Biology subjects

Tapper, S.

Publications and source records attributed to Tapper, S..

6 recordsLinked to original sources

bioRxiv2025

Evaluating transboundary connectivity to support cross-border conservation between Canada and the United States

Landscape connectivity is considered critical for maintaining biodiversity. Many jurisdictions have identified the importance of considering connectivity in land use plans, and connectivity has recently been included as a metric in international conservation agreements. Consequently, there is a need for measures of connectivity that can be applied at national and international scales; however, evaluating connectivity across international boundaries remains a challenge due to inconsistencies in mapping data, and differences in sociopolitical systems. Canada and the United States of America (USA) share a long international border, and thus, there is a need and opportunity to develop transboundary connectivity plans for this international region. We extended a previously published pan-Canadian multi-species connectivity model into the USA to produce a seamless and high-resolution omnidirectional connectivity map for the two countries. We identify several significant animal movement corridors across the transboundary region and show that about 20% of connectivity hotspots in the region are covered by protected areas. We also demonstrate the potential of the map for identifying important areas for wildlife movement and the spread of zoonotic diseases. Our map will be useful for supporting transboundary connectivity conservation between Canada and the USA and our modelling approach can easily be applied to other countries to support their own connectivity initiatives.

ecology↗

bioRxiv2021

The Macromolecular MR Spectrum in Healthy Aging

PurposeMobile macromolecules (MMs) from amino acids, cytosolic proteins and mobile lipids contribute a significant spectral background underlying the metabolite signals in the MR spectrum. A recent consensus recommends that MM contributions should be removed or included in modeling basis sets for determination of metabolite concentrations and/or metabolite ratios. The purpose of this study was to acquire the MM spectrum from healthy participants at a range of ages, and to investigate changes in the signals with age and sex groups. MethodsInversion time (TI) series were acquired to determine an optimal inversion time to null the metabolite signals. Experiments were carried out using a single adiabatic hyperbolic-secant inversion pulse. After the preliminary experiment, 102 volunteers (49M/53F) between 20 and 69 years were recruited for in vivo data acquisition in the centrum semiovale (CSO) and posterior cingulate cortex (PCC). The protocol consisted of a T1-weighted MPRAGE for structural images, followed by PRESS localization using a voxel size of 30 x 26 x 26 mm3 with pre-inversion (TR/TI 2000/600 ms) and CHESS water suppression. Metabolite-nulled spectra were modeled using a reduced basis set (NAA, Cr, Cho, Glu) and a flexible spline baseline (0.1 ppm knot spacing) followed by subtraction of the modeled metabolite signals to yield a clean MM spectrum, using the Osprey software. Pearsons correlation coefficient was calculated between integrals and age for the 14 MM signals between 0.9-4.2 ppm. One-way ANOVA was performed to determine differences between age groups. An independent t-test was carried out to determine differences between sexes. Relationships between brain tissues with age and sex groups were also measured. ResultsMM spectra were successfully acquired in 99 (CSO) and 96 (PCC) of 102 subjects. No significant correlations were seen between age and MM integrals. One-way ANOVA also suggested no age-group differences for any MM peak (all p > 0.004). No differences were observed between sex groups. The voxels were segmented as 80 {+/-} 4% white matter, 18 {+/-} 4% gray matter, and 2 {+/-} 1% CSF for CSO and 28 {+/-} 4% white matter, 61 {+/-} 4% gray matter and 11 {+/-} 1% CSF for PCC. WM and GM showed a significant (p < 0.05) negative linear association with age in the WM-predominant CSO (R = -0.29) and GM-predominant PCC regions (R = -0.57) respectively while CSF increased significantly with age in both regions. ConclusionOur findings indicate that the MM spectrum is stable across a large age range and between sexes, suggesting a pre-defined MM basis function can be used for linear combination modeling of metabolite data from different age and sex groups. HighlightsO_LIA large publicly available MM-aging dataset is presented. C_LIO_LIMacromolecule signals do not change with age between 20 and 70. C_LIO_LIThere is no sex difference for macromolecule integrals. C_LI

