Integrated social-ecological data for regional natural resource management.

Natural resource managers need information about both human and natural systems and interactions between those systems. Much data is available, but mostly from disparate sources and data have often been collected at different time steps and at different geographic scales. We used insights from the literature to select 270 relevant variables, available at national scale, from 33 unique (Australian) data sources. There were numerous with repeat measures, so in total we have 425 variables: 143 specific to 2016, 148 specific to 2021, and 134 available for both periods. We used GIS to summarize the variables spatially based on two geographic boundaries: one describes 63 Natural Resource Management Regions; the other describes 419 (sub) bioregions (formally, IBRA - Interim Biogeographic Regionalisation for Australia). Data deficiencies prevented us from being able to report on all variables for all regions. In the NRM dataset many regions are offshore islands, about which data are not generally available. Moreover, many IBRA regions are small and household level data are not always available at that scale. For analyses requiring a complete dataset at a single time step, our 2021 dataset for NRM regions includes 270 unique variables that describe 56 regions. Our IBRA data includes 214 variables describing 409 regions. To help managers select appropriate data for specific problems/contexts, the metadata file also categorises variables according to (a) whether they pertain to the social or ecological system, or interactions; (b) the segment of society described (where relevant); and (c) the frequency with which data are updated.

AusTraits, a curated plant trait database for the Australian flora.

We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.

LipidFinder 2.0: advanced informatics pipeline for lipidomics discovery applications.

SUMMARY: We present LipidFinder 2.0, incorporating four new modules that apply artefact filters, remove lipid and contaminant stacks, in-source fragments and salt clusters, and a new isotope deletion method which is significantly more sensitive than available open-access alternatives. We also incorporate a novel false discovery rate method, utilizing a target-decoy strategy, which allows users to assess data quality. A renewed lipid profiling method is introduced which searches three different databases from LIPID MAPS and returns bulk lipid structures only, and a lipid category scatter plot with color blind friendly pallet. An API interface with XCMS Online is made available on LipidFinder's online version. We show using real data that LipidFinder 2.0 provides a significant improvement over non-lipid metabolite filtering and lipid profiling, compared to available tools. AVAILABILITY AND IMPLEMENTATION: LipidFinder 2.0 is freely available at https://github.com/ODonnell-Lipidomics/LipidFinder and http://lipidmaps.org/resources/tools/lipidfinder. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Correction to: Timing rather than user traits mediates mood sampling on smartphones.

An amendment to this paper has been published and can be accessed via the original article.

Metabolic Dysregulation of the Lysophospholipid/Autotaxin Axis in the Chromosome 9p21 Gene SNP rs10757274.

BACKGROUND: Common chromosome 9p21 single nucleotide polymorphisms (SNPs) increase coronary heart disease risk, independent of traditional lipid risk factors. However, lipids comprise large numbers of structurally related molecules not measured in traditional risk measurements, and many have inflammatory bioactivities. Here, we applied lipidomic and genomic approaches to 3 model systems to characterize lipid metabolic changes in common Chr9p21 SNPs, which confer ≈30% elevated coronary heart disease risk associated with altered expression of ANRIL, a long ncRNA. METHODS: Untargeted and targeted lipidomics was applied to plasma from NPHSII (Northwick Park Heart Study II) homozygotes for AA or GG in rs10757274, followed by correlation and network analysis. To identify candidate genes, transcriptomic data from shRNA downregulation of ANRIL in HEK-293 cells was mined. Transcriptional data from vascular smooth muscle cells differentiated from induced pluripotent stem cells of individuals with/without Chr9p21 risk, nonrisk alleles, and corresponding knockout isogenic lines were next examined. Last, an in-silico analysis of miRNAs was conducted to identify how ANRIL might control lysoPL (lysophosphospholipid)/lysoPA (lysophosphatidic acid) genes. RESULTS: Elevated risk GG correlated with reduced lysoPLs, lysoPA, and ATX (autotaxin). Five other risk SNPs did not show this phenotype. LysoPL-lysoPA interconversion was uncoupled from ATX in GG plasma, suggesting metabolic dysregulation. Significantly altered expression of several lysoPL/lysoPA metabolizing enzymes was found in HEK cells lacking ANRIL. In the vascular smooth muscle cells data set, the presence of risk alleles associated with altered expression of several lysoPL/lysoPA enzymes. Deletion of the risk locus reversed the expression of several lysoPL/lysoPA genes to nonrisk haplotype levels. Genes that were altered across both cell data sets were DGKA, MBOAT2, PLPP1, and LPL. The in-silico analysis identified 4 ANRIL-regulated miRNAs that control lysoPL genes as miR-186-3p, miR-34a-3p, miR-122-5p, and miR-34a-5p. CONCLUSIONS: A Chr9p21 risk SNP associates with complex alterations in immune-bioactive phospholipids and their metabolism. Lipid metabolites and genomic pathways associated with coronary heart disease pathogenesis in Chr9p21 and ANRIL-associated disease are demonstrated.

