Aggregation of soil and climate input data can underestimate simulated biomass loss and nitrate leaching under climate change

Predicting areas of severe biomass loss and increased N leaching risk under climate change is critical for applying appropriate adaptation measures to support more sustainable agricultural systems. The frequency of annual severe biomass loss for winter wheat and its coincidence with an increase in N leaching in a temperate region in Germany was estimated including the error from using soil and climate input data at coarser spatial scales, using the soil-crop model CoupModel. We ran the model for a reference period (1980–2010) and used climate data predicted by four climate model(s) for the Representative Concentration Pathways (RCP) 2.6, 4.5 and 8.5. The annual median biomass estimations showed that for the period 2070–2100, under the RCP8.5 scenario, the entire region would suffer from severe biomass loss almost every year. Annual incidence of severe biomass loss and increased N leaching was predicted to increase from RCP4.5 to the 8.5 scenario. During 2070–2100 for RCP8.5, in more than half of the years an area of 95% of the region was projected to suffer from both severe biomass loss and increased N leaching. The SPEI3 predicted a range of 32 (P3 RCP4.5) to 55% (P3 RCP8.5) of the severe biomass loss episodes simulated in the climate change scenarios. The simulations predicted more severe biomass losses than by the SPEI index which indicates that soil water deficits are important in determining crop losses in future climate scenarios. There was a risk of overestimating the area where “no severe biomass loss + increased N leaching” occurred when using coarser aggregated input data. In contrast, underestimation of situations where “severe biomass loss + increased N leaching” occurred when using coarser aggregated input data. Larger annual differences in biomass estimations compared to the finest resolution of input data occurred when aggregating climate input data rather than soil data. The differences were even larger when aggregating both soil and climate input data. In half of the region, biomass could be erroneously estimated in a single year by more than 40% if using soil and climate coarser input data. The results suggest that a higher spatial resolution of especially climate input data would be needed to predict reliably annual estimates of severe biomass loss and N leaching under climate change scenarios.Peer reviewe

Dependence Logic with Generalized Quantifiers: Axiomatizations

We prove two completeness results, one for the extension of dependence logic by a monotone generalized quantifier Q with weak interpretation, weak in the meaning that the interpretation of Q varies with the structures. The second result considers the extension of dependence logic where Q is interpreted as "there exists uncountable many." Both of the axiomatizations are shown to be sound and complete for FO(Q) consequences.Comment: 17 page

River-to-ocean pathways of beryllium-9 through estuaries

Estuarine processes are key in modulating the riverine input of particle-reactive trace elements to the ocean. An important, but still under-utilized member of these elements is beryllium-9 (9Be) that together with cosmogenic 10Be has been suggested to serve as a quantitative tracer of present and past continental weathering flux. This study investigates different pathways of terrigenous 9Be through coastal areas into the ocean, based on dissolved 9Be concentrations in surface and bottom waters together with corresponding particulate 9Be concentrations along the salinity gradient in the Changjiang Estuary. Dissolved 9Be in the Changjiang Estuary shows a non-conservative behavior: At low to mid-salinity where water is well-mixed, 9Be is removed from both surface and bottom waters at low salinity and then released back into the water column at mid-salinity. At high salinity where water is stratified, dissolved 9Be is removed from surface waters, but is released back into bottom waters. In combination with hydrochemical (e.g., dissolved oxygen) and particulate 9Be data obtained from different extracted phases, we attribute the removal of dissolved 9Be at low salinity to salt-induced colloidal flocculation, whereas in surface waters at high salinity, we ascribe the removal to biological scavenging facilitated by phytoplankton blooms. The release of 9Be into mid- and high-salinity bottom waters is likely dominated by benthic processes, including porewater diffusion and/or submarine groundwater discharge. The contribution from desorption of 9Be from suspended particulate matter is negligible throughout the entire estuary. We propose that the release of 9Be through benthic processes potentially presents the most important contributor to the marine 9Be budget, where this benthic flux of 9Be is likely enhanced by hypoxic conditions in coastal bottom waters

Case-control diagnostic accuracy study of a non-sputum CD38-based TAM-TB test from a single milliliter of blood

