36 Works

Data from: Adaptation of brain functional and structural networks in aging

Annie Lee, Nagulan Ratnarajah, Ta Anh Tuan, Shen-Hsing Annabel Chen & Anqi Qiu
The human brain, especially the prefrontal cortex (PFC), is functionally and anatomically reorganized in order to adapt to neuronal challenges in aging. This study employed structural MRI, resting-state fMRI (rs-fMRI), and high angular resolution diffusion imaging (HARDI), and examined the functional and structural reorganization of the PFC in aging using a Chinese sample of 173 subjects aged from 21 years and above. We found age-related increases in the structural connectivity between the PFC and posterior...

Data from: Infection of male rats with Toxoplasma gondii results in enhanced delay aversion and neural changes in the nucleus accumbens core

Donna Tan, Linda Jing Ting Soh, Lee Wei Lim, Tan Chia Wei Daniel, Xiaodong Zhang & Ajai Vyas
Rats infected with the protozoan parasite Toxoplasma gondii exhibit reduced avoidance of predator odours. This behavioural change is likely to increase transmission of the parasite from rats to cats. Here, we show that infection with T. gondii increases the propensity of the infected rats to make more impulsive choices, manifested as delay aversion in an intertemporal choice task. Concomitantly, T. gondii infection causes reduction in dopamine content and neuronal spine density of the nucleus accumbens...

Data from: Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells

Anna Mattout, Yair Aaronson, Badi Sri Sailaja, Edupuganti V. Raghu Ram, Arigela Harikumar, Jan-Philipp Mallm, Kae Hwan Sim, Malka Nissim-Rafinia, Emmanuelle Supper, Prim B. Singh, Siu Kwan Sze, Susan M. Gasser, Karsten Rippe & Eran Meshorer
Background: Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. Results: Here we identify Heterochromatin Protein 1β (HP1β) as...

Data from: The contrasting phylodynamics of human influenza B viruses

Dhanasekaran Vijaykrishna, Edward C. Holmes, Udayan Joseph, Mathieu Fourment, Yvonne C. F. Su, Rebecca Halpin, Raphael T. C. Lee, Yi-Mo Deng, Vithiagaran Gunalan, Xudong Lin, Tim Stockwell, Nadia B. Fedorova, Bin Zhou, Natalie Spirason, Denise K. Kühnert, Veronika Bošková, Tanja Stadler, Anna-Maria Costa, Dominic E. Dwyer, Q. Sue Huang, Lance C. Jennings, William Rawlinson, Sheena G. Sullivan, Aeron C. Hurt, Sebastian Maurer-Stroh … & Raphael TC Lee
A complex interplay of viral, host and ecological factors shape the spatio-temporal incidence and evolution of human influenza viruses. Although considerable attention has been paid to influenza A viruses, a lack of equivalent data means that an integrated evolutionary and epidemiological framework has until now not been available for influenza B viruses, despite their significant disease burden. Through the analysis of over 900 full genomes from an epidemiological collection of more than 26,000 strains from...

Influence of grain size on strength of rocks: new insights from DEM grain-based modeling

Jun Peng, Louis Ngai Yuen Wong & Cee Ing Teh
Grain size effect on rock strength is a topic of great interest in solid earth science. From literature review, rock strength generally decreases with the increase of grain size for both silicate rock and carbonate rock in laboratory tests; however, some recent numerical simulation results conflict with those obtained in laboratory tests. To address this issue, the effect of grain size on rock strength is investigated numerically in this paper using the grain-based model by...

Data from: Impact of plant functional group and species removals on soil and plant nitrogen and phosphorus across a retrogressive chronosequence

David Wardle, Michael Gundale, Paul Kardol, Marie-Charlotte Nilsson Hegethorn & Nicolas Fanin
1. In the prolonged absence of catastrophic disturbance, ecosystem retrogression occurs, which is characterized by declining soil nitrogen (N) and phosphorus (P) availability, increasing plant and soil N to P ratios, and reduced plant biomass and productivity. It is, however, largely unknown as to how the effects of plant communities on soil nutrients change during retrogression or might contribute to declining nutrient availability as retrogression proceeds. 2. We studied a well characterized system of 30...

