Miracle-dz/UniFAR-FTUs huggingface dataset:
Epic studies of dietary restriction, feeding behaviour and insulin signalling in the fruit fly, Drosophila melanogaster

Dietary restriction (DR) extends lifespan in many organisms, through unknown mechanisms that may or may not be evolutionarily conserved. Currently, different diets and techniques exist in different laboratories to implement DR in the fruit fly, Drosophila melanogaster. Furthermore, DR is often implemented by food dilution, a technique that potentially enables flies to compensate for reduced nutrition by increasing their food intake. Thus, findings from DR experiments may not be strictly comparable because of these methodological differences and uncertainties. In this thesis, I examined the ability of DR to extend life in D. melanogaster with different genotypes and on different diet compositions. I demonstrate that many of the different diets used in different laboratories are inappropriate for DR and propose an optimised protocol to insure that DR studies are standardised. I also demonstrate, by combining two available feeding assays, that D. melanogaster do not compensate their food intake when exposed to DR by food dilution. The optimised feeding assay in this thesis provides a useful tool for researchers to measure fly total feeding, which is fundamental to studies involving their behaviour, nutrition and/ or drug administration. I demonstrate with this method that food intake is not altered in the lifespan extending mutation chico, the receptor substrate of the insulin/insulin-like signaling (IIS) pathway. IIS is a highly conserved pathway responsible for growth, development, stress resistance, metabolic homeostasis, reproduction, and recently, single gene mutations in the pathway have been shown to extend lifespan. One component of the pathway, dAkt, has yet to be established as a regulator of lifespan and fecundity in D. melanogaster. Although there is sufficient literature regarding its role in growth and development in fly larvae, it is much less understood in adults. Using viable dAkt mutants, I establish that for lifespan benefits to occur, the appropriate level of IIS reduction is required.
Hot Start 7-Deaza-dGTP Improves Sanger Dideoxy Sequencing Data of GC-Rich Targets

DNA sequencing has developed substantially over the years into a more cost-effective and accurate technique for scientific advancement in medical diagnostics, forensics, systematics, and genomics. Sanger dideoxy sequencing is currently one of the most established and popular sequencing methods (Sanger et al., 1977). Over the years, sequencing methods have become automated, faster and more specific and now allow sequencing of difficult and unknown regions of DNA. Several protocols have been developed over the years which include new dye chemistries, use of modified nucleotide analogs, use of additives in the sequencing reaction, and variations to the sequence cycling parameters (Prober et al., 1987; Kieleczawa, 2006). These modified protocols allow for sequencing through difficult regions of DNA and may be applied in the pre-sequencing PCR step or in the actual sequencing reaction itself. Despite these improvements, there continues to be DNA regions that are problematic to sequence, such as AT, GT, GC-rich regions, regions high in secondary structure, hairpins, homopolymer regions, and regions with repetitive DNA sequence (Kieleczawa, 2006; Frey et al., 2008). These challenging DNA templates often result in ambiguous sequencing data which include false stops, compressions, weak signals, and premature termination of signal. In particular, sequences high in GC content still suffer from several of these problems despite all the advancements.
Microbial Genome Methods