Background: CD4 T cell phenotyping-based blood assays have the potential to meet WHO target product profiles (TPP) of non-sputum-biomarker-based tests to diagnose tuberculosis (TB). Yet, substantial refinements are required to allow their implementation in clinical settings. This study assessed the real time performance of a simplified T cell activation marker (TAM)-TB assay to detect TB in adults from one millilitre of blood with a 24h turnaround time. Methods: We recruited 479 GeneXpert® positive cases and 108 symptomatic but GeneXpert® negativecontrols from presumptive adult TB patients in the Temeke District of Dar-es-Salaam, Tanzania. TAM-TB assay accuracy was assessed by comparison with a composite reference standard comprising GeneXpert® and solid culture. A single millilitre of fresh blood was processed to measure expression of CD38 or CD27 by CD4 T cells producing INF-γ and/or TNF-α in response to a synthetic peptide pool covering the sequences of Mycobacterium tuberculosis (Mtb) ESAT-6, CFP-10 and TB10.4 antigens on a 4-color FACSCalibur apparatus. Results: Significantly superior to CD27 in accurately diagnosing TB, the CD38-based TAM-TB assay specificity reached 93.4% for a sensitivity of 82.2% with an area under the receiver operating characteristics curve of 0.87 (95% CI 0.84-0.91). The assay performance was not significantly affected by HIV status. Conclusions: Wesuccessfully implemented TAM-TB immunoassay routine testing with a 24h turnaround time at district level in a resource limited setting. Starting from one millilitre of fresh blood and being not influenced by HIV status, TAM-TB assay format and performance appears closely compatible with the optimal TPP accuracy criteria defined by WHO for a non-sputum confirmatory TB test

Diagnostic accuracy of a sequence-specific Mtb-DNA hybridization assay in urine: a case-control study including subclinical TB cases.

Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) remains one of the deadliest infectious diseases globally. Timely diagnosis is a key step in the management of TB patients and in the prevention of further transmission events. Current diagnostic tools are limited in these regards. There is an urgent need for new accurate non-sputum-based diagnostic tools for the detection of symptomatic as well as subclinical TB. In this study, we recruited 52 symptomatic TB patients (sputum Xpert MTB/RIF positive) and 58 household contacts to assess the accuracy of a sequence-specific hybridization assay that detects the presence of Mtb cell-free DNA in urine. Using sputum Xpert MTB/RIF as a reference test, the magnetic bead-capture assay could discriminate active TB from healthy household contacts with an overall sensitivity of 72.1% [confidence interval (CI) 0.59-0.86] and specificity of 95.5% (CI 0.90-1.02) with a positive predictive value of 93.9% and negative predictive value of 78.2%. The detection of Mtb-specific DNA in urine suggested four asymptomatic TB infection cases that were confirmed in all instances either by concomitant Xpert MTB/RIF sputum testing or by follow-up investigation raising the specificity of the index test to 100%. We conclude that sequence-specific hybridization assays on urine specimens hold promise as non-invasive tests for the detection of subclinical TB. There is an urgent need for a non-sputum-based diagnostic tool allowing sensitive and specific detection of all forms of tuberculosis (TB) infections. In that context, we performed a case-control study to assess the accuracy of a molecular detection method enabling the identification of cell-free DNA from Mycobacterium tuberculosis that is shed in the urine of tuberculosis patients. We present accuracy data that would fulfill the target product profile for a non-sputum test. In addition, recent epidemiological data suggested that up to 50% of individuals secreting live bacilli do not present with symptoms at the time of screening. We report, here, that the investigated index test could also detect instances of asymptomatic TB infections among household contacts

Counter Machines and Distributed Automata: A Story about Exchanging Space and Time

We prove the equivalence of two classes of counter machines and one class of distributed automata. Our counter machines operate on finite words, which they read from left to right while incrementing or decrementing a fixed number of counters. The two classes differ in the extra features they offer: one allows to copy counter values, whereas the other allows to compute copyless sums of counters. Our distributed automata, on the other hand, operate on directed path graphs that represent words. All nodes of a path synchronously execute the same finite-state machine, whose state diagram must be acyclic except for self-loops, and each node receives as input the state of its direct predecessor. These devices form a subclass of linear-time one-way cellular automata.Comment: 15 pages (+ 13 pages of appendices), 5 figures; To appear in the proceedings of AUTOMATA 2018

