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1. Identification of Parkinsons disease PACE subtypes and repurposing treatments through integrative analyses of multimodal data.

Author

Su, Chang, Hou, Yu, Xu, Jielin, Xu, Zhenxing, Zhou, Manqi, Ke, Alison, Li, Haoyang, Xu, Jie, Brendel, Matthew, Maasch, Jacqueline, Bai, Zilong, Zhang, Haotan, Zhu, Yingying, Cincotta, Molly, Shi, Xinghua, Henchcliffe, Claire, Leverenz, James, Cummings, Jeffrey, Okun, Michael, Bian, Jiang, Cheng, Feixiong, and Wang, Fei

Abstract

Parkinsons disease (PD) is a serious neurodegenerative disorder marked by significant clinical and progression heterogeneity. This study aimed at addressing heterogeneity of PD through integrative analysis of various data modalities. We analyzed clinical progression data (≥5 years) of individuals with de novo PD using machine learning and deep learning, to characterize individuals phenotypic progression trajectories for PD subtyping. We discovered three pace subtypes of PD exhibiting distinct progression patterns: the Inching Pace subtype (PD-I) with mild baseline severity and mild progression speed; the Moderate Pace subtype (PD-M) with mild baseline severity but advancing at a moderate progression rate; and the Rapid Pace subtype (PD-R) with the most rapid symptom progression rate. We found cerebrospinal fluid P-tau/α-synuclein ratio and atrophy in certain brain regions as potential markers of these subtypes. Analyses of genetic and transcriptomic profiles with network-based approaches identified molecular modules associated with each subtype. For instance, the PD-R-specific module suggested STAT3, FYN, BECN1, APOA1, NEDD4, and GATA2 as potential driver genes of PD-R. It also suggested neuroinflammation, oxidative stress, metabolism, PI3K/AKT, and angiogenesis pathways as potential drivers for rapid PD progression (i.e., PD-R). Moreover, we identified repurposable drug candidates by targeting these subtype-specific molecular modules using network-based approach and cell line drug-gene signature data. We further estimated their treatment effects using two large-scale real-world patient databases; the real-world evidence we gained highlighted the potential of metformin in ameliorating PD progression. In conclusion, this work helps better understand clinical and pathophysiological complexity of PD progression and accelerate precision medicine.

Published
2024

3. Land-use Change Effects on Tropical Bird Communities: Abundance Patterns, Behavioral Shifts, and Reproductive Success

Author

Ke, Alison

Subjects
Ecology
Abstract

Land-use change currently constitutes the primary driver of modern biodiversity loss. One way that land conversion to agriculture can lead to biodiversity loss is through biotic homogenization where agriculture consistently favors the same species, causing communities to converge in species composition over space or time. Biotic homogenization could also occur phylogenetically, where species from the similar phylogenetic lineages are consistently favored by agriculture. However, whether phylogenetic homogenization occurs across multiple scales and in tropical regions is rarely investigated. In Chapter 1, I leveraged species’ phylogeny and traits to understand how land-use change affects tropical bird communities within Costa Rica and Colombia. We conducted bird surveys across Costa Rica and Colombia in 294 sites that varied in levels of local forest cover and annual precipitation. We then analyzed sites in Costa Rica and Colombia together to find that land conversion from forest to agriculture consistently favors the same types of species at a large scale. While most trait-based studies measure effects of global changes on species occurrences or abundances, changes in species abundance or occurrence provide little information about how species actually use the habitats where they occur. For example, a species detected in agriculture could simply be passing through (and not actually resilient to land-use change) or it could be using agriculture to forage, reproduce, or otherwise complete its lifecycle (meaning the species is resilient to land-use change). In Chapter 2, I developed and then validated a statistical model to analyze how species’ behavior differs between habitat types using observational data. To our knowledge, this is the first model to measure how animals use different environments while accounting for behavior-specific imperfect detection probability. We compared the model to an alternative model that did not account for imperfect detection probability and found that our new model produced more accurate estimates of the mean and uncertainty of the effects of environmental covariates on behaviors. Thus, this model allows researchers and managers to more accurately assess how species use the environments they are in using observational behavior data. In Chapter 3, I applied this model to over 14,000 behavioral observations across 55 bird species in Northwest Costa Rica to understand how local forest cover and forest protection level affect bird behaviors. We found that birds were more likely to perform reproductive behaviors in protected forest than private forest and agriculture, meaning that protected areas are likely important for bird reproduction and conservation. This chapter also demonstrates the importance of behavioral analyses in conservation planning, as species’ behavioral responses were not always consistent with their differences in abundance. Beyond measuring changes in occurrence and behavior, it is also critical to understand if habitats can support sufficient reproductive rates to allow for population persistence. Tropical cavity-nesting birds may be particularly threatened by agricultural land-use change, which removes the tree they rely on for nesting and roosting. In Chapter 4, I aimed to understand how land-use change affects tropical cavity-nesting bird reproduction by measuring nest site availability and conducting a nest-box addition experiment in forest and agriculture Northwest Ecuador. I found that land-use change likely limits the reproduction of cavity-nesting birds in agriculture, as nest boxes in agriculture had much higher levels of avian activity than nest boxes in forest. Nest boxes also had a relatively high rate of chicks fledged, meaning that nest boxes could be a successful conservation strategy for certain species. Overall, my dissertation explores the different effects of agricultural land-use change on tropical bird occurrence, behavior, and reproduction. I found that these effects can differ from each other and across scales. The results highlight the importance of forest conservation, especially in wet regions, and support investigating species’ responses beyond occurrence when comparing the conservation value of habitat types.

