Algae as nutritional and functional food sources: revisiting our understanding

Global demand for macroalgal and microalgal foods is growing, and algae are increasingly being consumed for functional benefits beyond the traditional considerations of nutrition and health. There is substantial evidence for the health benefits of algal-derived food products, but there remain considerable challenges in quantifying these benefits, as well as possible adverse effects. First, there is a limited understanding of nutritional composition across algal species, geographical regions, and seasons, all of which can substantially affect their dietary value. The second issue is quantifying which fractions of algal foods are bioavailable to humans, and which factors influence how food constituents are released, ranging from food preparation through genetic differentiation in the gut microbiome. Third is understanding how algal nutritional and functional constituents interact in human metabolism. Superimposed considerations are the effects of harvesting, storage, and food processing techniques that can dramatically influence the potential nutritive value of algal-derived foods. We highlight this rapidly advancing area of algal science with a particular focus on the key research required to assess better the health benefits of an alga or algal product. There are rich opportunities for phycologists in this emerging field, requiring exciting new experimental and collaborative approaches.

Vignette methodologies for studying clinicians' decision-making: Validity, utility, and application in ICD-11 field studies

Vignette-based methodologies are frequently used to examine judgments and decision-making processes, including clinical judgments made by health professionals. Concerns are sometimes raised that vignettes do not accurately reflect "real world" phenomena, and that this affects the validity of results and conclusions of these studies. This article provides an overview of the defining features, design variations, strengths, and weaknesses of vignette studies as a way of examining how health professionals form clinical judgments (e.g., assigning diagnoses, selecting treatments). As a "hybrid" of traditional survey and experimental methods, vignette studies can offer aspects of both the high internal validity of experiments and the high external validity of survey research in order to disentangle multiple predictors of clinician behavior. When vignette studies are well designed to test specific questions about judgments and decision-making, they can be highly generalizable to "real life" behavior, while overcoming the ethical, practical, and scientific limitations associated with alternative methods (e.g., observation, self-report, standardized patients, archival analysis). We conclude with methodological recommendations and a description of how vignette methodologies are being used to investigate clinicians' diagnostic decisions in case-controlled field studies for the ICD-11 classification of mental and behavioural disorders, and how these studies illustrate the preceding concepts and recommendations.

Introduction to SMART designs for the development of adaptive interventions: with application to weight loss research

The management of many health disorders often entails a sequential, individualized approach whereby treatment is adapted and readapted over time in response to the specific needs and evolving status of the individual. Adaptive interventions provide one way to operationalize the strategies (e.g., continue, augment, switch, step-down) leading to individualized sequences of treatment. Often, a wide variety of critical questions must be answered when developing a high-quality adaptive intervention. Yet, there is often insufficient empirical evidence or theoretical basis to address these questions. The Sequential Multiple Assignment Randomized Trial (SMART)-a type of research design-was developed explicitly for the purpose of building optimal adaptive interventions by providing answers to such questions. Despite increasing popularity, SMARTs remain relatively new to intervention scientists. This manuscript provides an introduction to adaptive interventions and SMARTs. We discuss SMART design considerations, including common primary and secondary aims. For illustration, we discuss the development of an adaptive intervention for optimizing weight loss among adult individuals who are overweight.

Optimization of the ultrasonic assisted removal of methylene blue by gold nanoparticles loaded on activated carbon using experimental design methodology

The present study was focused on the removal of methylene blue (MB) from aqueous solution by ultrasound-assisted adsorption onto the gold nanoparticles loaded on activated carbon (Au-NP-AC). This nanomaterial was characterized using different techniques such as SEM, XRD, and BET. The effects of variables such as pH, initial dye concentration, adsorbent dosage (g), temperature and sonication time (min) on MB removal were studied and using central composite design (CCD) and the optimum experimental conditions were found with desirability function (DF) combined response surface methodology (RSM). Fitting the experimental equilibrium data to various isotherm models such as Langmuir, Freundlich, Tempkin and Dubinin-Radushkevich models show the suitability and applicability of the Langmuir model. Analysis of experimental adsorption data to various kinetic models such as pseudo-first and second order, Elovich and intraparticle diffusion models show the applicability of the second-order equation model. The small amount of proposed adsorbent (0.01 g) is applicable for successful removal of MB (RE>95%) in short time (1.6 min) with high adsorption capacity (104-185 mg g(-1)).

