Miracle-dz/UniFAR-FTUs huggingface dataset:
Proteins, anatomy and networks of the fruit fly brain

Our understanding of the complexity of the brain is limited by the data we can collect and analyze. Because of experimental limitations and a desire for greater detail, most investigations focus on just one aspect of the brain. For example, brain function can be studied at many levels of abstraction including, but not limited to, gene expression, protein interactions, anatomical regions, neuronal connectivity, synaptic plasticity, and the electrical activity of neurons. By focusing on each of these levels, neuroscience has built up a detailed picture of how the brain works, but each level is understood mostly in isolation from the others. It is likely that interaction between all these levels is just as important. Therefore, a key hypothesis is that functional units spanning multiple levels of biological organization exist in the brain. This project attempted to combine neuronal circuitry analysis with functional proteomics and anatomical regions of the brain to explore this hypothesis, and took an evolutionary view of the results obtained. During the process we had to solve a number of technical challenges as the tools to undertake this type of research did not exist. Two informatics challenges for this research were to develop ways to analyze neurobiological data, such as brain protein expression patterns, to extract useful information, and how to share and present this data in a way that is fast and easy for anyone to access. This project contributes towards a more wholistic understanding of the fruit fly brain in three ways. Firstly, a screen was conducted to record the expression of proteins in the brain of the fruit fly, Drosophila melanogaster. Protein expression patterns in the fruit fly brain were recorded from 535 protein trap lines using confocal microscopy. A total of 884 3D images were annotated and made available on an easy to use website database, BrainTrap, available at fruitfly.inf. ed.ac. uk/braintrap. The website allows 3D images of the protein expression to be viewed interactively in the web browser, and an ontology-based search tool allows users to search for protein expression patterns in specific areas of interest. Different expression patterns mapped to a common template can be viewed simultaneously in multiple colours. This data bridges the gap between anatomical and biomolecular levels of understanding. Secondly, protein trap expression patterns were used to investigate the properties of the fruit fly brain. Thousands of protein-protein interactions have been recorded by methods such as yeast two-hybrid, however many of these protein pairs do not express in the same regions of the fruit fly brain. Using 535 protein expression patterns it was possible to rule out 149 protein-protein interactions. Also, protein expression patterns registered against a common template brain were used to produce new anatomical
Vertical Stratification Responses of an Arboreal Dung Beetle Species to Tropical Forest Fragmentation in Malaysia

Little is known about how arboreal arthropods respond to forest disturbance. We assessed how rain forest fragmentation affected the vertical stratification of arboreal dung beetles in Peninsular Malaysia. An arboreal dung beetle species (Onthophagus sp.) moved closer to the forest floor in smaller fragments, suggesting a downward shift in its foraging possibly in response to fragmentation.
ZINC HOMEOSTASIS IS CRITICAL FOR OPTIMISED ANTIOXIDANT DEFENSE IN FABA BEAN

SUMMARY Faba bean (Vicia faba L.) plants were grown with five levels of Zn supply ranging from 0.01 to 10 µM. Best growth and maximum biomass were obtained with 1 µM Zn. Leaves of plants with sub- and supra- optimal levels of Zn showed accumulation of lipid peroxides and alterations in the concentration of antioxidants (ascorbate, carotenoids). Activities of carbonic anyhydrase (CA) and total and Cu/Zn superoxide dismutase (SOD) increased with increase in Zn concentration. Activities of ascorbate peroxidase (APX) and catalase (CAT) were lower at both sub- and supra- optimal levels of Zn. Leaf tissue concentration of Zn (~30 µg Zn g -1 dw) was found optimum for biomass yield of faba bean and also provided defense against oxidative damage. Sub-optimal tissue Zn increased sensitivity to oxidative damage because of decreased activity of SOD that implied enhanced accumulation of superoxide. Supraoptimal tissue Zn produced similar, though less pronounced effect because of stimulation of SOD activity associated with inhibition of APX activity, which could impair efficacious scavenging of H 2 O 2 . The data shows that Zn homeostasis is critical for optimized defense against ROS. Deviation from this induces alterations in antioxidant enzyme activities resulting in weakening of antioxidant defense against the ROS.
Evaluation of the quality of protein sources for inclusion in diets for monogastric animals.

