Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecological Risk Assessment

Ecological Risk Assessments (ERA) are performed to evaluate the likelihood of adverse ecological effects occurring as a result of exposure to physical or chemical stressors. These stressors are defined as any biological, physical, or chemical factor that causes adverse responses in the environment. An ERA evaluates any potential harm that human activities have on living organisms within ecosystems. Within the framework of an Ecological Risk Assessment, scientific information is developed, organized and presented so that it is relevant to environmental decisions.
Bartonella henselae inhibits cellular apoptotic regulators to ensure survival

Human pathogens survive anti-pathogen host immune assault by either circumventing or evading the host immune response. Bartonella henselae, an intracellular pathogen previously shown to disrupt intrinsic apoptotic messengers to enhance its survival, exploits multiple facets of the cellular apoptotic mechanisms. Cellular pathways affected by apoptotic processes were assessed using real-time reversetranscriptase-polymerase-chain-reaction (rRT-PCR) to measure the effect of B. henselae on cell regulator gene expression (TRADD, FADD, caspase-8 and caspase-3), caspase activity, DNA cell cycle analysis, cell regulator protein expression and overall cell viability and morphology. The presence of B. henselae suppresses overall gene expression for TRADD and FADD and it dramatically suppresses ceramide-induced TRADD and FADD gene expression. The presence of B. henselae has a noticeable effect on ceramide-induced caspase-8 and caspase-3 gene expression. Only caspase-3 enzymatic activity was ceramide-induced and likewise supressed by the presence of B. henselae, whereas caspase-6 and caspase-8 were unaffected and equivalent to controls. The presence of B. henselae inhibits ceramide-induced DNA fragmentation, maintains overall cell morphology and enhances host cell viability. Lastly, B. henselae inhibits the timedependant ceramide-induction of TRADD protein and suppresses ubiquitous FADD protein expression. We demonstrated that B. henselae inhibits apoptotic induction in a systematic manner following exogenous apoptotic induction. B. henselae protection of microvascular endothelial cells from apoptosis induction begins at the modulation of cell surface receptor-dependent signaling. B. henselae minimizes, but does not completely abrogate, the cytotoxic effect of the apoptogenic shingolipid ceramide on human microvascular endothelial cells (CDC.EU.HMEC1). Broadening our understanding of the sequence of cell regulator suppression events by intracellular pathogens will provide insight into disease manifestation. Further, understanding how infected cells initiate and conclude apoptosis will open new avenues into the study of disease treatment. INDEX WORDS: Bartonella henselae, Apoptosis, Ceramide, TRADD, FADD, Caspase, Realtime RT-PCR BARTONELLA HENSELAE INHIBITS CELLULAR APOPTOTIC REGULATORS TO ENSURE SURVIVAL
Effects of Irradiation and Blast on Pulmonary Function in Sheep.

Abstract : The changes in pulmonary function that result following unilateral exposure to LD50 doses of neutron-gamma irradiation and/or sublethal blast overpressures were investigated in sheep. Animals exposed to blast-only and radiation-plus-blast demonstrated large increments in venous admixture on the day of insult followed by a major recovery toward baseline values during the first 24 hours following injury. The venous admixture of the blast-only animals approached baseline 7 days after exposure but that of the radiation-plus-blast sheep did not return to baseline until 21 days. The sheep exposed to radiation-only, blast-only, and radiation-plus-blast sustained similar reduction in means carbon monoxide diffusing capacity (DLCO) which were below that of the control mean at 2 days and 7 days post exposure. All of the radiation-only and radiation-plus-blast sheep that survived to or beyond 21 days displayed an overshoot or recovery to their individual baseline DLCO values. The blast-only and radiation-plus-blast animals also exhibited an increased mean ineffective alveolar ventilation (VAIneff) which persisted from 1 to 14 days following the onset of trauma. The radiation-only sheep had an increased VAIneff from 2 through 7 days post exposure. (Author)
Comparison of four DNA barcodes in identifying certain medicinal plants of Lamiaceae

