Miracle-dz/UniFAR-FTUs huggingface dataset:
Counterfactuals in the 'Aeneid'

This thesis examines the counterfactuals, both syntactic and structural, of Virgil's Aeneid. These are alternative stories presented by speakers (primary narrator and characters) as conceivable but only partly or not at all materialized; they clash with the more visible story of the fated advent of Rome and Augustus. The purpose of the study is to envisage some alternatives to the Aeneid as readable from the actualization, in some cases already under way, of the counterfactuals scrutinized; these include the universe and the text not starting or collapsing, Troy surviving, the Greeks losing the Trojan war, Aeneas repeatedly failing to carry out his mission, and Turnus defeating him. Virgil's counterfactual language and images are examined in relation to a number of obvious sources as well as developments contemporary to Virgil, as relevant to the individual case: Homer (particularly if not constructions in the Iliad: A would have happened, if not B), pre-Stoic and Stoic studies of conditionals, linguistic changes in Latin (uses of the indicative / subjunctive and coordination / subordination), the practice of comparison between pairs of differently actualized entities in Livy and earlier historians (synkrisis) and political language in Horace. The main strands of modern thought on counterfactuality from logical, linguistic, narratological and psychological viewpoints are also taken into consideration. An attempt has been made to examine all syntactic counterfactuals spoken in the Aeneid, including some but not all cases of possible counterfactuals, such as wishes, and two types of structural counterfactuals: those which become such when characters are saved through the diversion of weapons, and those which depict partial Troys. The different types of analyses have been as far as possible integrated. My conclusion is that Virgil was revealing but also deflecting alternative stories to that of the destiny of Rome and Augustus as well as those of Aeneas' career circulating at the time.
Design Genetic Fluorescent Probes to Detect Protease Activity and Calcium-Dependent Protein-Protein Interactions in Living Cells

Proteases are essential for regulating a wide range of physiological and pathological processes. The imbalance of protease activation and inhibition will result in a number of major diseases including cancers, atherosclerosis, and neurodegenerative diseases. Although fluorescence resonance energy transfer (FRET)-based protease probes, a small molecular dye and other methods are powerful, they still have drawbacks or limitations for providing significant information about the dynamics and pattern of endogenous protease activation and inhibition in a single living cell or in vivo. Currently protease sensors capable of quantitatively measuring specific protease activity in real time and monitoring activation and inhibition of enzymatic activity in various cellular compartments are highly desired. In this dissertation, we report a novel strategy to create protease sensors by grafting an enzymatic cleavage linker into a sensitive location for changing chromophore properties of enhanced green fluorescent protein (EGFP) following protease cleavage, which can be used to determine protease activity and track protease activation and inhibition with a ratiometric measurement mode in living cells. Our designed protease sensors exhibit large relative ratiometric optical signal change in both absorbance and fluorescence, and fast response to proteases. Meanwhile, these protease sensors exhibiting high enzymatic selectivity and kinetic responses are comparable or better than current small peptide probes and FRET-based protease probes. Additionally, our protease sensors can be utilized for real-time monitoring of cellular enzymogen activation and effects of inhibitors in living cells. This novel strategy opens a new avenue for developing specific protease sensors to investigate enzymatic activity in real time, to probe disease mechanisms corresponding to proteases in vitro and in vivo, and to screen protease inhibitors with therapeutic effects. Strong fluorescence was still retained in the cleaved EGFP-based protease sensors, which stimulated us to identify the EGFP fragment with fluorescence properties for further understanding chromophore formation mechanisms and investigating protein-protein interactions through fluorescence complementation of split EGFP fragments. Through fusing EF-hand motifs from calbindin D9k to split EGFP fragments, a novel molecular probe was developed to simultaneously track the calcium change or calcium signaling pathways and calcium-dependent protein-protein interaction in living cells in real time. INDEX WORDS: Protease sensor, Ratiometeric measurement, EGFP, Calcium-dependent, Protein-protein interactions, Fluorescence complementation DESIGN GENETIC FLUORESCENT PROBES TO DETECT PROTEASE ACTIVITY AND CALCIUM-DEPENDENT PROTEIN-PROTEIN INTERACTIONS IN LIVING CELLS
Identification of Sox8 and Ndp as Novel Targets of the Hedgehog Signaling Pathway in the Retina