For the precise formulation of the protein (amino acid) component of diets for monogastric animals such as the pig and chicken, it is of vital importance to have information regarding the nutritional quality of the protein sources available. Determinations of the nutritional availability of the amino acids must be carried out with ileal digesta rather than with feces. For feedstuffs that have not undergone processing (with heat and pressure, for example), true ileal amino acid digestibility coeffcients are the most appropriate for use in practical diet formulation. However, for feedstuffs that have undergone processing, the use of conventional methods to determine true ileal amino acid digestibility will overestimate the availability of amino acids such as lysine. In these cases, different methods must be used to determine the availability of lysine, such as the O-methylisourea or true reactive lysine bioassay method. The objective is to present a critical evaluation of the appropriateness of the use of the different methodologies currently available to determine the availability of amino acids in protein sources, both processed and non-processed, for the monogastric animals. Para una adecuada formulacion del componente proteico (aminoacidico) en dietas destinadas a animales monogastricos, como cerdos y aves, es necesario conocer la calidad nutricional de las fuentes de proteina. Con este proposito, es necesario estimar la disponibilidad de los aminoacidos de dichas fuentes de proteina. Esto se debe hacer utilizando la digestibilidad ileal, en vez de la digestibilidad fecal. Para alimentos sin procesar (ej. procesados con calor y presion) es mas apropiado utilizar coeficientes de digestibilidad verdadera, determinados a nivel del ileon en la formulacion de dietas. Sin embargo, en el caso de alimentos procesados, los metodos convencionales sobreestiman la disponibilidad de aminoacidos como la lisina. En estos casos, es necesario utilizar otros metodos para determinar la disponibilidad de lisina. Por ejemplo el metodo O-methylisourea o el bio-ensayo de lisina reactiva verdadera. Este trabajo tuvo por objetivo realizar una evaluacion critica de las metodologias actualmente existentes para determinar la disponibilidad de los aminoacidos en ingredientes, procesados y sin procesar, que son comunmente incorporados en dietas de animales monogastricos.
Agronomic evaluation of cocoa hybrids (Theobroma cacao L.) for high-yield selection and field resistance to moniliasis

In this study agronomic behavior of 11 hybrid families of cacao (Theobroma cacao L.) resistant to monilia (Moniliophthora roreri (Cif. & Par.) and established in the town of Tuxtla Chico, Chiapas, under humid tropical conditions was evaluated. Hybrid families were obtained through controlled pollination of reciprocal cross of UF- 273, PA-169, SCA-6, ICS-1, Santa Clara-3, RIM-117 and Pound-7 clones. Plants were seeded at a distance of 3 m between rows and 2 m between plants in a randomized block with four replications and eight plants per experimental unit. Evaluated variables were: grain fresh weight, grain dry weight, pod index, index seed and incidence of moniliasis. Results from cycles (2009, 2010, 2011 and 2012) showed that the best hybrid comes from cross Uf-273 x PA-169 and PA-169 x UF-273. Considering total pods of crop, the incidence of moniliasis reached 40% in the years of assessment. Hybrid families with low percentages of disease incidence and high grain yields per unit area were detected.
Dicer deletion and short RNA expression analysis in mouse embryonic stem cells

