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"Jamison, Sarah"
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Forecasting severe respiratory disease hospitalizations using machine learning algorithms
by
Castelino, Lorraine
,
Dost, Katharina
,
Wu, Milton
in
Age groups
,
Algorithms
,
Artificial neural networks
2024
Background
Forecasting models predicting trends in hospitalization rates have the potential to inform hospital management during seasonal epidemics of respiratory diseases and the associated surges caused by acute hospital admissions. Hospital bed requirements for elective surgery could be better planned if it were possible to foresee upcoming peaks in severe respiratory illness admissions. Forecasting models can also guide the use of intervention strategies to decrease the spread of respiratory pathogens and thus prevent local health system overload. In this study, we explore the capability of forecasting models to predict the number of hospital admissions in Auckland, New Zealand, within a three-week time horizon. Furthermore, we evaluate probabilistic forecasts and the impact on model performance when integrating laboratory data describing the circulation of respiratory viruses.
Methods
The dataset used for this exploration results from active hospital surveillance, in which the World Health Organization Severe Acute Respiratory Infection (SARI) case definition was consistently used. This research nurse-led surveillance has been implemented in two public hospitals in Auckland and provides a systematic laboratory testing of SARI patients for nine respiratory viruses, including influenza, respiratory syncytial virus, and rhinovirus. The forecasting strategies used comprise automatic machine learning, one of the most recent generative pre-trained transformers, and established artificial neural network algorithms capable of univariate and multivariate forecasting.
Results
We found that machine learning models compute more accurate forecasts in comparison to naïve seasonal models. Furthermore, we analyzed the impact of reducing the temporal resolution of forecasts, which decreased the model error of point forecasts and made probabilistic forecasting more reliable. An additional analysis that used the laboratory data revealed strong season-to-season variations in the incidence of respiratory viruses and how this correlates with total hospitalization cases. These variations could explain why it was not possible to improve forecasts by integrating this data.
Conclusions
Active SARI surveillance and consistent data collection over time enable these data to be used to predict hospital bed utilization. These findings show the potential of machine learning as support for informing systems for proactive hospital management.
Journal Article
The evolution of bone-eating worm diversity in the Upper Cretaceous Chalk Group of the United Kingdom
2025
The bone-eating worm Osedax is today a member of the highly adapted invertebrate assemblages associated with whale carcasses on the ocean floor. The worm has also been found in a variety of other vertebrates in marine environments. Osedax borings are represented by the trace fossil Osspecus , which has been identified in fossil whales and marine reptiles, with the earliest occurrence in the Albian. In studies of present-day whale bones it has been found that individual species of Osedax create distinct boring morphologies. The diversity of boring geometries therefore provides a proxy for species diversity that can be applied to the fossil record to better understand the diversity, ecology, and evolution of extinct Osedax species. We examined marine reptile fossils from the Upper Cretaceous Chalk Group of the United Kingdom, and found five previously undocumented boring morphologies. These results, coupled with a re-examination of previous records of Osspecus, led to the naming of seven new ichnospecies. Using nannofossil biostratigraphy from the chalk, we constrained the ages of these occurrences and found a high species diversity in the early Late Cretaceous, indicating either a rapid diversification or an earlier origin for Osedax than previously estimated. Furthermore, we recognise five Cretaceous ichnospecies that are also found in the Cenozoic, three of which are also found in present-day whale bones.
Journal Article
Correction: The evolution of bone-eating worm diversity in the Upper Cretaceous Chalk Group of the United Kingdom
2025
Higgs et al. 2012 [4] Holotype: Boring number 1 (Figs 3(a) and 4a–c) in [4] in a fossil cetacean radius stored in the Museo di Storia Naturale, Sezione di Geologia e Paleontologia, Florence, Italy (IGF 1134T). thumbnail Download: * PPT PowerPoint slide * PNG larger image * TIFF original image Fig 3. LSID urn:lsid:zoobank.org:act:7067E5BC-4DF3-4278-B14D-4B9051372BF6 Etymology In honour of Eunice Newton Foote (1819–1888), the first person to suggest on experimental grounds that an increase in atmospheric CO2 would in turn increase the temperature of the Earth [5,6]. (2024) [8], Fig 2, panels C and D. Diagnosis: Borings with chamber diameters ranging from 1.3–2.4 mm, and total depths from 2.3–3.7 mm. Aperture necks can be variable in length. The boring depth and the curvature of the aperture necks may be related to density differences within the dentine, but the histology of dentine is poorly documented in reptiles.