Abstract Many species in the family Lamiaceae have been widely used for the treatment of coronary heart disease, stroke, and other conditions, and authenticating each of these species has become an important topic of research. Due to the lack of distinct phenotypic differences between the species, morphological identification is often inaccurate. In the third Consortium for the Barcode of Life, the combination of matK and rbcL was recommended as the universal barcode for plants, but this combination resolved only 70% of the species; the psbA‐trnH intergenic region and internal transcribed spacer (ITS)/ITS2 were required for further study. In this study, we compared the sequences of the four candidate barcodes (matK, rbcL, ITS2, and psbA‐trnH), among different species of Lamiaceae medicinal plants based on three selection criteria: intraspecific and interspecific genetic divergences; Wilcoxon signed‐rank tests; and species identification ability. The results showed that ITS2 was the most variable region of the four tested barcodes. Of 672 samples collected from 314 species, ITS2 successfully identified 78.3% at the species level and 100% at the genus level. This strategy could widen the optimal range of divergence levels for the identification of Lamiaceae medicinal plants.
Numerical simulation of the MYRRHA reactor design v1.6

This study is embodied in the project of MYRRHA reactor, developed by the Belgian Nuclear Research Center (SCK-CEN), to which VKI is giving its contribution. This dissertation aims to perform a numerical simulation of the MYRRHA reactor design version 1.6 and analyse its results. It is important to point out that part of the information sources are confidential. The heavy metal considered is LBE (Lead Bismuth Eutectic). This reactor has originally a complex geometry, which was simplified for simulation purposes. The investigation is made through a single-phase flow CFD model in nominal conditions of the primary coolant circuit. Its objective is to provide a description of the flow and temperature fields of the entire pool loop while analysing the flow patterns that develop in the lower and the upper plenum of the MYRRHA v1.6 facility as complete as possible, while using a steady-state model. The model was prepared in the OpenFOAM software, due to its open source nature. Firstly the numerical set up is made, then the porous media is defined and finally the thermal modelling takes place. The solver used in these simulations to perform the thermal modelling is myrrhaSimpleFoam, developed at von Karman Institute and complemented with the most relevant thermal turbulence models for low Prandtl number liquids currently. The turbulence model applied is the Standard κ−ε and, in order to predict the effects of turbulent heat transfer, the Reynolds analogy is implemented, with a constant turbulent Prandtl number of 2.0. The flow is characterized for being steady state, incompressible and turbulent. Since we are dealing with a turbulent flow, the equations are solved based on the Reynolds Averaged Navier-Stokes (RANS) model. Finally, a comparison with the results from a previous study involving the design v1.4 of the reactor is made.
Study of grain growth, floret sterility and seed size of wheat cultivars as influenced by post-anthesis heat stress.

Four heat tolerant (Gourab, Sourav, Kanchan and Shatabdi) and two heat sensitive (Sonora and Kalyansona) wheat cultivars, were tested under normal and late growing post-anthesis heat stress conditions by seeding them November 30 and December 30 of 2005 to evaluate their grain growth pattern, floret sterility and seed size. A sigmoid pattern of grain growth was found in all the cultivars for both the growing conditions. At normal growing condition, both the heat tolerant and heat sensitive cultivars had similar grain growth duration (35 DAA). But in late growing heat stress condition, heat tolerant cultivars had longer grain filling duration (30 DAA) compared to heat sensitive cultivars (25 DAA). In both the growing conditions, heat tolerant cultivars had higher grain growth rate than the heat sensitive cultivars. Results showed that irrespective of growing conditions heat sensitive cultivars showed higher floret sterility compared to heat tolerant cultivars. Both the heat tolerant and heat sensitive cultivars showed a common tendency of higher floret sterility under post-anthesis condition. But the degree of increments of floret sterility was much lower in heat tolerant cultivars than those of heat sensitive cultivars. From heat susceptibility index it was observed that cultivars Gourab, Kanchan and Shatabdi were clearly lower heat susceptible (S<1.0) in individual seed weight compared to cultivars Sonora and Kalyansona
Characterization of cryptic components of the ancestral vertebrate genome

