Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of novel transcription factors in the development and function of the Drosophila renal tubule

The formation and development of an organ is a complex process which involves several programmed events, including changes in cell shape and adhesion, proliferation, and differentiation. Defects in any of them lead to malformations and lethality. Investigating these processes can lead to a mechanistic understanding of organ development in health and disease conditions. They are defined by the expression and combination of specific Transcription Factors (TFs). These are active during the development of the Malpighian Tubules (MTs), of Drosophila melanogaster, which perform equivalent functions to the human kidney. Therefore, research using Drosophila proved very useful for understanding the processes of cell differentiation, proliferation, and development. To investigate which novel TFs could be involved in the development and physiology of the Drosophila kidney, an initial genetic screen of candidate TFs was performed. These selection criteria included the identification of candidate TFs regarding their patterns of expression, previous literature and human homologues involved in renal diseases. This resulted in the selection GATAe, a member of the GATA family of TFs, as the focus of this project. The effects of GATAe downregulation and overexpression were studied in the context of the MTs employing diverse genetic manipulation techniques. Silencing GATAe in any of the three main cell-types of the MTs occasioned a diverse range of phenotypes. GATAe in the MT Principal Cells (PCs) is not required for the embryonic development of the tubule, but is crucial in to ensure the correct morphology and maintenance of the adult tubule from metamorphosis. As a consequence, loss of GATAe in PCs results in a reduced lifespan, less tolerance to diverse kinds of stress, and liquid retention. Further preliminary ChIP-Sequencing analysis using a tagged line of GATAe revealed potential downstream targets of GATAe in the PCs, reinforcing its roles in cell-to-cell communication, tissue maintenance and stress response in the MTs. In Stellate Cells (SCs), GATAe is required for their survival through metamorphosis. Therefore, loss of GATAe in SCs induces a sharp reduction in this cell population in the adult stage, and impairing their secretion capabilities. Furthermore, GATAe is necessary in the Renal and Nephritic Stem Cells (RNSCs) for their migration into the ureters and lower tubules during metamorphosis. Overall, the findings reported in this PhD thesis reveal the novel functions of GATAe as a potential master regulator in the events of tissue maintenance, cell survival and cell migration. Apart from GATAe, additional TFs were identified in this project, which could serve as a base for future investigation of their possible novel roles in the fly renal system. Altogether, the data showed here provides new insights into the molecular pathways involved in the formation and maintenance of a functional organ.
Choana Morphogenesis in Developmental Stages of Muscovy Ducks

This study was performed by using fourty nine Muscovy ducks to obtained sufficient information about the development of the choanal slit from 1 to 60 days old. The choanal slit formed nearly one third of the total length of the palate in all studied ages; consisted of rostral narrow and caudal wide parts. The ratio of the length of narrow part to the total length of the choanal slit was generally low at the young ducks and increased in the older ones, while that of the wide part reversing the ratio of the narrow part. By SEM, 2 rows of papillae can be identified on the edges of the wide part of the choanal slit in all studied ages. The papillae of those rows were mostly cone-shaped with pointed apices, but some of them are dome-shaped with blunt apices were demonstrated at 60 days old and numerous openings of the intraepithelial glands were scattered within the epithelium of the choanal slit. At the edges of the choanal slit at one day old, the stratified squamous epithelium continues for a short distance before transforming into ciliated respiratory epithelium. This epithelium was interrupted by intraepithelial mucous glands. These glands and their ducts surrounded by multiple lymphatic infiltration and nodules at 15- 60 days old. The lamina propria of the palate at the level of the choanal slit contained palatine salivary glands, these glands in older ages surrounded by numerous lymphatic nodules.
Differential gene expression of heat shock protein in response to thermal stress, in two Fundulus species endemic to the Gulf of Mexico

Expression of heat shock protein genes (Hsp) could be determinant for fish to survive an increase of water temperature due to global warming. Coastal lagoons, with their intrinsic high-water temperatures, test the resilience and adaptability of fish populations to environmental change. We analyze the variation in gene expression and genetic variation of 2 endemic Fundulus species in 2 lagoons to the north of the Yucatan Peninsula. We evaluated genetic distances between species using Hsp 70 gene sequences; our results showed low genetic differentiation between both Fundulus species and also showed individuals with high genetic variability, due to non-neutral polymorphisms. Expression of 2 isoforms of Hsp70 genes was higher in F. grandissimus than in F. persimilis. These variations are prompted by water temperature and genetic differentiation of species, induced in the fish thermal stress sensitivity. Our results suggest that both species are sensitive to thermal stress; however, populations exhibit wide genetic expression range and non-neutral polymorphisms, which could be an evidence of an adaptive process to thermal stress. This capacity of the fish populations to adapt to environmental variations could be affecting fish distribution.
Localized delivery and uncaging of glutamate from MRI-visible albumin nanoclusters in the rat hippocampus using focused ultrasound

