Miracle-dz/UniFAR-FTUs huggingface dataset:
An Adaptive Algorithm to Identify Ambiguous Prostate Capsule Boundary Lines for Three-Dimensional Reconstruction and Quantitation

Currently there are few parameters that are used to compare the efficiency of different methods of cancerous prostate surgical removal. An accurate assessment of the percentage and depth of extra-capsular soft tissue removed with the prostate by the various surgical techniques can help surgeons determine the appropriateness of surgical approaches. Additionally, an objective assessment can allow a particular surgeon to compare individual performance against a standard. In order to facilitate 3D reconstruction and objective analysis and thus provide more accurate quantitation results when analyzing specimens, it is essential to automatically identify the capsule line that separates the prostate gland tissue from its extra-capsular tissue. However the prostate capsule is sometimes unrecognizable due to the naturally occurring intrusion of muscle and connective tissue into the prostate gland. At these regions where the capsule disappears, its contour can be arbitrarily reconstructed by drawing a continuing contour line based on the natural shape of the prostate gland. Presented here is a mathematical model that can be used in deciding the missing part of the capsule. This model approximates the missing parts of the capsule where it disappears to a standard shape by using a Generalized Hough Transform (GHT) approach to detect the prostate capsule. We also present an algorithm based on a least squares curve fitting technique that uses a prostate shape equation to merge previously detected capsule parts with the curve equation to produce an approximated curve that represents the prostate capsule. We have tested our algorithms using three shapes on 13 prostate slices that are cut at different locations from the apex and the results are promising.
Déficience dans la réparation par excision de nucléotides en phase S induite par la séquestration du facteur de réplication RPA

III Table des matières. IV Liste des figures . VI Liste des abréviations . VII Remerciements . X Introduction: La réponse aux dommages à l'ADN . 11 Les types de dommages à l'ADN . 12 La provenance des dommages à l'ADN . 12 La réparation des dommages à l'ADN . 20 La réparation des lésions induites par les rayons UV . 21 Les mécanismes de tolérance . 25 La réponse cellulaire aux dommages à l'ADN . 27 Le cycle cellulaire chez la levure . 27 Le modèle de la levure : Saccharomyces cerevisiae . 34 Hypothèse . 36 Objectifs . 36 Matériel et Méthodes . 37 Culture cellulaire . 37 Irradiation aux rayons UV . 37 Détection par immunoblots de type western . 38 Quantification du contenu en ADN par cytométrie en flux . 38 Quantification de l’élimination des CPD par cytométrie en flux . 38 Quantification de l’élimination des CPD par slotblot . 39 Analyse par microscopie à fluorescence . 39 Résultats . 40
Effects of egg weight on the egg quality, chick quality, and broiler performance at the later stages of production (week 60) in broiler breeders

&NA; The objective of the present study was to determine the effect of broiler breeder egg weight on egg quality, chick quality, and broiler performance using Hubbard Classic broiler breeder flock. Hatching eggs from a commercial broiler breeder flock (Hubbard classic strain) were obtained at the age of 60 wk and divided into 3 egg‐weight categories, namely small, medium, and large. For this purpose, 930 eggs having weights 63.09 ± 0.21, 68.85 ± 0.23, and 74.81 ± 0.11g were divided into 3 egg categories labeled small, medium, and large respectively. We further divided these eggs into 2 categories, eggs for quality parameters and eggs for incubation and posthatch performance parameters. Eggs from the small egg category had greater proportion of the shell weight and more shell strength. Egg weight did not significantly affect the albumen and yolk weight percentage. Egg weight affected the shape index and specific gravity for which lower values were observed for large eggs. Egg weight positively affected the chick weight, chick yield, and chick length (P < 0.05) of both male and female chicks. Results of the body weight gain showed that effect of egg weight on the posthatch performance of chick diminishes with the age of broilers. Egg weight significantly affected the body weight gain of male and female chicks up to 3 wk of age. Egg weights did not significantly affect the feed intake and mortality of broiler. Different egg‐weight categories significantly affected the feed conversion ratio of female chicks at wk 2 and 3 of age and did not affect the feed conversion of male and female chicks at the end of wk 5. In conclusion, egg weight positively affected the chick characteristics (e.g., chick weight, chick length) and did not affect the final live body weight, feed conversion ratio, feed intake, and mortality in broilers.
Food Preference And Feeding Habit of Bonnet Macaque (Macaca Radiata)