Published
2023

4. Effects of agriculture and nature reserves on avian behavior in northwestern Costa Rica.

Author

Ke, Alison, Sollmann, Rahel, Frishkoff, Luke, Echeverri, Alejandra, Zook, Jim, and Karp, Daniel S.

Subjects
*NATURE reserves, *ANIMAL sexual behavior, *PASSIVITY (Psychology), *AGRICULTURE, *PROTECTED areas, *BIRD food, *BIRD populations
Abstract

Behavioral changes are often animals' first responses to environmental change and may act as a bellwether for population viability. Nonetheless, most studies of habitat conversion focus on changes in species occurrences or abundances. We analyzed >14,000 behavioral observations across 55 bird species in communities in northwestern Costa Rica to determine how land use affects reproductive, foraging, and other passive kinds of behaviors not associated with either foraging or reproduction. Specifically, we quantified differences in behaviors between farms, privately owned forests, and protected areas and implemented a novel modeling framework to account for variation in detection among behaviors. This framework entailed estimating abundances of birds performing different behaviors while allowing detection probabilities of individuals to vary by behavior. Birds were 1.2 times more likely to exhibit reproductive behaviors in forest than in agriculture and 1.5 times more likely to exhibit reproductive behaviors in protected areas than in private forests. Species were not always most abundant in the habitats where they were most likely to exhibit foraging or reproductive behaviors. Finally, species of higher conservation concern were less abundant in agriculture than in forest. Together, our results highlight the importance of behavioral analyses for elucidating the conservation value of different land uses. [ABSTRACT FROM AUTHOR]

Published
2024
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6. Same data, different analysts: variation in effect sizes due to analytical decisions in ecology and evolutionary biology