7 Zusammenfassung . 9 List of Figures . 13 List of Tables . 14 General introduction . 15 Chapter I . 21 Revisiting the origin of the vertebrate Hox14 by including its relict sarcopterygian members . 21 Abstract . 22. 22 Introduction . 22 Materials and methods . 25 Results . 29 Discussion . 37 Acknowledgments . 40 Chapter II . 41 Co-orthology of Pax4 and Pax6 to the fly eyeless gene: molecular phylogenetic, comparative genomic and embryological analyses . 41 Abstract . 42. 42 Introduction . 42 Materials and methods . 45 Results . 49 Discussion . 57 Acknowledgments . 62 Chapter III . 63 A novel Pax4/6 relative, Pax10, reveals a cryptic pan-vertebrate gene repertoire . 63 Abstract . 64. 64 Introduction . 64 Results . 68 Discussion . 77 Material and methods. 85 Acknowledgments . 89
Infestation of Laboratory Colonies of Rhodnius prolixus Stal, 1859 (Hemíptera: Reduviidae) by Megaselia scalaris (Loew, 1866) (Diptera: Phoridae)

The “humpbacked fly” Megaselia scalaris (Loew, 1866) is a Dipterous-Phoridae fly specie with a cosmopolitan distribution and a high degree of synantropy. Their larvae are very easyly reared in the laboratory, and can be found in detritivorous, facultative predators, parasites and parasitoids. In the present short communication is describe for the first time the infestation of laboratory colonies of Rhodnius prolixus Stal, 1859 (Hemiptera: Reduviidae: Triatominae), the main vector of Chagas disease in Venezuela, by M. scalaris (Loew, 1866) larvae. Nearly 90% (2687/2992: 89,81%) of triatomine individuals in a highly overcrowded and moisturized (>90%), colony containers were infested by M. scalaris (Loew, 1866) larvae. The significance of these results for the maintenance of triatomine colonies, is discussed.
Biogeographic, historical and environmental influences on the taxonomic and functional structure of Atlantic reef fish assemblages

Aim: To disentangle how historic, biogeographic and environmental factors have shaped the composition of different reef fish assemblages, we analysed assemblage structure from a taxonomic (proportions of species from different families) and functional perspective (diet and body size). Location: Atlantic Ocean. Methods: The distributions of 1629 fish species were compiled for 31 locations across the Atlantic Ocean (39°66' N, 27°50' S). These locations provide a richness gradient ranging from 54 species in St Paul's Rocks to 474 in Cuba. We used cluster analyses to assess how historical and biogeographic factors have shaped the taxonomic and functional structure (i.e. the distribution of species within families, diet and body size groups) of assemblages. We then employed a constrained analysis of principal coordinates (CAP) to test the relative influence of the distance from the biodiversity centre in the Atlantic, sea surface temperature, isolation, coral species richness and area, and coastal length on the observed patterns of assemblage structure. Results: The taxonomic and functional structure of reef fish assemblages across the Atlantic exhibits a biogeographic fingerprint, with a marked discrimination between species-rich biogenic reefs (concentrated primarily in the Caribbean and composed of small species feeding on invertebrates) and poorer peripheral regions dominated by larger species with more diverse diets. The first CAP axis explains 87% of body size distribution in assemblages, showing that the effects of sea surface temperature and coral richness and those of isolation are antagonistic and can be embedded into a single dimension. Environmental factors, such as temperature and habitat complexity, explain the disproportionate number of small species in the Caribbean, whereas in the remaining regions the predominance of large-bodied fish increases with isolation due to high dispersal ability. Main conclusions: We found that historical events, which have shaped the biogeography of reef fishes, and environmental characteristics (coral reefs versus periphery) have both played a role in structuring the taxonomic and functional components of Atlantic fish assemblages.
Epidemiology of internal parasites on Swiss organic dairy farms and phytotherapy as a possible worm control strategy

