Miracle-dz/UniFAR-FTUs huggingface dataset:
SPATIAL AND TEMPORAL VARIABILITY OF SOIL SURFACE ROUGHNESS AND THE APPLICATION IN HYDROLOGICAL AND SOIL EROSION MODELLING

Accurate estimations of water retention and detention are needed to simulate surface runoff and soil erosion following a rainfall event in a catchment. Several equations to estimate the amount of surface depressional storage, the fraction of the soil surface covered by water and the amount of rainfall excess needed to start surface runoff have been developed by Onstad (1984). The random roughness and slope gradient are needed for those estimations. Surface micro-elevation data have been gathered by a photographic method. The random roughness was determined from those elevation measurements. Several factors which have an impact on the soil surface roughness were taken into account. The main sources of influence are the type of land use, the crop stage within the growing period and tillage direction. Analyses of variance indicated that the variation in the RR-index could be explained mainly by type of land use, orientation and field type. The temporal variation was relatively small. Gradient data have been determined from a digital elevation model, constructed by digitizing contours. Combining the random roughness and the steepness of slope, the amounts of surface water retention and detention could be estimated. Knowledge of water retention and detention will improve the estimations of runoff and soil erosion modelling in catchments, such as those made with the LISEM model. The agricultural systems examined in this study have similar random roughness values in summer. Different soil erosion rates for several types of land use can not therefore be explained by the random roughness.
A Competitive Infection Model of Hematogenously Disseminated Candidiasis in Mice Redefines the Role of Candida albicans IRS4 in Pathogenesis

ABSTRACT Candida albicans IRS4 encodes a protein that regulates phosphatidylinositol-(4,5)-bisphosphate, which was shown to contribute to hematogenously disseminated candidiasis (DC) after several days in the standard mouse model. Our objective was to more accurately define the temporal contributions of IRS4 to pathogenesis. During competition assays in vitro, an irs4-null (Δirs4) mutant exhibited wild-type fitness. In DC experiments, mice were infected intravenously with the Δirs4 mutant, strain CAI-12 (1 × 105 CFU), or a mixture of the strains (0.5 × 105 CFU each). In single-strain infections, quantitative PCR revealed reduced Δirs4 mutant burdens within kidneys at days 1, 4, and 7 but not 6 h. In competitive infections, the Δirs4 mutant was outcompeted by CAI-12 in each mouse at ≥6 h (competitive indices, P ≤ 0.0001). At 4 and 7 days, the Δirs4 mutant burdens during competitive infections were significantly lower than those during single-strain infections (P = 0.01 and P < 0.001, respectively), suggesting increased susceptibility to inflammatory responses. Phagocytic infiltration of kidneys in response to CAI-12 or competitive infections was significantly greater than that in response to Δirs4 mutant infection at days 1 and 4 (P < 0.001), and the Δirs4 mutant was more susceptible to phagocytosis and killing by human polymorphonuclear cells (P = 0.01 and P = 0.006, respectively) and mouse macrophages in vitro (P = 0.04 and P = 0.01, respectively). Therefore, IRS4 contributes to tissue invasion at early stages of DC and mediates resistance to phagocytosis as DC progresses. Microarray analysis revealed remarkably similar gene expression by the Δirs4 mutant and reference strain CAI-12 within blood, suggesting that IRS4 is not significantly involved in the hematogenous stage of disease. A competitive DC model detects attenuated virulence that is not evident with the standard model.
Origin and Bioavailability of PAHs in the Mediterranean Sea from Mussel and Sediment Records