Author

Gould, Elliot, primary, Fraser, Hannah, additional, Parker, Timothy, additional, Nakagawa, Shinichi, additional, Griffith, Simon, additional, Vesk, Peter, additional, Fidler, Fiona, additional, Abbey-Lee, Robin, additional, Abbott, Jessica, additional, Aguirre, Luis, additional, Alcaraz, Carles, additional, Altschul, Drew, additional, Arekar, Kunal, additional, Atkins, Jeff, additional, Atkinson, Joe, additional, Barrett, Meghan, additional, Bell, Kristian, additional, Bello, Suleiman, additional, Berauer, Bernd, additional, Bertram, Michael, additional, Billman, Peter, additional, Blake, Charlie, additional, Blake, Shannon, additional, Bliard, Louis, additional, Bonisoli-Alquati, Andrea, additional, Bonnet, Timothée, additional, Bordes, Camille, additional, Bose, Aneesh, additional, Botterill-James, Thomas, additional, Boyd, Melissa, additional, Boyle, Sarah, additional, Bradfer-Lawrence, Tom, additional, Brand, Jack, additional, Brengdahl, Martin, additional, Bulla, Martin, additional, Bussière, Luc, additional, Camerlenghi, Ettore, additional, Campbell, Sara, additional, Campos, Leonardo, additional, Caravaggi, Anthony, additional, Cardoso, Pedro, additional, Carroll, Charles, additional, Catanach, Therese, additional, Chen, Xuan, additional, Chik, Heung Ying Janet, additional, Choy, Emily, additional, Christie, Alec, additional, Chuang, Angela, additional, Chunco, Amanda, additional, Clark, Bethany, additional, Cox, Murray, additional, Cressman, Kimberly, additional, Crouch, Connor, additional, D'Amelio, Pietro, additional, de Sousa, Alexandra, additional, Döbert, Timm, additional, Dobler, Ralph, additional, Dobson, Adam, additional, Doherty, Tim, additional, Drobniak, Szymon, additional, Duffy, Alexandra, additional, Dunn, Robert, additional, Dunning, Jamie, additional, Eberhart-Hertel, Luke, additional, Elmore, Jared, additional, Elsherif, Mahmoud, additional, English, Holly, additional, Ensminger, David, additional, Ernst, Ulrich, additional, Ferguson, Stephen, additional, Ferreira-Arruda, Thalita, additional, Fieberg, John, additional, Finch, Elizabeth, additional, Fiorenza, Evan, additional, Fisher, David, additional, Forstmeier, Wolfgang, additional, Fourcade, Yoan, additional, Francesca Santostefano, Francesca, additional, Frank, Graham, additional, Freund, Cathryn, additional, Gandy, Sara, additional, Gannon, Dustin, additional, García-Cervigón, Ana, additional, Géron, Charly, additional, Gilles, Marc, additional, Girndt, Antje, additional, Gliksman, Daniel, additional, Goldspiel, Harrison, additional, Gomes, Dylan, additional, Goslee, Sarah, additional, Gosnell, J., additional, Gratton, Paolo, additional, Grebe, Nicholas, additional, Greenler, Skye, additional, Griffith, Daniel, additional, Griffith, Frances, additional, Grossman, Jake, additional, Güncan, Ali, additional, Haesen, Stef, additional, Hagan, James, additional, Harrison, Natasha, additional, Hasnain, Sarah, additional, Havird, Justin, additional, Heaton, Andrew, additional, Hsu, Bin-Yan, additional, Iranzo, Esperanza, additional, Iverson, Erik, additional, Jimoh, Saheed, additional, Johnson, Douglas, additional, Johnsson, Martin, additional, Jorna, Jesse, additional, Jucker, Tommaso, additional, Jung, Martin, additional, Kačergytė, Ineta, additional, Ke, Alison, additional, Kelly, Clint, additional, Keogan, Katharine, additional, Keppeler, Friedrich, additional, Killion, Alexander, additional, Kim, Dongmin, additional, Kochan, David, additional, Korsten, Peter, additional, Kothari, Shan, additional, Kuppler, Jonas, additional, Kusch, Jillian, additional, Lagisz, Malgorzata, additional, Larkin, Daniel, additional, Larson, Courtney, additional, Lauck, Katherine, additional, Lauterbur, M., additional, Law, Alan, additional, Léandri-Breton, Don-Jean, additional, Lievens, Eva, additional, Lima, Daniela, additional, Lindsay, Shane, additional, Macphie, Kirsty, additional, Mair, Magdalena, additional, Malm, Lisa, additional, Mammola, Stefano, additional, Manhart, Michael, additional, Mäntylä, Elina, additional, Marchand, Philippe, additional, Marshall, Benjamin, additional, Martin, Dominic, additional, Martin, Jake, additional, Martin, Charles, additional, Martinig, April, additional, McCallum, Erin, additional, McNew, Sabrina, additional, Meiners, Scott, additional, Michelangeli, Marcus, additional, Moiron, Maria, additional, Moreira, Bruno, additional, Mortensen, Jennifer, additional, Mos, Benjamin, additional, Muraina, Taofeek, additional, Nelli, Luca, additional, Nilsonne, Gustav, additional, Nolazco, Sergio, additional, Nooten, Sabine, additional, Novotny, Jessie, additional, Olin, Agnes, additional, Organ, Chris, additional, Ostevik, Kate, additional, Palacio, Facundo, additional, Paquet, Matthieu, additional, Pascall, David, additional, Pasquarella, Valerie, additional, Payo-Payo, Ana, additional, Pedersen, Karen, additional, Perez, Grégoire, additional, Perry, Kayla, additional, Pottier, Patrice, additional, Proulx, Michael, additional, Proulx, Raphaël, additional, Pruett, Jessica, additional, Ramananjato, Veronarindra, additional, Randimbiarison, Finaritra, additional, Razafindratsima, Onja, additional, Rennison, Diana, additional, Riva, Federico, additional, Riyahi, Sepand, additional, Roast, Michael, additional, Rocha, Felipe, additional, Roche, Dominique, additional, Román-Palacios, Cristian, additional, Rosenberg, Michael, additional, Ross, Jessica, additional, Rowland, Freya, additional, Rugemalila, Deusdedith, additional, Russell, Avery, additional, Ruuskanen, Suvi, additional, Saccone, Patrick, additional, Sadeh, Asaf, additional, Salazar, Stephen, additional, sales, kris, additional, Salmón, Pablo, additional, Sanchez-Tojar, Alfredo, additional, Santos, Leticia, additional, Schilling, Hayden, additional, Schmidt, Marcus, additional, Schmoll, Tim, additional, Schneider, Adam, additional, Schrock, Allie, additional, Schroeder, Julia, additional, Schtickzelle, Nicolas, additional, Schultz, Nick, additional, Scott, Drew, additional, Shapiro, Julie, additional, Sharma, Nitika, additional, Shearer, Caroline, additional, Sitvarin, Michael, additional, Skupien, Fabrício, additional, Slinn, Heather, additional, Smith, Jeremy, additional, Smith, Grania, additional, Sollmann, Rahel, additional, Stack Whitney, Kaitlin, additional, Still, Shannon, additional, Stuber, Erica, additional, Sutton, Guy, additional, Swallow, Ben, additional, Taff, Conor, additional, Takola, Elina, additional, Tanentzap, Andrew, additional, Thawley, Christopher, additional, Tortorelli, Claire, additional, Trlica, Andrew, additional, Turnell, Biz, additional, Urban, Lara, additional, Van de Vondel, Stijn, additional, van Oordt, Francis, additional, Vanderwel, Mark, additional, Vanderwel, K., additional, Vanderwolf, Karen, additional, Verrelli, Brian, additional, Vieira, Marcus, additional, Vollering, Julien, additional, Walker, Xanthe, additional, Walter, Jonathan, additional, Waryszak, Pawel, additional, Weaver, Ryan, additional, Weller, Daniel, additional, Whelan, Shannon, additional, White, Rachel, additional, Wolfson, David, additional, Wood, Andrew, additional, Yanco, Scott, additional, Yen, Jian, additional, Youngflesh, Casey, additional, Zilio, Giacomo, additional, Zimmer, Cédric, additional, Zitomer, Rachel, additional, Villamil, Nora, additional, and Tompkins, Emily, additional

