Experimental Designs to Study the Aggregation and Colonization of Biofilms by Video Microscopy With Statistical Confidence

The goal of this study was to quantify the variability of confocal laser scanning microscopy (CLSM) time-lapse images of early colonizing biofilms to aid in the design of future imaging experiments. To accomplish this a large imaging dataset consisting of 16 independent CLSM microscopy experiments was leveraged. These experiments were designed to study interactions between human neutrophils and single cells or aggregates of Staphylococcus aureus (S. aureus) during the initial stages of biofilm formation. Results suggest that in untreated control experiments, variability differed substantially between growth phases (i.e., lag or exponential). When studying the effect of an antimicrobial treatment (in this case, neutrophil challenge), regardless of the inoculation level or of growth phase, variability changed as a frown-shaped function of treatment efficacy (i.e., the reduction in biofilm surface coverage). These findings were used to predict the best experimental designs for future imaging studies of early biofilms by considering differing (i) numbers of independent experiments; (ii) numbers of fields of view (FOV) per experiment; and (iii) frame capture rates per hour. A spreadsheet capable of assessing any user-specified design is included that requires the expected mean log reduction and variance components from user-generated experimental results. The methodology outlined in this study can assist researchers in designing their CLSM studies of antimicrobial treatments with a high level of statistical confidence.

Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission

BACKGROUND: Infectious disease spread in populations is controlled by individuals' susceptibility (propensity to acquire infection), infectivity (propensity to pass on infection to others) and recoverability (propensity to recover/die). Estimating the effects of genetic risk factors on these host epidemiological traits can help reduce disease spread through genetic control strategies. However, the effects of previously identified "disease resistance SNPs" on these epidemiological traits are usually unknown. Recent advances in computational statistics make it now possible to estimate the effects of single nucleotide polymorphisms (SNPs) on these traits from longitudinal epidemic data (e.g. infection and/or recovery times of individuals or diagnostic test results). However, little is known how to optimally design disease transmission experiments or field studies to maximise the precision at which pleiotropic SNP effects estimates for susceptibility, infectivity and recoverability can be estimated. RESULTS: We develop and validate analytical expressions for the precision of SNP effects estimates on the three host traits assuming a disease transmission experiment with one or more non-interacting contact groups. Maximising these leads to three distinct "experimental" designs, each specifying a different set of ideal SNP genotype compositions across groups: a) appropriate for a single contact-group, b) a multi-group design termed "pure", and c) a multi-group design termed "mixed", where "pure" and "mixed" refer to contact groups consisting of individuals with the same or different SNP genotypes, respectively. Precision estimates for susceptibility and recoverability were found to be less sensitive to the experimental design than infectivity. Data from multiple groups were found more informative about infectivity effects than from a single group containing the same number of individuals. Whilst the analytical expressions suggest that the multi-group pure and mixed designs estimate SNP effects with similar precision, the mixed design is preferable because it uses information from naturally occurring infections rather than those artificially induced. The same optimal design principles apply to estimating other categorical fixed effects, such as vaccinations status, helping to more effectively quantify their epidemiological impact. An online software tool SIRE-PC has been developed which calculates the precision of estimated substitution and dominance effects of a single SNP (or vaccine status) associated with all three traits depending on experimental design parameters. CONCLUSIONS: The developed methodology and software tool can be used to aid the design of disease transmission experiments for estimating the effect of individual SNPs and other categorical variables underlying host susceptibility, infectivity and recoverability.

