Miracle-dz/UniFAR-FTUs huggingface dataset:
Segmentation and Tracking Algorithms for in Vitro Cell Migration Analysis

This thesis describes a system for automatic in vitro cell migration analysis. Image sequences of adult neural stem/progenitor cells were acquired using a time-lapse bright-field microscopy setup. The adult neural stem/progenitor cell has the ability to differentiate into three different neural lineages; neuronal, astrocytic and oligodendrocytic. Different image analysis techniques were investigated for segmenting the cells in the images, such as watershed segmentation and boundary detection using dynamic programming. Some segmentation techniques required the positions of the cells to be detected first. This was done either using a multi-scale Laplace of Gaussian (LoG) filter, which detects blob-like objects in an image, or using the extended h-maxima transform. It was found that the performance of the multi-scale LoG-filter as a cell detector could be increased by using information about the cells-positions in the previous image. To track the individual cells through the sequence, the segmented cells in two consecutive images were associated using Bertsekas modified auction algorithm. The association weights were calculated based on distance, correlation and size between possible matching cells. A comparison of three different segmentation methods, evaluated after completing the tracking step, showed that the best system was an algorithm consisting of a multi-scale LoG-filter, followed by cell border detection using dynamic programming. Using that system, 93 % of the cell-to-cell associations in the evaluated sequences were correct. The obtained cell movement data was used for statistical modelling of the cell migration patterns. Using a Hidden Markov Model with two states, it was found that the motion of the glial progenitor cell was random 2/3 of the time, while the type-2 astrocyte showed a directed movement 2/3 of the time. This finding indicates possibilities for cell-type specific identification and cell sorting of live cells based on specific movement patterns in individual cell population, which would have a valuable application in neurobiological research.
Selection to Ensure Study Success: Looking for Multiple Criteria in the Case of a European Master of Science Program in Business

The authors report relations between entrance criteria and study success in a program for a master of science in business. Based on the admission criteria broadly used in European business schools and the findings of prior research, the present authors measured eight criteria for study success in the master's degree program. The authors applied the following criteria: verbal, quantitative, and analytical writing skills; prior knowledge; adjustment to college; social adjustment; personal-emotional adjustment; and attachment. Results revealed that a combination of verbal skills, prior knowledge, academic adjustment, and attachment best predicted study success.
Severe pollen limitation in populations of the New Zealand shrub Alseuosmia macrophylla (Alseuosmiaceae) can be attributed to the loss of pollinating bird species

The loss of bird species following human colonization of New Zealand has raised concerns about the consequences for crucial ecosystem functions such as pollination. The understorey shrub Alseuosmia macrophylla (Alseuosmiaceae) exhibits characteristics typical of a bird pollination syndrome, but populations still persist in northern North Island forest remnants despite the local extinction of most endemic bird pollinators, leading to the suggestion that moths – rather than birds – may be the primary pollinators. The aim of this study was to quantify the importance of endemic birds as pollinators of A. macrophylla over several years by comparing plants on Little Barrier Island (LBI), where all extant endemic bird pollinators still occur, to plants at sites on the adjacent North Island in the Waitakere Ranges (WTK), where only one of these species remains common. Flowers on LBI were visited by endemic bellbirds (Anthornis melanura) and stitchbirds (Notiomystis cincta), while at WTK sites the most common visitors were the recently arrived silvereye (Zosterops lateralis) and the introduced honeybee (Apis mellifera), both of which acted principally as nectar robbers. Caged flowers on LBI had significantly lower fruit set than open flowers, and plants at WTK were significantly more pollen-limited than plants on LBI. This provides evidence that the loss of endemic pollinating birds is the most likely reason for the high pollen limitation found in some North Island A. macrophylla populations, and the very low seed set of these populations could have serious implications for the long-term persistence of this species.
Evaluation of an immunoblotting test based on whole tachyzoite lysate for diagnosis of humoral response of domestic cats infected with Toxoplasma gondii, Rh strain