RNA interference (RNAi) manages many aspects of eukaryotic gene expression through sequence-specific interactions with RNA. Short RNAs, 20-30 nucleotides in length, guide the various effector proteins of RNAi to silence fully or partially complementary targets. The sequencing of endogenously expressed short RNA species coupled with genetic studies in various experimental organisms has revealed a role for RNAi in the silencing of protein-coding genes and repetitive elements in genomes. In mammals, it is unknown to what extent RNAi is involved in silencing processes other than the modulation of protein-coding gene expression, which is achieved through a class of short RNAs termed microRNAs (miRNAs). The work in this thesis quantitatively describes the short RNAs expressed in mouse embryonic stem (ES) cells. ES cell lines are derived from the pre-implantation blastocyst and can be cultured in vitro for extended periods while still maintaining pluripotency. It was demonstrated that approximately 130,000 5' phosphorylated short RNA molecules are present in a single ES cell. 10% of these short RNAs represent nonrandom fragments of larger, abundant non-coding RNA species, and have no known function. Low abundance short RNAs were discovered that cluster bidirectionally around the transcription start sites of protein-coding genes. These RNAs associate with features of active transcription, and may be evidence of widespread bidirectional initiation and pausing of RNA polymerase II in ES cells. There are on the order of 300 different miRNA species expressed in ES cells, comprising 85% of the total pool of 130,000 5' phosphorylated short RNAs. Based on experiments correlating miRNA abundance to target repression, only about 30 of these miRNAs are expected to carry significant ES cell regulatory capacity. ES cells lacking all miRNAs do not significantly change their morphology or gene expression patterns, but do show a significant drop in growth rate compared to controls, suggesting that a major function of ES cell miRNAs may be to govern cell division. A detailed comparison of short RNAs expressed in ES cells with and without the ribonuclease Dicer strongly suggests that miRNAs are the sole regulatory molecules that function through the RNAi pathway in ES cells. Considering previous work showing that repeating elements are frequently under Dicer-dependent repression, this observation raises the possibility that mammalian miRNAs may in certain contexts function to silence repeating genomic elements in addition to protein-coding genes.
Design and formal analysis of real-time memory controllers

Design and Formal Analysis of Real-Time Memory Controllers Modern multi-core embedded systems integrate an increasing number of heterogeneous resources to provide the necessary computational capacity for executing a variety of applications simultaneously. To reduce the cost, resources are shared by real-time and non-real-time applications. The former have timing requirements, such as a maximum response time or a minimum throughput, which must always be satis ed. The latter must be responsive and require good average performance. However, it is di cult to design these systems because of the complex sharing of resources between applications, making it challenging to meet their timing requirements. SDRAM is typically used as a main data storage device in embedded systems to store the data for the executed applications. It is shared by memory requestors, such as processors, DMAs, and hardware accelerators, which generate diverse memory tra c in terms of arbitrary read/write transactions with variable sizes on behalf of the applications they run. As a result, the memory controller coordinating between the requestors and the SDRAM has to provide guaranteed performance for real-time applications, while still giving good average performance to the rest, in the context of this diverse memory tra c. It is di cult for a memory controller to meet this requirement, because SDRAM is a complex resource, resulting in interference between requestors when they compete for the memory. Existing real-time memory controllers execute transactions by scheduling commands to the SDRAM either (semi-)statically based on pre-computed command schedules or dynamically. Static scheduling eases the analysis by sacri cing average performance, since run-time information cannot be exploited, and it does not e ciently support variable transaction sizes. On the other hand, dynamic scheduling achieves better average performance, while the analysis becomes harder. Therefore, existing dynamically-scheduled memory controllers and/or their analyses only support xed transaction sizes. The goal of this thesis is to overcome the problem of designing an e cient real-time memory controller for increasingly complex systems that feature a mix of real-time and non-real-time applications. The main contributions of this thesis are 1) a memory controller, named Run-DMC, designed to e ciently deal with the diverse tra c by dynamically scheduling commands for each transaction at run-time, and 2) three analysis approaches proposed to provide the worst-case response time (WCRT) and worst-case bandwidth (WCBW) based on a formalization, a data ow model, and a timed automata model, respectively.
Haemolytic Action of Non‐ionic Surfactants Derived from Lysine in Rat Erythrocytes

Monodisperse, non-ionic surfactants based on lysine contain two hydrophobic chains and one or two polyoxyethylene glycol chains with a methoxy group capping the terminal hydroxyl function. Because their structural resemblance to lecithins suggests they could be regarded as non-ionic molecular mimics of these compounds, their haemolytic action has been studied. The presence of 14 and 18 carbon atoms in the hydrophobic moiety seems to result in greater haemolytic action of the surfactants with one polyoxyethylene glycol chain. In the series with two polyoxyethylene glycol chains, the compounds tested at a concentration higher than their critical micellar concentration have greater haemolytic effect, irrespective of the shape of the micelles. When there is a single polyoxyethylene chain a relationship is observed between chain length and haemolytic effect. This correlation is not observed for compounds with two chains. The results show that it is not always possible to predict the haemolytic effect of a surfactant on the basis of its structure and composition.
Dinosaurian faunas of China