Social and Health System Complexities Impacting on Decision-Making for Utilization of Oncology and Palliative Care in an African Context: A Qualitative Study.

BACKGROUND: There is a dearth of research focusing on identifying the social complexities impacting on oncology and palliative care (PC), and no study has explored how the health-care system in Nigeria or other African contexts may be influencing utilization of these services. AIM: This study explored how social complexities and the organization of health-care influenced the decision-making process for the utilization of oncology and PC in a Nigerian hospital. METHODS: This qualitative study used an interpretive descriptive design. Data were collected using semistructured interview guides with 40 participants, comprising health-care professionals, patients, and their families. Thematic analysis was conducted to generate and analyze patterns within the data. FINDINGS: Three themes were identified: dysfunctional structural organization of the health-care delivery system, service-users' economic status, and the influence of social networks. The interrelationship between the themes result in patients and their family members decisions either to present late to the hospital, miss their clinical appointments, or not to seek oncological health care and PC. CONCLUSION: This article offers insights into the role of the health-care system, as organized currently in Nigeria, as "autoinhibitory" and not adequately prepared to address the increasing burden of cancer. We therefore argue that there is a need to restructure the Nigerian health-care system to better meet the needs of patients with cancer and their families as failure to do so will strengthen the existing inequalities, discourage usage, and increase mortality.

Identifying Indicators of Smartphone Addiction Through User-App Interaction.

We introduce a new approach to monitoring the activity of smartphone users based on their physical interactions with the interface. Typical events are taps, scrolling and typing, carried out to interact with apps. As compared to other measures, this directly encapsulates potential problematic physical smartphone behaviour as a signal. The approach contrasts against conventions such as self-reporting or timing activity sessions, and it focusses on active rather than passive smartphone activity. Using this alternative method, we collected all user interface interaction events from a sample of 64 participants over a period of 8 weeks, using a bespoke monitoring app called Tymer. User Smartphone Addiction was seen to significantly correlate with high levels of interaction with Lifestyle apps, particularly for female users. Interactions with Social apps in general were also associated with Smartphone Addiction. In particular, user interactions with Snapchat correlated with Smartphone Addiction, represented across all types of interface interaction. This is significant given the widespread usage of Snapchat by teenagers, and we hypothesise that the app's design provides a particularly strong pathway in support of Smartphone Addiction.

Construction of meanings during life-limiting illnesses and its impacts on palliative care: Ethnographic study in an African context.

OBJECTIVE: Knowledge about how people make meaning in cancer, palliative, and end-of-life care is particularly lacking in Africa, yet it can provide insights into strategies for improving palliative care (PC). This study explored ways in which cancer patients, their families, and health care professionals (HCPs) construct meaning of their life-limiting illnesses and how this impact on provision and use of PC in a Nigerian hospital. METHODS: This ethnographic study utilised participant observation, informal conversations during observation, and interviews to gather data from 39 participants, comprising service users and HCPs in a Nigerian hospital. Data were analysed using Spradley's framework for ethnographic data analysis. RESULTS: Meaning-making in life-limiting illness was predominantly rooted in belief systems. Most patients and their families, including some HCPs, perceived that cancer was caused by the devil, mystical, or supernatural beings. They professed that these agents manifested in the form of either spiritual attacks or that wicked people in society used either poison or acted as witches/wizards to inflict cancer on someone. These beliefs contributed to either nonacceptance of, or late presentation for, PC by most of patients and their families, while some professionals depended on supernatural powers for divine intervention and tacitly supporting religious practices to achieve healing/cure. CONCLUSIONS: Findings revealed that cultural and religious world views about life-limiting illnesses were used in decision-making process for PC. This, therefore, provided evidence that could improve the clinicians' cultural competence when providing PC to individuals of African descent, especially Nigerians, both in Nigerian societies and in foreign countries.

