The main strategies for soil pollution apportionment: A review of the numerical methods

Nowadays, a large number of compounds with different physical and chemical properties have been determined in soil. Environmental behaviors and source identification of pollutants in soil are the foundation of soil pollution control. Identification and quantitative analysis of potential pollution sources are the prerequisites for its prevention and control. Many efforts have made to develop methods for identifying the sources of soil pollutants. These efforts have involved the measurement of source and receptor parameters and the analysis of their relationships via numerical statistics methods. We have comprehensively reviewed the progress made in the development of source apportionment methodologies to date and present our synthesis. The numerical methods, such as spatial geostatistics analysis, receptor models, and machine learning methods are addressed in depth. In most cases, however, the effectiveness of any single approach for source apportionment remains limited. Combining multiple methods to address soil quality problems can reduce uncertainty about the sources of soil pollution. This review also constructively highlights the key strategies of combining mathematical models with the assessment of chemical profiles to provide more accurate source attribution. This review intends to provide a comprehensive summary of source apportionment methodologies to help promote further development.

Malondialdehyde Assays in Higher Plants

Malondialdehyde is a three-carbon dialdehyde produced as a byproduct of polyunsaturated fatty acid peroxidation widely used as a marker of the extent of lipid peroxidation in plants. There are several methodological approaches to quantify malondialdehyde contents in higher plants, ranging from the simplest, cheapest, and quickest spectrophotometric approaches to the more complex ones using tandem mass spectrometry. This chapter summarizes the advantages and limitations of approaches followed and provides brief protocols with some tips to facilitate the selection of the best method for each experimental condition and application.

Estimating foraging behavior in rodents using a modified paradigm measuring threat imminence dynamics

Animals need to respond to threats to avoid danger and approach rewards. In nature, these responses did not evolve alone but are always accompanied by motivational conflict. A semi-naturalistic threat imminence continuum model models the approach-avoidance conflict and is able to integrate multiple behaviors into a single paradigm. However, its comprehensive application is hampered by the lack of a detailed protocol and data about some fundamental factors including sex, age, and motivational level. Here, we modified a previously established paradigm measuring threat imminence continuum dynamics, involving modifications of training and testing protocols, and utilization of commercial materials combined with open science codes, making it easier to replicate. We demonstrate that foraging behavior is modulated by age, hunger level, and sex. This paradigm can be used to study foraging behaviors in animals in a more naturalistic manner with relevance to human approach-avoid conflicts and associated psychopathologies.

How to use the Surveillance, Epidemiology, and End Results (SEER) data: research design and methodology

In the United States (US), the Surveillance, Epidemiology, and End Results (SEER) program is the only comprehensive source of population-based information that includes stage of cancer at the time of diagnosis and patient survival data. This program aims to provide a database about cancer incidence and survival for studies of surveillance and the development of analytical and methodological tools in the cancer field. Currently, the SEER program covers approximately half of the total cancer patients in the US. A growing number of clinical studies have applied the SEER database in various aspects. However, the intrinsic features of the SEER database, such as the huge data volume and complexity of data types, have hindered its application. In this review, we provided a systematic overview of the commonly used methodologies and study designs for retrospective epidemiological research in order to illustrate the application of the SEER database. Therefore, the goal of this review is to assist researchers in the selection of appropriate methods and study designs for enhancing the robustness and reliability of clinical studies by mining the SEER database.

Getting to the Root of Branched Ubiquitin Chains: A Review of Current Methods and Functions

Nearly 20 years since the first branched ubiquitin (Ub) chains were identified by mass spectrometry, our understanding of these chains and their function is still evolving. This is due to the limitations of classical Ub research techniques in identifying these chains and the vast complexity of potential branched chains. Considering only lysine or N-terminal methionine attachment sites, there are already 28 different possible branch points. Taking into account recently discovered ester-linked ubiquitination, branch points of more than two linkage types, and the higher-order chain structures within which branch points exist, the diversity of branched chains is nearly infinite. This review breaks down the complexity of these chains into their general functions, what we know so far about the different linkage combinations, branched chain-optimized methodologies, and the future perspectives of branched chain research.