ii ACKNOWLEDGEMENTS iv LIST OF FIGURES viii . LIST OF TABLES x ABBREVIATIONS xi CHAPTER 1: INTRODUCTION 1 1.1 Hh Proteins 2 1.1.1 Hh isoforms 2 1.1.2 Hedgehog ligand processing 2 1.1.3 Hh signaling pathway 5 1.1.4 Hh binding proteins 13 1.2 Function of Hh signaling 14 1.2. 1 Embryonic development 14 . 1.2. 2 Homeostasis and regeneration 15 1.2. 3 Hh signaling, disease and cancer 15 1.3 The Retina 17 1.3. 1 Structure 17 1.3. 2 Retinal development 20 1.3. 3 Hh signaling during mouse retinal development 24 1.3. 4 Hh target genes in the retina 25 1.4 Sox8 and Ndp, novel targets of the Hh pathway 28 1.4. 1 Sox8 (Sry-like high-mobility-group box 8) 28
Metabolic Stability Screen in Drug Discovery

Optimizing metabolic stability is an important aspect of drug discovery. The optimal drug candidates should be metabolically stable enough to allow a convenient dosing schedule, such as once a day. At the same time, the drug should also be able to be metabolized and excreted from the body after the therapeutic goal is achieved, to avoid potential toxicity. Ideally, drug candidates should be cleared via multiple pathways to avoid possible drug-drug interactions or enzyme polymorphism effects. Keywords: cytochrome P450; human liver microsomes; S9 fractions; hepatocytes; metabolic stability; in vitro–in vivo correlation
Determining impacts of habitat modification on diversity of tropical forest fauna: the importance of spatial scale

1. There is an urgent need to understand the impacts of anthropogenic habitat disturbance on biodiversity in tropical forests, but no consensus has yet emerged. We reviewed the literature for the most frequently studied taxon (birds, 37 studies) and found that increased and decreased diversity in response to disturbance (selective logging and shifting agriculture) were reported with approximately equal frequency. 2. The spatial scale at which studies were carried out significantly affected the reported response to disturbance: studies where disturbed and undisturbed habitats were sampled at large spatial scales were more likely to report increased diversity following disturbance, whereas studies that sampled habitats at small spatial scales were more likely to report decreased diversity. These results were not a consequence of sampling method: we divided the studies into those using capture methods and those using observation methods and the same result was obtained when the analysis was restricted to only those studies using observation methods. 3. Previously, we have shown that reported impacts of disturbance on Lepidoptera are also affected by the spatial scale of study. We reviewed the Lepidoptera literature published since then and showed that all 12 new studies conformed to the predicted pattern. 4. While sampling scale significantly affected the reported responses of both birds and Lepidoptera, there were opposite effects of scale in the two taxa: large-scale bird studies and small-scale Lepidoptera studies were more likely to report increased diversity following disturbance. Bird studies were generally carried out at larger spatial scales than those of Lepidoptera and these opposite impacts of scale were probably due to a non-linear effect of habitat disturbance on habitat heterogeneity at different spatial scales. 5. Synthesis and applications. The rapid loss and degradation of tropical forests means that an understanding of the general patterns of responses of species to habitat disturbance is urgently needed. However, there has been little discussion of the most appropriate methods to ensure comparability of results between studies. Data presented here indicate that the spatial scale of sampling chosen in studies has a marked effect on the results obtained, and future studies need to account for this by examining explicitly the effects of disturbance at different spatial scales. The effect of spatial scale differs between taxa, and this may explain why the search for indicator taxa of disturbance effects has so far proved elusive.
Effects of the Double-Ovsynch program on some reproductive parameters at different postpartum days in dairy cows.