Published
2023
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7. Key knowledge gaps to achieve global sustainability goals

Author

Mastrángelo, Matías E., Pérez-Harguindeguy, Natalia, Enrico, Lucas, Bennett, Elena, Lavorel, Sandra, Cumming, Graeme S., Abeygunawardane, Dilini, Amarilla, Leonardo D., Burkhard, Benjamin, Egoh, Benis N., Frishkoff, Luke, Galetto, Leonardo, Huber, Sibyl, Karp, Daniel S., Ke, Alison, Kowaljow, Esteban, Kronenburg-García, Angela, Locatelli, Bruno, Martín-López, Berta, Meyfroidt, Patrick, Mwampamba, Tuyeni H., Nel, Jeanne, Nicholas, Kimberly A., Nicholson, Charles, Oteros-Rozas, Elisa, Rahlao, Sebataolo J., Raudsepp-Hearne, Ciara, Ricketts, Taylor, Shrestha, Uttam B., Torres, Carolina, Winkler, Klara J., and Zoeller, Kim

Published
2019
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10. Agriculture and hot temperatures interactively erode the nest success of habitat generalist birds across the United States.

Author

Lauck, Katherine S., Ke, Alison, Olimpi, Elissa M., Paredes, Daniel, Hood, Kees, Phillips, Thomas, Anderegg, William R. L., and Karp, Daniel S.

