title: A 3-factor epistatic model predicts digital ulcers in Italian scleroderma patients

authors: Beretta, Lorenzo

subjects: Cytokine

abstract: Background
The genetic background may predispose systemic sclerosis (SSc) patients to the development of digital ulcers (DUs).
Methods
Twenty-two functional cytokine single nucleotide polymorphisms (SNPs) and 3 HLA class I and II antigens were typed at the genomic level by polymerase chain reaction in 200 Italian SSc patients. Associations with DUs were sought by parametric models and with the Multifactor Dimensionality Reduction (MDR) algorithm to depict the presence of epistasis. Biological models consistent with MDR results were built by means of Petri nets to describe the metabolic significance of our findings.
Results
On the exploratory analysis, the diffuse cutaneous subset (dcSSc) was the only single factor statistically associated with DUs (p = 0.045, ns after Bonferroni correction). Gene–gene analysis showed that a 3-factor model comprising the IL-6 C-174G, the IL-2 G-330T SNPs and the HLA-B*3501 allele was predictive for the occurrence of DUs in our population (testing accuracy = 66.9%; p < 0.0001, permutation testing).
Conclusion
Biological interpretation via Petri net showed that IL-6 is a key factor in determining DUs occurrence and that this cytokines may synergise with HLA-B*3501 to determine DUs onset. Owing to the limited number of patients included in the study, future research are needed to replicate our statistical findings as well as to better determine their functional meaning.

text: A 3-factor epistatic model predicts digital ulcers in Italian scleroderma patients Background
The genetic background may predispose systemic sclerosis (SSc) patients to the development of digital ulcers (DUs).
Methods
Twenty-two functional cytokine single nucleotide polymorphisms (SNPs) and 3 HLA class I and II antigens were typed at the genomic level by polymerase chain reaction in 200 Italian SSc patients. Associations with DUs were sought by parametric models and with the Multifactor Dimensionality Reduction (MDR) algorithm to depict the presence of epistasis. Biological models consistent with MDR results were built by means of Petri nets to describe the metabolic significance of our findings.
Results
On the exploratory analysis, the diffuse cutaneous subset (dcSSc) was the only single factor statistically associated with DUs (p = 0.045, ns after Bonferroni correction). Gene–gene analysis showed that a 3-factor model comprising the IL-6 C-174G, the IL-2 G-330T SNPs and the HLA-B*3501 allele was predictive for the occurrence of DUs in our population (testing accuracy = 66.9%; p < 0.0001, permutation testing).
Conclusion
Biological interpretation via Petri net showed that IL-6 is a key factor in determining DUs occurrence and that this cytokines may synergise with HLA-B*3501 to determine DUs onset. Owing to the limited number of patients included in the study, future research are needed to replicate our statistical findings as well as to better determine their functional meaning.

year: 2010

title: Effects of anthropogenic land use on temperate mangrove forests

authors: Thomson, Timothy

subjects: Temperate mangrove forests

abstract: Coastal ecosystems worldwide are facing unprecedented challenges due to ever increasing human activities, resulting in increased land-derived stressors that can threaten the health and integrity of these systems. Mangrove forests are unique ecosystems that play a crucial role in filtering nutrients, retaining pollutants, and sequestering carbon. However, to what extent they are impacted by an intensification of human pressures is unclear and empirical evidence of landscape scale effects of a holistic view of the ecosystem is scarce. This thesis investigates the effects of human land use on several aspects of temperate mangrove ecosystems and aims to identify potential vulnerabilities of ecosystem processes to provide a holistic view on the impacts that humas are having on these important ecosystems.
By working across a broad gradient of human land use, the first chapter establishes a connection between human land use intensity in catchments and regionally generalizable trends in mangrove forest structure and physicochemical parameters in sediments. Highlighting the integrated nature of anthropogenic impacts, this chapter emphasizes the need for holistic evaluations in assessing responses of complex natural systems to change.
The second chapter investigates environmental controls on organic matter degradation in mangrove forests. Results from this study emphasize the importance of considering multiple factors influencing degradation processes, that vary with the quality of the decaying organic matter. Furthermore, using the human land use gradient from the previous chapter, this study identifies an impact of human land use through eutrophication on the rate of labile organic matter loss from mangrove sediments.
The third chapter provides insights into bacterial communities in temperate mangrove sediments, revealing the persistent effects of nutrient enrichment even after the biochemical signal is lost. The study highlights the spatial resolution needed to detect impacts on microbial communities, warning that functional changes may persist beyond observable eutrophication effects.