Neuropharmacological manipulations have been crucial for advancing fundamental neuroscience and elucidating the relationship between neurotransmitter function, channel kinetics, cellular signaling and behavior. However, systemic delivery of neuropharmacological agents can produce off-target effects that outweigh clinical benefit and confound preclinical results, preventing such interventions from reaching their full potential as therapeutic drugs and tools for research. Localization to specific brain regions requires injections, cannulae, pumps, or other invasive methods that can damage tissue and complicate or prevent translation to humans. Focused ultrasound (FUS) mediated blood-brain barrier (BBB) opening (BBBO) can deliver agents to specific brain regions non-invasively without damaging tissue. FUS can be targeted anywhere in the brain to open the BBB with high spatial resolution, but the use of BBB impermeable agents for localized delivery lacks temporal control, and circulating drugs can still cause systemic effects. Encapsulation of drugs prevents them from acting in non-target areas, and release from the capsules can provide temporal control. Here we demonstrate that MRI visible, albumin-based nanoclusters (NCs) can be used to encapsulate neuromodulators for non-invasive delivery to target rat brain regions via FUS facilitated BBBO. Glutamate and NBQX showed a very low baseline release rate from IV injected NCs. The NCs diffused locally into the brain with FUS facilitated BBBO and provided enhanced MRI contrast at the delivery site. Drug release into brain tissue was triggered by a second FUS treatment (FUS-release) using different parameters from the FUS used for BBBO. Furthermore, FUS-release caused a change in MRI contrast and provided in vivo confirmation of drug release. Using FUS, dye was locally released from NCs 30 minutes after delivery and release of dye into target brain regions was observed 24 hrs after delivery. The drug loading capacity of the NCs was sufficient for inducing localized changes in neural activity in response to glutamate release from NCs in vivo.
Biological Control of Insect Pest

Among all the crops, the total loss due to the pests varied for each crop likely for wheat 50%, cotton 80%, maize 31%, rice 37%, potatoes 40%, and soybean 26%. Environmental stewardship and food security are the most important factors that involved in agriculture. In many cases by the misuse of insecticide led to population resurgence, pesticide residues, and pest resistance. The microorganisms like virus, fungus, protozoan or bacterium are the active ingredient in this type of pesticides. Safety of food alludes to the conditions and practices that save the quality of food to anticipate tainting and food borne sicknesses. Natural enemies and botanicals play a vital role to control pests with different mechanisms. Microbial, for example, microscopic organisms, growths, and infections are the major biopesticides being concentrated generally to create contrasting options to chemicals. The number and development rate of biopesticides demonstrate an expanding promoting pattern in recent decades. Biopesticides are host particular and biodegradable bringing about slightest persis-tency of leftover poisonous quality. Biopesticides make key commitments to IPM and can enormously lessen ordinary pesticides. Nowadays, the globe is working on protein-based biopesticide, and it is very effective method to control the insect pest.
Determinants of resistance to nematode infection in Scottish blackface sheep

Gastrointestinal parasitism is one of the greatest causes of disease and lost productivity in domestic animals. It remains a major constraint on production and welfare in domestic animals in all geographical locations all over the world. Anthelmintic treatment is the mainstay of current control methods. However, with the widespread use of anthelmintics, the problem of parasite resistance has emerged. Other modalities of prevention and treatment are urgently needed. One of the most promising developments in this respect is the use of genetically resistant sheep. Selective breeding of animals resistant to gastrointestinal parasitism is particularly attractive, but identifying the phenotypic and genetic markers of resistance on which selection will be based is a major problem. Hence, this thesis has investigated some of the phenotypic and genetic determinants of resistance to nematode infection in Scottish Blackface sheep when naturally infected with the gastrointestinal nematodes, particularly Teladorsagia circumcincta, and how these determinants may facilitate the successful selection of resistant animals. Chapter three has investigated the seasonal pattern of T. circumcincta infection, as well as the changes in the mean and the distribution of faecal egg counts in Scottish Blackface sheep. There was no discernible pattern to egg counts with each season, and this could be attributed to factors like changes in grazing management, anthelmintic treatment, weather and humidity. Work described in chapter four has shown that there was considerable variation among populations. Faecal egg counts vary in naturally infected sheep, and mean egg counts vary among different populations and among the same population sampled at different times. In addition high mean faecal egg counts are not necessarily due to high intensities of infection, but probably reflect the contribution of species other than T. circumcincta. The present study has not found any correlations between plasma IgA activity against third-stage larvae of T. circumcincta and faecal egg (chapter five). Moreover, there was no significant correlation between growth rates in 24 week old lambs. The results suggest that IgA activity against fourth-stage larvae is probably a better marker of nematode resistance than IgA activity against third-stage larvae. This research has identified three new sequences at MHC class II DRB1 gene of Scottish Blackface sheep (chapter six). In addition, the study has provided evidence for QTL linked to parasitic infection and immune response on chromosome 3 and chromosome 20. The results reached in this study suggest that some aspects of parasite resistance are under strong genetic control, and with further research, this information could be used to select sheep for increased resistance to parasitic infection in marker assisted selection scheme. The work detailed in this thesis has further increased our understanding of the complex host/parasite relationship, and has confirmed that selective breeding, using the various phenotypic and genetic markers studied, is possible.
Comprehensive analysis of population genetics of Phoxinus phoxinus ujmonensis in the Irtysh River: Abiotic and biotic factors