Precipitation regime controls bryosphere carbon cycling similarly across contrasting ecosystems

Roger Grau-Andrés, David Wardle, Marie-Charlotte Nilsson & Paul Kardol
In arctic and boreal ecosystems, ground bryophytes play an important role in regulating carbon (C) exchange between vast belowground C stores and the atmosphere. Climate is changing particularly fast in these high-latitude regions, but it is unclear how altered precipitation regimes will affect C dynamics in the bryosphere (i.e., the ground moss layer including senesced moss, litter, and associated biota) and the closely associated upper humus layer, and how these effects will vary across contrasting...

Data from: Comparative and population mitogenomic analyses of Madagascar’s extinct, giant ‘subfossil’ lemurs

Logan Kistler, Aakrosh Ratan, Laurie R. Godfrey, Brooke E. Crowley, Cris E. Hughes, Runhua Lei, Yinqui Cui, Mindy L. Wood, Kathleen M. Muldoon, Haingoson Andriamialison, John J. McGraw, Lynn P. Tomsho, Stephan C. Schuster, Webb Miller, Edward E. Louis, Anne D. Yoder, Ripan S. Malhi, George H. Perry & Yinqiu Cui
Humans first arrived on Madagascar only a few thousand years ago. Subsequent habitat destruction and hunting activities have had significant impacts on the island's biodiversity, including the extinction of megafauna. For example, we know of 17 recently extinct ‘subfossil’ lemur species, all of which were substantially larger (body mass ∼11–160 kg) than any living population of the ∼100 extant lemur species (largest body mass ∼6.8 kg). We used ancient DNA and genomic methods to study...

Data from: Analysis of wild macaque stone tools used to crack oil palm nuts

Tomos Proffitt, V. Lydia Luncz, Suchinda Malaivijitnond, Michael Gumert, Magdalena S. Svensson & Micahel Haslam
The discovery of oil palm (Elaeis guineensis) nut-cracking by wild long-tailed macaques (Macaca fascicularis) is significant for the study of non-human primate and hominin percussive behaviour. Up until now, only West African chimpanzees (Pan troglodytes verus) and modern human populations were known to use stone hammers to crack open this particular hard-shelled palm nut. The addition of non-habituated, wild macaques increases our comparative dataset of primate lithic percussive behaviour focused on this one plant species....

Data from: Genetic variability, local selection and demographic history: genomic evidence of evolving towards allopatric speciation in Asian seabass

Le Wang, Zi YI Wan, Huan Sein Lim &
Genomewide analysis of genetic divergence is critically important in understanding the genetic processes of allopatric speciation. We sequenced RAD tags of 131 Asian seabass individuals of six populations from South-East Asia and Australia/Papua New Guinea. Using 32 433 SNPs, we examined the genetic diversity and patterns of population differentiation across all the populations. We found significant evidence of genetic heterogeneity between South-East Asian and Australian/Papua New Guinean populations. The Australian/Papua New Guinean populations showed a...

Data from: The role of bryophytes for tree seedling responses to winter climate change: implications for the stress gradient hypothesis

Signe Lett, David A. Wardle, Marie-Charlotte Nilsson, Laurenz M. Teuber & Ellen Dorrepaal
1.When tree seedlings establish beyond the current tree line due to climate warming, they encounter existing vegetation, such as bryophytes that often dominate in arctic and alpine tundra. The stress gradient hypothesis (SGH) predicts that plant interactions in tundra become increasingly negative as climate warms and conditions become less harsh. However, for seedlings climate warming might not result in lower winter stress, if insulating snow cover is reduced. 2.We aimed to understand to if bryophytes...

Data from: Coral settlement on a highly disturbed equatorial reef system

Andrew G. Bauman, James R. Guest, Glenn Dunshea, Jeffery Low, Peter A. Todd & Peter D. Steinberg
Processes occurring early in the life stages of corals can greatly influence the demography of coral populations, and successful settlement of coral larvae that leads to recruitment is a critical life history stage for coral reef ecosystems. Although corals in Singapore persist in one the world’s most anthropogenically impacted reef systems, our understanding of the role of coral settlement in the persistence of coral communities in Singapore remains limited. Spatial and temporal patterns of coral...