Keep it real: rethinking the primacy of experimental control in cognitive neuroscience

Naturalistic experimental paradigms in neuroimaging arose from a pressure to test the validity of models we derive from highly-controlled experiments in real-world contexts. In many cases, however, such efforts led to the realization that models developed under particular experimental manipulations failed to capture much variance outside the context of that manipulation. The critique of non-naturalistic experiments is not a recent development; it echoes a persistent and subversive thread in the history of modern psychology. The brain has evolved to guide behavior in a multidimensional world with many interacting variables. The assumption that artificially decoupling and manipulating these variables will lead to a satisfactory understanding of the brain may be untenable. We develop an argument for the primacy of naturalistic paradigms, and point to recent developments in machine learning as an example of the transformative power of relinquishing control. Naturalistic paradigms should not be deployed as an afterthought if we hope to build models of brain and behavior that extend beyond the laboratory into the real world.

Optimization of the combined ultrasonic assisted/adsorption method for the removal of malachite green by gold nanoparticles loaded on activated carbon: experimental design

The present study was aimed to experimental design optimization applied to removal of malachite green (MG) from aqueous solution by ultrasound-assisted removal onto the gold nanoparticles loaded on activated carbon (Au-NP-AC). This nanomaterial was characterized using different techniques such as FESEM, TEM, BET, and UV-vis measurements. The effects of variables such as pH, initial dye concentration, adsorbent dosage (g), temperature and sonication time on MG removal were studied using central composite design (CCD) and the optimum experimental conditions were found with desirability function (DF) combined response surface methodology (RSM). Fitting the experimental equilibrium data to various isotherm models such as Langmuir, Freundlich, Tempkin and Dubinin-Radushkevich models show the suitability and applicability of the Langmuir model. Kinetic models such as pseudo -first order, pseudo-second order, Elovich and intraparticle diffusion models applicability was tested for experimental data and the second-order equation and intraparticle diffusion models control the kinetic of the adsorption process. The small amount of proposed adsorbent (0.015 g) is applicable for successful removal of MG (RE>99%) in short time (4.4 min) with high adsorption capacity (140-172 mg g(-1)).

Methods for High-throughput Drug Combination Screening and Synergy Scoring

Gene products or pathways that are aberrantly activated in cancer but not in normal tissue hold great promises for being effective and safe anticancer therapeutic targets. Many targeted drugs have entered clinical trials but so far showed limited efficacy mostly due to variability in treatment responses and often rapidly emerging resistance. Toward more effective treatment options, we will need multi-targeted drugs or drug combinations, which selectively inhibit the viability and growth of cancer cells and block distinct escape mechanisms for the cells to become resistant. Functional profiling of drug combinations requires careful experimental design and robust data analysis approaches. At the Institute for Molecular Medicine Finland (FIMM), we have developed an experimental-computational pipeline for high-throughput screening of drug combination effects in cancer cells. The integration of automated screening techniques with advanced synergy scoring tools allows for efficient and reliable detection of synergistic drug interactions within a specific window of concentrations, hence accelerating the identification of potential drug combinations for further confirmatory studies.

Threats to the validity of eye-movement research in psychology

Eyetracking research in psychology has grown exponentially over the past decades, as equipment has become cheaper and easier to use. The surge in eyetracking research has not, however, been equaled by a growth in methodological awareness, and practices that are best avoided have become commonplace. We describe nine threats to the validity of eyetracking research and provide, whenever possible, advice on how to avoid or mitigate these challenges. These threats concern both internal and external validity and relate to the design of eyetracking studies, to data preprocessing, to data analysis, and to the interpretation of eyetracking data.

