Simulation of granular soil behaviour using the bullet physics library

A physics engine is computer software which provides a simulation of certain physical systems, such as rigid body dynamics, soft body dynamics and fluid dynamics. Physics engines were firstly developed for using in animation and gaming industry ; nevertheless, due to fast calculation speed they are attracting more and more attetion from researchers of the engineering fields. Since physics engines are capable of performing fast calculations on multibody rigid dynamic systems, soil particles can be modeled as distinct rigid bodies. However, up to date, it is not clear to what extent they perform accurately in modeling soil behaviour from a geotechnical viewpoint. To investigate this, examples of pluviation and vibration-induced desification were simulated using the physics engine called Bullet physics library. In order to create soil samples, first, randomly shaped polyhedrons, representing gravels, were generated using the Voronoi tessellation approach. Then, particles were pluviated through a funnel into a cylinder. Once the soil particles settled in a static state, the cylinder was subjected to horizontal sinusoidal vibration for a period of 20 seconds. The same procedure for sample perparation was performed in the laboratory. The results of pluviation and vibration tests weere recorded and compared to those of simulations. A good agreement has been found between the results of simulations and laboratory tests. The findings in this study reinforce the idea that physics engines can be employed as a geotechnical engineering simulation tool

Assessment of genotype x environment interaction on yield and yield components of durum wheat genotypes by multivariate analyses

Wheat breeders have to determine the new cultivars and lines responsive to the environmental changes for grain yield and yield components. Therefore, this study was conducted to evaluate 25 durum wheat (Triticum turgidum spp. durum) genotypes including 12 registered cultivars and 13 advanced breeding lines for their stability grown in three different locations (Tokat-Kazova, Diyarbakir and Sivas-Ulas) of Turkey for two growing seasons (2005-2006 and 2006-2007), and to select genotypes having desirable traits to be used in future durum wheat breeding program. Field trials were conducted in a randomized complete block design with three replications at each location. Days to heading, plant height, number of spikes per square meter, number of kernels per spike, spike weight, 1000 kernel weight and grain yield of the genotypes were evaluated in each location. The regression coefficient (bi) of Finlay and Wilkinson (1963) and mean square of deviation from regression (S2d) of Eberhart and Russell (1966) were used as the stability parameters. The results of combined analysis of variance showed a strong influence of the locations on plant height, number of spikes per square meter, number of kernels per spike,  spike weight, 1000 kernel weight and grain yield. Genotypic effects were mainly observed for spike length and test weight. Year had strong impact only on the days to heading. Ecological conditions of Diyarbakir among locations offer the better opportunity for production of durum wheat. Line 5 and cultivar Gidara were both stable in yield ability and also appeared the stable group based on the cluster analysis. In the first principal component days to heading, number of spikes per square meter and spike length  were the most important traits contributing to variation that obtained about 44.3%. There was a positive relationship between grain yield and number of spikes per square meter together test weight, whereas days to heading and spike length were negatively correlated to grain yield. The results of this study also imply that Line-5 and cultivar Gidara among genotypes were the most stable cultivars and can be used as breeding materials. The days to heading, number of spikes per square meter and spike length could be adequate to introduce the differences among genotypes.Key words: Durum wheat, stability, principal component analysis, cluster analysis

Uncertainty analysis for seismic hazard in Northern and Central Italy

In this study we examine uncertainty and parametric sensitivity of Peak Ground Acceleration (PGA) and 1-Hz Spectral Acceleration (1-Hz SA) in probabilistic seismic hazard maps (10% probability of exceedance in 50 years) of Northern and Central Italy. The uncertainty in hazard is estimated using a Monte Carlo approach to randomly sample a logic tree that has three input-variables branch points representing alternative values for bvalue, maximum magnitude (Mmax) and attenuation relationships. Uncertainty is expressed in terms of 95% confidence band and Coefficient Of Variation (COV). The overall variability of ground motions and their sensitivity to each parameter of the logic tree are investigated. The largest values of the overall 95% confidence band are around 0.15 g for PGA in the Friuli and Northern Apennines regions and around 0.35 g for 1-Hz SA in the Central Apennines. The sensitivity analysis shows that the largest contributor to seismic hazard variability is uncertainty in the choice of ground-motion attenuation relationships, especially in the Friuli Region (∼0.10 g) for PGA and in the Friuli and Central Apennines regions (∼0.15 g) for 1-Hz SA. This is followed by the variability of the b-value: its main contribution is evident in the Friuli and Central Apennines regions for both 1-Hz SA (∼0.15 g) and PGA (∼0.10 g). We observe that the contribution of Mmax to seismic hazard variability is negligible, at least for 10% exceedance in 50-years hazard. The overall COV map for PGA shows that the uncertainty in the hazard is larger in the Friuli and Northern Apennine regions, around 20-30%, than the Central Apennines and Northwestern Italy, around 10-20%. The overall uncertainty is larger for the 1-Hz SA map and reaches 50- 60% in the Central Apennines and Western Alps