Subjects
*BIRD nests, *BIRD habitats, *FOREST regeneration, *ENVIRONMENTAL degradation, *AGRICULTURE, *WILDLIFE conservation
Abstract

Habitat conversion and climate change are fundamental drivers of biodiversity loss worldwide but are often analyzed in isolation. We used a continental-scale, decades-long database of more than 150,000 bird nesting attempts to explore how extreme heat affects avian reproduction in forests, grasslands, and agricultural and developed areas across the US. We found that in forests, extreme heat increased nest success, but birds nesting in agricultural settings were much less likely to successfully fledge young when temperatures reached anomalously high levels. Species that build exposed cup nests and species of higher conservation concern were particularly vulnerable to maximum temperature anomalies in agricultural settings. Finally, future projections suggested that ongoing climate change may exacerbate the negative effects of habitat conversion on avian nesting success, thereby compromising conservation efforts in human-dominated landscapes. [ABSTRACT FROM AUTHOR]

Published
2023
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12. Inconsistent effects of landscape heterogeneity and land-use on animal diversity in an agricultural mosaic: a multi-scale and multi-taxon investigation

Author

Reynolds, Chevonne, Fletcher, Jr., Robert J., Carneiro, Celine M., Jennings, Nicole, Ke, Alison, LaScaleia, Michael C., Lukhele, Mbhekeni B., Mamba, Mnqobi L., Sibiya, Muzi D., Austin, James D., Magagula, Cebisile N., Mahlaba, Themba’alilahlwa, Monadjem, Ara, Wisely, Samantha M., and McCleery, Robert A.

Published
2018
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17. Inconsistent effects of landscape heterogeneity and land-use on animal diversity in an agricultural mosaic: a multi-scale and multi-taxon investigation

Author

Reynolds, Chevonne, primary, Fletcher, Robert J., additional, Carneiro, Celine M., additional, Jennings, Nicole, additional, Ke, Alison, additional, LaScaleia, Michael C., additional, Lukhele, Mbhekeni B., additional, Mamba, Mnqobi L., additional, Sibiya, Muzi D., additional, Austin, James D., additional, Magagula, Cebisile N., additional, Mahlaba, Themba’alilahlwa, additional, Monadjem, Ara, additional, Wisely, Samantha M., additional, and McCleery, Robert A., additional

Published
2017
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20. Remnant forest in Costa Rican working landscapes fosters bird communities that are indistinguishable from protected areas.

Author

Solar, Ricardo, Karp, Daniel S., Ke, Alison, Echeverri, Alejandra, Krishnan, Jaya, Chan, Kai M.A., Zook, Jim, Juárez, Pedro, and Frishkoff, Luke O.

Subjects
PROTECTED areas, BIRD communities, FRAGMENTED landscapes, TROPICAL forests, BIRD diversity, BIRDHOUSES
Abstract

Copyright of Journal of Applied Ecology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
2019
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21. Integrating disparate occurrence reports to map data-poor species ranges and occupancy: a case study of the Vulnerable bearded pig Sus barbatus.

Author

Ke, Alison and Luskin, Matthew Scott

Subjects
*BEARDED pigs, *DEFORESTATION, *CONSERVATION biology
Abstract

Monitoring species ranges and suitable and occupied habitat are core components of biogeography, ecology and conservation biology, but it is difficult to do for rare, cryptic, wide-ranging, migratory or nomadic species. We present a transparent and objective process to combine multiple types of locality data (peer-reviewed and grey literature, museum collections, camera-trap inventories, and citizen science reports). We illustrate the advantages of this pooled approach by assessing change in range and patch occupancy for a data-poor and threatened nomadic keystone species, the bearded pig Sus barbatus , in Borneo, Sumatra and Peninsular Malaysia. We used a collated set of all occurrence observations (n = 240) to create minimum convex polygons for forested habitats for two time periods. We evaluated confidence that a patch was truly occupied by the overlap among data types. We found that 62% of the forest habitat of the Sumatran bearded pig S. barbatus oi was lost during 1990–2010 and that its range contracted by 76%; the Bornean bearded pig S. barbatus barbatus lost 23 and 24% of its forest habitat and range, respectively, and in Peninsular Malaysia the 93% range collapse of this subspecies during 1985–2010 is more severe than the 33% habitat loss alone would suggest. We conclude that integrating data types can improve mapping of the ranges of many data-poor species. [ABSTRACT FROM AUTHOR]

Published
2019
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