Screening and optimization of highly effective ultrasound-assisted simultaneous adsorption of cationic dyes onto Mn-doped Fe3O4-nanoparticle-loaded activated carbon

The ultrasound-assisted simultaneous adsorption of brilliant green (BG) and malachite green (MG) onto Mn-doped Fe₃O₄ nanoparticle-loaded activated carbon (Mn-Fe₃O₄-NP-AC) as a novel adsorbent was investigated and analyzed using first derivative spectrophotometry. The adsorbent was characterized using FT-IR, FE-SEM, EDX and XRD. Plackett-Burman design was applied to reduce the total number of experiments and to optimize the ultrasound-assisted simultaneous adsorption procedure, where pH, adsorbent mass and sonication time (among six tested variables) were identified as the most significant factors. The effects of significant variables were further evaluated by a central composite design under response surface methodology. The significance of independent variables and their interactions was investigated by means of the analysis of variance (ANOVA) within 95% confidence level together with Pareto chart. Using this statistical tool, the optimized ultrasound-assisted simultaneous removal of basic dyes was obtained at 7.0, 0.02g, 3min for pH, adsorbent mass, and ultrasonication time, respectively. The maximum values of BG and MG uptake under these experimental conditions were found to be 99.50 and 99.00%, respectively. The adsorption process was found to be followed by the Langmuir isotherm and pseudo-second order model using equilibrium and kinetic studies, respectively. According to Langmuir isotherm model, the maximum adsorption capacities of the adsorbent were obtained to be 101.215 and 87.566mgg^-1 for MG and BG, respectively. The value of apparent energy of adsorption obtained from non-linear Dubinin-Radushkevich model (4.348 and 4.337kJmol^-1 for MG and BG, respectively) suggested the physical adsorption of the dyes. The studies on the well regenerability of the adsorbent in addition to its high adsorption capacity make it promising for such adsorption applications.

Spontaneous healing capacity of rabbit cranial defects of various sizes

Purpose

This study evaluated the spontaneous healing capacity of surgically produced cranial defects in rabbits with different healing periods in order to determine the critical size defect (CSD) of the rabbit cranium.

Methods

Thirty-two New Zealand white rabbits were used in this study. Defects of three sizes (6, 8, and 11 mm) were created in each of 16 randomly selected rabbits, and 15-mm defects were created individually in another 16 rabbits. The defects were analyzed using radiography, histologic analysis, and histometric analysis after the animal was sacrificed at 2, 4, 8, or 12 weeks postoperatively. Four samples were analyzed for each size of defect and each healing period.

Results

The radiographic findings indicated that defect filling gradually increased over time and that smaller defects were covered with a greater amount of radiopaque substance. Bony islands were observed at 8 weeks at the center of the defect in both histologic sections and radiographs. Histometrical values show that it was impossible to determine the precise CSD of the rabbit cranium. However, the innate healing capacity that originates from the defect margin was found to be constant regardless of the defect size.

Conclusions

The results obtained for the spontaneous healing capacity of rabbit cranial defects over time and the underlying factors may provide useful guidelines for the development of a rabbit cranial model for in vivo investigations of new bone materials.

A simple, robust and highly efficient transient expression system for producing antibodies

Transient expression systems in mammalian cells have become the method of choice for producing research quantities of antibodies. Both the speed and yield of the available transient systems and the natural posttranslational modifications favor these systems above expression in lower eukaryotes, prokaryotes or stable cell lines. We describe an optimized mammalian transient expression system, capable of producing up to 400mg/L of native secreted antibodies in less than a week. The system is composed of commercially available components and is based on expression in the fast growing suspension cell line, FreeStyle™ 293-F (HEK-293F). The method depends on an optimal combination of a gene transfer method, an expression vector and cotransfection with expression enhancing plasmids, encoding the large T antigen of the SV40 virus and the cell cycle inhibitors p21 and p27. Optimization of all components of the expression system, by experimental design techniques, yielded maximal expression levels (including antibody isotypes IgG1, 2, 3, 4 and Fab fragments of various species). Expression volumes were scalable from 0.1 ml up to 1.2L in a simple shaker flask system in animal component free, low protein medium, enabling consistent production of relatively high amounts of a large number of native antibodies.

