Bacterioplankton reveal years-long retention of Atlantic deep-ocean water by the Tropic Seamount.

Seamounts, often rising hundreds of metres above surrounding seafloor, obstruct the flow of deep-ocean water. While the retention of deep-water by seamounts is predicted from ocean circulation models, its empirical validation has been hampered by large scale and slow rate of the interaction. To overcome these limitations we use the growth of planktonic bacteria to assess the retention time of deep-ocean water by a seamount. The selected Tropic Seamount in the North-Eastern Atlantic is representative for the majority of isolated seamounts, which do not affect the surface ocean waters. We prove deep-water is retained by the seamount by measuring 2.4× higher bacterial concentrations in the seamount-associated or 'sheath'-water than in deep-ocean water unaffected by seamounts. Genomic analyses of flow-sorted, dominant sheath-water bacteria confirm their planktonic origin, whilst proteomic analyses of the sheath-water bacteria, isotopically labelled in situ, indicate their slow growth. According to our radiotracer experiments, it takes the sheath-water bacterioplankton 1.5 years to double their concentration. Therefore, the seamount should retain the deep-ocean water for 1.8 years for the deep-ocean bacterioplankton to grow to the 2.4× higher concentration in the sheath-water. We propose that turbulent mixing of the seamount sheath-water stimulates bacterioplankton growth by increasing cell encounter rate with ambient dissolved organic molecules.

Man against machine: diagnostic performance of a deep learning convolutional neural network for dermoscopic melanoma recognition in comparison to 58 dermatologists.

Background: Deep learning convolutional neural networks (CNN) may facilitate melanoma detection, but data comparing a CNN's diagnostic performance to larger groups of dermatologists are lacking. Methods: Google's Inception v4 CNN architecture was trained and validated using dermoscopic images and corresponding diagnoses. In a comparative cross-sectional reader study a 100-image test-set was used (level-I: dermoscopy only; level-II: dermoscopy plus clinical information and images). Main outcome measures were sensitivity, specificity and area under the curve (AUC) of receiver operating characteristics (ROC) for diagnostic classification (dichotomous) of lesions by the CNN versus an international group of 58 dermatologists during level-I or -II of the reader study. Secondary end points included the dermatologists' diagnostic performance in their management decisions and differences in the diagnostic performance of dermatologists during level-I and -II of the reader study. Additionally, the CNN's performance was compared with the top-five algorithms of the 2016 International Symposium on Biomedical Imaging (ISBI) challenge. Results: In level-I dermatologists achieved a mean (±standard deviation) sensitivity and specificity for lesion classification of 86.6% (±9.3%) and 71.3% (±11.2%), respectively. More clinical information (level-II) improved the sensitivity to 88.9% (±9.6%, P = 0.19) and specificity to 75.7% (±11.7%, P < 0.05). The CNN ROC curve revealed a higher specificity of 82.5% when compared with dermatologists in level-I (71.3%, P < 0.01) and level-II (75.7%, P < 0.01) at their sensitivities of 86.6% and 88.9%, respectively. The CNN ROC AUC was greater than the mean ROC area of dermatologists (0.86 versus 0.79, P < 0.01). The CNN scored results close to the top three algorithms of the ISBI 2016 challenge. Conclusions: For the first time we compared a CNN's diagnostic performance with a large international group of 58 dermatologists, including 30 experts. Most dermatologists were outperformed by the CNN. Irrespective of any physicians' experience, they may benefit from assistance by a CNN's image classification. Clinical trial number: This study was registered at the German Clinical Trial Register (DRKS-Study-ID: DRKS00013570; https://www.drks.de/drks_web/).

Low-Light Anoxygenic Photosynthesis and Fe-S-Biogeochemistry in a Microbial Mat.

