Comparative measurements of carbon dioxide fluxes from two nearby towers in a central Amazonian rainforest: the Manaus LBA site

Forests around Manaus have staged the oldest and the longest forest-atmosphere CO2 exchange studies made anywhere in the Amazon. Since July 1999 the exchange of CO2, water, and energy, as well as weather variables, have been measured almost continuously over two forests, 11 km apart, in the Cuieiras reserve near Manaus, Brazil. This paper presents the sites and climatology of the region based upon the new data sets. The landscape consists of plateaus dissected by often waterlogged valleys, and the two sites differ in terms of the relative areas of those two landscape components represented in the tower footprints. The radiation and wind climate was similar to both towers. Generally, both the long-wave and short-wave radiation input was less in the wet than in the dry season. The energy balance closure was imperfect (on average 80%) in both towers, with little variation in energy partitioning between the wet and dry seasons; likely a result of anomalously high rainfall in the 1999 dry season. Fluxes of CO2 also showed little seasonal variation except for a slightly shorter daytime uptake duration and somewhat lower respiratory fluxes in the dry season. The net effect is one of lower daily net ecosystem exchange (NEE) in the dry season. The tower, which has less waterlogged valley areas in its footprint, measured a higher overall CO2 uptake rate. We found that on first sight, NEE is underestimated during calm nights, as was observed in many other tower sites before. However, a closer inspection of the diurnal variation of CO2 storage fluxes and NEE suggests that at least part of the nighttime deficits is recovered from either lateral influx of CO2 from valleys or outgassing of soil storage. Therefore there is a high uncertainty in the magnitude of nocturnal NEE, and consequently preliminary estimates of annual carbon uptake reflecting this range from 1 to 8 T ha-1 y-1, with an even higher upper range for the less waterlogged area. The high uptake rates are clearly unsustainable and call for further investigations into the integral carbon balance of Amazon landscapes

“Omics”-Informed drug and biomarker discovery : opportunities, challenges and future perspectives

The pharmaceutical industry faces unsustainable program failure despite significant increases in investment. Dwindling discovery pipelines, rapidly expanding R&D budgets and increasing regulatory control, predict significant gaps in the future drug markets. The cumulative duration of discovery from concept to commercialisation is unacceptably lengthy, and adds to the deepening crisis. Existing animal models predicting clinical translations are simplistic, highly reductionist and, therefore, not fit for purpose. The catastrophic consequences of ever-increasing attrition rates are most likely to be felt in the developing world, where resistance acquisition by killer diseases like malaria, tuberculosis and HIV have paced far ahead of new drug discovery. The coming of age of Omics-based applications makes available a formidable technological resource to further expand our knowledge of the complexities of human disease. The standardisation, analysis and comprehensive collation of the “data-heavy” outputs of these sciences are indeed challenging. A renewed focus on increasing reproducibility by understanding inherent biological, methodological, technical and analytical variables is crucial if reliable and useful inferences with potential for translation are to be achieved. The individual Omics sciences—genomics, transcriptomics, proteomics and metabolomics—have the singular advantage of being complimentary for cross validation, and together could potentially enable a much-needed systems biology perspective of the perturbations underlying disease processes. If current adverse trends are to be reversed, it is imperative that a shift in the R&D focus from speed to quality is achieved. In this review, we discuss the potential implications of recent Omics-based advances for the drug development process

Protein Acetylation as an Integral Part of Metabolism in Cancer Development and Progression

Acetylation of lysine is one of the major post-translational modifications of histone and non-histone proteins of eukaryotic cells. Acetylation has been indicated as an avenue for cellular response to environmental, nutritional and behavioral factors. At the same time, aberrant protein acetylation has been related to cancer as well as many other diseases. Abnormal expression of some classes of histone deacetylases and histone acetyl transferases has been documented for the majority of cancers. These observations have led to extensive efforts in the development of inhibitors for these enzymes for the treatment of cancer as well as other diseases as well as pathogen control.Regulation of protein activities and gene expression by acetylation influences many processes relevant for cancer development, including metabolism. At the same time acetylation depends on a number of metabolic co-factors and a variety of metabolites act as inhibitors of acetylation proteins making acetylation enzymes an integral part of metabolism. Cancer metabolic phenotype is generally understood as one of the major hallmarks of cancer and thus the interplay between acetylation, anabolism and catabolism provides a very interesting forum for exploration of cancer development and for novel treatments. An ever increasing pool of publications shows relationships between the acetylation process and related enzymes with metabolites in cancerous and non-cancerous systems. In this review we are presenting previously established relationships between acetylation/deacetylation, metabolites and enzyme regulation particularly in relation to cancer development, progression and treatment

Energy and water dynamics of a central Amazonian rain forest

This paper presents measurements of the energy and water budgets of a tropical rain forest near Manaus, Brazil, in central Amazonia, collected between September 1995 and August 1996. Fluxes of sensible and latent heat were measured using a three-dimensional eddy covariance system mounted above the forest canopy. Using a new approach to analysis of eddy covariance data, we found that the measured fluxes increased significantly when turbulent transport on timescales of 1 to 4 hours was taken into account. With this new analysis, the measured turbulent fluxes almost balanced the incoming net radiation, giving increased confidence in the accuracy of the measured fluxes. Of the 5.56 GJ m-2 yr-1 of solar radiation supplied over the year, 11% were reflected, 15% were lost as net thermal emission, 27% were transported through sensible heat convection, 46% used in evapotranspiration, and 0.5% were used; in net carbon fixation. Total annual evapotranspiration was calculated to be 1123 mm; accounting for 54% of total precipitation. Seasohality was an important influence: limited water availability during the dry season caused evapotranspiration to reduce by 50%. Total canopy conductance was linearly correlated to soil moisture content, with typical midday values ranging between 0.8 mol m-2 s-1 in the wet season and 0.3 mol m-2 s-1 in the dry season. Such seasonal behavior is likely to be prevalent in most tropical forest regions, and correct description of dry-season evapotranspiration will require accurate modeling of plant and soil hydraulic properties and knowledge of root distributions. Copyright 2002 by the American Geophysical Union