A two-year study was performed on 34 organic dairy farms of the midland and alpine region in Switzerland to evaluate the situation of endoparasitic infections in first grazing season calves (FGSC), second grazing season cattle (SGSC) and cows. The animals were examined coprologically for presence of coccidia and helminth stages twice annually, in early summer and in autumn, and serologically once a year in autumn. The health status of the investigated flocks was generally good with only very few parasitological problems present. The most prevalent parasites during the whole observation period were the trichostrongylid nematodes with low-to-moderate mean egg counts per gram faeces (epg) in early summer and autumn (FGSC: 84-245 epg, SGSC: 27-37 epg, cows: 7-10 epg). Serum pepsinogen levels were also low to moderate. Separate grazing cycles for FGSC induced a higher risk for extensive infections with gastrointestinal trichostrongylids. Farm prevalences of Dictyocaulus viviparus, Fasciola hepatica, and Dicrocoelium dendriticum were 68, 12, and 82%, respectively. 50% of the organic farmers managed their livestock without using anthelmintics or vaccines, 35% used synthetic anthelmintics and 15% vaccinated against D. viviparus. The use of mixed or rotational grazing on most of the farms contributed to lower infection level. Despite the restriction in anthelmintic use and the daily access to pastures organic dairy farms did not have many problems with endoparasites.
Nuevo registro de Greenidea ficicola Takahashi (Hemiptera: Sternorrhyncha:Aphididae) en guayabo Psidium guajava (Myrtaceae) en Antioquia, Colombia.

Se encuentra por primera vez en el departamento de Antioquia (Colombia) y asociado al guayabo (Psidium guajava L.), la especie Greenidea ficicola Takahashi ( Hemiptera: Sternorrhyncha: Aphididae) colectada durante muestreos intensivos realizados durante el primer semestre de 2008 en el Valle de Aburra y municipios aledanos. Dicha especie de afido tambien fue colectada en falso laurel (Ficus benjamina). Dada la importancia que tienen los frutos de guayabo en la alimentacion humana y de los animales domesticos en Colombia, es necesario registrar esta especie con el fin de tomar medidas en lo referente a programas de muestreo de sus poblaciones, estudio de su ciclo de vida y determinar los posibles controladores biologicos, que conduzcan al mejor conocimiento de este insecto y faciliten la toma de medidas de contencion a su dispersion en el pais.
Clinical, morphologic, and neurochemical aspects in the aging central nervous system

Este livro contém os relatórios apresentados ao V I Simpósio Internacional sobre Fluxo Sangüíneo Cerebral, realizado em Filadelfia entre 6 e 9 de junho de 1 9 7 3 . Atenção especial foi focalizada no controle neurogênico da circulação e do metabolismo cerebrais, constituindo matéria de três sessões do congresso. Considerações sobre a metodologia para a medição do fluxo sangüíneo cerebral e decorrências dos respectivos resultados foram objeto de outras duas sessões. Interesse especial mereceram também as aplicações clínicas dos diversos métodos, principalmente no que concerne a traumatismos cranianos, doenças vasculares cerebrais, crises convulsivas, tumores intracranianos, doenças infecciosas e perturbações mentais. Em várias sessões adicionais foram considerados os efeitos experimentais do edema e da isquemia cerebrais e dos traumatismos cranianos. Finalmente, foram discutidos os efeitos de agentes farmacológicos sobre o fluxo sangüíneo e metabolismo cerebral. Os diversos relatórios que compunham cada sessão, foram reunidos em outros tantos capítulos, que eram encerrados por apreciações sintéticas de especialistas previamente convidados.
Role of RNA Polymerase, ρ Factor, and Ribosomes in Transcription Termination

INTRODUCTION Efficient transcription of the Escherichia coli genome depends on the ability of the cell to regulate the type and amount of mRNA produced from each of its 3000 to 4000 genes. This not only requires the information to specify precise starting points for transcription, but stopping points as well. The operon, as the functional polycistronic unit of gene expression, may in fact be defined by the occurrence of an efficient termination site at its distal end. This simple housekeeping function prevents transcriptional readthrough by RNA polymerase into adjoining regions of the genome. In addition, however, a termination site can be utilized within a regulatory region to alter gene expression by controlling the ability of RNA polymerase to transcribe beyond that site. Thus, sites that specify termination may have several purposes in the cell. (1) As efficient punctuation signals, they permit the differential regulation of adjacent gene clusters. (2) As modulating elements (e.g., in attenuation), they permit differential control of expression within operons. (3) As conditional abortive elements (e.g., in mutational polarity), they prevent wasteful depletion of cellular metabolites. (4) As barriers to elongation, they minimize sequestering of important enzymes (e.g., RNA polymerase or other RNA-binding macromolecules) that might be engaging in unnecessary transcription or binding to excess unusable products. It has been generally expected that all termination sites, regardless of their function in regulation, would contain certain common structural features required for the termination response of RNA polymerase at that site. The primary structures (sequences) of a large number.
Ancestors in Our Genome: The New Science of Human Evolution