Safety margins and adaptive capacity of vegetation to climate change.

Vegetation is composed of many individual species whose climatic tolerances can be integrated into spatial analyses of climate change risk. Here, we quantify climate change risk to vegetation at a continental scale by calculating the safety margins for warming and drying (i.e., tolerance to projected change in temperature and precipitation respectively) across plants sharing 100 km × 100 km grid cells (locations). These safety margins measure how much warmer, or drier, a location could become before its 'typical' species exceeds its observed climatic limit. We also analyse the potential adaptive capacity of vegetation to temperature and precipitation change (i.e., likelihood of in situ persistence) using median precipitation and temperature breadth across all species in each location. 47% of vegetation across Australia is potentially at risk from increases in mean annual temperature (MAT) by 2070, with tropical regions most vulnerable. Vegetation at high risk from climate change often also exhibited low adaptive capacity. By contrast, 2% of the continent is at risk from reductions in annual precipitation by 2070. Risk from precipitation change was isolated to the southwest of Western Australia where both the safety margin for drier conditions in the typical species is low, and substantial reductions in MAP are projected.

Understanding the Organization of Hospital-Based Palliative Care in a Nigerian Hospital: An Ethnographic Study.

CONTEXT: Organization and delivery of palliative care (PC) services vary from one country to another. In Nigeria, PC has continued to develop, yet the organization and scope of PC is not widely known by most clinicians and the public. OBJECTIVES: The aim of the study is to identify PC services available in a Nigerian Hospital and how they are organized. METHODS: This ethnographic study, utilized documentary analysis, participant observation, and ethnographic interviews (causal chat during observation and individual interviews) to gather data from members of PC team comprising doctors (n = 10), nurses (n = 4), medical social workers (n = 2), a physiotherapist, and a pharmacist, as well nurses from the oncology department (n = 3). Data were analyzed using Spradley's framework for ethnographic data analysis. RESULTS: PC was found to be largely adult patient-centered. A hospital-based care delivery model, in the forms of family meetings, in- and out-patients' consultation services, and a home-based delivery model which is primarily home visits conducted once in a week, were the two models of care available in the studied hospital. The members of the PC team operated two shift patterns from 7:00 am to 2.00 pm and a late shift from 2:00 pm to 7:00 pm instead of 24 h service provision. CONCLUSIONS: Although PC in this hospital has made significant developmental progress, the organization and scope of services are suggestive of the need for more development, especially in manpower and collaborative care. This study provided knowledge that could be used to improve the clinical practice of PC in various cross-cultural Nigerian societies and other African context, as well as revealing areas for PC development.

Evidence to support common application switching behaviour on smartphones.

We find evidence to support common behaviour in smartphone usage based on analysis of application (app) switching. This is an overlooked aspect of smartphone usage that gives additional insight beyond screen time and the particular apps that are accessed. Using a dataset of usage behaviour from 53 participants over a six-week period, we find strong similarity in the structure of networks built from app switching, despite diversity in the apps used, and the volume of app switching. App switch networks exhibit small-world, broad-scale network features, with a rapid popularity decay, suggesting that preferential attachment may drive next-app decision-making.

LipidFinder on LIPID MAPS: peak filtering, MS searching and statistical analysis for lipidomics.