Radiomics: Status quo and future challenges

Noninvasive imaging (computed tomography, magnetic resonance imaging, endoscopic ultrasonography, and positron emission tomography) as an important part of the clinical workflow in the clinic, but it still provides limited information for diagnosis, treatment effect evaluation and prognosis prediction. In addition, judgment and diagnoses made by experts are usually based on multiple years of experience and subjective impression which lead to variable results in the same case. With accumulation of medical imaging data, radiomics emerges as a relatively new approach for analysis. Via artificial intelligence techniques, high-throughput quantitative data which is invisible to the naked eyes extracted from original images can be used in the process of patients’ management. Several studies have evaluated radiomics combined with clinical factors, pathological, or genetic information would assist in the diagnosis, particularly in the prediction of biological characteristics, risk of recurrence, and survival with encouraging results. In various clinical settings, there are limitations and challenges needing to be overcome before transformation. Therefore, we summarize the concepts and method of radiomics including image acquisition, region of interest segmentation, feature extraction and model development. We also set forth the current applications of radiomics in clinical routine. At last, the limitations and related deficiencies of radiomics are pointed out to direct the future opportunities and development.

Towards robust and repeatable methods for studying interactions between jellyfish and microplastics

Studies of microplastics are increasing exponentially and standard protocols are only beginning to be established. Jellyfish are considered susceptible to ingesting microplastics because they feed on small, suspended particles. Inconsistent approaches used to study interactions between jellyfish and microplastics, however, make comparisons among studies difficult. Here we review aspects of the methods used to sample jellyfish in the field and experimental approaches used in the laboratory to study interactions between jellyfish and microplastics, recommend some standard protocols and identify areas for further research. We highlight the need for experiments to be environmentally relevant, to study a greater diversity of species and to study different life history stages.

A review on risk assessment in managed aquifer recharge

Managed aquifer recharge (MAR) refers to a suite of methods that is increasingly being applied worldwide for sustainable groundwater management to tackle drinking or irrigation water shortage or to restore and maintain groundwater ecosystems. The potential for MAR is far from being exhausted, not only due to geological and hydrogeological conditions or technical and economic feasibility but also due to its lack of acceptance by the public and policymakers. One approach to enable the safe and accepted use of MAR could be to provide comprehensive risk management, including the identification, analysis, and evaluation of potential risks related to MAR. This article reviews current MAR risk assessment methodologies and guidelines and summarizes possible hazards and related processes. It may help planners and operators select the appropriate MAR risk assessment approaches and support the risk identification process. In addition to risk assessment (and subsequent risk treatment) related to the MAR implementation phase, this review also addresses risk assessment for MAR operation. We also highlight the limitations and lessons learned from the application and development of risk assessment methodologies. Moreover, developments are recommended in the area of MAR-related risk assessment methodologies and regulation. Depending on data availability, collected methodologies may be applicable for MAR sites worldwide. Integr Environ Assess Manag 2022;18:1513-1529. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).

Recent advances in the screening methods of NPC1L1 inhibitors

NPC1L1 is a crucial protein involved in sterol lipid absorption and has been shown to play an important role in intestinal cholesterol absorption. Hypercholesterolemia is a significant risk factor for cardiovascular diseases such as coronary heart disease. Screening of NPC1L1 inhibitors is critical for gaining a full understanding of lipid metabolism, developing new cholesterol-lowering medicines, and treating cardiovascular diseases. This work summarized existing methodologies for screening NPC1L1 inhibitors and evaluated their challenges, and will assist the development of novel cholesterol-lowering medications and therapeutic strategies for hypercholesterolemia and other cholesterol-related metabolic disorders.

The Relationship Between Different Bench Test Methodologies and Accuracy of Insulin Infusion Pumps: A Systematic Literature Review

Diabetes technology has rapidly evolved, and insulin infusion pumps (IIPs) have gained worldwide acceptance in diabetes care. The safety of medical equipment is highly discussed, imposing complex challenges in its use. The accuracy of IIPs can be determined through laboratory tests, generally following the IEC 60601-2-24 protocol. Studies have evaluated the accuracy and precision of IIPs, and there are discrepant results. So, we conducted a Systematic Literature Review to assess the methodologies used to evaluate the accuracy of IIPs, organizing the findings in a compiled perspective. The methodology was based on Kitchenham and Biolchini guidelines, and when possible it was carried out the Bayesian meta-analyses to compare the accuracy of IIPs. Most studies used the microgravimetric technique to evaluate the device accuracy, and some proposed adaptations for the standard protocol. The variation of results was recurrent, and the establishment of a protocol, especially to evaluate patch pumps, is necessary. The present study gives enough data to understand the scenario of the IIPs evaluation, as well as the different protocols that can be explored for its evaluation. This highlights the need for a reliable, practical, and low-cost methodology to assist the evaluation of IIPs.