bioengineering↗

bioRxiv2021

Comparison of linear combination modeling strategies for GABA-edited MRS at 3T

PurposeJ-difference-edited spectroscopy is a valuable approach for the in vivo detection of {gamma}-aminobutyric-acid (GABA) with MRS. A recent expert consensus article recommends linear combination modeling (LCM) of edited MRS but does not give specific details of implementation. This study explores different modeling strategies to adapt LCM for GABA-edited MRS. Methods61 medial parietal lobe GABA-edited MEGA-PRESS spectra from a recent 3T multi-site study were modeled using 102 different strategies combining six different approaches to account for co-edited macromolecules, three modeling ranges, three baseline knot spacings, and the use of basis sets with or without homocarnosine. The resulting GABA and GABA+ estimates (quantified relative to total creatine), the residuals at different ranges, SDs and CVs, and Akaike information criteria, were used to evaluate the models performance. ResultsSignificantly different GABA+ and GABA estimates were found when a well-parameterized MM3co basis function was included in the model. The mean GABA estimates were significantly lower when modeling MM, while the CVs were similar. A sparser spline knot spacing led to lower variation in the GABA and GABA+ estimates, and a narrower modeling range - only including the signals of interest - did not substantially improve or degrade modeling performance. Additionally, results suggest that LCM can separate GABA and the underlying co-edited MM3co. Incorporating homocarnosine into the modeling did not significantly improve variance in GABA+ estimates. ConclusionGABA-edited MRS is most appropriately quantified by LCM with a well-parameterized co-edited MM3co basis function with a constraint to the non-overlapped MM0.93, in combination with a sparse spline knot spacing (0.55 ppm) and a modeling range between 0.5 and 4 ppm. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/445817v3_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@129ce60org.highwire.dtl.DTLVardef@1ac3797org.highwire.dtl.DTLVardef@1759d69org.highwire.dtl.DTLVardef@b190a3_HPS_FORMAT_FIGEXP M_FIG C_FIG 102 strategies to model GABA-edited MRS with linear combination modeling were evaluated to quantify GABA and GABA+ in Osprey. Significantly different GABA and GABA+ estimates were found when a well-parameterized macro-molecule at 3 ppm was included. The findings suggest that linear combination modeling needs to be adapted for quantification of GABA-edited MRS.

biochemistry↗

bioRxiv2020

Comparison of algorithms for linear-combination modelling of short-echo-time magnetic resonance spectra

Short-TE proton MRS is used to study metabolism in the human brain. Common analysis methods model the data as linear combination of metabolite basis spectra. This large-scale multi-site study compares the levels of the four major metabolite complexes in short-TE spectra estimated by three linear-combination modelling (LCM) algorithms. 277 medial parietal lobe short-TE PRESS spectra (TE = 35 ms) from a recent 3T multi-site study were pre-processed with the Osprey software. The resulting spectra were modelled with Osprey, Tarquin and LCModel, using the same three vendor-specific basis sets (GE, Philips, and Siemens) for each algorithm. Levels of total N-acetylaspartate (tNAA), total choline (tCho), myoinositol (mI), and glutamate+glutamine (Glx) were quantified with respect to total creatine (tCr). Group means and CVs of metabolite estimates agreed well for tNAA and tCho across vendors and algorithms, but substantially less so for Glx and mI, with mI systematically estimated lower by Tarquin. The cohort mean coefficient of determination for all pairs of LCM algorithms across all datasets and metabolites was [Formula], indicating generally only moderate agreement of individual metabolite estimates between algorithms. There was a significant correlation between local baseline amplitude and metabolite estimates (cohort mean [Formula]). While mean estimates of major metabolite complexes broadly agree between linear-combination modelling algorithms at group level, correlations between algorithms are only weak-to-moderate, despite standardized pre-processing, a large sample of young, healthy and cooperative subjects, and high spectral quality. These findings raise concerns about the comparability of MRS studies, which typically use one LCM software and much smaller sample sizes. Graphical Abstract O_TBL View this table: org.highwire.dtl.DTLVardef@6775bdorg.highwire.dtl.DTLVardef@62f27borg.highwire.dtl.DTLVardef@1d77ccorg.highwire.dtl.DTLVardef@a4049aorg.highwire.dtl.DTLVardef@2a1feb_HPS_FORMAT_FIGEXP M_TBL C_TBL Three linear-combination algorithms (Osprey, Tarquin and LCMode) were used to quantify the levels of tNAA, tCho, mI, and Glx in 277 short-TE PRESS. Group means and CVs of metabolite estimates agreed well for tNAA and tCho, but substantially less so for Glx and mI with a cohort mean correlation coefficient of [Formula], indicating moderate agreement between algorithms. These findings raise concerns about the comparability of MRS studies, which typically use one LCM software and much smaller sample sizes.

