Routine full characterization of
is culture based, taking many weeks. Whole-genome sequencing (WGS) can generate antibiotic susceptibility profiles to inform treatment, augmented with strain ...information for global surveillance; such data could be transformative if provided at or near the point of care. We demonstrate a low-cost method of DNA extraction directly from patient samples for
WGS. We initially evaluated the method by using the Illumina MiSeq sequencer (40 smear-positive respiratory samples obtained after routine clinical testing and 27 matched liquid cultures).
was identified in all 39 samples from which DNA was successfully extracted. Sufficient data for antibiotic susceptibility prediction were obtained from 24 (62%) samples; all results were concordant with reference laboratory phenotypes. Phylogenetic placement was concordant between direct and cultured samples. With Illumina MiSeq/MiniSeq, the workflow from patient sample to results can be completed in 44/16 h at a reagent cost of £96/£198 per sample. We then employed a nonspecific PCR-based library preparation method for sequencing on an Oxford Nanopore Technologies MinION sequencer. We applied this to cultured
strain BCG DNA and to combined culture-negative sputum DNA and BCG DNA. For flow cell version R9.4, the estimated turnaround time from patient to identification of BCG, detection of pyrazinamide resistance, and phylogenetic placement was 7.5 h, with full susceptibility results 5 h later. Antibiotic susceptibility predictions were fully concordant. A critical advantage of MinION is the ability to continue sequencing until sufficient coverage is obtained, providing a potential solution to the problem of variable amounts of
DNA in direct samples.
A generic level of chromatin organization generated by the interplay between cohesin and CTCF suffices to limit promiscuous interactions between regulatory elements, but a lineage-specific chromatin ...assembly that supersedes these constraints is required to configure the genome to guide gene expression changes that drive faithful lineage progression. Loss-of-function approaches in B cell precursors show that IKAROS assembles interactions across megabase distances in preparation for lymphoid development. Interactions emanating from IKAROS-bound enhancers override CTCF-imposed boundaries to assemble lineage-specific regulatory units built on a backbone of smaller invariant topological domains. Gain of function in epithelial cells confirms IKAROS' ability to reconfigure chromatin architecture at multiple scales. Although the compaction of the Igκ locus required for genome editing represents a function of IKAROS unique to lymphocytes, the more general function to preconfigure the genome to support lineage-specific gene expression and suppress activation of extra-lineage genes provides a paradigm for lineage restriction.
We developed a low-cost and reliable method of DNA extraction from as little as 1 ml of early positive mycobacterial growth indicator tube (MGIT) cultures that is suitable for whole-genome sequencing ...to identify mycobacterial species and predict antibiotic resistance in clinical samples. The DNA extraction method is based on ethanol precipitation supplemented by pretreatment steps with a MolYsis kit or saline wash for the removal of human DNA and a final DNA cleanup step with solid-phase reversible immobilization beads. The protocol yielded ≥0.2 ng/μl of DNA for 90% (MolYsis kit) and 83% (saline wash) of positive MGIT cultures. A total of 144 (94%) of the 154 samples sequenced on the MiSeq platform (Illumina) achieved the target of 1 million reads, with <5% of reads derived from human or nasopharyngeal flora for 88% and 91% of samples, respectively. A total of 59 (98%) of 60 samples that were identified by the national mycobacterial reference laboratory (NMRL) as Mycobacterium tuberculosis were successfully mapped to the H37Rv reference, with >90% coverage achieved. The DNA extraction protocol, therefore, will facilitate fast and accurate identification of mycobacterial species and resistance using a range of bioinformatics tools.
We describe simple finite element schemes for approximating spatially extended predator–prey dynamics with the Holling type II functional response and logistic growth of the prey. The finite element ...schemes generalize ‘Scheme 1’ in the paper by Garvie (Bull Math Biol 69(3):931–956,
2007
). We present user-friendly, open-source
Matlab
code for implementing the finite element methods on arbitrary-shaped two-dimensional domains with Dirichlet, Neumann, Robin, mixed Robin–Neumann, mixed Dirichlet–Neumann, and Periodic boundary conditions. Users can download, edit, and run the codes from
http://www.uoguelph.ca/~mgarvie/
. In addition to discussing the well posedness of the model equations, the results of numerical experiments are presented and demonstrate the crucial role that habitat shape, initial data, and the boundary conditions play in determining the spatiotemporal dynamics of predator–prey interactions. As most previous works on this problem have focussed on square domains with standard boundary conditions, our paper makes a significant contribution to the area.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
We present a new fully spatially structured PDE metapopulation model for predator–prey dynamics in d≤3 space dimensions. A nonlinear reaction–diffusion system of Rosenzweig–MacArthur form models ...predator–prey dynamics in two ‘high’ quality patches embedded in a ‘low’ quality subdomain, where species can diffuse, convect and die. Our model substantially generalizes and improves earlier fully structured metapopulation models. After a nondimensionalization procedure, in order to approximate the metapopulation model we present a fully discrete Galerkin finite element method in two space dimensions, which is a generalization of the finite element method analyzed in a previous single patch predator–prey model. The numerical solutions are illustrated for some test cases using MATLAB. Numerical experiments demonstrate that the initial local extinction of predators in one patch leads to waves of recolonization from another patch. In an appendix we also give an outline for the proof of the well-posedness of the model.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
Studies of the chronic effects of MDMA, or ‘ecstasy’, in humans have been largely inconsistent. We explored whether study-level characteristics are associated with the effect size estimate reported. ...We based our analyses on the recent systematic review by Rogers and colleagues, focusing on those meta-analyses within this report where there was a relatively large number of studies contributing to each individual meta-analysis. Linear regression was used to investigate the association between study level variables and effect size estimate, weighted by the inverse of the SE of the effect size estimate, with cluster correction for studies which contributed multiple estimates. This indicated an association between effect size estimate and both user group, with smaller estimates among studies recruiting former users compared with those recruiting current users, and control group, with smaller estimates among studies recruiting polydrug user controls compared with those recruiting drug-naïve controls. In addition, increasing year of publication was associated with reduced effect size estimate, and there was a trend level association with prevalence of ecstasy use, reflecting smaller estimates among studies conducted in countries with higher prevalence of ecstasy use. Our data suggest a number of study-level characteristics which appear to influence individual study effect size estimates. These should be considered when designing future studies, and also when interpreting the ecstasy literature as a whole.