We report extremely low-light-adapted anoxygenic photosynthesis in a thick microbial mat in Magical Blue Hole, Abaco Island, The Bahamas. Sulfur cycling was reduced by iron oxides and organic carbon limitation. The mat grows below the halocline/oxycline at 30 m depth on the walls of the flooded sinkhole. In situ irradiance at the mat surface on a sunny December day was between 0.021 and 0.084 µmol photons m-2 s-1, and UV light (<400 nm) was the most abundant part of the spectrum followed by green wavelengths (475-530 nm). We measured a light-dependent carbon uptake rate of 14.5 nmol C cm-2 d-1. A 16S rRNA clone library of the green surface mat layer was dominated (74%) by a cluster (>97% sequence identity) of clones affiliated with Prosthecochloris, a genus within the green sulfur bacteria (GSB), which are obligate anoxygenic phototrophs. Typical photopigments of brown-colored GSB, bacteriochlorophyll e and (ß-)isorenieratene, were abundant in mat samples and their absorption properties are well-adapted to harvest light in the available green and possibly even UV-A spectra. Sulfide from the water column (3-6 µmol L-1) was the main source of sulfide to the mat as sulfate reduction rates in the mats were very low (undetectable-99.2 nmol cm-3 d-1). The anoxic water column was oligotrophic and low in dissolved organic carbon (175-228 µmol L-1). High concentrations of pyrite (FeS2; 1-47 µmol cm-3) together with low microbial process rates (sulfate reduction, CO2 fixation) indicate that the mats function as net sulfide sinks mainly by abiotic processes. We suggest that abundant Fe(III) (4.3-22.2 µmol cm-3) is the major source of oxidizing power in the mat, and that abiotic Fe-S-reactions play the main role in pyrite formation. Limitation of sulfate reduction by low organic carbon availability along with the presence of abundant sulfide-scavenging iron oxides considerably slowed down sulfur cycling in these mats.

Assembling cheap, high-performance microphones for recording terrestrial wildlife: the Sonitor system.

Passive acoustic monitoring of wildlife requires sound recording systems. Several cheap, high-performance, or open-source solutions currently exist for recording soundscapes, but all rely on commercial microphones. Commercial microphones are relatively expensive, specialized for particular taxa, and often have incomplete technical specifications. We designed Sonitor, an open-source microphone system to address all needs of ecologists that sample terrestrial wildlife acoustically. We evaluated the cost and durability of our system and measured trade-offs that are seldom acknowledged but which universally limit microphones' functions: weatherproofing versus sound attenuation, windproofing versus transmission loss after rain, signal loss in long cables, and analog sound amplification versus directivity with acoustic horns. We propose five microphone configurations suiting different budgets (from 8 to 33 EUR per unit), and fulfilling different sound quality and flexibility requirements. The Sonitor system consists of sturdy acoustic sensors that cover the entire sound frequency spectrum of sonant terrestrial wildlife at a fraction of the cost of commercial microphones.

Recoding of the stop codon UGA to glycine by a BD1-5/SN-2 bacterium and niche partitioning between Alpha- and Gammaproteobacteria in a tidal sediment microbial community naturally selected in a laboratory chemostat.

Sandy coastal sediments are global hotspots for microbial mineralization of organic matter and denitrification. These sediments are characterized by advective porewater flow, tidal cycling and an active and complex microbial community. Metagenomic sequencing of microbial communities sampled from such sediments showed that potential sulfur oxidizing Gammaproteobacteria and members of the enigmatic BD1-5/SN-2 candidate phylum were abundant in situ (>10% and ~2% respectively). By mimicking the dynamic oxic/anoxic environmental conditions of the sediment in a laboratory chemostat, a simplified microbial community was selected from the more complex inoculum. Metagenomics, proteomics and fluorescence in situ hybridization showed that this simplified community contained both a potential sulfur oxidizing Gammaproteobacteria (at 24 ± 2% abundance) and a member of the BD1-5/SN-2 candidate phylum (at 7 ± 6% abundance). Despite the abundant supply of organic substrates to the chemostat, proteomic analysis suggested that the selected gammaproteobacterium grew partially autotrophically and performed hydrogen/formate oxidation. The enrichment of a member of the BD1-5/SN-2 candidate phylum enabled, for the first time, direct microscopic observation by fluorescent in situ hybridization and the experimental validation of the previously predicted translation of the stop codon UGA into glycine.

