Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiological studies (parasitological, serological and molecular techniques) of Trypanosoma evansi infection in camels (Camelus dromedarius) in Egypt

Trypanosomosis in camel caused by Trypanosoma evansi is still a serious problem in camel husbandry causes considerable economic losses in many camel-rearing regions of the world. In the present study 193 camels clinically suspected for surra were examined parasitologically by Giemsa stained blood smear (GSBS) and haematocrit centrifugation technique, serologically for detection of anti-trypanosomal antibodies by card agglutination test for trypanosomes (CATT), and for DNA amplification, by Polymerase chain reaction (PCR), with primers yielding a 177 bp PCR product for the specific detection of Trypanozoan parasites. Out of 193, eight camels were positive by GSBS (4.1%) while 12 were positive with haematocrit centrifugation technique (6.2%). Detection of anti-trypanosomal antibodies with CATT yielded 84 positive samples (43.5%). Using PCR 110 out of 193 were positive (56.9 %). PCR technique is accurate, more sensitive and specific method for diagnosis of trypanosome infected camels than parasitological techniques; it overcomes the problem of specificity and can detect low parasitemic camels in chronic cases. The PCR proved to be the best test used for detection of camel trypanosomosis in Egypt.
The Role of Spirochetes in Periodontal Disease

The spirochetal accumulation in subgingival plaque appears to be a function of the clinical severity of periodontal disease. It is not known how many different spirochetal species colonize the plaque, but based upon size alone, there are small, intermediate-sized, and large spirochetes. Four species of small spirochetes are cultivable, and of these, T. denticola has been shown to possess proteolytic and keratinolytic enzymes as well as factors or mechanisms which suppress lymphocyte blastogenesis and inhibit fibroblast and polymorphonuclear leukocyte (PMNL) function. All of these attributes could contribute to periodontal tissue insult. Yet independent of these potential virulence mechanisms, the overgrowth of spirochetes can be clinically useful if simply interpreted as indicating the result of tissue damage. In this case, the spirochetes would be indicators of disease and could be easily monitored by microscopic examination of plaque, or possibly by the measurement of benzoyl-DL-arginine-2-naphthylamide (BANA) hydrolytic activity in the plaque.
Eigenmode Analysis of Boundary Conditions for the One-dimensional Preconditioned Euler Equations

An analysis of the effect of local preconditioning on boundary conditions for the subsonic, one-dimensional Euler equations is presented. Decay rates for the eigenmodes of the initial boundary value problem are determined for different boundary conditions. Riemann invariant boundary conditions based on the unpreconditioned Euler equations are shown to be reflective with preconditioning, and, at low Mach numbers, disturbances do not decay. Other boundary conditions are investigated which are non-reflective with preconditioning and numerical results are presented confirming the analysis. 1. Introduction. Local preconditioning has been successfully utilized to accelerate the convergence to a steady-state for Euler and Navier-Local preconditioning is introduced into a time-dependent problem as,
Examining Committee

A diet high in saturated fat and similar in composition to western diets (WD) has been shown to exacerbate injury following traumatic brain injury. Thus, we investigated the effects of a WD on cell death and functional outcome following global ischemia. First we assessed the effects of a 60day WD regimen on temperature, activity and glucose levels in normal rats (Experiment 1). Second, we evaluated the influence of a 60-day WD regimen on hippocampal CA1 injury and learning and memory impairments following global ischemia in rats (Experiment 2). Briefly, results from experiment 1 revealed no differences in glucose or temperature profiles between animals fed the WD and CD; however, WD animals were significantly less active than CD animals. Eight minutes of ischemia in experiment 2 induced severe hippocampal CA1 cell loss (~90%) and severe learning and memory impairments relative to unoperated controls. However, the WD did not exacerbate CA1 injury or behavioural deficits. These findings suggest that a 60day WD regimen does not significantly influence recovery following global ischemia. However, previous literature on saturated fat and neuronal plasticity suggest that our feeding protocol was not long enough. Thus, the second portion of my thesis examined the effects of a 120-day WD regimen on stroke severity and cognition following global ischemia. We hypothesized that a prolonged WD would aggravate hippocampal CA1 cell death and spatial learning and memory deficits as compared to animals fed a CD. Briefly, I found that the surgical protocol used to induce a global ischemic insult, in this case, did not produce consistent damage across all animals. Plausible reasons for this surgical variability and future directions are discussed.
Pennerstorfer Network migration : do neighbouring regions matter ?