CD38 expression by antigen-specific CD4 t cells is significantly restored 5 months after treatment initiation independently of sputum bacterial load at the time of tuberculosis diagnosis

T cell activation markers (TAM) expressed by antigen-specific T cells constitute promising candidates to attest the presence of an active infection by Mycobacterium tuberculosis (Mtb). Reciprocally, their modulation may be used to assess antibiotic treatment efficacy and eventually attest disease resolution. We hypothesized that the phenotype of Mtb-specific T cells may be quantitatively impacted by the load of bacteria present in a patient. We recruited 105 Tanzanian adult tuberculosis (TB) patients and obtained blood before and after 5 months of antibiotic treatment. We studied relationships between patients' clinical characteristics of disease severity and microbiological as well as molecular proxies of bacterial load in sputum at the time of diagnosis. Besides, we measured by flow cytometry the expression of CD38 or CD27 on CD4+ T cells producing interferon gamma (IFN-γ) and/or tumor necrosis factor alpha (TNF-α) in response to a synthetic peptide pool covering the sequences of Mtb antigens ESAT-6, CFP-10, and TB10.4. Reflecting the difficulty to extrapolate bacterial burden from a single end-point read-out, we observed statistically significant but weak correlations between Xpert MTB/RIF, molecular bacterial load assay and time to culture positivity. Unlike CD27, the resolution of CD38 expression by antigen-specific T cells was observed readily following 5 months of antibiotic therapy. However, the intensity of CD38-TAM signals measured at diagnosis did not significantly correlate with Mtb 16S RNA or rpoB DNA detected in patients' sputa. Altogether, our data support CD38-TAM as an accurate marker of infection resolution independently of sputum bacterial load

Parametrised Complexity of Model Checking and Satisfiability in Propositional Dependence Logic

In this paper, we initiate a systematic study of the parametrised complexity in the field of Dependence Logics which finds its origin in the Dependence Logic of V\"a\"an\"anen from 2007. We study a propositional variant of this logic (PDL) and investigate a variety of parametrisations with respect to the central decision problems. The model checking problem (MC) of PDL is NP-complete. The subject of this research is to identify a list of parametrisations (formula-size, treewidth, treedepth, team-size, number of variables) under which MC becomes fixed-parameter tractable. Furthermore, we show that the number of disjunctions or the arity of dependence atoms (dep-arity) as a parameter both yield a paraNP-completeness result. Then, we consider the satisfiability problem (SAT) showing a different picture: under team-size, or dep-arity SAT is paraNP-complete whereas under all other mentioned parameters the problem is in FPT. Finally, we introduce a variant of the satisfiability problem, asking for teams of a given size, and show for this problem an almost complete picture.Comment: Update includes refined result

Impacts of Climate Change on Maize and Beans Production and Compatibility of Adaptation Strategies in Pangani River Basin, Tanzania

Climate change present new development challenges particularly in Sub-Saharan countries where the majority of the population depend on climate-sensitive activities such as rain-fed agriculture. This necessitates for a need to focus on impacts of climate change and compatibility of adaptation as a way of providing sustainable solutions to reduce the vulnerability of the majority of poor Sub-Saharan communities. This study employed Ricardian approach to assess the impacts of temperature and rainfall variability on the net revenue from two main food crops (maize and beans) from Pangani River Basin produced primarily under rain fed agriculture. The study also employed the gross margin to assess the compatibility of irrigation adaptation strategy. The results indicate that increase in temperature and decrease in rainfall has decreased the net revenue from maize and beans production and raised rent for irrigated farms particularly in the middle and low altitudes of the basin. Increase in temperature has increased the net revenue from maize and beans production in the upper altitudes of basin. The results clearly demonstrate that climate change have affected the livelihood of the majority of the poor small scale farmers found in the middle and lower altitudes and improved that of farmers living in the upper. They also demonstrate that irrigation is a significant technique for adaptation to climate change in the basin