Cortical bone size deficit in adult patients with type 1 diabetes mellitus

Context: The increased fracture risk associated with type 1 diabetes mellitus (T1DM) remains unexplained by traditional risk factors such as low areal bone mineral density (aBMD). Nonetheless, few data exist on other determinants of bone strength in T1DM, including volumetric bone mineral density (vBMD) and bone geometry. Objective: Wecompared areal and volumetric bone parameters and cortical bone geometry in adult T1DM patients and sex-and age-matched controls. Design: Cross-sectional study including 64 adult T1DM patients (38 men; mean age, 41.168.1 years) and 63 sex-and age-matched controls. Main Outcome Measures: Areal bone parameters using dual-energy X-ray absorptiometry; volumetric bone parameters and cortical bone geometry using peripheral quantitative computed tomography. Results: T1DM was associated with lower aBMD at the total body, femoral neck, and total hip; lower trabecular vBMD at the distal radius; and higher cortical but lower total vBMD at the radial shaft. In addition, subjects with T1DM had a similar periosteal but larger endosteal circumference, smaller cortical thickness, and lower cortical over total bone area ratio. Differences in bone parameters could not be explained by differences in bone turnover markers or body composition, but cortical area was inversely associated with glycemic variability and long-term glycemic control. Conclusions: Besides decreased aBMD and trabecular vBMD, adult T1DM patients present with a cortical bone size deficit, which may contribute to their increased fracture risk. This deficit is mainly situated at the endosteal envelope, suggesting imbalanced remodeling rather than compromised modeling processes as the underlying mechanism

Most Permissive Semantics of Boolean Networks

As shown in (http://dx.doi.org/10.1101/2020.03.22.998377), the usual update modes of Boolean networks (BNs), including synchronous and (generalized) asynchronous, fail to capture behaviors introduced by multivalued refinements. Thus, update modes do not allow a correct abstract reasoning on dynamics of biological systems, as they may lead to reject valid BN models.This technical report lists the main definitions and properties of the most permissive semantics of BNs introduced in http://dx.doi.org/10.1101/2020.03.22.998377. This semantics meets with a correct abstraction of any multivalued refinements, with any update mode. It subsumes all the usual updating modes, while enabling new behaviors achievable by more concrete models. Moreover, it appears that classical dynamical analyzes of reachability and attractors have a simpler computational complexity:- reachability can be assessed in a polynomial number of iterations. The computation of iterations is in NP in the very general case, and is linear when local functions are monotonic, or with some usual representations of functions of BNs (binary decision diagrams, Petri nets, automata networks, etc.). Thus, reachability is in P with locally-monotonic BNs, and P$^{\text{NP}}$ otherwise (instead of being PSPACE-complete with update modes);- deciding wherever a configuration belongs to an attractor is in coNP with locally-monotonic BNs, and coNP$^{\text{coNP}}$ otherwise (instead of PSPACE-complete with update modes).Furthermore, we demonstrate that the semantics completely captures any behavior achievable with any multilevel or ODE refinement of the BN; and the semantics is minimal with respect to this model refinement criteria: to any most permissive trajectory, there exists a multilevel refinement of the BN which can reproduce it.In brief, the most permissive semantics of BNs enables a correct abstract reasoning on dynamics of BNs, with a greater tractability than previously introduced update modes

First Field Release of a Genetically Engineered, Self-Limiting Agricultural Pest Insect:Evaluating Its Potential for Future Crop Protection

Alternative, biologically-based approaches for pest management are sorely needed and one approach is to use genetically engineered insects. Herein we describe a series of integrated field, laboratory and modeling studies with the diamondback moth, Plutella xylostella, a serious global pest of crucifers. A “self-limiting” strain of Plutella xylostella (OX4319L), genetically engineered to allow the production of male-only cohorts of moths for field releases, was developed as a novel approach to protect crucifer crops. Wild-type females that mate with these self-limiting males will not produce viable female progeny. Our previous greenhouse studies demonstrated that releases of OX4319L males lead to suppression of the target pest population and dilution of insecticide-resistance genes. We report results of the first open-field release of a non-irradiated, genetically engineered self-limiting strain of an agricultural pest insect. In a series of mark-release-recapture field studies with co-releases of adult OX4319L males and wild-type counterparts, the dispersal, persistence and field survival of each strain were measured in a 2.83 ha cabbage field. In most cases, no differences were detected in these parameters. Overall, 97.8% of the wild-type males and 95.4% of the OX4319L males recaptured dispersed <35 m from the release point. The predicted persistence did not differ between strains regardless of release rate. With 95% confidence, 75% of OX4319L males released at a rate of 1,500 could be expected to live between 3.5 and 5.4 days and 95% of these males could be expected to be detected within 25.8–34.9 m from the release point. Moth strain had no effect on field survival but release rate did. Collectively, these results suggest similar field behavior of OX4319L males compared to its wild-type counterpart. Laboratory studies revealed no differences in mating competitiveness or intrinsic growth rates between the strains and small differences in longevity. Using results from these studies, mathematical models were developed that indicate release of OX4319L males should offer efficacious pest management of P. xylostella. Further field studies are recommended to demonstrate the potential for this self-limiting P. xylostella to provide pest suppression and resistance management benefits, as was previously demonstrated in greenhouse studies

