The development of a classification system for inland aquatic ecosystems in South Africa

A classification system is described that was developed for inland aquatic ecosystems in South Africa, including wetlands. The six-tiered classification system is based on a top-down, hierarchical  classification of aquatic ecosystems, following the functionally-oriented hydrogeomorphic (HGM)  approach to classification but incorporating structural attributes at the lower levels of the hierarchy. At Level 1, a distinction is made between inland, estuarine and shallow marine systems using the degree of connectivity to the open ocean as the key discriminator. Inland systems are characterised by the  complete absence of marine exchange and/or tidal influence. At Level 2, inland systems are grouped according to the most appropriate spatial framework for the particular application. At Level 3, four  primary Landscape Units are distinguished (Valley floor, Slope, Plain, Bench) on the basis of the  topographic position within which a particular inland aquatic ecosystem is situated, in recognition of the influence that the landscape setting has over hydrological and hydrodynamic processes acting within an aquatic ecosystem. Level 4 identifies HGM Units, defined primarily according to landform, hydrological characteristics and hydrodynamics. The following primary HGM Units (or HGM Types), which represent the main units of analysis for the classification system, are distinguished at Level 4A: (1) River; (2) Floodplain Wetland; (3) Channelled Valley-Bottom Wetland; (4) Unchannelled Valley-Bottom Wetland; (5) Depression; (6) Seep; (7) Wetland Flat. Secondary discriminators are applied at Level 5 to classify the hydrological regime of an HGM Unit, and Descriptors at Level 6 to categorise a range of biophysical attributes. The HGM Unit at Level 4 and the Hydrological Regime at Level 5 together constitute a Functional Unit, which represents the focal point of the classification system. The utility of the  classification system is ultimately dependent on the level to which ecosystem units are classified, which is in turn constrained by the type and extent of information available.Keywords: freshwater ecosystems, hydrogeomorphic (HGM) units, inland water ecosystems,  wetlands, wetland classification syste

A comparison of photographic, replication and direct clinical examination methods for detecting developmental defects of enamel

Different methods have been used for detecting developmental defects of enamel (DDE). This study aimed to compare photographic and replication methods with the direct clinical examination method for detecting DDE in children's permanent incisors

Bacterial Genomes: Habitat Specificity and Uncharted Organisms

The capability and speed in generating genomic data have increased profoundly since the release of the draft human genome in 2000. Additionally, sequencing costs have continued to plummet as the next generation of highly efficient sequencing technologies (next-generation sequencing) became available and commercial facilities promote market competition. However, new challenges have emerged as researchers attempt to efficiently process the massive amounts of sequence data being generated. First, the described genome sequences are unequally distributed among the branches of bacterial life and, second, bacterial pan-genomes are often not considered when setting aims for sequencing projects. Here, we propose that scientists should be concerned with attaining an improved equal representation of most of the bacterial tree of life organisms, at the genomic level. Moreover, they should take into account the natural variation that is often observed within bacterial species and the role of the often changing surrounding environment and natural selection pressures, which is central to bacterial speciation and genome evolution. Not only will such efforts contribute to our overall understanding of the microbial diversity extant in ecosystems as well as the structuring of the extant genomes, but they will also facilitate the development of better methods for (meta)genome annotation

Confiabilidad de un instrumento para clasificar al recién nacido de acuerdo con la complejidad de la atención

