bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laboratory experiments and simulations for solitary internal waves with trapped cores
Authors: Luzzatto-Fegiz Paolo , Helfrich Karl R. 
Published: September 2014

AbstractWe perform simultaneous coplanar measurements of velocity and density in solitary internal waves with trapped cores, as well as viscous numerical simulations. Our set-up comprises a thin stratified layer (approximately 15 % of the overall fluid depth) overlaying a deep homogeneous layer. We consider waves propagating near a free surface, as well as near a rigid no-slip lid. In the free-surface case, all trapped-core waves exhibit a strong shear instability. We propose that Marangoni effects are responsible for this instability, and use our velocity measurements to perform quantitative calculations supporting this hypothesis. These surface-tension effects appear to be difficult to avoid at the experimental scale. By contrast, our experiments with a no-slip lid yield robust waves with large cores. In order to consider larger-amplitude waves, we complement our experiments with viscous numerical simulations, employing a longer virtual tank. Where overlap exists, our experiments and simulations are in good agreement. In order to provide a robust definition of the trapped core, we propose bounding it as a Lagrangian coherent structure (instead of using a closed streamline, as has been done traditionally). This construction is less sensitive to small errors in the velocity field, and to small three-dimensional effects. In order to retain only flows near equilibrium, we introduce a steadiness criterion, based on the rate of change of the density in the core. We use this criterion to successfully select within our experiments and simulations a family of quasi-steady robust flows that exhibit good collapse in their properties. The core circulation is small (at most, around 10 % of the baroclinic wave circulation). The core density is essentially uniform; the standard deviation of the density, in the core region, is less than 4 % of the full density range. We also calculate the circulation, kinetic energy and available potential energy of these waves. We find that these results are consistent with predictions from Dubreil-Jacotin–Long theory for waves with a uniform-density irrotational core, except for an offset, which we suggest is associated with viscous effects. Finally, by computing Richardson-number fields, and performing a temporal stability analysis based on the Taylor–Goldstein equation, we show that our results are consistent with empirical stability criteria in the literature.
Asymmetric flux models for particle-size segregation in granular avalanches
Authors: Gajjar P. , Gray J. M. N. T. 
Published: September 2014

AbstractParticle-size segregation commonly occurs in both wet and dry granular free-surface flows through the combined processes of kinetic sieving and squeeze expulsion. As the granular material is sheared downslope, the particle matrix dilates slightly and small grains tend to percolate down through the gaps, because they are more likely than the large grains to fit into the available space. Larger particles are then levered upwards in order to maintain an almost uniform solids volume fraction through the depth. Recent experimental observations suggest that a single small particle can percolate downwards through a matrix of large particles faster than a large particle can be levered upwards through a matrix of fines. In this paper, this effect is modelled by using a flux function that is asymmetric about its maximum point, differing from the symmetric quadratic form used in recent models of particle-size segregation. For illustration, a cubic flux function is examined in this paper, which can be either a convex or a non-convex function of the small-particle concentration. The method of characteristics is used to derive exact steady-state solutions for non-diffuse segregation in two dimensions, with an inflow concentration that is (i) homogeneous and (ii) normally graded, with small particles above the large. As well as generating shocks and expansion fans, the new asymmetric flux function generates semi-shocks, which have characteristics intersecting with the shock just from one side. In the absence of diffusive remixing, these can significantly enhance the distance over which complete segregation occurs.
Similar worldwide patterns in the sex pheromone signal and response in the oriental fruit moth, Grapholita molesta (Lepidoptera: Tortricidae)
Authors: Knight A.L. , Barros-Parada W. , Bosch D. , Escudero-Colomar L.A. , Fuentes-Contreras E. , Hernández-Sánchez J. , Yung C. , Kim Y. , Kovanci O.B. , Levi A. , Lo P. , Molinari F. , Valls J. , Gemeno C. 
Published: September 2014

