Time-resolved single-cell RNA-seq using metabolic RNA labelling

Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal RNA dynamics. Here we present single-cell metabolically labeled new RNA tagging sequencing (scNT-seq), a method for massively parallel analysis of newly transcribed and pre-existing mRNAs from the same cell. This droplet microfluidics-based method enables high-throughput chemical conversion on barcoded beads, efficiently marking newly transcribed mRNAs with T-to-C substitutions. Using scNT-seq, we jointly profiled new and old transcriptomes in ~55,000 single cells. These data revealed time-resolved transcription factor activities and cell-state trajectories at the single-cell level in response to neuronal activation. We further determined rates of RNA biogenesis and decay to uncover RNA regulatory strategies during stepwise conversion between pluripotent and rare totipotent two-cell embryo (2C)-like stem cell states. Finally, integrating scNT-seq with genetic perturbation identifies DNA methylcytosine dioxygenase as an epigenetic barrier into the 2C-like cell state. Time-resolved single-cell transcriptomic analysis thus opens new lines of inquiry regarding cell-type-specific RNA regulatory mechanisms

Radiographic assessment of the femorotibial joint of the CCLT rabbit experimental model of osteoarthritis

<p>Abstract</p> <p>Background</p> <p>The purposes of the study were to determine the relevance and validity of in vivo non-invasive radiographic assessment of the CCLT (Cranial Cruciate Ligament Transection) rabbit model of osteoarthritis (OA) and to estimate the pertinence, reliability and reproducibility of a radiographic OA (ROA) grading scale and associated radiographic atlas.</p> <p>Methods</p> <p>In vivo non-invasive extended non weight-bearing radiography of the rabbit femorotibial joint was standardized. Two hundred and fifty radiographs from control and CCLT rabbits up to five months after surgery were reviewed by three readers. They subsequently constructed an original semi-quantitative grading scale as well as an illustrative atlas of individual ROA feature for the medial compartment. To measure agreements, five readers independently scored the same radiographic sample using this atlas and three of them performed a second reading. To evaluate the pertinence of the ROA grading scale, ROA results were compared with gross examination in forty operated and ten control rabbits.</p> <p>Results</p> <p>Radiographic osteophytes of medial femoral condyles and medial tibial condyles were scored on a four point scale and dichotomously for osteophytes of medial fabella. Medial joint space width was scored as normal, reduced or absent. Each ROA features was well correlated with gross examination (p < 0.001). ICCs of each ROA features demonstrated excellent agreement between readers and within reading. Global ROA score gave the highest ICCs value for between (ICC 0.93; CI 0.90-0.96) and within (ICC ranged from 0.94 to 0.96) observer agreements. Among all individual ROA features, medial joint space width scoring gave the highest overall reliability and reproducibility and was correlated with both meniscal and cartilage macroscopic lesions (r_s= 0.68 and r_s= 0.58, p < 0.001 respectively). Radiographic osteophytes of the medial femoral condyle gave the lowest agreements while being well correlated with the macroscopic osteophytes (r_s= 0.64, p < 0.001).</p> <p>Conclusion</p> <p>Non-invasive in vivo radiography of the rabbit femorotibial joint is feasible, relevant and allows a reproducible grading of experimentally induced OA lesion. The radiographic grading scale and atlas presented could be used as a template for in vivo non invasive grading of ROA in preclinical studies and could allow future comparisons between studies.</p

Searching for stochastic gravitational waves using data from the two colocated LIGO Hanford detectors

Searches for a stochastic gravitational-wave background (SGWB) using terrestrial detectors typically involve cross-correlating data from pairs of detectors. The sensitivity of such cross-correlation analyses depends, among other things, on the separation between the two detectors: the smaller the separation, the better the sensitivity. Hence, a colocated detector pair is more sensitive to a gravitational-wave background than a noncolocated detector pair. However, colocated detectors are also expected to suffer from correlated noise from instrumental and environmental effects that could contaminate the measurement of the background. Hence, methods to identify and mitigate the effects of correlated noise are necessary to achieve the potential increase in sensitivity of colocated detectors. Here we report on the first SGWB analysis using the two LIGO Hanford detectors and address the complications arising from correlated environmental noise. We apply correlated noise identification and mitigation techniques to data taken by the two LIGO Hanford detectors, H1 and H2, during LIGO’s fifth science run. At low frequencies, 40–460 Hz, we are unable to sufficiently mitigate the correlated noise to a level where we may confidently measure or bound the stochastic gravitational-wave signal. However, at high frequencies, 460–1000 Hz, these techniques are sufficient to set a 95% confidence level upper limit on the gravitational-wave energy density of Ω(f) < 7.7 × 10[superscript -4](f/900  Hz)[superscript 3], which improves on the previous upper limit by a factor of ~180. In doing so, we demonstrate techniques that will be useful for future searches using advanced detectors, where correlated noise (e.g., from global magnetic fields) may affect even widely separated detectors.National Science Foundation (U.S.)United States. National Aeronautics and Space AdministrationCarnegie TrustDavid & Lucile Packard FoundationAlfred P. Sloan Foundatio

