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Deoxyribonuclease I (DNase I)-hypersensitive site sequencing (DNase-seq) has been widely used to determine chromatin accessibility and its underlying regulatory lexicon. However, exploring DNase-seq data requires sophisticated downstream bioinformatics analyses. In this study, we first review computational methods for all of the major steps in DNase-seq data analysis, including experimental design, quality control, read alignment, peak calling, annotation of cis-regulatory elements, genomic footprinting and...
Existing retrosynthesis tools generally traverse production routes from a source to a sink metabolite using known enzymes or de novo steps. Generally, important considerations such as blending known transformations with putative steps, complexity of pathway topology, mass conservation, cofactor balance, thermodynamic feasibility, microbial chassis selection, and cost are largely dealt with in a posteriori fashion. The computational procedure we present here designs bioconversion routes while simultaneously ...
[This corrects the article DOI: 10.1371/journal.pone.0183342.].
Chromosomal instability and associated chromosomal aberrations are hallmarks of cancer and play a critical role in disease progression and development of resistance to drugs. Single-cell genome analysis has gained interest in latest years as a source of biomarkers for targeted-therapy selection and drug resistance, and several methods have been developed to amplify the genomic DNA and to produce libraries suitable for Whole Genome Sequencing (WGS). However, most protocols require several enzymatic and clean...
Walk ratio, defined as step length divided by cadence, indicates the coordination of gait. During free walking, deviation from the preferential walk ratio may reveal abnormalities of walking patterns. The purpose of this study was to examine the impact of rhythmic auditory cueing (metronome) on the neuromotor control of gait at different walking speeds. Forty adults (mean age 26.6 ± 6.0 years) participated in the study. Gait characteristics were collected using a computerized walkway. In the preferred wal...
Avian monitoring strategies are usually linked to bird singing or calling behavior. Individual availability for detection can change as a result of conspecific factors affecting bird behavior, though the magnitude of these effects is difficult to quantify. We evaluated behavioral and temporal factors affecting Northern Bobwhite (Colinus virginianus) breeding season individual availability for detection during three common survey times (3 min, 5 min, 10 min). We conducted 10-minute surveys associated with ra...
The purpose of this study was to assess the accuracy of energy expenditure (EE) estimation and step tracking abilities of six activity monitors (AMs) in relation to indirect calorimetry and hand counted steps and assess the accuracy of the AMs between high and low fit individuals in order to assess the impact of exercise intensity. Fifty participants wore the Basis watch, Fitbit Flex, Polar FT7, Jawbone, Omron pedometer, and Actigraph during a maximal graded treadmill test. Correlations, intra-class correla...
The goal of the article is to describe a systematic approach through core principles and steps for the transition of the patient with a neurological disorder to the adult model of care, to provide steps and principles to help receiving providers successfully integrate the patient into their practice, and to discuss cultural, systemic, and discipline-based barriers to transition.