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1. SCIsegV2: A Universal Tool for Segmentation of Intramedullary Lesions in Spinal Cord Injury

Author

Karthik, Enamundram Naga, Valošek, Jan, Farner, Lynn, Pfyffer, Dario, Schading-Sassenhausen, Simon, Lebret, Anna, David, Gergely, Smith, Andrew C., Weber II, Kenneth A., Seif, Maryam, Group, RHSCIR Network Imaging, Freund, Patrick, and Cohen-Adad, Julien

Subjects
Computer Science - Computer Vision and Pattern Recognition, Computer Science - Artificial Intelligence
Abstract

Spinal cord injury (SCI) is a devastating incidence leading to permanent paralysis and loss of sensory-motor functions potentially resulting in the formation of lesions within the spinal cord. Imaging biomarkers obtained from magnetic resonance imaging (MRI) scans can predict the functional recovery of individuals with SCI and help choose the optimal treatment strategy. Currently, most studies employ manual quantification of these MRI-derived biomarkers, which is a subjective and tedious task. In this work, we propose (i) a universal tool for the automatic segmentation of intramedullary SCI lesions, dubbed \texttt{SCIsegV2}, and (ii) a method to automatically compute the width of the tissue bridges from the segmented lesion. Tissue bridges represent the spared spinal tissue adjacent to the lesion, which is associated with functional recovery in SCI patients. The tool was trained and validated on a heterogeneous dataset from 7 sites comprising patients from different SCI phases (acute, sub-acute, and chronic) and etiologies (traumatic SCI, ischemic SCI, and degenerative cervical myelopathy). Tissue bridges quantified automatically did not significantly differ from those computed manually, suggesting that the proposed automatic tool can be used to derive relevant MRI biomarkers. \texttt{SCIsegV2} and the automatic tissue bridges computation are open-source and available in Spinal Cord Toolbox (v6.4 and above) via the \texttt{sct\_deepseg -task seg\_sc\_lesion\_t2w\_sci} and \texttt{sct\_analyze\_lesion} functions, respectively., Comment: Accepted at MICCAI AMAI 2024 workshop

Published
2024

6. Factors influencing terrestriality in primates of the Americas and Madagascar

Author

Eppley, Timothy M, Hoeks, Selwyn, Chapman, Colin A, Ganzhorn, Jörg U, Hall, Katie, Owen, Megan A, Adams, Dara B, Allgas, Néstor, Amato, Katherine R, Andriamahaihavana, McAntonin, Aristizabal, John F, Baden, Andrea L, Balestri, Michela, Barnett, Adrian A, Bicca-Marques, Júlio César, Bowler, Mark, Boyle, Sarah A, Brown, Meredith, Caillaud, Damien, Calegaro-Marques, Cláudia, Campbell, Christina J, Campera, Marco, Campos, Fernando A, Cardoso, Tatiane S, Carretero-Pinzón, Xyomara, Champion, Jane, Chaves, Óscar M, Chen-Kraus, Chloe, Colquhoun, Ian C, Dean, Brittany, Dubrueil, Colin, Ellis, Kelsey M, Erhart, Elizabeth M, Evans, Kayley JE, Fedigan, Linda M, Felton, Annika M, Ferreira, Renata G, Fichtel, Claudia, Fonseca, Manuel L, Fontes, Isadora P, Fortes, Vanessa B, Fumian, Ivanyr, Gibson, Dean, Guzzo, Guilherme B, Hartwell, Kayla S, Heymann, Eckhard W, Hilário, Renato R, Holmes, Sheila M, Irwin, Mitchell T, Johnson, Steig E, Kappeler, Peter M, Kelley, Elizabeth A, King, Tony, Knogge, Christoph, Koch, Flávia, Kowalewski, Martin M, Lange, Liselot R, Lauterbur, M Elise, Louis, Edward E, Lutz, Meredith C, Martínez, Jesús, Melin, Amanda D, de Melo, Fabiano R, Mihaminekena, Tsimisento H, Mogilewsky, Monica S, Moreira, Leandro S, Moura, Letícia A, Muhle, Carina B, Nagy-Reis, Mariana B, Norconk, Marilyn A, Notman, Hugh, O’Mara, M Teague, Ostner, Julia, Patel, Erik R, Pavelka, Mary SM, Pinacho-Guendulain, Braulio, Porter, Leila M, Pozo-Montuy, Gilberto, Raboy, Becky E, Rahalinarivo, Vololonirina, Raharinoro, Njaratiana A, Rakotomalala, Zafimahery, Ramos-Fernández, Gabriel, Rasamisoa, Delaïd C, Ratsimbazafy, Jonah, Ravaloharimanitra, Maholy, Razafindramanana, Josia, Razanaparany, Tojotanjona P, Righini, Nicoletta, Robson, Nicola M, da Rosa Gonçalves, Jonas, Sanamo, Justin, Santacruz, Nicole, Sato, Hiroki, Sauther, Michelle L, Scarry, Clara J, Serio-Silva, Juan Carlos, Shanee, Sam, de Souza Lins, Poliana GA, and Smith, Andrew C

