Are Nurse Residents Ready for Evidence-Based Practice?

A nursing professional development practitioner and clinical nurse specialists developed a curriculum, including supportive materials to complete evidence-based practice projects, as part of a new nurse residency program. Residents were guided through the evidence-based practice process. Challenges uncovered during the implementation phase suggested a need to reevaluate resident readiness.

Supercontinuum generation in a graded-index multimode tellurite fiber.

We report the generation of a broadband supercontinuum (SC) from 790 to 2900 nm in a tellurite graded-index (GRIN) multimode fiber with a nanostructured core. We study the SC dynamics in different dispersion regimes and observe near-single-mode spatial intensity distribution at high input energy values. Numerical simulations of the (3 + 1)D generalized nonlinear Schrödinger equation are in good agreement with our experiments.

Space-efficient computation of k-mer dictionaries for large values of k.

Computing k-mer frequencies in a collection of reads is a common procedure in many genomic applications. Several state-of-the-art k-mer counters rely on hash tables to carry out this task but they are often optimised for small k as a hash table keeping keys explicitly (i.e.

SAKE: Strobemer-assisted k-mer extraction.

K-mer-based analysis plays an important role in many bioinformatics applications, such as de novo assembly, sequencing error correction, and genotyping. To take full advantage of such methods, the k-mer content of a read set must be captured as accurately as possible. Often the use of long k-mers is preferred because they can be uniquely associated with a specific genomic region.

Tailored supercontinuum generation using genetic algorithm optimized Fourier domain pulse shaping.

We report the generation of a spectrally tailored supercontinuum using Fourier-domain pulse shaping of femtosecond pulses injected into a highly nonlinear fiber controlled by a genetic algorithm. User-selectable spectral enhancement is demonstrated over the 1550-2000-nm wavelength range, with the ability to both select a channel with target central wavelength and bandwidth in the range of 1-5 nm. The spectral enhancement factor relative to unshaped input pulses is typically ∼5-20 in the range 1550-1800 nm and increases for longer wavelengths, exceeding a factor of 160 around 2000 nm.

Chaining for accurate alignment of erroneous long reads to acyclic variation graphs.

Motivation: Aligning reads to a variation graph is a standard task in pangenomics, with downstream applications such as improving variant calling. While the vg toolkit [Garrison et al. (Variation graph toolkit improves read mapping by representing genetic variation in the reference.

ViQUF: De Novo Viral Quasispecies Reconstruction Using Unitig-Based Flow Networks.

During viral infection, intrahost mutation and recombination can lead to significant evolution, resulting in a population of viruses that harbor multiple haplotypes. The task of reconstructing these haplotypes from short-read sequencing data is called viral quasispecies assembly, and it can be categorized as a multiassembly problem. We consider the de novo version of the problem, where no reference is available.

HGGA: hierarchical guided genome assembler.

Background: De novo genome assembly typically produces a set of contigs instead of the complete genome. Thus additional data such as genetic linkage maps, optical maps, or Hi-C data is needed to resolve the complete structure of the genome. Most of the previous work uses the additional data to order and orient contigs.

Machine learning analysis of instabilities in noise-like pulse lasers.

Neural networks have been recently shown to be highly effective in predicting time-domain properties of optical fiber instabilities based only on analyzing spectral intensity profiles. Specifically, from only spectral intensity data, a suitably trained neural network can predict temporal soliton characteristics in supercontinuum generation, as well as the presence of temporal peaks in modulation instability satisfying rogue wave criteria. Here, we extend these previous studies of machine learning prediction for single-pass fiber propagation instabilities to the more complex case of noise-like pulse dynamics in a dissipative soliton laser.

Two octave supercontinuum generation in a non-silica graded-index multimode fiber.

The generation of a two-octave supercontinuum from the visible to mid-infrared (700-2800 nm) in a non-silica graded-index multimode fiber is reported. The fiber design is based on a nanostructured core comprised of two types of drawn lead-bismuth-gallate glass rods with different refractive indices. This yields an effective parabolic index profile and ten times increased nonlinearity when compared to silica fibers.

Feed-forward neural network as nonlinear dynamics integrator for supercontinuum generation: erratum.

We present an erratum to our Letter [Opt. Lett.47, 802 (2022)10.

Feed-forward neural network as nonlinear dynamics integrator for supercontinuum generation.

The nonlinear propagation of ultrashort pulses in optical fibers depends sensitively on the input pulse and fiber parameters. As a result, the optimization of propagation for specific applications generally requires time-consuming simulations based on the sequential integration of the generalized nonlinear Schrödinger equation (GNLSE). Here, we train a feed-forward neural network to learn the differential propagation dynamics of the GNLSE, allowing emulation of direct numerical integration of fiber propagation, and particularly the highly complex case of supercontinuum generation.

Extraction of long k-mers using spaced seeds.