Na maioria das maternidades, a classificação, a avaliação e a definição da unidade a encaminhar o recém-nascido (RN) após o nascimento são realizadas pelo médico. A\ud avaliação ocorre na sala de parto considerando: peso ao nascer; idade gestacional;\ud condutas que definem quadro clínico e doença. Este estudo observacional teve\ud como objetivo avaliar a confiabilidade de um instrumento de classificação de RN. A pesquisa foi realizada no berçário de um hospital público, São Paulo. Nove enfermeiras\ud aplicaram o instrumento a 63 RN, sendo duas simultaneamente em cada um dos\ud cinco setores do berçário. Verificou-se que o nível de concordância Kappa entre as enfermeiras foi excelente para a maioria das áreas de cuidado (69,0%). Concluiu-se que houve consenso e concordância das enfermeiras quanto ao instrumento ser completo, de fácil entendimento e aplicável, porém despende muito tempo. As enfermeiras reconhecem a importância do instrumento para o dimensionamento dos profissionais, organização e planejamento do cuidado.In most maternity units, the physician classifies, evaluates, and determines which unit will receive the newborn (NB) after birth. Evaluation occurs in the delivery room, taking into consideration the following factors: birth weight, gestational age, and behaviors that define the clinical picture and disease. This observational study evaluates the reliability of an NB classification instrument. The study was conducted at the nursery of a public hospital in São Paulo. Nine nurses applied the instrument to 63 NB, with two of the nurses working simultaneously in each of the nursery’s fi ve sectors. The Kappa level of agreement among the nurses was found to be excellent for most care areas\ud (69.0%). It was concluded that there was a consensus and agreement among the\ud nurses that the instrument was complete, easy to understand and applicable, but was\ud very time consuming. The nurses recognize the instrument’s importance for the allocation of professionals, organization, and care planning.En la mayoría de las maternidades la clasificación, la evaluación y la definición de la unidad para referir el recién nacido (RN), son realizadas por el médico. La evaluación se realiza en la sala de parto, considerando: peso al nacer, edad gestacional y conductas que definen el cuadro clínico y la enfermedad. Este estudio observacional tuvo como objetivo evaluar la confiabilidad de un instrumento de clasificación del RN. Fue realizada en el servicio de neonatología de un hospital público en Sao Paulo. Nueve enfermeras\ud aplicaron el instrumento a 63 RN, siendo aplicados dos de forma simultánea en los cinco sectores de la unidad neonatal. El nivel de concordancia Kappa fue excelente para la mayoría de las áreas de atención (69,0%). Se concluyó que hubo consenso y\ud concordancia entre las enfermeras, quienes expresaron que el instrumento es completo, fácil de entender y de aplicar, pero se necesita mucho tempo. Las enfermeras reconocen la importancia de este instrumento para dimensionar el número de profesionales, la organización y la planificación de la atención

Apoptotic HPV Positive Cancer Cells Exhibit Transforming Properties

Previous studies have shown that DNA can be transferred from dying engineered cells to neighboring cells through the phagocytosis of apoptotic bodies, which leads to cellular transformation. Here, we provide evidence of an uptake of apoptotic-derived cervical cancer cells by human mesenchymal cells. Interestingly, HeLa (HPV 18+) or Ca Ski (HPV16+) cells, harboring integrated high-risk HPV DNA but not C-33 A cells (HPV-), were able to transform the recipient cells. Human primary fibroblasts engulfed the apoptotic bodies effectively within 30 minutes after co-cultivation. This mechanism is active and involves the actin cytoskeleton. In situ hybridization of transformed fibroblasts revealed the presence of HPV DNA in the nucleus of a subset of phagocytosing cells. These cells expressed the HPV16/18 E6 gene, which contributes to the disruption of the p53/p21 pathway, and the cells exhibited a tumorigenic phenotype, including an increased proliferation rate, polyploidy and anchorage independence growth. Such horizontal transfer of viral oncogenes to surrounding cells that lack receptors for HPV could facilitate the persistence of the virus, the main risk factor for cervical cancer development. This process might contribute to HPV-associated disease progression in vivo

Development and Validation of an In Silico Decision Tool To Guide Optimization of Intravenous Artesunate Dosing Regimens for Severe Falciparum Malaria Patients