Eukaryotic MicrobesMolecular Dissection of G Protein-Mediated Signal Transduction Using Random Mutagenesis in Dictyostelium, C.A. Parent and P.N. DevreotesCloning and Characterizing Developmentally Regulated Genes in Candida albicans, D.R. Soll, T. Srikantha, and S.R. LockhartMethods in the Analysis of Telomere Function in Saccharomyces cerevisiae, A.J. LustigGeneration, Screening, and Analysis of LACZ Fusions in Yeast, N. Burns, P. Ross-MacDonald, G.S. Roeder, and M. SnyderDevelopment of a Genetic Selection for Transcription Factor Mutants Based on a Promoter Fusion to a G418 Resistance Gene in Saccharomyces cerevisiae, A.E. Pepper and M.J. HollandGeneration of Chimeric Proteins by in Vivo Homologous Gene Recombination in Yeast: Example of an Essential P-Type ATPase, A. de Kerchove d'Exaerde, P. Supply, and A. GoffeauComparative Gene Analysis and Dominant Negative Mutations in DNA Repair, G.T. Milne, J.W. Donovan, Y. Xiao, and D.T. WeaverDNA Repair and Checkpoint Controls in Fission Yeast: A Practical Guide, A.M. Carr and J.M. MurrayProkaryotic MicrobesTechniques for the Introduction of Specific DNA Lesions Downstream from Prokaryotic RNA Polymerase Promoters and Analysis of the Transcription Products, W. Zhou and P.W. DoetschBacteria Identification by PCR-Based Techniques, G. Damiani, P. Amedeo, C. Bandi, R. Fani, D. Bellizzi, and V. SgaramellaLive Time Quantification of Bacterial Interactions in Various Environments, C.I. KadoIsolation of Complexes Containing an Escherichia coli Chaperone Protein, SecB, Bound to Newly Synthesized Polypeptides, O. Francetic and C.A. KumamotoPathogenesis and Host Resistance to Infection: A Model System and an Analysis of Capsule Synthesis and Regulation by Bacillus anthracis, S.L. Welkos and R. MarreroGenetic Manipulation of Bordetella, V. Scarlato, S. Ricci, R. Rappuoli, and M. Pizza
Influence of road transportation during hot summer conditions on oxidative status biomarkers in Iranian dromedary camels

Transportation causes stress in livestock that may alter numerous physiological variables with a negative impact on production and health. The objective of the current study was to investigate the effects of road transport on oxidative stress biomarkers in camels. Ten Iranian dromedary camels were selected and subjected to a journey of approximately 300 km in a truck by road in August 2008. Blood samples were collected immediately before loading at 8:30 A.M., after 1 h transportation, at 9:30 A.M., and at the end of the journey after unloading at 1:30 PM. Final blood sample was taken 24 h after arrival. Plasma concentrations of malondialdehyde and
The Right to Vote, The Right to Health: Voter Suppression as a Determinant of Racial Health Disparities

Civic participation is beneficial to one’s health. Conversely, being unable to participate, such as being unable to vote, may be detrimental for health. Barriers that prevent voting and civic participation, which constitute voter suppression, disproportionately impact people of color. Therefore, voter suppression may explain intractable racial health disparities. However, few studies have examined the connection between voter suppression and health. In consideration of the frequent, and increasing, reports of voter suppression in recent elections, including the rise in voter identification laws, the reduction in early voting opportunities, and the closing of polling places, the field of public health should address voter suppression as a significant determinant of health inequities. This paper suggests a framework for how voter suppression may operate to negatively impact health and well-being, especially for people of color. Lastly, directions for future research are recommended to begin to disentangle the complex relationship between civic participation and health.
Raw And Processed Hydro-Meteorological Variables Of Jucar River Basin For Feature Selection

The dataset Processed data – input WQEISS.csv was employed for the input variable selection step in Zaniolo et al., 2018. It includes monthly values of 28 hydro-meteorological variables and indexes of Jucar river basin, Spain, for the period 1986-2000, namely: 2 temporal features: day and month of the year; 12 inputs to the Jucar State Index: average monthly storage and groundwater levels, average three months river runoff, and cumulated areal precipitation over 12 months; 8 additional observed variables in the basin: three months average outflows from, and inflows to, the main reservoirs, and mean monthly areal temperatures; 6 traditional drought indicators: Standardized Precipitation Index (SPI) and Standardized Precipitation and Evaporation Index (SPEI). SPI and SPEI indicators are computed on mean monthly data over the entire basin for 3, 6, and 12 months time aggregations. The last column of the dataset reports the target variable, i.e., the monthly nominal shortage of water conveyed to the irrigation districts simulated via AQUATOOL model. For further details on the dataset please consult Zaniolo et al., 2018, or the dedicated website http://www.nrm. deib.polimi. it/? page_id=2438 The unprocessed data used to compute indices and temporal cumulations in Processed data – input WQEISS.csv are reported in table Raw Data.csv. Public observations of rainfall, streamflows and storage levels come from the SAIH (Hydrological Automatic Information System) of the CHJ (Jucar Hydrological Confederation). Users can directly download data for the last 12 months on the dedicated webpage http://saih.chj. es/chj/saih/? f while previous data records are provided for free by CHJ upon request. Observations from piezometers are downloadable from the Piezometric Network Information section section of the CHJ https://www.chj. es/es-es/medioambiente/redescontrol/Paginas/Piezometr%C3%ADa.aspx.
Caracteres epidérmicos foliares de valor diagnóstico en la identificación de plantas leñosas del Chaco occidental

