Miracle-dz/UniFAR-FTUs huggingface dataset:
Retrospective study of clinical CT dose trends at St. Vincent’s Hospital and evaluation of the impacts of patient size and tube current modulation with an anthropomorphic phantom

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Global patterns of mobile carbon stores in trees at the high‐elevation tree line

Aim Across all latitudes, high-elevation tree lines represent a drastic change in the dominant plant life-form, from upright trees to low-stature alpine plants. Although associated with low temperatures, the physiological mechanisms controlling this boundary are still not clear. The growth-limitation hypothesis assumes a direct low-temperature restriction of tissue formation at otherwise sufficient photoassimilation. In order to test this hypothesis, we present a global synthesis of previously published and new data on tree carbon supply status at high-elevation tree lines. Location Global; 13 regions between 68° N and 45° S. Methods Late-season concentrations of non-structural carbohydrates (NSC) in foliage and branch wood were measured at three elevations across the tree line ecotones, from upper tall forests (timber line) to the edges of aborescent tree growth (tree line). Year-round records of −10 cm soil temperatures were taken at the tree line. Results Despite large differences in elevation and season length, the mean growing season temperature at the tree line was similar (approximately 6.6 °C) between all sites. NSC concentrations were not depleted at any of the elevation gradients between timber line and tree line, indicating no shortage of C at the uppermost tree stands. Tested across all sites, NSC concentrations in fact significantly increased with elevation. On average, NSC increased by 18% in leaves and 26% in branch wood from the lowest to the highest stands, primarily due to higher starch concentrations rather than free sugars. Hence, these responses do not reflect osmotic adjustments to lower temperatures at the end of the growing season. Main conclusions This global data set contributes to a mechanistic understanding of tree line formation based on biological principles across climatic zones and tree genera. No evidence of C shortage was found at the high-elevation tree line in either seasonal and non-seasonal regions. The increasing trend of NSC concentrations with elevation is in line with the growth-limitation hypothesis.
Resistência natural à estreptomicina e eficiência de estirpes de Rhizobium nativas nos cerrados associadas a Stylosanthes

Foram efetuados isolamentos de Rhizobium sp nativos nos Cerrados, associados a Stylosanthes spp, com o objetivo de estudar a natureza dos fatores que interferem no estabelecimento das estirpes de Rhizobium inoculadas, e de avaliar o potencial de fixacao de N 2 das estirpes nativas. Dentre 122 estirpes isoladas em solo sob Cerrado cultivado, 35% foram resistentes a concentracoes iguais ou superiores a 40 μg/ml, enquanto que apenas 10% dentre 92 estirpes isoladas em solo sob Cerrado virgem apresentaram esse nivel de resistencia. Esses dados sugerem que modificacoes ecologicas promovidas pelo cultivo dos Cerrados podem induzir a vantagens competitivas para estirpes de Rhizobium sp. resistentes a estreptomicina. Experimentos conduzidos em vasos Leonard com areia e solucao nutritiva esterilizada indicaram que cerca de 61% das estirpes isoladas em S . guianensis var. Canescens e S. grandifolia eram pouco ou moderadamente efetivas no hospedeiro homologo, enquanto que apenas 14% das estirpes apresentaram um nivel elevado de fixacao do N 2 . Esse baixo indice de estirpes eficientes sugere a necessidade de se iniciar um trabalho de selecao de Rhizobium sp. adaptado as condicoes dos Cerrados, visando a producao de inoculantes de alta qualidade para a regiao.
The Dutch Head and Neck Audit: The First Steps

Objective: The treatment of Head and Neck Cancer (HNC) is an example of low volume, highly complex, multidisciplinary integrated care. To monitor and effectively improve high quality integrated care, the Dutch Head and Neck Audit (DHNA) was set up in 2014 (with quality indicators as a basis) to monitor, benchmark and find areas for improvement. This paper gives an overview of the development, first results, and implications. Methods: Quality Indicators (QIs) were developed from three perspectives: Medical specialists, allied health professionals and patients. Data were collected in an online registration system. Results: Setting up a multidisciplinary quality registration is challenging and time-consuming. Involvement of all health professionals and development of good QIs is crucial. Efforts should be made on national level to solve privacy and juridical restrictions for quality registrations. It is crucial to decrease registration burden, for example with an IT-reliable automatic subtraction system. Although the registration was recently launched, it already visualizes hospital variation in current care. More data are needed to better define case-mix, obtain more insight into long-term Patient Reported Outcomes (PROs) and Patients' Experiences (PREs), and to define the relation between PROs and PREs and patient outcomes such as survival. Conclusion: The development of a multidisciplinary quality registration from different perspectives is feasible. Obtained experiences in this project can be used to set up other oncological quality registrations. In the upcoming years, more data has to be obtained, enabling more reliable feedback to improve quality of health care for patients with HNC in the Netherlands.
Transcriptome responses in herbivorous insects towards host plant and toxin feeding