Summary This study was aimed to detect anti-Toxoplasma gondii antibodies in cats infected with Rh strain of T. gondii by using an immunoblotting method. For this, cats were experimentally infected using tachyzoites harvested from Vero cell cultures. Tachyzoites were then lysed and transferred to polyacrylamide gels followed by blotting to PVDF membranes. An immunoblotting was performed using these membranes to detect IgG antibodies. Protein bands were detected in regions related to the presence of T. gondii surface antigens, dense granular or rhoptry proteins. No positive bands were detected in serum samples of kittens that received only Vero cell lysates (controls). Positive or negative results were in concordance to the results of IFAT. The results of this study revealed that whole tachyzoite antigen based immunoblotting is an appropriate diagnostic test for serological detection of anti-T. gondii antibodies in recently infected kittens with this Apicomplexan parasite.
PROTEOMICS AND IN VIVO LABELING OF PROTEIN THIOLS IN SULFOLOBUS SOLFATARICUS DURING EXPOSURE TO ANTIMONY

Antimony (Sb) has a long history in both the chemical and social literature. As a metalloid it is often found in the environment with Arsenic (As). Extended exposure in humans causes heart disease, lung disease, diarrhea, severe vomiting and ulcers. In plants, it inhibits early crop growth. A large body of data on bacterial response and mechanisms for detoxification also exists. In contrast, knowledge about how archaeal species respond to Sb is much less extensive. The model crenarchaeal organism Sulfolobus solfataricus, can survive in environments with high antimony concentrations, and the genetic and biochemical mechanisms responsible for antimony tolerance have yet to be reported. As a first step in bringing to light the biological response of S. solfataricus to antimony, a set of proteomic and chemical tagging experiments were undertaken. Twodimensional differential gel electrophoresis (2D-DIGE) showed a limited response from intracellular and membrane proteins with respect to their abundance. In contrast,
hox Gene Regulation and Function During Zebrafish Embryogenesis: A Dissertation

Hox genes encode a conserved family of homeodomain containing transcription factors essential for metazoan development. The establishment of overlapping Hox expression domains specifies tissue identities along the anterior-posterior axis during early embryogenesis and is regulated by chromatin architecture and retinoic acid (RA). Here we present the role nucleosome positioning plays in hox activation during embryogenesis. Using four stages of early embryo development, we map nucleosome positions at 37 zebrafish hox promoters. We find nucleosome arrangement to be progressive, taking place over several stages independent of RA. This progressive change in nucleosome arrangement on invariant sequence suggests that trans-factors play an important role in organizing nucleosomes. To further test the role of trans-factors, we created hoxb1b and hoxb1a mutants to determine if the loss of either protein effected nucleosome positions at the promoter of a known target, hoxb1a . Characterization of these mutations identified hindbrain segmentation defects similar to targeted deletions of mouse orthologs Hoxa1 and Hoxb1 and zebrafish hoxb1b and hoxb1a morpholino (MO) loss-of-function experiments. However, we also identified differences in hindbrain segmentation as well as phenotypes in facial motor neuron migration and reticulospinal neuron formation not previously observed in the MO experiments. Finally, we find that nucleosomes at the hoxb1a promoter are positioned differently in hoxb1b -/- embryos compared to wild-type. Together, our data provides new insight into the roles of hoxb1b and hoxb1a in zebrafish hindbrain segmentation and reticulospinal neuron formation and indicates that nucleosome positioning at hox promoters is dynamic, depending on sequence specific factors such as Hox proteins.
Monoterpenoid Indole Alkaloid Biosynthesis

