Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources

The large amount of biological data available in the current times, makes it necessary to use tools and applications based on sophisticated and efficient algorithms, developed in the area of bioinformatics. Further, access to high performance computing resources is necessary, to achieve results in reasonable time. To speed up applications and utilize available compute resources as efficient as possible, software developers make use of parallelization mechanisms, like multithreading. Many of the available tools in bioinformatics offer multithreading capabilities, but more compute power is not always helpful. In this study we investigated the behavior of well-known applications in bioinformatics, regarding their performance in the terms of scaling, different virtual environments and different datasets with our benchmarking tool suite BOOTABLE. The tool suite includes the tools BBMap, Bowtie2, BWA, Velvet, IDBA, SPAdes, Clustal Omega, MAFFT, SINA and GROMACS. In addition we added an application using the machine learning framework TensorFlow. Machine learning is not directly part of bioinformatics but applied to many biological problems, especially in the context of medical images (X-ray photographs). The mentioned tools have been analyzed in two different virtual environments, a virtual machine environment based on the OpenStack cloud software and in a Docker environment. The gained performance values were compared to a bare-metal setup and among each other. The study reveals, that the used virtual environments produce an overhead in the range of seven to twenty-five percent compared to the bare-metal environment. The scaling measurements showed, that some of the analyzed tools do not benefit from using larger amounts of computing resources, whereas others showed an almost linear scaling behavior. The findings of this study have been generalized as far as possible and should help users to find the best amount of resources for their analysis. Further, the results provide valuable information for resource providers to handle their resources as efficiently as possible and raise the user community’s awareness of the efficient usage of computing resources.     

Die Auferstehung Christi aus medizinischer Sicht

Did Jesus Christ die on the cross? It has been repeatedly speculated that Jesus of Nazareth did not really die on the cross when he was crucified. The spear thrust into his side and the flow of blood and water when pierced with a spear suggests that Jesus must have had some sort of hydrothorax and/or haemothorax at the time he was crucified. Management of hydrothorax and/or haemothorax in modern medicine is the establishment of chest drains. Further one might speculate that the thrust of the spear on the side, carried out to ensure the death of Jesus, may have had, in fact, an opposite effect, namely relief of hypoxemia, which might have been followed by recovery of consciousness after he was taken down from the cross.     

(E)-2-(2-(2-hydroxyphenyl)hydrazono)-1-phenylbutane-1,3-dione: Tautomery and coordination to copper(II)

(E)-2-(2-(2-hydroxyphenyl)hydrazono)-1-phenylbutane-1,3-dione (H₂L) was synthesized by azocoupling of diazonium salt of 2-hydroxyaniline with 1-phenylbutane-1,3-dione and characterized by IR, ¹H and ¹³C NMR spectroscopies and X-ray diffraction analysis. In solution, H₂L exists as a mixture of the enol-azo and hydrazone tautomeric forms and a decrease of temperature and of solvent polarity shifts the tautomeric balance to the hydrazone form. In the solid state, H₂L crystallizes from ethanol-water in the monohydrate hydrazone form, as shown by X-ray analysis. The dissociation constants of H₂L (pK₁ = 5.98 ± 0.04, pK₂ = 9.72 ± 0.03) and the stability constants of its copper(II) complex (log β₁ = 11.01 ± 0.07, log β₂ = 20.19 ± 0.08) were determined by the potentiometric method in aqueous-ethanol solution. The copper(II) complex [Cu₂(μ-L)₂]_n was isolated in the solid state and found by X-rays to be a coordination polymer of a binuclear core with a distorted square pyramidal metal coordination geometry.     

Patchy bed disturbance and fish predation independently influence the distribution of stream invertebrates and algae

1. The identification of factors determining the patchy distribution of organisms in space and time is a central concern of ecology. Predation and abiotic disturbance are both well-known drivers of this patchiness, but their interplay is still poorly understood, especially for communities dominated by mobile organisms in frequently disturbed ecosystems. 2. We investigated the separate and interactive influences of bed disturbance by floods and predation by fish on the benthic community in a flood-prone stream. Electric fields excluded fish predators from half of 48 stream bed patches (area 0·49 m(2) ) with contrasting disturbance treatments. Three types of bed disturbance were created by either scouring or filling patches to a depth of 15-20 cm or by leaving the patches undisturbed, thus mimicking the mosaic of scour and fill caused by a moderate flood. Benthic invertebrates and algae were sampled repeatedly until 57 days after the disturbance. 3. Disturbance influenced all ten investigated biological response variables, whereas predation affected four variables. Averaged across time, invertebrate taxon richness and total abundance were highest in stable patches. Algal biomass and densities of five of the seven most common invertebrate taxa (most of which were highly mobile) were higher in fill than in scour patches, whereas two taxa were more abundant in scour and stable than in fill patches. Furthermore, two common invertebrate grazers were more abundant and algal biomass tended to be reduced in fish exclusion patches, suggesting a patch-scale trophic cascade from fish to algae. 4. Our results highlight the importance of patchy physical disturbance for the microdistribution of mobile stream organisms and indicate a notable, but less prevalent, influence of fish predation at the patch scale in this frequently disturbed environment. Disturbance and predation treatments interacted only once, suggesting that the observed predation effects were largely independent of local bed disturbance patterns.     