Food source is a major determinant of physiological performance and a strong selection force for insect herbivores. The ability to adequately respond to chemical challenges posed by their host plants is the primary determinant of larval fitness. Most herbivorous insects must consume large quantities of plant material to meet their nutritional requirements and, at the same time, cope with numerous mechanical, chemical and protein-based defences posed by their sessile hosts. Despite the importance of host plants on essential life history traits of insect herbivores, data on global responses to both individual plant-derived compounds and plant feeding is scarce. Here we discuss the existing data on herbivore responses to host plant exposure, toxin feeding or nutrient limitations, and we make an attempt at identifying changes in genome-wide expression patterns of generalist and/or specialist herbivores. While generalists face an array of different plant defences, and therefore likely need to invest in broad detoxifying strategies, specialist herbivores need to fine-tune their adaptation to specific plant defences.
Prebiotic Isomalto-oligosaccharide Production from Thai Rice

This study aimed to evaluate the potential usage of Thai rice for the production of prebiotic isomalto-oligosaccharides through fungal fermentation. Solid-state fermentations (SSF) of two rice varieties, waxy rice RD6 and non-waxy rice KDM 105 with Aspergillus oryzae TISTR 3108 were compared. The effects of the main parameters such as incubation time, temperature, pH, fungal spore inoculum size and moisture content were also studied individually to maximise the isomalto-oligosaccharides yield. Results showed that the maximum values of amylolytic activity and total reducing sugar were observed when using rice in SSF with initial moisture content of 70% and inoculated with the inoculum size of 10 spores/g. The optimal conditions of SSF were performed at initial pH 6 and 30°C for 5 days. SSF of waxy rice RD6 with Aspergillus oryzae produced highest concentrations of isomalto-oligosaccharides which consisted of isomaltose, panose and isomaltotriose. After fermentation, mashing was used to further hydrolyse the remaining starch in rice slurry. The subsequent rice syrup contained higher amounts of isomaltose, panose and isomaltotriose with the values of 44, 10 and 7 g/l respectively.
Physiological profiling of microbial communities.

While novel methods to discover new types and characterize microbial diversity are valuable, alternative approaches for describing microbial communities in ecologically relevant terms are needed to provide insight into the spatial and temporal patterns in both natural and man-made ecosystems. This chapter concludes with a synthesis of the various community-level physiological profiling (CLPP) approaches, including comparison of their relative strengths and weaknesses, discussion of appropriate applications, and definition of future areas of research. The CLPP assay is a sensitive, simple, rapid, and relatively inexpensive means of discriminating among microbial communities in environmental samples. A number of factors (high substrate concentrations, indirect evaluation of respiration via the redox chemistry, and presence of unknown proprietary ingredients) limit the ability of the Biolog CLPP to examine functionally relevant shifts in microbial communities. Alternative techniques developed to improve functional relevance involve direct measurement of respiration, either based on substrate consumption (O2) or product appearance (CO2), eliminating bias in the Biolog assay as a result of cells that cannot take up or are inhibited by the redox dye. While further incorporation of new technologies to continually improve CLPP is encouraged, the existing techniques represent valuable tools for evaluating factors affecting the metabolic state of heterotrophic microbial communities.
Computational modeling and simulation of cellular growth and migration in angiogenesis

Cancer is one of the leading causes of death in today’s society, with an approximated diagnosis rate of 14 million cases per year, contributing to an estimate of 13% of all deaths world wide. Whereas surgery and treatment, in many cases, can provide cure from well confined, primary tumors, over 90% of patients who succumb to cancer die because of cancer metastasis. Tumor induced angiogenesis, the outgrowth of a tumor-associated vasculature, constitutes a key enabling factor in the cancers route towards metastasis. Recent advances in the field of molecular biology have lead to the identification of key mechanisms involved in the regulation of angiogenesis, paving the way for integrative studies in mathematical models and computer simulations. The study of cancer in an in silico environment allows to address the underlying bio-mechanical principles at a granularity not accessible in experimental models and promises to provide a systematic approach for the identification of organizing principles regulating this complex disease. In this thesis, we propose mathematical models and numerical methods for the simulation of angiogenesis and cell migration pertinent to cancer progression and metastasis. The models are employed to study the influence of the tumor microenvironment on sprouting angiogenesis and shed light on the role played by the structure of the extracellular matrix and its affinity to molecular growth factors and adhesion signals that orchestrate cell migration and proliferation during vascular growth. The modeling work is supported by experimental investigations that provide the basis for parameter estimation and model validation. The exploration of experimental systems in biology hinges on the availability of image analysis methods that can provide a quantitative description of the investigated phenomena. In this thesis, we develop image analysis methods and metrics for the quantification of vascular networks and cell migration investigated in in vitro wound healing assays. The methods are employed to establish a quantitative database describing vertical sprouting progression and maturation of developmental angiogenesis in the retina of the mouse and cell migration on topographic substrates. The algorithms are integrated into distributable software packages made accessible to a broad range of researchers in the fields of experimental and computational biology.
The value of species distribution models as a tool for conservation and ecology in Egypt and Britain