Bu çalışmada postpartum farklı günlerde uygulamaya başlanan Double-Ovsynch protokolünün çeşitli fertilite parametreleri üzerine olan etkilerinin değerlendirilmesi amaçlanmıştır. Çalışma 51 adet Holstein ırkı inek üzerinde yürütüldü ve hayvanlar 4 gruba ayrıldı. Grup 1, grup 2 ve grup 3’ün her birinde bulunan 12 hayvan sırasıyla postpartum 25. , 32. ve 39. günlerde bulunuyordu. Grup 4 kontrol grubu olarak değerlendirildi ve bu gruptaki hayvanlara (n=15) postpartum 40. güne kadar hiçbir uygulama yapılmadı, bu günden sonra östrus gösterenlere suni tohumlama işlemi uygulandı. Çalışma grubundaki ineklere ise 0. gün GnRH, 7. gün PGF2, 10. gün GnRH, 17. gün GnRH ve 24. gün PGF2 uygulandı. PGF2 uygulamasından sonraki 56. saatte GnRH uygulaması yapıldı ve bunu takiben 16-20. (ortalama 18. saatte) saatlerde suni tohumlama işlemi uygulandı. Çalışma gruplarında senkronizasyon oranları %66.67 ile %91.67 arasında değişirken, grup 2 ve grup 3’de yüksek oranda senkronizasyon gözlendi. Çalışma grubundaki hayvanlarda ilk suni tohumlama sırasında çok az oranda östrus belirtileri gözlendi (P<0.05). Çalışmada birinci tohumlamada en yüksek gebe kalma oranları (%58.33) grup 2 ve grup 3’de belirlendi. Kümülatif gebelik oranları en yüksek olarak (%91.67) grup 1 ve grup 2’de gözlendi. Sonuç olarak, ineklerde değişik postpartum dönemlerde başlanan Double-Ovsynch uygulaması ile östrus tespitine gerek kalmadan yüksek oranlarda reprodüktif performans elde edilebileceği belirlendi.
Carbohydrate Digestibility and Resistant Starch of Steamed Bread

Sixteen Australian hard and soft wheats and two U.S. hard wheats were milled into flours (break and reduction) for preparation of steamed breads. Chemical composition and rheological properties of the flour were determined. Steamed breads were analyzed for carbohydrate digestibility and resistant starch. There was no relationship between flour type, protein content and specific volume of steamed breads. Carbohydrate digestibility of steamed breads from soft wheat flour was higher than that of breads from hard wheat flour. Reduction flours produced steamed breads with higher carbohydrate digestibility than break flours. Resistant starch was higher in steamed breads from soft wheat flours than in those from hard wheat flours. Reduction flour produced higher resistant starch levels than break flours. Commercial white bread had resistant starch levels similar to those of steamed breads from soft wheat flour and hard wheat reduction flour. Verdaulichkeit der Kohlenhydrate und resistente Starke in bedampftem Brot. Sechzehn australische Hart- und Weichweizen sowie zwei U.S.-Hartweizen wurden zu Mehlen (grob und fein) vermahlen zur Herstellung von bedampften Broten. Die chemische Zusammensetzung und die rheologischen Eigenschaften des Mehls wurden bestimmt. Bedampfte Brote wurden hinsichtlich Verdaulichkeit und resistenter Starke analysiert. Es gab keinen Zusammenhang zwischen Mehyltype, Proteingehalt und spezifischem Volumen der bedampften Brote. Die Kohlenhydratverdaulichkeit bedampfter Brote von Weichweizenmehlen war hoher als die der Brote aus Hartweizenmehl. Feine Mehle ergaben bedampfte Brote mit hoherer Kohlenhydratverdaulichkeit als die aus Grobmehlen. Der Gehalt an resistenter Starke war bei Weichweizenmehlen hoher als bei Hartweizenmehlen. Feinweizenmehle erzeugten mehr resistente Starke als Grobmehle. Handelsubliches Weisbrot enthielt ahnliche Mengen an resistenter Starke wie bedampfte Brote aus Weichweizenmehl und Hartweizen-Feinmehl.
Light and nutrient effects on the settling characteristics of the sea ice diatom Nitzschia frigida

Sea ice‐algae contribute significantly to Arctic primary production and play an important role in the life histories of planktonic and benthic consumers after the algae are released from the sea ice habitat. Following export from the ice, the extent to which fresh algal material is available to planktonic or benthic consumers is dependent on residence time in the water column, initially related to particle settling rate. Laboratory experiments using isolated Nitzschia frigida, a common sea ice diatom, were conducted to ascertain the effects of nutrient (N, P, and Si) and light limitation on settling characteristics of the algal material. While settling characteristics of N‐ and P‐limited cultures were not significantly different from controls grown under light and nutrient‐replete conditions, significant differences from the controls were found for light and Si limitation. Differences between treatments were evidenced by changes in the proportion of each population that had particular settling rates, rather than by changes in the range of settling rates measured within a treatment. Thus, fast (> 20 m d−1) and slow‐sinking particles (< 2 m d−1) were found in all cultures, but compared to the controls, a larger percentage of fast‐sinking particles were observed under Si limitation while a larger percentage of slow‐sinking material was observed under light limitation. While N. frigida is just one member of the sea ice algal assemblage, its prevalence in Arctic land‐fast sea ice means these results may be representative of the broader Arctic nearshore ice‐algae community. As such, abiotic conditions within Arctic sea ice, such as nutrient availability and depth of overlying snow (which affects the light field in the ice), could influence the amount of algae‐derived material available to different components of the underlying marine food web.
Feature regularization and learning for human activity recognition.

