The Lotic Intersite Nitrogen Experiments: an example of successful ecological research collaboration

Collaboration is an essential skill for modern ecologists because it brings together diverse expertise, viewpoints, and study systems. The Lotic Intersite Nitrogen eXperiments (LINX I and II), a 17-y research endeavor involving scores of early- to late-career stream ecologists, is an example of the benefits, challenges, and approaches of successful collaborative research in ecology. The scientific success of LINX reflected tangible attributes including clear scientific goals (hypothesis-driven research), coordinated research methods, a team of cooperative scientists, excellent leadership, extensive communication, and a philosophy of respect for input from all collaborators. Intangible aspects of the collaboration included camaraderie and strong team chemistry. LINX further benefited from being part of a discipline in which collaboration is a tradition, clear data-sharing and authorship guidelines, an approach that melded field experiments and modeling, and a shared collaborative goal in the form of a universal commitment to see the project and resulting data products through to completion

Higher mortality and intubation rate in COVID-19 patients treated with noninvasive ventilation compared with high-flow oxygen or CPAP

COVID-19; Noninvasive ventilation; High-flow oxygenCOVID-19; Ventilación no invasiva; Oxígeno de alto flujoCOVID-19; Ventilació no invasiva; Oxigen d'alt cabalThe effectiveness of noninvasive respiratory support in severe COVID-19 patients is still controversial. We aimed to compare the outcome of patients with COVID-19 pneumonia and hypoxemic respiratory failure treated with high-flow oxygen administered via nasal cannula (HFNC), continuous positive airway pressure (CPAP) or noninvasive ventilation (NIV), initiated outside the intensive care unit (ICU) in 10 university hospitals in Catalonia, Spain. We recruited 367 consecutive patients aged ≥ 18 years who were treated with HFNC (155, 42.2%), CPAP (133, 36.2%) or NIV (79, 21.5%). The main outcome was intubation or death at 28 days after respiratory support initiation. After adjusting for relevant covariates and taking patients treated with HFNC as reference, treatment with NIV showed a higher risk of intubation or death (hazard ratio 2.01; 95% confidence interval 1.32-3.08), while treatment with CPAP did not show differences (0.97; 0.63-1.50). In the context of the pandemic and outside the intensive care unit setting, noninvasive ventilation for the treatment of moderate to severe hypoxemic acute respiratory failure secondary to COVID-19 resulted in higher mortality or intubation rate at 28 days than high-flow oxygen or CPAP. This finding may help physicians to choose the best noninvasive respiratory support treatment in these patients.Clinicaltrials.gov identifier: NCT04668196

Structure of the {001} talc surface as seen by atomic force microscopy: Comparison with X-ray and electron diffraction results

In this study the surface structure of a centimetre sized crystal of talc from the Trimouns deposit (Ariège, France) was imaged by atomic force microscopy. The direct image shows detailed characteristics of clay tetrahedral surfaces. The unit-cell dimensions obtained 30 using atomic force microscopy (aor = 5.47±0.28 and bor = 9.48±0.28 Å) are found to be slightly higher, with an increased uncertainty, than those obtained using X-ray diffraction (aor = 5.288±0.007 and bor = 9.159±0.010 Å) and selected-area electron diffraction (aor = 5.32±0.03 and bor = 9.22±0.05 Å). Talc has a quasi-ideal surface, clean of strong 34 structural distortion as compared to most of other clay minerals and unlikely surface 35 relaxation. The observation on the obtained image of apparent cell dimension enlargement is 36 then more likely attributed to instrumental artefacts, also responsible for scattered values of unit-cell parameters rather than related to any surface structural features

3-D Magnetotelluric Image of Offshore Magmatism at the Walvis Ridge and Rift Basin