SUMMARY: We present LipidFinder online, hosted on the LIPID MAPS website, as a liquid chromatography/mass spectrometry (LC/MS) workflow comprising peak filtering, MS searching and statistical analysis components, highly customized for interrogating lipidomic data. The online interface of LipidFinder includes several innovations such as comprehensive parameter tuning, a MS search engine employing in-house customized, curated and computationally generated databases and multiple reporting/display options. A set of integrated statistical analysis tools which enable users to identify those features which are significantly-altered under the selected experimental conditions, thereby greatly reducing the complexity of the peaklist prior to MS searching is included. LipidFinder is presented as a highly flexible, extensible user-friendly online workflow which leverages the lipidomics knowledge base and resources of the LIPID MAPS website, long recognized as a leading global lipidomics portal. AVAILABILITY AND IMPLEMENTATION: LipidFinder on LIPID MAPS is available at: http://www.lipidmaps.org/data/LF.

Personality Homophily and Geographic Distance in Facebook.

Personality homophily remains an understudied aspect of social networks, with the traditional focus concerning sociodemographic variables as the basis for assortativity, rather than psychological dispositions. We consider the effect of personality homophily on one of the biggest constraints to human social networks: geographic distance. We use the Big Five model of personality to make predictions for each of the five facets: Openness to experience, Conscientiousness, Extraversion, Agreeableness, and Neuroticism. Using a network of 313,669 Facebook users, we investigate the difference in geographic distance between homophilous pairs, in which both users scored similarly on a particular facet, and mixed pairs. In accordance with our hypotheses, we find that pairs of open and conscientious users are geographically further apart than mixed pairs. Pairs of extraverts, on the other hand, tend to be geographically closer together. We find mixed results for the Neuroticism facet, and no significant effects for the Agreeableness facet. The results are discussed in the context of personality homophily and the impact of geographic distance on social connections.

Timing rather than user traits mediates mood sampling on smartphones.

OBJECTIVE: Recent years have seen an increasing number of studies using smartphones to sample participants' mood states. Moods are usually collected by asking participants for their current mood or for a recollection of their mood states over a specific period of time. The current study investigates the reasons to favour collecting mood through current or daily mood surveys and outlines design recommendations for mood sampling using smartphones based on these findings. These recommendations are also relevant to more general smartphone sampling procedures. RESULTS: N=64 participants completed a series of surveys at the beginning and end of the study providing information such as gender, personality, or smartphone addiction score. Through a smartphone application, they reported their current mood 3 times and daily mood once per day for 8 weeks. We found that none of the examined intrinsic individual qualities had an effect on matches of current and daily mood reports. However timing played a significant role: the last followed by the first reported current mood of the day were more likely to match the daily mood. Current mood surveys should be preferred for a higher sampling accuracy, while daily mood surveys are more suitable if compliance is more important.

LipidFinder: A computational workflow for discovery of lipids identifies eicosanoid-phosphoinositides in platelets.

Accurate and high-quality curation of lipidomic datasets generated from plasma, cells, or tissues is becoming essential for cell biology investigations and biomarker discovery for personalized medicine. However, a major challenge lies in removing artifacts otherwise mistakenly interpreted as real lipids from large mass spectrometry files (>60 K features), while retaining genuine ions in the dataset. This requires powerful informatics tools; however, available workflows have not been tailored specifically for lipidomics, particularly discovery research. We designed LipidFinder, an open-source Python workflow. An algorithm is included that optimizes analysis based on users' own data, and outputs are screened against online databases and categorized into LIPID MAPS classes. LipidFinder outperformed three widely used metabolomics packages using data from human platelets. We show a family of three 12-hydroxyeicosatetraenoic acid phosphoinositides (16:0/, 18:1/, 18:0/12-HETE-PI) generated by thrombin-activated platelets, indicating crosstalk between eicosanoid and phosphoinositide pathways in human cells. The software is available on GitHub (https://github.com/cjbrasher/LipidFinder), with full userguides.

A Dominant Social Comparison Heuristic Unites Alternative Mechanisms for the Evolution of Indirect Reciprocity.