Resistivity studies under hydrostatic pressure on a low-resistance variant of the quasi-2D organic superconductor kappa-(BEDT-TTF)2Cu[N(CN)2]Br: quest for intrinsic scattering contributions

Resistivity measurements have been performed on a low (LR)- and high (HR)-resistance variant of the kappa-(BEDT-TTF)_2Cu[N(CN)_2]Br superconductor. While the HR sample was synthesized following the standard procedure, the LR crystal is a result of a somewhat modified synthesis route. According to their residual resistivities and residual resistivity ratios, the LR crystal is of distinctly superior quality. He-gas pressure was used to study the effect of hydrostatic pressure on the different transport regimes for both variants. The main results of these comparative investigations are (i) a significant part of the inelastic-scattering contribution, which causes the anomalous rho(T) maximum in standard HR crystals around 90 K, is sample dependent, i.e. extrinsic in nature, (ii) the abrupt change in rho(T) at T* approx. 40 K from a strongly temperature-dependent behavior at T > T* to an only weakly T-dependent rho(T) at T < T* is unaffected by this scattering contribution and thus marks an independent property, most likely a second-order phase transition, (iii) both variants reveal a rho(T) proportional to AT^2 dependence at low temperatures, i.e. for T_c < T < T_0, although with strongly sample-dependent coefficients A and upper bounds for the T^2 behavior measured by T_0. The latter result is inconsistent with the T^2 dependence originating from coherent Fermi-liquid excitations.Comment: 8 pages, 6 figure

Uncertainty analysis for seismic hazard in Northern and Central Italy

In this study we examine uncertainty and parametric sensitivity of Peak Ground Acceleration (PGA) and 1-Hz Spectral Acceleration (1-Hz SA) in probabilistic seismic hazard maps (10% probability of exceedance in 50 years) of Northern and Central Italy. The uncertainty in hazard is estimated using a Monte Carlo approach to randomly sample a logic tree that has three input-variables branch points representing alternative values for bvalue, maximum magnitude (Mmax) and attenuation relationships. Uncertainty is expressed in terms of 95% confidence band and Coefficient Of Variation (COV). The overall variability of ground motions and their sensitivity to each parameter of the logic tree are investigated. The largest values of the overall 95% confidence band are around 0.15 g for PGA in the Friuli and Northern Apennines regions and around 0.35 g for 1-Hz SA in the Central Apennines. The sensitivity analysis shows that the largest contributor to seismic hazard variability is uncertainty in the choice of ground-motion attenuation relationships, especially in the Friuli Region (?0.10 g) for PGA and in the Friuli and Central Apennines regions (?0.15 g) for 1-Hz SA. This is followed by the variability of the b-value: its main contribution is evident in the Friuli and Central Apennines regions for both 1-Hz SA (?0.15 g) and PGA (?0.10 g). We observe that the contribution of Mmax to seismic hazard variability is negligible, at least for 10% exceedance in 50-years hazard. The overall COV map for PGA shows that the uncertainty in the hazard is larger in the Friuli and Northern Apennine regions, around 20-30%, than the Central Apennines and Northwestern Italy, around 10-20%. The overall uncertainty is larger for the 1-Hz SA map and reaches 50- 60% in the Central Apennines and Western Alps

An interaction network of mental disorder proteins in neural stem cells

Mental disorders (MDs) such as intellectual disability (ID), autism spectrum disorders (ASD) and schizophrenia have a strong genetic component. Recently, many gene mutations associated with ID, ASD or schizophrenia have been identified by high-throughput sequencing. A substantial fraction of these mutations are in genes encoding transcriptional regulators. Transcriptional regulators associated with different MDs but acting in the same gene regulatory network provide information on the molecular relation between MDs. Physical interaction between transcriptional regulators is a strong predictor for their cooperation in gene regulation. Here, we biochemically purified transcriptional regulators from neural stem cells, identified their interaction partners by mass spectrometry and assembled a protein interaction network containing 206 proteins, including 68 proteins mutated in MD patients and 52 proteins significantly lacking coding variation in humans. Our network shows molecular connections between established MD proteins and provides a discovery tool for novel MD genes. Network proteins preferentially co-localize on the genome and cooperate in disease-relevant gene regulation. Our results suggest that the observed transcriptional regulators associated with ID, ASD or schizophrenia are part of a transcriptional network in neural stem cells. We find that more severe mutations in network proteins are associated with MDs that include lower intelligence quotient (IQ), suggesting that the level of disruption of a shared transcriptional network correlates with cognitive dysfunction

