A standard variation file format for human genome sequences

Here we describe the Genome Variation Format (GVF) and the 10Gen dataset. GVF, an extension of Generic Feature Format version 3 (GFF3), is a simple tab-delimited format for DNA variant files, which uses Sequence Ontology to describe genome variation data. The 10Gen dataset, ten human genomes in GVF format, is freely available for community analysis from the Sequence Ontology website and from an Amazon elastic block storage (EBS) snapshot for use in Amazon's EC2 cloud computing environment

Recommendations for change in infection prevention programs and practice

Fifty years of evolution in infection prevention and control programs have involved significant accomplishments related to clinical practices, methodologies, and technology. However, regulatory mandates, and resource and research limitations, coupled with emerging infection threats such as the COVID-19 pandemic, present considerable challenges for infection preventionists. This article provides guidance and recommendations in 14 key areas. These interventions should be considered for implementation by United States health care facilities in the near future

Herschel observations of extra-ordinary sources: Detection of Hydrogen Fluoride in absorption towards Orion~KL

We report a detection of the fundamental rotational transition of hydrogen fluoride in absorption towards Orion KL using Herschel/HIFI. After the removal of contaminating features associated with common molecules ("weeds"), the HF spectrum shows a P-Cygni profile, with weak redshifted emission and strong blue-shifted absorption, associated with the low-velocity molecular outflow. We derive an estimate of 2.9 x 10^13 cm^-2 for the HF column density responsible for the broad absorption component. Using our best estimate of the H2 column density within the low-velocity molecular outflow, we obtain a lower limit of ~1.6 x 10^-10 for the HF abundance relative to hydrogen nuclei, corresponding to 0.6% of the solar abundance of fluorine. This value is close to that inferred from previous ISO observations of HF J=2--1 absorption towards Sgr B2, but is in sharp contrast to the lower limit of 6 x 10^-9 derived by Neufeld et al. (2010) for cold, foreground clouds on the line of sight towards G10.6-0.4.Comment: 5 pages, 3 figures, paper to be published in the Herschel special issue of A&A letter

EGASP: the human ENCODE Genome Annotation Assessment Project

Background: Non-long terminal repeat (non-LTR) retrotransposons have contributed to shaping the structure and function of genomes. In silico and experimental approaches have been used to identify the non-LTR elements of the urochordate Ciona intestinalis. Knowledge of the types and abundance of non-LTR elements in urochordates is a key step in understanding their contribution to the structure and function of vertebrate genomes. Results: Consensus elements phylogenetically related to the I, LINE1, LINE2, LOA and R2 elements of the 14 eukaryotic non-LTR clades are described from C. intestinalis. The ascidian elements showed conservation of both the reverse transcriptase coding sequence and the overall structural organization seen in each clade. The apurinic/apyrimidinic endonuclease and nucleic-acid-binding domains encoded upstream of the reverse transcriptase, and the RNase H and the restriction enzyme-like endonuclease motifs encoded downstream of the reverse transcriptase were identified in the corresponding Ciona families. Conclusions: The genome of C. intestinalis harbors representatives of at least five clades of non-LTR retrotransposons. The copy number per haploid genome of each element is low, less than 100, far below the values reported for vertebrate counterparts but within the range for protostomes. Genomic and sequence analysis shows that the ascidian non-LTR elements are unmethylated and flanked by genomic segments with a gene density lower than average for the genome. The analysis provides valuable data for understanding the evolution of early chordate genomes and enlarges the view on the distribution of the non-LTR retrotransposons in eukaryotes

Frequency and properties of bars in cluster and field galaxies at intermediate redshifts

We present a study of large-scale bars in field and cluster environments out to redshifts of ~0.8 using a final sample of 945 moderately inclined disk galaxies drawn from the EDisCS project. We characterize bars and their host galaxies and look for relations between the presence of a bar and the properties of the underlying disk. We investigate whether the fraction and properties of bars in clusters are different from their counterparts in the field. The total optical bar fraction in the redshift range z=0.4-0.8 (median z=0.60), averaged over the entire sample, is 25% (20% for strong bars). For the cluster and field subsamples, we measure bar fractions of 24% and 29%, respectively. We find that bars in clusters are on average longer than in the field and preferentially found close to the cluster center, where the bar fraction is somewhat higher (~31%) than at larger distances (~18%). These findings however rely on a relatively small subsample and might be affected by small number statistics. In agreement with local studies, we find that disk-dominated galaxies have a higher optical bar fraction (~45%) than bulge-dominated galaxies (~15%). This result is based on Hubble types and effective radii and does not change with redshift. The latter finding implies that bar formation or dissolution is strongly connected to the emergence of the morphological structure of a disk and is typically accompanied by a transition in the Hubble type. (abridged)Comment: 17 pages, accepted for publication in A&

