Miracle-dz/UniFAR-FTUs huggingface dataset:
Deriving compositional random generators

Generating good random values described by algebraic data types is often quite intricate. State-of-the-art tools for synthesizing random generators serve the valuable purpose of helping with this task, while providing different levels of invariants imposed over the generated values. However, they are often not built for composability nor extensibility, a useful feature when the shape of our random data needs to be adapted while testing different properties or sub-systems. In this work, we develop an extensible framework for deriving compositional generators, which can be easily combined in different ways in order to fit developers' demands using a simple type-level description language. Our framework relies on familiar ideas from the à la Carte technique for writing composable interpreters in Haskell. In particular, we adapt this technique with the machinery required in the scope of random generation, showing how concepts like generation frequency or terminal constructions can also be expressed in the same type-level fashion. We provide an implementation of our ideas, and evaluate its performance using real-world examples.
The Zebra Finch: A Synthesis of Field and Laboratory Studies

1. Systematics and phylogeny 2. Distribution and habitat 3. Morphology, domestication, and moult 4. Feeding ecology 5. Drinking, water relations, and temperature regulation 6. Coloniality and breeding ecology 7. Breeding periodicity 8. Populations 9. Social and reproductive behaviour 10. Vocalizations 11. Song 12. Sexual selection and mate choice 13. Life history and adaptations Appendices References Index
Inferring genomic sequences

Recent advances in next generation sequencing have provided unprecedented opportunities for high-throughput genomic research, inexpensively producing millions of genomic sequences in a single run. Analysis of massive volumes of data results in a more accurate picture of the genome complexity and requires adequate bioinformatics support. We explore computational challenges of applying next generation sequencing to particular applications, focusing on the problem of reconstructing viral quasispecies spectrum from pyrosequencing shotgun reads and problem of inferring informative single nucleotide polymorphisms (SNPs), statistically covering genetic variation of a genome region in genomewide association studies. The genomic diversity of viral quasispecies is a subject of a great interest, particularly for chronic infections, since it can lead to resistance to existing therapies. High-throughput sequencing is a promising approach to characterizing viral diversity, but unfortunately standard assembly software cannot be used to simultaneously assemble and estimate the abundance of multiple closely related (but non-identical) quasispecies sequences. Here, we introduce a new Viral Spectrum Assembler (ViSpA) for inferring quasispecies spectrum and compare it with the state-of-the-art ShoRAH tool on both synthetic and real 454 pyrosequencing shotgun reads from HCV and HIV quasispecies. While ShoRAH has an advanced error correction algorithm, ViSpA is better at quasispecies assembling, producing more accurate reconstruction of a viral population. We also foresee ViSpA application to the analysis of high-throughput sequencing data from bacterial metagenomic samples and ecological samples of eukaryote populations. Due to the large data volume in genome-wide association studies, it is desirable to find a small subset of SNPs (tags) that covers the genetic variation of the entire set. We explore the trade-off between the number of tags used per non-tagged SNP and possible overfitting and propose an efficient 2LR-Tagging heuristic. INDEX WORDS: Haplotype assembling, Viral quasispecies, Hepatitis C virus, Next generation sequencing, NGS, 454 pyrosequencing, Shotgun reads, VISPA, Read graph, Expectation maximization, Tagging, SNP, Genotype, Correlation, Linear Programming, Bioinformatics, Georgia State University INFERRING GENOMIC SEQUENCES
A few strokes to the family portrait of translational GTPases.

This theoretical work covers structural and biochemical aspects of nucleotide binding and GDP/GTP exchange of GTP hydrolases belonging to the family of small GTPases. Current models of GDP/GTP exchange regulation are often based on two specific assumptions. The first is that the conformation of a GTPase is switched by the exchange of the bound nucleotide from GDP to GTP or vice versa. The second is that GDP/GTP exchange is regulated by a guanine nucleotide exchange factor, which stabilizes a GTPase conformation with low nucleotide affinity. Since, however, recent biochemical and structural data seem to contradict this view, we present a generalized scheme for GTPase action. This novel ansatz accounts for those important cases when conformational switching in addition to guanine nucleotide exchange requires the presence of cofactors, and gives a more nuanced picture of how the nucleotide exchange is regulated. The scheme is also used to discuss some problems of interpretation that may arise when guanine nucleotide exchange mechanisms are inferred from experiments with analogs of GTP, like GDPNP, GDPCP, and GDP gamma S.
Exploring Opencl on a CPU-FPGA heterogeneous architecture research platform (HARP)

