Observed communication semantics for classical processes

Classical Linear Logic (CLL) has long inspired readings of its proofs as communicating processes. Wadler's CP calculus is one of these readings. Wadler gave CP an operational semantics by selecting a subset of the cut-elimination rules of CLL to use as reduction rules. This semantics has an appealing close connection to the logic, but does not resolve the status of the other cut-elimination rules, and does not admit an obvious notion of observational equivalence. We propose a new operational semantics for CP based on the idea of observing communication, and use this semantics to define an intuitively reasonable notion of observational equivalence. To reason about observational equivalence, we use the standard relational denotational semantics of CLL. We show that this denotational semantics is adequate for our operational semantics. This allows us to deduce that, for instance, all the cut-elimination rules of CLL are observational equivalences

Exoplanet diversity in the era of space-based direct imaging missions

Community White Paper: submitted to the National Academy of Sciences Exoplanet Science StrategyThis white paper discusses the diversity of exoplanets that could be detected by future observations, so that comparative exoplanetology can be performed in the upcoming era of large space-based flagship missions. The primary focus will be on characterizing Earth-like worlds around Sun-like stars. However, we will also be able to characterize companion planets in the system simultaneously. This will not only provide a contextual picture with regards to our Solar system, but also presents a unique opportunity to observe size dependent planetary atmospheres at different orbital distances. We propose a preliminary scheme based on chemical behavior of gases and condensates in a planet's atmosphere that classifies them with respect to planetary radius and incident stellar flux

A reversal of climatic trends in the North Atlantic since 2005

In the mid-1990s the North Atlantic subpolar gyre warmed rapidly, which had important climate impacts, such as increased hurricane numbers, and changes to rainfall over Africa, Europe and North America. Evidence suggests that the warming was largely due to a strengthening of the ocean circulation, particularly the Atlantic Meridional Overturning Circulation (AMOC). Since the mid-1990s direct and indirect measurements have suggested a decline in the strength of the ocean circulation, which is expected to lead to a reduction in northward heat transport. Here we show that since 2005 a large volume of the upper North Atlantic Ocean has cooled significantly by approximately -0.45C or 1.5x10^22 J, reversing the previous warming trend. By analysing observations and a state-of-the-art climate model, we show that this cooling is consistent with a reduction in the strength of the ocean circulation and heat transport, linked to record low densities in the deep Labrador Sea. The low density in the deep Labrador Sea is primarily due to deep ocean warming since 1995, but a long-term freshening also played a role. The observed upper ocean cooling since 2005 is not consistent with the hypothesis that anthropogenic aerosols directly drive Atlantic temperatures

Search for rare quark-annihilation decays, B --> Ds(*) Phi

We report on searches for B- --> Ds- Phi and B- --> Ds*- Phi. In the context of the Standard Model, these decays are expected to be highly suppressed since they proceed through annihilation of the b and u-bar quarks in the B- meson. Our results are based on 234 million Upsilon(4S) --> B Bbar decays collected with the BABAR detector at SLAC. We find no evidence for these decays, and we set Bayesian 90% confidence level upper limits on the branching fractions BF(B- --> Ds- Phi) Ds*- Phi)<1.2x10^(-5). These results are consistent with Standard Model expectations.Comment: 8 pages, 3 postscript figues, submitted to Phys. Rev. D (Rapid Communications

Mechanisms of decadal variability in the Labrador Sea and the wider North Atlantic in a high-resolution climate model

A necessary step before assessing the performance of decadal predictions is the evaluation of the processes that bring memory to the climate system, both in climate models and observations. These mechanisms are particularly relevant in the North Atlantic, where the ocean circulation, related to both the Subpolar Gyre and the Meridional Overturning Circulation (AMOC), is thought to be important for driving significant heat content anomalies. Recently, a rapid decline in observed densities in the deep Labrador Sea has pointed to an ongoing slowdown of the AMOC strength taking place since the mid 90s, a decline also hinted by in-situ observations from the RAPID array. This study explores the use of Labrador Sea densities as a precursor of the ocean circulation changes, by analysing a 300-year long simulation with the state-of-the-art coupled model HadGEM3-GC2. The major drivers of Labrador Sea density variability are investigated, and are characterised by three major contributions. First, the integrated effect of local surface heat fluxes, mainly driven by year-to-year changes in the North Atlantic Oscillation, which accounts for 62% of the total variance. Additionally, two multidecadal-to-centennial contributions from the Greenland-Scotland Ridge outflows are quantified; the first associated with freshwater exports via the East Greenland Current, and the second with density changes in the Denmark Strait Overflow. Finally, evidence is shown that decadal trends in Labrador Sea densities are followed by important atmospheric impacts. In particular, a negative winter NAO response appears to follow the positive Labrador Sea density trends, and provides a phase reversal mechanism

Recent progress in understanding and predicting Atlantic decadal climate variability

Recent Atlantic climate prediction studies are an exciting new contribution to an extensive body of research on Atlantic decadal variability and predictability that has long emphasized the unique role of the Atlantic Ocean in modulating the surface climate. We present a survey of the foundations and frontiers in our understanding of Atlantic variability mechanisms, the role of the Atlantic Meridional Overturning Circulation (AMOC), and our present capacity for putting that understanding into practice in actual climate prediction systems

The role of emergency department HIV care in resource-poor settings: lessons learned in western Kenya