Comparative study on ultrasonic assisted adsorption of dyes from single system onto Fe3O4 magnetite nanoparticles loaded on activated carbon: Experimental design methodology

The present study the ultrasound assisted adsorption of dyes in single system onto Fe₃O₄ magnetite nanoparticles loaded on activated carbon (Fe₃O₄-MNPs-AC) was described following characterization and identification of this adsorbent by conventional techniques likes field emission scanning electron microscopy, transmission electron microscopy, particle-size distribution, X-ray diffraction and Fourier transform infrared spectroscopy. A central composite design in conjunction with a response surface methodology according to f-test and t-test for recognition and judgment about significant term led to construction of quadratic model which represent relation among responses and effective terms. This model has unique ability to predict adsorption data behavior over a large space around central and optimum point. Accordingly Optimum conditions for well and quantitative removal of present dyes was obtained best operation and conditions: initial SY, MB and EB dyes concentration of 15, 15 and 25mgL^-1, 4.0, 6.0 and 5.0 of pH, 360, 360 and 240s sonication time and 0.04, 0.03 and 0.032g of Fe₃O₄-MNPs-AC. Replication of similar experiment (N=5) guide that average removal percentage of SY, MB and EB were found to be 96.63±2.86%, 98.12±1.67% and 99.65±1.21% respectively. Good agreement and closeness of Predicted and experimental result and high adsorption capacity of dyes in short time strongly confirm high suitability of present method for waste water treatment, while easy separation of present nanoparticle and its good regeneration all support good applicability of Fe₃O₄-MNPs-AC for waste water treatment. The kinetic study can be represented by combination of pseudo second-order and intraparticle diffusion. The obtained maximum adsorption capacities correspond to Langmuir as best model for representation of experimental data correspond to dyes adsorption onto Fe₃O₄-MNPs-AC were 76.37, 78.76 and 102.00mgg^-1 for SY, MB and EB, respectively. In addition, the performance comparison of ultrasound-assisted, magnetic stirrer assisted and vortex assisted adsorption methods demonstrates that ultrasound is an effective and good choice for facilitation of adsorption process via. Compromise of simple and facile diffusion.

The effect of thin and muscular images on women's body satisfaction

A substantial body of research documents that exposure to images depicting a "thin ideal" body figure effects women's state-oriented body satisfaction. However, there is evidence that the societal ideal body figure of females is evolving to be not just thin, but also muscular or toned. Therefore, the purpose of this research was to test the effect of exposure to ideal body figures that are both thin and muscular on female state body satisfaction. Researchers recruited female participants (N=366) from an online community (Amazon's Mechanical Turk) and randomly assigned them to view images in one of four conditions: thin, thin and muscular, thin and hypermuscular, and control (images of cars). Results indicated that state-oriented body satisfaction decreased in the thin condition and thin and muscular condition, but not the hypermuscular or control conditions. These findings have implications for clinical initiatives as well as future research.

A review on experimental design for pollutants removal in water treatment with the aid of artificial intelligence

Water pollution occurs mainly due to inorganic and organic pollutants, such as nutrients, heavy metals and persistent organic pollutants. For the modeling and optimization of pollutants removal, artificial intelligence (AI) has been used as a major tool in the experimental design that can generate the optimal operational variables, since AI has recently gained a tremendous advance. The present review describes the fundamentals, advantages and limitations of AI tools. Artificial neural networks (ANNs) are the AI tools frequently adopted to predict the pollutants removal processes because of their capabilities of self-learning and self-adapting, while genetic algorithm (GA) and particle swarm optimization (PSO) are also useful AI methodologies in efficient search for the global optima. This article summarizes the modeling and optimization of pollutants removal processes in water treatment by using multilayer perception, fuzzy neural, radial basis function and self-organizing map networks. Furthermore, the results conclude that the hybrid models of ANNs with GA and PSO can be successfully applied in water treatment with satisfactory accuracies. Finally, the limitations of current AI tools and their new developments are also highlighted for prospective applications in the environmental protection.

Sample size calculation while controlling false discovery rate for differential expression analysis with RNA-sequencing experiments

Background

RNA-Sequencing (RNA-seq) experiments have been popularly applied to transcriptome studies in recent years. Such experiments are still relatively costly. As a result, RNA-seq experiments often employ a small number of replicates. Power analysis and sample size calculation are challenging in the context of differential expression analysis with RNA-seq data. One challenge is that there are no closed-form formulae to calculate power for the popularly applied tests for differential expression analysis. In addition, false discovery rate (FDR), instead of family-wise type I error rate, is controlled for the multiple testing error in RNA-seq data analysis. So far, there are very few proposals on sample size calculation for RNA-seq experiments.