Intel introduced the Heterogeneous Architecture Research Platform (HARPv2)[1]. The platform interconnects a CPU (Broadwell Xeon) and a Field-Programmable Gate Array (Intel Arria 10 GX) through a high speed, low latency QPI/PCI data path providing cache coherency and shared memory. To program the FPGA, a High Level Synthesis (HLS) language, OpenCL, is made available [2]. By using HLS, a faster design cycle can be achieved compared to programming in a traditional Hardware Description Language (HDL). This, however, comes at the cost of having less control over the hardware implementation. We will investigate how efficiently OpenCL can be applied on the HARP platform.
Phospholipids of Virus-Induced Membranes in Cytoplasm of Escherichia coli

Infection of Escherichia coli with amber mutants of phage fd, in contrast to infection with wild-type phage, leads to cell death and the proliferation of intracytoplasmic membranes observed in electron micrographs at the poles of the cells. The accumulation of membranes correlates with changes in structural phospholipids, especially a marked increase in the apparent rate of formation and total amount of cardiolipin (from 4 to 20% of total radioactive phospholipids), and a compensating decline in phosphatidylethanolamine.
Quantitative trait loci associated with kernel weight and test weight in durum wheat

Kernel weight and test weight are complex traits associated with grain yield and end use quality of durum wheat (Triticum turgidum L. spp. durum (Desf)Husn. ). A doubled haploid population segregating for kernel weight (KW) and test weight (TW) was developed using the maize pollen method from the cross Kofa//Kyle*2/ Biodur (W9262-260D3). The Kofa parent has higher KW and lower TW compared to the other parent, W9262-260D3 (an F9 selection). KW and TW were determined in replicated field trials grown at three locations in western Canada, in 2000 through 2002 (7 environments). Data were analysed using mixed-model ANOVA to assess differences among genotypes. The parents were screened for polymorphism with wheat microsatellite markers, and 208 polymorphic markers that followed a 1:1 ratio of parental bands were used to genotype the population. The QTL analysis was performed by composite interval mapping using MapQTL5. Ten QTL affecting KW were localized on chromosomes 1A, 2A, 2B, 3B, 4B, 5B, 6B and 7B. Six QTL were associated with KW at six and seven environments, with substantial differences in phenotypic variation explained in this trait. QTLs at four loci were significantly associated with KW in five or fewer environments and tended to explain less of the variation. The two QTL on 2A and 4B were also significantly related to TW at five and seven environments and explained 5-13% and 4-45% of variation.
Regulation of microRNAs and Transcription

Regulation of Transcription Factors and microRNAs (miRNAs) are coordinated in the cellular genomic responses. In general, the transcription of mRNAs is regulated by transcription factors binding to the promoter regions of the targeted mRNAs. The miRNAs regulate the transcription of mRNAs to suppress the expression. The miRNAs are regulated by transcription factors, followed by the regulation of mRNAs. In this editorial, the regulatory networks of mRNAs and miRNAs are described, mainly focused on the regulatory regions of the genome. The Transcription Factors (TFs) and microRNAs (miRNAs) regulate gene expression by its binding towards the regulatory regions of genome [1]. TFs and miRNAs share many features to regulate the gene expression, in which TFs bind to the promoter regions of mRNAs and miRNAs bind to the 3 prime regions of mRNAs [1]. TFs regulate the gene expression through promoter activation or repression. Epigenetic regulations of genes include the miRNAdriven gene suppression. There are several studies in which mutation and methylation in promoter regions of miRNAs playing important roles are identified [2-4]. The SNP in promoter region of miR-10b gene is associated with breast cancer risk [2]. CpG dinucleotide methylation of the promoter region of miR-29c gene is associated with breast cancer, where the inhibition of CpG methylation with 5-aza-CdR increases miR-29c expression in basal-like breast cancer cells [3]. Demethylation in SP1 sites within promoter region of miR-23a-27a-24-2 is associated with up-regulation of the expression, proliferation and apoptosis inhibition in laryngeal cancer cells [4]. The miRNA-target interactions contain the multiple targeting of the genes in which miRNA targets 3’-untranslated region (UTR) for several genes [5]. The miR-27b targets 3’-UTR of pyruvate dehydrogenase protein X (PDHX), leading to the repression of PDHX expression and promotion of growth in breast cancer [6]. The miRNA target sites in the 3’-UTRs of genes can be predicted using known mammalian miRNA sequences [7]. The 3’UTRs from the Homo sapiens, Mus musculus and Rattus norvegicus genomes were scanned with the algorithm based on sequence complementarity between the mature miRNAs and the target site, binding energy of the miRNAtarget duplex, and evolutionary conservation of the target site sequence and target position in aligned UTRs of homologous genes [7]. The miRNA-dependent regulation of transcription Regulation of microRNAs and Transcription
Digestión del heno de trigo en comparación con la de alfalfa y ballico en novillos