AbstractThe response of Grapholita molesta (Busck) males to three-component sex pheromone blends containing a 100% ratio of the major sex pheromone component, (Z)-8-dodecenyl acetate and a 10% ratio of (Z)-8-dodecenol, but with varying ratios of (E)-8-dodecenyl acetate (0.4, 5.4, 10.4, 30.4, and 100.1% E-blends) was tested with populations in eight stone and pome fruit orchards in Europe, Asia, and North and South America. Traps baited with the 5.4% E-blend caught significantly more males than traps with any other blend with all populations. Significantly more males were caught in traps baited with the 10.4% E-blend than in traps with the remaining blends, except with the 0.4% E-blend in Turkey. Significant differences in male moth catches occurred between the other blends with the 0.4>30.4% E-blend, and the 30.4>100.1% E-blend. Male moth catches with the 100.1% E-blend only differed from the hexane control in Chile. No apparent differences were noted to these blends in populations collected from pome or stone fruits. Flight tunnel assays to synthetic blends with a subset of populations were similar to the field results, but the breadth of the most attractive E-blends was wider. Flight tunnel assays also demonstrated a high level of male–female cross-attraction among field-collected populations. Female gland extracts from field-collected populations did not show any significant variation in their three-component blends. The only exceptions in these assays were that long-term laboratory populations were less responsive and attractive, and produced different blend ratios of the two minor components than recently collected field populations.
Effect of changes in milking routine on milking related behaviour and milk removal in Tunisian dairy dromedary camels
Authors: Atigui Moufida , Marnet Pierre-Guy , Ayeb Naziha , Khorchani Touhami , Hammadi Mohamed 
Published: September 2014

We studied the effects of changes in the milking routine (lack or presence of 30-s prestimulation, 0 or 1, 2 or 4-min delay between preparation and cluster attachment) and environmental perturbation (unusual loud sounds capable of frightening animals just after stall entry or during the course of milking) on milk removal and milking-related behaviour in dairy dromedary camels. A 30-s prestimulation decreased incidence of bimodal milk flow curves and increased occurrence of the best milk ejection patterns with higher milk flow but had limited effect on milk production in our well-trained animals within a good machine milking setting. However, unusual sounds heard from the beginning of milking or even after milk ejection caused inhibition or disruption of milk removal and modification of camels’ behaviour. Milk ejection was significantly delayed (1·58±0·17 min), residual milk increased over 40% of total milk yield and average and peak milk flow rates were significantly lowered when unusual noises were heard from the beginning of milking. These environmental perturbations increased signs of vigilance and the number of attempts to escape the milking parlour. Delaying cluster attachment for over 1 min after the end of udder preparation caused serious milk losses. Up to 62% of total milk was withheld in the udder when the delay reached 4 min. Average and peak milk flow rates also decreased significantly with delayed milking. Signs of vigilance and attempts to escape from the milking parlour appeared when camels waited for over 2 min. After a 4-min delay, camels showed signs of acute stress. Defaecation prior to milk ejection (solid faeces) and rumination during milking can be used to assess camels’ milk ejection during milking. Animal welfare and milking efficiency can be ensured when camels are pre-stimulated, milked in calm conditions and with cluster attachment within a maximum of a 1-min delay after stimulation
The Euthyphro, Divine Command Theory and Moral Realism
Authors: Harrison Gerald K. 
Published: September 2014

AbstractDivine command theories of metaethics are commonly rejected on the basis of the Euthyphro problem. In this paper, I argue that the Euthyphro can be raised for all forms of moral realism. I go on to argue that this does not matter as the Euthyphro is not really a problem after all. I then briefly outline some of the attractions of a divine command theory of metaethics. I suggest that given one of the major reasons for rejecting such an analysis has been found to be unsound divine command theories deserve to be taken more seriously in contemporary metaethics.
Revisiting Styblo's law: could mathematical models aid in estimating incidence from prevalence data?
Authors: BEGUN M. , NEWALL A. T. , MARKS G. B. , WOOD J. G. 
Published: September 2014

SUMMARYEstimation of the true incidence of tuberculosis (TB) is challenging. The approach proposed by Styblo in 1985 is known to be inaccurate in the modern era where there is widespread availability of treatment for TB. This study re-examines the relationship of incidence to prevalence and other disease indicators that can be derived from surveys. We adapt a simple, previously published model that describes the epidemiology of TB in the presence of treatment to investigate a revised ratio-based approach to estimating incidence. We show that, following changes to treatment programmes for TB, the ratio of incidence to prevalence reaches an equilibrium value rapidly; long before other model indicators have stabilized. We also show that this ratio relies on few parameters but is strongly dependent on, and requires knowledge of, the efficacy and timeliness of treatment.
Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea
Authors: Salter Ian , Galand Pierre E , Fagervold Sonja K , Lebaron Philippe , Obernosterer Ingrid , Oliver Matthew J , Suzuki Marcelino T , Tricoire Cyrielle 
Published: September 2014

AbstractA seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time&lt;5 h). We propose a conceptual framework in which physical mixing of the water column periodically resets SAR11 communities to a high diversity state and the seasonal evolution of phosphate limitation competitively excludes deeper-dwelling ecotypes to promote low diversity states dominated (&gt;80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q2=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study.
Warped linear mixed models for the genetic analysis of transformed phenotypes
Authors: Fusi Nicolo , Lippert Christoph , Lawrence Neil D. , Stegle Oliver 
Published: September 2014