Rigidity for Monogamy-Of-Entanglement Games

In a monogamy-of-entanglement (MoE) game, two players who do not communicate try to simultaneously guess a referee's measurement outcome on a shared quantum state they prepared. We study the prototypical example of a game where the referee measures in either the computational or Hadamard basis and informs the players of her choice. We show that this game satisfies a rigidity property similar to what is known for some nonlocal games. That is, in order to win optimally, the players' strategy must be of a specific form, namely a convex combination of four unentangled optimal strategies generated by the Breidbart state. We extend this to show that strategies that win near-optimally must also be near an optimal state of this form. We also show rigidity for multiple copies of the game played in parallel. As an application, we construct for the first time a weak string erasure scheme where the security does not rely on limitations on the parties' hardware. Instead, we add a prover, which enables security via the rigidity of this MoE game. Furthermore, we show that this can be used to achieve bit commitment in a model where it is impossible classically.Comment: 46 pages, 3 figure

New Approaches to Complexity via Quantum Graphs

Problems based on the structure of graphs -- for example finding cliques, independent sets, or colourings -- are of fundamental importance in classical complexity. It is well motivated to consider similar problems about quantum graphs, which are an operator system generalisation of graphs. Defining well-formulated decision problems for quantum graphs faces several technical challenges, and consequently the connections between quantum graphs and complexity have been underexplored. In this work, we introduce and study the clique problem for quantum graphs. Our approach utilizes a well-known connection between quantum graphs and quantum channels. The inputs for our problems are presented as quantum channels induced by circuits, which implicitly determine a corresponding quantum graph. We also use this approach to reimagine the clique and independent set problems for classical graphs, by taking the inputs to be circuits of deterministic or noisy channels which implicitly determine confusability graphs. We show that, by varying the collection of channels in the language, these give rise to complete problems for the classes $\textsf{NP}$, $\textsf{MA}$, $\textsf{QMA}$, and $\textsf{QMA}(2)$. In this way, we exhibit a classical complexity problem whose natural quantisation is $\textsf{QMA}(2)$, rather than $\textsf{QMA}$, which is commonly assumed. To prove the results in the quantum case, we make use of methods inspired by self-testing. To illustrate the utility of our techniques, we include a new proof of the reduction of $\textsf{QMA}(k)$ to $\textsf{QMA}(2)$ via cliques for quantum graphs. We also study the complexity of a version of the independent set problem for quantum graphs, and provide preliminary evidence that it may be in general weaker in complexity, contrasting to the classical case where the clique and independent set problems are equivalent.Comment: 45 pages, 3 figure

Rank lower bounds on non-local quantum computation

A non-local quantum computation (NLQC) replaces an interaction between two quantum systems with a single simultaneous round of communication and shared entanglement. We study two classes of NLQC, $f$-routing and $f$-BB84, which are of relevance to classical information theoretic cryptography and quantum position-verification. We give the first non-trivial lower bounds on entanglement in both settings, but are restricted to lower bounding protocols with perfect correctness. Within this setting, we give a lower bound on the Schmidt rank of any entangled state that completes these tasks for a given function $f(x,y)$ in terms of the rank of a matrix $g(x,y)$ whose entries are zero when $f(x,y)=0$, and strictly positive otherwise. This also leads to a lower bound on the Schmidt rank in terms of the non-deterministic quantum communication complexity of $f(x,y)$. Because of a relationship between $f$-routing and the conditional disclosure of secrets (CDS) primitive studied in information theoretic cryptography, we obtain a new technique for lower bounding the randomness complexity of CDS

A study into the impacts of water table and nitrogen pulse on cellulose decomposition rates and carbon release in active peatland

Since the 1980s overstocking of sheep has become an increasing problem on UK uplands. This study examined the effect of livestock urination, and also water table depth, on active peatland on cellulose decomposition and fluvial carbon release. Urination was simulated using synthetic sheep urine (SSU) and applied to quadrats of active peatland at Redlake Mire on South Dartmoor and compared to quadrats without SSU treatment. Cellulose decomposition was measured using the cotton strip assay (CSA) method as a measure of microbial activity by examining a loss in tensile strength of cotton strips buried for 45 days from September 20th to November 3rd 2012. Carbon release was measured via dissolved and particulate organic carbon (DOC and POC) concentration analyses. Application of SSU caused a biologically significant (P < 0.1) reduction in cotton tensile strength (CTSL) of approximately 8% compared to cotton strips buried with SSU, which is less than previous studies. Despite this, no statistically significant effects of SSU were found, which was most likely due to wet weather conditions during the fieldwork causing a high water table, meaning an anaerobic environment was maintained, making oxygen the limiting factor. This study suggests livestock urination does have some detrimental impact on peat so stocking patterns should be carefully considered; however peatland restoration and preservation projects will be most beneficial if they focus on hydrology making rewetting and maintenance of a high water table a priority