From Model Organisms to Humans, the Opportunity for More Rigor in Methodologic and Statistical Analysis, Design, and Interpretation of Aging and Senescence Research

This review identifies frequent design and analysis errors in aging and senescence research and discusses best practices in study design, statistical methods, analyses, and interpretation. Recommendations are offered for how to avoid these problems. The following issues are addressed: (a) errors in randomization, (b) errors related to testing within-group instead of between-group differences, (c) failing to account for clustering, (d) failing to consider interference effects, (e) standardizing metrics of effect size, (f) maximum life-span testing, (g) testing for effects beyond the mean, (h) tests for power and sample size, (i) compression of morbidity versus survival curve squaring, and (j) other hot topics, including modeling high-dimensional data and complex relationships and assessing model assumptions and biases. We hope that bringing increased awareness of these topics to the scientific community will emphasize the importance of employing sound statistical practices in all aspects of aging and senescence research.

Disrupting the Systems: Opportunities to Enhance Methodological Approaches to Address Socio-Structural Determinants of HIV and End the Epidemic Through Effective Community Engagement

A world without HIV is only possible by addressing the socio-structural determinants of health. Our understanding of socio-structural determinants is constantly changing, and parallel changes must occur with the methodologies used to explain the drivers of the HIV epidemic. We argue for the need to engage communities in the planning, implementation, and dissemination of research on the socio-structural determinants of HIV. Community engagement should cross-cut various types of research including rigorous measurement development of socio-structural determinants and novel analytic techniques to model their role in the trajectory of the epidemic and the impact of interventions. Considering the role of place, we recommend collaboration between scientists and communities in the interpretation of results from studies that map HIV-related behaviors and movement. As we collectively delve into historically oppressive systems with colonial antecedents, we must be ready to challenge these systems and replace them with collaborative models. The success of research-driven HIV policy and programming will best be evaluated with methodologies derived from the insights of the very individuals that these policies and programs aim to serve.

The Differential Relations Between ADHD and Reading Comprehension: A Quantile Regression and Quantile Genetic Approach

This paper extends the understanding of the relation between ADHD and reading comprehension, through examining how this relation differs depending on the quantile an individual falls in for each. Samples from three twin projects around the United States were used (Florida Twin Project, Colorado component of International Longitudinal Twin Study of Early Reading Development, & Western Reserve Reading and Math Projects). Phenotypic analysis using quantile regression showed relations between ADHD related behaviors and reading comprehension to be stronger in the lower quantiles of reading comprehension in two of three samples. A new method was developed extending this analysis into the bivariate genetic space. Results of this quantile genetic analysis revealed that overlapping common environmental influences accounted for a larger proportion of variance in the lower quantiles of these variables in two of three samples. Finally, in all three samples the phenotypic relation was strongest when shared environmental influences accounted for a larger proportion of the overall variance.

Current strategies to determine antifungal and antimicrobial activity of natural compounds

Fungal and microbial infections are increasingly common diseases affecting not only humans, but also animals. Despite the fact that there are wide ranges of antifungal drugs that can be used as therapy against different types of mycosis, the large-scale needed for new antifungal and antimicrobial agents is undeniable. The reasons for a great demand for new agents are low effectiveness due to the development of resistance, host toxicity and various side effects of currently used therapeutics. In order to develop novel drugs against fungal infections, scientists need to search for new molecules that show antimicrobial activity. However, there are various methods to determine antifungal and antimicrobial activity such as diffusion methods, bioautography methods, dilution methods and other frequently used methods. This review aims to explain the methodologies mentioned, to highlight the functioning, usage, advantages and disadvantages and to compare the techniques using different sources of the last years. Additionally, some of the currently investigated natural compounds such as essential oils, which show promising results in the medication of fungal diseases, are mentioned.