Trade in Palm Products in North-Western South America

More than 200 scientific publications and Internet sources dealing with trade in palm products in north-western South America are reviewed. We focus on value chains, trade volumes, prices, and recent developments for some of the most important raw materials derived from native palms. Trade in palm products takes place at local, regional, national, and international levels. For local communities and individual households palm products may play a key role as the most important or only source of cash income. Most of these palm products are inadequately or not at all captured in trade statistics at the local and regional economic levels. Only products such as vegetable ivory and palm heart are monitored statistically, mainly because they are exported. Most raw materials derived from palms are extracted from the wild, and mainly by destructive harvesting. Reduced availability and rising prices on local and regional markets reflect incipient resource depletion. Only in vegetable ivory more or less sustainable wild harvesting methods prevail. Palm heart is increasingly being harvested from orchards and non-sustainable exploitation of wild populations is loosing ground. The international market for native palm oils and pulp (esp. Euterpe oleracea or açaí) is currently served almost exclusively from Brazil. Due to low oil contents and high production costs palm oils are currently used mainly for cosmetics. Based on their content of protein, starch, tocols, and carotenoids palm fruits have high nutritional value and represent a considerable potential for the development of functional foods, food supplements and animal fodder. Palms could undoubtedly play a more important role in the socio-economic development of north-western South America. Sustainability and marketing potential of palm products are negatively affected by the low income obtained by primary producers which often represents no more than 0.01–3% of the retail value. Poor governance, insecurity of land tenure and unequal sharing of profits endanger a sustainable long-term development of these valuable resources.     

A stability analysis of the power-law steady state of marine size spectra

This paper investigates the stability of the power-law steady state often observed in marine ecosystems. Three dynamical systems are considered, describing the abundance of organisms as a function of body mass and time: a “jump-growth” equation, a first order approximation which is the widely used McKendrick–von Foerster equation, and a second order approximation which is the McKendrick–von Foerster equation with a diffusion term. All of these yield a power-law steady state. We derive, for the first time, the eigenvalue spectrum for the linearised evolution operator, under certain constraints on the parameters. This provides new knowledge of the stability properties of the power-law steady state. It is shown analytically that the steady state of the McKendrick–von Foerster equation without the diffusion term is always unstable. Furthermore, numerical plots show that eigenvalue spectra of the McKendrick–von Foerster equation with diffusion give a good approximation to those of the jump-growth equation. The steady state is more likely to be stable with a low preferred predator:prey mass ratio, a large diet breadth and a high feeding efficiency. The effects of demographic stochasticity are also investigated and it is concluded that these are likely to be small in real systems.     

Ammonium and attachment of <Emphasis Type="Italic">Rhodopirellula baltica</Emphasis>

A dimorphic life cycle has been described for the planctomycete Rhodopirellula baltica SH1^T, with juvenile motile, free-swimming cells and adult sessile, attached-living cells. However, attachment as a response to environmental factors was not investigated. We studied the response of R. baltica to nitrogen limitation. In batch cultures, ammonium limitation coincided with a dominance of free-swimming cells and a low number of aggregates. Flow cytometry revealed a quantitative shift with increasing ammonium availability, from single cells towards attached cells in large aggregates. During growth of R. baltica on glucose and ammonium in chemostats, an ammonium addition caused a macroscopic change of the growth behaviour, from homogeneous growth in the liquid phase to a biofilm on the borosilicate glass wall of the chemostat vessel. Thus, an ammonium limitation—a carbon to nitrogen supply ratio of 30:1—sustained free-living growth without aggregate formation. A sudden increase in ammonium supply induced sessile growth of R. baltica. These observations reveal a response of Rhodopirellula baltica cells to ammonium: they abandon the free-swimming life, attach to particles and form biofilms.     