The distribution of selected polycyclic aromatic hydrocarbons (PAHs) in surface sediments and in mussels (Mytilus galloprovincialis) of the western Mediterranean Sea (French, Spanish and Balearic coasts) has been investigated by gas chromatography–mass spectrometry (GC–MS). The sediment PAH concentrations ranged from less than 1 to 8500 ng g−1. The most contaminated sediments have been sampled in harbours while the mean concentration of the Balearic Island sediments, far away from contamination sources, is low (≈30 ng g−1). The main pollution source is pyrolytic with an overimposition of petrogenic/diagenetic PAHs in a few sediments. The mussels are contaminated at very low levels (25–80 ng g−1) with the exception of those collected in two harbours (Port Vendres and Barcelona) and whose tissue PAH content is medium. In the Mediterranean Sea, the bioavailability from sediment of adsorbed hydrophobic organic compounds such as PAHs seems to be mainly governed by the origin of the contaminants. Pyrolytic compounds (penta- and hexa-aromatics) are not readily available. In contrast, petroleum hydrocarbons (some tetra-aromatics, methylated PAHs) are accumulated by mussels to a great extent.
The identification and differentiation of the Candida parapsilosis complex species by polymerase chain reaction-restriction fragment length polymorphism of the internal transcribed spacer region of the rDNA

Currently, it is accepted that there are three species that were formerly grouped under Candida parapsilosis: C. para- psilosis sensu stricto, Candida orthopsilosis, andCandida metapsilosis. In fact, the antifungal susceptibility profiles and distinct virulence attributes demonstrate the differences in these nosocomial pathogens. An accurate, fast, and economical identification of fungal species has been the main goal in mycology. In the present study, we searched sequences that were available in the GenBank database in order to identify the complete sequence for the internal transcribed spacer (ITS)1-5.8S-ITS2 region, which is comprised of the forward and reverse primers ITS1 and ITS4. Subsequently, an in silico polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was performed to differentiate the C. parapsilosis complex species. Ninety-eight clinical isolates from patients with fungaemia were submitted for analysis, where 59 isolates were identified as C. parapsilosis sensu stricto, 37 were identified as C. orthopsilosis, and two were identified as C. metapsilosis. PCR-RFLP quickly and accurately identified C. parapsilosis complex species, making this method an alternative and routine identification system for use in clinical mycology laboratories.
Population-Based Genetic and Evolutionary Analysis of Chlamydia trachomatis Urogenital Strain Variation in the United States

ABSTRACT Chlamydia trachomatis is a major cause of ocular and sexually transmitted diseases worldwide. While much of our knowledge about its genetic diversity comes from serotyping or ompA genotyping, no quantitative assessment of genetic diversity within serotypes has been performed. To accomplish this, 507 urogenital samples from a multicenter U.S. study were analyzed by phylogenetic and statistical modeling. No B, Da, or I serotypes were represented. Based on our analyses, all but one previous urogenital B serotype was identified as Ba. This, coupled with the lack of B serotypes in our population, suggests that B has specific tropism for ocular mucosa. We identified a Ba/D recombinant (putative crossover nucleotide 477; P < 0.0001) similar to a B/D mosaic we described previously from an African trachoma patient. Computational analyses of the Ba/D recombinant indicated that upstream changes were less important for tissue tropism than downstream incorporation of the D sequence. Since most serotypes had nonsynonymous/synonymous ratios of <1.0, the major outer membrane protein, encoded by ompA, has many functional constraints and is under purifying selection. Surprisingly, all serotype groups except for J had a unimodal population structure indicating rapid clonal expansion. Of the groups with a unimodal structure, E and Ia and, to a lesser extent, G and K were prevalent, had infrequent incorporation of mutations, and, compared to other groups, had a relatively greater degree of diversifying selection, consistent with a selective sweep of mutations within these groups. Collectively, these data suggest a diverse evolutionary strategy for different serogroups of the organism.
Preparation of a Porous Composite Film for the Fabrication of a Hydrogen Peroxide Sensor