Journal Article
The earliest fossil cetacean with Osedax borings: narrowing the spatiotemporal gap between Cretaceous marine reptiles and late Cenozoic whales
by
Upchurch, Paul
,
Jamison-Todd, Sarah
,
Mannion, Philip D.
in
Aquatic mammals
,
Biodiversity
,
Bioerosion
2025
Borings of the extant bone-eating worm Osedax have previously been found in Cenozoic cetaceans and Cretaceous marine reptiles. The stratigraphically youngest Cretaceous example is from the Maastrichtian, and, until now, the oldest Cenozoic example was from the Oligocene. This leaves a substantial temporal and taxonomic gap between examples from both Osedax-hosting tetrapod groups. Here, we report nine fossil cetacean specimens with Osspecus (Osedax bioerosion), identified via CT scans. These include a late Eocene occurrence of the basilosaurid Zyghorhiza kochii from the eastern USA, which represents the earliest known Cenozoic occurrence of Osedax borings, narrowing the temporal gap between occurrences of Osspecus in Cretaceous marine reptiles and Cenozoic whales. These specimens also include the first Osspecus-bearing fossil cetaceans from the northwestern Atlantic, expanding the Cenozoic biogeography of Osedax. Six ichnospecies of Osspecus are found in these cetacean fossils, including one newly described ichnospecies. The high morphological diversity of Osspecus in these Cenozoic specimens is broadly consistent with that of the Late Cretaceous, with several ichnospecies now known from both time intervals. Surviving lineages of other large marine vertebrates, such as turtles, crocodyliforms and fish, likely acted as suitable resources for Osedax across the Cretaceous–Paleogene boundary, bridging both the temporal and taxonomic gap.
Journal Article
Aggregate Trait Evolvability and Macroevolution in Two Sister Species of the Bryozoan Stylopoma
by
Leventhal, Sarah
,
Simpson, Carl
,
Jamison-Todd, Sarah
in
Animal Genetics and Genomics
,
Biomedical and Life Sciences
,
Colonies
2023
The study of trait evolution in modular animals is more complicated than that in solitary animals, because a single genotype of a modular colony can express an enormous range of phenotypic variation. Furthermore, traits can occur either at the module level or at the colony level. However, it is unclear how the traits at the colony level evolve. We test whether colony-level aggregate traits, defined as the summary statistics of a phenotypic distribution, can evolve. To quantify this evolutionary potential, we use parent-offspring pairs in two sister species of the bryozoan
Stylopoma
, grown and bred in a common garden breeding experiment. We find that the medians of phenotypic distributions are evolvable between generations of colonies. We also find that the structure of this evolutionary potential differs between these two species. Ancestral species align more closely with the direction of species divergence than the descendent species. This result indicates that aggregate trait evolvability can itself evolve.
Journal Article
The prevalence of invertebrate bioerosion on Mesozoic marine reptile bone from the Jurassic and Cretaceous of the United Kingdom: new data and implications for taphonomy and environment
by
Upchurch, Paul
,
Jamison-Todd, Sarah
,
Mannion, Philip D.