Results

In this paper, we propose a procedure for sample size calculation while controlling FDR for RNA-seq experimental design. Our procedure is based on the weighted linear model analysis facilitated by the voom method which has been shown to have competitive performance in terms of power and FDR control for RNA-seq differential expression analysis. We derive a method that approximates the average power across the differentially expressed genes, and then calculate the sample size to achieve a desired average power while controlling FDR. Simulation results demonstrate that the actual power of several popularly applied tests for differential expression is achieved and is close to the desired power for RNA-seq data with sample size calculated based on our method.

Conclusions

Our proposed method provides an efficient algorithm to calculate sample size while controlling FDR for RNA-seq experimental design. We also provide an R package ssizeRNA that implements our proposed method and can be downloaded from the Comprehensive R Archive Network (http://cran.r-project.org).

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-0994-9) contains supplementary material, which is available to authorized users.

Individual differences in visual science: What can be learned and what is good experimental practice?

We all pass out our lives in private perceptual worlds. The differences in our sensory and perceptual experiences often go unnoticed until there emerges a variation (such as 'The Dress') that is large enough to generate different descriptions in the coarse coinage of our shared language. In this essay, we illustrate how individual differences contribute to a richer understanding of visual perception, but we also indicate some potential pitfalls that face the investigator who ventures into the field.

Multivariate optimization of capillary electrophoresis methods: a critical review

In this article a review on the recent applications of multivariate techniques for optimization of electromigration methods, is presented. Papers published in the period from August 2007 to February 2013, have been taken into consideration. Upon a brief description of each of the involved CE operative modes, the characteristics of the chemometric strategies (type of design, factors and responses) applied to face a number of analytical challenges, are presented. Finally, a critical discussion, giving some practical advices and pointing out the most common issues involved in multivariate set-up of CE methods, is provided.

Reducing Ageism: Education About Aging and Extended Contact With Older Adults

BACKGROUND AND OBJECTIVES

Ageism is of increasing concern due to the growing older population worldwide and youth-centered focus of many societies.

RESEARCH DESIGN AND METHODS

The current investigation tested the PEACE (Positive Education about Aging and Contact Experiences) model for the first time. Two online experimental studies examined 2 key factors for reducing ageism: education about aging (providing accurate information about aging) and extended contact (knowledge of positive intergenerational contact) as well as their potential combined effect (education plus extended contact).

RESULTS AND DISCUSSION

In Study 1, 354 undergraduates in all 3 experimental conditions (vs. control participants) reported less negative attitudes toward older adults (delayed post-test) and greater aging knowledge (immediate and delayed post-tests), when controlling for pre-study attitudes. In Study 2, 505 national community participants (ages 18-59) in all experimental conditions (vs. control participants) reported less negative attitudes toward older adults (immediate post-test) and greater aging knowledge (immediate and delayed post-tests). In summary, across 2 online studies, education about aging and knowledge of intergenerational extended contact improved attitudes toward older adults and aging knowledge.

IMPLICATIONS

Thus, brief, online ageism-reduction strategies can be an effective way to combat ageism. These strategies hold promise to be tested in other settings, with other samples, and to be elaborated into more in-depth interventions that aim to reduce ageism in everyday culture.

Development and validation of an ultra-high-performance liquid chromatography tandem mass spectrometric method for the simultaneous determination of free and conjugated Alternaria toxins in cereal-based foodstuffs