Microenvironments of reduced salinity harbour biofilms in Dead Sea underwater springs.

The Dead Sea is a hypersaline lake where only few types of organisms can grow. Recently, abundant and diverse microbial life was discovered in biofilms covering rocks and permeable sediments around underwater freshwater springs and seeps. We used a newly developed salinity mini-sensor (spatial resolution 300 µm) to investigate the salinity environment around these biofilms in a flume that simulates an underwater spring. Compared with the hypersaline bulk water, salinity at the sediment surface decreased to zero at seeping velocities of 7 cm s(-1). At similar flow velocities, salinity above rocks decreased to 100-200 g L(-1) at a distance of 300 µm from the surface. This depended on the position on the rock, and coincided with locations of natural biofilms. The salinity reduction substantially diminished at flow velocities of 3.5 cm s(-1). We suggest that locally decreased salinity due to freshwater input is one of the main factors that make areas around underwater freshwater springs and seeps in the Dead Sea more favourable for life. However, due to frequent fluctuations in the freshwater flow, the locally decreased salinity is unstable. Therefore, microorganisms that inhabit these environments must be capable of withstanding large and rapid salinity fluctuations.

S1 guideline diagnosis and therapy of cutaneous larva migrans (creeping disease).

GUIDELINE OBJECTIVES: These guidelines aim to enhance patient care by optimizing the diagnosis and treatment of infections due to creeping disease (cutaneous larva migrans) and to raise awareness among doctors of current treatment options. METHODS: S1 guideline, non-systematic literature search, consensus process using a circular letter.

Marine sulfate-reducing bacteria cause serious corrosion of iron under electroconductive biogenic mineral crust.

Iron (Fe(0) ) corrosion in anoxic environments (e.g. inside pipelines), a process entailing considerable economic costs, is largely influenced by microorganisms, in particular sulfate-reducing bacteria (SRB). The process is characterized by formation of black crusts and metal pitting. The mechanism is usually explained by the corrosiveness of formed H(2) S, and scavenge of 'cathodic' H(2) from chemical reaction of Fe(0) with H(2) O. Here we studied peculiar marine SRB that grew lithotrophically with metallic iron as the only electron donor. They degraded up to 72% of iron coupons (10 mm × 10 mm × 1 mm) within five months, which is a technologically highly relevant corrosion rate (0.7 mm Fe(0) year(-1) ), while conventional H(2) -scavenging control strains were not corrosive. The black, hard mineral crust (FeS, FeCO(3) , Mg/CaCO(3) ) deposited on the corroding metal exhibited electrical conductivity (50 S m(-1) ). This was sufficient to explain the corrosion rate by electron flow from the metal (4Fe(0) → 4Fe(2+) + 8e(-) ) through semiconductive sulfides to the crust-colonizing cells reducing sulfate (8e(-) + SO(4) (2-) + 9H(+) → HS(-) + 4H(2) O). Hence, anaerobic microbial iron corrosion obviously bypasses H(2) rather than depends on it. SRB with such corrosive potential were revealed at naturally high numbers at a coastal marine sediment site. Iron coupons buried there were corroded and covered by the characteristic mineral crust. It is speculated that anaerobic biocorrosion is due to the promiscuous use of an ecophysiologically relevant catabolic trait for uptake of external electrons from abiotic or biotic sources in sediments.

Azathioprine in the treatment of autoimmune blistering diseases.

Although there are no standard guidelines for the treatment of autoimmune blistering diseases, azathioprine has shown good efficacy in acquired autoimmune blistering diseases, and is well tolerated. Side effects of azathioprine normally occur in mild variants. Severe reactions are due to reduced thiopurine S-methyltransferase (TPMT) or inosine triphosphate pyrophosphohydrolase (ITPA) activity. Therefore, screening for TPMT activity should be conducted in white patients and Africans, whereas Japanese should be screened for ITPA activity before therapy with azathioprine is started. Azathioprine is clinically meaningful for the treatment of pemphigus.