A series of dopant-type polyaniline-polyacrylic acid composite (PAn-PAA) films with porous structures were prepared and developed for an enzyme-free hydrogen peroxide (H2O2) sensor. The composite films were highly electroactive in a neutral environment as compared to polyaniline (PAn). In addition, the carboxyl group of the PAA was found to react with H2O2 to form peroxy acid groups, and the peroxy acid could further oxidize the imine structure of PAn to form N-oxides. The N-oxides reverted to their original form via electrochemical reduction and increased the reduction current. Based on this result, PAn-PAA was used to modify a gold electrode (PAn-PAA/Au) as a working electrode for the non-enzymatic detection of H2O2. The characteristics of the proposed sensors could be tuned by the PAA/PAn molar ratio. Blending PAA with PAn enhanced the surface area, electrocatalytic activity, and conductivity of these sensors. Under optimal conditions, the linear concentration range of the H2O2 sensor was 0.04 to 12 mM with a sensitivity of 417.5 μA/mM-cm2. This enzyme-free H2O2 sensor also exhibited a rapid response time, excellent stability, and high selectivity.
www.druid.dk DRUID Working Paper No. 05-18 Entrepreneurial Founder Effects in the Growth of Regional Clusters: How Early Success is a Key Determinant By

How can the growth of regional clusters be explained? This paper studies in great detail the growth of the wireless communication cluster in Northern Denmark. Unlike the dominant theories, we argue that initial success of the first firms are the main driving force behind the generation of new firms that eventually lead to the formation of clusters. The success of the first firms tends to generate spin-offs, which become successful themselves due to the background of the founders.
Marmousi-2: An Updated Model for the Investigation of AVO in Structurally Complex Areas

We have created an elastic version of the IFF Marmousi model for use in AVO analysis in the presence of complex structure. The model is larger, includes larger offsets, lies in deeper water, includes surface streamer, multicomponent OBC and VSP acquisition, and contains more hydrocarbons than its predecessor. In addition to AVO analysis, we believe these data will be suitable for calibrating emerging technologies including converted wave tomography and vector seismic processing.
An Extraction and Expansion Approach for Graph Coloring

This paper presents an extraction and expansion approach for the graph coloring problem. The extraction phase transforms a large graph into a sequence of progressively smaller graphs by removing large independent sets from the graph. The expansion phase starts by generating an approximate coloring for the smallest graph in the sequence. Then it expands the smallest graph by progressively adding back the extracted independent sets and determine a coloring for each intermediate graph. To color each graph, a simple perturbation based tabu search algorithm is used. The proposed approach is evaluated on the DIMACS challenge benchmarks showing competitive results in comparison with the state-of-the-art methods.
Spectrotemporal Processing Differences between Auditory Cortical Fast-Spiking and Regular-Spiking Neurons

Excitatory pyramidal neurons and inhibitory interneurons constitute the main elements of cortical circuitry and have distinctive morphologic and electrophysiological properties. Here, we differentiate them by analyzing the time course of their action potentials (APs) and characterizing their receptive field properties in auditory cortex. Pyramidal neurons have longer APs and discharge as regular-spiking units (RSUs), whereas basket and chandelier cells, which are inhibitory interneurons, have shorter APs and are fast-spiking units (FSUs). To compare these neuronal classes, we stimulated cat primary auditory cortex neurons with a dynamic moving ripple stimulus and constructed single-unit spectrotemporal receptive fields (STRFs) and their associated nonlinearities. FSUs had shorter latencies, broader spectral tuning, greater stimulus specificity, and higher temporal precision than RSUs. The STRF structure of FSUs was more separable, suggesting more independence between spectral and temporal processing regimens. The nonlinearities associated with the two cell classes were indicative of higher feature selectivity for FSUs. These global functional differences between RSUs and FSUs suggest fundamental distinctions between putative excitatory and inhibitory interneurons that shape auditory cortical processing.
Human Dendritic Cells Are Activated by Dengue Virus Infection: Enhancement by Gamma Interferon and Implications for Disease Pathogenesis

