Quality Output Checklist and Content Assessment (QuOCCA): a new tool for assessing research quality and reproducibility.

Research must be well designed, properly conducted and clearly and transparently reported. Our independent medical research institute wanted a simple, generic tool to assess the quality of the research conducted by its researchers, with the goal of identifying areas that could be improved through targeted educational activities. Unfortunately, none was available, thus we devised our own. Here, we report development of the Quality Output Checklist and Content Assessment (QuOCCA), and its application to publications from our institute's scientists. Following consensus meetings and external review by statistical and methodological experts, 11 items were selected for the final version of the QuOCCA: research transparency (items 1-3), research design and analysis (items 4-6) and research reporting practices (items 7-11). Five pairs of raters assessed all 231 articles published in 2017 and 221 in 2018 by researchers at our institute. Overall, the results were similar between years and revealed limited engagement with several recommended practices highlighted in the QuOCCA. These results will be useful to guide educational initiatives and their effectiveness. The QuOCCA is brief and focuses on broadly applicable and relevant concepts to open, high-quality, reproducible and well-reported science. Thus, the QuOCCA could be used by other biomedical institutions and individual researchers to evaluate research publications, assess changes in research practice over time and guide the discussion about high-quality, open science. Given its generic nature, the QuOCCA may also be useful in other research disciplines.

Substitution, delegation or addition? Implications of workforce skill mix on efficiency and interruptions in computed tomography.

Objectives This study evaluated multiple computed tomography (CT) workforce models to identify any implications on efficiency (length of stay, scan frequency and workforce cost) and scanning radiographer interruptions through substituting or supplementing with a trained CT assistant. Methods The study was conducted in a CT unit of a tertiary Queensland hospital and prospectively compared four workforce models, including usual practice: Model 1 used an administrative assistant (AA) and one radiographer; Model 2 substituted a medical imaging assistant (MIA) for the AA; Model 3 was usual practice, consisting of two radiographers; and Model 4 included two radiographers, with a supplemented MIA. Observational data were collected over 7 days per model and were cross-checked against electronic records. Data for interruption type and frequency, as well as scan type and duration, were collected. Annual workforce costs were calculated as measures of efficiency. Results Similar scan frequency and parameters (complexity) occurred across all models, averaging 164 scans (interquartile range 160-172 scans) each. The median times from patient arrival to examination completion in Models 1-4 were 47, 35, 46 and 33min respectively. There were between 34 and 104 interruptions per day across all models, with the 'assistant role' fielding the largest proportion. Model 4 demonstrated the highest workforce cost, and Model 2 the lowest. Conclusion This study demonstrated that assistant models offer similar patient throughput to usual practice at a reduced cost. Model 2 was the most efficient of all two-staff models (Models 1-3), offering the cheapest workforce, slightly higher throughput and faster examination times. Not surprisingly, the additional staff model (Model 4) offered greater overall examination times and throughput, with fewer interruptions, although workforce cost and possible role ambiguity were both limitations of this model. These findings may assist decision makers in selecting the optimal workforce design for their own individual contexts. What is known about the topic? Innovative solutions are required to address ongoing health workforce sustainability concerns. Workforce substitution models using trained assistants have demonstrated numerous benefits internationally, with translation to the Australian allied health setting showing promise. What does this paper add? Building on existing research, this study provides clinical workforce alternatives that maintain patient throughput while offering cost efficiencies. This study also quantified the many daily interruptions that occur within the CT setting, highlighting a potential clinical risk. To the best of our knowledge, this study is the first to empirically test the use of allied health assistants within CT. What are the implications for practitioners? Role substitution in CT may offer solutions to skills shortages, increasing expenditure and service demand. Incorporating appropriate assistant workforce models can maintain throughput while demonstrating implications for efficiency and interruptions, potentially affecting staff stress and burnout. In addition, the assistant's scope and accepted level of interruptions should be considerations when choosing the most appropriate model.

A novel multiplex-protein array for serum diagnostics of colon cancer: a case-control study.

