Quasiperiodic Dynamics in Bose-Einstein Condensates in Periodic Lattices and Superlattices

We employ KAM theory to rigorously investigate quasiperiodic dynamics in cigar-shaped Bose-Einstein condensates (BEC) in periodic lattices and superlattices. Toward this end, we apply a coherent structure ansatz to the Gross-Pitaevskii equation to obtain a parametrically forced Duffing equation describing the spatial dynamics of the condensate. For shallow-well, intermediate-well, and deep-well potentials, we find KAM tori and Aubry-Mather sets to prove that one obtains mostly quasiperiodic dynamics for condensate wave functions of sufficiently large amplitude, where the minimal amplitude depends on the experimentally adjustable BEC parameters. We show that this threshold scales with the square root of the inverse of the two-body scattering length, whereas the rotation number of tori above this threshold is proportional to the amplitude. As a consequence, one obtains the same dynamical picture for lattices of all depths, as an increase in depth essentially only affects scaling in phase space. Our approach is applicable to periodic superlattices with an arbitrary number of rationally dependent wave numbers.Comment: 29 pages, 6 figures (several with multiple parts; higher-quality versions of some of them available at http://www.its.caltech.edu/~mason/papers), to appear very soon in Journal of Nonlinear Scienc

Orthology prediction at scalable resolution by phylogenetic tree analysis

BACKGROUND: Orthology is one of the cornerstones of gene function prediction. Dividing the phylogenetic relations between genes into either orthologs or paralogs is however an oversimplification. Already in two-species gene-phylogenies, the complicated, non-transitive nature of phylogenetic relations results in inparalogs and outparalogs. For situations with more than two species we lack semantics to specifically describe the phylogenetic relations, let alone to exploit them. Published procedures to extract orthologous groups from phylogenetic trees do not allow identification of orthology at various levels of resolution, nor do they document the relations between the orthologous groups. RESULTS: We introduce "levels of orthology" to describe the multi-level nature of gene relations. This is implemented in a program LOFT (Levels of Orthology From Trees) that assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable. CONCLUSION: The "levels of orthology" concept offers high resolution, reliable orthology, while preserving the relations between orthologous groups. A Windows as well as a preliminary Java version of LOFT is available from the LOFT website

Could 3D food printing help to improve the food supply chain resilience against disruptions such as caused by pandemic crises

SummaryThe ongoing COVID‐19 pandemic is having a tremendous effect on the current food system. The situation urges us to face many issues never experienced before, aimed at mitigating a multitude of sanitary and social risks. The current pandemic has affected the food system in many ways: significant changes in dietary habits and in the health status of people; the food chain is broken, which has an effect on food security (including making it difficult to find or to buy fresh food at affordable prices); unemployment or underemployment is rising due to the damages of the food sector; there is a lack of food‐socialising events which has an effect on people's mental status; and there are concerns about food safety. To mitigate all these issues, the implementation of innovative technologies urges. We have mapped the scientific studies and online information on 3D food printing (3DFP) about the effects of 3DFP on the food system and people's health when adopted in food industry, restaurants, hospitals, schools, offices, homes, etc. Finally, this information has been examined in light to the future challenges of the food chain also considering the ongoing COVID‐19 pandemic, demonstrating its potential benefits to mitigate this and future pandemics

Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence

Contains fulltext : 129351.pdf (publisher's version ) (Open Access)Background Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. Methodology/Principal Findings We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. Conclusions/Significance Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo

Dose–Exposure–Response Analysis of the Nonsteroidal Mineralocorticoid Receptor Antagonist Finerenone on UACR and eGFR:An Analysis from FIDELIO-DKD

