General principles of preclinical study design.

Preclinical studies using animals to study the potential of a therapeutic drug or strategy are important steps before translation to clinical trials. However, evidence has shown that poor quality in the design and conduct of these studies has not only impeded clinical translation but also led to significant waste of valuable research resources. It is clear that experimental biases are related to the poor quality seen with preclinical studies. In this chapter, we will focus on hypothesis testing type of preclinical studies and explain general concepts and principles in relation to the design of in vivo experiments, provide definitions of experimental biases and how to avoid them, and discuss major sources contributing to experimental biases and how to mitigate these sources. We will also explore the differences between confirmatory and exploratory studies, and discuss available guidelines on preclinical studies and how to use them. This chapter, together with relevant information in other chapters in the handbook, provides a powerful tool to enhance scientific rigour for preclinical studies without restricting creativity

Sensory profiles in women with neuropathic pain after breast cancer surgery

Purpose We performed a detailed analysis of sensory function in patients with chronic post-surgical neuropathic pain (NP) after breast cancer treatments by quantitative sensory testing (QST) with DFNS (German Research Network on Neuropathic Pain) protocol and bed side examination (BE). The nature of sensory changes in peripheral NP may reflect distinct pathophysiological backgrounds that can guide the treatment choices. NP with sensory gain (i.e., hyperesthesia, hyperalgesia, allodynia) has been shown to respond to Na+-channel blockers (e.g., oxcarbazepine). Methods 104 patients with at least "probable" NP in the surgical area were included. All patients had been treated for breast cancer 4-9 years ago and the handling of the intercostobrachial nerve (ICBN) was verified by the surgeon. QST was conducted at the site of NP in the surgical or nearby area and the corresponding contralateral area. BE covered the upper body and sensory abnormalities were marked on body maps and digitalized for area calculation. The outcomes of BE and QST were compared to assess the value of QST in the sensory examination of this patient group. Results Loss of function in both small and large fibers was a prominent feature in QST in the area of post-surgical NP. QST profiles did not differ between spared and resected ICBN. In BE, hypoesthesia on multiple modalities was highly prevalent. The presence of sensory gain in BE was associated with more intense pain. Conclusions Extensive sensory loss is characteristic for chronic post-surgical NP several years after treatment for breast cancer. These patients are unlikely to respond to Na+-channel blockers.Peer reviewe

Designing a Locally Manufacturable Wheelchair for Nepal

Persons with disabilities in developing countries often lack the basic equipment needed to assist them in their daily lives. International Nepal Fellowship (INF) is a Christian medical organization located in Nepal that provides medical care and assistance to people with disabilities and other conditions. Currently, INF imports expensive wheelchairs that undergo a prolonged border process before being received by INF. INF has reached out to the Collaboratory to design a wheelchair that can withstand the challenges of Nepal’s terrain and can be manufactured from local materials. The Nepal Wheelchair team accepted this challenge and set out to design a wheelchair that can fulfill the needs of INF. The team began by researching wheelchair models for inspiration and eventually settled on two preliminary designs. In January 2020, the team traveled to Pokhara, Nepal to gain feedback from the staff at INF and select a final design based on their comments. During this trip, the team acquired and brought back locally available materials and parts in order to be able to construct a prototype using materials which are actually available in Nepal. After returning, the team began performing Finite Element Analysis on the frame design and tested the steel from the trip to determine its physical properties. With prototyping progress stalled by recent events, the team is focusing on perfecting the design and preparing an instruction manual for INF.https://mosaic.messiah.edu/engr2020/1005/thumbnail.jp

Choice ofy-axis can mislead readers

Using two examples from the non-scientific literature, we show how choice of unit of measure and scaling of y-axis can caused a biased perception of data, a phenomenon we propose to call perception bias. We recommend to pre-specify unit of measure or how it will be determined, whether outcome variables will be shown as absolute or relative/normalized changes, and to typically start y-axis at 0 for ratio variables

Mechanical detection and pain thresholds: comparability of devices using stepped and ramped stimuli