This paper analyses the role of the spatial structure of migrant networks in the location decision of migrants to the European Union at the regional level. Using a random parameters logit specification, a significant positive effect of migrant networks in neighbouring regions on migrants’ location decisions is found. Although this spatial spillover effect is smaller than the effect of networks in the host regions, omitting to control for this spatial dependence results in a 40% overestimation of the effect of regional migrant networks on the location decision of newly arriving migrants.
Study the vulnerability and blocking of streets after earthquake (case study: Kerman Shariati and Shahid Beheshti Streets and Jomhuri Boulevard)

Background: Despite achieving great technologies in last century, earthquakes seem unbridled. When an earthquake occurs, city is affected as a system and not only urban elements are affected by earthquake shocks and its other side effects, but as interaction of system, affects other elements of city. One of the most important elements is road network. Passages blocking roads due to their length and width and may disrupt Relief after earthquake. Aims: In this study, we provide a model in order to assess the damages and vulnerability of Kerman main passages (Shariati Street, Shahid Beheshti and Jomhuri Boulevard). Materials and Methods: Methodology of study is based on descriptive nature and method and is applied study in terms of aim. GIS maps of Kerman have been used in order to get the best routes. Results: Longitudinal and transverse blocking of passages and their effectiveness after an earthquake was determined through conducting the necessary studies and obtaining GIS results.
Dissertation submitted to the Combined Faculties for the Natural Sciences and for Mathematics of the Ruperto-Carola University of Heidelberg , Germany for the degree of Doctor of Natural Sciences

The far-field light microscope is a valuable scientific instrument in modern life sciences, nevertheless, its full potential was constrained by the diffraction-limited resolution. A concept exploiting a saturable optical transition of fluorescent molecules, namely stimulated emission depletion (STED), allowed to overcome this restriction and provides diffraction-unlimited resolution in far-field light microscopy. In this thesis STED microscopy as a tool in cell biology is further established by revealing the ring-like structure of the Bruchpilot protein in larval Drosophila neuromuscular junctions and clustering behavior of the nicotinic acetylcholine receptor in mammalian cells. Moreover, the performance of STED microscopes is further improved by examining photobleaching behavior of fluorescent dyes and presenting a new illumination scheme for reduced photobleaching and increased signal. For the first time a new approach to STED microscopy with a Q-switched microchip laser, replacing a Ti:Sapphire-based laser system, was successfully implemented. The applicability of this approach and an increase in resolution beyond the diffraction limit to below 25 nm is demonstrated with colloidal nanoparticles and in biological samples. The range of applicable dyes for STED microscopy is further extended into the blue regime, widening the field of possible applications.
SOCIODEMOGRAPHIC CHARACTERISTICS OF INTERPERSONAL VIOLENCE ASSOCIATED WITH ALCOHOL CONSUMPTION

HOW TO REFERENCE THIS ARTICLE: Silva ER, Hino P, Fernandes H. Sociodemographic characteristics of interpersonal violence associated with alcohol consumption. Cogitare Enferm. [Internet]. 2022 [accessed “insert day, monh and year”]; 27. Available from: http://dx.doi. org/10.5380/ce.v27i0. 77876. ABSTRACT Objective: to identify the sociodemographic profile of interpersonal violence associated with alcohol consumption in São Paulo-SP, Brazil. Method: a cross-sectional study carried out through notifications of suspected or confirmed cases of interpersonal violence from the Notifiable Diseases Information System submitted between 2016 and 2019. Collection took place between March and June 2020. Chi-square or Fisher’s exact tests were performed in the statistical analysis. Results: 27,775 notifications were obtained, whose prevalent profile was female victims (60.6%), aged between 20 and 34 years old (41.4%), brownor black-skinned (51%), and with complete high school (18.8%). Physical violence was more frequent (81.9%), perpetrated by an intimate partner (20.3%), motivated by sexism (9.9%) and generational conflict (11.2%). In sexual violence, rape prevailed with 69.4% and there was a low supply of emergency contraception methods (14.7%). Conclusion: the study contributes to reflections and subsidies in the planning of public policies to control the problem.
OSGeo Journal

Debris flows are rapid mass movements of water and debris, constituting a considerable hazard when interfering with people, buildings, or infrastructure. They are often triggered by heavy or prolonged rainfall or by extreme snow melt. Mobilization of the material occurs due to translational or rotational failure of saturated or undercut slopes, or by detachment due to surface runoff or the debris flow itself. Various models do exist for simulating sub-processes included into debris flows, for example for detachment (r.sim.sediment within the GRASS GIS environment), for soil hydrology and slope stability (14), or for debris flow runout (9; 7). More integrated GISbased approaches as attempted for example by (1) or (11) are scarce. Such approaches would be valuable for a quick assessment of hydrological thresholds for potential debris flow hazard regarding specified features at risk. This paper describes and discusses the development of such a model as GRASS GIS raster module. The model is designed for small catchments (few square kms) and is tested at the moment with seven study areas along the international road corridor from Mendoza (Western Argentina) to Central Chile, crossing the highest section of the Andes (figure 1). The preliminary results for the study area Guido A are presented.
Thymocyte Development CD 8 Locus Nuclear Dynamics during

