Using Distributed Temperature Sensing for Long-Term Monitoring of Pockmark Activity in the Gulf of Patras (Greece): Data Processing Hints and Preliminary Findings.

Patras Gulf pockmark field (Western Greece) is a tectonically controlled field that has been activated at least twice by strong earthquakes (M5.4, 14 July 1993 and M6.4, 8 June 2008), and episodic gas seepages have been recorded in the past using geophysical means. A distributed temperature sensor (DTS) system was deployed inside a shallow pockmark and along an active fault at the northern end of the field. This ongoing experiment represents the first long-term monitoring ever conducted on gas-bearing pockmarks and active faults by the DTS system. For now, we have acquired and analyzed data regarding about 1.56 years. One of the primary objectives of this study is to establish methodological queues for data processing and analysis, including spectral analysis and incomplete data treatment techniques, to be standardized for use in further stages of the experiment. Spectral analysis was proven capable of separating the temperature footprint of background environmental components, such as sea-atmosphere heat flux, tides, and winds/waves, from high-frequency temperature residuals. Those residuals represent unusual events that might be correlated to seismicity. Monitoring the causal relationship between seismic activity and seabed water temperature changes in the field was thus attempted. No significant local earthquakes occurred during the monitoring period. Although the relation between seismicity and irregular seabed water temperature events was not systematic, we postulate that four thermal events have a causative link with the local seismicity. The DTS system constitutes a low-cost monitoring system, and the promising preliminary results of this experiment suggest that it is worth testing for a longer period.

Long-term history dependence of growth rates of E. coli after nutrient shifts.

According to a widely accepted paradigm of microbiology, steady-state growth rates are determined solely by current growth conditions1-3 and adaptations between growth states are rapid, as recently recapitulated by simple resource allocation models4. However, even in microbes overlapping regulatory networks can yield multi-stability or long-term cellular memory. Species like Listeria monocytogenes5 and Bacillus subtilis "distinguish" distinct histories for the commitment to sporulation6, but it is unclear if these states can persist over many generations. Remarkably, studying carbon co-utilization of Escherichia coli, we found that growth rates on combinations of carbon sources can depend critically on the previous growth condition. Growing in identical conditions, we observed differences in growth rates of up to 25% and we did not observe convergence of growth rates over 15 generations. We observed this phenomenon occurs across combinations of different phosphotransferase (PTS) substrates with various gluconeogenic carbon sources and found it to depend on the transcription factor Mlc.

Gravity beyond Einstein? Yes, but in which direction?

We present qualitative arguments in favour of an extension of the theory of the gravitational interaction beyond that resulting from the Hilbert-Einstein action. To this end, we consider a locally conformal invariant theory of gravity, discussed some 30 years ago by Mannheim and Kazanas. We discuss its exact solution of the static, spherically symmetric configurations and, based on these, we revisit some of the outstanding problems associated with gravity, high energy interactions and sketch potential resolutions within the conformal gravity framework. This article is part of the theme issue 'The future of mathematical cosmology, Volume 2'.

Insights into seafloor litter spatiotemporal dynamics in urbanized shallow Mediterranean bays. An optimized monitoring protocol using towed underwater cameras.

Monitoring of marine litter at the sea surface, the beaches and the seafloor is essential to understanding their sources, pathways and sinks and design effective clean-up programs or increase public awareness for reducing litter waste. Up until today, seafloor litter is the least exploited component of marine litter. Although the protocols for recording and assessing seafloor litter in the deep-sea environments are currently being actively defined and practiced, shallow seafloor litter survey protocols are still notably under-developed. Moreover, trawling for fishing, which is the main means for collecting seafloor litter data, needs to be phased out in the coming years due to its high environmental footprint and be replaced by less destructive ways based on underwater imagery. In this paper we propose an integrated approach for assessing in detail the spatiotemporal distribution and composition of seafloor litter in shallow coastal environments, using common towed underwater cameras. Effort has been put to correctly estimating spatial litter densities regarding the true coverage of the visualized area, which was efficiently extracted through photogrammetric reconstruction of the seafloor. Interpretation of the spatial distribution of litter was aided by auxiliary bathymetric and swath sonar backscatter datasets, to determine the seabed geomorphological features that control their dispersion and composition. Local geo-morphology, along with any reported coastal anthropogenic activity, are correlated to seafloor litter densities to investigate the temporal and spatial dynamics that control their distribution and temporal trends in Syros Island, Cyclades, Greece. There, in the context of LIFE DEBAG project, monitoring of an urbanized shallow bay for 3 consecutive years has been performed to assess the impact of an intensive local awareness raising campaign to the local environment. A significant reduction of litter densities under the impact of this campaign has been documented, while links between the seafloor litter transport dynamics and the seabed micro- and macro-topography were made evident. Monitoring litter densities on the seafloor of urbanized shallow bays proved to be a prospective way of tracking marine litter pressures on the local marine environment.