Reflections on Methodological Congruence in Systems and Complexity-Informed Research Comment on "What Can Policy-Makers Get Out of Systems Thinking? Policy Partners' Experiences of a Systems-Focused Research Collaboration in Preventive Health"

In this paper we argue, for an increased congruence between the conceptual frameworks and the research methodology in studies focused on the theory or practice of systems and complexity-informed thinking (SCT). In doing so, we believe we can build more complex forms of knowledge with clearer and more impactful implications for practice. There is scope for both methodological innovations and the adaptation of traditional research methods to enact properties congruent with the systemic complexity of our targeted realities. We organise our reflection around the paper of Haynes et al. We provide examples of how a research methodology more deeply embedded in systems and complexity-thinking may add depth and meaning to the research results and their interpretation. We explore the creative adaptation of the interview techniques to integrate systemic forms of questioning (eg, circular and reflexive questioning) to map the patterns of interaction contributing to the outcomes of interventions.

Evaluation of Viral Recovery Methodologies from Solid Waste Landfill Leachate

Leachate from solid waste landfill is a dark liquid of variable composition and possible source of contamination of groundwater and surface waters. This study aims to assess skimmed milk flocculation and ultracentrifugation as viral concentration methods associated to different nucleic acid extraction protocols in order to establish a methodology for virus recovery from sanitary landfill leachate. Spiking experiments using human adenovirus (HAdV) and bacteriophage PP7 revealed the association of QIAamp Fast DNA Stool mini kit® nucleic acid extraction and ultracentrifugation as an effective method for recovering HAdV (346.18%) and PP7 (523.97%) when compared to organic flocculation method (162.64% for HAdV and 0.61% for PP7) that presented PCR inhibition in all undiluted samples. Ultracentrifugation applied in three landfill samples confirm efficiency of the methodology detecting HAdV in all samples with a mean of 3.44E + 06 ± 1.56E + 06 genomic copies/mL. Nucleotide sequencing characterized HAdV as belonging to group B and F. JC polyomavirus (JCPyV) was also investigated in those samples; however, detection was not observed. Methodologies for detection of viruses in leachate can be useful to generate data for future health risk analysis of workers who have contact with solid urban waste, as well as populations exposed to different environmental matrices contaminated by these effluents.

A meta-analysis of methodologies adopted by microplastic studies in China

China is the world's largest plastic producer and has been a focus of research on microplastic pollution. An increasing number of studies have documented plastics in the sediment, water and biota of China over the past decades. This systematic review compares different methodologies adopted by microplastic studies in China, including sampling equipment and methods; laboratory procedures in microplastic extraction and identification; and the characterisation and quantification of particles. In general, sediment samples were primarily collected with a grab sampler, while water samples were mostly taken from the surface using trawl nets. Different techniques, including density separation, chemical digestion, sieving and filtration, were applied to extract microplastics from the sample matrix. Visual sorting was an obligatory step that identifies microplastics by their morphological characteristics, such as size, shape and colour. Most studies in China reported the prevalence of irregular-shaped particles with sizes smaller than 1 mm. The chemical properties of microplastics were also assessed using infrared and Raman spectroscopy. Quantitative units commonly used for sediment, water and biota samples were "items per kg", "items per m³" and "items per individual", respectively. The inconsistencies in methods have marked the urgent warrant of a standardised methodology. It is believed that the findings of the present review can serve as an important waypoint contributing towards a more efficient and long-acting methodology for microplastic research, that can enable meaningful inter-study comparisons.

Complexity of matrix phenotypes

The extracellular matrix is engaged in an ever-evolving and elegant ballet of dynamic reciprocity that directly and bi-directionally regulates cell behavior. Homeostatic and pathophysiological changes in cell-matrix signaling cascades manifest as complex matrix phenotypes. Indeed, the extracellular matrix can be implicated in virtually every known human disease, thus, making it the most critical and dynamic "organ" in the human body. The overall goal of this Special Issue is to provide an accurate and inclusive functional definition that addresses the inherent complexity of matrix phenotypes. This goal is summarily achieved via a corpus of expertly written articles, reviews and original research, focused at answering this question empirically and fundamentally via state-of-the-art methods and research strategies.