A UPLC-ESI^+/--MS/MS method for the simultaneous determination of free (alternariol, alternariol monomethyl ether, altenuene, tenuazonic acid, tentoxin, altertoxin-I) and conjugated (sulfates and glucosides of alternariol and alternariol monomethyl ether) Alternaria toxins in cereals and cereal products (rice, oat flakes and barley) was developed. Optimization of the sample preparation and extraction methodology was achieved through experimental design, using full factorial design for extraction solvent composition optimization and fractional factorial design to identify the critical factors in the sample preparation protocol, which were in turn subjected to optimization. Final extracts were analysed using an Waters Acquity UPLC system coupled to a Quattro Premier XE mass spectrometer equipped with an electrospray interface operated in both positive and negative ionization mode. Chromatographic separation was achieved using an Acquity UPLC HSS T3 column, and the applied gradient elution programme allowed for the simultaneous determination of 10 Alternaria toxins in a one-step chromatographic run with a total run time of only 7min. Subsequently, the method, applying isotopically labelled internal standards ([²H₄]-alternariol monomethyl ether and [¹³C₆,¹⁵N]-tenuazonic acid), was validated for several parameters such as linearity, apparent recovery, limit of detection, limit of quantification, precision, measurement uncertainty and specificity (in agreement with the criteria mentioned in Commission Regulation No. 401/2006/EC and Commission Decision No. 2002/657/EC). During validation, quality of the bioanalytical data was improved by counteracting the observed heteroscedasticity through the application of weighted least squares linear regression (WLSLR). Finally, 24 commercially available cereal-based foodstuffs were subjected to analysis, revealing the presence of tenuazonic acid in both rice and oat flake samples (<LOQ - 68±7μgkg^-1) and tentoxin in rice samples (<LOQ - 10.9±2.0μgkg^-1).

Preparation and optimization of poly (lactic acid) nanoparticles loaded with fisetin to improve anti-cancer therapy

Fisetin is a natural flavonoid with promising antitumor activity, whereas its clinical application is limited by its hydrophobic property. In this study, we aimed to load fisetin into poly(lactic acid) (PLA) nanoparticles to increase fisetin's solubility and therapeutic efficacy. Based on spontaneous emulsification solvent diffusion (SESD) method, the formulation of PLA nanoparticles was optimized by two successive experimental designs. One-factor-at-a-time variation experiments were first applied to investigate the effects of four process variables on three responses, including drug encapsulation efficiency, average particles size and cumulative drug release ratio, followed by determining the possible ranges of these variables. Subsequently, the combinations of four variables at best levels were evaluated using a Taguchi orthogonal array design with regard to the same three responses. Eventually, the nanoparticle prepared by optimized procedure showed a narrow size distribution around 226.85 ± 4.78 nm with a high encapsulation efficiency of 90.35%. The incorporation of fisetin in nanoparticles was subsequently confirmed by FT-IR and DSC spectroscopy. Furthermore, cytotoxicity assay against HCT116 colon cancer cells in vitro and antitumor test in a xenograft 4T1 breast cancer model in vivo demonstrated that the antitumor effect of drug-loaded nanoparticles was superior to that of free drug solution.

Comparison of extraction methods for the identification and quantification of polyphenols in virgin olive oil by ultra-HPLC-QToF mass spectrometry

In this work, liquid-liquid extraction (LLE) and solid phase extraction (SPE), of polyphenols from a VOO sample were optimised by a Plackett-Burman experimental design; then the two extraction techniques capabilities were compared. By using HPLC-DAD, the extraction ability of SPE with the diol phase and LLE were similar. The two methods were further evaluated with ultra HPLC-ESI QToF in negative ion mode by recoveries of standards and matched comparison of the peak area of 40 identified and 27 unidentified compounds. Conclusions indicate that LLE gives better recoveries for highly polar, non-polar, and some polyphenols suspected to contain a nitrogen atom, while for the others the two methods seem to be equally suitable. The presence of nitrogen-containing polyphenols was confirmed in positive ionisation mode in LLE extract, whereas in the SPE extract they were not present. One of them was tentatively identified as a compound containing tyrosine and methyl-decarboxymetyl-eleanoic acid moieties.

Considerations on the use of enzyme-assisted extraction in combination with pressurized liquids to recover bioactive compounds from algae

Pressurized liquids, PLE, and enzyme-assisted extraction, EAE, have been tested to improve the extraction of phlorotannins from the seaweed Sargassum muticum. Enzymatic treatment with proteases and carbohydrases, alkaline hydrolysis and PLE with ethanol:water as extracting solvent have been studied in terms of extraction yield, total phenolic content and antioxidant activity (TEAC assay). Results demonstrated that the application of PLE alone provided the highest yields and relevant antioxidant activity. An experimental design was employed to further optimize the PLE extraction conditions; optimum parameters included the use of 160 °C and 95% ethanol. Under these conditions, values of 21.9%, 94.0mg gallic acid equivalents g(-1), 5.018 mg phloroglucinol equivalents g(-1) and 1.275 mmol trolox equivalents g(-1) were obtained for extraction yield, total phenols, total phlorotannins and TEAC, respectively. A preliminary chemical characterization by liquid chromatography coupled to mass spectrometry provided insight in terms of the mechanisms involved in the different processes.

