Subarachnoid-Pleural Fistula: Applied Anatomy of the Thoracic Spinal Nerve Root

Subarachnoid-pleural fistula (SPF) is a rare complication of chest or spine operations for neoplastic disease. Concomitant dural and parietal pleural defects permit flow of cerebrospinal fluid into the pleural cavity or intrapleural air into the subarachnoid space. Dural injury recognized intraoperatively permits immediate repair, but unnoticed damage may cause postoperative pleural effusion, intracranial hypotension, meningitis, or pneumocephalus. We review two cases of SPF following surgical intervention for chest wall metastatic disease to motivate a detailed review of the anatomy of neural, osseous, and ligamentous structures at the intervertebral foramen. We further provide recommendations for avoidance and detection of such complication

Water regime history drives responses of soil Namib Desert microbial communities to wetting events

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.The South African National Research Foundation (NRF 88303) and the University of Pretoria.http://www.nature.com/scientificreportsam201

Heel strike detection based on human walking movement for surveillance analysis

Heel strike detection is an important cue for human gait recognition and detection in visual surveillance since the heel strike position can be used to derive the gait periodicity, stride and step length. We propose a novel method for heel strike detection using a gait trajectory model, which is robust to occlusion, camera view, and low resolution. When a person walks, the movement of the head is conspicuous and sinusoidal. The highest point of the trajectory of the head occurs when the feet cross (stance) and the lowest point is when the gait stride is the largest (heel strike). Our gait trajectory model is constructed from trajectory data using non-linear optimisation. Then, the key frames in which the heel strikes take place are calculated. A Region Of Interest (ROI) is extracted using the silhouette image of the key frame as a filter. For candidate detection, Gradient Descent is applied to detect maxima which are considered to be the time of the heel strikes. For candidate verification, two filtering methods are used to reconstruct the 3D position of a heel strike using the given camera projection matrix. The contribution of this research is the first use of the gait trajectory in the heel strike position estimation process and we contend that it is a new approach for basic analysis in surveillance imagery

A sequential co-extraction method for DNA, RNA and protein recovery from soil for future system-based approaches

A co-extraction protocol that sequentially isolates core biopolymer fractions (DNA, RNA, protein) from edaphic microbial communities is presented. In order to confirm compatibility with downstream analyses, bacterial T-RFLP profiles were generated from the DNA- and RNA-derived fractions of an arid-based soil, with metaproteomics undertaken on the corresponding protein fraction.National Research Foundation Grant no. 81779 (South Africa).http://www.elsevier.com/ locate/jmicmethhb2016Genetic

The influence of surface soil physicochemistry on the edaphic bacterial communities in contrasting terrain types of the Central Namib Desert

Notwithstanding, the severe environmental conditions, deserts harbour a high diversity of adapted micro-organisms. In such oligotrophic environments, soil physicochemical characteristics play an important role in shaping indigenous microbial communities. This study investigates the edaphic bacterial communities of three contrasting desert terrain types (gravel plains, sand dunes and ephemeral rivers) with different surface geologies in the Central Namib Desert. For each site, we evaluated surface soil physicochemistries and used explorative T-RFLP methodology to get an indication of bacterial community diversities. While grain size was an important parameter in separating the three terrain types physicochemically and specific surface soil types could be distinguished, the desert edaphic bacterial communities displayed a high level of local spatial heterogeneity. Ten variables contributed significantly (P < 0.05) to the variance in the T-RFLP data sets: fine silt, medium and fine sand content, pH, S, Na, Zn, Al, V and Fe concentrations, and 40% of the total variance could be explained by these constraining variables. The results suggest that local physicochemical conditions play a significant role in shaping the bacterial structures in the Central Namib Desert and stress the importance of recording a wide variety of environmental descriptors to comprehensively assess the role of edaphic parameters in shaping microbial communities.University of Pretoria and the South African National Research Foundation (NRF).http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1472-46692016-09-30hb201

Namib Desert edaphic bacterial, fungal and archaeal communities assemble through deterministic processes but are influenced by different abiotic parameters

The central Namib Desert is hyperarid, where limited plant growth ensures that biogeochemical processes are largely driven by microbial populations. Recent research has shown that niche partitioning is critically involved in the assembly of Namib Desert edaphic communities. However, these studies have mainly focussed on the Domain Bacteria. Using microbial community fingerprinting, we compared the assembly of the bacterial, fungal and archaeal populations of microbial communities across nine soil niches from four Namib Desert soil habitats (riverbed, dune, gravel plain and salt pan). Permutational multivariate analysis of variance indicated that the nine soil niches presented significantly different physicochemistries (R 2 = 0.8306, P ≤ 0.0001) and that bacterial, fungal and archaeal populations were soil niche specific (R 2 ≥ 0.64, P ≤ 0.001). However, the abiotic drivers of community structure were Domain-specific (P < 0.05), with P, clay and sand fraction, and NH4 influencing bacterial, fungal and archaeal communities, respectively. Soil physicochemistry and soil niche explained over 50% of the variation in community structure, and communities displayed strong non-random patterns of co-occurrence. Taken together, these results demonstrate that in central Namib Desert soil microbial communities, assembly is principally driven by deterministic processes.The South African National Research Foundation (Grant Number N00113-95565) and the University of Pretoria (UP).http://link.springer.com/journal/7922018-01-31hb2017Genetic