"Dinosaurian Faunas of China" describes all dinosaur genera ever found in China and gives their characteristics, stratigraphic occurrence and a brief history of their discovery. The author introduces a comprehensive classification of all Chinese dinosaurs. More than 100 illustrations including those of the skeletons of many of the dinosaurs illustrate this exciting subject of paleontology. This monograph on paleontology and vertebrate biology is intended for researchers and museums of natural history.
Cells expressing Desiccate are essential for morphogenesis of labial sensilla in Drosophila melanogaster adults

We recently discovered a new gene, Desiccate (Desi), that is expressed in the epidermis and protects larvae from desiccation stress in Drosophila melanogaster. In the present study, we found that taste organs express more Desi than the epidermis both in larvae and adults. Green fluorescent protein (GFP) expression in larvae under the direction of a Desi promoter‐Gal4 line containing the 1,010‐bp 5′ flanking region of Desi produced no signal in the epidermis but strong signals in cells of the larval gustatory sense organs, indicating that this driver works specifically in the gustatory organs. In adults, GFP expression was also observed in basal cells of sensilla on labella, tarsi and wings. More precise morphological analysis of GFP expression located its expression in the outer accessory cells rather than neurons of the labial sensilla. Although Desi knockdown or induction of cell death in Desi‐expressing cells did not change the morphological or physiological characters of the larvae, larvae lacking Desi‐expressing cells failed to metamorphose normally, and all of them died inside puparia. Dying pharate adults were found to lack all labial sensilla. The proneural genes Achaete and Scute, which are involved in the development of the adult central and peripheral nervous system, were normally expressed in the pupae lacking Desi‐expressing cells. These results suggested that the lack of Desi‐expressing cells makes it impossible to produce outer accessory cells for development of the sensilla, thereby signifying that cells expressing Desi are essential for normal morphogenesis of the labial sensilla in Drosophila adults.
Fatty acid composition of cooked and fermented beans of the wild legumes (Canavalia) of coastal sand dunes.

Changes in total lipids and fatty acid methyl esters (FAMEs) of dry beans of two wild legumes of coastal sand dunes (CSD) (Canavalia cathartica and C. maritima) using different treatments (cooked and cooked + solid-state fermentation with Rhizopus oligosporus) and extraction methods (Soxhlet and cold extraction) were evaluated. Significant variations in total lipids as well as FAMEs were found between beans, treatments and extraction methods. Cold extraction (Bligh and Dyer method) resulted in significantly highest quantity of total lipids in both beans. The polyunsaturated/saturated ratios were ≥ 0.45 in cooked as well as fermented beans. Stearic acid was significantly elevated in fermented beans of both species in Soxhlet and cold extraction, while palmitic acid in both beans was significantly increased only in Soxhlet method. Oleic acid was significantly raised in C. maritima beans on Soxhlet extraction. There is scope for value-addition by following solid-state fermentation of protein-, carbohydrate-, energy-rich and low lipid Canavalia beans using R. oligosporus. Further studies required to evaluate the yield and acceptability of FAMEs in beans of CSD Canavalia spp. to human and or livestock using R. oligosporus at different temperature regimes, incubation periods and amendment of minerals.
Methane oxidation associated with submerged brown mosses reduces methane emissions from Siberian polygonal tundra

1. Methane (CH4) oxidation (methanotrophy) associated with submerged brown moss species occurs in polygonal tundra environments of the Siberian Arctic. Methanotrophic bacteria living in close association with mosses are thus not restricted to Sphagnum species and low‐pH peatlands.
Professional Development for Technology Integration into Differentiated Math Instruction