AbstractLinear mixed models (LMMs) are a powerful and established tool for studying genotype–phenotype relationships. A limitation of the LMM is that the model assumes Gaussian distributed residuals, a requirement that rarely holds in practice. Violations of this assumption can lead to false conclusions and loss in power. To mitigate this problem, it is common practice to pre-process the phenotypic values to make them as Gaussian as possible, for instance by applying logarithmic or other nonlinear transformations. Unfortunately, different phenotypes require different transformations, and choosing an appropriate transformation is challenging and subjective. Here we present an extension of the LMM that estimates an optimal transformation from the observed data. In simulations and applications to real data from human, mouse and yeast, we show that using transformations inferred by our model increases power in genome-wide association studies and increases the accuracy of heritability estimation and phenotype prediction.
Kainate receptor activation induces glycine receptor endocytosis through PKC deSUMOylation
Authors: Sun Hao , Lu Li , Zuo Yong , Wang Yan , Jiao Yingfu , Zeng Wei-Zheng , Huang Chao , Zhu Michael X. , Zamponi Gerald W. , Zhou Tong , Xu Tian-Le , Cheng Jinke , Li Yong 
Published: September 2014

AbstractSurface expression and regulated endocytosis of glycine receptors (GlyRs) play a critical function in balancing neuronal excitability. SUMOylation (SUMO modification) is of critical importance for maintaining neuronal function in the central nervous system. Here we show that activation of kainate receptors (KARs) causes GlyR endocytosis in a calcium- and protein kinase C (PKC)-dependent manner, leading to reduced GlyR-mediated synaptic activity in cultured spinal cord neurons and the superficial dorsal horn of rat spinal cord slices. This effect requires SUMO1/sentrin-specific peptidase 1 (SENP1)-mediated deSUMOylation of PKC, indicating that the crosstalk between KARs and GlyRs relies on the SUMOylation status of PKC. SENP1-mediated deSUMOylation of PKC is involved in the kainate-induced GlyR endocytosis and thus plays an important role in the anti-homeostatic regulation between excitatory and inhibitory ligand-gated ion channels. Altogether, we have identified a SUMOylation-dependent regulatory pathway for GlyR endocytosis, which may have important physiological implications for proper neuronal excitability.
Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes
Authors: Jones Siân , Stransky Nicolas , McCord Christine L. , Cerami Ethan , Lagowski James , Kelly Devon , Angiuoli Samuel V. , Sausen Mark , Kann Lisa , Shukla Manish , Makar Rosemary , Wood Laura D. , Diaz Luis A. , Lengauer Christoph , Velculescu Victor E. 
Published: September 2014

AbstractMalignant mixed Müllerian tumours, also known as carcinosarcomas, are rare tumours of gynaecological origin. Here we perform whole-exome analyses of 22 tumours using massively parallel sequencing to determine the mutational landscape of this tumour type. On average, we identify 43 mutations per tumour, excluding four cases with a mutator phenotype that harboured inactivating mutations in mismatch repair genes. In addition to mutations in TP53 and KRAS, we identify genetic alterations in chromatin remodelling genes, ARID1A and ARID1B, in histone methyltransferase MLL3, in histone deacetylase modifier SPOP and in chromatin assembly factor BAZ1A, in nearly two thirds of cases. Alterations in genes with potential clinical utility are observed in more than three quarters of the cases and included members of the PI3-kinase and homologous DNA repair pathways. These findings highlight the importance of the dysregulation of chromatin remodelling in carcinosarcoma tumorigenesis and suggest new avenues for personalized therapy.
An Efficient Genotyping Method for Genome-modified Animals and Human Cells Generated with CRISPR/Cas9 System
Authors: Zhu Xiaoxiao , Xu Yajie , Yu Shanshan , Lu Lu , Ding Mingqin , Cheng Jing , Song Guoxu , Gao Xing , Yao Liangming , Fan Dongdong , Meng Shu , Zhang Xuewen , Hu Shengdi , Tian Yong 
Published: September 2014