Roles of TRPM2 in oxidative stress

Reactive oxygen species (ROS) play critical roles in cell death, diseases, and normal cellular processes. TRPM2 is a member of transient receptor potential (TRP) protein superfamily and forms a Ca²⁺-permeable nonselective cation channel activated by ROS, specifically by hydrogen peroxide (H₂O₂), and at least in part via second-messenger mechanisms. Accumulating evidence has indicated that TRPM2 mediates multiple cellular responses, after our finding that Ca²⁺ influx via TRPM2 regulates H₂O₂-induced cell death. Recently, we have demonstrated that Ca²⁺ influx through TRPM2 induces chemokine production in monocytes and macrophages, which aggravates inflammatory neutrophil infiltration in mice. However, understanding is still limited for in vivo physiological or pathophysiological significance of ROS-induced TRPM2 activation. In this review, we summarize mechanisms underlying activation of TRPM2 channels by oxidative stress and downstream biological responses, and discuss the biological importance of oxidative stress-activated TRP channels.     

Variation in carbon isotope discrimination in Cleistogenes squarrosa (Trin.) Keng: patterns and drivers at tiller, local, catchment, and regional scales

Understanding the patterns and drivers of carbon isotope discrimination in C(4) species is critical for predicting the effects of global change on C(3)/C(4) ratio of plant community and consequently on ecosystem functioning and services. Cleistogenes squarrosa (Trin.) Keng is a dominant C(4) perennial bunchgrass of arid and semi-arid ecosystems across the Mongolian plateau of the Eurasian steppe. Its carbon isotope discrimination (((13))Δ) during photosynthesis is relatively large among C(4) species and it is variable. Here the ((13))Δ of C. squarrosa and its potential drivers at a nested set of scales were examined. Within cohorts of tillers, ((13))Δ of leaves increased from 5.1‰ to 8.1‰ from old to young leaves. At the local scale, ((13))Δ of mature leaves varied from 5.8‰ to 8.4‰, increasing with decreasing grazing intensity. At the catchment scale, ((13))Δ of mature leaves varied from 6.2‰ to 8.5‰ and increased with topsoil silt content. At the regional scale, ((13))Δ of mature leaves varied from 5.5‰ to 8.9‰, increasing with growing-season precipitation. At all scales, ((13))Δ decreased with increasing leaf nitrogen content (N(leaf)). N(leaf) was positively correlated with grazing intensity and leaf position along tillers, but negatively correlated with precipitation. The presence of the correlations across a range of different environmental contexts strongly implicates N(leaf) as a major driver of ((13))Δ in C. squarrosa and, possibly, other C(4) species.     

Environmental impacts of decommissioning nuclear power plants: methodical challenges,case study,and implications

Purpose

Environmental impacts of the decommissioning of nuclear power plants are brought into focus by the nuclear phase-out in Germany and a worldwide growing number of decommissioning projects. So far, life cycle assessments of decommissioning nuclear power plants have been conducted very rarely or are based on rather uncertain assumptions. Against this background, environmental impacts of the ongoing decommissioning of the nuclear power plant in Lubmin (KGR), Germany are examined. Methodological aspects like transferability to other decommissioning projects as well as influence of assumptions about the lifespan of a power plant are discussed.

Methods

A life cycle assessment of the decommissioning according to ISO 14040/44 is conducted. The decommissioning of one power plant (of the assessed KGR) is chosen as functional unit. The system boundaries include removal and demolition of plant components and buildings as well as decontamination, conditioning, interim storage, and final repository of low-level and interim-level nuclear waste together with disposal and recycling of conventional waste. Interim storage and final repository of high-level nuclear waste such as fuel rods are excluded from the system boundaries as they are assigned to the use phase of the plant. Primary data was obtained from the plant decommissioning firm (Energiewerke Nord GmbH, EWN) in Lubmin. The GaBi database was used to model background processes. Environmental impacts are estimated using the CML2001 methodology.

Results and discussion

Environmental impacts are mainly caused by on-site energetic demands of component removal and peripheral tasks. Further significant impacts are caused by the handling, storage, and final repository of low-level and intermediate-level nuclear waste. Recycling conventional, nonradioactive metallic waste has the potential to unburden the process in a significant scale, depending on recycling rates.

Conclusions

The dismantling of nuclear power plants shows a relevant environmental impact. Regarding the environmental impacts per kilowatt-hour assumptions concerning the plant’ lifespan are a crucial factor. Comparing the result from this study to recent datasets for nuclear power poses the question if LCA datasets represent environmental burdens of nuclear power accurately. The transferability of LCA results to other studies using one parameter for scaling is problematic and needs further research.