Optimization of formulation and process parameters for the production of carvedilol nanosuspension by wet media milling

The aim of this study is to develop nanosuspension of carvedilol (CRV) by wet media milling. Concentration of polymeric stabilizer (hydroxypropyl cellulose-HPC-SL), milling speed and size of milling beads were identified as critical formulation and process parameters and their effect on CRV particle size after 60 min of milling was assessed using a Box-Behnken experimental design. Optimized nanosuspension was solidified using spray drying and freeze drying and subjected to solid state characterization. Low stabilizer concentration (10%), low milling speed (300 rpm) with small milling beads (0.1 mm) were found as optimal milling conditions. Crystal lattice simulation identified potential slip plane within CRV crystals, where fractures are the most likely to occur. Calculated mechanical properties of CRV crystal indicates that low energy stress is sufficient to initiate fracture, if applied in the correct direction, explaining the advantage of using smaller milling beads. Only spray dried nanosuspension redispersed to original nanoparticles, while particle agglomeration during freeze drying prevented sample redispersion. Wet milling and spray drying did not induce polymorphic transition of CRV, while there is indication of polymorphic transition during freeze drying, making spray drying as the preferred solidification method.

Rigor and reproducibility in rodent behavioral research

Behavioral neuroscience research incorporates the identical high level of meticulous methodologies and exacting attention to detail as all other scientific disciplines. To achieve maximal rigor and reproducibility of findings, well-trained investigators employ a variety of established best practices. Here we explicate some of the requirements for rigorous experimental design and accurate data analysis in conducting mouse and rat behavioral tests. Novel object recognition is used as an example of a cognitive assay which has been conducted successfully with a range of methods, all based on common principles of appropriate procedures, controls, and statistics. Directors of Rodent Core facilities within Intellectual and Developmental Disabilities Research Centers contribute key aspects of their own novel object recognition protocols, offering insights into essential similarities and less-critical differences. Literature cited in this review article will lead the interested reader to source papers that provide step-by-step protocols which illustrate optimized methods for many standard rodent behavioral assays. Adhering to best practices in behavioral neuroscience will enhance the value of animal models for the multiple goals of understanding biological mechanisms, evaluating consequences of genetic mutations, and discovering efficacious therapeutics.

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

Background

In gene expression studies, RNA sample pooling is sometimes considered because of budget constraints or lack of sufficient input material. Using microarray technology, RNA sample pooling strategies have been reported to optimize both the cost of data generation as well as the statistical power for differential gene expression (DGE) analysis. For RNA sequencing, with its different quantitative output in terms of counts and tunable dynamic range, the adequacy and empirical validation of RNA sample pooling strategies have not yet been evaluated. In this study, we comprehensively assessed the utility of pooling strategies in RNA-seq experiments using empirical and simulated RNA-seq datasets.

Result

The data generating model in pooled experiments is defined mathematically to evaluate the mean and variability of gene expression estimates. The model is further used to examine the trade-off between the statistical power of testing for DGE and the data generating costs. Empirical assessment of pooling strategies is done through analysis of RNA-seq datasets under various pooling and non-pooling experimental settings. Simulation study is also used to rank experimental scenarios with respect to the rate of false and true discoveries in DGE analysis. The results demonstrate that pooling strategies in RNA-seq studies can be both cost-effective and powerful when the number of pools, pool size and sequencing depth are optimally defined.

Conclusion

For high within-group gene expression variability, small RNA sample pools are effective to reduce the variability and compensate for the loss of the number of replicates. Unlike the typical cost-saving strategies, such as reducing sequencing depth or number of RNA samples (replicates), an adequate pooling strategy is effective in maintaining the power of testing DGE for genes with low to medium abundance levels, along with a substantial reduction of the total cost of the experiment. In general, pooling RNA samples or pooling RNA samples in conjunction with moderate reduction of the sequencing depth can be good options to optimize the cost and maintain the power.