Article
Biochemistry & Molecular Biology
Mateu Menendez-Serra, Vicente J. Ontiveros, Joan Caliz, David Alonso, Emilio O. Casamayor
Summary: This study examines the assembly processes of bacterial and microeukaryotic communities along a salinity gradient and reveals that increasing salinity leads to a dominant role of selection over dispersal, resulting in decreased community turnover. The richness of microeukaryotes decreases with increasing salinity, suggesting that the net effect of selection and dispersal is determined by environmental conditions and microbial ecologies.
Article
Environmental Sciences
James Gahan, David R. Bellwood, Leo Nankervis, Sterling B. Tebbett
Summary: This study analyzed the characteristics of zooplankton communities in the offshore regions of the Queensland shelf using Australian data and found that the composition of these communities was predictable at a broad taxonomic level, but the variation in relative abundance was unpredictable.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Genetics & Heredity
Logan S. Whitehouse, Daniel R. Schrider
Summary: Timesweeper is a convolutional neural network-based tool that can identify selective sweeps using continuous genomic time-series data. It demonstrates that more accurate inferences about natural selection can be made using genomic time-series data.
Article
Computer Science, Artificial Intelligence
Jianing Teng, Dong Zhang, Wei Zou, Ming Li, Dah-Jye Lee
Summary: Typical Facial Expression Network (TFEN) proposes a new network structure to address the challenges in facial expression recognition. It uses two 2D CNNs to extract facial and expression features, and a facial feature decoupler to minimize the influence of individual facial characteristics. Experimental results show that TFEN achieves better recognition accuracy than state-of-the-art approaches on four popular dynamic FER datasets.
IEEE TRANSACTIONS ON AFFECTIVE COMPUTING
(2023)
Article
Ecology
Fearghal O'Donncha, Yihao Hu, Paulito Palmes, Meredith Burke, Ramon Filgueira, Jon Grant
Summary: This study introduces a novel spatio-temporal LSTM architecture for time series forecasting in environmental datasets, demonstrating its ability to accurately replicate complex signals and provide high performance. Learning from multiple sensors simultaneously can enhance robustness to missing data.
ECOLOGICAL INFORMATICS
(2022)
Article
Multidisciplinary Sciences
Arnau Pujol, Nanna Brokhattingen, Gloria Matambisso, Henriques Mbeve, Pau Cistero, Anna Escoda, Sonia Maculuve, Boaventura Cuna, Cardoso Melembe, Nelo Ndimande, Humberto Munguambe, Julia Montana, Lidia Nhamussua, Wilson Simone, Kevin K. A. Tetteh, Chris Drakeley, Benoit Gamain, Chetan E. Chitnis, Virander Chauhan, Llorenc Quinto, Arlindo Chidimatembue, Helena Marti-Soler, Beatriz Galatas, Caterina Guinovart, Francisco Saute, Pedro Aide, Eusebio Macete, Alfredo Mayor
Summary: The study found a spatio-temporal relationship between malaria trends in pregnant women attending first antenatal care visits and in children and health facilities. The P. falciparum rates detected in antenatal care mirrored rates in children, with a 2-3 months lag. The seroprevalence of pregnancy-specific antigen VAR2CSA reflected declining malaria trends. ANC-based malaria surveillance offers valuable information on temporal trends and geographic distribution of malaria burden.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Kaiya Provost, Stephanie Yun Shue, Meghan Forcellati, Brian Tilston Smith
Summary: Spatial models can explain genetic differentiation between populations based on factors such as geographic distance and environmental resistance. The genomic landscape of differentiation is diverse, indicating different evolutionary histories. This study compared different geographic predictors of differentiation in ten bird species and found that the characteristics of genomic landscapes varied, influenced by population structuring and admixture. Historical and contemporary mechanisms both played a role in genetic distance, with climate and habitat being particularly important. Different regions of the genome captured different evolutionary histories, suggesting that the genomic landscape of differentiation is associated with alternative geographic factors.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Computer Science, Artificial Intelligence
Yuchen Pan, Yuanyuan Shang, Tie Liu, Zhuhong Shao, Guodong Guo, Hui Ding, Qiang Hu
Summary: This paper proposes a novel Spatial-Temporal Attention Depression Recognition Network (STA-DRN) that enhances feature extraction and relevance of depression recognition by capturing global and local spatial-temporal information. The experimental results demonstrate competitive performance and visualization analysis shows significant responses in specific locations related to depression.