Approximately 20% of plant species contain alkaloids with a broad range of physiological properties that protect them from various types of herbivores and pathogens. Within this abundant group of nitrogen-containing secondary metabolites, the monoterpenoid indole alkaloids (MIAs) make up the largest and most diverse class of compounds that are characteristically found within the Apocynaceae, Loganiaceae and Rubiaceae plant families. The complexity of MIA chemistry is matched by their remarkably diverse effects on living organisms which has led to their use as drugs (Figure 10.1) for treating neurological disorders (reserpine), cancer (camptothecin, vinblastine and vincristine) and as vasodilators (yohimbine) in humans. Serpentine has recently been shown to be a powerful acetylcholinesterase inhibitor with potential use for treatment of Alzheimer’s disease (Pereira et al., 2010). Catharanthus roseus is the best characterised MIA-producing plant, mostly due to the commercial value of its anticancer alkaloids, vinblastine and vincristine. Several recent reviews have been published on the analysis (Hisiger and Jolicoeur, 2007), chemistry (O’Connor and Maresh, 2006), biosynthesis (Facchini and De Luca, 2008; Oudin et al., 2007a; El-Sayed and Verpoorte, 2007; Loyola-Vargas et al., 2007; Hedhili et al., 2007), regulation (Memelink and Gantet, 2007; Memelink, 2009), intracellular, intercellular and organ-specific compartmentation (Mahroug et al., 2007), plant cell culture-based
Properties of the thioredoxin system in microaerophiles from the Streptococcus genus

The Streptococcus genus includes the pathogenic species S. mutans, the main responsible of dental caries, and the safe microorganism S. thermophilus, used for the manufacture of dairy products. These facultative anaerobes control the levels of reactive oxygen species (ROS) and indeed, both S. mutans and S. thermophilus possess a cambialistic superoxide dismutase, the key enzyme for a preventive action against ROS. To evaluate the properties of a crucial mechanism for repairing ROS damages, the molecular and functional characterization of the thioredoxin system in these streptococci was investigated. The putative genes encoding its protein components in S. mutans and S. thermophilus were analysed and the corresponding recombinant proteins were purified. A single thioredoxin reductase was obtained from either S. mutans (SmTrxB) or S. thermophilus (StTrxB1), whereas two thioredoxins were prepared from either S. mutans (SmTrxA and SmTrxH1) or S. thermophilus (StTrxA1 and StTrxA2). Both SmTrxB and StTrxB1 reduced the synthetic substrate DTNB in the presence of NADPH, whereas only SmTrxA and StTrxA1 accelerated the insulin reduction in the presence of DTT. To reconstitute an in vitro streptococcal thioredoxin system, the combined activity of the thioredoxin components was tested through the insulin precipitation in the absence of DTT. The assay functions with a combination of SmTrxB or StTrxB1 with either SmTrxA or StTrxA1. These results suggest that the streptococcal members of the thioredoxin system display a direct functional interaction between them and that these protein components are interchangeable within the Streptococcus genus. In conclusion, our data prove the existence of a functioning thioredoxin system even in these microaerophiles.
Effect of Feeding Expander Extruder Processed Complete Diet Containing Sugarcane Bagasse on Performance of Murrah Buffaloes

A complete diet was formulated with sugarcane bagasse as sole roughage source (28.5%) and processed with expander-extruder. The extruded diet was compared with a traditional system of feeding comprising concentrate mixture, ad libitum chopped sorghum straw and limited quantity of green hybrid Napier (10kg/animal/day) in terms of nutrient utilization and milk characteristics in 12 lactating Murrah buffaloes (6 in each group) for 180 days. The buffaloes consumed less (P<0.01) dry matter (DM) per kg metabolic body weight when fed processed complete diet than those fed conventional ration. However, the DM intakes in both the groups were higher than the standard recommended requirements (Kearl, 1982). The water intake/kg DM intake was higher (P<0.01) in expander extruder processed complete diet fed animals. Blending of bagasse with concentrates and expander extruder processing complete diet resulted in higher (P<0.01) crude protein digestibility. The digestibility of other nutrients and fibre fractions remained comparable among the groups. The digestible crude protein of complete ration was higher (P<0.05) than the conventional ration. The higher (P<0.01) intakes of total digestible nutrients and metabolizable energy by buffaloes fed conventional ration was a reflection of more roughage consumption (61.9% Vs 28.5%) by these animals. Milk yield, fat corrected milk (FCM) yield, fat and SNF % was similar between both the groups. The DMI/kg FCM production was significantly (P<0.05) lower on processed complete diet compared to conventional diet. The cost of feeding/kg milk production was lower (P<0.01) and reduced by 31.53% when expander extruder pellet complete diet containing sugarcane bagasse was fed to animals.
Improved tolerance of Cu/Zn superoxide dismutase and ascorbate peroxidase expressing transgenic tobacco seeds and seedlings against multiple abiotic stresses.

