Stoichiometric N:P Ratios, Temperature, and Iron Impact Carbon and Nitrogen Uptake by Ross Sea Microbial Communities

The Southern Ocean is one of the most biologically important ecosystems on our planet. Microscopic plants, called phytoplankton, form the base of the food web in the Southern Ocean and play a direct role in regulating how much and how fast elements like nitrogen and carbon are cycled throughout the world ocean. The goal of this research was to determine how predicted changes in the environment will impact how fast phytoplankton use these elements. The conditions that we tested included elevated temperature, addition of iron, and the proportion of nitrogen to phosphorus in the seawater. These parameters were selected because temperatures are increasing in the Southern Ocean, and the relative availability of nutrients can alter what species of phytoplankton are present and how fast they grow. Phytoplankton were collected from two locations in the Ross Sea, Antarctica, and grown for a few weeks under experimental conditions. Our results demonstrate that all three parameters, warmer temperatures, the addition of iron, and changing nitrogen to phosphorus ratios will increase how fast phytoplankton use nitrogen and carbon, but the impact of elevated temperature and the addition of iron had a much larger impact than the nitrogen to phosphorus ratio

Molecular Hydrodynamics: Vortex Formation and Sound Wave Propagation

In the present study, quantitative feasibility tests of the hydrodynamic description of a two-dimensional fluid at the molecular level are performed, both with respect to length and time scales. Using high-resolution fluid velocity data obtained from extensive molecular dynamics simulations, we computed the transverse and longitudinal components of the velocity field by the Helmholtz decomposition and compared them with those obtained from the linearized Navier-Stokes (LNS) equations with time-dependent transport coefficients. By investigating the vortex dynamics and the sound wave propagation in terms of these field components, we confirm the validity of the LNS description for times comparable to or larger than several mean collision times. The LNS description still reproduces the transverse velocity field accurately at smaller times, but it fails to predict characteristic patterns of molecular origin visible in the longitudinal velocity field. Based on these observations, we validate the main assumptions of the mode-coupling approach. The assumption that the velocity autocorrelation function can be expressed in terms of the fluid velocity field and the tagged particle distribution is found to be remarkably accurate even for times comparable to or smaller than the mean collision time. This suggests that the hydrodynamic-mode description remains valid down to the molecular scale

Group memory rehabilitation for people with multiple sclerosis: a feasibility randomized controlled trial

Objective: To assess the feasibility and effectiveness of a group memory rehabilitation programme combining compensation and restitution strategies. Design: Randomized controlled trial. Setting: Community. Participants: People with multiple sclerosis who reported memory difficulties were recruited. Interventions: A group memory rehabilitation programme, comprising ten 1.5-hour sessions, was compared with a waiting list control. Main measures: The primary outcome was the Everyday Memory Questionnaire. Secondary outcomes included the General Health Questionnaire 28 and MS Impact Scale administered four and eight months after randomization. In addition, those in the intervention group gave feedback about the intervention. Results: Forty-eight participants were recruited. They were aged 34–72 years (mean 54.3, SD 11.0) and 33 (69%) were women. There were no significant differences between the two groups on the Everyday Memory Questionnaire or MS Impact Scale (P > 0.05) at four or eight months after randomization. However, the intervention group reported significantly better mood than controls on the GHQ-28 at eight months (P = 0.04). Participants showed minimal benefit from the memory rehabilitation programme on quantitative measures but the intervention was well received, as indicated by positive feedback at the end of the intervention. Conclusions: There was no significant effect of the intervention on memory but there was a significant effect on mood. The results suggest a larger scale study is justified

RevManHAL: towards automatic text generation in systematic reviews

Background: Systematic reviews are a key part of healthcare evaluation. They involve important painstaking but repetitive work. A major producer of systematic reviews, the Cochrane Collaboration, employs Review Manager (RevMan) programme—a software which assists reviewers and produces XML-structured files. This paper describes an add-on programme (RevManHAL) which helps auto-generate the abstract, results and discussion sections of RevMan-generated reviews in multiple languages. The paper also describes future developments for RevManHAL. Methods: RevManHAL was created in Java using NetBeans by a programmer working full time for 2 months. Results: The resulting open-source programme uses editable phrase banks to envelop text/numbers from within the prepared RevMan file in formatted readable text of a chosen language. In this way, considerable parts of the review’s ‘abstract’, ‘results’ and ‘discussion’ sections are created and a phrase added to ‘acknowledgements’. Conclusion: RevManHAL’s output needs to be checked by reviewers, but already, from our experience within the Cochrane Schizophrenia Group (200 maintained reviews, 900 reviewers), RevManHAL has saved much time which is better employed thinking about the meaning of the data rather than restating them. Many more functions will become possible as review writing becomes increasingly automated