Most deaths from severe falciparum malaria occur within 24 h of presentation to a hospital. Intravenous (i.v.) artesunate is the first-line treatment for severe falciparum malaria, but its efficacy may be compromised by delayed parasitological responses. In patients with severe malaria, the life-saving benefit of the artemisinin derivatives is their ability to clear circulating parasites rapidly, before they can sequester and obstruct the microcirculation. To evaluate the dosing of i.v. artesunate for the treatment of artemisinin-sensitive and reduced ring stage sensitivity to artemisinin severe falciparum malaria infections, Bayesian pharmacokinetic-pharmacodynamic modeling of data from 94 patients with severe malaria (80 children from Africa and 14 adults from Southeast Asia) was performed. Assuming that delayed parasite clearance reflects a loss of ring stage sensitivity to artemisinin derivatives, the median (95% credible interval) percentage of patients clearing ≥99% of parasites within 24 h (PC24≥99%) for standard (2.4 mg/kg body weight i.v. artesunate at 0 and 12 h) and simplified (4 mg/kg i.v. artesunate at 0 h) regimens was 65% (52.5% to 74.5%) versus 44% (25% to 61.5%) for adults, 62% (51.5% to 74.5%) versus 39% (20.5% to 58.5%) for larger children (≥20 kg), and 60% (48.5% to 70%) versus 36% (20% to 53.5%) for smaller children (<20 kg). The upper limit of the credible intervals for all regimens was below a PC24≥99% of 80%, a threshold achieved on average in clinical studies of severe falciparum malaria infections. In severe falciparum malaria caused by parasites with reduced ring stage susceptibility to artemisinin, parasite clearance is predicted to be slower with both the currently recommended and proposed simplified i.v. artesunate dosing regimens

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

Little is known about the factors affecting the relative influences of stochastic and deterministic processes that govern the assembly of microbial communities in successional soils. Here, we conducted a meta-analysis of bacterial communities using six different successional soil datasets distributed across different regions. Different relationships between pH and successional age across these datasets allowed us to separate the influences of successional age (i.e., time) from soil pH. We found that extreme acidic or alkaline pH conditions lead to assembly of phylogenetically more clustered bacterial communities through deterministic processes, whereas pH conditions close to neutral lead to phylogenetically less clustered bacterial communities with more stochasticity. We suggest that the influence of pH, rather than successional age, is the main driving force in producing trends in phylogenetic assembly of bacteria, and that pH also influences the relative balance of stochastic and deterministic processes along successional soils. Given that pH had a much stronger association with community assembly than did successional age, we evaluated whether the inferred influence of pH was maintained when studying globally distributed samples collected without regard for successional age. This dataset confirmed the strong influence of pH, suggesting that the influence of soil pH on community assembly processes occurs globally. Extreme pH conditions likely exert more stringent limits on survival and fitness, imposing strong selective pressures through ecological and evolutionary time. Taken together, these findings suggest that the degree to which stochastic vs. deterministic processes shape soil bacterial community assembly is a consequence of soil pH rather than successional age

The Microbiome of Brazilian Mangrove Sediments as Revealed by Metagenomics

Here we embark in a deep metagenomic survey that revealed the taxonomic and potential metabolic pathways aspects of mangrove sediment microbiology. The extraction of DNA from sediment samples and the direct application of pyrosequencing resulted in approximately 215 Mb of data from four distinct mangrove areas (BrMgv01 to 04) in Brazil. The taxonomic approaches applied revealed the dominance of Deltaproteobacteria and Gammaproteobacteria in the samples. Paired statistical analysis showed higher proportions of specific taxonomic groups in each dataset. The metabolic reconstruction indicated the possible occurrence of processes modulated by the prevailing conditions found in mangrove sediments. In terms of carbon cycling, the sequences indicated the prevalence of genes involved in the metabolism of methane, formaldehyde, and carbon dioxide. With respect to the nitrogen cycle, evidence for sequences associated with dissimilatory reduction of nitrate, nitrogen immobilization, and denitrification was detected. Sequences related to the production of adenylsulfate, sulfite, and H2S were relevant to the sulphur cycle. These data indicate that the microbial core involved in methane, nitrogen, and sulphur metabolism consists mainly of Burkholderiaceae, Planctomycetaceae, Rhodobacteraceae, and Desulfobacteraceae. Comparison of our data to datasets from soil and sea samples resulted in the allotment of the mangrove sediments between those samples. The results of this study add valuable data about the composition of microbial communities in mangroves and also shed light on possible transformations promoted by microbial organisms in mangrove sediments