Glycolysis/gluconeogenesis specialization in microbes is driven by biochemical constraints of flux sensing.

Central carbon metabolism is highly conserved across microbial species, but can catalyze very different pathways depending on the organism and their ecological niche. Here, we study the dynamic reorganization of central metabolism after switches between the two major opposing pathway configurations of central carbon metabolism, glycolysis, and gluconeogenesis in Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas putida. We combined growth dynamics and dynamic changes in intracellular metabolite levels with a coarse-grained model that integrates fluxes, regulation, protein synthesis, and growth and uncovered fundamental limitations of the regulatory network: After nutrient shifts, metabolite concentrations collapse to their equilibrium, rendering the cell unable to sense which direction the flux is supposed to flow through the metabolic network. The cell can partially alleviate this by picking a preferred direction of regulation at the expense of increasing lag times in the opposite direction. Moreover, decreasing both lag times simultaneously comes at the cost of reduced growth rate or higher futile cycling between metabolic enzymes. These three trade-offs can explain why microorganisms specialize for either glycolytic or gluconeogenic substrates and can help elucidate the complex growth patterns exhibited by different microbial species.

Spatiotemporal assessment of the environmental quality of bottom waters through the study of benthic foraminifera in a semi-enclosed gulf.

The evolution of the bottom water in Amvrakikos Gulf in Ionian Sea at western Greece for a 50-year timespan was assessed by benthic foraminifera assemblages. The degradation of the bottom water of Amvrakikos has been a catalyst for the surface water degradation. The east basin has shown permanent low environmental quality in bottom waters since 1980, while the west basin has been under seasonal hypoxic regime since 2000. The most adverse environmental conditions occurred in 1990-2000 and 2005-2010 coinciding with the recorded fish mortality events. The major cause of the environmental quality improvement of the bottom water is the intrusion of seawater. In western areas of the gulf, where the influence of the seawater is high, the decreased temperature improves the environmental conditions, while in the areas influenced by river discharges (east and northern), the environmental conditions are depended on multiple causes like organic matter input and surface salinity.

A universal trade-off between growth and lag in fluctuating environments.

The rate of cell growth is crucial for bacterial fitness and drives the allocation of bacterial resources, affecting, for example, the expression levels of proteins dedicated to metabolism and biosynthesis1,2. It is unclear, however, what ultimately determines growth rates in different environmental conditions. Moreover, increasing evidence suggests that other objectives are also important3-7, such as the rate of physiological adaptation to changing environments8,9. A common challenge for cells is that these objectives cannot be independently optimized, and maximizing one often reduces another. Many such trade-offs have indeed been hypothesized on the basis of qualitative correlative studies8-11. Here we report a trade-off between steady-state growth rate and physiological adaptability in Escherichia coli, observed when a growing culture is abruptly shifted from a preferred carbon source such as glucose to fermentation products such as acetate. These metabolic transitions, common for enteric bacteria, are often accompanied by multi-hour lags before growth resumes. Metabolomic analysis reveals that long lags result from the depletion of key metabolites that follows the sudden reversal in the central carbon flux owing to the imposed nutrient shifts. A model of sequential flux limitation not only explains the observed trade-off between growth and adaptability, but also allows quantitative predictions regarding the universal occurrence of such tradeoffs, based on the opposing enzyme requirements of glycolysis versus gluconeogenesis. We validate these predictions experimentally for many different nutrient shifts in E. coli, as well as for other respiro-fermentative microorganisms, including Bacillus subtilis and Saccharomyces cerevisiae.

Reserve Flux Capacity in the Pentose Phosphate Pathway by NADPH Binding Is Conserved across Kingdoms.