European lipodystrophy registry: Background and structure

Background: Lipodystrophy syndromes comprise a group of extremely rare and heterogeneous diseases characterized by a selective loss of adipose tissue in the absence of nutritional deprivation or catabolic state. Because of the rarity of each lipodystrophy subform, research in this area is difficult and international co-operation mandatory. Therefore, in 2016, the European Consortium of Lipodystrophies (ECLip) decided to create a registry for patients with lipodystrophy. Results: The registry was build using the information technology Open Source Registry System for Rare Diseases in the EU (OSSE), an open-source software and toolbox. Lipodystrophy specific data forms were developed based on current knowledge of typical signs and symptoms of lipodystrophy. The platform complies with the new General Data Protection Regulation (EU) 2016/679 by ensuring patient pseudonymization, informational separation of powers, secure data storage and security of communication, user authentication, person specific access to data, and recording of access granted to any data. Inclusion criteria are all patients with any form of lipodystrophy (with the exception of HIV-associated lipodystrophy). So far 246 patients from nine centres (Amsterdam, Bologna, Izmir, Leipzig, M\ufcnster, Moscow, Pisa, Santiago de Compostela, Ulm) have been recruited. With the help from the six centres on the brink of recruitment (Cambridge, Lille, Nicosia, Paris, Porto, Rome) this number is expected to double within the next one or 2 years. Conclusions: A European registry for all patients with lipodystrophy will provide a platform for improved research in the area of lipodystrophy. All physicians from Europe and neighbouring countries caring for patients with lipodystrophy are invited to participate in the ECLip Registry. Study registration: ClinicalTrials.gov (NCT03553420). Registered 14 March 2018, retrospectively registered

Acting Intuition into Sense: How Film Crews Make Sense with Embodied Ways of Knowing

This study contributes to a holistic understanding of sensemaking by going beyond the mind–body dualism. To do so, we focus analytically on a phenomenon that operates at the nexus of mind and body: intuition. By observing four film crews, we unpack how people act their intuition into sense – that is, how they transform, through action, an initial sense (intuition) that is tacit, intimate, and complex into one that is publicly displayed, simpler, and ordered (i.e., a developed sense). Our model identifies two sensemaking trajectories, each of which involves several bodily actions (e.g., displaying feelings, working hands-on, speaking assertively). These actions enable intuition to express a facet of itself and acquire new properties. This study makes three important contributions. First, it develops the holistic-relational character of sensemaking by locating it in the relations among multiple loci (cognition, language, body, and materiality) rather than in each one disjunctively. Second, it theorizes embodied sensemaking as a transformative process entailing a rich repertoire of bodily actions. Third, it extends sensemaking research by attending to the physicality and materiality of language in embodied sensemaking

Loss of thymidine phosphorylase activity disrupts adipocyte differentiation and induces insulin-resistant lipoatrophic diabetes.

BACKGROUND: Thymidine phosphorylase (TP), encoded by the TYMP gene, is a cytosolic enzyme essential for the nucleotide salvage pathway. TP catalyzes the phosphorylation of the deoxyribonucleosides, thymidine and 2'-deoxyuridine, to thymine and uracil. Biallelic TYMP variants are responsible for Mitochondrial NeuroGastroIntestinal Encephalomyopathy (MNGIE), an autosomal recessive disorder characterized in most patients by gastrointestinal and neurological symptoms, ultimately leading to death. Studies on the impact of TYMP variants in cellular systems with relevance to the organs affected in MNGIE are still scarce and the role of TP in adipose tissue remains unexplored. METHODS: Deep phenotyping was performed in three patients from two families carrying homozygous TYMP variants and presenting with lipoatrophic diabetes. The impact of the loss of TP expression was evaluated using a CRISPR-Cas9-mediated TP knockout (KO) strategy in human adipose stem cells (ASC), which can be differentiated into adipocytes in vitro. Protein expression profiles and cellular characteristics were investigated in this KO model. RESULTS: All patients had TYMP loss-of-function variants and first presented with generalized loss of adipose tissue and insulin-resistant diabetes. CRISPR-Cas9-mediated TP KO in ASC abolished adipocyte differentiation and decreased insulin response, consistent with the patients' phenotype. This KO also induced major oxidative stress, altered mitochondrial functions, and promoted cellular senescence. This translational study identifies a new role of TP by demonstrating its key regulatory functions in adipose tissue. CONCLUSIONS: The implication of TP variants in atypical forms of monogenic diabetes shows that genetic diagnosis of lipodystrophic syndromes should include TYMP analysis. The fact that TP is crucial for adipocyte differentiation and function through the control of mitochondrial homeostasis highlights the importance of mitochondria in adipose tissue biology