El cultivo de trigo (Triticum aestivum) es el de mayor importancia en el valle de Mexicali, Mexico. Con base en su composicion quimica, la planta completa de trigo es considerada de calidad similar a la alfalfa (Medicago sativa) o al ballico (Lolium multiflorum). Por ello, se comparo la digestion del heno de trigo para grano cosechado en dos estados de crecimiento (45 y 90 d) con henos de alfalfa (floracion media) y ballico (120 d despues de sembrado). Cuatro novillos Holstein (326 ±20 kg PV) con canulas ruminales y duodenales se usaron en un diseno cuadro latino 4X4. Los tratamientos (henos) fueron: 1) alfalfa, 2) ballico, 3) trigo cosechado a 45 d (T45d) y 4) trigo cosechado a 90 d (T90d). Los novillos alimentados con T45d y T90d consumieron menos N (0.10 y 0.11 kg d–1) (p≤0.05) que aquellos alimentados con alfalfa y ballico (0.16 y 0.19 kg d–1). El flujo duodenal de FDN (1.49 kg d–1) fue mayor (p 0.05) a la de alfalfa y ballico, y superior al trigo cosechado a los 90 d. Se concluye que la digestion del heno de trigo cosechado a los 45 d fue similar a los henos de alfalfa y ballico, pero superior al trigo cosechado a los 90 d
Influenza A virus

Influenza A viruses (IAVs) are important veterinary and human health pathogens that are present worldwide. The category of viruses has a diverse host range, including a large number of avian and mammalian species. The ecology and epidemiology of influenza A viruses are very complex, involving various free-living, captive-raised, and domestic bird hosts as well as various wild and domesticated mammalian hosts within diverse environments, including humans, pigs, horses, dogs, bats, and sporadic infections in miscellaneous mammalian hosts (Figure 1.1). The other key characteristic of the virus is the genetic and antigenic variation that occurs through the combination of a high mutation rate and a segmented genome that provides an ability to rapidly change and adapt to new hosts. In the right conditions, an IAV can adapt to a new host such that it replicates and transmits efficiently to become endemic in a particular species. In general, this adaptation process produces a viral lineage that has some level of host specificity, so that it becomes more difficult to infect other species. For example, a virus that becomes endemic in horses becomes less able to infect other species such as swine or humans. The species barrier can be less clear in avian species, as a chicken-adapted virus will typically also infect other gallinaceous species, but other classes of birds, such as ducks or pigeons, may be resistant to infection. The IAV can cause a wide range of clinical disease that generally relates to the pathogenesis of the virus, whether it infects just on mucosal surfaces or causes systemic infection. The control of IAVs in animals has used a variety of tools, including vaccines, quarantines, and even culling of infected animals. The goal of eradication of the virus from a host population
An investigation of gardening in the sedentary caddisfly Tinodes waeneri across a nutrient gradient

4 Acknowledgements 5 Published chapter 6 Tables 11 Figures 12 Chapter 1 Introduction 15 1.1 General introduction 15 1.2 Periphyton 18 1.3 Nutrients and periphyton 19 1.4 Impacts of grazers on periphyton 20 1.5 Resource fertilisation and consumer-mediated nutrient recycling 22 1.6 Sedentary grazers 23 1.7 Gardening 26 1.8 The study organism Tinodes waeneri 27 1.8. 1 General ecology 27 1.8. 2 Preliminary evidence for gardening 28 1.9 Use of natural abundance stable isotopes (C and N) to investigate trophic relationships and nitrogen cycling 29 1.10 Aims of the research 31 1.11 Structure of the thesis 34 Chapter 2 Gardening by the psychomyiid caddisfly Tinodes waeneri: evidence from stable isotopes 36 2.
An efficient method for generation of bi-allelic null mutant mouse embryonic stem cells and its application for investigating epigenetic modifiers