All organisms evolved defense mechanisms to counteract oxidative stress and buildup of reactive oxygen species (ROS). To test whether a potentially conserved mechanism exists for the rapid response, we investigated immediate metabolic dynamics of Escherichia coli, yeast, and human dermal fibroblasts to oxidative stress that we found to be conserved between species. To elucidate the regulatory mechanisms that implement this metabolic response, we developed mechanistic kinetic models for each organism's central metabolism and systematically tested activation and inactivation of each irreversible reaction by each metabolite. This ensemble modeling predicts in vivo relevant metabolite-enzyme interactions based on their ability to quantitatively describe metabolite dynamics. All three species appear to inhibit their oxidative pentose phosphate pathway during normal growth by the redox cofactor NADPH and relieve this inhibition to increase the pathway flux for detoxification of ROS during stress, with the sole exception of yeast when exposed to high levels of stress.

Capacity for instantaneous catabolism of preferred and non-preferred carbon sources in Escherichia coli and Bacillus subtilis.

Making the right choice for nutrient consumption in an ever-changing environment is a key factor for evolutionary success of bacteria. Here we investigate the regulatory mechanisms that enable dynamic adaptation between non-preferred and preferred carbon sources for the model Gram-negative and -positive species Escherichia coli and Bacillus subtilis, respectively. We focus on the ability for instantaneous catabolism of a gluconeogenic carbon source upon growth on a glycolytic carbon source and vice versa. By following isotopic tracer dynamics on a 1-2 minute scale, we show that flux reversal from the preferred glucose to non-preferred pyruvate as the sole carbon source is primarily transcriptionally regulated. In the opposite direction, however, E. coli can reverse its flux instantaneously by means of allosteric regulation, whereas in B. subtilis this flux reversal is transcriptionally regulated. Upon removal of transcriptional regulation, B. subtilis assumes the ability of instantaneous glucose catabolism. Using an approach that combines quantitative metabolomics and kinetic modelling, we then identify the additionally necessary key metabolite-enzyme interactions that implement the instantaneous flux reversal in the transcriptionally deregulated B. subtilis, and validate the most relevant allosteric interactions.

Reserve Flux Capacity in the Pentose Phosphate Pathway Enables Escherichia coli's Rapid Response to Oxidative Stress.

To counteract oxidative stress and reactive oxygen species (ROS), bacteria evolved various mechanisms, primarily reducing ROS through antioxidant systems that utilize cofactor NADPH. Cells must stabilize NADPH levels by increasing flux through replenishing metabolic pathways like pentose phosphate (PP) pathway. Here, we investigate the mechanism enabling the rapid increase in NADPH supply by exposing Escherichia coli to hydrogen peroxide and quantifying the immediate metabolite dynamics. To systematically infer active regulatory interactions governing this response, we evaluated ensembles of kinetic models of glycolysis and PP pathway, each with different regulation mechanisms. Besides the known inactivation of glyceraldehyde 3-phosphate dehydrogenase by ROS, we reveal the important allosteric inhibition of the first PP pathway enzyme by NADPH. This NADPH feedback inhibition maintains a below maximum-capacity PP pathway flux under non-stress conditions. Relieving this inhibition instantly increases PP pathway flux upon oxidative stress. We demonstrate that reducing cells' capacity to rapidly reroute their flux through the PP pathway increases their oxidative stress sensitivity.

Interposing a Varying Gravitational Constant Between Modified Newtonian Dynamics and Weak Weyl Gravity.

The Newtonian gravitational constant G obeys the dimensional relation [G][M][a] = [v]4, where M, a, and v denote mass, acceleration, and speed, respectively. Since the baryonic Tully-Fisher (BTF) and Faber-Jackson (BFJ) relations are observed facts, this relation implies that G a = constant. This result cannot be obtained in Newtonian dynamics which cannot explain the origin of the BTF and BFJ relations. An alternative, modified Newtonian dynamics (MOND) assumes that G = G 0 is constant in space and derives naturally a characteristic constant acceleration a = a 0, as well as the BTF and BFJ relations. This is overkill and it comes with a penalty: MOND cannot explain the origin of a 0. A solid physical resolution of this issue is that G ∝ a -1, which implies that in lower-acceleration environments the gravitational force is boosted relative to its Newtonian value because G increases. This eliminates all problems related to MOND's empirical cutoff a 0 and yields a quantitative method for mapping the detailed variations of G(a) across each individual galaxy as well as on larger and smaller scales. On the opposite end, the large accelerations produced by G(a) appear to be linked to the weak-field limit of the fourth-order theory of conformal Weyl gravity.

Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity.

Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small molecule-enzyme regulatory interactions. Here, we develop a framework leveraging the vast, but fragmented, biochemical literature to reconstruct and analyze the small molecule regulatory network (SMRN) of the model organism Escherichia coli, including the primary metabolite regulators and enzyme targets. Using metabolic control analysis, we prove a fundamental trade-off between regulation and enzymatic activity, and we combine it with metabolomic measurements and the SMRN to make inferences on the sensitivity of enzymes to their regulators. Generalizing the analysis to other organisms, we identify highly conserved regulatory interactions across evolutionarily divergent species, further emphasizing a critical role for small molecule interactions in the maintenance of metabolic homeostasis.

Few regulatory metabolites coordinate expression of central metabolic genes in Escherichia coli.

Transcription networks consist of hundreds of transcription factors with thousands of often overlapping target genes. While we can reliably measure gene expression changes, we still understand relatively little why expression changes the way it does. How does a coordinated response emerge in such complex networks and how many input signals are necessary to achieve it? Here, we unravel the regulatory program of gene expression in Escherichia coli central carbon metabolism with more than 30 known transcription factors. Using a library of fluorescent transcriptional reporters, we comprehensively quantify the activity of central metabolic promoters in 26 environmental conditions. The expression patterns were dominated by growth rate-dependent global regulation for most central metabolic promoters in concert with highly condition-specific activation for only few promoters. Using an approximate mathematical description of promoter activity, we dissect the contribution of global and specific transcriptional regulation. About 70% of the total variance in promoter activity across conditions was explained by global transcriptional regulation. Correlating the remaining specific transcriptional regulation of each promoter with the cell's metabolome response across the same conditions identified potential regulatory metabolites. Remarkably, cyclic AMP, fructose-1,6-bisphosphate, and fructose-1-phosphate alone explained most of the specific transcriptional regulation through their interaction with the two major transcription factors Crp and Cra. Thus, a surprisingly simple regulatory program that relies on global transcriptional regulation and input from few intracellular metabolites appears to be sufficient to coordinate E. coli central metabolism and explain about 90% of the experimentally observed transcription changes in 100 genes.

The Great Pretenders Among the ULX Class.

The recent discoveries of pulsed X-ray emission from three ultraluminous X-ray (ULX) sources have finally enabled us to recognize a subclass within the ULX class: the great pretenders, neutron stars (NSs) that appear to emit X-ray radiation at isotropic luminosities L X = 7 × 1039 erg s-1 - 1 × 1041 erg s-1 only because their emissions are strongly beamed toward our direction and our sight lines are offset by only a few degrees from their magnetic-dipole axes. The three known pretenders appear to be stronger emitters than the presumed black holes of the ULX class, such as Holmberg II & IX X-1, IC10 X-1, and NGC300 X-1. For these three NSs, we have adopted a single reasonable assumption, that their brightest observed outbursts unfold at the Eddington rate, and we have calculated both their propeller states and their surface magnetic-field magnitudes. We find that the results are not at all different from those recently obtained for the Magellanic Be/X-ray pulsars: the three NSs reveal modest magnetic fields of about 0.3-0.4 TG and beamed propeller-line X-ray luminosities of ~ 1036-37 erg s-1, substantially below the Eddington limit.

Active knee range of motion assessment in elite track and field athletes: normative values.

BACKGROUND: flexibility is an important physical characteristic in athletes in terms of performance and injury prevention. Active Range Of Motion (AROM) was assessed in elite Greek track and field athletes. METHODS: prospective cohort study was carried out. In the period 2000-2010, the AROM was measured bilaterally with the Active Knee Extension (AKE) test during an in-season period with a goniometer in 127 athletes. RESULTS: male runners and jumpers had a higher mean AROM than throwers, but this result was not statistically significant. Female jumpers had a higher mean AROM than both runners and throwers, but the difference was also not statistically significant. CONCLUSION: in athletes, mean posterior thigh muscle flexibility is likely to be between 72.3° and 73.9°. Posterior thigh muscle flexibility is associated with performance, the higher the AROM, the better performance is achieved athletes have generally high AROM, and this may be a result of their increased muscle flexibility. The normative values of posterior thigh flexibility may assist in better monitoring rehabilitation of the posterior thigh muscle injuries and be useful in pre-season screening of athletes' flexibility.

Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.