Se describen y se ilustran las estructuras de la epidermis foliar de 36 especies de plantas lenosas presentes en el Chaco occidental argentino (provincia de Salta),incluyendo una clave para la identificacion de fragmentos de hojas que se encuentran en las heces y en el contenido estomacal y ruminal de animales. Los principales caracteres utilizados para la identificacion fueron la pared de las celulas epidermicas propiamente dichas, tricomas, estomas y ornamentacion de la cuticula.
Complex pedigree analysis to detect quantitative trait loci in dairy cattle

In dairy cattle, many quantitative traits of economic importance show phenotypic variation. For breeding purposes the analysis of this phenotypic variation and uncovering the contribution of genetic factors is very important. Usually, the individual gene effects contributing to the quantitative genetic variation can not be distinguished. Developments in molecular genetics, however, have resulted in the identification of polymorphic sites in the genome, which are called genetic markers. Genetic markers have opened the way to follow segregation of chromosomal segments in families. Through the use of these genetically marked chromosomal segments, detection and mapping the genes affecting quantitative traits ("quantitative trait loci" or "QTL") becomes possible. After identifying QTL, genetic markers may, for example, be used to select animals at a younger age and/or to improve the accuracy of predictions of genetic merit. The aim of this thesis is to contribute to the efficient utilization of genetic marker and quantitative trait data in detecting and utilizing single QTL in complex pedigrees in dairy cattle breeding programs. Implementation of marker-assisted selection in dairy cattle has been hampered by the lack of identified QTL, and the lack of efficient methods for marker-assisted genetic evaluation for situations with incomplete marker data. The development of statistical methods forms the core of this thesis. Methodology is based on Bayes theory and implemented via Markov chain Monte Carlo algorithms, such as the Metropolis-Hastings algorithm and the Gibbs sampler. Throughout this thesis, a mixed linear model with two random genetic components, i.e., effects due to a marked QTL and residual polygenes, was assumed. These components are assumed to be normally distributed and independent in the base population. To arrive at a flexible method for full pedigree analysis, an animal model is taken as the starting point. Covariances among genetic effects of related individuals are taken into account via the numerator relationship matrix for polygenes and the gametic relationship matrix for QTL.In most chapters, the developed methodology is empirically tested by the use of simulated data. In one chapter, however, experimental data on bovine chromosome six is analyzed to estimate the position and size of a putative QTL for protein percent. At bovine chromosome six , a QTL for protein percent was identified. The most likely position of this QTL is similar to that previously reported by Spelman and co-workers. The presence of a second putative QTL for protein percent is uncertain and requires further research probably with a two-QTL model. In the general discussion, the presented Bayesian method is compared to other methods for QTL analysis in complex pedigrees. Our method at this moment is unique in being able to handle complex pedigrees in outbred populations with missing marker data. The general discussion is completed with a brief review of issues related to practical implications for marker-assisted genetic evaluation in dairy cattle breeding schemes.
Presumed Chemosensory Hairs in Talitrid Amphipods (Crustacea)

Abstract Sensory hairs in a number of Talitrid Amphipods were studied by means of scanning electron microscopy. The general pattern is closely similar in all species although minor specific differences seem to occur. Two main morphological types of sensory hairs are present, viz (1) thin-walled hairs and (2) hairs protected by a spine from which only the distal part of the hair protrudes subterminally, giving the impression of a two-tipped spine. Some intermediate types also occur. The terminal part of both types of hair, however, is of exactly the same type with leaf-like protecting cuticular structures and a terminal pore. Therefore it is concluded that they all have at least a similar function, and a previously published analysis of antennular thin-walled hairs in two of the species makes it highly probable on morphological grounds that this function is chemosensory. Both types of hairs are widely distributed on the appendages, although the spine-hairs are more prevalent on the pereiopods, uropods, and telson. Practically every spine carries a sensory appendage and it can be concluded that a wealth of sensory information is received by them. The body wall is provided with numerous structures described in the paper, the function of which is unknown but may well be sensory.
Model logitowy jako narzędzie prognozowania obciążeń podatkowych działek gruntu w wyniku wprowadzenia podatku ad valorem