The human immunodeficiency virus (HIV) pandemic in sub-Saharan Africa and other high prevalence regions continues to overwhelm health care systems. While there has been a global response to improve the delivery of antiretroviral therapy in these high prevalence regions, there are few models that have developed an adequate plan to deal with HIV specifically in resource-poor emergency department settings. In this manuscript, we report on the experience scaling up HIV care at one emergency department in a large referral hospital located in western Kenya. Specifically, we describe how rapid bedside HIV testing helps to narrow the differential diagnosis of disease processes in acute care patients and how HIV screening of patients discharged from the emergency department can detect HIV-infected individuals

The Pentameric Vertex Proteins Are Necessary for the Icosahedral Carboxysome Shell to Function as a CO2 Leakage Barrier

BACKGROUND: Carboxysomes are polyhedral protein microcompartments found in many autotrophic bacteria; they encapsulate the CO(2) fixing enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) within a thin protein shell and provide an environment that enhances the catalytic capabilities of the enzyme. Two types of shell protein constituents are common to carboxysomes and related microcompartments of heterotrophic bacteria, and the genes for these proteins are found in a large variety of bacteria. METHODOLOGY/PRINCIPAL FINDINGS: We have created a Halothiobacillus neapolitanus knockout mutant that does not produce the two paralogous CsoS4 proteins thought to occupy the vertices of the icosahedral carboxysomes and related microcompartments. Biochemical and ultrastructural analyses indicated that the mutant predominantly forms carboxysomes of normal appearance, in addition to some elongated microcompartments. Despite their normal shape, purified mutant carboxysomes are functionally impaired, although the activities of the encapsulated enzymes are not negatively affected. CONCLUSIONS/SIGNIFICANCE: In the absence of the CsoS4 proteins the carboxysome shell loses its limited permeability to CO(2) and is no longer able to provide the catalytic advantage RubisCO derives from microcompartmentalization. This study presents direct evidence that the diffusion barrier property of the carboxysome shell contributes significantly to the biological function of the carboxysome

A framework for generalized subspace pattern mining in high-dimensional datasets

Background A generalized notion of biclustering involves the identification of patterns across subspaces within a data matrix. This approach is particularly well-suited to analysis of heterogeneous molecular biology datasets, such as those collected from populations of cancer patients. Different definitions of biclusters will offer different opportunities to discover information from datasets, making it pertinent to tailor the desired patterns to the intended application. This paper introduces ‘GABi’, a customizable framework for subspace pattern mining suited to large heterogeneous datasets. Most existing biclustering algorithms discover biclusters of only a few distinct structures. However, by enabling definition of arbitrary bicluster models, the GABi framework enables the application of biclustering to tasks for which no existing algorithm could be used. Results First, a series of artificial datasets were constructed to represent three clearly distinct scenarios for applying biclustering. With a bicluster model created for each distinct scenario, GABi is shown to recover the correct solutions more effectively than a panel of alternative approaches, where the bicluster model may not reflect the structure of the desired solution. Secondly, the GABi framework is used to integrate clinical outcome data with an ovarian cancer DNA methylation dataset, leading to the discovery that widespread dysregulation of DNA methylation associates with poor patient prognosis, a result that has not previously been reported. This illustrates a further benefit of the flexible bicluster definition of GABi, which is that it enables incorporation of multiple sources of data, with each data source treated in a specific manner, leading to a means of intelligent integrated subspace pattern mining across multiple datasets. Conclusions The GABi framework enables discovery of biologically relevant patterns of any specified structure from large collections of genomic data. An R implementation of the GABi framework is available through CRAN (http://cran.r-project.org/web/packages/GABi/index.html)

Comparison of a low carbohydrate and low fat diet for weight maintenance in overweight or obese adults enrolled in a clinical weight management program

<p>Abstract</p> <p>Background</p> <p>Recent evidence suggests that a low carbohydrate (LC) diet may be equally or more effective for short-term weight loss than a traditional low fat (LF) diet; however, less is known about how they compare for weight maintenance. The purpose of this study was to compare body weight (BW) for participants in a clinical weight management program, consuming a LC or LF weight maintenance diet for 6 months following weight loss.</p> <p>Methods</p> <p>Fifty-five (29 low carbohydrate diet; 26 low fat diet) overweight/obese middle-aged adults completed a 9 month weight management program that included instruction for behavior, physical activity (PA), and nutrition. For 3 months all participants consumed an identical liquid diet (2177 kJ/day) followed by 1 month of re-feeding with solid foods either low in carbohydrate or low in fat. For the remaining 5 months, participants were prescribed a meal plan low in dietary carbohydrate (~20%) or fat (~30%). BW and carbohydrate or fat grams were collected at each group meeting. Energy and macronutrient intake were assessed at baseline, 3, 6, and 9 months.</p> <p>Results</p> <p>The LC group increased BW from 89.2 ± 14.4 kg at 3 months to 89.3 ± 16.1 kg at 9 months (<it>P </it>= 0.84). The LF group decreased BW from 86.3 ± 12.0 kg at 3 months to 86.0 ± 14.0 kg at 9 months (<it>P </it>= 0.96). BW was not different between groups during weight maintenance (<it>P </it>= 0.87). Fifty-five percent (16/29) and 50% (13/26) of participants for the LC and LF groups, respectively, continued to decrease their body weight during weight maintenance.</p> <p>Conclusion</p> <p>Following a 3 month liquid diet, the LC and LF diet groups were equally effective for BW maintenance over 6 months; however, there was significant variation in weight change within each group.</p