Hundreds of molecular-level changes within central metabolism allow a cell to adapt to the changing environment. A primary challenge in cell physiology is to identify which of these molecular-level changes are active regulatory events. Here, we introduce pseudo-transition analysis, an approach that uses multiple steady-state observations of (13)C-resolved fluxes, metabolites, and transcripts to infer which regulatory events drive metabolic adaptations following environmental transitions. Pseudo-transition analysis recapitulates known biology and identifies an unexpectedly sparse, transition-dependent regulatory landscape: typically a handful of regulatory events drive adaptation between carbon sources, with transcription mainly regulating TCA cycle flux and reactants regulating EMP pathway flux. We verify these observations using time-resolved measurements of the diauxic shift, demonstrating that some dynamic transitions can be approximated as monotonic shifts between steady-state extremes. Overall, we show that pseudo-transition analysis can explore the vast regulatory landscape of dynamic transitions using relatively few steady-state data, thereby guiding time-consuming, hypothesis-driven molecular validations.

Development and validation of a questionnaire (FASH--Functional Assessment Scale for Acute Hamstring Injuries): to measure the severity and impact of symptoms on function and sports ability in patients with acute hamstring injuries.

OBJECTIVE: To develop a condition-specific patient-reported outcome measure, the Functional Assessment Scale for Acute Hamstring Injuries (FASH), de novo in three languages, following distinct and rigorous methodology for content generation, analysis and validation and to assess its psychometric properties. BACKGROUND: To our knowledge, there is no patient-reported functional scale specific for acute hamstring injuries. METHODS: The development of the scale followed specific guidelines, as well as de novo construction in three languages (Greek, English and German). Item generation was accomplished by selecting three different sources of items: literature review, focus group and key informant interviews. Content analysis was conducted by an expert committee. The 21 items selected as appropriate were tested through a structured content analytic method and item-content validity coefficient, and 10 were retained for the FASH. The validation and assessment of its psychometric properties followed theConsensus-based Standards for the selection of health status Measurement Instruments (COSMIN) recommendations to ensure quality, in a convenience sample of 140 participants. RESULTS: The face validity was adequate and tested by expert committees, authors and participants. Content validity was characterised as well addressed and conducted independently by experts and through specific content validation procedures. The dimensionality analysis indicated a one-factor solution explaining the 95.8% of total variance. Known group validity was demonstrated by significant differences between patients and controls (p<0.001). The FASH exhibited very good test-retest reliability (intraclass correlation coefficient=0.9, p<0.001), internal consistency (α=0.98) and responsiveness (3.81 and 5.23 using baseline and pooled SD, respectively; standardised response mean (SRD)=4.68). CONCLUSION: This study provides initial evidence for psychometric properties of the first scale assessing hamstring injuries.

Advancing metabolic models with kinetic information.

Kinetic models are crucial to quantitatively understand and predict how functional behavior emerges from dynamic concentration changes of cellular components. The current challenge is on resolving uncertainties about parameter values of reaction kinetics. Additionally, there are also major structural uncertainties due to unknown molecular interactions and only putatively assigned regulatory functions. What if one or few key regulators of biochemical reactions are missing in a metabolic model? By reviewing current advances in building kinetic models of metabolism, we found that such models experience a paradigm shift away from fitting parameters towards identifying key regulatory interactions.

Low-level laser therapy in meniscal pathology: a double-blinded placebo-controlled trial.

We performed a randomized, double-blinded, placebo-controlled study (ISRCTN24203769) to assess the effectiveness of low-level laser therapy (LLLT) in patients with meniscal pathology, including only symptomatic patients with tiny focus of grade 3 attenuation (seen only on 0.7 thickness sequences) or intrasubstance tears with spot of grade 3 signal intensity approaching the articular surface. None of the patients in the study group underwent arthroscopy or new magnetic resonance imaging investigation. Paired-samples t test was used to detect significant changes in subjective knee pain over the experimental period within groups, and ANOVA was used to detect any significant differences between the two groups. Pain was significantly improved for the LLLT group than for the placebo group (F = 154, p < 0.0001). Pain scores were significantly better after LLLT. Four (12.5 %) patients did not respond to LLLT. At baseline, the average Lysholm score was 77 ± 4.6 for the LLLT group and 77.2 ± 2.6 for the placebo group (p > 0.05). Four weeks after LLLT or placebo therapy, the laser group reported an average Lysholm score of 82.5 ± 4.6, and the placebo group scored 79.0 ± 1.9. At 6 months, the laser group had an average Lysholm score of 82.2 ± 5.7, and after 1 year, they scored 81.6 ± 6.6 (F = 14.82923, p = 0.002). Treatment with LLLT was associated with a significant decrease of symptoms compared to the placebo group: it should be considered in patients with meniscal tears who do not wish to undergo surgery.