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NUK, OILJ, SAZU, UKNU, UL, UM, UPUK
Formalized participation in professional service is not often part of the college experience, especially for first-year students in chemistry courses. When service opportunities are offered, they are ...most often through elective credit, upper-level courses, extracurricular clubs, and the rare service-learning courses. We have successfully incorporated a large science service-learning opportunity into the general chemistry laboratory that provides multidisciplinary educational experiences for children and the community. The experience for the college students involves several weeks of preparation for a two-week laboratory module and participation in the public event on the university campus. College students involved in the second year of the event were surveyed to determine the impact of formalized participation in professional service on their attitude toward science and participation in future professional service events. Highly positive responses on the surveys and public interest in the event suggest continuing and expanding on the science offerings in our geographic location.
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IJS, KILJ, NUK, PNG, UL, UM
Access to healthcare delivery programs and systems is a primary correlate to the overall health and well-being of Veterans and the general population. Participation in clinical research is a gateway ...to novel therapies that are intended to address current global health issues. Meeting or exceeding recruitment goals in clinical research is one of the key determinants of the timely and successful completion of a study. The travel and time burdens experienced by study participants are often considered barriers to their enrollment into clinical research. The Department of Veterans Affairs (VA) Cooperative Studies Program (CSP) established a consortium of nine VA medical centers (VAMCs) called the Network of Dedicated Enrollment Sites (NODES). The NODES program provides study site-level expertise and innovative approaches that address challenges to clinical research execution. In alignment with our mission, our program developed an approach to increase study participant access to clinical research through implementing “Mobile Recruitment (MoRe)” units. This manuscript describes the utility and challenges associated with employing this strategy to address three common barriers to clinical research participation: 1) research participant travel burden, 2) participant access to study opportunities, and 3) low participant enrollment.
A plan to introduce the Mobile Recruitment (MoRe) unit as a recruitment strategy was piloted for a high-volume, observational cohort study and mega biobank in the VA health care system, the “Million Veteran Program (MVP)”. MoRe is a recruitment strategy for CSP research integrating mobile technology and atypical research recruitment locations. Recruitment locations include primary or main VA hospitals and their assigned VA Community-Based Outpatient Clinics (CBOCs). Each Node site (n = 9) received components of the MoRe unit including a laptop, printer, portable cart with storage space, cooler/ice packs for specimen storage and transport. Each site's usage of these components varied based on its respective needs. Activities focused on both VA main facilities and CBOC facilities for recruitment.
Seven of the nine Node sites compared the effectiveness of the MoRe unit on MVP study enrollment outcomes over three-time points: pre-intervention period, intervention period, and post-intervention period. The utilization of MoRe in the intervention period demonstrated a 36.9% increase in enrollment compared to the previous six months (pre-intervention period). There was a 2% enrollment increase at the six-month post-intervention period as compared to the intervention period. When comparing the pre-intervention period to the post-intervention period (duration of eighteen months), enrollment increased by 38.9%.
Five of the seven sites experienced an increase in enrollment during the intervention and post-intervention periods. The two sites without an increase in enrollment experienced various extenuating factors. Characteristics of sites using MoRe included the ability to utilize a smaller, unconventional space, i.e. not a traditional clinical research exam space for recruitment. MoRe was utilized in hospital laboratory space, CBOCs, primary care clinics, and other subspecialty clinics that allowed recruitment activities but did not have dedicated space to offer the research teams for that purpose. This initiative successfully demonstrated the benefit of deploying the unit, proving its utility in cases in where there was a lack of space or alternative workstations for research activities. The implementation of MoRe by NODES as a recruitment strategy for MVP may be transferable to other VA clinical research studies, as well as to other healthcare settings executing similar clinical research activities.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
Risk of suicidality during smoking cessation treatment is an important, but often overlooked, aspect of nicotine addiction research and treatment. We explore the relationship between smoking ...cessation interventions and suicidality and explore common treatments, their associated risks, and effectiveness in promoting smoking reduction and abstinence. Although active smokers have been reported to have twofold to threefold increased risk of suicidality when compared to nonsmokers,
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research regarding the safest way to stop smoking does not always provide clear guidelines for practitioners wishing to advise their patients regarding smoking cessation strategies. In this article, we review pharmacological and cognitive behavioral therapy (CBT) options that are available for people seeking to quit smoking, focusing on the relationship between the ability of these therapies to reduce smoking behavior and promote abstinence and suicidality risks as assessed by reported suicidality on validated measures, reports of suicidal ideation, behaviors, actual attempts, or completed suicides. Pharmacotherapies such as varenicline, bupropion, and nicotine replacement, and CBTs, including contextual CBT interventions, have been found to help reduce smoking rates and promote and maintain abstinence. Suicidality risks, while present when trying to quit smoking, do not appear to demonstrate a consistent or significant rise associated with use of any particular smoking cessation pharmacotherapy or CBT/contextual CBT intervention reviewed.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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