ABSTRACT The ability of dendritic cells (DCs) to shape the adaptive immune response to viral infection is mediated largely by their maturation and activation state as determined by the surface expression of HLA molecules, costimulatory molecules, and cytokine production. Dengue is an emerging arboviral disease where the severity of illness is influenced by the adaptive immune response to the virus. In this report, we have demonstrated that dengue virus infects and replicates in immature human myeloid DCs. Exposure to live dengue virus led to maturation and activation of both the infected and surrounding, uninfected DCs and stimulated production of tumor necrosis factor alpha (TNF-α) and alpha interferon (IFN-α). Activation of the dengue virus-infected DCs was blunted compared to the surrounding, uninfected DCs, and dengue virus infection induced low-level release of interleukin-12 p70 (IL-12 p70), a key cytokine in the development of cell-mediated immunity (CMI). Upon the addition of IFN-γ, there was enhanced activation of dengue virus-infected DCs and enhanced dengue virus-induced IL-12 p70 release. The data suggest a model whereby DCs are the early, primary target of dengue virus in natural infection and the vigor of CMI is modulated by the relative presence or absence of IFN-γ in the microenvironment surrounding the virus-infected DCs. These findings are relevant to understanding the pathogenesis of dengue hemorrhagic fever and the design of new vaccination and therapeutic strategies.
ANÁLISE ECOMORFOLÓGICA DE TRÊS ESPÉCIES DE PEIXES DO PARQUE ESTADUAL MARINHO DO PARCEL DE MANUEL LUIZ, MARANHÃO, BRASIL

O objetivo deste trabalho foi descrever padroes ecologicos relacionados com aspectos morfologicos de Balistes vetula , Ocyurus chrysurus e Haemulon plumieri , especies que representam cerca de 10% da abundância da comunidade de peixes do Parque Estadual Marinho Parcel de Manuel Luiz. Dez individuos de cada especie foram utilizados no estudo e, sobre cada um, 12 medidas morfometricas foram obtidas para o calculo de nove atributos morfologicos. Uma matriz combinada de atributos e especies foi submetida a uma ACP para identificar os padroes ecomorfologicos. Os resultados mostraram diferencas entre as especies relacionados com o uso de microhabitat. B. vetula tem maior capacidade para realizar giros verticais e possui habito associado com o fundo. H. plumieri e O. chrysurus , por sua vez, estao associados com o fundo e possuem fenotipo adaptado para natacao rapida. Estas duas especies podem ser diferenciadas pelo tamanho da presa ingerida, que e maior em H. plumieri. ABSTRACT Ecomorphological analysis of three species of fishes from Parcel de Manuel Luiz Marine State Park, Brazilian northeast The goal of this paper was to describe ecological patterns related to morphological characteristics of Balistes vetula , Ocyurus chrysurus and Haemulon plumieri , which represent 10% of the total abundance of the Marine State Park of Parcel Manuel Luiz fish community. Ten individuals of each species were used for an ecomorphological analysis. On each exemplar, 12 morphometric measures were obtained in order to compute nine morphological attributes. A matrix with attributes and species was submited to a Principal Components Analysis (PCA) aiming to identify ecomorphological patterns. The results showed differences among species, related to the microhabitat uses. B. vetula has the highest capacity to do vertical turns and has a benthic habit. H. plumieri and O. chrysurus are associated with the bottom and bear phenotype adaptated to high swim velocities. These two species are yet diferenciated by the size of the prey ingested, which is larger in H. plumieri. Key words: Ecomorphology, Reef fishes, Northeastern Brazil, Parcel de Manuel Luiz.
Metazoan endoparasites of Pygocentrus nattereri (Characiformes: Serrasalminae) in the Negro River, Pantanal, Brazil.

In the period of October 2007 to August 2008, 152 specimens of Pygocentrus nattereri were caught in the Negro River in the Nhecolândia region, central Pantanal wetland, State of Mato Grosso do Sul, Brazil. The specimens were necropsied and a total of 4,212 metazoan endoparasites were recovered, belonging to 10 taxons: Procamallanus (Spirocamallanus) inopinatus, Philometridae gen. sp. , Eustrongylides sp. , Brevimulticaecum sp. , Contracaecum sp. (Nematoda), Echinorhynchus paranensis (Acanthocephala), Leiperia gracile, Sebekia oxycephala, Subtriquetra sp. 1 and Subtriquetra sp. 2 (Pentastomida). This is the first record of two parasite species from P. nattereri: E. paranensis and L. gracile.
Ovarian function is preserved in women with severe systemic lupus erythematosus after a 6-month course of cyclophosphamide followed by mycophenolate mofetil.