EXPERT SYSTEMS WITH APPLICATIONS
(2024)
Article
Plant Sciences
Wenjin Li, Xi Zhou, Zhiqiang Xiang, Jinhua Li, Shaopeng Wang, Michel Loreau, Lin Jiang
Summary: During secondary succession, both plant diversity and functional and compositional stability increase at different spatial scales. The study provides empirical evidence that biodiversity-mediated effects on ecosystem temporal stability strengthen over successional time.
JOURNAL OF ECOLOGY
(2023)
Article
Engineering, Civil
Richard D. Crago, Russell Qualls, Jozsef Szilagyi
Summary: This study aims to compare multiple versions of the Complementary Relationship (CR) between actual regional evaporation and apparent potential evaporation, and investigate their response to changes in spatial and temporal scaling. By using data from seven eddy-covariance flux stations in Australia and global ERA5 reanalysis data, the performance and parameter values of these versions were assessed.
JOURNAL OF HYDROLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Christopher P. Kozakiewicz, Alexandra K. Fraik, Austin H. Patton, Manuel Ruiz-Aravena, David G. Hamilton, Rodrigo Hamede, Hamish McCallum, Paul A. Hohenlohe, Mark J. Margres, Menna E. Jones, Andrew Storfer
Summary: Transcriptomics studies play a crucial role in oncology and infectious disease fields, helping to identify the molecular basis of phenotypic variations. Tasmanian devils, affected by DFTD, show different levels of survival, with host response heterogeneity likely playing a key role, but the fundamental processes underlying this variation remain unclear.
Article
Neurosciences
Zhihao Zhang, Tong Chen, Ye Liu, Chongyang Wang, Ke Zhao, Chang Hong Liu, Xiaolan Fu
Summary: The ability of humans to discern facial expressions is mediated by distributed face selective regions, such as the LO-faces and IP-faces. Through time-resolved decoding of neural responses, it was found that facial expressions could be successfully classified within 100 to 150 ms after stimulus onset. Additionally, similarity analyses with a convolutional neural network revealed that the LO-faces and IP-faces exhibited stronger correlations with deep representations of emotional categories rather than image-level information.
Article
Computer Science, Information Systems
Cun Ji, Mingsen Du, Yanxuan Wei, Yupeng Hu, Shijun Liu, Li Pan, Xiangwei Zheng
Summary: Time series classification is widely used in various domains, including EEG/ECG classification, device anomaly detection, and speaker authentication. Despite the existence of many methods, selecting intuitive temporal features for accurate classification remains a challenge. Therefore, this paper proposes a new method called TSC-RTF, which utilizes random temporal features, and shows that it can compete with state-of-the-art methods.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2023)
Article
Neurosciences
Tatiana A. Engel, Marieke L. Schoelvinck, Christopher M. Lewis
Summary: Human macroscopic neuroimaging reveals the organization of brain-wide activity, but hides the detailed responses and connections of individual neurons. New invasive approaches in animals allow for recording and manipulating neural activity at finer scales, shedding light on the significance of neural activity for global brain states and adaptive behavior.
Article
Forestry
Kathryn L. Purcell, Eric L. McGregor
Summary: White-headed woodpeckers prefer and nest more successfully in higher elevation true fir forests. Congruence exists between habitat preferences and nest survival, particularly at the landscape scale, indicating adaptive selection. However, at the nest site scale, they may exhibit maladaptive habitat selection.
FOREST ECOLOGY AND MANAGEMENT
(2021)
Article
Biochemistry & Molecular Biology
Casia Nursyifa, Anna Bruniche-Olsen, Genis Garcia-Erill, Rasmus Heller, Anders Albrechtsen
Summary: The SATC method is proposed to assign sex to samples and identify sex-linked scaffolds from NGS data, working for species with a homogametic/heterogametic sex determination system. It uses scaffold depth distribution and PCA to achieve sex assignment and sex-linked scaffold identification, without prior knowledge of sample sex, using WGS data.
MOLECULAR ECOLOGY RESOURCES
(2022)
Review
Biology
Janan Sykes, Barbara R. Holland, Michael A. Charleston
Summary: Proteins play a crucial role in connecting genotype and phenotype, but understanding the relationship between protein sequence and structure, and applying this knowledge to predict function, is challenging. Investigating the space of protein folds can provide insights into protein evolution and function.