Primate demography and behavior are profoundly affected by ecological variables and that even short term changes in environmental conditions affects species population densities and group sizes. Food preference and feeding habit of Macaca radiata in a sacred grove was studied. Macaca radiata are generalistic feeders, although they exploited a wide variety of food items they concentrated on young leaves, fruits & leaf buds which provide crude proteins, fibers, minerals and sugars. They utilized food sources in a very balanced form that they achieve their nutritional requirement from it. Macaca radiata space themselves out as they forage on widely dispersed leaves, flowers and fruits of commonly available plants. Opportunities for monopolization of foods are therefore rare during natural foraging and strong competition may not occur under these circumstances are noted.
Variation of physical seed dormancy and its ecological role in fire-prone ecosystems

University of Wollongong Copyright Warning You may print or download ONE copy of this document for the purpose of your own research or study. The University does not authorise you to copy, communicate or otherwise make available electronically to any other person any copyright material contained on this site. You are reminded of the following: This work is copyright. Apart from any use permitted under the Copyright Act 1968, no part of this work may be reproduced by any process, nor may any other exclusive right be exercised, without the permission of the author. Copyright owners are entitled to take legal action against persons who infringe their copyright. A reproduction of material that is protected by copyright may be a copyright infringement. A court may impose penalties and award damages in relation to offences and infringements relating to copyright material. Higher penalties may apply, and higher damages may be awarded, for offences and infringements involving the conversion of material into digital or electronic form. Unless otherwise indicated, the views expressed in this thesis are those of the author and do not necessarily represent the views of the University of Wollongong.
Real-time chromatin dynamics at the single gene level during transcription activation

Genome dynamics relate to regulation of gene expression, the most fundamental process in biology. Yet we still do not know whether the very process of transcription drives spatial organization and chromatin conformation at specific gene loci. To address this issue, we have optimized the ANCHOR/ParB DNA labeling system for real-time imaging and quantitative analysis of the dynamics of a single-copy transgene in human cells. Transcription of the transgene under the control of the endogenous Cyclin D1 promoter was induced by addition of 17β-estradiol. Motion of the ANCHOR3-tagged DNA locus was recorded in the same cell prior to and during appearance of nascent mRNA visualized using the MS2 system. We found that transcription initiation resulted in rapid confinement of the mRNA-producing gene. The confinement was maintained even upon inhibition of pol2 elongation. It did not occur when recruitment of pol2 or transcription initiation was blocked by anti-estrogens or Triptolide. These results suggest that preinitiation complex formation and concomitant reorganization of the chromatin domain constrains freedom of movement of an induced gene’s promoter within minutes. Confined diffusion reflects assembly of functional protein hubs and DNA processing during the rate-limiting steps of transcription.
Pectic and Galacturonic Acid Oligosaccharides on the Postharvest Performance of Citrus Fruits

Araceli M. Vera-Guzman is a doctoral student in the graduate program of CIAD, and received a graduate fellowship from CONACyT, Mexico. Part of this work was supported by the Spanish Ministry of Science and Technology (Research Grant AGL2013-41734-R and AGL2014-55802-R) and by the Generalitat Valenciana, Spain (Grant PROMETEOII/2014/027).
Molecular studies on hepatitis E viruses

Oliveira-Filho, E.F. , H-J. Thiel, M. König (2012). Sequence and expression of the capsid protein of swine Hepatitis E virus (HEV) from Germany. 22nd Annual Meeting of the Society for Virology, Essen. Oliveira-Filho, E.F. , M. König, H. -J. Thiel (2012). Genetic variability of HEV isolates: inconsistencies of current classification. IX International Congress of Veterinary Virology, Madrid. Oliveira-Filho, E.F. , H. -J.Thiel, M. König (2012). Hepatitis E Virus in domestic swine and wild boar from Germany. European association for veterinary laboratory diagnosticians Congress, Kazimierz Dolny. Oliveira-Filho, E.F. , M. König, H. -J. Thiel (2011). Phylogeny of Hepatitis E Virus (HEV) based on complete genomic sequences. Anual meeting of the Society of veterinary epidemiology and preventive medicine, Leipzig. Oliveira-Filho, E. F. , B. R. Bank-Wolf, M. König, H. -J. Thiel (2009). Molecular epidemiology of hepatitis E virus in swine and wild boar in Germany. 8th International Congress of Veterinary Virology, Budapeste. (oral presentation)
Heritability and its use in animal breeding