Feature extraction is an essential component in the design of human activity recognition model. However, relying on extracted features alone for learning often makes the model a suboptimal model. Therefore, this research work seeks to address such potential problem by investigating feature regularization. Feature regularization is used for encapsulating discriminative patterns that are needed for better and efficient model learning. Firstly, a within-class subspace regularization approach is proposed for eigenfeatures extraction and regularization in human activity recognition. In this approach, the within-class subspace is modelled using more eigenvalues from the reliable subspace to obtain a four-parameter modelling scheme. This model enables a better and true estimation of the eigenvalues that are distorted by the small sample size effect. This regularization is done in one piece, thereby avoiding undue complexity of modelling eigenspectrum differently. The whole eigenspace is used for performance evaluation because feature extraction and dimensionality reduction are done at a later stage of the evaluation process. Results show that the proposed approach has better discriminative capacity than several other subspace approaches for human activity recognition. Secondly, with the use of likelihood prior probability, a new regularization scheme that improves the loss function of deep convolutional neural network is proposed. The results obtained from this work demonstrate that a well regularized feature yields better class discrimination in human activity recognition. The major contribution of the thesis is the development of feature extraction strategies for determining discriminative patterns needed for efficient model learning.
Molecular methods in developmental biology : xenopus and zebrafish

The Animal Cap Assay, Jeremy Green. Cell and Tissue Transplantation in Zebrafish Embryos, Toshiro Mizuno, Minori Shinya, and Hiroyuki Takeda. Ribonuclease Protection Analysis of Gene Expression in Xenopus, Craig S. Newman and Paul A. Krieg. Quantitative Analysis of mRNA Levels in Xenopus Embryos by Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR), Oliver C. Steinbach and Ralph A. W. Rupp. Wholemount In Situ Hybridization of Xenopus and Zebrafish Embryos, Joanne Broadbent and E. Mary Read. In Situ Hybridization to Sections of Xenopus Embryos, David Bertwistle. Zebrafish Immunohistochemistry, Rachel Macdonald. Immunohistochemistry of Xenopus Embryos, Carl Robinson and Matthew Guille. Preparation and Testing of Synthetic mRNA for Microinjection, Wendy Moore and Matthew Guille. Microinjection into Xenopus Oocytes and Embryos, Matthew Guille. Microinjection into Zebrafish Embryos, Qiling Xu. Expression from DNA Injected into Xenopus Embryos, Ondine Cleaver and Paul A. Krieg. Promoter Analysis in Zebrafish Embryos, Jos Joore. Transient Transgenesis in Xenopus laevis Facilitated by AAV-ITRs, Yuchang Fu, Donghui Kan, and Sylvia Evans. Band-Shift Analysis Using Crude Oocyte and Embryo Extracts from Xenopus laevis, Rob Orford and Matthew Guille. DNA Footprinting Using Crude Embryo Extracts from Xenopus laevis, Rob Orford, Darren Mernagh, and Matthew Guille. Mapping Protein-DNA Interactions Using In Vivo Footprinting, David Warshawsky and Leo Miller. Index.
The Functional Role of Dystrophin in the Heart: Implications for Inherited and Non-Inherited Heart Disease.