BACKGROUND: More than 1.2 million new cases of colorectal cancer are reported each year worldwide. Despite actual screening programs, about 50% of the patients are diagnosed at advanced tumor stages presenting poor prognosis. Innovative screening tools could aid the detection at early stages and allow curative treatment interventions. METHODS: A nine target multiplex serum protein biochip was generated and evaluated using a training- and validation-set of 317 highly standardized, liquid nitrogen preserved serum samples comprising controls, adenomas, and colon cancers. RESULTS: Serum levels of CEA, IL-8, VEGF, S100A11, MCSF, C3adesArg, CD26, and CRP showed significant differences between cases and controls. The largest areas under the receiver operating characteristics curve were observed for CEA, IL-8, and CRP. At threshold levels yielding 90% specificity, sensitivities for CEA, IL-8 and CRP were 26%, 22%, and 17%, respectively. The most promising marker combinations were CEA + IL-8 reaching 37% sensitivity at 83% specificity and CEA + CRP with 35% sensitivity at 81% specificity. In an independent validation set CEA + IL-8 reached 47% sensitivity at 86% specificity while CEA + CRP obtained 39% sensitivity at 86% specificity. Early carcinomas were detected with 33% sensitivity for CEA + IL-8 and 28% for CEA + CRP. CONCLUSIONS: Apart from CEA, IL-8, and CRP, the screening value of additional blood markers and the potential advantage of combining serum biochip testing with fecal occult blood testing needs to be studied. Multiplex biochip array technology utilizing serum samples offers an innovative approach to colorectal cancer screening.

Toward standardized high-throughput serum diagnostics: multiplex-protein array identifies IL-8 and VEGF as serum markers for colon cancer.

Development and progression of colon cancer may be related to cytokines. Cytokines with diagnostic value have been identified individually but have not been implemented into clinical praxis. Using a multiplex protein array, the authors explore a panel of cytokines simultaneously and compared its performance to carcinoembryonic antigen (CEA) and carbohydrate antigen 19-9 (CA 19-9). Serum concentrations of 12 cytokines were simultaneously determined by multiplex biochip technology in 50 colon cancer patients and 50 healthy controls. Serum levels of interleukin-8 (IL-8) and CEA were significantly higher in cancer patients than in healthy controls. Areas under the receiver operating characteristic curves (AUCs) were largest for IL-8, followed by CEA, vascular endothelial growth factor (VEGF), and CA 19-9. Analyses regarding marker combinations showed an advantage over single marker performance for CEA, VEGF, and CA 19-9 but not for IL-8. Multiplex biochip array technology represents a practical tool in cytokine and cancer research when simultaneous determination of different biomarkers is of interest. The results suggest that the assessment of IL-8, CEA, VEGF, and possibly CA 19-9 serum levels could be useful for colon cancer screening with the potential of also detecting early stage tumors. Further validation studies using these and additional markers on a multiplex array format are encouraged.

Aging, depot origin, and preadipocyte gene expression.

Fat distribution changes with aging. Inherent changes in fat cell progenitors may contribute because fat cells turn over throughout life. To define mechanisms, gene expression was profiled in preadipocytes cultured from epididymal and perirenal depots of young and old rats. 8.4% of probe sets differed significantly between depots, particularly developmental genes. Only 0.02% differed with aging, despite using less stringent criteria than for comparing depots. Twenty-five genes selected based on fold change with aging were analyzed in preadipocytes from additional young, middle-aged, and old animals by polymerase chain reaction. Thirteen changed significantly with aging, 13 among depots, and 9 with both. Genes involved in inflammation, stress, and differentiation changed with aging, as occurs in fat tissue. Age-related changes were greater in perirenal than epididymal preadipocytes, consistent with larger declines in replication and adipogenesis in perirenal preadipocytes. Thus, age-related changes in preadipocyte gene expression differ among depots, potentially contributing to fat redistribution and dysfunction.

Characterisation of thorium-ethylenediaminetetraacetic acid and thorium-nitrilotriacetic acid species by electrospray ionisation-mass spectrometry.