Environmental Factors in the Relapse and Recurrence of Inflammatory Bowel Disease:A Review of the Literature

The causes of relapse in patients with Crohn's disease (CD) and ulcerative colitis (UC) are largely unknown. This paper reviews the epidemiological and clinical data on how medications (non-steroidal anti-inflammatory drugs, estrogens and antibiotics), lifestyle factors (smoking, psychological stress, diet and air pollution) may precipitate clinical relapses and recurrence. Potential biological mechanisms include: increasing thrombotic tendency, imbalances in prostaglandin synthesis, alterations in the composition of gut microbiota, and mucosal damage causing increased permeability

Elasticity and Petri nets

Digital electronic systems typically use synchronous clocks and primarily assume fixed duration of their operations to simplify the design process. Time elastic systems can be constructed either by replacing the clock with communication handshakes (asynchronous version) or by augmenting the clock with a synchronous version of a handshake (synchronous version). Time elastic systems can tolerate static and dynamic changes in delays (asynchronous case) or latencies (synchronous case) of operations that can be used for modularity, ease of reuse and better power-delay trade-off. This paper describes methods for the modeling, performance analysis and optimization of elastic systems using Marked Graphs and their extensions capable of describing behavior with early evaluation. The paper uses synchronous elastic systems (aka latency-tolerant systems) for illustrating the use of Petri nets, however, most of the methods can be applied without changes (except changing the delay model associated with events of the system) to asynchronous elastic systems.Peer ReviewedPostprint (author's final draft

Observational rotation curves and density profiles versus the Thomas-Fermi galaxy structure theory

The Thomas-Fermi approach to galaxy structure determines self-consistently the gravitational potential of the fermionic warm dark matter (WDM) given its distribution function f(E). This framework is appropriate for macroscopic quantum systems as neutron stars, white dwarfs and WDM galaxies. Compact dwarf galaxies are near the quantum degenerate regime, while large galaxies are in the classical Boltzmann regime. We derive analytic scaling relations for the main galaxy magnitudes: halo radius rh, mass Mh and phase-space density. Small deviations from the exact scaling show up for compact dwarfs due to quantum macroscopic effects. We contrast the theoretical curves for the circular galaxy velocities vc(r) and density profiles \u3c1(r) with those obtained from observations using the empirical Burkert profile. Results are independent of any WDM particle physics model, they only follow from the gravitational interaction of the WDM particles and their fermionic nature. The theoretical rotation curves and density profiles reproduce very well the observational curves for r 72 rh obtained from 10 different and independent sets of data for galaxy masses from 5 7 109 to 5 7 1011M 99. Our normalized theoretical circular velocities and normalized density profiles turn to be universal functions of r/rh for all galaxies. In addition, they agree extremely well with the observational curves described by the Burkert profile for r 72 2 rh. These results showthat the Thomas-Fermi approach correctly describes the galaxy structures

Toward an internally consistent astronomical distance scale

Accurate astronomical distance determination is crucial for all fields in astrophysics, from Galactic to cosmological scales. Despite, or perhaps because of, significant efforts to determine accurate distances, using a wide range of methods, tracers, and techniques, an internally consistent astronomical distance framework has not yet been established. We review current efforts to homogenize the Local Group's distance framework, with particular emphasis on the potential of RR Lyrae stars as distance indicators, and attempt to extend this in an internally consistent manner to cosmological distances. Calibration based on Type Ia supernovae and distance determinations based on gravitational lensing represent particularly promising approaches. We provide a positive outlook to improvements to the status quo expected from future surveys, missions, and facilities. Astronomical distance determination has clearly reached maturity and near-consistency.Comment: Review article, 59 pages (4 figures); Space Science Reviews, in press (chapter 8 of a special collection resulting from the May 2016 ISSI-BJ workshop on Astronomical Distance Determination in the Space Age