Widening of Hydrous Shear Zones During Incipient Eclogitization of Metastable Dry and Rigid Lower Crust— Holsnøy, Western Norway

The partially eclogitized crustal rocks on Holsnøy in the Bergen Arcs, Norway, indicate that eclogitization is caused by the interplay of brittle and ductile deformation promoted by fluid infiltration and fluid-rock interaction. Eclogitization generated an interconnected network of millimeterto- kilometer-wide hydrous eclogite-facies shear zones, which presumably caused transient weakening of the mechanically strong lower crust. To decipher the development of those networks, we combine detailed lithological and structural mapping of two key outcrops with numerical modeling. Both outcrops are largely composed of preserved granulite with minor eclogite-facies shear zones, thus representing the beginning phases of eclogitization and ductile deformation. We suggest that deformation promoted fluidrock interaction and eclogitization, which gradually consumed the granulite until fluid-induced reactions were no longer significant. The shear zones widen during progressive deformation. To identify the key parameters that impact shear zone widening, we generated scale-independent numerical models, which focus on different processes affecting the shear zone evolution: (i) rotation of the shear zones caused by finite deformation, (ii) mechanical weakening due to a limited amount of available fluid, and (iii) weakening and further hydration of the shear zones as a result of continuous and unlimited fluid supply. A continuous diffusion-type fluid infiltration, with an effective diffusion coefficient around 2 10 16 m s D , coupled with deformation is prone to develop structures similar to the ones mapped in field. Our results suggest that the shear zones formed under a continuous fluid supply, causing shear zone widening, rather than localization, during progressive deformation

VITRAIL : Acquisition, Modelling and Rendering of Stained Glass

Stained glass windows are designed to reveal their powerful artistry under diverse and time-varying lighting conditions; virtual relighting of stained glass, therefore represents an exceptional tool for the appreciation of this age old art form. However, as opposed to most other artifacts, stained glass windows are extremely difficult if not impossible to analyze using controlled illumination because of their size and position. In this paper we present novel methods built upon image based priors to perform virtual relighting of stained glass artwork by acquiring the actual light transport properties of a given artefact. In a preprocessing step we build a material-dependent dictionary for light transport by studying the scattering properties of glass samples in a laboratory setup. We can now use the dictionary to recover a light transport matrix in two ways: under controlled illuminations the dictionary constitutes a sparsifying basis for a compressive sensing acquisition, while in the case of uncontrolled illuminations the dictionary is used to perform sparse regularization. The proposed basis preserves volume impurities and we show that the retrieved light transport matrix is heterogeneous, as in the case of real world objects. We present the rendering results of several stained glass artifacts, including the Rose Window of the cathedral of Lausanne, digitized using the presented methods

Investigating the Extent of Primer Dropout in SARS-CoV-2 Genome Sequences During the Early Circulation of Delta Variants

The SARS-CoV-2 Delta variant, corresponding to the Pangolin lineage B.1.617.2, was first detected in India in July 2020 and rapidly became dominant worldwide. The ARTIC v3 protocol for SARS-CoV-2 whole-genome sequencing, which relies on a large number of PCR primers, was among the first available early in the pandemic, but may be prone to coverage dropouts that result in incomplete genome sequences. A new set of primers (v4) was designed to circumvent this issue in June 2021. In this study, we investigated whether the sequencing community adopted the new sets of primers, especially in the context of the spread of the Delta lineage, in July 2021. Because information about protocols from individual laboratories is generally difficult to obtain, the aims of the study were to identify whether large under-sequenced regions were present in deposited Delta variant genome sequences (from April to August 2021), to investigate the extent of the coverage dropout among all the currently available Delta sequences in six countries, and to propose simple PCR primer modifications to sequence the missing region, especially for the first circulating Delta variants observed in 2021 in Switzerland. Candidate primers were tested on few clinical samples, highlighting the need to further pursue primer optimization and validation on a larger and diverse set of samples

Saproxylic species are linked to the amount and isolation of dead wood across spatial scales in a beech forest

ContextDead wood is a key habitat for saproxylicspecies, which are often used as indicators of habitatquality in forests. Understanding how the amount andspatial distribution of dead wood in the landscapeaffects saproxylic communities is therefore importantfor maintaining high forest biodiversity.ObjectivesWe investigated effects of the amountand isolation of dead wood on the alpha and betadiversity of four saproxylic species groups, with afocus on how the spatial scale influences results.MethodsWe inventoried saproxylic beetles, wood-inhabiting fungi, and epixylic bryophytes and lichenson 62 plots in the Sihlwald forest reserve in Switzer-land. We used GLMs to relate plot-level speciesrichness to dead wood amount and isolation on spatialscales of 20–200 m radius. Further, we used GDMs todetermine how dead wood amount and isolationaffected beta diversity.ResultsA larger amount of dead wood increasedbeetle richness on all spatial scales, while isolation hadno effect. For fungi, bryophytes and lichens this wasonly true on small spatial scales. On larger scales ofour study, dead wood amount had no effect, whilegreater isolation decreased species richness. Further,we found no strong consistent patterns explaining betadiversity