Abstract As a widely distributed species along the Irtysh River, Phoxinus phoxinus ujmonensis (Kaschtschenko, 1899) was used as a model to investigate genetic diversity and population structure as well as the influence of environmental factors on population genetics. In this study, we specifically developed 12 polymorphic microsatellite loci. The analysis of microsatellite and mtDNA markers revealed a high and a moderate genetic diversity across seven populations, respectively. Moderate differentiation was also detected among several populations, indicating the impact of habitat fragmentation and divergence. The absence of isolation by distance implied an extensive gene flow, while the presence of isolation by adaptation implied that these populations might be in the process of adapting to divergent habitats. Correlation analysis showed that abiotic factors like dissolved oxygen, pH, total dissolved solids, and conductivity in water as well as biotic factors like plankton diversity and fish species diversity had impact on genetic diversity and divergence in P. phoxinus ujmonensis populations. The results of this study will provide an insight into the effect of environmental factors on genetic diversity and contribute to the study of population genetics of sympatric species.
Composition and Functional Diversity of the Urban Flora of Alfenas-MG, Brazil

Urban tree cover has important environmental and social functions and can act as ecological refuges. The objective of the present study was to investigate the taxonomic and functional diversities of urban plant communities in Alfenas, Minas Gerais State, Brazil. We sampled all trees DBH ≥ 3 cm in eight different urban green areas, recording 1,138 individuals and 119 species; two species were dominant: Poincianella pluviosa (Fabaceae) and Syagrus romanzoffiana (Arecaceae). The high species richness encountered reflected, in part, the presence of exotic species, which corresponded to 40% of the species and 25% of the total abundance. The functional diversity index (HF’) was considered low, with the predominant functional traits among the species being small size, entomophily, zoochory, evergreen leaves, and dry fruits. We recommend that future urban afforestation projects incorporate strategies that increase the use of regional species as well as the functional diversity/complexity of those environments.
Notes on Lagothrix flavicauda (Primates: Atelidae): oldest known specimen and the importance of the revisions of museum specimens

The yellow-tailed woolly monkey,Lagothrixflavicauda(Humboldt, 1812), is a large atelid endemic to the cloud forests of Peru. The identity of this species was uncertain for at least 150 years, since its original description in 1812 without a voucher specimen. Additionally, the absence of expeditions to the remote Peruvian cloud forests made it impossible to collect material that would help to confirm the true identity ofL.flavicaudaduring the 19th and first half of the 20th century. Until now, the specimens ofL.flavicaudacollected by H. Watkins, in 1925, in La Lejía (Amazonas, Peru) were thought to be the oldest ones deposited in any scientific collection. Nevertheless, after reviewing the databases of the several international museums and literature, we found one specimen ofL.flavicaudadeposited at the Muséum National d’histoire Naturelle (Paris, France) collected in 1900 by G.A. Baër, in the most eastern part of San Martín (Peru), where the presence of this species was not confirmed until 2011. Thus, Baër’s specimen represents the oldest known specimen of the yellow-tailed woolly monkey and the only one coming from the eastern part of the species’ distribution. Finally, we highlight the importance of online scientific databases for easily diagnosable species. However, caution needs to be taken when using them. We also discuss the value of scientific collections as sources of new discoveries.
Estimation and Control of Dynamical Systems with Applications to Multi-Processor Systems