The extraction of k-mers from reads is an important task in many bioinformatics applications, such as all DNA sequence analysis methods based on de Bruijn graphs. These methods tend to be more accurate when the used k-mers are unique in the analyzed DNA, and thus the use of longer k-mers is preferred. When the read lengths of short read sequencing technologies increase, the error rate will become the determining factor for the largest possible value of k.

Innovative Utilization of Wright's Model for Competency Validation.

Wright's competency assessment model is well known, yet implementation has been largely challenging. Some organizations have attempted enterprise-wide implementation. This article summarizes how Wright's model was used from a specific topic perspective.

Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data.

A key problem in processing raw optical mapping data (Rmaps) is finding Rmaps originating from the same genomic region. These sets of related Rmaps can be used to correct errors in Rmap data, and to find overlaps between Rmaps to assemble consensus optical maps. Previous Rmap overlap aligners are computationally very expensive and do not scale to large eukaryotic data sets.

Fast and efficient Rmap assembly using the Bi-labelled de Bruijn graph.

Genome wide optical maps are high resolution restriction maps that give a unique numeric representation to a genome. They are produced by assembling hundreds of thousands of single molecule optical maps, which are called Rmaps. Unfortunately, there are very few choices for assembling Rmap data.

Algorithms meet sequencing technologies - 10th edition of the RECOMB-Seq workshop.

DNA and RNA sequencing is a core technology in biological and medical research. The high throughput of these technologies and the consistent development of new experimental assays and biotechnologies demand the continuous development of methods to analyze the resulting data. The RECOMB Satellite Workshop on Massively Parallel Sequencing brings together leading researchers in computational genomics to discuss emerging frontiers in algorithm development for massively parallel sequencing data.

Implementation of a "Serenity Room": Promoting resiliency in the ED.

Work-related stress is common within the nursing profession, especially in the ED. Studies have shown that interventions to improve hospital working environments positively impact retention and help prevent burnout. This nursing practice innovation project describes the development, implementation, and evaluation of a restorative space (the "Serenity Room") in a busy regional ED.

Inference of viral quasispecies with a paired de Bruijn graph.

Motivation: RNA viruses exhibit a high mutation rate and thus they exist in infected cells as a population of closely related strains called viral quasispecies. The viral quasispecies assembly problem asks to characterize the quasispecies present in a sample from high-throughput sequencing data. We study the de novo version of the problem, where reference sequences of the quasispecies are not available.

Optical map guided genome assembly.

Background: The long reads produced by third generation sequencing technologies have significantly boosted the results of genome assembly but still, genome-wide assemblies solely based on read data cannot be produced. Thus, for example, optical mapping data has been used to further improve genome assemblies but it has mostly been applied in a post-processing stage after contig assembly.

Results: We propose OPTICALKERMIT which directly integrates genome wide optical maps into contig assembly.

Machine learning analysis of rogue solitons in supercontinuum generation.

Supercontinuum generation is a highly nonlinear process that exhibits unstable and chaotic characteristics when developing from long pump pulses injected into the anomalous dispersion regime of an optical fiber. A particular feature associated with this regime is the long-tailed "rogue wave"-like statistics of the spectral intensity on the long-wavelength edge of the supercontinuum, linked to the generation of a small number of "rogue solitons" with extreme red-shifts. Whilst the statistical properties of rogue solitons can be conveniently measured in the spectral domain using the real-time dispersive Fourier transform technique, we cannot use this technique to determine any corresponding temporal properties since it only records the spectral intensity and one loses information about the spectral phase.

Low-noise octave-spanning mid-infrared supercontinuum generation in a multimode chalcogenide fiber.

We demonstrate the generation of a low-noise, octave-spanning mid-infrared supercontinuum from 1700 to 4800 nm by injecting femtosecond pulses into the normal dispersion regime of a multimode step-index chalcogenide fiber with 100 µm core diameter. We conduct a systematic study of the intensity noise across the supercontinuum spectrum and show that the initial fluctuations of the pump laser are at most amplified by a factor of three. We also perform a comparison with the noise characteristics of an octave-spanning supercontinuum generated in the anomalous dispersion regime of a multimode fluoride fiber with similar core size and show that the normal dispersion supercontinuum in the multimode chalcogenide fiber has superior noise characteristics.

Succinct dynamic de Bruijn graphs.

Motivation: The de Bruijn graph is one of the fundamental data structures for analysis of high throughput sequencing data. In order to be applicable to population-scale studies, it is essential to build and store the graph in a space- and time-efficient manner. In addition, due to the ever-changing nature of population studies, it has become essential to update the graph after construction, e.

Fast and accurate correction of optical mapping data via spaced seeds.

Motivation: Optical mapping data is used in many core genomics applications, including structural variation detection, scaffolding assembled contigs and mis-assembly detection. However, the pervasiveness of spurious and deleted cut sites in the raw data, which are called Rmaps, make assembly and alignment of them challenging. Although there exists another method to error correct Rmap data, named cOMet, it is unable to scale to even moderately large sized genomes.