The LHCb configuration database

The aim of the LHCb configuration database is to store information about all the controllable devices of the detector. The experiment's control system (that uses PVSS ) will configure, start up and monitor the detector from the information in the configuration database. The database will contain devices with their properties, connectivity and hierarchy. The ability to store and rapidly retrieve huge amounts of data, and the navigability between devices are important requirements. We have collected use cases to ensure the completeness of the design. Using the entity relationship modelling technique we describe the use cases as classes with attributes and links. We designed the schema for the tables using relational diagrams. This methodology has been applied to the TFC (switches) and DAQ system. Other parts of the detector will follow later. The database has been implemented using Oracle to benefit from central CERN database support. The project also foresees the creation of tools to populate, maintain, and configure the configuration database. To communicate between the control system and the database we have developed a system which sends queries to the database and displays the results in PVSS. This database will be used in conjunction with the configuration database developed by the CERN JCOP (Joint Controls Project) project for PVSS

Response of diatom and dinoflagellate lifeforms to reduced phosphorus loading: a case study in the Thau lagoon, France

The basin of Thau in southern France is a shallow, weakly flushed lagoon which is an important location for oyster cultivation. Phytoplankton analyses were carried out in 1975-1976 and then (almost) continuously since 1987. We report an investigation of 'the balance of organisms' in phytoplankton in relation to reductions in phosphorus loading, using two new tools based on phytoplankton lifeforms: the Plankton Index for Phytoplankton (PIp); Euclidean distance in state space. Our results show the utility of the tools for analysing changes in the ‘balance of organisms’ at the level of functional groups (in our study diatoms and dinoflagellates), but also illustrate the difficulties in demonstrating the reversal of human impacts resulting from eutrophication. The comparison between 1987-89 and 1976 showed the expected 'de-eutrophication' due to the reduction in dissolved inorganic phosphate (DIP), with a decrease in dinoflagellate abundance. Since 1989, year-to-year variation in annual mean concentrations of (DIP) may have contributed to inter-annual variability in the balance of the two lifeforms, but the data suggest that the system has remained in a dynamically stable regime because: (i) there was no long-term trend in Euclidean distance from the reference; and (ii) there was no increase in inter-annual variability about the time-series mean Euclidean distance suggesting there has been no decrease in resilience which might signal a regime change. Integrated management of human activities will be required to manage (and reduce) total P in the system. Monitoring phytoplankton and nutrients concentrations to determine how primary production and the balance of species respond to further changes in the nutrient status of the lagoon should be an integral part of any management programme

STARECAPMED, des indices pour La Méditerranée

Le projet STARECAPMED (STAtion of Reference and rEsearch on Change of local and global Anthropogenic Pressures on Mediterranean Ecosystems Drifts) a pour objectif (i) d’améliorer la compréhension du fonctionnement des différents écosystèmes marins côtiers présents en Méditerranée et (ii) de décrire l’influence des activités humaines sur les processus qui gouvernent ce fonctionnement. La baie de Calvi, par sa situation exceptionnelle, est un site de référence de la Directive Européenne Cadre sur l’Eau (DCE), du monitoring de l’eutrophisation et de la contamination par les éléments traces. La Station de recherches océanographiques STARESO, implantée dans la baie depuis près de 50 ans, possède un accès unique à la mer et de nombreuses facilités logistiques. Elle a développé au fil du temps une expertise scientifique reposant notamment sur l’acquisition de longues séries temporelles de données environnementales. Ensemble, Baie et Station s’intègrent en un site atelier dédié à l’évaluation de l’état de santé des écosystèmes marins côtiers de Méditerranée Nord-Occidentale. En particulier, différents indices et indicateurs y sont développés en collaboration avec de nombreux laboratoires partenaires. Ainsi, nous avons développé, d’une part, une version non destructive de l’indice PREI (Posidonia Rapid Easy Index) d’évaluation de la qualité des eaux côtières reposant sur le suivi des herbiers à Posidonia oceanica, et d’autre part, deux indices d’évaluation de l’impact des ancrages, puis testé   l’indice EBQI (Ecosystem Based Quality Index), une approche sur la diversité écologique. Les indices TEPI (Trace Element Pollution Index) et TESVI (Trace Element Spatial Variation Index) permettent d’évaluer la contamination par les éléments traces. Le BeMSI (BEnthic Methodology Simplification) est un nouvel indicateur de la qualité du milieu défini à partir de la composition des peuplements macrobenthiques des substrats meubles et plus généralement, l’indice LIMA traduit l’attrait paysager et la richesse patrimoniale du benthos méditerranéen entre 0 et –40 m. Quant à l’indice ICAR (Indice paysager CAulerpa Racemosa), il permet d’évaluer les niveaux de colonisation par l’algue invasive Caulerpa cylindracea. Enfin, une approche innovante reposant sur l’enregistrement des sons permet d’évaluer la qualité du milieu à partir d’un paysage acoustique sous-marin. En conclusion, le développement et l’application combinée de ces différents indices et indicateurs développés dans le cadre du programme pluridisciplinaire STARECAPMED fournissent une estimation globale des états du milieu côtier méditerranéen à différents niveaux d’organisation, depuis l’espèce jusqu’à l’écosystème. De plus, leur mise en œuvre dans ce même site atelier privilégié permet de les confronter, de les ajuster et de les intercalibrer pour à terme les proposer aux gestionnaires du milieu côtier.STARECAMPE

Guidelines for clinical studies assessing the efficacy of drugs for the management of acute low back pain

In this paper we propose guidelines for clinical trials aimed at assessing the efficacy of drugs for acute non-specific low back pain (LBP) with or without radicular pain, preliminary to their approval and registration. To this end, consensus statements were obtained from a group of experts in the fields of rheumatology, clinical medicine, public health and epidemiology. EBM resources were systematically used as references