Streamability of nested word transductions

We consider the problem of evaluating in streaming (i.e., in a single left-to-right pass) a nested word transduction with a limited amount of memory. A transduction T is said to be height bounded memory (HBM) if it can be evaluated with a memory that depends only on the size of T and on the height of the input word. We show that it is decidable in coNPTime for a nested word transduction defined by a visibly pushdown transducer (VPT), if it is HBM. In this case, the required amount of memory may depend exponentially on the height of the word. We exhibit a sufficient, decidable condition for a VPT to be evaluated with a memory that depends quadratically on the height of the word. This condition defines a class of transductions that strictly contains all determinizable VPTs

Optimized approach to retrieve information on the tropospheric and stratospheric carbonyl sulfide (OCS) vertical distributions above Jungfraujoch from high-resolution FTIR solar spectra

Carbonyl sulfide (OCS), which is produced in the troposphere from both biogenic and anthropogenic sources, is the most abundant gaseous sulfur species in the unpolluted atmosphere. Due to its low chemical reactivity and water solubility, a significant fraction of OCS is able to reach the stratosphere where it is converted to SO2 and ultimately to H2SO4 aerosols (Junge layer). These aerosols have the potential to amplify stratospheric ozone destruction on a global scale and may influence Earth’s radiation budget and climate through increasing solar scattering. The transport of OCS from troposphere to stratosphere is thought to be the primary mechanism by which the Junge layer is sustained during nonvolcanic periods. Because of this, long-term trends in atmospheric OCS concentration, not only in the troposphere but also in the stratosphere, are of great interest. A new approach has been developed and optimized to retrieve atmospheric abundance of OCS from high-resolution ground-based infrared solar spectra by using the SFIT-2 (v3.91) algorithm, including a new model for solar lines simulation (solar lines often produce significant interferences in the OCS microwindows). The strongest lines of the nu3 fundamental band of OCS at 2062 cm-1 have been systematically evaluated with objective criteria to select a new set of microwindows, assuming the HITRAN 2004 spectroscopic parameters with an increase in the OCS line intensities of the nu3band main isotopologue 16O12C32S by 15.79% as compared to HITRAN 2000 (Rothman et al., 2008, and references therein). Two regularization schemes have further been compared (deducted from ATMOS and ACE-FTS measurements or based on a Tikhonov approach), in order to select the one which optimizes the information content while minimizing the error budget. The selected approach has allowed us to determine updated OCS long-term trend from 1988 to 2009 in both the troposphere and the stratosphere, using spectra recorded on a regular basis with Fourier Transform Infrared spectrometers (FTIRs), under clear-sky conditions, at the NDACC site (Network for the Detection of Atmospheric Composition Change, visit http://www.ndacc.org) of the International Scientific Station of the Jungfraujoch (Swiss Alps, 46.5°N, 8.0°E, 3580m asl). Trends and seasonal cycles deduced from our results will be compared to values published in the literature and critically discussed. In particular, we will confirm the recent change in the OCS total column trend, which has become positive since 2002 before undergoing a slowing down over the last years

Paleontology in France: 200 years in the footsteps of Cuvier and Lamarck

International audienceDue to its richness in fossil localities and Fossil-Lagerstätten, France played a major role in the 18th and 19th centuries in establishing paleontology and biostratigraphy as scientific disciplines. The French naturalist and zoologist Cuvier (1769-1832) established the fields of comparative anatomy and paleontology, and proposed the concept of 'catastrophism' in geology. The naturalist Lamarck (1744-1829) is considered the founder of invertebrate paleontology and biostratigraphy and an early pioneer in the studies of evolution, developing the idea of 'transformism' and creating the word 'fossil', while his successor Blainville (1777-1850) was the first to use the word 'paleontology'. Based on this rich heritage, numerous French scientists strengthened paleontology as an important discipline during the 19th and 20th centuries. Paleontology was present at the universities of most major French cities, as documented by the rich collections in over 50 natural history museums and university collections. The most significant paleontological collection is that housed in the Muséum National d'Histoire Naturelle (MNHN) at Paris that currently hosts the largest research unit in paleontology of France with over 100 scientists, curators and technicians. The second largest collection (and the largest in terms of invertebrate fossils) is housed at the University of Lyon1, where the most important university paleontology research team is present. About 250 professional paleontologists are currently working in research units that are mostly affiliated to the Centre National de Recherche Scientifique (CNRS), in public or private museums, or in the numerous natural parcs. A significant generation change took place in the early 2000s, with the retirement of the paleontologists recruited in the 1960s and 1970s, that were often specialized in alpha-taxonomy and stratigraphy, and the arrival of a young generation of scientists that attempts to answer more 'modern' questions, such as global (climate) change, biodiversity, or evolution. This new generation of paleontologists faces modified funding schemes with project-based supporting structures in a more and more competitive environment. In the present paper we attempt to summarize the current situation of paleontology as a discipline in the very complex academic and scientific context of France. After a short overview on the history of French paleontology in the last centuries, a synopsis on institutions and funding agencies is presented briefly. The major research departments and their research themes are then described, together with the most important collections, the paleontological associations, journals, and databases, etc. Paleontological training possibilities and job opportunities, in particular in academia, are next documented, concluding with a summary of the prospects of the discipline