in
Aquatic reptiles
,
Archosauria
,
Art galleries & museums
2023
Invertebrate bioerosion on fossil bone can contribute to reconstructions of benthic taxonomic assemblages and inform us about oxygenation levels, water depth and exposure time on the seafloor prior to burial. However, these traces are not commonly described in the fossil record. To date, there have been only 13 published studies describing a total of 15 instances of invertebrate bioerosion on marine reptile fossil bones from the Mesozoic globally. We surveyed the collections of several UK museums with substantial occurrences of Mesozoic marine reptiles for evidence of invertebrate bioerosion. Here, we document 153 specimens exhibiting 171 newly recorded instances of invertebrate bioerosion on Jurassic and Cretaceous marine reptile bones. Several major bioeroding taxonomic groups are identified. Within the geological strata of the United Kingdom, there is a higher prevalence of bioerosion in the Cretaceous relative to the Jurassic, despite greater sampling of specimens from the Jurassic. Although biotic turnover and food web restructuring might have played a role, potentially pertaining to heightened productivity during the later stages of the Mesozoic Marine Revolution, we consider it more likely that this temporal change corresponds to differences in depositional environment and taphonomic history between the sampled rock units. In particular, the Cretaceous deposits are characterized by heightened oxygenation levels relative to their Jurassic counterparts, as well as reworking, which would have allowed two phases of bioerosion. A spatiotemporally broader dataset on invertebrate bioerosion on vertebrate bone will be important in further testing this and other hypotheses.
Journal Article
Establishing components of cultural competence healthcare models to better cater for the needs of migrants with disability: a systematic review
2016
This study examined the challenges of providing services to migrants with disability (MWD), including healthcare providers’ (HCP) level of cultural competence, and documented components of the cultural competence framework required to reduce disability-related health inequalities. This systematic review was undertaken according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Six databases were searched from January 2000 to August 2013: Ovid Medline, Ovid PsychINFO, EMBASE, CINHAL plus, Informit health databases and Scopus. The search focused on MWD, carers of MWD and HCP working with MWD in industrialised countries. The search yielded 271 articles of which 11 met the inclusion criteria (10 qualitative and 1 quantitative). While HCP perceived themselves as being culturally competent, carers of MWD felt that HCP needed to be more culturally competent as MWD’s needs were not being adequately addressed due to cultural misunderstandings and disrespect of cultural values, beliefs and traditions. The review found one existing healthcare model intended for use with MWD; however, the lack of specific attention to cultural competency limits its clinical utility. The findings of this review led to the development of suggested components to be included in a cultural competence model for HCP working with MWD.
Journal Article
Aggregate trait evolvability and macroevolution in two sister species of the bryozoan Stylopoma
2022
The study of trait evolution in modular animals is more complicated than that in solitary animals, because a single genotype of a modular colony can express an enormous range of phenotypic variation. Furthermore, traits can occur either at the module level or at the colony level. However, it is unclear how the traits at the colony level evolve. We test whether colony-level aggregate traits, defined as the summary statistics of a phenotypic distribution, can evolve. To quantify this evolutionary potential, we use parent-offspring pairs in two sister species of the bryozoan Stylopoma, grown and bred in a common garden breeding experiment. We find that the medians of phenotypic distributions are evolvable between generations of colonies. We also find that the structure of this evolutionary potential differs between these two species. Ancestral species align more closely with the direction of species divergence than the descendent species. This result indicates that aggregate trait evolvability can itself evolve.
Micro- and macroevolutionary change of colony-level traits in bryozoans
by
Leventhal, Sarah E
,
Simpson, Carl
,
Jamison-Todd, Sarah
in
Colonies
,
Divergence
,
Division of labor
2021
The evolution of trait variation among populations of animals is difficult to study due to the many overlapping genetic and environmental influences that control phenotypic expression. In a group of animals, bryozoans, it is possible to isolate genetic contributions to phenotypic variation, due to the modular nature of bryozoan colonies. Each bryozoan colony represents a snapshot of the phenotypes that correspond to a single genotype, which can be summarized as a phenotypic distribution. We test whether these phenotypic distributions are heritable across generations of colonies in two sister species of the bryozoan Stylopoma, grown and bred in a common garden breeding experiment. We find that components of phenotypic distributions, specifically median trait values of colony members, are heritable between generations of colonies. Furthermore, this heredity has macroevolutionary importance because it correlates with the morphological distance between these two species. Because parts of phenotypic distributions are heritable, and this heritability corresponds to evolutionary divergence between species, we infer that these distributions have the potential to evolve. The evolutionary potential of these phenotypic distributions may underpin the emergence of colony-level traits, like division of labor in colonies. Competing Interest Statement The authors have declared no competing interest.