MRSA eradication in dermatologic outpatients - theory and practice.

BACKGROUND: The dissemination of methicillin resistant staphylococcus aureus (MRSA) is an increasing challenge in medical care. Apart from hospital acquired MRSA, there has also been an increase in community acquired and livestock associated MRSA. While the risks of MRSA (e. g. wound infections) and consequences (e. g. rejection of patients) are well known, there are little data on the effectiveness of eradication procedures. PATIENTS AND METHODS: 32 patients with proven MRSA colonization were monitored during eradication for the following aspects: (1) localization of MRSA (swabs from hairline, anterior nares, throat, axillae, groins, perineum, and wounds, if present), (2) presence of eradication-impairing factors, (3) length of time needed for eradication, (4) cost of eradication, (5) molecular fingerprint and risk assessment (spa-types). RESULTS: We describe the successful eradication of MRSA in all 32 patients. Most positive nasal swabs were obtained from the anterior nares and the throat and only rarely from the hairline or axillae. The greater the number of positive swabs, the more time was needed for eradication. In most patients (37.5%), eradication with topical antiseptics was successful. The average time for eradication was 12.97 (± 7.6) days. Twelve patients required systemic antibiotic therapy. Treatment costs associated with the use of systemic antibiotics were significantly higher. The most frequent spa types were t032 and t003. CONCLUSIONS: We report successful MRSA eradication in outpatients. Systemic antibiotics are unnecessary in the majority of patients. A combined anti-MRSA strategy for inpatients and outpatients is recommended.

Differential diagnosis and therapy of leg ulcers.

A leg ulcer is a symptom and the treating physician needs to find out its origin by differential diagnostic approaches and procedures. The correct diagnosis leads to a specific therapy that ideally accelerates the healing of the ulceration. Identifying the pathogenesis of a leg ulcer is the first and main step towards healing. Although vascular diseases are the major causes of leg ulcers, one needs to consider, in addition to venous and arterial disorders, autoimmune, infectious, metabolic and neoplastic causes. The simple truth that one can only make a diagnosis that was considered holds particularly true in leg ulcers. The differential diagnostic considerations presented here appear in the daily routine of a dermatologist and the article provides help in diagnostic approaches and therapeutic decisions.

Azathioprine in the treatment of autoimmune blistering diseases.

Although there are no standard guidelines for the treatment of autoimmune blistering diseases, azathioprine has shown good efficacy in acquired autoimmune blistering diseases, and is well tolerated. Side effects of azathioprine normally occur in mild variants. Severe reactions are due to reduced thiopurine S-methyltransferase (TPMT) or inosine triphosphate pyrophosphohydrolase (ITPA) activity. Therefore, screening for TPMT activity should be conducted in white patients and Africans, whereas Japanese should be screened for ITPA activity before therapy with azathioprine is started. Azathioprine is clinically meaningful for the treatment of pemphigus.

Successful treatment of palmoplantar hyperkeratotic psoriasis with a combination of etanercept and alitretinoin.

Palmoplantar hyperkeratotic psoriasis can be challenging to treat since micro-trauma induced by manual labor supports the development of new lesions via the isomorphic Koebner reaction. In this article, the authors report the successful treatment of severe palmoplantar hyperkeratotic psoriasis with etanercept and alitretinoin combination therapy. The results indicate that the new retinoid alitretinoin can be effectively used in combination with anti-tumor necrosis factor blocking agents for the treatment of psoriasis in individual cases.

High-pressure systems for gas-phase free continuous incubation of enriched marine microbial communities performing anaerobic oxidation of methane.