Cooperation is a fundamental human trait but our understanding of how it functions remains incomplete. Indirect reciprocity is a particular case in point, where one-shot donations are made to unrelated beneficiaries without any guarantee of payback. Existing insights are largely from two independent perspectives: i) individual-level cognitive behaviour in decision making, and ii) identification of conditions that favour evolution of cooperation. We identify a fundamental connection between these two areas by examining social comparison as a means through which indirect reciprocity can evolve. Social comparison is well established as an inherent human disposition through which humans navigate the social world by self-referential evaluation of others. Donating to those that are at least as reputable as oneself emerges as a dominant heuristic, which represents aspirational homophily. This heuristic is found to be implicitly present in the current knowledge of conditions that favour indirect reciprocity. The effective social norms for updating reputation are also observed to support this heuristic. We hypothesise that the cognitive challenge associated with social comparison has contributed to cerebral expansion and the disproportionate human brain size, consistent with the social complexity hypothesis. The findings have relevance for the evolution of autonomous systems that are characterised by one-shot interactions.

Mapping the Human Platelet Lipidome Reveals Cytosolic Phospholipase A2 as a Regulator of Mitochondrial Bioenergetics during Activation.

Human platelets acutely increase mitochondrial energy generation following stimulation. Herein, a lipidomic circuit was uncovered whereby the substrates for this are exclusively provided by cPLA2, including multiple fatty acids and oxidized species that support energy generation via ß-oxidation. This indicates that acute lipid membrane remodeling is required to support energetic demands during platelet activation. Phospholipase activity is linked to energy metabolism, revealing cPLA2 as a central regulator of both lipidomics and energy flux. Using a lipidomic approach (LipidArrays), we also estimated the total number of lipids in resting, thrombin-activated, and aspirinized platelets. Significant diversity between genetically unrelated individuals and a wealth of species was revealed. Resting platelets demonstrated ∼5,600 unique species, with only ∼50% being putatively identified. Thrombin elevated ∼900 lipids >2-fold with 86% newly appearing and 45% inhibited by aspirin supplementation, indicating COX-1 is required for major activation-dependent lipidomic fluxes. Many lipids were structurally identified. With ∼50% of the lipids being absent from databases, a major opportunity for mining lipids relevant to human health and disease is presented.

Central oxytocin and food intake: focus on macronutrient-driven reward.

Centrally acting oxytocin (OT) is known to terminate food consumption in response to excessive stomach distension, increase in salt loading, and presence of toxins. Hypothalamic-hindbrain OT pathways facilitate these aspects of OT-induced hypophagia. However, recent discoveries have implicated OT in modifications of feeding via reward circuits: OT has been found to differentially affect consumption of individual macronutrients in choice and no-choice paradigms. In this mini-review, we focus on presenting and interpreting evidence that defines OT as a key component of mechanisms that reduce eating for pleasure and shape macronutrient preferences. We also provide remarks on challenges in integrating the knowledge on physiological and pathophysiological states in which both OT activity and macronutrient preferences are affected.

Oxygen limitation induces acid tolerance and impacts simulated gastro-intestinal transit in Listeria monocytogenes J0161.

UNLABELLED: ᅟ: Listeria monocytogenes is a food-borne pathogen and the causative agent of listeriosis, a severe infection to those with a pre-disposition. Infections often arise through consumption of contaminated foods, where high intrinsic resistance to food processing practises permit survival and growth. Several practises, including refrigeration, acidification and oxygen limitation are ineffective in controlling L. monocytogenes, therefore foods which do not undergo thermal processing, e.g. ready-to-eat products, are considered high risk. While the responses to several food processing practises have been investigated, there are few reports on the responses of L. monocytogenes to oxygen limitation. Therefore the aim of this study was to investigate the effects of oxygen limitation on stress response andsurvival capacity during simulated gastro-intestinal transit. FINDINGS: Anaerobiosis induced an acid tolerance response, causing cells to be more resistant to organic and inorganic acids than aerobically grown counterparts (p < 0.05). Using a gastro-intestinal transit model it was found that anaerobic growth induced an acid tolerance response which enhanced resistance to pH 2.5 simulated gastric juice (SGJ) compared to aerobically grown cells (p < 0.05). This response was most pronounced in exponential phase cells. However, exposure of stationary phase cells to pH 3.5 SGJ enhanced bile tolerance, suggesting a link between acid and bile tolerance. CONCLUSIONS: The responses of L. monocytogenes to oxygen limitation are not extensively studied. These findings provide an initial insight into the effects of anaerobiosis on stress response and survival potential in L. monocytogenes. While it appears anaerobiosis may impact these, further work is required to confirm these findings are not strain specific.