Perhaps a wee bit of sugar would help.
Ontology highlight
ABSTRACT:
SUBMITTER: Freeze HH
PROVIDER: S-EPMC5428893 | biostudies-literature | 2016 Jun
REPOSITORIES: biostudies-literature
Publications
A new genetic disorder might be treatable through consumption of a simple sugar, but the relative contributions of endogenous and dietary sources are mostly unknown. It's time to change that. ...[more]
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Project description: Not available
| S-EPMC4609180 | biostudies-literature
Project description:ObjectiveTo determine the feasibility of conducting a longitudinal prospective study to evaluate functional recovery and predictors of impaired functional recovery in critically ill children.DesignProspective pilot study.SettingSingle-center PICU at McMaster Children's Hospital, Hamilton, Canada.PatientsChildren aged 12 months to 17 years, with at least one organ dysfunction, limited mobility or bed rest during the first 48 hours of PICU admission, and a minimum 48-hour PICU length of stay, were eligible. Patients transferred from a neonatal ICU prior to ever being discharged home, already mobilizing well or at baseline functional status at time of screening, with an English language barrier, and prior enrollment into this study, were excluded.InterventionsNone.Measurements and main resultsThe primary outcome was feasibility, as defined by the ability to screen, enroll eligible patients, and execute the study procedures and measurements on participants. Secondary outcomes included functional status at baseline, 3 and 6 months, PICU morbidity, and mortality. Functional status was measured using the Pediatric Evaluation of Disability Inventory and the Participation and Environment Measure for Children and Youth. Thirty-three patients were enrolled between October 2012 and April 2013. Consent rate was 85%, and follow-up rates were 93% at 3 months and 71% at 6 months. We were able to execute the study procedures and measurements, demonstrating feasibility of conducting a future longitudinal study. Functional status deteriorated following critical illness. Recovery appears to be influenced by baseline health or functional status and severity of illness.ConclusionLongitudinal research is needed to understand how children recover after a critical illness. Our results suggest factors that may influence the recovery trajectory and were used to inform the methodology, outcomes of interest, and appropriate sample size of a larger multicenter study evaluating functional recovery in this population.
| S-EPMC4499478 | biostudies-literature
Project description:Transcription factors regulate gene activity by binding specific regions of genomic DNA thanks to a subtle interplay of specific and nonspecific interactions that is challenging to quantify. Here, we exploit Reflective Phantom Interface (RPI), a label-free biosensor based on optical reflectivity, to investigate the binding of the N-terminal domain of Gal4, a well-known gene regulator, to double-stranded DNA fragments containing or not its consensus sequence. The analysis of RPI-binding curves provides interaction strength and kinetics and their dependence on temperature and ionic strength. We found that the binding of Gal4 to its cognate site is stronger, as expected, but also markedly slower. We performed a combined analysis of specific and nonspecific binding-equilibrium and kinetics-by means of a simple model based on nested potential wells and found that the free energy gap between specific and nonspecific binding is of the order of one kcal/mol only. We investigated the origin of such a small value by performing all-atom molecular dynamics simulations of Gal4-DNA interactions. We found a strong enthalpy-entropy compensation, by which the binding of Gal4 to its cognate sequence entails a DNA bending and a striking conformational freezing, which could be instrumental in the biological function of Gal4.
| S-EPMC8067546 | biostudies-literature
Project description:Oryza sativa cultivar:Goda Wee Genome sequencing
| PRJNA384107 | ENA
Project description:MotivationGraphs are commonly used to represent sets of sequences. Either edges or nodes can be labeled by sequences, so that each path in the graph spells a concatenated sequence. Examples include graphs to represent genome assemblies, such as string graphs and de Bruijn graphs, and graphs to represent a pan-genome and hence the genetic variation present in a population. Being able to align sequencing reads to such graphs is a key step for many analyses and its applications include genome assembly, read error correction and variant calling with respect to a variation graph.ResultsWe generalize two linear sequence-to-sequence algorithms to graphs: the Shift-And algorithm for exact matching and Myers' bitvector algorithm for semi-global alignment. These linear algorithms are both based on processing w sequence characters with a constant number of operations, where w is the word size of the machine (commonly 64), and achieve a speedup of up to w over naive algorithms. For a graph with |V| nodes and |E| edges and a sequence of length m, our bitvector-based graph alignment algorithm reaches a worst case runtime of O(|V|+⌈mw⌉|E| log w) for acyclic graphs and O(|V|+m|E| log w) for arbitrary cyclic graphs. We apply it to five different types of graphs and observe a speedup between 3-fold and 20-fold compared with a previous (asymptotically optimal) alignment algorithm.Availability and implementationhttps://github.com/maickrau/GraphAligner.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC6761980 | biostudies-literature
Project description:Members of the Wee family of kinases negatively regulate the cell cycle via phosphorylation of CDK1 and are considered potential drug targets. Herein, we investigated the structure-function relationship of human Wee1, Wee2, and Myt1 (PKMYT1). Purified recombinant full-length proteins and kinase domain constructs differed substantially in phosphorylation states and catalytic competency, suggesting complex mechanisms of activation. A series of crystal structures reveal unique features that distinguish Wee1 and Wee2 from Myt1 and establish the structural basis of differential inhibition by the widely used Wee1 inhibitor MK-1775. Kinome profiling and cellular studies demonstrate that, in addition to Wee1 and Wee2, MK-1775 is an equally potent inhibitor of the polo-like kinase PLK1. Several previously unrecognized inhibitors of Wee kinases were discovered and characterized. Combined, the data provide a comprehensive view on the catalytic and structural properties of Wee kinases and a framework for the rational design of novel inhibitors thereof.