Knowledge about the distribution of species is limited, with extensive gaps in our knowledge, particularly in tropical areas and in arid environments. Species distribution models offer a potentially very powerful tool for filling these gaps in our knowledge. They relate a set of recorded occurrences of a species to environmental variables thought to be important in determining the distributions of species, in order to predict where species will be found throughout an area of interest. In this thesis, I explore the development, potential applications and possible limitations of distribution models using species from various taxonomic groups in two regions of the world: butterflies, mammals, reptiles and amphibians in Egypt, and butterflies, hoverflies and birds in Great Britain. Specifically I test: 1) which modelling methods produce the best models; 2) which variables correlate best with the distributions of species, and in particular whether interactions among species can explain observed distributions; 3) whether the distributions of some species correlate better with environmental variables than others and whether this variation can be explained by ecological characteristics of the species; 4) whether the same environmental variables that explain species’ occurrence can also explain species richness, and whether distribution models can be combined to produce an accurate model of species richness; 5) whether the apparent accuracy of distribution models is supported by ground-truthing; and 6) whether the models can predict the impact of climate change on the distribution of species. Overall the use of distribution models is supported; my models for species in both Egypt and Britain explained observed occurrence very well. My results shed some light on factors that may be important in determining the distributions of species, particularly on the importance of interactions among species. As they currently stand, distribution models appear unable to predict accurately the impacts of climate change.
Crown gall of stone fruit. II. Identification and nomenclature of Agrobacterium isolates.

Twenty-seven local isolates of Agrobacterium and twenty-three isolates supplied by other laboratories were compared by biochemical tests, serology, protein patterns following gel electrophoresis, and by pathogenicity. All isolates fell into two distinct biotypes and this was supported by their serological reactions and by their protein patterns. Biotype 1 contained tumour-inducing, root-proliferating, and non-pathogenic forms; biotype 2 contained both these pathogenic forms but no non-pathogens. We believe the present division of the genus into species based on pathogenicity is untenable. If the genus is to be retained, we propose that it should consist of one species, A. radiobacter, with pathogenicity indicated by a varietal epithet and the biotype specified.
Plasticity, its cost, and phenotypic selection under water and nutrient stress in two annual grasses

A comparative approach can prove to be a useful tool for studying phenotypic plasticity, if applied to specific traits involved in adaptation to particular environment in more than one species across co-located populations. The present study tested whether two annual grasses, Hordeum spontaneum and Avena sterilis, belonging to the same guild, having similar stature, seed dispersal mechanism, breeding system, and genetic variation, and sampled in exactly the same environmentally specific locations, differed with respect to: (1) plasticity in traits involved in adaptation, namely the onset of reproduction and maternal investment involving the number of inflorescences, spikelets per inflorescence, the weight of individual spikelets, and abortion rate; (2) the cost of this plasticity, and (3) the pattern of phenotypic selection on the above traits. The two species exhibited highly differing amounts of phenotypic plasticity in the onset of flowering and several reproductive traits (number of inflorescences, spikelets per inflorescence, abortion rate), but no plasticity costs in any experimental environment. The two species demonstrated a decreasing similarity in the regulation of reproduction in four experimental environments: benign, water, nutrients and water × nutrient deficient. Correlational selection appears to contribute, although not solely, to the observed species differences with respect to the regulation of reproduction. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 581–593.
Enhancing sugarcane (Saccharum hybrid complex) productivity through modified trench method of planting in sub-tropical India