Data from: Coordinated responses of soil communities to elevation in three subarctic vegetation types

G. F. Ciska Veen, Jonathan R. De Long, Paul Kardol, Maja K. Sundqvist, L. Basten Snoek & David A. Wardle
Global warming has begun to have a major impact on the species composition and functioning of plant and soil communities. However, long-term community and ecosystem responses to increased temperature are still poorly understood. In this study, we used a well-established elevational gradient in northern Sweden to elucidate how plant, microbial and nematode communities shift with elevation and associated changes in temperature in three highly contrasting vegetation types (i.e. heath, meadow and Salix vegetation). We found...

Bryosphere loss impairs litter decomposition consistently across moss species, litter types, and micro-arthropod abundance

Roger Grau-Andrés, David A. Wardle & Paul Kardol
The bryosphere (i.e., ground mosses and their associated biota) is a key driver of nutrient and carbon dynamics in many terrestrial ecosystems, in part because it regulates litter decomposition. However, we have a poor understanding of how litter decomposition responds to changes in the bryosphere, including changes in bryosphere cover, moss species, and bryosphere-associated biota. Specifically, the contribution of micro-arthropods to litter decomposition in the bryosphere is unclear. Here, we used a 16-month litterbag field...

Data from: Patterns of nitrogen-fixing tree abundance in forests across Asia and America

Duncan N. L. Menge, Ryan A. Chisholm, Stuart J. Davies, Kamariah Abu Salim, David Allen, Mauricio Alvarez, Norm Bourg, Warren Y. Brockelman, Sarayudh Bunyavejchewin, Nathalie Butt, Min Cao, Wirong Chanthorn, Wei-Chun Chao, Keith Clay, Richard Condit, Susan Cordell, João Batista Da Silva, H. S. Dattaraja, Ana Cristina Segalin De Andrade, Alexandre A. Oliveira, Jan Den Ouden, Michael Drescher, Christine Fletcher, Christian P. Giardina, C. V. Savitri Gunatilleke … & Tak Fung
Symbiotic nitrogen (N)‐fixing trees can provide large quantities of new N to ecosystems, but only if they are sufficiently abundant. The overall abundance and latitudinal abundance distributions of N‐fixing trees are well characterised in the Americas, but less well outside the Americas. Here, we characterised the abundance of N‐fixing trees in a network of forest plots spanning five continents, ~5,000 tree species and ~4 million trees. The majority of the plots (86%) were in America...

Semi‐quantitative metabarcoding reveals how climate shapes arthropod community assembly along elevation gradients on Hawaii Island

Jun Ying Lim, Jairo Patiño, Suzuki Noriyuki, Henrik Krehenwinkel, Luis Simmari, Rosemary Gillespie, Luis Cayetano & Rosemary G. Gillespie
Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche...

Data from: Ecological and evolutionary significance of primates’ most consumed plant families

Jun Ying Lim, Michael D. Wasserman, Jorin Veen, Marie-Lynne Despres-Einspenner & W. Daniel Kissling
Angiosperms have been essential components of primate diet for millions of years, but the relative importance of different angiosperm families in primate diets and their influence on primate evolution and ecology remains unclear. Here, we assess the contribution and ecological and evolutionary significance of plant families to the diets of wild primates based on an unprecedented dietary dataset of over 8,000 dietary records, compiled from 140 primary sources encompassing 109 primate species. Out of the...

Data from: Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

Victor C. Mason, Gang Li, Patrick Minx, Jurgen Schmitz, Gennady Churakov, Liliya Doronina, Amanda D. Melin, Nathaniel J. Dominy, Norman T-L. Lim, Mark S. Springer, Richard K. Wilson, Wesley C. Warren, Kristofer M. Helgen & William J. Murphy
Colugos are one of the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculo-skeletal related genes that likely underlie their nocturnal...

Data from: Revisiting the measurement of anomie

Ali Teymoori, Jolanda Jetten, Brock Bastian, Amarina Ariyanto, Frédérique Autin, Nadia Ayub, Constantina Badea, Tomasz Besta, Fabrizio Butera, Rui Costa-Lopes, Lijuan Cui, Carole Fantini, Gillian Finchilesc, Lowell Gaertner, Mario Gollwitzer, Ángel Gómez, Roberto González, Ying Yi Hong, Dorthe Høj Jensen, Minoru Karasawa, Thomas Kessler, Olivier Klein, Marcus Lima, Tuuli Anna Mähönen, Laura Megevand … & Gillian Finchilescu
Sociologists coined the term "anomie" to describe societies that are characterized by disintegration and deregulation. Extending beyond conceptualizations of anomie that conflate the measurements of anomie as 'a state of society' and as a 'state of mind', we disentangle these conceptualizations and develop an analysis and measure of this phenomenon focusing on anomie as a perception of the 'state of society'. We propose that anomie encompasses two dimensions: a perceived breakdown in social fabric (i.e.,...