Electrospray ionisation-mass spectrometry (ESI-MS) has been used to investigate the speciation of Th in the presence of two common organic complexing agents found in radioactive wastes, EDTA and NTA. These ligands may enhance radionuclide migration from nuclear wastes and contaminated land, and characterisation of the complexes formed will improve our understanding of their environmental mobility. When acetic acid and ammonia were used to adjust the pH, the dominant Th-EDTA species changed from the mixed ligand [ThEDTAac](-) complex to [ThEDTAOH](-) and [ThEDTA(OH)(2)ac](3-) as the pH increased, with all species co-existing, to some extent, over the pH range (2.5-10.8). A previously suggested Th-NTA species, [ThNTA(2)](2-), dominates from pH 6.0-8.5 but at high pH (10.0-10.8) NTA was not able to solubilise Th to a measurable extent. In the presence of both EDTA and NTA, Th formed a mixed ligand complex, [ThEDTANTA](3-) which has also been characterised in independent experiments. The identification of the importance of [ThNTA(2)](2-), [ThEDTANTA](3-) and [ThEDTA(OH)(2)](2-) (with an additional acetate ligand) highlights that these species are not included in current speciation databases and thus may impact on predictions of the environmental mobility of Th. ESI-MS has therefore been used to identify and confirm fundamentally important Th complexes. It has proved to be a useful tool for elucidating radionuclide speciation, adding to our knowledge of Th geochemistry and providing a means of critically examining existing stability constant data.

Identification of depot-specific human fat cell progenitors through distinct expression profiles and developmental gene patterns.

Anatomically separate fat depots differ in size, function, and contribution to pathological states, such as the metabolic syndrome. We isolated preadipocytes from different human fat depots to determine whether the basis for this variation is partly attributable to differences in inherent properties of fat cell progenitors. We found that genome-wide expression profiles of primary preadipocytes cultured in parallel from abdominal subcutaneous, mesenteric, and omental fat depots were distinct. Interestingly, visceral fat was not homogeneous. Preadipocytes from one of the two main visceral depots, mesenteric fat, had an expression profile closer to that of subcutaneous than omental preadipocytes, the other main visceral depot. Expression of genes that regulate early development, including homeotic genes, differed extensively among undifferentiated preadipocytes isolated from different fat depots. These profiles were confirmed by real-time PCR analysis of preadipocytes from additional lean and obese male and female subjects. We made preadipocyte strains from single abdominal subcutaneous and omental preadipocytes by expressing telomerase. Depot-specific developmental gene expression profiles persisted for 40 population doublings in these strains. Thus, human fat cell progenitors from different regions are effectively distinct, consistent with different fat depots being separate mini-organs.

Aging results in paradoxical susceptibility of fat cell progenitors to lipotoxicity.

Aging is associated with metabolic syndrome, tissue damage by cytotoxic lipids, and altered fatty acid handling. Fat tissue dysfunction may contribute to these processes. This could result, in part, from age-related changes in preadipocytes, since they give rise to new fat cells throughout life. To test this hypothesis, preadipocytes cultured from rats of different ages were exposed to oleic acid, the most abundant fatty acyl moiety in fat tissue and the diet. At fatty acid concentrations at which preadipocytes from young animals remained viable, cells from old animals accumulated lipid in multiple small lipid droplets and died, with increased apoptotic index, caspase activity, BAX, and p53. Rather than inducing apoptosis, oleic acid promoted adipogenesis in preadipocytes from young animals, with appearance of large lipid droplets. CCAAT/enhancer-binding protein-alpha (C/EBPalpha) and peroxisome proliferator-activated receptor-gamma (PPARgamma) increased to a greater extent in cells from young than old animals after oleate exposure. Oleic acid, but not glucose, oxidation was impaired in preadipocytes and fat cells from old animals. Expression of carnitine palmitoyltransferase (CPT)-1, which catalyzes the rate-limiting step in fatty acid beta-oxidation, was not reduced in preadipocytes from old animals. At lower fatty acid levels, constitutively active CPT I expression enhanced beta-oxidation. At higher levels, CPT I was not as effective in enhancing beta-oxidation in preadipocytes from old as young animals, suggesting that mitochondrial dysfunction may contribute. Consistent with this, medium-chain acyl-CoA dehydrogenase expression was reduced in preadipocytes from old animals. Thus preadipocyte fatty acid handling changes with aging, with increased susceptibly to lipotoxicity and impaired fatty acid-induced adipogenesis and beta-oxidation.

Effect of organic co-contaminants on technetium and rhenium speciation and solubility under reducing conditions.