Heritability is the single most important consideration in determining appropriate animal evaluation methods, selection methods and mating systems. Heritability measures the relative importance of hereditary and environmental influences on the development of a specific quantitative trait. More specifically, it measures that part of the total variability of the trait caused by genetic differences among the animals on which the
Quantitative chemical imaging in atom probe tomography

Atom Probe Tomography (APT) resolves atoms in real space and detects their chemical identity. In the realm of microscopic techniques, it has its unique place with sub nanometer spatial resolution and high chemical sensitivity. In this thesis, data driven techniques have been developed to identify nano scale chemical features from reconstructed atomic data obtained from APT experiments. Main drawbacks in present day methods, to detect nano scale features, are use of input parameters involving heuristics on part of user. Techniques developed in this work use the APT data to determine the input parameters, thereby making the process more quantitative. In particular, techniques have been developed to select optimal voxel size to calculate the concentration profile, and to select the concentration threshold using ideas from computational topology. Voxel size is selected using an error minimization technique. A framework to quantify and visualize spatial uncertainty in isosurface has also been developed. Approaches developed in this work are generic in nature and can be applied on any APT data. In this work, results have been shown for Ni based superalloy data.
Impacto da qualidade do sêmen sobre a fertilidade a campo em bovinos

Fertilization involves a complex process and requires many sperm attributes for its success. There is great variation in the semen of different bulls and batch, which causes an oscillation in fertility potential. The use in TAI of semen batch with reduced fertility potential causes a great impact on the productivity of the herd. Semen batches that exhibit characteristics of progressive motility, vigor, morphological defects and concentration within those acceptable for use in AI may show reduction in fertility potential, which may be attributed to changes in structures or sperm functions not contemplated in these evaluations. Several techniques have been developed to identify sperm alterations that result in failure of fertility; revealing more accurately sperm cell lesions after the cryopreservation process. This paper aims to address, essentially based on our experiences, fertility failures inherent to semen and how laboratory techniques can predict the fertility potential of a semen batch prior to use in TAI and its impact on herd fertility.
Restored tallgrass prairies have reduced phylogenetic diversity compared with remnants

Summary Ecological restoration is critical for mitigating habitat loss and providing ecosystem services. However, restorations often have lower diversity than remnant, reference sites. Phylogenetic diversity is an important component of biodiversity and ecosystem function that has only recently been used to evaluate restoration outcomes. To move towards prediction in the restoration of biodiversity, it is necessary to understand how phylogenetic diversity of restorations compares with that of reference sites, and where deficits are found, to evaluate factors constraining phylogenetic diversity. We quantified plant taxonomic and phylogenetic diversity in eastern tallgrass prairie, one of the most endangered ecosystems on earth. We measured diversity at large (site) and small (plot) scales in 19 restored prairies and compared patterns with those from 41 remnant prairies. To evaluate how environmental conditions and management actions influence outcomes, we tested the effects of soil properties and seed mix composition on diversity of restorations. Restored prairies were less phylogenetically diverse than remnants at both spatial scales. On the other hand, the total species richness of remnant and restored prairies did not significantly differ, but remnants had higher native richness. Restored communities were taxonomically and phylogenetically distinct from remnants. Soil properties (moisture and pH) influenced phylogenetic diversity and composition. There were positive relationships between the taxonomic and phylogenetic diversity of seed mixes and resulting diversity of planted assemblages (excluding volunteer species). Species in seed mixes were more closely related than expected by chance, and several clades found in remnant prairies were missing from seed mixes. Synthesis and applications. Restored tallgrass prairies had lower phylogenetic diversity than remnant prairies, which may contribute to the widely observed phenomenon of restorations not being functionally equivalent to reference sites. It is encouraging for restoration efforts that seed mix phylogenetic diversity predicted phylogenetic diversity of planted assemblages. This indicates that designing phylogenetically diverse seed mixes for restoration is beneficial. In addition, clades found in reference sites that are missing from restoration seed mixes could be added to new or existing restorations to reduce gaps in phylogenetic diversity. Further work on the effects of management on phylogenetic diversity is needed to advance restoration of biodiversity.
Biosystematic studies in the Loganiaceae (series 1): Foliar trichomemorphology of Tree Species of Anthocleista Afzel Found in Parts of the NigerDelta, Nigeria