Carbon offset market methodologies applicable for coastal wetland restoration and conservation in the United States: A review

Coastal wetlands have been valued for a variety of ecosystem services including carbon sequestration and long term storage. The carbon sequestered and stored in coastal habitat including mangroves, salt marshes, and seagrass beds is termed as blue carbon. However, these systems are threatened mainly due to sea level rise, limited sediment supply, edge erosion, and anthropogenic influences. These habitats require restoration and conservation to continue providing ecosystem services. The incentive for emission reductions, referred to as carbon offsets, is well established for other ecosystems like forestry and agriculture. Some blue carbon offset methodologies or protocols have been certified by various voluntary carbon markets; however to date, a few wetland restoration carbon offset in the US has been transacted. Thus, the goal of this paper is to discuss the existing carbon market and carbon market methodologies applicable to coastal wetland restoration and conservation in the US. Currently, four wetland carbon offset methodologies have been approved in the carbon market. These methodologies are site and/or project-specific depending on the type of the wetlands, vulnerability to loss, and restoration need. The appropriate carbon stock and Green House Gas (GHG) emission assessment is the basis of determining carbon offsets. Simplification of the existing methodologies and development of new site and project-specific methodologies could potentially help to realize blue carbon offsets in practice. The slowly growing demand for carbon offsets in the carbon market could potentially be fulfilled from the blue carbon pool. While this carbon offset is in the early stages, this review may help the inclusion of carbon offset component in the coastal restoration and conservation projects in United States and potentially across the globe.

Tumor-educated platelet as liquid biopsy in lung cancer patients

Lung cancer is the most frequent cancer for males and third most frequent cancer for females. Targeted therapy drugs based on molecular alterations, such as angiogenesis inhibitors, epidermal growth factor receptor (EGFR) inhibitors, and anaplastic lymphoma kinase (ALK) inhibitors are important part of treatment of NSCLC. However, the quality of the available tumor biopsy and/or cytology material is sometimes not adequate to perform the necessary molecular testing, which has prompted the search for alternatives. This review examines the use of tumor-educated platelet (TEP) as a liquid biopsy in lung cancer patients. The development of sensitive and accurate techniques have made it possible to detect the specific genetic alterations for which targeted therapies are already available. Liquid biopsy offers opportunities to detect resistance mechanisms at an early stage. To conclude, tumor-educated platelet has the potential to be used as liquid biopsy for a variety of clinical and investigational applications.

Understanding Diseases from Single-Cell Sequencing and Methylation

Clinical single-cell biomedicine has become a new emerging discipline, which integrates single-cell RNA and DNA sequencing, proteomics, and functions with clinical phenomes, therapeutic responses, and prognosis. It is of great value to discover disease-, phenome-, and therapy-specific diagnostic biomarkers and therapeutic targets on the basis of the principle of clinical single-cell biomedicine. This book reviews the roles of single-cell sequencing and methylation in diseases and explores disease-specific alterations of single-cell sequencing and methylation, especially focusing on potential applications of methodologies on human single-cell sequencing and methylation, on potential correlations between those changes with pulmonary diseases, and on potential roles of signaling pathways that cause heterogeneous cellular responses during treatment. This book also emphasizes the importance of methodologies in clinical practice and application, the potential of perspectives, challenges and solutions, and the significance of single-cell preparation standardization. Alterations of DNA and RNA methylation, demethylation in lung diseases, and a deep knowledge about the regulation and function of target gene methylation for diagnosing and treating diseases at the early stage are also provided. Importantly, this book aims to apply the measurement of single-cell sequencing and methylation for clinical diagnosis and treatment and to understand clinical values of those parameters and to headline and foresee the potential values of the application of single-cell sequencing in non-cancer diseases.