Carbon cycling of Lake Kivu (East Africa): net autotrophy in the epilimnion and emission of CO2 to the atmosphere sustained by geogenic inputs

peer reviewedWe report organic and inorganic carbon distributions and fluxes in a large (>2000 km2) oligotrophic, tropical lake (Lake Kivu, East Africa), acquired during four field surveys, that captured the seasonal variations (March 2007–mid rainy season, September 2007–late dry season, June 2008–early dry season, and April 2009–late rainy season). The partial pressure of CO2 (pCO2) in surface waters of the main basin of Lake Kivu showed modest spatial (coefficient of variation between 3% and 6%), and seasonal variations with an amplitude of 163 ppm (between 579±23 ppm on average in March 2007 and 742±28 ppm on average in September 2007). The most prominent spatial feature of the pCO2 distribution was the very high pCO2 values in Kabuno Bay (a small sub-basin with little connection to the main lake) ranging between 11213 ppm and 14213 ppm (between 18 and 26 times higher than in the main basin). Surface waters of the main basin of Lake Kivu were a net source of CO2 to the atmosphere at an average rate of 10.8 mmol m−2 d−1, which is lower than the global average reported for freshwater, saline, and volcanic lakes. In Kabuno Bay, the CO2 emission to the atmosphere was on average 500.7 mmol m−2 d−1 (~46 times higher than in the main basin). Based on whole-lake mass balance of dissolved inorganic carbon (DIC) bulk concentrations and of its stable carbon isotope composition, we show that the epilimnion of Lake Kivu was net autotrophic. This is due to the modest river inputs of organic carbon owing to the small ratio of catchment area to lake surface area (2.15). The carbon budget implies that the CO2 emission to the atmosphere must be sustained by DIC inputs of geogenic origin from deep geothermal springs.AFRIVA

Assessment of the effects of sulfate and nitrate on the temporal evolution of Klebsiella oxytoca and Staphylococcus aureus abundance under shaking conditions, in aquatic microcosm

Most chemicals in natural aquatic media can be assimilated by bacteria. The impact of various environmental conditions on this microbial process is not always clear. This study aimed at investigating changes in the abundance of Klebsiella oxytoca and Staphylococcus aureus under different shaking conditions, in aquatic microcosms containing nitrate and sulfate. Sodium chloride solution (8.5 g NaCl•L-1), and nitrate and sulfate solutions (0.005, 0.05, 0.5 and 5 g•L-1) containing bacteria were supplemented with tryptic peptone at a final concentration of 10 g•L-1. The solutions were incubated under shaking conditions (300, 350 and 400 rev•min-1). Bacteriological analyses were performed hourly over a 6-h period. During the first 3 h of incubation, results showed that the highest values of the apparent cell growth rates (CAGRs) with K2SO4 in pure cultures, at a shaking speed 400 rev•min-1, were 0.656 h-1 for S. aureus, and 0.364 h-1 for K. oxytoca. In mixed culture, the CAGR was 0.235 h-1 for S. aureus, and 0.388 h-1 for K. oxytoca, both recorded at 300 rev•min-1. With KNO3 in pure culture solutions, the CAGR was 0.353 h-1 for S. aureus at 300 rev•min-1, and 0.367 h-1 for K. oxytoca at 350 rev•min-1. In mixed culture it was 0.454 h-1 for S. aureus and 0.393 h-1 for K. oxytoca, both recorded at 350 rev•min-1. The highest value of the apparent cell inhibition rate (CAIR) for S. aureus was 0.520 h-1 in K2SO4 (5 g•L-1, 400 rev•min-1), and 0.115 h-1 in KNO3 (5 g•L-1, 300 rev•min-1). For K. oxytoca, it was 0.07 h-1 in K2SO4 in pure culture (0.05 g•L-1, 300 rev•min-1), and 0.044 h-1 in mixed culture (0.05 g•L-1, 350 rev•min-1). In KNO3 it was 0.239 h-1 in mixed culture (5 g•L-1, 300 rev•min-1). The growth and inhibition potentials of different microbial species were impacted by the chemical concentrations and the movement speeds.L’impact de diverses conditions environnementales sur l’assimilation bactérienne dans l’eau, des composés chimiques est peu connu. La présente étude a visé l’évaluation de la dynamique d’abondance de Klebsiella oxytoca et Staphylococcus aureus sous diverses conditions, en milieu aquatique microcosme contenant du sulfate ou nitrate. Des solutions du NaCl (8,5 g•L-1), sulfate et nitrate (0,005, 0,05, 0,5 et 5 g•L-1) contenant des cellules ont été enrichies à la peptone trypsique (concentration finale 10 g•L-1), puis incubées sous conditions dynamiques (300, 350 et 400 tr•min-1). Les analyses bactériologiques ont été effectuées pendant 6 h. Il ressort qu’au cours des trois premières heures d'incubation, le taux de croissance cellulaire apparent (TCCA) le plus élevé en culture pure, contenant du K2SO4, est de 0,656 h-1 pour S. aureus, et 0,364 h-1 pour K. oxytoca, enregistrés à 400 tr•min-1. En culture mixte, il est de 0,235 h-1 pour S. aureus, et 0,388 h-1 pour K. oxytoca, enregistrés à 300 tr•min-1. Avec du KNO3, en culture pure, le TCCA est de 0,353 h-1 pour S. aureus à 300 tr•min-1, et 0,367 h-1 à 350 tr•min-1 pour K. oxytoka. En culture mixte, il est de 0,454 h-1 pour S. aureus et 0,393 h-1 pour K. oxytoca, enregistrés à 350 tr•min-1. Le taux d’inhibition cellulaire apparent (TICA) le plus élevé de S. aureus est de 0,520 h-1 en présence du K2SO4 (5 g•L-1, 400 tr•min-1), et 0,115 h-1 en présence de KNO3 (5 g•L-1, 300 tr•min-1). Pour K. oxytoca, il est de 0,07 h-1 avec du K2SO4 en culture pure (0,05 g•L-1, 300 tr•min-1), et 0,044 h-1 en culture mixte (0,05 g•L-1, 350 tr•min-1). Avec du KNO3, il est de 0,239 h-1 en culture mixte (5 g•L-1, 300 tr•min-1). La croissance et l’inhibition des microorganismes sont affectées par les concentrations en sels et la vitesse de mouvements du milieu