Comparative systematic study of foliar epidermal trichome morphology of species of Anthocleista found in Nigeria was carried out in parts of Niger Delta area of the country. The area covered includes parts of Rivers, Bayelsa, Akwa-Ibom and Cross River States. The present study brings out the trichome morphology in leaf epidermal surfaces in four species belonging to the genus Anthocleista of the Loganiaceae. The micromorphological observations reveal some interesting features with reference to the type, and frequency or abundance of trichomes on foliar surfaces of the species studied. Though there could be similarity in terms of type and morphology in both surfaces of the species, A. liebrechtsiana showed a lesser abundance of trichome on both surface. Anthocleista djalonesis has in addition to other types, conical, falcate and stellate trichomes. Based on the variations in the above feature 10 types of trichomes among the four groups of species of Anthocleista are recognized. These include: cylindrical unbranched, 3- armed, 5- armed, dendritic, scale, 2- armed, conical, falcate, stellate and simple unbranched trichomes. The adaptive variation and taxonomic significance of the trichome epidermal features observed in this study further highlight the usefulness of micro anatomical structures in taxonomic delimitation. This therefore confirms earlier suggestions on the use of this epidermal structure including trichomes in plant classification.
Identifikasi Bakteri Asam Laktat dan Aktivitas Penghambatan Radikal pada Jaruk Tigarun (Crataeva nurvala, Buch Ham)

Jaruk tigarun is a traditional fermented food from South Borneo made from tigarun flower that was fermented in water without salt addition. The objectives of the research were to isolate and identify the Lactic Acid Bacteria (LAB) from jaruk tigarun then to determine the DPPH radical scavenging activities of jaruk tigarun extracts. LAB was isolated from jaruk tigarun which was fermented for 7 days at room temperature. Media of MRS+CaCO 3 were used to isolate the LAB while API 50 CHL kit was utilised to identify them. Fresh flowers and jaruk tigarun were also freeze-dryed, crushed and extracted using methanol, ethanol and ethyl acetate. The total phenolic and antioxidant activity of each extract were determine with Folin-Ciocalteu method and DPPH. Three isolates of LAB were isolated and identified as Lactobacillus plantarum . The fermentation was able to increase total phenolic of jaruk tigarun which was extracted with methanol, ethanol, and ethyl acetate (53.24 ± 0.73, 44.86 ± 0.90 and 23.95 ± 0.13 mg GAE/g extract, respectively). Similarly, the antioxidant activity of jaruk tigarun that were extracted with methanol, ethanol and ethyl acetate increased to 92.68 ± 0.02 %, 92.43 ± 0.11 %, and 42.94 ± 0.02 %. Methanolic extract of jaruk tigarun has the highest IC 50 that was equal to 1.511 μg/mL. UV-Vis spectrum analysis and FT-IR were used to identify the compounds isolated from methanolic extract of jaruk tigarun resulting flavonoid as tentative identified compounds. ABSTRAK Jaruk tigarun adalah salah satu makanan fermentasi tradisional dari Kalimantan Selatan yang dibuat dengan cara merendam bunga tigarun dalam air matang selama beberapa hari. Penelitian ini bertujuan untuk mengisolasi dan mengidentifikasi bakteri asam laktat yang terlibat selama fermentasi jaruk serta mengetahui aktivitas penghambatan radikal DPPH pada jaruk tigarun. BAL diisolasi dari bunga tigarun yang difermentasi selama 7 hari pada suhu kamar sampai menjadi jaruk. Isolasi BAL menggunakan media MRS+CaCO 3 dan diidentifikasi dengan API 50 CHL Kit. Bunga segar dan jaruk tigarun juga masing-masing dikeringbekukan, dihaluskan dan diekstraksi dengan metanol, etanol dan etil asetat. Total fenolik dan aktivitas antioksidan dari masing masing ekstrak ditentukan dengan metoda Folin Ciocalteu dan DPPH. Tiga isolat BAL berhasil diisolasi dan diidentifikasi sebagai Lactobacillus plantarum . Fermentasi berhasil meningkatkan total fenolik dari jaruk tigarun yang diekstrak dengan metanol, etanol dan etil asetat berturut-turut sebesar 53,24 ± 0,73, 44,86 ± 0,90 dan 23,95 ± 0,13 mg GAE/g ekstrak. Demikian pula halnya dengan aktivitas antioksidan dari jaruk yang diekstrak dengan metanol, etanol dan etil asetat meningkat menjadi 92,68 ± 0,02 %, 92,43 ± 0,11 %, dan 42,94 ± 0,02 %. Ekstrak metanol dari jaruk tigarun memiliki IC 50 yang paling baik yaitu sebesar 1.511 μg/mL. Hasil isolasi dan identifikasi senyawa yang dimurnikan dari ekstrak metanol jaruk menggunakan analisis spektrum UV-Vis dan FT-IR diperoleh dugaan senyawa adalah golongan flavonoid.
The C02-Concentrating Mechanism and Photorespiration