To make a connection between pedagogy and technology in teaching, this chapter will explore whether or not a professional development design and practice, whose aim is to help teachers use technology for personal purposes, readily translates into the ability to effectively teach and learn with technology. Adopting a conceptual framework known as self-efficacy beliefs and TPACK, or technological pedagogical content knowledge (Mishra & Koehler, 2006), this chapter discusses the design of a professional development model, the goal of which is increasing the critical attribute of the successful professional development: self-efficacy. In an effort to provide empirical knowledge to support this design, this chapter further showcases a faculty member’s approaches to connecting technology and pedagogy using the TPACK approach, while implementing a model designed to improve teachers’ self-efficacy. Implications and guidelines for developing teachers’ self-efficacy, through activities during the professional development workshop, are discussed.
Paving the way for molecular biological quantification of Listeria monocytogenes in food

Das Thema dieser Arbeit war die Bearbeitung von grundlegenden Fragestellungen im Zusammenhang mit dem molekular-biologischen Nachweis von lebensmittelpathogenen Bakterien. Die Methode der welche dafur eingesetzt werden sollte war die Real-time Polymerase-Kettenreaktion (qPCR). Dieser Ansatz des molekularbiologischen Nachweises lebensmittelpathogener Bakterien sollte beispielhaft mit Listeria monocytogenes durchgefuhrt werden. In einem ersten Schritt sollte ein existierender L. monocytogenes spezifischer konventioneller PCR-Assay erweitert werden werden um den Assay in einer qPCR Anwendung verwenden zu konnen. Basierend auf diesem qPCR-Assay wurde im folgenden eine kombinierte Anreicherungs/qPCR Methode entwickelt. Parallel dazu wurde die Moglichkeit der direkten quantitativen Analyse aus dem Lebensmittel ohne vorbereitende Schritte untersucht. Der Einfluss der Lebensmittelmatrix und der verwendeten Anreicherungsmedien auf die Efffizienz der qPCR Reaktion wurde untersucht. Ein weiterer Schritt in Richtung zuverlassiger molekularbiologischer Nachweisverfahren fur die Detektion lebensmittelpathogener Bakterien ist letztendlichen die Berucksichtigung der Notwendigkeit einer analytischen Kette bestehend aus Probenvorbereitung, DNA Isolation/Aufreinigung und qPCR Detektion. Daher wurde eine neue Probenvorbereitungsmethode entwickelt um die Nachteile bestehender Methodik zu vermeiden. Ein kritischer Punkt wahrend der Entwicklung der neuen Probenvorbereitungsmethode war das Auffinden der prasumptiven Zielkeime. Da lebensmittelpathogene Bakterien farblos und daher in der Probe unsichtbar sind war es notwendig sie wahrend der Entwicklung durch farbige Indikatoren zu ersetzen. Es wurde daher der chromogene Gram positive Bakterienstamm Micrococcus roseus eingesetzt um die Untersuchung einer so grosen Anzahl an zu testenden physikalischen und chemischen Parametern in akzeptabler Zeit und mit den vorhandenen Resourcen durchzufuhren.
DNA EXTRACTION AND QUANTIFICATION OF DIPLOID AND TETRAPLOID RED CLOVER (TRIFOLIUM PRATENSE L.) FROM LEAF TISSUE USING KIT EXTRACTION (SIGMA)

This paper describes the process of DNA extraction and quantification of diploid and tetraploid red clover (Trifolium pratense L.). Red clover is an important forage crop for research purposes which has seen a gradual decline in use for a century. The paper begins by describing the advantages of red clover and arguing that its use may become important once again within the context of sustainable agriculture. The process of DNA extraction using a commercial extraction kit is then described in detail. The results section considers DNA quantification using both spectrophotometer and electrophoresis processes. Quantification is used to determine the concentration and purity of the laboratory samples of red clover used in the research laboratory
Influence of 5’-untranslated region (UTR) sequence on the regulation of human tissue plasminogen activator (t-PA) mRNA expression

Human tissue plasminogen activator (t-PA) is a serine protease that plays a key role infibrinolysis, a process of dissolving blood clot. t-PA is produced by a variety of cells andtissues and many tumor cell lines. It is well known that t-PA expression in these cell lines
Geometric Modeling of Muscle Cells

Progress in biological sciences asks for modeling tools that would allow simple communication of complex biological objects. According to electron microscopic studies, cells are packed with intracellular organelles that vary widely in size and shape and are in complex spatial relations to each other. We introduce here a modeling concept that allows building of complex structures such as muscle cells according to imagination of scholars.