System and control theory is playing an increasingly important role in the design and analysis of computing systems. This thesis investigates a set of estimation and control problems that are driven by new challenges presented by next-generation Multi-Processor Systems on Chips (MPSoCs). Specifically, we consider problems related to state norm estimation, state estimation for positive systems, sensor selection, and nonlinear output tracking. Although these problems are motivated by applications to multi-processor systems, the corresponding theory and algorithms are developed for general dynamical systems. We first study state norm estimation for linear systems with unknown inputs. Specifically, we consider a formulation where the unknown inputs and initial condition of the system are bounded in magnitude, and the objective is to construct an unknown input norm-observer which estimates an upper bound for the norm of the states. This class of problems is motivated by the need to estimate the maximum temperature across a multi-core processor, based on a given model of the thermal dynamics. In order to characterize the existence of the norm observer, we propose a notion of bounded-input-bounded-output-bounded-state (BIBOBS) stability; this concept supplements various system properties, including bounded-input-bounded-output (BIBO) stability, bounded-input-bounded-state (BIBS) stability, and input-output-to-state stability (IOSS). We provide necessary and sufficient conditions on the system matrices under which a linear system is BIBOBS stable, and show that the set of modes of the system with magnitude 1 plays a key role. A construction for the unknown input norm-observer follows as a byproduct. Then we investigate the state estimation problem for positive linear systems with unknown inputs. This problem is also motivated by the need to monitor the temperature of a multi-processor system and the property of positivity arises due to the physical nature of the thermal model. We extend the concept of strong observability to positive systems and as a negative result, we show that the additional information on positivity does not help in state estimation. Since the states of the system are always positive, negative state estimates are meaningless and the positivity of the observers themselves may be desirable in certain applications. Moreover, positive systems possess certain desired robustness properties. Thus, for positive systems where state estimation with unknown inputs is possible, we provide a linear programming based design procedure for delayed positive observers. Next we consider the problem of selecting an optimal set of sensors to estimate the states of linear dynamical systems; in the context of multi-core processors, this problem arises due to the need to place thermal sensors in order to perform state estimation. The goal is to choose (at design-time) a subset of sensors (satisfying certain budget constraints) from a given set in order to minimize the trace of the steady state a priori or a posteriori error covariance produced by a
From Darkness to Light: Art Therapy for Homeless Women with Co-occurring Opioid Use Disorder

This paper discusses the importance of art therapy for homeless women with opioid addiction. It details the importance of aspects such as mindfulness-based relapse prevention, art therapy and mindfulness, spirituality, shame reduction and anxiety reduction. The therapeutic approaches that art therapy consists of allow for women to comprehend their mental illness and better be able to understand their addictive nature. The author being an artist and one who understands family dynamics of addiction provides the reader the ability to recognize how appropriate steps are necessary for preventative measures and maintaining stability.
Authorship decisions in ecology, evolution, organismal biology and natural resource management: who, why, and how

Publication in peer–reviewed journals is essential for scientific progress including: (1) advancement of knowledge, (2) societal benefits including scientifically–based decision–making, (3) evaluation of researcher productivity, and (4) obtaining and retaining a research or faculty position and facilitating future scientific contributions. As science becomes increasingly complex so do the results necessary for publication, which frequently necessitates collaboration among scientists from multiple and diverse fields. Nevertheless, collaborative publication always includes the possibility of misunderstandings and differences of opinion. Here we first review the published literature on authorship determination for scientific publications in ecology, evolution, organismal biology and natural resource management, including consideration of what constitutes authorship, consideration of author contributions, author order in a byline, and power relationships, after which we provide several examples of realistic authorship conflict scenarios for purposes of pedagogy and discussion with colleagues and students.
Value of Supplementary Feeding for Lactating Cows Grazing Fertilized Grass Pastures in Puerto Rico

There were 282 cows that completed one or more lactations on grazing alone (T1); or grazing plus supplements of molasses (T2), ground corn (T3), high concentrate feeding (T4), limited concentrate feeding (T5), and urea + molasses (T6). Supplements for T2, T3, T5, and T6 were fed at the rate of 1 lb/2 lb of milk in excess of 22 lb/day and for T4 at the rate of 1 lb of concentrate per 2 1b of milk irrespective of level of production. Stocking rate was one cow per acre for all groups on highly fertilized pastures of star, pangola or guineagrasses in a humid area of Puerto Rico. During the dry period all cows were on grazing alone. Calvings were for the period October 1969 to February 1974. Temperature conditions and rainfall were adequate for growth of grass throughout the year. Average milk and fat yields, using age-month of calving adjusted records, were 6,912 and 245; 8,005 and 275; 8,080 and 284; 9,861 and 335; 9,300 and 315; and 8,424 and 286 1b for T1, T2, T3, T4, T5, and T6, respectively. Treatment effects were significant (P < .05) for lactation length, milk and fat yields, and final body weight but were not significant for fat percent, gain in body weight, or measures of breeding efficiency. There was no association between initial body weight and treatments. Breeding efficiency, determined as time from parturition to first estrus, and calving interval were below average on grazing alone (T1) and high supplement (T4). When milk yields were adjusted to expected yield per cow per year, the gains over grazing alone were 20.2, 21.4, 42.0, 39.0, and 33.3% for T2, T3, T4, T5, and T6, respectively. From these results medium, but not high, levels of supplementary feeding of lactating cows on high quality tropical grass pastures are economically feasible.