Localization Transition in Incommensurate non-Hermitian Systems

A class of one-dimensional lattice models with incommensurate complex potential $V(\theta)=2[\lambda_r cos(\theta)+i \lambda_i sin(\theta)]$ is found to exhibit localization transition at $|\lambda_r|+|\lambda_i|=1$. This transition from extended to localized states manifests in the behavior of the complex eigenspectum. In the extended phase, states with real eigenenergies have finite measure and this measure goes to zero in the localized phase. Furthermore, all extended states exhibit real spectrum provided $|\lambda_r| \ge |\lambda_i|$. Another novel feature of the system is the fact that the imaginary part of the spectrum is sensitive to the boundary conditions {\it only at the onset to localization}

webGQT: A Shiny Server for Genotype Query Tools for Model-Based Variant Filtering

Genotype Query Tools (GQT) were developed to discover disease-causing variations from billions of genotypes and millions of genomes, processes data at substantially higher speed over other existing methods. While GQT has been available to a wide audience as command-line software, the difficulty of constructing queries among non-IT or non-bioinformatics researchers has limited its applicability. To overcome this limitation, we developed webGQT, an easy-to-use tool with a graphical user interface. With pre-built queries across three modules, webGQT allows for pedigree analysis, case-control studies, and population frequency studies. As a package, webGQT allows researchers with less or no applied bioinformatics/IT experience to mine potential disease-causing variants from billions. Results webGQT offers a flexible and easy-to-use interface for model-based candidate variant filtering for Mendelian diseases from thousands to millions of genomes at a reduced computation time. Additionally, webGQT provides adjustable parameters to reduce false positives and rescue missing genotypes across all modules. Using a case study, we demonstrate the applicability of webGQT to query non-human genomes. In addition, we demonstrate the scalability of webGQT on large data sets by implementing complex population-specific queries on the 1000 Genomes Project Phase 3 data set, which includes 8.4 billion variants from 2504 individuals across 26 different populations. Furthermore, webGQT supports filtering single-nucleotide variants, short insertions/deletions, copy number or any other variant genotypes supported by the VCF specification. Our results show that webGQT can be used as an online web service, or deployed on personal computers or local servers within research groups. Availability webGQT is made available to the users in three forms: 1) as a webserver available at https://vm1138.kaj.pouta.csc.fi/webgqt/, 2) as an R package to install on personal computers, and 3) as part of the same R package to configure on the user's own servers. The application is available for installation at https://github.com/arumds/webgqt.Peer reviewe

Transport and retention of artificial and real wastewater particles inside a bed of settled aerobic granular sludge assessed applying magnetic resonance imaging

The removal or degradation of particulate organic matter is a crucial part in biological wastewater treatment. This is even more valid with respect to aerobic granular sludge and the impact of particulate organic matter on the formation and stability of the entire granulation process. Before the organic part of the particulate matter can be hydrolyzed and finally degraded by the microorganism, the particles have to be transported towards and retained within the granulated biomass. The understanding of these processes is currently very limited. Thus, the present study aimed at visualizing the transport of particulate organic matter into and through an aerobic granular sludge bed. Magnetic Resonance Imaging (MRI) was successfully applied to resolve the different fractions of a granular sludge bed over time and space. Quantification and merging of 3D data sets allowed for a clear determination of the particle distribution within the granular sludge bed. Dextran coated super paramagnetic iron oxide nanoparticles (SPIONs

Pancreatic Exocrine Insufficiency as a Complication of Gastrointestinal Surgery and the Impact of Pancreatic Enzyme Replacement Therapy

BACKGROUND: Pancreatic exocrine insufficiency (PEI) is characterized by inadequate production, insufficient secretion, and/or inactivation of pancreatic enzymes, resulting in maldigestion. The aim of this review was to analyze the prevalence and pathophysiology of PEI resulting from gastrointestinal (GI) surgery and to examine the use of pancreatic enzyme replacement therapy (PERT) for effectively managing PEI. SUMMARY: A targeted PubMed search was conducted for studies examining the prevalence and pathophysiology of PEI in patients following GI surgery and for studies assessing the effects of PERT in these patients. PEI is a common complication following GI surgery that can lead to nutritional deficiencies, which may contribute to morbidity and mortality in patients. Timely treatment of PEI with PERT can prevent malnutrition, increase quality of life, and possibly reduce the associated mortality. Treatment of PEI should aim not only to alleviate symptoms but also to achieve significant improvements in nutritional parameters. Dose optimization of PERT is required for effective management of PEI, in addition to regular assessment of nutritional status, appropriate patient education, and reassessment if symptoms return. Key Messages: Difficulties in detecting PEI following GI surgery can result in undiagnosed and untreated maldigestion, leading to metabolic complications and increased morbidity. Both are preventable by early administration and monitoring for optimal doses of PERT

Higher education, mature students and employment goals: policies and practices in the UK

This article considers recent policies of Higher Education in the UK, which are aimed at widening participation and meeting the needs of employers. The focus is on the growing population of part-time students, and the implications of policies for this group. The article takes a critical perspective on government policies, using data from a major study of mature part-time students, conducted in two specialist institutions in the UK, a London University college and a distance learning university. Findings from this study throw doubt on the feasibility of determining a priori what kind of study pathway is most conducive for the individual in terms of employment gains and opportunities for upward social mobility. In conclusion, doubts are raised as to whether policies such as those of the present UK government are likely to achieve its aims. Such policies are not unique to the UK, and lessons from this country are relevant to most of the developed world

Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections

Motivation: The comparison of diverse genomic datasets is fundamental to understanding genome biology. Researchers must explore many large datasets of genome intervals (e.g., genes, sequence alignments) to place their experimental results in a broader context and to make new discoveries. Relationships between genomic datasets are typically measured by identifying intervals that intersect: that is, they overlap and thus share a common genome interval. Given the continued advances in DNA sequencing technologies, efficient methods for measuring statistically significant relationships between many sets of genomic features is crucial for future discovery. Results: We introduce the Binary Interval Search (BITS) algorithm, a novel and scalable approach to interval set intersection. We demonstrate that BITS outperforms existing methods at counting interval intersections. Moreover, we show that BITS is intrinsically suited to parallel computing architectures such as Graphics Processing Units (GPUs) by illustrating its utility for efficient Monte-Carlo simulations measuring the significance of relationships between sets of genomic intervals