Despite previous reports of no apparent photorespiration in C. , plants based on measurements of gas exchange under 2 versus 21% O, at varying [CO,], photosynthesis in maize (Zea mays) shows a dual response to varying [O,]. lhe maximum rate of photosynthesis in maize is dependent on 0, (approximately 10Y0). lhis O2 dependence is not related to stomatal conductance, because measurements were made at constant intercellular CO, concentration (Ci); it may be linked to respiration or pseudocyclic electron flow. At a given Ci, increasing [O,] above 10% inhibits both the rate of photosynthesis, measured under high light, and the maximum quantum yield, measured under limiting light (Qco,). lhe dual effect of O2 is masked if measurements are made under only 2 versus 21% O,. lhe inhibition of both photosynthesis and Qco, by O, (measured above 10% O,) with decreasing Ci increases in a very similar manner, characteristically of O, inhibition due to photorespiration. There is a sharp increase in 0, inhibition when the Ci decreases below 50 wbar of CO,. Also, increasing temperature, which favors photorespiration, causes a decrease in QCO, under limiting CO, and 40% 0,. By comparing the degree of inhibition of photosynthesis in maize with that in the CI species wheat (Triticum aestivum) at varying Ci, the effectiveness of C. , photosynthesis in concentrating CO, in the leaf was evaluated. Under high light, 30"C, and atmospheric levels of C02 (340 pbar), where there is little inhibition of photosynthesis in maize by O,, the estimated leve1 of C02 around ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in the bundle sheath compartment was 900 pbar, which is about 3 times higher than the value around Rubisco in mesophyll cells of wheat. A high [COZI is maintained in the bundle sheath compartment in maize until Ci decreases below approximately 100 Mbar. lhe results from these gas exchange measurements indicate that photorespiration occurs in maize but that the rate is low unless the intercellular [COJ is severely limited by stress.
Investigating the Determinants of Host Range Specificity of Pseudomonas aeruginosa Phage

Phage therapy, or the use of bacteriophages (phages) to kill pathogenic bacteria, represents an alternative strategy to antibiotics in combating bacterial disease in the face of growing antibiotic resistance. To use phage therapy as an antibacterial treatment, we need to understand how the phages choose their host. The following thesis outlines my work studying two particular Pseudomonas aeruginosa phages, D3 and JBD44a, which I have chosen based on structural similarity and host diversity. I have shown that D3-27 and JBD44-39 are required for complete phage particles as well as involved in specificity through heterologous complementation experiments. I have determined that JBD44a can be blocked by LPS from its host strain PA14. I have also determined that D3-27 specifically and immediately modifies LPS from its host strain PAO1 through the Cterminus. The experiments outlined have shown that D3-27 and JBD44 are involved in specificity and are found in the phage tail.