Reactive oxygen species (ROS) are produced during seed germination but remain under-control in optimum germination conditions. Seeds being germinated in single or multiple stress conditions such as drought, excessive salt and low-temperature may face burst of ROS, which leads to poor germination and weak seedling establishment. Enzymatic activities, germination rates and seedling growth of the seeds of transgenic tobacco plants simultaneously expressing Cu/Zn-superoxide dismutase (CuZnSOD) and ascorbate peroxidase (APX) in plastids (CA seeds) under various combinations of environmental stresses (drought, salt and low temperature) were investigated and compared with the non-transgenic seeds (NT seeds). CA seeds maintained higher CuZnSOD and APX activities during seed imbibitions than NT seeds. CA seeds depicted less ion leakage after salt stress than NT seeds providing the evidence of proper functioning of CuZnSOD and APX to keep ROS production under control. When germinated in stress conditions, CA seeds germinated earlier than NT seeds and this character was more profound under double or triple stress conditions. Moreover, CA seedlings accumulated more shoot and root dry weight as compared to NT seedlings under single, double and triple stress conditions. These investigations strongly suggest that overexpression of CuZnSOD and APX helped CA seeds to keep ROS under control by detoxifying superoxide radicals and H2O2, which paved the way for increased germination and seedling growth in various combinations of environmental stresses. © 2013 Friends Science Publishers
Reproduction and Sexuality in Marine Fishes: Patterns and Processes

Marine fishes represent astonishing diversity with respect to practically every aspect of their biology. Reproductive modes and sexual patterns are especially fascinating and provide deep insight into general evolutionary problems. In this volume, chapters focus on reproduction and sexuality among groups of fishes defined by habitat, taxon, and the reproductive processes that are critical for reproductive success. The book illustrates how knowledge of reproductive biology among marine fishes can help identify vulnerable and potentially vulnerable species in the face of changing environmental conditions and increasing human-based pressures.
Design and Implementation of the CloudMdsQL Multistore System

The blooming of different cloud data management infrastructures has turned multistore systems to a major topic in the nowadays cloud landscape. In this paper, we give an overview of the design of a Cloud Multidatastore Query Language (CloudMdsQL), and the implementation of its query engine. CloudMdsQL is a functional SQL-like language, capable of querying multiple heterogeneous data stores (relational, NoSQL, HDFS) within a single query that can contain embedded invocations to each data storeâ? s native query interface. The major innovation is that a CloudMdsQL query can exploit the full power of local data stores, by simply allowing some local data store native queries (e.g. a breadth-first search query against a graph database) to be called as functions, and at the same time be optimized.
Design, development and construction of open sea floating cage device for breeding and farming marine fish in Indian waters

The floating cage device described in the present study is the first of its kind in Indian seas and consists of a cylindrical floating cage structure along with suitable netting materials for mariculture of finfishes and shellfishes in open sea. The cage structure was made of high density polyethylene (HDPE) top support, inner and outer rings and a middle catwalk. The inner and outer collar had provisions for connecting outer predator, inner growout and bird nets. Catwalk in the middle served for regular cage management and safety of the workers. There were HDPE vertical and diagonal supports for the cage frame. Ballast was used at the bottom to maintain the shape of the cage. The total weight of the cage frame was 447.7 kg in air and 74.2 kg in water. The floatation force of the cage was 211.2 kg while the effective floatation force was 131.8 kg. The total weight of netting materials including rope was 46.7 kg in air and 5.2 kg in water. A floating net cage device of 6 m inner and 8 m outer collar dia with 6 m net depth and an effective inner volume of 169.7 m3 was designed and successfully tested in open sea, during the present study. The floating sea cage structure and nets were designed and standardised in such a way to suit the current and wave conditions of Indian seas.
Does Organizational Support Affect Employees' Commitment to Implement Biogas Programs?