OBJECTIVE To evaluate whether a short duration treatment with cyclophosphamide (CYC) followed by mycophenolate mofetil (MMF) is associated with preservation of the ovarian function in female patients with systemic lupus erythematosus (SLE). METHODS We retrospectively evaluated 61 premenopausal women with SLE treated for lupus nephritis (n=58), autoimmune hemolytic anemia (n=1) and central nervous system involvement (n=2). Thirty-nine patients received prolonged treatment with 1 g/m2 intravenous (IV) CYC pulses (group I). 22 patients received 5-7 monthly 1 g/m2 IV CYC pulses and afterwards 2 g/day MMF (group II). RESULTS Disease activity was equally controlled using either regimen (p=0.76 and p=0.31 for disease remission and relapse respectively). Amenorrhea developed in 56% of women in group I (n=22) and 14% in group II (n=3) (p=0.01), whereas sustained amenorrhea developed in 51% (n=20) of women in group I versus 4% (n=1) in group II (p=0.05). Most women with amenorrhea in group I (86%) did not resume menses after the cessation of therapy versus one woman (33%) in group II. In logistic regression, group I had a 4-fold higher risk of amenorrhea and 5-fold higher risk of sustained amenorrhea compared to group II (p=0.001 and p=0.009 respectively). Age (p<0.001), cumulative CYC dose (p=0.001) and anti-Ro antibodies (p=0.002) were significant in terms of amenorrhea, while sustained amenorrhea was significantly associated with the patient age (p=0.026). CONCLUSION We suggest that treatment with MMF following 5-7 IV pulses of CYC is an effective mean to control disease activity and preserve ovarian function in premenopausal women with SLE.
Healthy travel and child socialisation:policy implications for social and cultural change

The way people travel has a substantial impact on health. Over reliance on car transportation has personal as well as social health effects. This thesis reports research designed to investigate the role of cultural factors on children's travel. It examined the home and the school in a project that had theoretical and practical objectives. Theoretically the research sought to ascertain if there is transmission of parental attitudes, norms and patterns of travel behaviour to children. A practical objective was to determine if school travel initiatives are effective in reducing car dependency for school journeys. The primary argument is that children learn about travel modes in the same way as other aspects of culture, through agents of socialisation: the family, school, media and peer groups. The findings were used to develop a social theory of travel mode behaviour, 'travel socialisation'. This focuses on behaviour in the context of the culture in which people live, examining the role of every day life on travel. A secondary argument is that to remove 'car dependency' involves changing the social and cultural emphasis on cars as a mode of transport. There is a need to tackle this from a social policy approach rather than just a 'travel demand' management perspective. The policy implications of the findings address how children, as the next generation of adults, should be socialised to avoid future dependency on car transportation. These include measures aimed at families, employers and everyone who shares the community. A 'mixed methods' research design utilised qualitative and quantitative data and the main conclusions were strengthened by methodological triangulation. A 'comparative methods' approach was used in the design and analysis of the research instruments. Key variables were 'number of cars in household' and 'type of school attended'. Primary school children completed travel diaries, pictorial questionnaires and some participated in focus groups. Parents and key persons in schools completed a questionnaire and some were interviewed. A documentary analysis of the governmental school travel plan promotional literature was undertaken.
Low-Frequency Variations in Currents near the Shelf Break: Northeast Gulf of Alaska

Abstract We present current observations from depths of 20, 50, 100 and 175 m obtained over a 3-year period near the northeast Gulf of Alaska shelf break, and emphasize a 2-year continuous segment from 50 m depth. These records indicate that a moderate (∼16 cm s−1 at 50 m) mean flow was directed, at all depths, along-shelf toward the northwest. Variance was high and had nearly normal distributions in along- and across-shelf components. The mean alongshelf speed varied from ∼12 cm s−1 in summer to ∼20 cm s−1 in winter and a more distinct seasonal cycle was evident in monthly kinetic energies of wind and current. Very low-frequency (VLF) ( 0.8 at 95% level). Fluctuating kinetic energy of the current contained in the VLF band was a significant fraction (34%) of the total kinetic energy, and displayed an increase over the two years with no seasonal trend. Trends in the wind ki.