Nuclear architecture and chromatin reorganization have recently been shown to orchestrate gene expression and act as key players in developmental pathways. To investigate how regulatory elements in the mouse CD8 gene locus are arranged in space and in relation to each other, three-dimensional fluorescence in situ hybridization and chromosome conformation capture techniques were employed to monitor the repositioning of the locus in relation to its subchromosomal territory and to identify long-range interactions between the different elements during development. Our data demonstrate that CD8 gene expression in murine lymphocytes is accompanied by the relocation of the locus outside its subchromosomal territory. Similar observations in the CD4 locus point to a rather general phenomenon during T cell development. Furthermore, we show that this relocation of the CD8 gene locus is associated with a clustering of regulatory elements forming a tight active chromatin hub in CD8-expressing cells. In contrast, in nonexpressing cells, the gene remains close to the main body of its chromosomal domain and the regulatory elements appear not to interact with each other. A lthough epigenetic studies examining histone modifications and chromatin remodeling originally gave contradictory and controversial results, recently a more educated view on how the genome is organized in the nucleus and how genes respond to environmental signals to initiate and establish a tran-scriptional program has evolved. A number of histone modifications can be used as markers of active transcription (3meK4H3, 3meK36H3, AcH3, AcH4) and a number of chromatin-associated proteins (HP1a, Suv39H) and histone modifications (3meK9H3, 3meK27H3) as hallmarks for silent chromatin. In addition, nuclear architecture has emerged as a key player in creating the conditions for gene activation or silencing. A prevalent model of nuclear architecture proposes that, with some exceptions, transcribing or permissive euchromatin is located toward the center of the nucleus, whereas the silent heterochro-matin lies near the nuclear periphery. Recently, powerful tools, such as three-dimensional (3D) fluorescence in situ hybridization (FISH) and chromosome conformation capture (3C), have helped toward a better understanding of the functional organization of the genome in lymphocytes and other cell types (1–4) and of how the tran-scriptional activity could be correlated to a preferential positioning of a gene within the nucleoplasm. Thus, it has been shown that CD4 and CD8 coreceptor genes associate with heterochromatin when silenced during T cell development (5–7). As transcription and RNA editing factors and RNA pol II are in limiting numbers in the nucleus, their accumulation …
A Two-Dimensional Gravest Empirical Mode Determined from Hydrographic Observations in the Subantarctic Front

Abstract South of Australia, where the baroclinicity in the Subantarctic Front extends almost to the seafloor, the geopotential height of the sea surface (ϕ) and the vertical acoustic travel time (τ) exhibit a tight empirical relationship to each other and to the entire vertical structure of temperature T(p), salinity S(p), and specific volume anomaly δ(p). Measurements of τ provide proxy estimates of the profiles TG(τ, p), SG(τ, p), and δG(τ, p), based on a two-dimensional “gravest empirical mode” (GEM) representation of the vertical structure fitted to 212 hydrographic stations. A seasonal model was fitted in the near-surface layers using additional historical data. At each depth in the range 150–3000 dbar, more than 96% of the variance in both the T and δ fields is captured by the GEM representation. During the Subantarctic Flux and Dynamics Experiment (Mar 1995–Mar 1997), inverted echo sounders (IES) and current meters were moored in a 2D array along the WOCE SR3 transect south of Australia. At each I.
Interventional Pulmonary/Bronchology 1 Oral Presentations

Introduction: Studies suggest that 10% of children with an ARI have persistent cough at day 21. There are no studies in Indigenous children who have a high risk of chronic lung disease. We aimed to identify the incidence and outcomes of ARI with cough as a symptom in urban Indigenous children. Methods:This is a prospective study of Indigenous children aged<5 years registered with a primary health service. Children are followed for a period of 12 months via monthly contacts. Children who develop cough as a symptom at any time are followed weekly for 4 weeks to ascertain cough outcomes. Results: To date, 162 children are enrolled, totalling 1065 child-months of observation. Two-hundred ARI episodes with cough have been reported (29.6 episodes/100 child-months at risk). Thirty-four ARIs (17%) have progressed to persistent cough at day 28 in 24 children. Of these, 15 children had 1 episode, 5 had 2, 4 had 3 and 1 had 4 during the follow-up period. The majority of children with persistent cough were diagnosed (by a respiratory physician) with protracted bacterial bronchitis and/or bronchiectasis. Conclusions:The proportion of children developing persistent cough postARI is higher than that currently reported (10%) with the majority suggesting protracted bacterial infection. GrantSupport:AQUTAPAaward, aQCMRIProgramGrant, UQFoundation Research Excellence Award, a QUT Indigenous Health Research StartUpGrant and the NHMRCCRE for LungHealth in Aboriginal and TorresStrait Islander Children. Declaration of Interest: None to Declare
Accessibility in a post-apartheid city: Comparison of two approaches for the computation of accessibility indicators