EFEKTIVITAS MODEL PEMBELAJARAN BLENDED LEARNING TERHADAP HASIL BELAJAR MAHASISWA DI MASA PANDEMI COVID 19

Blended Learning merupakan salah satu model pembelajaran yang memadukan pembelajaran tatap muka (konvensional) dan pembelajaran online. Metode penelitian yang digunakan adalah Pre-Experimental Designs dengan model One –Group Pretest- Postest Design, yang bertujuan untuk menilai perbedaan hasil belajar model pembelajaran blended learning dengan model pembelajaran tatap muka langsung (konvensional). Penelitian dilakukan pada mahasiswa Prodi Pendidikan Bahasa Inggris UIN Ar-raniry di semester Genap 2020/2021 yang berjumlah 30 orang yang dipilih dengan teknik purposive sampling. Pengumpulan data dilakukan dengan menggunakan instrumen tes, sedangkan teknik analisis data menggunakan uji prasyarat dan uji hipotesis. Berdasarkan penelitian diperoleh nilai t hitung sebesar 9,517 dan pada taraf signifikansi 0,05 diperoleh nilai t tabel sebesar 2,045 yang artinya t hitung > t tabel (9,517 > 2,045) maka Ho ditolak dan Ha diterima artinya terdapat perbedaan rata-rata antara hasil belajar Pretest dan Posttest yang berarti bahwa pembelajaran model blended learning memberikan efektivitas yang signifikan dan lebih baik dibandingkan dengan pembelajaran tatap muka (konvensional). Namun berdasarkan nilai rata-rata N-gain Score sebesar 29,90. atau 29,90% termasuk dalam kategori tidak efektif. Hal ini cukup dimaklumi mengingat berbagai kendala dan keterbatasan yang menyebabkan pembelajaran belum dapat dilaksanakan secara maksimal. Sehingga wajar sekali efektivitas model pembelajaran Blended learning dalam penelitian ini tidak efektif untuk meningkatkan hasil belajar.

The Contribution of Social Representations Theory for a Social Psychology of Communication Laboratory

This chapter describes the mission and research of the Social Psychology of Communication and Cognition Laboratory (Laboratório de Psicologia Social da Comunicação e Cognição) at the Federal University of Santa Catarina (LACCOS–UFSC). After explaining how the lab was set up, the authors illustrate the communication systems model from the social representations perspective. This goes beyond previous communication paradigms that use metaphors like the machine, the organism, or Frankenstein and toward a contextualized conception of social communication. Studies conducted by the Lab exemplify how change and continuity might be experimentally explored. Some of them concern scientific knowledge on HIV/AIDS and show how to tackle the dialogical knowledge generated by the ternary Ego-Alter-Object view proposed by means of experimental designs in the social representation domain. The chapter closes with some considerations on the COVID-19 pandemic and the dynamics of social representations.

The evidence of after-death survival of human consciousness according to the winners of the Bigelow contest: a scientific examination

The aim of this study was to examine the strength of scientific evidence, reproducibility and replicability of the 29 essays of the winners of the Bigelow contest.Six essays (20.5%) were included in the category with the high strength of scientific evidence. Four essays (14%) were included in the category with medium strength of scientific evidence and the remaining 19 essays (65.5%) in the category with low strength of scientific evidence. The overall agreement between our strength of scientific evidence categories and the Bigelow ones, was only 48.8%, sufficient to demonstrate a clear difference between our scientific criteria and those adopted by the judges of the Bigelow contest.The essays that obtained the highest strength of scientific evidence level were related to near-death experiences and mental mediumship.For other phenomena, more studies with refined experimental designs are necessary to increase the evidence of the survival of human consciousness.

Rapid profiling of protein complex re-organization in perturbed systems

Protein complexes constitute the primary functional modules of cellular activity. To respond to perturbations, complexes undergo changes in their abundance, subunit composition or state of modification. Understanding the function of biological systems requires global strategies to capture this contextual state information on protein complexes and interaction networks. Methods based on co-fractionation paired with mass spectrometry have demonstrated the capability for deep biological insight but the scope of studies using this approach has been limited by the large measurement time per biological sample and challenges with data analysis. As such, there has been little uptake of this strategy beyond a few expert labs into the broader life science community despite rich biological information content. We present a rapid integrated experimental and computational workflow to assess the re-organization of protein complexes across multiple cellular states. It enables complex experimental designs requiring increased sample/condition numbers. The workflow combines short gradient chromatography and DIA/SWATH mass spectrometry with a data analysis toolset to quantify changes in complex organization. We applied the workflow to study the global protein complex rearrangements of THP-1 cells undergoing monocyte to macrophage differentiation and a subsequent stimulation of macrophage cells with lipopolysaccharide. We observed massive proteome organization in functions related to signaling, cell adhesion, and extracellular matrix during differentiation, and less pronounced changes in processes related to innate immune response induced by the macrophage stimulation. We therefore establish our integrated differential pipeline for rapid and state-specific profiling of protein complex organization with broad utility in complex experimental designs.