Chapter 1. The Trees Within the Forest: The Molecular Quest for Our Nearest Primate Relative Chapter 2. Looks Can Be Deceiving: Evolution Does a Double-Take Chapter 3. The Great Divorce: The Human Lineage Emerges Chapter 4. A Population Crash: The Down and Upsides to It Chapter 5. What Makes Us Human? : Searching the Genome for our Species-Wide Adaptations Chapter 6. The Ongoing Evolutionary Journey: Human Adaptations Around the World Chapter 7: Kissing Cousins: Clues from Ancient Genomes Chapter 8. The Future of the Genome
Virus evolution in the progression of natural feline immunodeficiency virus infection

Feline immunodeficiency virus (FIV) is an important pathogen of domestic cats which in some cases can lead to feline AIDS. It shares many similarities with its human counterpart and is studied to understand correlates of immune-protection and mechanisms of disease progression in cats, both to improve the welfare of infected cats and as an animal model for the pathogenesis of HIV infection in humans. FIV is believed to evolve during the course of infection as a result of the error prone nature of reverse transcriptase and recombination between viral variants, but relatively little is known about this process in naturally occurring infection. Ultimately, it remains unknown why some infected cats remain healthy while others progress to AIDS rapidly. The studies reported in this thesis addressed this lack of knowledge by examining sequential blood samples obtained during the course of natural FIV infection in a population of 44 privately owned domestic cats. Employing Bayesian coalescent framework, it was demonstrated that the FIV env gene is relatively stable genetically. Although not necessary a prerequisite, this is likely to explain why many naturally infected cats can remain healthy and do not progress to AIDS. By determining the cell tropism of isolated viral variants, it was shown that sick cats were more likely to harbour viruses of the “late” phenotype than healthy animals, similar to the co-receptor switch observed during the progression of HIV infection. Intra-host diversity analyses highlighted a likely role for the leader region of the env gene in viral pathogenesis. Furthermore, recombination was demonstrated to be abundant in natural infection, indicating a requirement for the current phylogenetic classification of FIV to be revised. By assessing the strength and breadth of neutralising antibodies (NAbs), it was shown that NAbs did not appear to influence the course of natural FIV infection, arguing against a role in controlling infection and disease progression. Following an examination of samples collected from a group of privately owned Australian vaccinates, it was shown that the Fel-O-Vax FIV vaccine did not induce cross-reactive neutralising antibodies. Furthermore, in the country where commercial FIV vaccine is licenced, we identified and characterised the virus strain which was likely able to establish infection in vaccinated cat and raised concerns of vaccine’s efficacy. Overall this study broadens our understanding of natural FIV infection, and highlights that much can be learned, not from the similarities but rather by studying the differences between the feline and human lentiviruses. Such comparative studies are likely to contribute to design of highly desirable, safe and fully efficacious lentiviral vaccines.
Microhabitat Segregation between Apodemus argenteus and A. speciosus in Northern Kyushu

The structure of microhabitats used by Apodemus argenteus and A. speciosus, which are generally regarded as sympatric at the macrohabitat level, was analysed ; and habitat segregation patterns and interspecific competition between these two species were discussed. Transects of 50 Sherman live-traps set 10 m apart were laid in forests at four ' sites in northern Kyushu. After mark-and-release, variables reflecting the structure, diversity of vegetation and physical factors were examined in a quadrat of 10 m2 and a circle with the radius of 10 m both of which were centered on the trapping point. A discriminant function analysis by the stepwise method resulted in 66.6-100% of correct discrimination of microhabitats for the two species both at each site and at the four sites en bloc, indicating that A. argenteus selected microhabitats with characteristics of climax forests, and that A. speciosus did those with features of secondary forests. A principal component analysis on five selected variables revealed that the macrohabitat segregation between these two species was flexible. The more the two species approached each other, the more A. argenteus selected the microhabitat with complex strata of vegetation cover. The flexible horizontal and vertical microhabitat segregations would play a role in decreasing competition between these two species.