The stakeholders must support the important process of generating renewable energy. One source of renewable energy is biogas produced from palm oil liquid waste. The organizations and employees’ support are expected to succeed biogas program and to generate the renewable energy. This research investigates organizational support and employees’ commitment in implementing biogas programs. The research was conducted in PTPN III Region of North Sumatera with a sample of 98 employees in eight areas proportionally. The explorative research aims to predict the effect of organizational support and employee’s commitment in implementing biogas program. The results show that the organizational support and employees’ commitment have either direct or indirect influence on biogas program. In conclusion, the biogas program needs organizational support and increased employees’ commitment so that it can be implemented in accordance with the intended purpose.
Le rôle des cellulases dans les interactions entre les mycobactéries du complexe Mycobacterium tuberculosis et les amibes libres

Le genome de Mycobacterium tuberculosis, l’agent causal de la tuberculose, code pour une proteine ayant la capacite de se fixer sur la cellulose (Rv1987), une cellulase potentielle (Rv1090), et une cellulase pleinement active (Rv0062). Cette observation est surprenante, car la cellulose est un composant majeur des parois des cellules vegetales, tandis que M. tuberculosis est un pathogene humain sans contact connu avec des plantes. Nous avons emis l’hypothese que ces proteines pourraient jouer un role dans les interactions entre les mycobacteries du complexe M. tuberculosis avec les kystes d’amibes libres, dont la paroi contient egalement de la cellulose. Dans notre travail de these, nous avons cherche par une analyse in silico la presence de ces trois genes chez toutes les bacteries ayant un genome completement sequence presentes dans la base de donnees CAZy (accessible en ligne a l’adresse www.cazy.org). Cette etude a montre que seulement 2,5% des bacteries codent pour les trois genes simultanement. Parmi ces bacteries, nous avons ensuite confirme experimentalement par PCR et sequencage la presence des genes Rv0062, Rv1090 et Rv1987 chez les mycobacteries du complexe M. tuberculosis. Nous avons ensuite verifie la transcription de ces trois genes chez la souche de reference M. tuberculosis H37Rv, puis produit dans Escherichia coli des proteines de fusion Rv1090 et Rv1987 et montre qu'elles etaient capables d'hydrolyser la cellulose (Rv1090) et de s’y fixer (Rv1987). De plus, nous avons mis en place un model experimental d’interaction entre les mycobacteries du complexe M. tuberculosis et les amibes libres dans le but de comprendre le role des genes Rv0062, Rv1090 et Rv1987. Dans un premier temps nous avons montre que M. tuberculosis, Mycobacterium bovis, Mycobacterium canettii ainsi que Mycobacterium avium utilise ici comme un controle positif etaient capables de survivre dans le cytoplasme des amibes libres telles que Acanthamoeba polyphaga. Ensuite, nous avons montre que M. tuberculosis et M. bovis mais pas M. canettii etaient capables de survivre a l’interieur des kystes d’amibes. Enfin nous avons montre que M. tuberculosis, M. bovis et M. canettii etaient capables de survivre dans le sol pendant au moins 6 mois. Les donnees etablies dans cette these soutiennent le role des cellulases dans la survie environnementale des mycobacteries du complexe M. tuberculosis, et ouvrent la voie a l’etude de cette phase meconnue dans le cycle de ces organismes
A redescription of Paragotoea bathybia Kramp 1942 (Hydroidomedusae: Corymorphidae) with a new diagnosis for the genus Paragotoea

A redescription is given for the 1-tentacled Anthomedusa Paragotoea bathybia from new specimens collected in the Weddell Sea. The comparative study of the previous descriptions of this species permitted to define a new diagnosis for the genus which has been ascribed to the family Corymorphidae. The family Paragotoeidae Ralph, where P. bathybia was formerly included, is supressed. The 4-tentacled reconstructed stage considered by Ralph (1959) as the adult stage of P. bathybia is a new species placed in a new genus: Tetraralphia hypothetica, (Capitata incertae sedis).