Pitfalls in Sleep and Memory Research and How to Avoid Them: A Consensus Paper

Understanding the complex relationship between sleep and memory is a major challenge in neuroscience. Thousands of studies on memory consolidation in humans suggest that sleep triggers offline memory processes, resulting in less forgetting of declarative memory and performance stabilization in non-declarative memory. However, an increasing number of contradictory findings reveal potential issues with how research is conducted in this field and call into question the reliability and interpretation of the results. In this consensus paper, we describe four sets of prevalent methodological pitfalls in human sleep and memory research: (i) non-optimal experimental designs, (ii) task complexity, (iii) fatigue effects in repetitive tasks, and (iv) inappropriate data analysis practices. We then offer solutions to each of these pitfalls. We believe that implementing these solutions in future research of sleep and memory will lead to more reliable results and significantly advance our understanding in this field.

Experimental Applications and Factors Involved in Validating Thermal Windows Using Infrared Thermography to Assess the Health and Thermostability of Laboratory Animals

Evaluating laboratory animals’ health and thermostability are fundamental components of all experimental designs. Alterations in either one of these parameters have been shown to trigger physiological changes that can compromise the welfare of the species and the replicability and robustness of the results obtained. Due to the nature and complexity of evaluating and managing the species involved in research protocols, non-invasive tools such as infrared thermography (IRT) have been adopted to quantify these parameters without altering them or inducing stress responses in the animals. IRT technology makes it possible to quantify changes in surface temperatures that are derived from alterations in blood flow that can result from inflammatory, stressful, or pathological processes; changes can be measured in diverse regions, called thermal windows, according to their specific characteristics. The principal body regions that were employed for this purpose in laboratory animals were the orbital zone (regio orbitalis), auricular pavilion (regio auricularis), tail (cauda), and the interscapular area (regio scapularis). However, depending on the species and certain external factors, the sensitivity and specificity of these windows are still subject to controversy due to contradictory results published in the available literature. For these reasons, the objectives of the present review are to discuss the neurophysiological mechanisms involved in vasomotor responses and thermogenesis via BAT in laboratory animals and to evaluate the scientific usefulness of IRT and the thermal windows that are currently used in research involving laboratory animals.

Design Choices in the Infant Habituation Paradigm: A Pre-registered Crowd-Sourced Systematic Review and Meta-Analysis

Methodological variations and inconsistency in reporting practices pose considerable challenges to the interpretation and generalizability of outcomes derived from the habituation paradigm - one of the most prominent methods for studying infant cognition. In a systematic review, we map out experimental design choices in habituation study samples aged 0-18 months using looking time measures. 2,853 records published in peer-reviewed journals between 2000-2019 were extracted from PsycInfo and Web of Science. 785 (27.5%) papers were identified after screening (Fleiss kappa = .60, 95%, CI[.40 - .80], 6 blind raters). We adopt a collaborative, multi-lab approach for crowd-sourced data collection involving raters from the developmental research community. In a meta-analysis, we assess the impact of habituation detection criteria on the novelty effect size, moderated by age. Our results will inform a detailed evaluation of experimental designs and a set of specific guidelines to improve research and reporting practices in infant habituation research.

Catalogue of selected experimental plans

Summary There are many works in the literature on the construction of experimental plans based on weighing designs. Hence, it is useful to compile a catalogue of experimental designs with specific properties. In this work, we investigate the properties of experimental plans constructed using the matrices of spring balance weighing designs. Additionally, an even number of experimental objects is assumed. An overview of the construction methods of these designs and classes of design matrices with selected properties are given. The results make it possible to create a catalogue of experimental designs constructed on the basis of spring balance weighing designs.