Abstract Mouse embryonic stem (ES) cells are a popular model system to study biological processes, though uncovering recessive phenotypes requires inactivating both alleles. Building upon resources from the International Knockout Mouse Consortium (IKMC), we developed a targeting vector for second allele inactivation in conditional-ready IKMC ‘knockout-first’ ES cell lines. We applied our technology to several epigenetic regulators, recovering bi-allelic targeted clones with a high efficiency of 60% and used Flp recombinase to restore expression in two null cell lines to demonstrate how our system confirms causality through mutant phenotype reversion. We designed our strategy to select against re-targeting the ‘knockout-first’ allele and identify essential genes in ES cells, including the histone methyltransferase Setdb1. For confirmation, we exploited the flexibility of our system, enabling tamoxifen inducible conditional gene ablation while controlling for genetic background and tamoxifen effects. Setdb1 ablated ES cells exhibit severe growth inhibition, which is not rescued by exogenous Nanog expression or culturing in naive pluripotency ‘2i’ media, suggesting that the self-renewal defect is mediated through pluripotency network independent pathways. Our strategy to generate null mutant mouse ES cells is applicable to thousands of genes and repurposes existing IKMC Intermediate Vectors.
Bacillus Thuringiensis: Biology, Ecology and Safety

Characterisation. Natural Occurrence and Role in the Environment. Production and Formulation. Toxicity to Insects. Effects on Non-target Microbes and Invertebrates. Effects on Vertebrates. Persistence and Activity in the Environment. Insect and Environmental Factors Affecting Toxicity. Transmission and Dispersal. Effects in Combination with Other Insecticidal Agents. Gene Transfer. Transgenic Use of Bt Toxin Genes. Resistance. Conclusions: Safety and Risks. References. Appendices. Index.
Antimicrobial Characteristics of Edible Medicinal Herbs Extracts

To develop a natural food preservatives from medicinal herbs (62 species), antimicrobial test was performed with hot water and ethanol extracts against Escherchia coli, Listeria monocytogens and Candida albicans by paper disk method. And its result as a first screening test, 7 kinds of medicinal herbs were selected, and more precise analysis was conducted at last 3 kinds of medicinal herbs was finally selected. Therminalia chebula Retz and Rhus javanica has a broad antimicrobial spectrums and has a low MIC values. In growth inhibition test, they showed a very strong antimicrobial activity aganist Listeria monocytogens. If there has a elaborate approaches in its characteristics and properties, some good result must followed in making a powerful natural antimicrobial preservatives.
Medium and large-sized mammals in a Cerrado area of the state of Goiás, Brazil

Brazilian mammal fauna is considered to be the richest of the Neotropical region. However, in several regions of the country, there are gaps in the knowledge of its mammal fauna. Thus, we conducted a survey of the medium and large-sized mammal species in the fragmented Cerrado region in the southeast area of the state of Goias. Nonlinear transects were conducted in 28 sessions over 13 months using direct observation methods, indirect observation methods (scratches, footprints, feces and lairs) and camera trapping. Twenty-five species belonging to eight orders were recorded. The species richness estimated by the Jackknife 1 method was 24.89 (±1.61) species in the transects and 16.88 (±1.29) species in camera trap, with stabilization of the species accumulation curves. Among the recorded species, 5 were endangered at the national level, and three were globally endangered. The high species richness found in the area in addition to the presence of endangered species highlights the need for conservation measures for the study site.
Investigation of myelin membrane adhesion and compaction in the central nervous system