Subjects
Life Below Water, Americas, Animals, Biological Evolution, Cercopithecidae, Haplorhini, Humans, Madagascar, Mammals, Primates, Trees, primate communities, primate evolution, evolutionary transitions, niche shift, climate change
Abstract

Among mammals, the order Primates is exceptional in having a high taxonomic richness in which the taxa are arboreal, semiterrestrial, or terrestrial. Although habitual terrestriality is pervasive among the apes and African and Asian monkeys (catarrhines), it is largely absent among monkeys of the Americas (platyrrhines), as well as galagos, lemurs, and lorises (strepsirrhines), which are mostly arboreal. Numerous ecological drivers and species-specific factors are suggested to set the conditions for an evolutionary shift from arboreality to terrestriality, and current environmental conditions may provide analogous scenarios to those transitional periods. Therefore, we investigated predominantly arboreal, diurnal primate genera from the Americas and Madagascar that lack fully terrestrial taxa, to determine whether ecological drivers (habitat canopy cover, predation risk, maximum temperature, precipitation, primate species richness, human population density, and distance to roads) or species-specific traits (body mass, group size, and degree of frugivory) associate with increased terrestriality. We collated 150,961 observation hours across 2,227 months from 47 species at 20 sites in Madagascar and 48 sites in the Americas. Multiple factors were associated with ground use in these otherwise arboreal species, including increased temperature, a decrease in canopy cover, a dietary shift away from frugivory, and larger group size. These factors mostly explain intraspecific differences in terrestriality. As humanity modifies habitats and causes climate change, our results suggest that species already inhabiting hot, sparsely canopied sites, and exhibiting more generalized diets, are more likely to shift toward greater ground use.

Published
2022

11. OPTIMIZATION OF A BALL'S LAUNCH IN SPORTS

Author

Smith, Andrew C. and Hasbun, Javier E.

Subjects
Sports -- Physiological aspects -- Psychological aspects -- United States, Magnus effect -- Evaluation, Differential equations -- Evaluation, Science and technology
Abstract

Newton's laws are used to study the effects of air resistance on an object's motion. In ball-related sports such as baseball, soccer, etc., understanding the effects of air resistance is essential to optimize ball launch performance. This performance optimization can be studied by identifying the minimal time it takes for a ball with speed v to travel a certain distance. We work with two models that apply to an object's motion. One of the models assumes a linear air drag while a second model makes use of a quadratic air drag. We do investigate known differential equations for when the Magnus force is present as well as absent. This is done through numerical and analytic solutions, when possible. The development of approximations leads to differential equations that are suitable for time optimization studies The analytic calculations are compared to MATLAB's numerical results. We concentrate on situations for which the speed of the projectile parallel to the ground is much greater than its speed perpendicular to it. Keywords: Mechanics, speed, sports, motion, air drag, INTRODUCTION The use of technology in sports allows for a deeper understanding of the physics of a sport, leading to increased knowledge and skill of play. In ball-related sports, such [...]

Published
2023

13. An Academic and Cultural Transition Course for International Students: Efficacy and Socioemotional Outcomes

Author

Brunsting, Nelson C., Smith, Andrew C., and Zachry, Corinne

Abstract

The current study details changes in first-year international undergraduate students' perceived knowledge of, confidence in, and usefulness of intercultural skills in specific US university contexts after completing a semester-long academic and cultural transition course at a mid-sized private university. Results revealed significant increases in participants' (n = 42) perceived intercultural competence, perspective shifting, suspending judgment, self-advocacy, and interacting in class with students of other cultures; participants also reported significantly higher campus belonging and social support than a comparison group of students at the university who were not enrolled in the course (n = 32). These findings provide initial evidence for the potential of transition courses to increase intercultural skills and campus belonging for first-year undergraduate international students attending US universities.