Background and Objective: Finerenone reduces the risk of kidney failure in patients with chronic kidney disease and type 2 diabetes. Changes in the urine albumin-to-creatinine ratio (UACR) and estimated glomerular filtration rate (eGFR) are surrogates for kidney failure. We performed dose–exposure–response analyses to determine the effects of finerenone on these surrogates in the presence and absence of sodium glucose co-transporter-2 inhibitors (SGLT2is) using individual patient data from the FIDELIO-DKD study. Methods: Non-linear mixed-effects population pharmacokinetic/pharmacodynamic models were used to quantify disease progression in terms of UACR and eGFR during standard of care and pharmacodynamic effects of finerenone in the presence and absence of SGLT2i use. Results: The population pharmacokinetic/pharmacodynamic models adequately described effects of finerenone exposure in reducing UACR and slowing eGFR decline over time. The reduction in UACR achieved with finerenone during the first year predicted its subsequent effect in slowing progressive eGFR decline. SGLT2i use did not modify the effects of finerenone. The population pharmacokinetic/pharmacodynamic model demonstrated with 97.5% confidence that finerenone was at least 94.1% as efficacious in reducing UACR in patients using an SGLT2i compared with patients not using an SGLT2i based on the 95% confidence interval of the SGLT2i-finerenone interaction from 94.1 to 122%. The 95% confidence interval of the SGLT2i-finerenone interaction for the UACR-mediated effect on chronic eGFR decline was 9.5–144%. Conclusions: We developed a model that accurately describes the finerenone dose–exposure–response relationship for UACR and eGFR. The model demonstrated that the early UACR effect of finerenone predicted its long-term effect on eGFR decline. These effects were independent of concomitant SGLT2i use

Current and future trends in VRU accidents in Europe - why we need ITS solutions

Vulnerable Road Users (VRUs) is a collective term used to describe cyclists, motorcyclists, moped riders and pedestrians. This paper describes work undertaken within the EC’s VRUITS project which focuses on reducing VRU accidents through the use of ITS solutions. The paper determines the current accident numbers within Europe for VRUs between the years 2002 and 2012 using the CARE database. Accident forecasting is then applied to predict future accident numbers if current trends continue and no successful countermeasures including ITS solutions are introduced into the Road Transport System. This shows the number of VRU fatalities in 2030 to be almost comparable to those of car accidents since car fatality rates are reducing at a far increased proportion compared to VRUs. The results of the study emphasise why the introduction of effective ITS solutions are necessary to improve the overall safety of VRUs

A headway to improve PTW rider safety within the EU through three types of ITS

Introduction: The current safety situation for Powered Two Wheelers (PTW) within the EU is alarming. According to EU statistics, PTW riders account for 17% of all fatal road injuries in the region and twice as many fatalities per hundred thousand registered vehicles compared with occupants of cars. In recent years, too little attention has been given to Vulnerable Road Users (VRUs), including PTW users, in the development of Intelligent Transport Systems (ITS). Therefore, ITS should be developed that consider PTW riders an integral part of traffic; we focus on three systems that we believe have the potential to improve safety among PTW riders, namely Intersection Safety (INS), the Powered Two Wheeler oncoming vehicle information system (PTW2V), and the Vulnerable road user Beacon System (VBS). The present study aims to estimate quantitatively the safety impacts of the selected ITS for PTW riders in the EU-28, once the systems are fully adopted and meet selected future scenarios for 2020 and 2030. Method: An ex-ante method suggested by Kulmala [1] was further developed and applied to assess the safety impacts of ITS specifically designed for VRUs. As suggested by the method, the analysis started by determining the impact mechanisms through which the selected ITS systems affect the safety of PTW riders. Results: According to the main results, all the systems we studied have a positive impact on PTW rider safety by preventing fatalities and injuries. The greatest effects, based on 2012 accident data and full penetration, could be attained by implementing PTW2V (283 fewer yearly fatalities) and INS (261 fewer yearly fatalities). The weakest effect was found with VBS (216 fewer yearly fatalities). Forecasts for 2030, also based on estimated accident trends and penetration rates, confirm an expected edge for INS and PTW2V in terms of safety

Are intelligent transport systems effective in improving the safety of vulnerable road users?

This paper presents the results of safety impact assessment, providing quantitative estimates of the safety impacts of ten ITS which were designed to improve safety, mobility and comfort of VRUs. The evaluation method originally developed to assess safety impacts of ITS for cars was now adapted for assessing safety impacts of ITS for VRUs. The main results of the assessment showed that nine services included in the quantitative safety impact assessment affected traffic safety in a positive way by preventing fatalities and injuries. At full penetration the highest effects were obtained for the systems PCDS+EBR, VBS and INS. The estimates for PCDS+EBR showed the maximum reduction of 7.5% on all road fatalities and 5.8% on all road injuries, which came down to an estimate of over 2,100 fatalities and over 62,900 injuries saved per year in the EU-28 when exploiting the 2012 accident levels adjusted with the estimated accident trends