Biomedical subjects

Matthew O'Brien

Publications and source records attributed to Matthew O'Brien.

6 recordsLinked to original sources

PubMed2025

Giotto Suite: a multiscale and technology-agnostic spatial multiomics analysis ecosystem.

Emerging spatial multiomics technologies provide an increasingly large amount of information content at multiple scales. However, it remains challenging to efficiently represent and harmonize diverse spatial datasets. Here we present Giotto Suite, a suite of modular packages that provides scalable and extensible end-to-end solutions for multiscale and multiomic data analysis, integration and visualization. At its core, Giotto Suite is centered around an innovative data framework, allowing the representation and integration of spatial omics data in a technology-agnostic manner. Giotto Suite integrates molecular, morphology, spatial and annotated feature information to create a responsive and flexible workflow, as demonstrated by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science in R, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive and multiscale ecosystem for spatial multiomic data analysis.

Genomics↗

PubMed2006

In situ observation of homogeneous nucleation of nanosized zeolite A.

The formation of zeolite A (LTA) in the presence of tetramethylammonium cations is studied using in situ small angle and wide angle X-ray scattering (SAXS/WAXS) techniques. The SAXS measurements show the formation of homogeneous precursors 10 nm in size prior to the crystallization of LTA which were consumed during the crystallization. The crystal size is estimated by fitting the SAXS patterns with an equation for a cubic particle, and it is revealed that the final crystal size of the LTA depends on the synthesis temperature. However, although such temperature dependence is noted for the final crystal size, the initial precursor particles size appears to be closely similar (ca. 10 nm) irrespective of the synthesis temperature.

Journal Article↗

PubMed2005

A second-generation total synthesis of (+)-discodermolide: the development of a practical route using solely substrate-based stereocontrol.

A novel total synthesis of the complex polyketide (+)-discodermolide, a promising anticancer agent of sponge origin, has been completed in 7.8% overall yield over 24 linear steps, with 35 steps altogether. This second-generation approach was designed to rely solely on substrate control for introduction of the required stereochemistry, eliminating the use of all chiral reagents or auxiliaries. The common 1,2-anti-2,3-syn stereotriad found in each of three subunits, aldehyde 9 (C(1)-C(5)), ester 40 (C(9)-C(16)), and aldehyde 13 (C(17)-C(24)), was established via a boron-mediated aldol reaction of ethyl ketone 15 and formaldehyde, followed by hydroxyl-directed reduction to give 1,3-diol 14. Alternatively, a surrogate aldehyde 22 was employed for formaldehyde in this aldol reaction, leading to the beta-hydroxy aldehyde 20 as a common building block, corresponding to the discodermolide stereotriad. Key fragment unions were achieved by a lithium-mediated anti aldol reaction of ester 40 and aldehyde 13 under Felkin-Anh control to provide (16S,17S)-adduct 51 and a boron-mediated aldol reaction between enone 10 and aldehyde 9, exploiting unprecedented remote 1,6-stereoinduction, to give the (5S)-adduct 57.

Alkanes↗

PubMed2005

Exploration of the contribution of biobehavioral variables to the energy expenditure of preterm infants.

Variation in energy expended by preterm infants may be due to infant maturity and history of resolved acute lung disease (respiratory distress syndrome [RDS]) as well as growth, caloric intake, and activity. Indirect calorimetry was used in this exploratory, short-term longitudinal study to estimate energy expenditure (EE) from measures of inspired and expired O2 and CO2. The sample included 35 assessments for 10 preterm infants (5 with and 5 without RDS history). Lung disease history (resolved RDS, no RDS diagnosis), weight gain (g/d) from the day on which birth weight had been regained to the study day, mean activity level, the number of the assessment (1-6), and the interaction of lung disease history and time were included in a linear mixed model for repeated measures. Time was an index of postconceptional and postnatal age; all 3 were highly correlated. Because of high correlation with weight gain, caloric intake was not included in the analytic model. Lung disease history, mean activity level, and time were significant contributors to EE. A more precise measure of medical status than absence or presence of lung disease history, evenly spaced repetitions of EE assessment, and exploration of contexts in which the infants exhibit a higher activity level are needed in a replication study with a larger sample.

Acute Disease↗

PubMed2004

The effect of walking speed on peak plantar pressure.

BACKGROUND: Plantar pressure measurements often are used as a tool to evaluate pathologic gait. Previous studies, often done at self-selected walking speeds, have used peak plantar pressure to try to predict ulcer formation, compare surgical outcomes, and evaluate orthotic device efficacy. However, the relationship between walking speed and plantar pressures at specific plantar regions has not been clearly defined. METHODS: Twenty normal subjects walked on a treadmill at six speeds (0.75 to 2.00 m/s). In-shoe peak plantar pressure was measured at five plantar regions and compared across the range of speeds. RESULTS: Walking speed affected peak plantar pressure differently at the five examined plantar regions. The hallux and heel regions had the highest pressures, which increased linearly with faster speeds. The central and medial forefoot pressures initially increased but plateaued at the faster speeds, while the lateral forefoot had the lowest overall peak pressures, which decreased at the faster walking speeds. Therefore, significant quadratic effects were found at the forefoot. Best-fit regression equations defined distinct pressure-speed relationships at each plantar region (p < 0.0001). CONCLUSION: The effect of walking speed on peak plantar pressure varied with plantar region. To achieve more robust peak plantar pressure measurements, walking speed should be controlled. Determining the normal plantar function across a range of speeds can aid in the development of shoes and foot orthoses. The pressure-speed relationships presented in this study can be used as a comparative tool for evaluating the efficacy of clinical interventions for pressure reduction, especially when walking speed changes may confound the outcomes.

Adult↗

PubMed1999

The antibacterial effects of ciprofloxacin and trovafloxacin against Streptococcus pneumoniae in an in vitro dynamic model.

OBJECTIVE: To determine whether the newer fluoroquinolone antibiotics such as trovafloxacin posses enhanced activity against Gram-positive organisms, including Streptococcus pneumoniae, because the clinical activity of older quinolones against pneumococci has been questioned. METHODS: In this study, the bactericidal activities of ciprofloxacin and trovafloxacin against six strains of penicillin-resistant and -sensitive strains of Streptococcus pneumoniae were compared using an in vitro model that simulates human pharmacokinetics. Ciprofloxacin was administered at 750 mg every 12 h, higher than the usual daily dose of 500 mg twice a day. Trovafloxacin was administered at 300 mg every 24 h for the six strains and at 200 mg every 24 h for three of the strains. RESULTS: The single 300-mg dose of trovafloxacin killed five of the six strains in 4 h, with no bacterial regrowth. Ciprofloxacin reduced the initial inoculum by 3--5 logs by 24 h. Although the 300-mg dose of trovafloxacin more rapidly eradicated susceptible strains, the activity of trovafloxacin at 200 mg every 24 h was similar to that of ciprofloxacin at 750 mg every 12 h against the three strains tested. CONCLUSION: Trovafloxacin (and ciprofloxacin at high doses) eradicates susceptible strains of pneumococci in an in vitro dynamic model.

Journal Article↗