BIOLOGICAL REVIEWS
(2023)
Article
Biology
Joshua Stevenson, Barbara Holland, Michael Charleston, Jeremy Sumner
Summary: The algebraic properties of flattenings and subflattenings can be used to identify edges in the true phylogeny and complete tree using pattern counts from sequence alignment. This method is attractive due to the relatively small number of possible internal edges among a set of taxa. However, more evaluation is needed for their effectiveness in inferring phylogenetic trees, especially for subflattenings.
BULLETIN OF MATHEMATICAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Liam Quinn, Genis Garcia-Erill, Cindy Santander, Anna Bruniche-Olsen, Xiaodong Liu, Mikkel-Holger S. Sinding, Michael P. P. Heaton, Timothy P. L. Smith, Patricia Pecnerova, Laura D. D. Bertola, Kristian Hanghoj, Malthe Sebro Rasmussen, Deon de Jager, Hans R. R. Siegismund, Anders Albrechtsen, Rasmus Heller, Ida Moltke
Summary: The iconic Cape buffalo has experienced population declines attributed to multiple factors, including the rinderpest pandemic and recent human activity. This study analyzed whole genome sequencing data to assess genetic diversity in Cape buffalo populations. The results indicate that recent inbreeding and colonialism-associated events have significantly impacted the genetic diversity of the southernmost populations.
Article
Virology
Christopher P. Kozakiewicz, Christopher P. Burridge, Justin S. Lee, Simona J. Kraberger, Nicholas M. Fountain-Jones, Robert N. Fisher, Lisa M. Lyren, Megan K. Jennings, Seth P. D. Riley, Laurel E. K. Serieys, Meggan E. Craft, W. Chris Funk, Kevin R. Crooks, Sue VandeWoude, Scott Carver
Summary: Spatially heterogeneous landscape factors, such as urbanisation, can impact the spread of wildlife diseases. However, there is limited research on the connection between pathogen transmission patterns and landscape features. This study used phylogeographic and machine learning approaches to investigate the influence of landscape and host factors on the genetic variation and spread of FIVLru among bobcats in coastal southern California. The results suggest that urban barriers to host movement constrain the spread of FIVLru and that natural habitat plays a role in virus transmission and spread.
Article
Genetics & Heredity
Felicia Bardan, Denice Higgins, Jeremy J. Austin
Summary: Massively parallel sequencing allows for high-throughput genetic testing, but its application to forensic testing is limited by the need for initial PCR amplification and the lack of customization for different markers. This study presents an alternative approach using hybridisation enrichment, which successfully enriches target DNA and provides comprehensive biological profiling for forensic intelligence testing. The custom panel of hybridisation baits accurately estimated biogeographic ancestry, hair and eye colour, and paternal lineage in modern male and female samples, demonstrating the utility of this approach.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2023)
Article
Ecology
E. M. Ringwaldt, B. W. Brook, J. C. Buettel, C. X. Cunningham, C. Fuller, R. Gardiner, R. Hamer, M. Jones, A. M. Martin, S. Carver
Summary: This study investigates the dynamics and drivers of landscape-scale wildlife disease using the case of sarcoptic mange in bare-nosed wombats in Tasmania, Australia. The research finds that the Tasmanian landscape is almost universally suitable for wombats, except in areas with high mean annual precipitation. However, the clinical signs of sarcoptic mange are widespread but heterogeneously distributed. The disease is most likely to occur in areas with high host habitat suitability, low annual precipitation, near freshwater sources, and minimal topographic roughness.
JOURNAL OF ANIMAL ECOLOGY
(2023)
Article
Zoology
Stevie N. Florent, Judy Clarke, Meredith J. Bashaw, Rodrigo Hamede, Menna E. Jones, Elissa Z. Cameron
Summary: Captivity can have physiological and behavioral effects on animals, potentially affecting conservation efforts. This study investigated the long-term effects of captivity on Tasmanian devils and found that both intensive captive and free-range captive environments maintained stress profiles similar to wild devils, indicating potential success in future reintroductions.
JOURNAL OF ZOOLOGY
(2023)
Article
Ecology
Jessica Stanhope, Jeremy J. Austin, Emily Skelly, Philip Weinstein
Summary: Methods guides are helpful for researchers, but they should be based on up-to-date scientific evidence to avoid outdated methodologies. A recent example of recommending UV sterilization for sample collection in microbiota restoration studies highlights the importance of accurate recommendations. Omissions or inaccurate guidance materials may lead to inaccurate research findings.