Marqueurs moléculaires utilisables en sélection chez la canne à sucre : cas de la résistance à la rouille brune

Les cultivars modernes de canne à sucre (Saccharum spp., 2n=100 à 130) sont hautement polyploïdes, aneuploïdes et d'origine interspécifique. Un gène majeur (Bru1) conférant la résistance à la rouille brune, causée par le champignon Puccinia melanocephala, a été identifié chez le cultivar R570. Nous avons analysé 380 cultivars modernes et clones en cours de sélection, représentatifs de la diversité mondiale, à l'aide de 22 marqueurs moléculaires regroupés dans un segment de 8,2cM génétiquement lié à Bru1 chez R570. Nos résultats révèlent un fort déséquilibre de liaison dans la région autour de Bru1 et de fortes associations entre la plupart des marqueurs et la résistance à la rouille. Deux marqueurs PCR flanquant le segment portant Bru1 sont complètement associés et sont présents uniquement chez les clones résistants. Ces marqueurs constituent des marqueurs moléculaires diagnostics de Bru1. 86% des 194 clones de canne à sucre résistants possèdent les marqueurs diagnostics de Bru1, révélant que ce gène constitue la principale source de résistance à la rouille brune chez les cultivars modernes. Les marqueurs PCR diagnostics de Bru1 devraient être particulièrement utiles pour identifier des cultivars possédant des sources de résistance alternatives à Bru1 afin de diversifier la base génétique de la résistance à la rouille brune dans les programmes de sélection. (Résumé d'auteur

Enabling dynamic and intelligent workflows for HPC, data analytics, and AI convergence

The evolution of High-Performance Computing (HPC) platforms enables the design and execution of progressively larger and more complex workflow applications in these systems. The complexity comes not only from the number of elements that compose the workflows but also from the type of computations they perform. While traditional HPC workflows target simulations and modelling of physical phenomena, current needs require in addition data analytics (DA) and artificial intelligence (AI) tasks. However, the development of these workflows is hampered by the lack of proper programming models and environments that support the integration of HPC, DA, and AI, as well as the lack of tools to easily deploy and execute the workflows in HPC systems. To progress in this direction, this paper presents use cases where complex workflows are required and investigates the main issues to be addressed for the HPC/DA/AI convergence. Based on this study, the paper identifies the challenges of a new workflow platform to manage complex workflows. Finally, it proposes a development approach for such a workflow platform addressing these challenges in two directions: first, by defining a software stack that provides the functionalities to manage these complex workflows; and second, by proposing the HPC Workflow as a Service (HPCWaaS) paradigm, which leverages the software stack to facilitate the reusability of complex workflows in federated HPC infrastructures. Proposals presented in this work are subject to study and development as part of the EuroHPC eFlows4HPC project.This work has received funding from the European High-Performance Computing Joint Undertaking (JU) under grant agreement No 955558. The JU receives support from the European Union’s Horizon 2020 research and innovation programme and Spain, Germany, France, Italy, Poland, Switzerland and Norway. In Spain, it has received complementary funding from MCIN/AEI/10.13039/501100011033, Spain and the European Union NextGenerationEU/PRTR (contracts PCI2021-121957, PCI2021-121931, PCI2021-121944, and PCI2021-121927). In Germany, it has received complementary funding from the German Federal Ministry of Education and Research (contracts 16HPC016K, 6GPC016K, 16HPC017 and 16HPC018). In France, it has received financial support from Caisse des dépôts et consignations (CDC) under the action PIA ADEIP (project Calculateurs). In Italy, it has been preliminary approved for complimentary funding by Ministero dello Sviluppo Economico (MiSE) (ref. project prop. 2659). In Norway, it has received complementary funding from the Norwegian Research Council, Norway under project number 323825. In Switzerland, it has been preliminary approved for complimentary funding by the State Secretariat for Education, Research, and Innovation (SERI), Norway. In Poland, it is partially supported by the National Centre for Research and Development under decision DWM/EuroHPCJU/4/2021. The authors also acknowledge financial support by MCIN/AEI /10.13039/501100011033, Spain through the “Severo Ochoa Programme for Centres of Excellence in R&D” under Grant CEX2018-000797-S, the Spanish Government, Spain (contract PID2019-107255 GB) and by Generalitat de Catalunya, Spain (contract 2017-SGR-01414). Anna Queralt is a Serra Húnter Fellow.With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2018-000797-S)