Namib Desert primary productivity is driven by cryptic microbial community N-fixation

Carbon exchange in drylands is typically low, but during significant rainfall events (wet anomalies) drylands act as a C sink. During these anomalies the limitation on C uptake switches from water to nitrogen. In the Namib Desert of southern Africa, the N inventory in soil organic matter available for mineralisation is insufficient to support the observed increase in primary productivity. The C4 grasses that flourish after rainfall events are not capable of N fixation, and so there is no clear mechanism for adequate N fixation in dryland ecosystems to support rapid C uptake. Here we demonstrate that N fixation by photoautotrophic hypolithic communities forms the basis for the N budget for plant productivity events in the Namib Desert. Stable N isotope (δ15N) values of Namib Desert hypolithic biomass, and surface and subsurface soils were measured over 3 years across dune and gravel plain biotopes. Hypoliths showed significantly higher biomass and lower δ15N values than soil organic matter. The δ15N values of hypoliths approach the theoretical values for nitrogen fixation. Our results are strongly indicative that hypolithic communities are the foundation of productivity after rain events in the Namib Desert and are likely to play similar roles in other arid environments.The South African National Research Foundation (Grant number: N00113-95565) and the University of Pretoria (Research and Development Programme for J-BR).http://www.nature.com/srepam2018BiochemistryGeneticsMammal Research InstituteMicrobiology and Plant Patholog

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

8 páginas, 4 figuras. -- The first publication is available at https://www.nature.comThe temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.We gratefully acknowledge financial support from the National Research Foundation of South Africa (grant no.81779 and TTK2008052000003), the Research Council of Norway (grant No. 180352) and the University of the Western Cape. Partial support was also provided under the Laboratory Directed Research and Development Program at PNNL, a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy under contract DE-AC05-76RL01830.Peer reviewe

Unique microbial phylotypes in Namib desert dune and gravel plain fairy circle soils

Fairy Circles (FCs) are barren circular patches of soil surrounded by grass species, the origin of which is poorly understood. FCs feature in both the gravel plains and dune fields of the Namib Desert. While a substantial number of hypotheses to explain the origin and/or sustainability of fairy circles have been presented, none are completely consistent with either their properties or distribution. In this study, we investigated the hypothesis that dune and gravel plain FC formation is due to microbial phytopathogenesis. Surface soils from five gravel plain and five dune FCs, together with control soil samples, were analysed using high-throughput sequencing of bacterial/archaeal (16S rRNA gene) and fungal (ITS region) phylogenetic markers. Our analyses showed that gravel plain and dune FC microbial communities are phylogenetically distinct and that FC communities differ from adjacent vegetated soils. Furthermore, various soil physicochemical properties, particularly pH, Ca, P, Na, SO4, soil particle size and % carbon, significantly influenced dune and gravel plain FC microbial community compositions but none were found to segregate FC and vegetated soil communities. Nevertheless, 9 bacterial, 1 archaeal and 57 fungal phylotypes were identified as FC-specific, being present only within the gravel plain and dune FCs soils but not in the vegetated soils. Some of these FC-specific phylotypes were assigned to taxa known to harbour phytopathogenic microorganisms. This suggests that these FC-specific microbial taxa may be involved in the formation and/or maintenance of Namib Desert FCs.South African National Research Foundation (NRF, Grant No: 90312) and the University of Pretoria.http://aem.asm.org2017-02-28hb2016Genetic

Effect of selenium supplementation on CD4 T-cell recovery, viral suppression, morbidity and quality of life of HIV-infected patients in Rwanda: study protocol for a randomized controlled trial

<p>Abstract</p> <p>Background</p> <p>Low levels of serum selenium are associated with increased risk of mortality among HIV+ patients in East Africa. We aim to assess the effect of selenium supplementation on CD4 cell count, HIV viral load, opportunistic infections, and quality of life in HIV-infected patients in Rwanda.</p> <p>Methods and Design</p> <p>A 24-month, multi-centre, patient and provider-blinded, randomized, placebo-controlled clinical trial involving 300 pre-antiretroviral therapy (ART) HIV-infected patients will be carried out at two sites in Rwanda. Patients ≥ 21 years of age with documented HIV infection, CD4 cell count of 400-650 cells/mm³, and not yet on ART will be recruited. Patients will be randomized at each study site using a randomized block design to receive either the selenium micronutrient supplement or an identically appearing placebo taken once daily. The primary outcome is a composite of time from baseline to reduction of CD4 T lymphocyte count below 350 cells/mm³ (confirmed by two measures at least one week apart), or start of ART, or the emergence of a documented CDC-defined AIDS-defining illness. An intention-to-treat analysis will be conducted using stepwise regression and structural equation modeling.</p> <p>Discussion</p> <p>Micronutrient interventions that aim to improve CD4 cell count, decrease opportunistic infections, decrease HIV viral load, and ultimately delay initiation of more costly ART may be beneficial, particularly in resource-constrained settings, such as sub-Saharan Africa. Additional trials are needed to determine if micro-supplementation can delay the need for more costly ART among HIV-infected patients. If shown to be effective, selenium supplementation may be of public health importance to HIV-infected populations, particularly in sub-Saharan Africa and other resource-constrained settings.</p> <p>Trial Registration</p> <p><a href="http://www.clinicaltrials.gov/ct2/show/NCT01327755">NCT01327755</a></p