RESTORATION ECOLOGY
(2023)
Article
Ecology
Floriaan Devloo-Delva, Christopher P. Burridge, Peter M. Kyne, Juerg M. Brunnschweiler, Demian D. Chapman, Patricia Charvet, Xiao Chen, Geremy Cliff, Ryan Daly, J. Marcus Drymon, Mario Espinoza, Daniel Fernando, Laura Garcia Barcia, Kerstin Glaus, Blanca I. Gonzalez-Garza, Michael I. Grant, Rasanthi M. Gunasekera, Sebastian Hernandez, Susumu Hyodo, Rima W. Jabado, Sebastien Jaquemet, Grant Johnson, James T. Ketchum, Helene Magalon, James R. Marthick, Frederik H. Mollen, Stefano Mona, Gavin J. P. Naylor, John E. G. Nevill, Nicole M. Phillips, Richard D. Pillans, Bautisse D. Postaire, Amy F. Smoothey, Katsunori Tachihara, Bree J. Tillet, Jorge A. Valerio-Vargas, Pierre Feutry
Summary: In this study, the population structure of the Bull Shark was assessed globally for the first time. The results revealed reproductive isolation between and across ocean basins, with distinct island populations in Japan and Fiji. The Bull Sharks maintain gene flow through shallow coastal waters as dispersal corridors, but large oceanic distances and historical land-bridges act as barriers. Protecting these insular populations of Bull Sharks is crucial for ecosystem stability and functioning.
ECOLOGY AND EVOLUTION
(2023)
Article
Biodiversity Conservation
Cyril Scomparin, Caitlan Geale, Christopher N. Johnson, Menna E. Jones
Summary: Controlling invasive predators is crucial for protecting island biodiversity. This study investigates the effectiveness of a cat-trapping program on reducing feral cat density and its potential influence on native and invasive mammal species. The results show that trapping can effectively reduce cat density in a focused landscape context. However, the study found no direct effect of cat reduction on the abundance or behavior of native or invasive mammalian prey species. The study highlights the complexity of subsequent effects of invasive predator control on the broader ecosystem.
BIOLOGICAL INVASIONS
(2023)
Article
Fisheries
Mark Adams, Michael P. P. Hammer, Peter J. J. Unmack, Tarmo A. A. Raadik, Charlotte Jense, Christopher P. P. Burridge
Summary: This study synthesized historic and published molecular data to provide a systematic framework for the conservation and taxonomic efforts of Galaxiids in Tasmania. The study found phylogenetic diversity among Tasmanian Galaxiids, supporting the accepted taxonomy while also uncovering potential species-level diversity and taxonomic ambiguities. The results highlight the value of multi-locus studies in validating taxonomy and addressing conservation priorities.
MARINE AND FRESHWATER RESEARCH
(2023)
Article
Zoology
Tessa P. Manning, Jeremy J. Austin, Katherine E. Moseby, Melissa A. Jensen
Summary: Reintroduction programs face challenges in maintaining genetic diversity due to founder effects and subsequent reproductive skews. In a reintroduced western quoll population, pedigree analysis revealed multiple paternity but with skewed results, as one male fathered 65% of sampled offspring. The most successful male had a smaller body mass but a larger home range, and additional genetic management measures may be needed to address genetic drift and inbreeding risks.
AUSTRALIAN MAMMALOGY
(2023)
Article
Zoology
Calum X. Cunningham, Zach Aandahl, Menna E. Jones, Rowena Hamer, Christopher N. Johnson
Summary: Eastern quolls in Tasmania have experienced a significant decline in population over the past few decades, with evidence of declines in the early 2000s, mid-1990s, and more recently. The ongoing declines suggest that factors other than unfavorable weather are contributing to the decrease in numbers. Urgent conservation efforts are needed to protect the remaining populations in Tasmania and ensure the long-term survival of the species.
AUSTRALIAN MAMMALOGY
(2023)
Article
Ecology
Holly Rickards, John L. Read, Chris N. Johnson, Menna E. Jones, Matthew D. Pauza, Joss Bentley, Andry Sculthorpe, Morgan Humphrey, Rowena Hamer
Summary: This study aimed to test the target specificity of the Felixer grooming device in Tasmania. The results showed that the Felixer could successfully differentiate quoll species from feral cats, but could not reliably identify Tasmanian devils and common wombats as non-target species.