Data from: Toxoplasma gondii infection enhances testicular steriodogeneis in rat

Audrey Lim, Vineet Kumar, Shantala A. Hari Dass & Ajai Vyas
The protozoan parasite Toxoplasma gondii enhances the sexual attractiveness of infected male rats and attenuates the innate fear of cat odor in infected individuals. These behavioral changes plausibly lead to greater transmission of parasites through sexual and trophic routes, respectively. Testosterone, a testicular steroid, is known to reduce fear and enhance sexual attractiveness in males. Here, we show that Toxoplasma gondii infection enhances expression of genes involved in facilitating synthesis of testosterone, resulting in greater...

Data from: Biotic and abiotic plant-soil feedback depends on nitrogen-acquisition strategy and shifts during long-term ecosystem development

Guochen Kenny Png, Hans Lambers, Paul Kardol, Benjamin L. Turner, David A. Wardle & Etienne Laliberté
1. Feedback between plants and soil is an important driver of plant community structure, but it remains unclear whether plant-soil feedback (PSF): (i) reflects changes in biotic or abiotic properties, (ii) depends on environmental context in terms of soil nutrient availability, and (iii) varies among plant functional groups. Because soil nutrient availability strongly affects plant distribution and performance, soil chemical properties and plant nutrient-acquisition strategies might serve as important drivers of PSF. 2. We used...

Data from: Toxoplasma gondii infection reduces predator aversion in rats through epigenetic modulation in the host medial amygdala

Shantala Arundhati Hari Dass & Ajai Vyas
Male rats (Rattus novergicus) infected with protozoan Toxoplasma gondii relinquish their innate aversion to the cat odors. This behavioral change is postulated to increase transmission of the parasite to its definitive felid hosts. Here, we show that the Toxoplasma gondii infection institutes an epigenetic change in the DNA methylation of the arginine vasopressin promoter in the medial amygdala of male rats. Infected animals exhibit hypomethylation of arginine vasopressin promoter, leading to greater expression of this...

Data from: Cross-cultural similarity in relationship-specific social touching

Juulia T. Suvilehto, Lauri Nummenmaa, Tokiko Harada, Robin I. M. Dunbar, Riitta Hari, Robert Turner, Norihiro Sadato & Ryo Kitada
Many species use touching for reinforcing social structures, and particularly non-human primates use social grooming for managing their social networks. However, it is still unclear how social touch contributes to maintenance and reinforcement of human social networks. Human studies in Western cultures suggest that the body locations where touch is allowed are associated with the strength of the emotional bond between the person touched and the toucher. However, it is unknown to what extent this...

Post‐agriculture rain forest succession on a tropical Pacific island

Edward L. Webb, Avele Iofi Lalogafu’afu’a, Martin Van De Bult, Wei Kit Lee, Siaifoi Fa'aumu, Muhammad Izuddin, Mark A. MacDonald, Roger Meyer, Rachel Rui Ying Oh, Alden P. Tagarino, Rachel C. Webb, Adam C. Miles & Martin Bult
We surveyed the tree and seedling community in 34 vegetation plots in mature and >50 y old secondary lowland rain forest on the Polynesian island of Tutuila, American Samoa. The main data set includes original data from the tree surveys as well as all repeat surveys of seedling plots. We also include all R code and data sets used in analyses, including soil and environmental data, species by plot matrices for NMDS, and processed data...

Data from: Dung beetle-megafauna trophic networks in Singapore’s fragmented forests

Xin Rui Ong, Eleanor M. Slade & Matthew L. M. Lim
We investigated trophic networks between dung beetles and megafauna species in five forest fragments in Singapore varying in size and isolation. We found that Singapore’s dung beetle communities were attracted to extant and extinct dung types from different dietary groups. All forest fragment networks were similar, and displayed high generalism and high nestedness.

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Affiliations

  • Nanyang Technological University
    36
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    10
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    3
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