Variability of carbon dioxide and methane in the epilimnion of Lake Kivu

peer reviewedWe report a dataset of the partial pressure of CO2 (pCO2) and me-thane concentrations (CH4) in the surface waters of Lake Kivu ob-tained during four cruises covering the two main seasons (rainy and dry). Spatial gradients of surface pCO2 and CH4 concentrations were modest in the main basin. In Kabuno Bay, pCO2 and CH4 concentra-tions in surface waters were higher, owing to the stronger influence of subaquatic springs from depth. Seasonal variations of pCO2 and CH4 in the main basin of Lake Kivu were strongly driven by deepen-ing of the epilimnion and the resulting entrainment of water charac-terized by higher pCO2 and CH4 concentrations. Physical and chem-ical vertical patterns in Kabuno Bay were seasonally stable, owing to a stronger stratification and smaller surface area inducing fetch limi-tation of wind driven turbulence. A global and regional cross-system comparison of pCO2 and CH4 concentrations in surface waters of lakes highlights the peculiarity of Kabuno Bay in terms of pCO2 values in surface waters. In terms of surface CH4 concentrations, both Kabuno Bay and the main basin of Lake Kivu are at the lower end of values in lakes globally, despite the huge amounts of CH4 and CO2 in the deeper layers of the lake.AFRIVA

Impact of safety-related dose reductions or discontinuations on sustained virologic response in HCV-infected patients: Results from the GUARD-C Cohort

BACKGROUND: Despite the introduction of direct-acting antiviral agents for chronic hepatitis C virus (HCV) infection, peginterferon alfa/ribavirin remains relevant in many resource-constrained settings. The non-randomized GUARD-C cohort investigated baseline predictors of safety-related dose reductions or discontinuations (sr-RD) and their impact on sustained virologic response (SVR) in patients receiving peginterferon alfa/ribavirin in routine practice. METHODS: A total of 3181 HCV-mono-infected treatment-naive patients were assigned to 24 or 48 weeks of peginterferon alfa/ribavirin by their physician. Patients were categorized by time-to-first sr-RD (Week 4/12). Detailed analyses of the impact of sr-RD on SVR24 (HCV RNA <50 IU/mL) were conducted in 951 Caucasian, noncirrhotic genotype (G)1 patients assigned to peginterferon alfa-2a/ribavirin for 48 weeks. The probability of SVR24 was identified by a baseline scoring system (range: 0-9 points) on which scores of 5 to 9 and <5 represent high and low probability of SVR24, respectively. RESULTS: SVR24 rates were 46.1% (754/1634), 77.1% (279/362), 68.0% (514/756), and 51.3% (203/396), respectively, in G1, 2, 3, and 4 patients. Overall, 16.9% and 21.8% patients experienced 651 sr-RD for peginterferon alfa and ribavirin, respectively. Among Caucasian noncirrhotic G1 patients: female sex, lower body mass index, pre-existing cardiovascular/pulmonary disease, and low hematological indices were prognostic factors of sr-RD; SVR24 was lower in patients with 651 vs. no sr-RD by Week 4 (37.9% vs. 54.4%; P = 0.0046) and Week 12 (41.7% vs. 55.3%; P = 0.0016); sr-RD by Week 4/12 significantly reduced SVR24 in patients with scores <5 but not 655. CONCLUSIONS: In conclusion, sr-RD to peginterferon alfa-2a/ribavirin significantly impacts on SVR24 rates in treatment-naive G1 noncirrhotic Caucasian patients. Baseline characteristics can help select patients with a high probability of SVR24 and a low probability of sr-RD with peginterferon alfa-2a/ribavirin