| S-EPMC6200136 | biostudies-literature
Project description:DNA has been employed to either store digital information or to perform parallel molecular computing. Relatively unexplored is the ability to combine DNA-based memory and logical operations in a single platform. Here, we show a DNA tri-level cell non-volatile memory system capable of parallel random-access writing of memory and bit shifting operations. A microchip with an array of individually addressable electrodes was employed to enable random access of the memory cells using electric fields. Three segments on a DNA template molecule were used to encode three data bits. Rapid writing of data bits was enabled by electric field-induced hybridization of fluorescently labeled complementary probes and the data bits were read by fluorescence imaging. We demonstrated the rapid parallel writing and reading of 8 (23) combinations of 3-bit memory data and bit shifting operations by electric field-induced strand displacement. Our system may find potential applications in DNA-based memory and computations.
| S-EPMC5773625 | biostudies-literature
Project description:We study Bell scenarios with binary outcomes supplemented by one bit of classical communication. We developed a method to find facet inequalities for such scenarios even when direct facet enumeration is not possible, or at least difficult. Using this method, we partially solved the scenario where Alice and Bob choose between three inputs, finding a total of 668 inequivalent facet inequalities (with respect to relabelings of inputs and outputs). We also show that some of these inequalities are constructed from facet inequalities found in scenarios without communication, that is, the well-known Bell inequalities.
| S-EPMC7514653 | biostudies-literature
Project description:A design for genetically encoded counters is proposed via repressor-based circuits. An N-bit counter reads sequences of input pulses and displays the total number of pulses, modulo 2 N . The design is based on distributed computation with specialized cell types allocated to specific tasks. This allows scalability and bypasses constraints on the maximal number of circuit genes per cell due to toxicity or failures due to resource limitations. The design starts with a single-bit counter. The N-bit counter is then obtained by interconnecting (using diffusible chemicals) a set of N single-bit counters and connector modules. An optimization framework is used to determine appropriate gate parameters and to compute bounds on admissible pulse widths and relaxation (inter-pulse) times, as well as to guide the construction of novel gates. This work can be viewed as a step toward obtaining circuits that are capable of finite automaton computation in analogy to digital central processing units.
| S-EPMC8666654 | biostudies-literature
Project description:BackgroundThe internal thoracic artery (ITA) is a descendant branch of the subclavian artery. The former is located bilaterally in both internal sides of the thorax near the sternum and is accompanied by two internal thoracic veins (ITV). From a practical point of view, the ITA (and the ITV) identification is important because these vessels can be injured when pericardiocentesis with the parasternal approach is used. Other advantage of the ITA recognition is to check the patency of the ITA grafts in coronary artery revascularizated patients with new onset chest pain. The purpose of this article is to introduce a simple ultrasonographic technique for recognition of the aforementioned vessels and to highlight the utility of this finding in clinical practice.FindingsWith linear probe and along paraesternal line, the internal thoracic vessels are recognized on grayscale imaging as an anechoic tubular structure immediately anterior to pleural line. Color Doppler identifies a pulsatile (ITA) and a non-pulsatile (ITV) flow. Spectral Doppler normally shows a high resistance velocity profile in non-grafted ITA and a phasic flow in ITV. A biphasic low resistance velocity profile is normally expected in the grafted and permeable ITA.ConclusionsThe ITA (non-grafted) and ITV are recognized routinely along the parasternal line. The operators should identify these vessels when the parasternal approach pericardiocentesis is required and should also consider obtaining spectral Doppler images to check permeability of grafted ITA in coronary artery bypass graft patients with chest pain.
| S-EPMC4255330 | biostudies-literature