Inbred mouse strains play a critical role in biomedical research. Genetic homogeneity within inbred strains and their general amenability to genetic manipulation has made them an ideal resource for dissecting the physiological function(s) of individual genes. However, the inbreeding that makes inbred mice so useful also results in genetic divergence between them. This genetic divergence is often unaccounted for, but may be a confounding factor when comparing studies which have utilized distinct inbred strains. Here, we compared the cardiac function of C57BL/6J mice to seven other commonly used inbred mouse strains: FVB/NJ, DBA/2J, C3H/HeJ, BALB/cJ, 129X1/SvJ, C57BL/10SnJ and 129SvImJ. The assays used to compare cardiac function were the ex vivo isolated Langendorff heart preparation and in vivo real time hemodynamic analysis using conductance micromanometry. We report significant strain–dependent differences in cardiac function between C57BL/6J 1 This manuscript was previously published in Physiological Genomics and is copyrighted by the American Physiological Society (APS). It has been reproduced here in accordance with APS copyright policy (http://www.the-aps.org/publications/authorinfo/copyright.htm). 56 and other commonly used inbred strains. C57BL/6J maintained better cardiac function than most inbred strains during ex vivo ischemia, particularly when compared to 129SvImJ, 129X1/SvJ and C57BL/10SnJ strains. However, during in vivo acute hypoxia 129X1/SvJ and 129SvImJ maintained relatively normal cardiac function, whereas C57BL/6J animals showed dramatic cardiac decompensation. Additionally, C3H/HeJ showed rapid and marked cardiac decompensation in response to esmolol infusion compared with other strains. These findings demonstrate the complexity of genetic divergence between inbred strains on cardiac function. These results may help inform analysis of gene ablation or transgenic studies and further demonstrate specific quantitative traits that could be useful in discovery of genetic modifiers relevant to cardiac health
Molecular Mapping in Barley: Shifting from the Structural to the Functional Level

As a resource for structural and functional barley genome analysis, more than 140 000 ESTs (expressed sequence tags) were generated from 22 cDNA libraries that yielded 25 224 tentative unigenes. About 50% of them belong to gene families. The size of the complete transcriptome is estimated to comprise between 35 000 and 75 000 genes. The barley EST collection is a rich source for the development of novel markers including SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). Several bioinformatic tools have been developed facilitating the computer-assisted analysis of EST databases for the presence of either SNPs or SSRs and the development of SNP-derived CAPS (cleaved amplified polymorphic sequences) markers. In an attempt to systematically map barley genes a high-density transcript map is under construction and presently comprises more than 1000 markers. This map is a gateway to comparative genomics with particular emphasis on the rice genome. 65% of the mapped ESTs showing a significant homology to rice ESTs were found to display a syntenic relationship between barley and rice. Thus, the barley EST resource facilitates the rapid and systematic transfer of genetic information from rice to barley and other Triticeae, which can readily be exploited for marker saturation of defined chromosome regions and their detailed comparison to rice. In the context of a functional genomics study, the complex trait “malting quality” is investigated using a barley cDNA array. By correlating the phenotypic malting trait data of selected barley lines with the corresponding expression profiles, a set of candidate genes was identified and further verified by genetic analysis.
Frecuencia del alelo Q204X del gen miostatina, en hatos de ganado Charolais de la región noreste de México

Frequency of the myostatin Q204X allele in Charolais cattle herds in northeast Mexico was determined by sampling 289 animals from four herds. Each herd had allele carriers, with a total of 15 carriers identified, and overall genotypicfrequency of 5.2 % and allelic frequency of 2.6 %. The number of carriers per herd was not significantly different (P>0.05) between herds, although two herds had more than 8 % carriers. The allele was in Hardy-Weinberg equilibrium within the studied herds. Evaluation of genes that affect quantitative traits, such as the myostatin Q204X allele, is vital to determining their role and potential applications in breeding strategies.
Original Article Induction of antigen-specific immune tolerance by TGF-β- induced CD4+Foxp3+ regulatory T cells

Like natural CD4+CD25+ Treg cells, TGF-β-induced Treg cells also prevent allograft rejection in MHC- mismatched organ transplantation models. In analyzing this effect with greater detail, we determined that injection of TGF-β-induced, alloactivated CD4+CD25+ cells induces antigen-specific immune tolerance in vivo. Increased CD4+CD25+ cells in recipients contribute to this immune tolerance. In addition, adoptive transfer of TGF-β-induced CD4+CD25+ cells did not result in significant toxic and side effects in recipients. These results indicate that TGF-β-induced, alloactivated CD4+CD25+ cells may provide a safe and effective approach to protect MHC-mismatched organ grafts from rejection in a clinical setting.