Accessibility indicators take land use, the transport system, and their interdependencies into account in a holistic fashion. In many areas, however, spatial data to perform accessibility calculations are hard to obtain or not available at all. Freely available volunteered geographic information (VGI) like from OpenStreetMap (OSM), which is increasingly becoming a world-wide standard for geo-spatial data, may be a solution to this problem. In fact, some accessibility studies use data from OSM to create representations of the transport network and to perform network-based computations. In this paper, two approaches for accessibility assessment for Nelson Mandela Bay Municipality in South Africa are presented. The approaches possess different levels of utilization of OSM data which both exceed the use of OSM data for network creation. In the first approach, the transport network as well as locations and types of activity facilities are taken from OSM. Additionally, a synthetic population is created based on a census. The corresponding travel demand is generated based on a travel survey. Local expert knowledge is applied to design a household-specific accessibility indicator that takes into account various characteristics of travel and land use, such as travel time to work and/or education, travel time to the nearest health/shopping facility, availability of different transport options, and availability of various facilities within walking distance. Weights are used to combine the respective values of aforementioned characteristics into a composite, household-based accessibility score. This approach appears particularly suitable in the South African context where housing locations and travel characteristics are highly diverse among the population. The second approach relies exclusively on OSM data, which is -- as before -- used to create the network and activity facilities in the model. The approach applies an econometric accessibility indicator, which calculates the accessibility of a given measuring point as the weighted sum over the utilities of all opportunities including the costs of reaching them. In contrast to the first approach, no synthetic population, but only household locations -- collected from OSM in the same way as (other) activity facilities -- are used for the calculation. The approach is highly portable since no input data other than those from OSM are used. It is found that the second approach, though being much more lightweight in terms of data requirements, yields the same quality of insights concerning accessibilities of different areas of the region. Both approaches detect areas where levels of accessibility deprivation are high and where interventions in the transport-land-use system are advisable. Consequently, the paper is a contribution to accessibility analyses based on easily obtainable and ubiquitously available OSM data to obtain similar results as with respective approaches based on traditional spatial data.
Roles of Solvent Accessibility and Gene Expression in Modeling Protein Sequence Evolution

Models of protein evolution tend to ignore functional constraints, although structural constraints are sometimes incorporated. Here we propose a probabilistic framework for codon substitution that evaluates joint effects of relative solvent accessibility (RSA), a structural constraint; and gene expression, a functional constraint. First, we explore the relationship between RSA and codon usage at the genomic scale as well as at the individual gene scale. Motivated by these results, we construct our framework by determining how probable is an amino acid, given RSA and gene expression, and then evaluating the relative probability of observing a codon compared to other synonymous codons. We come to the biologically plausible conclusion that both RSA and gene expression are related to amino acid frequencies, but, among synonymous codons, the relative probability of a particular codon is more closely related to gene expression than RSA. To illustrate the potential applications of our framework, we propose a new codon substitution model. Using this model, we obtain estimates of 27N s, the product of effective population size N, and relative fitness difference of allele s. For a training data set consisting of human proteins with known structures and expression data, 2N s is estimated separately for synonymous and nonsynonymous substitutions in each protein. We then contrast the patterns of synonymous and nonsynonymous 2N s estimates across proteins while also taking gene expression levels of the proteins into account. We conclude that our 2N s estimates are too concentrated around 0, and we discuss potential explanations for this lack of variability.
Making 3D binary digital images well-composed

A 3D binary digital image is said to be well-composed if and only if the set of points in the faces shared by the voxels of foreground and background points of the image is a 2D manifold. Well-composed images enjoy important topological and geometric properties; in particular, there is only one type of connected component in any well-composed image, as 6-, 14-, 18-, and 26-connected components are equal. This implies that several algorithms used in computer vision, computer graphics, and image processing become simpler. For example, thinning algorithms do not suffer from the irreducible thickness problem if the image is well-composed, and the extraction of isosurfaces from well-composed images using the Marching Cubes (MC) algorithm or some of its enhanced variations can be simplified, as only six out of the fourteen canonical cases of cube-isosurface intersection can occur. In this paper, we introduce a new randomized algorithm for making 3D binary digital images that are not well-composed into well-composed ones. We also analyze the complexity and convergence of our algorithm, and present experimental evidence of its effectiveness when faced with practical medical imaging data.