A field experiment was conducted during autumn seasons of 2007–09 and 2008–10 to study the effect of modified trench method of sugarcane planting at 120 cm apart placing setts across the furrow and covering them with 2.5 cm of soil layer, followed by light irrigation (T5) over other planting methods, viz. conventional furrow planting at 90 cm apart (T1), deep furrow (20 cm) planting at 90 cm apart covering setts with 2.5 cm of soil layer (T2), paired row furrow planting at 120 : 60:120 cm (T3), paired row deep furrow (20 cm) planting at 120: 60:120 cm covering setts with 2.5 cm of soil layer (T4) on the growth, yield and quality of sugarcane (Saccharum hybrid complex) under sub-tropical climatic conditions. Experimental results revealed that T5 planting method produced significantly higher cane yields of 118.7 and 121.7 tonnes/ ha compared with other planting methods during both the years of experimentation. The cane yield thus obtained under T5 was 18.72, 23.87, 21.22 and 27.01% higher than that of T4, T3, T2 and T1 treatments, respectively. Increase in sugar yield exhibited almost similar trend as the yield of cane under different treatments, and accordingly the T5 treatment produced significantly higher sugar yield (14.18 tonnes/ha) than that obtained under rest of the treatments ranging from 10.85 to 11.70 tonnes/ha in the study. Economics of different treatments clearly indicated that by virtue of higher cane yield, the T5 treatment exhibited a net returns and B:C ratio of ` 154 436/ha and 2.23 which were higher to the tune of 18.63 and 10.86, 20.17 and 3.59, 21.20 and 13.00 and 22.73 and 5.83% under T4, T3, T2 and T1 treatments, respectively. Conclusively, since the modified trench method of planting (T5) offers benefit in terms of producing higher yields of cane and sugar over other conventional methods of planting and that would be worth adopting by farmers for increased sugarcane productivity in sub-tropical India.
Phylogenetic Relationships Among Advanced Snakes: A Molecular Perspective

This monograph addresses questions concerning the evolutionary history of advanced snakes using molecular phylogenetic data. Viperids are the sister group of the other clades examined. "Atractaspis" may share a lineage with elapids. The study concludes that, because of sampling problems, many generalizations concerning snake evolution derived from the fossil record, particularly those about the age of lineages, are probably in error.
Aktivitas Antioksidan Jus Ubi Jalar Kultivar Lokal sebagai Penangkal Radikal Bebas 1,1-diphenyl-2-picrylhydrazyl (DPPH)

Sweet potatoes (Ipomoea batatas) are tuber that have high antioxidant activity. The determination of antioxidant activity based on as percentage of inhibition of free radical DPPH. The purpose of this research was to observe the activity of three local cultivars of sweet potatoes by using DPPH method and by using vitamine C as compparison. The measurement of antioxidant activity which performed on sweet potatoes juice and vitamine C with concentration 625 ppm, 1250 ppm, 2500 ppm, 5000 ppm and 10000 ppm by using free radical of DPPH 0,004% that was soluble in ethanol pa and then was measure by using spectrofotometer. Data were analyzed by using ANOVA and LSD (a = 0.05). The result of this research showed that the three cultivar of sweet potatoes juice have antioxidant activity and the purple sweet potatoes cultivar Biru Mangsi had the highest antioxidant activity, although lower than vitamine C. The highest of antioxidant activity were vitamine C, followed by purple sweet potatoe, yellow sweet potatoes (cultivar Kuning Madu) and white sweet potatoes (cultivar Kapasan).
The Tannase Gene: Metaphylogenomics, Global Distribution and Presence in the Midgut Flora of the Forest Tent Caterpillar Malacosoma disstria Hübner

Tannase enzymes hydrolyze tannins, a class of plant polyphenolics that defend against herbivory. Prior to the 1980’s, most studies were focused on the tannase gene in fungi owing to the interest surrounding their industrial value. Since then a large number of bacterial tannase genes have also been discovered. I performed phylogenetic analysis on 110 fungal and bacterial tannase reference sequences in an effort to observe the relationships between fungal and bacterial tannase. The generated maximum likelihood tree shows eight strongly supported tannase clades, with a rift among fungal tannases, which either align with proteobacterial tannase or actinobacterial tannase. Metagenomes were used to assess the biogeographical distribution of the tannase clades, revealing that they may have environmental specificity. An unpublished observation made by the Despland lab of Concordia University suggested that forest tent caterpillars (Malacosoma disstria) from western Canada are unable to survive on tannin-rich sugar maple foliage (Acer saccharum), whereas populations in eastern Canada develop on sugar maple. In Chapter 2 I examine this observation, and explore the possibility of tannase-expressing secondary symbionts in eastern M. disstria. For the first time, the microbiome of M. disstria has been described using 16S rRNA gene sequencing and is shown to contain several genera known for expressing the tannase gene.