Novel high-pressure biotechnical systems that were developed and applied for the study of anaerobic oxidation of methane (AOM) are described. The systems, referred to as high-pressure continuous incubation system (HP-CI system) and high-pressure manifold-incubation system (HP-MI system), allow for batch, fed-batch, and continuous gas-phase free incubation at high concentrations of dissolved methane and were designed to meet specific demands for studying environmental regulation and kinetics as well as for enriching microbial biomass in long-term incubation. Anoxic medium is saturated with methane in the first technical stage, and the saturated medium is supplied for biomass incubation in the second stage. Methane can be provided in continuous operation up to 20 MPa and the incubation systems can be operated during constant supply of gas-enriched medium at a hydrostatic pressure up to 45 MPa. To validate the suitability of the high-pressure systems, we present data from continuous and fed-batch incubation of highly active samples prepared from microbial mats from the Black Sea collected at a water depth of 213 m. In continuous operation in the HP-CI system initial methane-dependent sulfide production was enhanced 10- to 15-fold after increasing the methane partial pressure from near ambient pressure of 0.2 to 10.0 MPa at a hydrostatic pressure of 16.0 MPa in the incubation stage. With a hydraulic retention time of 14 h a stable effluent sulfide concentration was reached within less than 3 days and a continuing increase of the volumetric AOM rate from 1.2 to 1.7 mmol L(-1) day(-1) was observed over 14 days. In fed-batch incubation the AOM rate increased from 1.5 to 2.7 and 3.6 mmol L(-1) day(-1) when the concentration of aqueous methane was stepwise increased from 5 to 15 mmol L(-1) and 45 mmol L(-1). A methane partial pressure of 6 MPa and a hydrostatic pressure of 12 MPa in manifold fed-batch incubation in the HP-MI system yielded a sixfold increase in the volumetric AOM rate. Over subsequent incubation periods AOM rates increased from 0.6 to 1.2 mmol L(-1) day(-1) within 26 days of incubation. No inhibition of biomass activity was observed in all continuous and fed-batch incubation experiments. The organisms were able to tolerate high sulfide concentrations and extended starvation periods.

Flood risk assessment in European river basins--concept, methods, and challenges exemplified at the Mulde River.

Flood risk assessment is an essential part of flood risk management, a concept that is becoming more and more popular in European flood policy and is part of the new European Union flood directive. This paper gives a brief introduction into the general concept and methods of flood risk assessment. Furthermore, 3 problems in the practical application of flood risk assessment, particularly on the river basin scale, are discussed: First, uncertainties in flood risk assessment; second, the inclusion of social and environmental flood risk factors; and third, the consideration of the spatial dimension of flood risk. In the 2nd part of the paper a multicriteria risk mapping approach is introduced that is intended to address these 3 problems.

In situ applications of a new diver-operated motorized microsensor profiler.

Microsensors are powerful tools for microenvironment studies, however their use has often been restricted to laboratory applications due to the lack of adequate equipment for in situ deployments. Here we report on new features, construction details, and examples of applications of an improved diver-operated motorized microsensor profiler for underwater field operation to a water depth of 25 m. The new motorized profiler has a final precision of 5 microm, and can accommodate amperometric Clark-type microsensors for oxygen and hydrogen sulfide, potentiometric microsensors (e.g., for pH, Ca2+), and fiber-optic irradiance microsensors. The profiler is interfaced by a logger with a signal display, and has pushbuttons for underwater operation. The system can be pre-programmed to autonomous operation or interactively operated by divers. Internal batteries supply power for up to 24 h of measurements and 36 h of data storage (max. 64 million data points). Two flexible stands were developed for deployment on uneven or fragile surfaces, such as coral reefs. Three experimental pilot studies are presented, where (1) the oxygen distribution in a sand ripple was 3-D-mapped, (2) the microenvironment of sediment accumulated on a stony coral was studied, and (3) oxygen dynamics during an experimental sedimentation were investigated. This system allows SCUBA divers to perform a wide array of in situ measurements, with deployment precision and duration similar to those possible in the laboratory.