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.

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.

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.

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.

Clinic and ambulatory heart rates in patients with ischaemic heart disease and/or chronic heart failure taking rate-limiting medications: are they interchangeable?

BACKGROUND: The prognostic benefit from heart rate (HR) reduction in patients with ischaemic heart disease (IHD) and/or chronic heart failure (CHF) is now firmly established. Most decisions regarding initiation and/or dose adjustment of HR-limiting medications in such patients are based on clinic HR. Yet, this is a highly variable parameter that may not necessarily reflect HR control over the 24 h period. OBJECTIVE: To examine the level of agreement between mean clinic and mean ambulatory HRs in patients with IHD and/or CHF taking rate-limiting medications. METHODS: Prospective, observational study. Fifty patients with IHD and/or CHF who attended cardiology outpatient clinics at the Manchester Heart Centre and underwent same-day 24 h continuous ECG recording between March and October 2013 were included in the study. Mean clinic HR was compared with mean 24 h, daytime and night-time HRs. Limits-of-agreement plots were constructed to examine the relationship between the two HR measures in more detail. RESULTS: The mean clinic HR was numerically similar to the mean HRs of all ambulatory time periods examined. However, on Bland-Altman plots, the limits of agreement between clinic and ambulatory HR means were quite wide, with the mean clinic HR ranging between 10.93 and 13.58 bpm below and 8.4 and 18.15 bpm above the mean ambulatory HR. CONCLUSIONS: Although numerically similar, the means of clinic and ambulatory HRs in patients with IHD and/or CHF display wide limits of agreement. As such, the two measures cannot be regarded as interchangeable.

A comparison of the sensitivity of four Staphylococcus aureus isolates to two chlorine-based disinfectants and an eco-friendly commercially available cleaning agent.

The aim of this study was to determine the effect of household bleach, a sodium dichloroisocyanurate (NaDCC)-based disinfectant and an eco-friendly cleaning agent (EFCA) on four Staphylococcus aureus strains, including two isolated from community infections. The products were assessed using the suspension (EN 1276) and surface (EN 13697) tests, while biofilm activity was determined using the 96-well plate method. Bleach and NaDCC caused > 5 log reduction in viable counts within 5 min in suspension, whilst on surfaces the reduction was < 3 log. Bleach at 5000 ppm free available chlorine completely eradicated MSSA NCTC 13297 and PVL CA MSSA biofilms within 10 min, but not at 500 and 50 ppm, NaDCC was less effective against biofilms. The EFCA demonstrated no antimicrobial activity. It is of concern that at the recommended "use" dilution, bleach did not eradicate biofilms. Although increasing contact time and/or concentration should improve the activity, this may not be acceptable to the user.

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.

Not all pacemakers are created equal: MRI conditional pacemaker and lead technology.

Due to expanding clinical indications and an aging society there has been an increase in the use of implantable pacemakers. At the same time, due to increased diagnostic yield over other imaging modalities and the absence of ionizing radiation, there has been a surge in demand for magnetic resonance imaging (MRI) assessment, of both cardiac and noncardiac conditions. Patients with an implantable device have a 50-75% chance of having a clinical indication for MRI during the lifetime of their device. The presence of an implantable cardiac device has been seen as a relative contraindication to MRI assessment, limiting the prognostic and diagnostic utility of MRI in many patients with these devices. The introduction of MRI conditional pacemakers will enable more patients to undergo routine MRI assessment without risk of morbidity or device malfunction. This review gives a general overview of the principles and current evidence for the use of MRI conditional implantable cardiac devices. Furthermore, we appraise the differences between those pacemakers currently released to market.

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.

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.

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.

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.

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.

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.

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.

A hybrid form of cardiac resynchronisation therapy in patients with failing systemic right ventricles.

INTRODUCTION: Late systemic right ventricular (RV) dysfunction after atrial redirection surgery is common. Patients may require cardiac transplantation in early adulthood. METHODS: We undertook cardiac resynchronisation (CRT)/defibrillator therapy in two patients as a bridge to transplantation. RESULTS: Two males (aged 24, 110 kg and 26 years, 106 kg); having undergone a Mustard procedure for dextro-transposition of the great arteries at 7 and 6 months of age respectively, presented with impaired systemic RV function and New York Heart Association III symptoms. Both patients had dual chamber pacemakers in-situ for sinus bradycardia. Upgrade to CRT was performed by conserving the existing endocardial leads and placement of epicardial electrodes. One demonstrated sustained improvement over a 24 month follow-up period. CONCLUSION: A hybrid CRT strategy is feasible in patients with failing systemic RVs and pre-existent endocardial dual chamber pacemakers. Appropriate patient selection criteria and optimum lead placement, however, still needs further evaluation in this population.