Phytoplankton-bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge

Southern Ocean primary productivity plays a key role in global ocean biogeochemistry and climate. At the Southern Ocean sea ice edge in coastal McMurdo Sound, we observed simultaneous cobalamin and iron limitation of surface water phytoplankton communities in late Austral summer. Cobalamin is produced only by bacteria and archaea, suggesting phytoplankton-bacterial interactions must play a role in this limitation. To characterize these interactions and investigate the molecular basis of multiple nutrient limitation, we examined transitions in global gene expression over short time scales, induced by shifts in micronutrient availability. Diatoms, the dominant primary producers, exhibited transcriptional patterns indicative of co-occurring iron and cobalamin deprivation. The major contributor to cobalamin biosynthesis gene expression was a gammaproteobacterial population, Oceanospirillaceae ASP10-02a. This group also contributed significantly to metagenomic cobalamin biosynthesis gene abundance throughout Southern Ocean surface waters. Oceanospirillaceae ASP10-02a displayed elevated expression of organic matter acquisition and cell surface attachment-related genes, consistent with a mutualistic relationship in which they are dependent on phytoplankton growth to fuel cobalamin production. Separate bacterial groups, including Methylophaga, appeared to rely on phytoplankton for carbon and energy sources, but displayed gene expression patterns consistent with iron and cobalamin deprivation. This suggests they also compete with phytoplankton and are important cobalamin consumers. Expression patterns of siderophore-related genes offer evidence for bacterial influences on iron availability as well. The nature and degree of this episodic colimitation appear to be mediated by a series of phytoplankton-bacterial interactions in both positive and negative feedback loops

NuRV: A nuXmv Extension for Runtime Verification

We present NuRV, an extension of the nuXmv model checker for assumption-based LTL runtime verification with partial observability and resets. The tool provides some new commands for online/offline monitoring and code generations into standalone monitor code. Using the online/offline monitor, LTL properties can be verified incrementally on finite traces from the system under scrutiny. The code generation currently supports C, C++, Common Lisp and Java, and is extensible. Furthermore, from the same internal monitor automaton, the monitor can be generated into SMV modules, whose characteristics can be verified by Model Checking using nuXmv. We show the architecture, functionalities and some use scenarios of NuRV, and we compare the performance of generated monitor code (in Java) with those generated by a similar tool, RV-Monitor. We show that, using a benchmark from Dwyer's LTL patterns, besides the capacity of generating monitors for long LTL formulae, our Java-based monitors are about 200x faster than RV-Monitor at generation-time and 2–5x faster at runtime

Evaluation of Cell Cycle Arrest in Estrogen Responsive MCF-7 Breast Cancer Cells: Pitfalls of the MTS Assay

Endocrine resistance is a major problem with anti-estrogen treatments and how to overcome resistance is a major concern in the clinic. Reliable measurement of cell viability, proliferation, growth inhibition and death is important in screening for drug treatment efficacy in vitro. This report describes and compares commonly used proliferation assays for induced estrogen-responsive MCF-7 breast cancer cell cycle arrest including: determination of cell number by direct counting of viable cells; or fluorescence SYBR®Green (SYBR) DNA labeling; determination of mitochondrial metabolic activity by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay; assessment of newly synthesized DNA using 5-ethynyl-2′-deoxyuridine (EdU) nucleoside analog binding and Alexa Fluor® azide visualization by fluorescence microscopy; cell-cycle phase measurement by flow cytometry. Treatment of MCF-7 cells with ICI 182780 (Faslodex), FTY720, serum deprivation or induction of the tumor suppressor p14ARF showed inhibition of cell proliferation determined by the Trypan Blue exclusion assay and SYBR DNA labeling assay. In contrast, the effects of treatment with ICI 182780 or p14ARF-induction were not confirmed using the MTS assay. Cell cycle inhibition by ICI 182780 and p14ARF-induction was further confirmed by flow cytometric analysis and EdU-DNA incorporation. To explore this discrepancy further, we showed that ICI 182780 and p14ARF-induction increased MCF-7 cell mitochondrial activity by MTS assay in individual cells compared to control cells thereby providing a misleading proliferation readout. Interrogation of p14ARF-induction on MCF-7 metabolic activity using TMRE assays and high content image analysis showed that increased mitochondrial activity was concomitant with increased mitochondrial biomass with no loss of mitochondrial membrane potential, or cell death. We conclude that, whilst p14ARF and ICI 182780 stop cell cycle progression, the cells are still viable and potential treatments utilizing these pathways may contribute to drug resistant cells. These experiments demonstrate how the combined measurement of metabolic activity and DNA labeling provides a more reliable interpretation of cancer cell response to treatment regimens

Interval temporal logic model checking: The border between good and bad HS fragments

The model checking problem has thoroughly been explored in the context of standard point-based temporal logics, such as LTL, CTL, and CTL 17, whereas model checking for interval temporal logics has been brought to the attention only very recently. In this paper, we prove that the model checking problem for the logic of Allen\u2019s relations started-by and finished-by is highly intractable, as it can be proved to be EXPSPACE-hard. Such a lower bound immediately propagates to the full Halpern and Shoham\u2019s modal logic of time intervals (HS). In contrast, we show that other noteworthy HS fragments, namely, Propositional Neighbourhood Logic extended with modalities for the Allen relation starts (resp., finishes) and its inverse started-by (resp., finished-by), turn out to have\u2014maybe unexpectedly\u2014the same complexity as LTL (i.e., they are PSPACE-complete), thus joining the group of other already studied, well-behaved albeit less expressive, HS fragments