AbstractThe rapid generation of various species and strains of laboratory animals using CRISPR/Cas9 technology has dramatically accelerated the interrogation of gene function in vivo. So far, the dominant approach for genotyping of genome-modified animals has been the T7E1 endonuclease cleavage assay. Here, we present a polyacrylamide gel electrophoresis-based (PAGE) method to genotype mice harboring different types of indel mutations. We developed 6 strains of genome-modified mice using CRISPR/Cas9 system and utilized this approach to genotype mice from F0 to F2 generation, which included single and multiplexed genome-modified mice. We also determined the maximal detection sensitivity for detecting mosaic DNA using PAGE-based assay as 0.5%. We further applied PAGE-based genotyping approach to detect CRISPR/Cas9-mediated on- and off-target effect in human 293T and induced pluripotent stem cells (iPSCs). Thus, PAGE-based genotyping approach meets the rapidly increasing demand for genotyping of the fast-growing number of genome-modified animals and human cell lines created using CRISPR/Cas9 system or other nuclease systems such as TALEN or ZFN.
Pharmacologic rescue of an enzyme-trafficking defect in primary hyperoxaluria 1
Authors: Miyata Non , Steffen Janos , Johnson Meghan E. , Fargue Sonia , Danpure Christopher J. , Koehler Carla M. 
Published: September 2014

Significance
The lethal disorder, primary hyperoxaluria 1 (PH1), is caused by mutations in peroxisomal-localized alanine:glyoxylate aminotransferase (AGT). AGT contains a C-terminal peroxisomal targeting sequence, but mutations generate a strong N-terminal mitochondrial targeting sequence that directs AGT to mitochondria. Although mutant AGT is functional, the enzyme must be in the peroxisome to detoxify glyoxylate and prevent oxalate accumulation. We have identified a Food and Drug Administration-approved drug, dequalinium chloride (DECA), from a chemical genetic screen to identify probes that attenuate mitochondrial protein import. DECA treatment restores trafficking of mutant AGT from mitochondria to peroxisomes with a subsequent reduction in oxalate levels. Thus, repurposing DECA has potential in therapeutic strategies for PH1 because current clinical trials have not produced an effective treatment, short of organ transplant.
Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge
Authors: Rhrissorrakrai Kahn , Belcastro Vincenzo , Bilal Erhan , Norel Raquel , Poussin Carine , Mathis Carole , Dulize Rémi H. J. , Ivanov Nikolai V. , Alexopoulos Leonidas , Jeremy Rice J. , Peitsch Manuel C. , Stolovitzky Gustavo , Meyer Pablo , Hoeng Julia 
Published: September 2014

Motivation: Inferring how humans respond to external cues such as drugs, chemicals, viruses or hormones is an essential question in biomedicine. Very often, however, this question cannot be addressed because it is not possible to perform experiments in humans. A reasonable alternative consists of generating responses in animal models and ‘translating’ those results to humans. The limitations of such translation, however, are far from clear, and systematic assessments of its actual potential are urgently needed. sbv IMPROVER (systems biology verification for Industrial Methodology for PROcess VErification in Research) was designed as a series of challenges to address translatability between humans and rodents. This collaborative crowd-sourcing initiative invited scientists from around the world to apply their own computational methodologies on a multilayer systems biology dataset composed of phosphoproteomics, transcriptomics and cytokine data derived from normal human and rat bronchial epithelial cells exposed in parallel to 52 different stimuli under identical conditions. Our aim was to understand the limits of species-to-species translatability at different levels of biological organization: signaling, transcriptional and release of secreted factors (such as cytokines). Participating teams submitted 49 different solutions across the sub-challenges, two-thirds of which were statistically significantly better than random. Additionally, similar computational methods were found to range widely in their performance within the same challenge, and no single method emerged as a clear winner across all sub-challenges. Finally, computational methods were able to effectively translate some specific stimuli and biological processes in the lung epithelial system, such as DNA synthesis, cytoskeleton and extracellular matrix, translation, immune/inflammation and growth factor/proliferation pathways, better than the expected response similarity between species.Contact: pmeyerr@us.ibm.com or Julia.Hoeng@pmi.comSupplementary information: Supplementary Data are available at Bioinformatics online.
Environmental dependence of star formation induced by cloud collisions in a barred galaxy
Authors: Fujimoto Yusuke , Tasker Elizabeth J. , Habe Asao 
Published: September 2014

Abstract
Cloud collision has been proposed as a way to link the small-scale star formation process with the observed global relation between the surface star formation rate and gas surface density. We suggest that this model can be improved further by allowing the productivity of such collisions to depend on the relative velocity of the two clouds. Our adjustment implements a simple step function that results in the most successful collisions being at the observed velocities for triggered star formation. By applying this to a high-resolution simulation of a barred galaxy, we successfully reproduce the observational result that the star formation efficiency (SFE) in the bar is lower than that in the spiral arms. This is not possible when we use an efficiency dependent on the internal turbulence properties of the clouds. Our results suggest that high-velocity collisions driven by the gravitational pull of the clouds are responsible for the low bar SFE.