Proposal for an optimized method for sustainable remediation evaluation and application: implementation of a multi-criteria process

As sustainable remediation methods do not yet have a consolidated approach, a detailed assessment of the level of satisfaction for sustainability prospects is necessary. So, this study aims to evaluate the sustainability level of sustainable remediation methods according to the visions of decision makers in this field, in order to propose an optimized method that best represents its approach. We considered eight methods applied to sustainable remediation and nine decision criteria for evaluation. The analytical hierarchy process (AHP) of multi-criteria decision analysis (MCDA) was applied to judge and weigh the criteria by stakeholders. These weights were used to calculate the degrees of sustainability for all the methods, to classify these within a ranking, and to optimize the one that obtained the best performance. The results indicated that when the criteria were weighted, the criterion (C7), protection of human health and the environment in general, obtained the best placement, and the degree of sustainability achieved by each method indicates that ITRC (Interstate Technology and Regulatory Council) had the best performance. Finally, the proposal method resulted in an explicit approach of all the considered criteria. This article presents a new approach compared with those already applied in this context and provides more robust resources to examine to what extent the methods integrate the premises of sustainable remediation. Graphical Abstract .

A systematic review of the effect of infrastructural interventions to promote cycling: strengthening causal inference from observational data

BACKGROUND

Previous reviews have suggested that infrastructural interventions can be effective in promoting cycling. Given inherent methodological complexities in the evaluation of such changes, it is important to understand whether study results obtained depend on the study design and methods used, and to describe the implications of the methods used for causality. The aims of this systematic review were to summarize the effects obtained in studies that used a wide range of study designs to assess the effects of infrastructural interventions on cycling and physical activity, and whether the effects varied by study design, data collection methods, or statistical approaches.

METHODS

Six databases were searched for studies that evaluated infrastructural interventions to promote cycling in adult populations, such as the opening of cycling lanes, or the expansion of a city-wide cycling network. Controlled and uncontrolled studies that presented data before and after the intervention were included. No language or date restrictions were applied. Data was extracted for any outcome presented (e.g. bikes counted on the new infrastructure, making a bike trip, cycling frequency, cycling duration), and for any purpose of cycling (e.g. total cycling, recreational cycling, cycling for commuting). Data for physical activity outcomes and equity effects was extracted, and quality assessment was conducted following previous methodologies and the UK Medical Research Council guidance on natural experiments. The PROGRESS-Plus framework was used to describe the impact on subgroups of the population. Studies were categorized by outcome, i.e. changes in cycling behavior, or usage of the cycling infrastructure. The relative change was calculated to derive a common outcome across various metrics and cycling purposes. The median relative change was presented to evaluate whether effects differed by methodological aspects.

RESULTS

The review included 31 studies and all were conducted within urban areas in high-income countries. Most of the evaluations found changes in favor of the intervention, showing that the number of cyclists using the facilities increased (median relative change compared to baseline: 62%; range: 4 to 438%), and to a lesser extent that cycling behavior increased (median relative change compared to baseline: 22%; range: - 21 to 262%). Studies that tested for statistical significance and studies that used subjective measurement methods (such as surveys and direct observations of cyclists) found larger changes than those that did not perform statistical tests, and those that used objective measurement methods (such as GPS and accelerometers, and automatic counting stations). Seven studies provided information on changes of physical activity behaviors, and findings were mixed. Three studies tested for equity effects following the opening of cycling infrastructure.

CONCLUSIONS

Study findings of natural experiments evaluating infrastructural interventions to promote cycling depended on the methods used and the approach to analysis. Studies measuring cycling behavior were more likely to assess actual behavioral change that is most relevant for population health, as compared to studies that measured the use of cycling infrastructure. Triangulation of methods is warranted to overcome potential issues that one may encounter when evaluating environmental changes within the built environment.

TRIAL REGISTRATION

The protocol of this study was registered at PROSPERO (CRD42018091079).

An overview of methods/techniques for the detection of Cryptosporidium in food samples

Cryptosporidium is one of the most important parasitic protozoa of concern within the food production industry, worldwide. This review describes the evolution and its development, and it monitors the methodology that has been used for Cryptosporidium in food material since 1984, when the first publication appeared regarding the detection of Cryptosporidium parvum in food materials. The methods that are currently being used for the detection of Cryptosporidium oocysts in food material (mainly vegetables) and all of the other available published methods are discussed in this review. Generating more consistent and reliable data should lead to a better understanding of the occurrence, transport and fate of the oocysts in food material. Improvements in monitoring and developing effective methodology, along with food security, offer more practical possibilities for both the developed and developing worlds.