Obowiązujący w Polsce system opodatkowania nieruchomości zurbanizowanych bazuje na powierzchni (w przypadku opodatkowania gruntow) oraz powierzchni uzytkowe (w przypadku budynkow i lokali). W wielu krajach, takze niektorych nalezących do krajow postsocjalistycznych, obowiązującym system opodatkowania jest system oparty na wartości nieruchomości. W Polsce wielokrotnie rozpoczynano dyskusje polityczne dotyczące reformy opodatkowania nieruchomości. Podstawowa obawa dotycząca podatku od wartości nieruchomości to zwiekszenie obciązen podatkowych. W artykule zaproponowano wykorzystanie modelu logitowego do prognozowania zwiekszenia tych obciązen. Podstawą rozwazan bylo przeprowadzenie (we wcześniejszych badaniach) masowej wyceny gruntow zlokalizowanych na terenie wybranej gminy. Dzieki zastosowaniu modelu logitowego powstaje mozliwośc prognozy zwiekszenia obciązen podatkowych. Wyniki takich prognoz mogą sie przyczynic do zmiany przekonania o tym, ze reforma opodatkowania nieruchomości musi doprowadzic do wzrostu obciązen podatkowych dla kazdego podmiotu opodatkowania.
Serious Game Patterns

Social development theory claims that social interactions play a key role in learning. This dissertation has developed several serious games patterns, in particular the synchronization point and motivational leaderboard pattern, to increase social interaction in serious games. These patterns were empirically evaluated in several experiments with up to 306 participants. The results demonstrate that the synchronization point pattern increases collaboration and the motivational leaderboard pattern increases retention and performance significantly.
Modelling the elimination of hepatitis C virus infection as a public health threat

The revolution in hepatitis C virus treatment through the development of direct-acting antivirals has generated international interest in the elimination of the disease as a public health threat. This led the World Health Organization to establish viral hepatitis elimination targets. Whether these targets can be met and how intervention programmes should be scaled up in specific settings are open questions. This thesis details how mathematical models were developed and used to answer these questions. A model of the hepatitis C epidemic was designed and the impact of a range of intervention strategies estimated. A comprehensive package of prevention, screening and treatment interventions could avert 15million new infections and 1.5million premature deaths, falling narrowly short of the WHO targets. Nevertheless, achieving these gains relies on a dramatic scaling up of harm reduction interventions to people who inject drugs (to 40% coverage), continued reductions in risk of hepatitis C infection in the remaining population and implementation of screening programmes that result in 90% of hepatitis C infected people being diagnosed. Meeting global targets will only occur if concrete strategies are implemented at the local level. We worked with policy makers in Yunnan Province, China, to devise and assess a range of screening strategies. A combined suite of interventions could reduce incidence by 49% andmortality by 56% by 2030 with treatment costs over that period of 492 million Chinese Yuan. Targeted screening that averts future infections is more cost effective than general screening; cost effectiveness hinges upon reducing DAA costs below current list prices in China. Implementing hepatitis C interventions offers a net economic benefit. This work provides a two-sided view of tackling the public health burden of hepatitis C. Considered globally, significant steps towards elimination can be taken provided ambitious intervention targets are met. Considered locally, our analysis of the hepatitis C epidemic in Yunnan illustrates that interventions can be scaled up in a pragmatic way that offers economic benefits in addition to reducing the burden of disease ultimately borne by patients.
Skeletal Muscle Function, Morphology, and Biochemistry in Ts65Dn Mice: A Model of Down Syndrome