Published
2018

18. Novel approaches in long term mechanical circulatory support

Author

Morley-Smith, Andrew C., Pepper, John, and Lyon, Alexander

Subjects
616.1
Abstract

Long term mechanical circulatory support using left ventricular assist devices (LVADs) remains an essential tool in managing patients with advanced heart failure, and in some patients can facilitate reverse remodelling of ventricular function. However, large groups of patients remain poorly served by current technologies, and understanding of reverse remodelling, including how to assess it in vivo, remains poor. I evaluate new approaches in long term mechanical support. Specifically, I assess: (1) the CircuLite Synergy LVAD and Sunshine Heart C-Pulse counterpulsation device as novel methods for partial LV support, considering particularly their ability to facilitate reverse remodelling and propensity to induce coagulopathy; (2) gene therapy with the AAV1.SERCA2a product as a novel adjunctive therapy, considering particularly its safety and feasibility in LVAD patients in the SERCA-LVAD trial; and (3) novel biomarkers for use in LVAD patients, with focus on strain echocardiography and circulating microRNA. I report that (1) partial LV support is plausible as a concept and is beneficial in some patients, but there was no consistent evidence of ventricular reverse remodelling and, at the present time, high complication rates and difficulties with patient selection preclude its widespread adoption; (2) there were high rates of pump thrombosis in the Synergy LVAD, though there is no evidence of a device-specific coagulopathy to explain it; (3) gene therapy with AAV1.SERCA2a is safe and feasible in LVAD patients, though there was no evidence of significant efficacy benefit, in line with other clinical trials of this gene therapy in heart failure; (4) assessment of global circumferential strain is feasible in LVAD patients, but inconsistent image quality and effect of loading conditions limit its use; and (5) assessment of circulating microRNA profiles is feasible in LVAD patients, and preliminary data shows roles for specific miRs in patient selection and monitoring of LV function.

Published
2018
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24. Expanding National Vocational Education and Training Statistical Collections: Private Provider Engagement

Author

National Centre for Vocational Education Research, Smith, Andrew C., Potter, Rosemary, and Smith, Peter J.

Abstract

The research reported was intended to identify the barriers and facilitators to the participation of private education and training providers in the supply of data to the national vocational education and training (VET) statistical collection. In addition, the research process developed a number of strategies to assist private registered training organisations (RTOs) to participate in the training market and tested those strategies with the industry. The larger context for the research can be found in the growing recognition that the private provision of VET in Australia has grown into a thriving industry that makes a considerable contribution to the national training effort. However, the nation holds only poor data on the size of this contribution, its profile, or its participants. From the private training sector viewpoint, that is an unsatisfactory position since it does not develop a public perception of the value of the sector to the nation; it is also unsatisfactory from a government perspective in that, without a clear knowledge of the total VET effort, there can only be partial planning of future growth in VET, its outputs, its contribution to the economy and economic development, and to its role in providing greater equity. The purpose of this research: (1) to identify the barriers to private providers in supplying statistical data to the National VET Provider Collection; (2) to identify drivers that would encourage private providers to supply those data; (3) to identify some data requirements that private providers would either not be able to, or would not wish to, provide to the National VET Provider Collection; and (4) to develop and provide strategies that would assist private provider participation. Survey questions and response options are appended. (Contains 4 tables.)

Published
2010

36. Identifying sulphate-reducing and magnetotactic bacteria in a hyperalkaline cave system

Author

Shen, Jianxun, Smith, Andrew C., Barnett, Megan J., Morgan, Alistair, Wynn, Peter M., Shen, Jianxun, Smith, Andrew C., Barnett, Megan J., Morgan, Alistair, and Wynn, Peter M.

Abstract

Sulphate-reducing bacteria (SRB) and magnetotactic bacteria (MTB) are two special groups of prokaryotes that emerged early in Earth's history. These extremotolerant bacterial groups have rarely been identified or studied within cave and karst environments, especially hyperalkaline cave systems (pH > 9), such as Poole's Cavern in Derbyshire, England. In this study, we identify the sulphate-reducing MTB Desulfovibrio magneticus, within this hyperalkaline cave system. It appears to survive in a diverse range of environments including soil, stalactites and cave sediments. Additionally, we identify various extremotolerant SRB in similar Poole's Cavern environments. We show that these SRB and MTB can move successfully into subsurface environments and adapt concomitantly to the anomalous pH, saline, and relatively nutrient-poor conditions found in Poole's Cavern. These findings are significant to our understanding of microorganisms on early Earth because it is believed, but not proven, that underground environments might have been hot spots for early microbial life. We expect that these early bacteria would have been able to adopt similar adaptation strategies, transferring and acclimatizing to underground environments, in ways comparable to the SRB and MTB identified in this study.