The role of mucus as an invisible cloak to transepithelial drug delivery by nanoparticles

Mucosal administration of drugs and drug delivery systems has gained increasing interest. However, nanoparticles intended to protect and deliver drugs to epithelial surfaces require transport through the surface-lining mucus. Translation from bench to bedside is particularly challenging for mucosal administration since a variety of parameters will influence the specific barrier properties of the mucus including the luminal fluids, the microbiota, the mucus composition and clearance rate, and the condition of the underlying epithelia. Besides, after administration, nanoparticles interact with the mucosal components, forming a biomolecular corona that modulates their behavior and fate after mucosal administration. These interactions are greatly influenced by the nanoparticle properties, and therefore different designs and surface-engineering strategies have been proposed. Overall, it is essential to evaluate these biomolecule-nanoparticle interactions by complementary techniques using complex and relevant mucus barrier matrices.

Concepts and Methodologies to Study Protein SUMOylation: An Overview

Protein modification by the small ubiquitin-related modifier (SUMO) was simultaneously discovered by several groups at the middle of the 1990s. Although distinct names were proposed including Sentrin, GMP1, PIC1, or SMT3, SUMO became the most popular. Early studies on the functions of SUMOylation focused on activities in the nucleus, including transcription activation, chromatin structure, and DNA repair. However, it is now recognized that SUMOylation affects a large diversity of cellular processes both in the nucleus and the cytoplasm and functions of SUMOylation appear to have undefined limits. SUMO-conjugating enzymes and specific proteases actively regulate the modification status of target proteins. The recent discoveries of ubiquitin-SUMO hybrid chains, multiple SUMO-interacting motifs, and macromolecular complexes regulated by SUMOylation underscore the high complexity of this dynamic reversible system. New conceptual frameworks suggested by these findings have motivated the development of new methodologies to study pre- and post-SUMOylation events in vitro and in vivo, using distinct model organisms. Here we summarize some of the new developments and methodologies in the field, particularly those that will be further elaborated on in the chapters integrating this book.

3D tumor spheroids: an overview on the tools and techniques used for their analysis. Biotechnol Adv. 2016;34:1427-1441. [PMID: 27845258 DOI: 10.1016/j.biotechadv.2016.11.002]

In comparison with 2D cell culture models, 3D spheroids are able to accurately mimic some features of solid tumors, such as their spatial architecture, physiological responses, secretion of soluble mediators, gene expression patterns and drug resistance mechanisms. These unique characteristics highlight the potential of 3D cellular aggregates to be used as in vitro models for screening new anticancer therapeutics, both at a small and large scale. Nevertheless, few reports have focused on describing the tools and techniques currently available to extract significant biological data from these models. Such information will be fundamental to drug and therapeutic discovery process using 3D cell culture models. The present review provides an overview of the techniques that can be employed to characterize and evaluate the efficacy of anticancer therapeutics in 3D tumor spheroids.

Circulating microRNAs and long non-coding RNAs in gastric cancer diagnosis: An update and review

Gastric cancer (GC) is the fourth most common cancer and the third leading cause of cancer mortality worldwide. MicroRNAs (miRNAs) and long non-coding RNAs (lncRNAs) are the most popular non-coding RNAs in cancer research. To date, the roles of miRNAs and lncRNAs have been extensively studied in GC, suggesting that miRNAs and lncRNAs represent a vital component of tumor biology. Furthermore, circulating miRNAs and lncRNAs are found to be dysregulated in patients with GC compared with healthy individuals. Circulating miRNAs and lncRNAs may function as promising biomarkers to improve the early detection of GC. Multiple possibilities for miRNA secretion have been elucidated, including active secretion by microvesicles, exosomes, apoptotic bodies, high-density lipoproteins and protein complexes as well as passive leakage from cells. However, the mechanism underlying lncRNA secretion and the functions of circulating miRNAs and lncRNAs have not been fully illuminated. Concurrently, to standardize results of global investigations of circulating miRNAs and lncRNAs biomarker studies, several recommendations for pre-analytic considerations are put forward. In this review, we summarize the known circulating miRNAs and lncRNAs for GC diagnosis. The possible mechanism of miRNA and lncRNA secretion as well as methodologies for identification of circulating miRNAs and lncRNAs are also discussed. The topics covered here highlight new insights into GC diagnosis and screening.