Highlights • We report on marine 3D Magnetotelluric study on Walvis Ridge • Derived 3D electrical resistivity model shows a large scale resistive zone, which we link to crustal extension due to local uplift. It might indicate the location where the hot-spot impinged on the crust prior to rifting • Smaller scale resistive region is attributed to magma ascent during rifting • Rift basin is identified by low resistivity region The Namibian continental margin marks the starting point of the Tristan da Cunha hotspot trail, the Walvis Ridge. This section of the volcanic southwestern African margin is therefore ideal to study the interaction of hotspot volcanism and rifting, which occurred in the late Jurassic/early Cretaceous. Offshore magnetotelluric data image electromagnetically the landfall of Walvis Ridge. Two large-scale high resistivity anomalies in the 3-D resistivity model indicate old magmatic intrusions related to hot-spot volcanism and rifting. The large-scale resistivity anomalies correlate with seismically identified lower crustal high velocity anomalies attributed to magmatic underplating along 2-D offshore seismic profiles. One of the high resistivity anomalies (above 500 Ωm) has three arms of approximately 100 km width and 300 km to 400 km length at 120 degree angles in the lower crust. One of the arms stretches underneath Walvis Ridge. The shape is suggestive of crustal extension due to local uplift. It might indicate the location where the hot-spot impinged on the crust prior to rifting. A second, smaller anomaly of 50 km width underneath the continent ocean boundary may be attributed to magma ascent during rifting. We attribute a low resistivity anomaly east of the continent ocean boundary and south of Walvis Ridge to the presence of a rift basin that formed prior to the rifting

Fuzzy species limits in Mediterranean gorgonians (Cnidaria, Octocorallia): inferences on speciation processes

The study of the interplay between speciation and hybridization is of primary importance in evolutionary biology. Octocorals are ecologically important species whose shallow phylogenetic relationships often remain to be studied. In the Mediterranean Sea, three congeneric octocorals can be observed in sympatry: Eunicella verrucosa, Eunicella cavolini and Eunicella singularis. They display morphological differences and E.singularis hosts photosynthetic Symbiodinium, contrary to the two other species. Two nuclear sequence markers were used to study speciation and gene flow between these species, through network analysis and Approximate Bayesian Computation (ABC). Shared sequences indicated the possibility of hybridization or incomplete lineage sorting. According to ABC, a scenario of gene flow through secondary contact was the best model to explain these results. At the intraspecific level, neither geographical nor ecological isolation corresponded to distinct genetic lineages in E.cavolini. These results are discussed in the light of the potential role of ecology and genetic incompatibilities in the persistence of species limits.French National Research Agency (ANR) program Adacni (ANR) [ANR-12-ADAP-0016]CNRSHubert Curien 'Tassili' program [12MDU853]CCMAR Strategic Plan from Fundacao para a Ciencia e a Tecnologia-FCT [PEst-C/MAR/LA0015/2011,FEDERinfo:eu-repo/semantics/publishedVersio

Keras R-CNN: library for cell detection in biological images using deep neural networks

Background: A common yet still manual task in basic biology research, high-throughput drug screening and digital pathology is identifying the number, location, and type of individual cells in images. Object detection methods can be useful for identifying individual cells as well as their phenotype in one step. State-of-the-art deep learning for object detection is poised to improve the accuracy and efficiency of biological image analysis. Results: We created Keras R-CNN to bring leading computational research to the everyday practice of bioimage analysts. Keras R-CNN implements deep learning object detection techniques using Keras and Tensorflow (https://github.com/broadinstitute/keras-rcnn). We demonstrate the command line tool’s simplified Application Programming Interface on two important biological problems, nucleus detection and malaria stage classification, and show its potential for identifying and classifying a large number of cells. For malaria stage classification, we compare results with expert human annotators and find comparable performance. Conclusions: Keras R-CNN is a Python package that performs automated cell identification for both brightfield and fluorescence images and can process large image sets. Both the package and image datasets are freely available on GitHub and the Broad Bioimage Benchmark Collection

HamLib: A library of Hamiltonians for benchmarking quantum algorithms and hardware

In order to characterize and benchmark computational hardware, software, and algorithms, it is essential to have many problem instances on-hand. This is no less true for quantum computation, where a large collection of real-world problem instances would allow for benchmarking studies that in turn help to improve both algorithms and hardware designs. To this end, here we present a large dataset of qubit-based quantum Hamiltonians. The dataset, called HamLib (for Hamiltonian Library), is freely available online and contains problem sizes ranging from 2 to 1000 qubits. HamLib includes problem instances of the Heisenberg model, Fermi-Hubbard model, Bose-Hubbard model, molecular electronic structure, molecular vibrational structure, MaxCut, Max-k-SAT, Max-k-Cut, QMaxCut, and the traveling salesperson problem. The goals of this effort are (a) to save researchers time by eliminating the need to prepare problem instances and map them to qubit representations, (b) to allow for more thorough tests of new algorithms and hardware, and (c) to allow for reproducibility and standardization across research studies