Myelin is a multi-layered membrane which enwraps the axons in peripheral (PNS) and central nervous system (CNS). The formation and assembly of this structure is a multi-step process that is regulated by a variety of extracellular factors. In the CNS, myelin is produced by oligodendrocytes. During development, the progenitors of these cells differentiate into mature oligodendrocytes that start to enwrap axons by myelin membrane sheaths after receiving the appropriate signal(s) from the microenvironment. However, the responsible signals to initiate this process are unknown. Here, we showed that oligodendrocytes release small microvesicles, exosomes, into the extracellular space that prevent the terminal differentiation of oligodendrocytes and subsequently myelin formation. These inhibitory effects were revealed to be mediated by activity of the RhoA-ROCK signalling cascade. Importantly, the exosome release by oligodendrocytes was significantly reduced when cells were incubated with the conditioned medium from neurons. Our results suggest that exosomes produced by oligodendrocytes maintain the cells in pre-myelinating stage, whereas in the presence of neuronal signals, exosomes secretion by oligodendrocytes is reduced and the autoinhibitory signals are relieved. Thus neurons may regulate the formation and release of oligodendroglial-derived exosomes in order to coordinate myelin membrane biogenesis and assembly. In the second part of the thesis, the question of how myelin compaction is mediated was addressed. Whereas MBP is known to organize the interaction between myelin membranes from cytoplasmic side, the molecular mechanisms underlying the interaction between the outer leaflets still remain unclear. In general, the interaction between two opposite membranes requires the expression of adhesion molecules and the removal of repulsive components. Therefore, we investigated the role of proteolipid protein (PLP), as a putative adhesive molecule, and the glycocalyx, as a repulsive structure, during myelin compaction in the CNS. We analyzed the adhesion of purified myelin particles with the primary oligodendrocytes in order to mimic the interaction between myelin layers. Using this system we showed that PLP increases the adhesiveness of myelin membrane. We also found that PLP enhances physical stability of myelin using single particle force spectrometry. In addition, we observed a significant reduction in the glycocalyx during oligodendrocyte maturation which correlated with an increase in their surface affinity towards myelin particles. Further analysis indicated that the negative charge of sugar moieties, mainly sialic acid, is responsible for the reduction in myelin adhesiveness. Therefore, we propose that the adhesive properties of PLP along with the reduction of the glycocalyx, orchestrate myelin membrane adhesion and compaction in the CNS.
Putting theory into practice: Predicting the invasion and stability of Wolbachia using simulation models and empirical studies

OF DISSERTATION PUTTING THEORY INTO PRACTICE: PREDICTING THE INVASION AND STABILITY OF WOLBACHIA USING SIMULATION MODELS AND EMPIRICAL STUDIES A new strategy to fight mosquito-borne disease is based on infections of the maternally-transmitted, intracellular bacterium Wolbachia pipientis. Estimates predict that Wolbachia infects nearly half of all insect species, as well as other arthropods and some nematodes. Wolbachia manipulates the reproduction of its host to promote infection, most commonly causing a form of conditional sterility known as cytoplasmic incompatibility. Generally, Wolbachia infections are benign and do not inflict significant costs upon its host. However, studies demonstrate that some infections are associated with substantial costs to its host. These same infections can also induce pathogen interference and decrease vector competency of important disease vectors. Theory predicts that organisms that incur costs relative to conspecifics are less competitive and their competitive exclusion is expected. In the case of Wolbachia, the bacterium can influence reproduction such that phenotypes with lower fitness may still reach fixation in natural populations. In this dissertation, I describe theoretical and empirical experiments that aim to understand the invasion and stability of Wolbachia infections that impose costs on their host. Particular attention is paid to immature insect lifestages, which have been previously marginalized. These results are discussed in relation to ongoing vector control strategies that would use Wolbachia to manipulate vector populations. Specifically, I discuss the cost of novel Wolbachia infections in Aedes polynesiensis, which decreases larval survival and overall fitness relative to wild-type mosquitoes. Then, a theoretical framework was developed to determine the significance of reductions in larval viability in relation to the population replacement disease control strategy. Further theoretical studies determined that Wolbachia infections, once established, resist re-invasion by uninfected individuals despite relatively high costs associated with infection so long as the infection produces reproductive manipulations. Additional studies determined that larvae hatched from old eggs experience reduced survival in mosquito strains with novel Wolbachia infections when compared to the wild-type. To validate the theoretical studies, model predictions were tested empirically to determine the importance of the larval viability. Finally, a COPAS PLUS machine was evaluated and its role in understanding early larval development in mosquitoes is discussed. The importance of integrated research in disease control is highlighted.