Published
2023

44. Factors influencing terrestriality in primates of the Americas and Madagascar

Author

Eppley, Timothy M., Hoeks, Selwyn, Chapman, Colin A., Ganzhorn, Jörg U., Hall, Katie, Owen, Megan A., Adams, Dara B., Allgas, Néstor, Amato, Katherine R., Andriamahaihavana, McAntonin, Aristizabal, John F., Baden, Andrea L., Balestri, Michela, Barnett, Adrian A., Bicca-Marques, Júlio César, Bowler, Mark, Boyle, Sarah A., Brown, Meredith, Caillaud, Damien, Calegaro-Marques, Cláudia, Campbell, Christina J., Campera, Marco, Campos, Fernando A., Cardoso, Tatiane S., Carretero-Pinzón, Xyomara, Champion, Jane, Chaves, Óscar M., Chen-Kraus, Chloe, Colquhoun, Ian C., Dean, Brittany, Dubrueil, Colin, Ellis, Kelsey M., Erhart, Elizabeth M., Evans, Kayley J.E., Fedigan, Linda M., Felton, Annika M., Ferreira, Renata G., Fichtel, Claudia, Fonseca, Manuel L., Fontes, Isadora P., Fortes, Vanessa B., Fumian, Ivanyr, Gibson, Dean, Guzzo, Guilherme B., Hartwell, Kayla S., Heymann, Eckhard W., Hilário, Renato R., Holmes, Sheila M., Irwin, Mitchell T., Johnson, Steig E., Kappeler, Peter M., Kelley, Elizabeth A., King, Tony, Knogge, Christoph, Koch, Flávia, Kowalewski, Martin M., Lange, Liselot R., Lauterbur, M. Elise, Louis, Edward E., Jr., Lutz, Meredith C., Martínez, Jesús, Melin, Amanda D., de Melo, Fabiano R., Mihaminekena, Tsimisento H., Mogilewsky, Monica S., Moreira, Leandro S., Moura, Letícia A., Muhle, Carina B., Nagy-Reis, Mariana B., Norconk, Marilyn A., Notman, Hugh, O’Mara, M. Teague, Ostner, Julia, Patel, Erik R., Pavelka, Mary S.M., Pinacho-Guendulain, Braulio, Porter, Leila M., Pozo-Montuy, Gilberto, Raboy, Becky E., Rahalinarivo, Vololonirina, Raharinoro, Njaratiana A., Rakotomalala, Zafimahery, Ramos-Fernández, Gabriel, Rasamisoa, Delaïd C., Ratsimbazafy, Jonah, Ravaloharimanitra, Maholy, Razafindramanana, Josia, Razanaparany, Tojotanjona P., Righini, Nicoletta, Robson, Nicola M., da Rosa Gonçalves, Jonas, Sanamo, Justin, Santacruz, Nicole, Sato Hiroki, Sauther, Michelle L., Scarry, Clara J., Serio-Silva, Juan Carlos, Shanee, Sam, de Souza Lins, Poliana G.A., Smith, Andrew C., Smith Aguilar, Sandra E., Souza-Alves, João Pedro, Stavis, Vanessa Katherinne, Steffens, Kim J.E., Stone, Anita I., Strier, Karen B., Suarez, Scott A., Talebi, Maurício, Tecot, Stacey R., Tujague, M. Paula, Valenta, Kim, Van Belle, Sarie, Vasey, Natalie, Wallace, Robert B., Welch, Gilroy, Wright, Patricia C., Donati, Giuseppe, and Santini, Luca

Subjects
Mammals, Primates, primate communities, evolutionary transitions, Cercopithecidae, Haplorhini, Biological Evolution, Trees, climate change, Madagascar, Animals, Humans, Americas, Life Below Water, primate evolution, niche shift
Abstract

Significance. Primates from the Americas and Madagascar are predominantly arboreal but occasionally descend to the ground. This increased ground use was associated with multiple ecological drivers, including increased temperature and a decrease in canopy cover, as well as species-specific traits, including a dietary shift away from fruits and larger group size. As anthropogenic impacts to habitats and climate worsen, our results suggest that diurnal species already inhabiting hot, sparsely canopied sites, and exhibiting more generalized diets, are more likely to shift toward greater ground use., Among mammals, the order Primates is exceptional in having a high taxonomic richness in which the taxa are arboreal, semiterrestrial, or terrestrial. Although habitual terrestriality is pervasive among the apes and African and Asian monkeys (catarrhines), it is largely absent among monkeys of the Americas (platyrrhines), as well as galagos, lemurs, and lorises (strepsirrhines), which are mostly arboreal. Numerous ecological drivers and species-specific factors are suggested to set the conditions for an evolutionary shift from arboreality to terrestriality, and current environmental conditions may provide analogous scenarios to those transitional periods. Therefore, we investigated predominantly arboreal, diurnal primate genera from the Americas and Madagascar that lack fully terrestrial taxa, to determine whether ecological drivers (habitat canopy cover, predation risk, maximum temperature, precipitation, primate species richness, human population density, and distance to roads) or species-specific traits (body mass, group size, and degree of frugivory) associate with increased terrestriality. We collated 150,961 observation hours across 2,227 months from 47 species at 20 sites in Madagascar and 48 sites in the Americas. Multiple factors were associated with ground use in these otherwise arboreal species, including increased temperature, a decrease in canopy cover, a dietary shift away from frugivory, and larger group size. These factors mostly explain intraspecific differences in terrestriality. As humanity modifies habitats and causes climate change, our results suggest that species already inhabiting hot, sparsely canopied sites, and exhibiting more generalized diets, are more likely to shift toward greater ground use.

Published
2022

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