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.

The isolation and characterization of temperature-dependent ricin A chain molecules in Saccharomyces cerevisiae.

Ricin is a heterodimeric plant protein that is potently toxic to mammalian cells. Toxicity results from the catalytic depurination of eukaryotic ribosomes by ricin toxin A chain (RTA) that follows toxin endocytosis to, and translocation across, the endoplasmic reticulum membrane. To ultimately identify proteins required for these later steps in the entry process, it will be useful to express the catalytic subunit within the endoplasmic reticulum of yeast cells in a manner that initially permits cell growth. A subsequent switch in conditions to provoke innate toxin action would permit only those strains containing defects in genes normally essential for toxin retro-translocation, refolding or degradation to survive. As a route to such a screen, several RTA mutants with reduced catalytic activity have previously been isolated. Here we report the use of Saccharomyces cerevisiae to isolate temperature-dependent mutants of endoplasmic reticulum-targeted RTA. Two such toxin mutants with opposing phenotypes were isolated. One mutant RTA (RTAF108L/L151P) allowed the yeast cells that express it to grow at 37 degrees C, whereas the same cells did not grow at 23 degrees C. Both mutations were required for temperature-dependent growth. The second toxin mutant (RTAE177D) allowed cells to grow at 23 degrees C but not at 37 degrees C. Interestingly, RTAE177D has been previously reported to have reduced catalytic activity, but this is the first demonstration of a temperature-sensitive phenotype. To provide a more detailed characterization of these mutants we have investigated their N-glycosylation, stability, catalytic activity and, where appropriate, a three-dimensional structure. The potential utility of these mutants is discussed.

Study protocol: a randomised controlled trial of multiple and single dose activated charcoal for acute self-poisoning.

BACKGROUND: The case fatality for intentional self-poisoning in rural Asia is 10-30 times higher than in the West, mostly due to the use of highly toxic poisons. Activated charcoal is a widely available intervention that may - if given early - bind to poisons in the stomach and prevent their absorption. Current guidelines recommend giving a single dose of charcoal (SDAC) if patients arrive within an hour of ingestion. Multiple doses (MDAC) may increase poison elimination at a later time by interrupting any enterohepatic or enterovascular circulations. The effectiveness of SDAC or MDAC is unknown. Since most patients present to hospital after one hour, we considered MDAC to have a higher likelihood of clinical benefit and set up a study to compare MDAC with no charcoal. A third arm of SDAC was added to help determine whether any benefit noted from MDAC resulted from the first dose or all doses. METHODS/DESIGN: We set up a randomised controlled trial assessing the effectiveness of superactivated charcoal in unselected adult self-poisoning patients admitted to the adult medical wards of three Sri Lankan secondary hospitals. Patients were randomised to standard treatment or standard treatment plus either a single 50 g dose of superactivated charcoal dissolved in 300 ml of water or six doses every four hours. All patients with a history of poison ingestion were approached concerning the study and written informed consent taken from each patient, or their relative (for unconscious patients or those <16 yrs), recruited to the study. The exclusion criteria were: age under 14 yrs; prior treatment with activated charcoal during this poisoning episode; pregnancy; ingestion of a corrosive or hydrocarbon; requirement for oral medication; inability of the medical staff to intubate the patient with a Glasgow Coma Score <13; presentation >72 hrs post-ingestion, and previous recruitment. The primary outcome was in-hospital mortality; secondary outcomes included the occurrence of serious complications (need for intubation, time requiring assisted ventilation, fits, cardiac dysrhythmias). Analysis will be on an intention-to-treat basis; the effects of reported time to treatment after poisoning and status on admission will also be assessed. DISCUSSION: This trial will provide important information on the effectiveness of both single and multiple dose activated charcoal in the forms of poisoning commonly seen in rural Asia. If charcoal is found to be effective, it should be possible to make it widely available across rural Asia in an affordable formulation. TRIAL REGISTRATION: Current Controlled Trials ISRCTN02920054.