A common clinical observation of persons with Down syndrome at all developmental stages is hypotonia and generalized muscle weakness. The cause of muscle weakness in Down syndrome is not known and there is an immediate need to establish an acceptable animal model to explore the muscle dysfunction that is widely reported in the human population. Using a combination of functional, histological, and biochemical analyses this dissertation provides the initial characterization of skeletal muscle from the Ts65Dn mouse, a model of Down syndrome. The experiments revealed that Ts65Dn muscle over-expresses SOD1 protein but this did not lead to oxidative stress. Ts65Dn soleus muscles displayed normal force generation in the unfatigued state, but exhibited muscle weakness following fatiguing contractions. We show that a reduction in cytochrome c oxidase expression may contribute to the impaired muscle performance in Ts65Dn soleus. These findings support the use of the Ts65Dn mouse model of Down syndrome to delineate mechanisms of muscle dysfunction in the human condition. SKELETAL MUSCLE FUNCTION, MORPHOLOGY, AND BIOCHEMISTRY IN TS65DN MICE: A MODEL OF DOWN SYNDROME By Patrick M. Cowley B.A. Ithaca College, 2002 M.S. Ithaca College, 2005
Fitness in Narcissus hybrids: low fertility is overcome by early hybrid vigour, absence of exogenous selection and high bulb propagation

1. The evolutionary fate of natural hybridization is determined by the fitness of hybrids. Specifically, the survival of newly formed hybrids is affected by intrinsic genetic incompatibilities and/or genotype–environment interactions. The influence of these factors on the evolutionary potential of two natural hybrids of Narcissus has been assessed. Fitness components were estimated in early experimental F1 hybrids as well as in natural hybrids of unknown descent.
Etude des fonctions mitotiques du domaine amino-terminal de CENP-A

Le variant d'histone CENP-A est le facteur responsable de la determination epigene- tique du centromere. Il permet le recrutement de nombreuses proteines centromeriques, et constitue ainsi la brique fondatrice du kinetochore. Il possede un domaine amino-terminal non structure dont la fonction precise reste encore a elucider, bien qu'il soit deja etabli chez certaines especes que ce domaine est requis pour le bon fonctionnement du cen- tromere et consequemment le bon deroulement de la mitose. Nous avons construit des lignees cellulaires humaines exprimant stablement diverses formes mutantes de CENP-A, qui nous ont permis de realiser des experiences de pseudogenetique en supprimant l'ex- pression de la proteine CENP-A endogene. Nous observons une augmentation drastique du taux de defauts de segregation des chromosomes et de cellules plurinucleees dans des cellules exprimant uniquement le domaine globulaire de CENP-A, ce qui est en accord avec les donnees de la litterature et confirme l'importance du domaine amino-terminal. Un phenotype similaire est observe dans des cellules exprimant une proteine CENP-A entiere mais dont le domaine amino-terminal n'est pas phosphorylable. Nos resultats montrent l'implication de la phosphorylation de la serine de CENP-A dans le bon deroulement de la mitose, et suggerent que la fonction mitotique du domaine amino-terminal est centree sur cette seule phosphorylation.
Use of Sodium Dithionite for Groundwater Restoration Following Uranium In-Situ Recovery Mining at the Smith Ranch-Highalnd Site in Wyoming

Uranium in-situ recovery (ISR) is a subsurface aqueous mining technique used to extract uranium from sandstone roll-front deposits. After ISR mining, groundwater restoration is conducted to decrease concentrations of residual U(VI) and other contaminants leftover in the groundwater. Sodium dithionite, a strong chemical reductant, is being tested for use in groundwater restoration following uranium ISR at the Smith Ranch-Highland site in Wyoming. Sodium dithionite has been used to remediate chromium plumes by creating an in-situ permeable reactive barrier, but there has been no work using sodium dithionite for groundwater restoration following uranium ISR mining. Laboratory batch and column experiments, and two push-pull field tests were conducted to test the reductive capacity imparted to post-mined sediments from the Smith Ranch-Highland site after treatment with sodium dithionite. In one laboratory column and batch experiment, where sediments had high uranium and organic carbon content, sodium dithionite did not impart a reductive capacity to the post-mined sediments, suggesting dithionite reacts differently with organic carbon which inhibits the reduction of U(VI) to U(IV). In laboratory batch and column experiments with post-mined sediments low in organic carbon content, and in the push-pull field tests, sodium dithionite imparted a