The value of Retrospective and Concurrent Think Aloud in formative usability testing of a physician data query tool

OBJECTIVE

To compare the performance of the Concurrent (CTA) and Retrospective (RTA) Think Aloud method and to assess their value in a formative usability evaluation of an Intensive Care Registry-physician data query tool designed to support ICU quality improvement processes.

METHODS

Sixteen representative intensive care physicians participated in the usability evaluation study. Subjects were allocated to either the CTA or RTA method by a matched randomized design. Each subject performed six usability-testing tasks of varying complexity in the query tool in a real-working context. Methods were compared with regard to number and type of problems detected. Verbal protocols of CTA and RTA were analyzed in depth to assess differences in verbal output. Standardized measures were applied to assess thoroughness in usability problem detection weighted per problem severity level and method overall effectiveness in detecting usability problems with regard to the time subjects spent per method.

RESULTS

The usability evaluation of the data query tool revealed a total of 43 unique usability problems that the intensive care physicians encountered. CTA detected unique usability problems with regard to graphics/symbols, navigation issues, error messages, and the organization of information on the query tool's screens. RTA detected unique issues concerning system match with subjects' language and applied terminology. The in-depth verbal protocol analysis of CTA provided information on intensive care physicians' query design strategies. Overall, CTA performed significantly better than RTA in detecting usability problems. CTA usability problem detection effectiveness was 0.80 vs. 0.62 (p<0.05) respectively, with an average difference of 42% less time spent per subject compared to RTA. In addition, CTA was more thorough in detecting usability problems of a moderate (0.85 vs. 0.7) and severe nature (0.71 vs. 0.57).

CONCLUSION

In this study, the CTA is more effective in usability-problem detection and provided clarification of intensive care physician query design strategies to inform redesign of the query tool. However, CTA does not outperform RTA. The RTA additionally elucidated unique usability problems and new user requirements. Based on the results of this study, we recommend the use of CTA in formative usability evaluation studies of health information technology. However, we recommend further research on the application of RTA in usability studies with regard to user expertise and experience when focusing on user profile customized (re)design.

Hypothesis exploration with visualization of variance

Background

The Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes—to explore whether they are linked to syndromes including ADHD, Bipolar disorder, and Schizophrenia. An aim of the consortium was in moving from traditional categorical approaches for psychiatric syndromes towards more quantitative approaches based on large-scale analysis of the space of human variation. It represented an application of phenomics—wide-scale, systematic study of phenotypes—to neuropsychiatry research.

Results

This paper reports on a system for exploration of hypotheses in data obtained from the LA2K, LA3C, and LA5C studies in CNP. ViVA is a system for exploratory data analysis using novel mathematical models and methods for visualization of variance. An example of these methods is called VISOVA, a combination of visualization and analysis of variance, with the flavor of exploration associated with ANOVA in biomedical hypothesis generation. It permits visual identification of phenotype profiles—patterns of values across phenotypes—that characterize groups. Visualization enables screening and refinement of hypotheses about variance structure of sets of phenotypes.

Conclusions

The ViVA system was designed for exploration of neuropsychiatric hypotheses by interdisciplinary teams. Automated visualization in ViVA supports ‘natural selection’ on a pool of hypotheses, and permits deeper understanding of the statistical architecture of the data. Large-scale perspective of this kind could lead to better neuropsychiatric diagnostics.

Community Engagement using World Café: The Well London Experience

The Well London programme was launched across twenty boroughs in London during late 2007 to improve the health and well-being of residents living in some of the most deprived communities in London. Well London employed a multi-stage community engagement process which informed the overall project strategy for each intervention area. In this article we establish and describe the key principles that guided the design of this innovative community engagement process. Principles included building collaborative partnerships, working with whole-systems, privileging community knowledge and working with the deficit of experience in each area. The article then describes in detail how these principles were operationalised throughout the preparation and delivery of forty World Cafes, which were the first open community activities of the Well London community engagement process. Finally, this article reflects on and summarises the lessons learned when employing innovative, inclusive and transparent community engagement for health promotion.