The synthesis of these chapters provides a holistic view of the effects of anthropogenic impacts on temperate mangrove ecosystems across various scales. While some components of the system may benefit from moderate amounts of nutrient enrichment, others can deteriorate, ultimately diminishing overall service provisioning of the system. To understand and quantify these effects, this thesis calls for a nuanced understanding of disturbance effects on mangrove ecosystems, emphasizing their complexity and the interconnectedness of their components. It adds a valuable information about the functional resilience of mangrove forests in the face of human pressures and highlights the importance of an ecosystem-based perspective when assessing the effects of external stressors on these important ecosystems.

text: Effects of anthropogenic land use on temperate mangrove forests Coastal ecosystems worldwide are facing unprecedented challenges due to ever increasing human activities, resulting in increased land-derived stressors that can threaten the health and integrity of these systems. Mangrove forests are unique ecosystems that play a crucial role in filtering nutrients, retaining pollutants, and sequestering carbon. However, to what extent they are impacted by an intensification of human pressures is unclear and empirical evidence of landscape scale effects of a holistic view of the ecosystem is scarce. This thesis investigates the effects of human land use on several aspects of temperate mangrove ecosystems and aims to identify potential vulnerabilities of ecosystem processes to provide a holistic view on the impacts that humas are having on these important ecosystems.
By working across a broad gradient of human land use, the first chapter establishes a connection between human land use intensity in catchments and regionally generalizable trends in mangrove forest structure and physicochemical parameters in sediments. Highlighting the integrated nature of anthropogenic impacts, this chapter emphasizes the need for holistic evaluations in assessing responses of complex natural systems to change.
The second chapter investigates environmental controls on organic matter degradation in mangrove forests. Results from this study emphasize the importance of considering multiple factors influencing degradation processes, that vary with the quality of the decaying organic matter. Furthermore, using the human land use gradient from the previous chapter, this study identifies an impact of human land use through eutrophication on the rate of labile organic matter loss from mangrove sediments.
The third chapter provides insights into bacterial communities in temperate mangrove sediments, revealing the persistent effects of nutrient enrichment even after the biochemical signal is lost. The study highlights the spatial resolution needed to detect impacts on microbial communities, warning that functional changes may persist beyond observable eutrophication effects.

The synthesis of these chapters provides a holistic view of the effects of anthropogenic impacts on temperate mangrove ecosystems across various scales. While some components of the system may benefit from moderate amounts of nutrient enrichment, others can deteriorate, ultimately diminishing overall service provisioning of the system. To understand and quantify these effects, this thesis calls for a nuanced understanding of disturbance effects on mangrove ecosystems, emphasizing their complexity and the interconnectedness of their components. It adds a valuable information about the functional resilience of mangrove forests in the face of human pressures and highlights the importance of an ecosystem-based perspective when assessing the effects of external stressors on these important ecosystems.

year: 2024

title: Tōku tūrangawaewae: Culture, identity, and belonging for Māori homeless people

authors: Groot, Shiloh Ann Maree

subjects: Māori

abstract: To be Māori is to have a tūrangawaewae (a place of strength and belonging, a place to stand). If so, is it conceivable that Māori are homeless in our own homeland? This presentation focuses on the experiences of two Māori homeless people who took part in a 3-year research project conducted in partnership with not-for-profit service agencies. Previous research into street homelessness has all but ignored indigenous histories, circumstances and worldviews. The situation in which indigenous people find themselves requires us to rethink how we understand homelessness and the development of culturally based roles and identities on the street and beyond.

text: Tōku tūrangawaewae: Culture, identity, and belonging for Māori homeless people To be Māori is to have a tūrangawaewae (a place of strength and belonging, a place to stand). If so, is it conceivable that Māori are homeless in our own homeland? This presentation focuses on the experiences of two Māori homeless people who took part in a 3-year research project conducted in partnership with not-for-profit service agencies. Previous research into street homelessness has all but ignored indigenous histories, circumstances and worldviews. The situation in which indigenous people find themselves requires us to rethink how we understand homelessness and the development of culturally based roles and identities on the street and beyond.

year: 2010