The chemical and biogeochemical reduction of pertechnetate (TcO4-) and perrhenate (ReO4-) have been compared alongside complexation of the reduced species by three anthropogenic ligands relevant to nuclear waste (ethylenediaminetetraacetic acid (EDTA), nitrilotriacetic acid (NTA), and isosaccharinic acid (ISA)). An HPLC size-exclusion column coupled to ICP-MS was used to separate the species and quantify Tc and Re. During method development, ReO4- showed recalcitrance to direct chemical reduction by Sn(ll) under conditions that readily reduced TcO4- and resulted in Tc(IV)-organic complexes. In microcosm experiments of a silty loam soil containing Tc04-, ReO4-, and ISA (3.0 mM), EDTA (0.17 mM), or NTA (2.4 mM), anoxia developed to iron-reducing conditions during the 42 day experimental period. The majority of the TcO4- was reduced to particle-reactive Tc(IV) and removed from solution during nitrate reduction, but there was no chromatographic evidence of Tc(IV)-organic complexes in the porewater. Overall, the excess organic complexants added did not cause a measurable difference in the solubility of Tc(IV) over the control experiments in this organic-rich (12% organic carbon) soil. ReO4- did not undergo reduction, as shown by the constant porewater concentration and the chromatographic data, and thus Re does notfunction as an analogue forTc under environmental nitrate- and iron-reducing conditions.

Increased CUG triplet repeat-binding protein-1 predisposes to impaired adipogenesis with aging.

Preadipocyte differentiation capacity declines between middle and old age. Expression of the adipogenic transcription factors, CCAAT/enhancer-binding protein (C/EBP) alpha and peroxisome proliferator-activated receptor gamma (PPARgamma), is lower in differentiating preadipocytes from old than young animals, although no age-related changes occur in C/EBPbeta mRNA, which is upstream of C/EBPalpha and PPARgamma. C/EBPbeta-liver-enriched inhibitory protein (C/EBPbeta-LIP), a truncated C/EBPbeta isoform that is a dominant inhibitor of differentiation, increases with aging in rat fat tissue and preadipocytes. CUG triplet repeat-binding protein-1 (CUGBP1) binds to C/EBPbeta mRNA, increasing C/EBPbeta-LIP translation. Abundance and nucleotide binding activity of CUGBP1 increased with aging in preadipocytes. CUGBP1 overexpression in preadipocytes from young animals increased C/EBPbeta-LIP and impaired adipogenesis. Decreasing CUGBP1 in preadipocytes from old rats by RNA interference reduced C/EBPbeta-LIP abundance and promoted adipogenesis. Tumor necrosis factor-alpha, levels of which are elevated in fat tissue with aging, increased CUGBP1 protein, CUGBP1 binding activity, and C/EBPbeta-LIP in preadipocytes from young rats. Thus, CUGBP1 contributes to regulation of adipogenesis in primary preadipocytes and is responsive to tumor necrosis factor-alpha. With aging, preadipocyte CUGBP1 abundance and activity increases, resulting in enhanced translation of the C/EBPbeta-LIP isoform, thereby blocking effects of adipogenic transcription factors, predisposing preadipocytes from old animals to resist adipogenesis. Altered translational processing, possibly related to changes in cytokine milieu and activation of stress responses, may contribute to changes in progenitor differentiation and tissue function with aging.

Derivatisation of carboxylic acid groups in pharmaceuticals for enhanced detection using liquid chromatography with electrospray ionisation tandem mass spectrometry.

Tris(2,4,6-trimethoxyphenyl)phosphonium propylamine bromide (TMPP) has been used for the derivatisation of maleic, fumaric, sorbic and salicylic acids to facilitate determination using liquid chromatography/electrospray ionisation tandem mass spectrometry (LC/ESI-MS/MS) in positive ion mode. Detection limits, achieved using multiple reaction monitoring mode, were 2, 4, 0.4 and 540 fmol (5 muL injection) for derivatised fumaric, sorbic, maleic and salicylic acids, respectively. In comparison, detection limits achieved in negative ion mode for the underivatised acids were 24, 51, 2, and 117 fmol, respectively. The method was successfully used for the determination of sorbic acid in a sample of Panadol. The derivatisation of salicylic acid was not as successful, probably due to poor reaction efficiency.

Abundance of two human preadipocyte subtypes with distinct capacities for replication, adipogenesis, and apoptosis varies among fat depots.

