Island that is Widespread among Urease-producing Uropathogens and Shares Features with a Diverse Group of Mobile Elements. Infection and Immunity. 2009 Nov; 77(11):4887-94. 35 presence of ICEPm1 among P. mirabilis colonizing isolates showed that ICEPm1 is more prevalent in urine isolates compared to P. mirabilis strains isolated from other body sites (p<.0001) further suggesting it contributes to niche specificity and is positively selected for in the urinary tract.
Phytotoxity of Fusarium subglutinans culture filtrates on in vitro plantlets and calli of resistant and susceptible pineapple (Ananas comosus)

Various concentrations of culture filtrates from Fusarium subglutinans were tested for their effect on in vitro multiplication of plantlets and regeneration from calli of pineapple. The cultivars tested were the resistant Perolera and Spring and the susceptible Perola and Smooth Cayenne. The culture filtrate reduced shoot formation of in vitro plantlets and regeneration of plants from calli derived from the susceptible cultivars but plantlets and calli from resistant plants showed resistance. These results show the potential for culture filtrates of F. subglutinans to provide a method of in vitro screening of pineapple for resistance to the pathogen.
Impact of photo manipulation and visual literacy on consumers’ responses to persuasive communication

Abstract As digital manipulation capabilities in image-based advertising become more ubiquitous, this project investigated whether knowledge of photo manipulation techniques might alter the way audiences perceive photography-based appeals. Using an experimental design with images manipulated to communicate product effectiveness (e.g. fuller hair, longer lashes and smoother skin), we found photo manipulation is a persuasive advertising technique to positively influence consumer choices and attitudes towards brands, regardless of higher societal knowledge that digital images are easily manipulated. These findings call into question the efficacy of visual literacy skills as a defence against visual manipulation.
Foundations in Microbiology: Basic Principles.

1 The Main Themes of Microbiology 2 The Chemistry of Biology 3 Tools of the Laboratory: The Methods for Studying Microorganisms 4 A Survey of Prokaryotic Cells and Microorganisms 5 A Survey of Eukaryotic Cells and Microorganisms 6 An Introduction to Viruses 7 Elements of Microbial Nutrition, Ecology, and Growth 8 An Introduction to Microbial Metabolism: The Chemical Crossroads of Life 9 Microbial Genetics 10 Genetic Engineering: A Revolution in Molecular Biology 11 Physical and Chemical Agents for Microbial Control 12 Drugs, Microbes, Host--The Elements of Chemotherapy 13 Microbe-Human Interactions: Infection and Disease 14 Nonspecific Host Defenses 15 Adaptive, Specific Immunity and Immunization 16 Disorders in Immunity 17 Diagnosing Infections APPENDIX A APPENDIX B APPENDIX C APPENDIX D APPENDIX E
Nuclear EGFR modulation of DNA repair

Overexpression of the epidermal growth factor receptor (EGFR) is associated with resistance to chemotherapy and radiotherapy. EGFR involvement, in repair of radiation-induced DNA damage, is mediated by association with the catalytic subunit of DNA protein kinase (DNAPKcs). This study investigated the role of EGFR nuclear import, and its association with DNAPKcs, on DNA repair following treatment either with cisplatin or ionizing radiation (IR). EGFR- null murine NIH3T3 cells were transfected with wild type or with mutated EGFR (mutations found in human cancers L858R, EGFRvIII and mutations in the EGFR nuclear localization signal (NLS) sequence NLS123, LNLS123). Comet assay analysis, which measures unhooking of cisplatin crosslinks and repair of IR induced strand breaks, demonstrated that wtEGFR and EGFRvIII completely repair cisplatin and IR induced DNA damage. Immunoprecipitation studies show that repair is associated with the binding of both wtEGFR and EGFRvIII to DNAPKcs, which increases by 2- fold 18 hours following cisplatin treatment. Confocal analysis and proximity ligation assay indicated that this association takes place both in the cytoplasm and in the nucleus resulting in a significant increase of DNA-PK kinase activity. Intermediate levels of repair as shown by the L858R construct with impaired nuclear localization demonstrated that EGFR kinase activity is partially involved in repair but is not sufficient to determine EGFR nuclear expression. EGFR-NLS mutants showed impaired nuclear localization and impaired DNAPKcs association resulting in significant inhibition of DNA repair and downregulation of DNA-PK kinase activity. Our data suggest that EGFR nuclear localization is required for the modulation of cisplatin and IR induced DNA damage repair. The EGFR-DNAPKcs binding is triggered by cisplatin or IR and not by EGFR nuclear translocation per se. Understanding mechanisms regulating EGFR subcellular distribution in relation to DNA repair kinetics will be a critical determinant of improved molecular targeting and response to therapy.