biochemistry↗

bioRxiv2020

Osprey: Open-Source Processing, Reconstruction & Estimation of Magnetic Resonance Spectroscopy Data

BackgroundProcessing and quantitative analysis of magnetic resonance spectroscopy (MRS) data are far from standardized and require interfacing with third-party software. Here, we present Osprey, a fully integrated open-source data analysis pipeline for MRS data, with seamless integration of pre-processing, linear-combination modelling, quantification, and data visualization. New MethodOsprey loads multiple common MRS data formats, performs phased-array coil combination, frequency-and phase-correction of individual transients, signal averaging and Fourier transformation. Linear combination modelling of the processed spectrum is carried out using simulated basis sets and a spline baseline. The MRS voxel is coregistered to an anatomical image, which is segmented for tissue correction and quantification is performed based upon modelling parameters and tissue segmentation. The results of each analysis step are visualized in the Osprey GUI. The analysis pipeline is demonstrated in 12 PRESS, 11 MEGA-PRESS, and 8 HERMES datasets acquired in healthy subjects. ResultsOsprey successfully loads, processes, models, and quantifies MRS data acquired with a variety of conventional and spectral editing techniques. Comparison with Existing Method(s)Osprey is the first MRS software to combine uniform pre-processing, linear-combination modelling, tissue correction and quantification into a coherent ecosystem. Compared to existing compiled, often closed-source modelling software, Ospreys open-source code philosophy allows researchers to integrate state-of-the-art data processing and modelling routines, and potentially converge towards standardization of analysis. ConclusionsOsprey combines robust, peer-reviewed data processing methods into a modular workflow that is easily augmented by community developers, allowing the rapid implementation of new methods.

biochemistry↗

bioRxiv2019

Heat dissipation capacity influences reproductive performance in an aerial insectivore

Climatic warming will likely increase the frequency of extreme weather events, which may reduce an individuals capacity for sustained activity due to thermal limits. We tested whether the risk of overheating may limit parental provisioning of an aerial insectivorous bird in population decline. For many seasonally breeding birds, parents are thought to operate close to an energetic ceiling during the 2-3 week chick-rearing period. The factors determining the ceiling remain unknown, although it may be set by an individuals capacity to dissipate body heat (the heat dissipation limitation hypothesis). To test this hypothesis, over two breeding seasons we experimentally trimmed the ventral feathers of female tree swallows (Tachycineta bicolor) to provide a thermal window. We then monitored maternal provisioning rates, nestling growth rates, and fledging success. We found the effect of our experimental treatment was context-dependent and varied with environmental conditions. Females with trimmed plumage fed their nestlings at higher rates than controls when conditions were hot and non-windy, but the reverse was true under cool and windy conditions. On average, nestlings of trimmed females were heavier than controls, and had a higher probability of fledging. We suggest that removal of a thermal constraint allowed females to increase provisioning rates, but additionally provided nestlings with a thermal advantage via increased heat transfer during maternal brooding. Our data provide partial support for the heat dissipation limitation hypothesis, and suggest that depending on weather patterns, heat dissipation capacity can influence reproductive success in aerial insectivores.

zoology↗