Fat depots vary in function and size. The preadipocytes that fat cells develop from exhibit distinct regional characteristics that persist in culture. Human abdominal subcutaneous cultured preadipocytes undergo more extensive lipid accumulation, higher adipogenic transcription factor expression, and less TNF-alpha-induced apoptosis than omental preadipocytes. We found higher replicative potential in subcutaneous and mesenteric than in omental preadipocytes. In studies of colonies arising from single preadipocytes, two preadipocyte subtypes were found, one capable of more extensive replication, differentiation, and adipogenic transcription factor expression and less apoptosis in response to TNF-alpha than the other. The former was more abundant in subcutaneous and mesenteric than in omental preadipocyte populations, potentially contributing to regional variation in replication, differentiation, and apoptosis. Both subtypes were found in strains derived from single human preadipocytes stably expressing telomerase, confirming that both subtypes are of preadipocyte lineage. After subcloning of cells of either subtype, both subtypes were found, indicating that switching can occur between subtypes. Thus proportions of preadipocyte subtypes with distinct cell-dynamic properties vary among depots, potentially permitting tissue plasticity through subtype selection during development. Furthermore, mesenteric preadipocyte cell-dynamic characteristics are distinct from omental cells, indicating that visceral fat depots are not functionally uniform.

Behavioural characteristics of the quick phase of vestibular nystagmus before and after unilateral labyrinthectomy in guinea pig.

The aim of this paper was to characterise the conditions under which the quick phase of vestibular nystagmus is generated in response to sinusoidal horizontal angular accelerations in guinea pig and to determine whether the characteristics of the quick phase are altered following unilateral vestibular deafferentation (UVD). In experiment 1, the quick-phase response to 2-Hz sinusoidal stimuli with different peak head velocities was measured before and after UVD. In experiment 2, lower-frequency stimuli with a fixed amplitude (+/-20 degrees ) were used to measure the eye-movement response. In experiment 1, at 2 Hz, the most noticeable difference between UVD animals and normal animals was a reduction in the number of quick phases generated, particularly when rotating towards the lesioned side: the onset of the quick phase was delayed and occurred at a lower value of peak head velocity compared to normals. However, both these measures probably reflect the depressed slow-phase eye-velocity gain rather than a change in the quick-phase mechanism itself, because if a quick phase was generated there was no difference between UVDs and normals on a variety of measures (duration, position, peak eye velocity) for a 2-Hz stimulus. For both UVD and normal animals there did appear to be a position threshold for the onset of a quick-phase eye movement (approximately +/-7.5 degrees ), although it should be noted that the threshold is not an absolute value. In experiment 2, with lower-frequency stimuli, the characteristics of the quick phase itself were altered in UVD animals. At these lower accelerations, although the head velocity and average eye position for the onset of the quick phase did not differ between UVD and normal animals, there were significant differences between UVD and normal animals in the number of quick phases generated (fewer), the duration of the quick phase (longer) and the peak eye velocity of the quick phase (slower). For lower-frequency stimuli there was no evidence of a specific eye-position threshold for the generation of a quick phase, although the position at which a quick phase occurred rarely exceeded the +/-7.5 degrees value obtained in experiment 1. The behavioural data were used to produce a biologically based neural-network simulation of both the slow- and quick-phase components of the vestibulo-ocular reflex, the results of which are presented in a companion paper.

A realistic neural-network simulation of both slow and quick phase components of the guinea pig VOR.

A realistic neural-network model was constructed to simulate production of both the slow-phase and quick-phase components of vestibular nystagmus by incorporating a quick-phase pathway into a previous model of the slow phase. The neurons in the network were modelled by multicompartmental Hodgkin-Huxley-style spiking neurons based on known responses and projections of physiologically identified vestibular neurons. The modelling used the GENESIS software package. The slow-phase network consisted of ganglion and medial vestibular nucleus (MVN) neurons; the latter were constructed using biophysical models of MVN type A and B neurons. The quick-phase network contained several types of bursting cells which have been shown to have major roles in the generation of the quick phase: burster-driver neurons, long-lead burst neurons, pause neurons, excitatory burst neurons and inhibitory burst neurons. Comparison of the output neural responses from the model with guinea pig behavioural responses from the companion paper showed consistency between model and animal data for neuron firing patterns, maximal firing rates, and timing, duration and number of quick phases. Comparisons were made for stable head input and for sinusoidal angular stimuli at a range of frequencies from 0.1 to 2 Hz. Except for data at 0.1 Hz, where the simulation produced one more quick phase per half cycle than the animal data, the number of quick phases was consistent between the model and the animal data. The model was also used to simulate the effects both of unilateral vestibular deafferentation (UVD) and of vestibular compensation after UVD, and the responses in the modelled MVN neurons were affected in a way similar to those measured in guinea pig MVN neurons: the number of quick phases and their timing changed in a similar fashion to that observed in behavioural data.