Quantitative sensory testing is used to assess somatosensory function in humans. The protocol of the German Research Network on Neuropathic Pain (DFNS) provides comprehensive normative values using defined tools; however, some of these may not be feasible in low-resource settings. Objectives: To compare the standard DFNS devices for assessment of mechanosensory function to a low resource tool, the Sorri-Bauru-monofilaments. Methods: Mechanical detection thresholds (MDT), pain thresholds (MPT), and suprathreshold pinprick ratings (pain sensitivity: MPS) were measured over cheek, hand dorsum, and fingertip in 13 healthy subjects (7 female, aged 21-44 years). Mechanical detection threshold was assessed with DFNS standard glass monofilaments (0.25-512 mN, 0.5 mm tip) and nylon monofilaments (Sorri-Bauru; 0.5-3000 mN). MPT was assessed with DFNS standard cylindrical probes (8-512 mN, 0.25 mm tip), Sorri-Bauru monofilaments, and with ramped stimuli using an electronic von Frey aesthesiometer (10 mN/s or 100 mN/s, 0.20 mm tip). MPS was measured in response to stepped and ramped pinpricks (128 and 256 mN). Results: Mechanical detection thresholds were the same for DFNS and Sorri-Bauru monofilaments. For MPT, Sorri-Bauru filaments yielded lower values than PinPricks over face but not hand. Pain thresholds were higher at all test sites for ramped than stepped pinpricks (P < 0.01). Suprathreshold ratings were lower for ramped than stepped pinpricks (P < 0.05). Conclusion: Sorri-Bauru filaments are acceptable substitutes for DFNS standards in estimating tactile sensitivity, but are not consistent with standard probes for pinprick sensitivity because of their nonstandardized tips. Ramped stimuli overestimated MPT and underestimated MPS due to reaction time artefacts and therefore need their own normative values

A protocol for the systematic review and meta-analysis of thigmotactic behaviour in the open field test in rodent models associated with persistent pain

ObjectiveThigmotaxis is an innate predator avoidance behaviour of rodents and is enhanced when animals are under stress. It is characterised by the preference of a rodent to seek shelter, rather than expose itself to the aversive open area. The behaviour has been proposed to be a measurable construct that can address the impact of pain on rodent behaviour. This systematic review will assess whether thigmotaxis can be influenced by experimental persistent pain and attenuated by pharmacological interventions in rodents.Search strategyWe will conduct search on three electronic databases to identify studies in which thigmotaxis was used as an outcome measure contextualised to a rodent model associated with persistent pain. All studies published until the date of the search will be considered.Screening and annotationTwo independent reviewers will screen studies based on the order of (1) titles and abstracts, and (2) full texts.Data management and reportingFor meta-analysis, we will extract thigmotactic behavioural data and calculate effect sizes. Effect sizes will be combined using a random-effects model. We will assess heterogeneity and identify sources of heterogeneity. A risk-of-bias assessment will be conducted to evaluate study quality. Publication bias will be assessed using funnel plots, Egger’s regression and trim-and-fill analysis. We will also extract stimulus-evoked limb withdrawal data to assess its correlation with thigmotaxis in the same animals. The evidence obtained will provide a comprehensive understanding of the strengths and limitations of using thigmotactic outcome measure in animal pain research so that future experimental designs can be optimised. We will follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses reporting guidelines and disseminate the review findings through publication and conference presentation.</jats:sec

Machine learning and artificial intelligence in neuroscience: A primer for researchers

This is the final version. Available on open access from Elsevier via the DOI in this recordData availability: No data was used for the research described in the article.Artificial intelligence (AI) is often used to describe the automation of complex tasks that we would attribute intelligence to. Machine learning (ML) is commonly understood as a set of methods used to develop an AI. Both have seen a recent boom in usage, both in scientific and commercial fields. For the scientific community, ML can solve bottle necks created by complex, multi-dimensional data generated, for example, by functional brain imaging or *omics approaches. ML can here identify patterns that could not have been found using traditional statistic approaches. However, ML comes with serious limitations that need to be kept in mind: their tendency to optimise solutions for the input data means it is of crucial importance to externally validate any findings before considering them more than a hypothesis. Their black-box nature implies that their decisions usually cannot be understood, which renders their use in medical decision making problematic and can lead to ethical issues. Here, we present an introduction for the curious to the field of ML/AI. We explain the principles as commonly used methods as well as recent methodological advancements before we discuss risks and what we see as future directions of the field. Finally, we show practical examples of neuroscience to illustrate the use and limitations of ML

Sensory bedside testing: a simple stratification approach for sensory phenotyping

Introduction: Stratification of patients according to the individual sensory phenotype has been suggested a promising method to identify responders for pain treatment. However, many state-of-the-art sensory testing procedures are expensive or time-consuming. Objectives: Therefore, this study aimed to present a selection of easy-to-use bedside devices. Methods: In total, 73 patients (39 m/34 f) and 20 controls (11 m/9 f) received a standardized laboratory quantitative sensory testing (QST) and a bedside-QST. In addition, 50 patients were tested by a group of nonexperienced investigators to address the impact of training. The sensitivity, specificity, and receiver-operating characteristics were analyzed for each bedside-QST parameter as compared to laboratory QST. Furthermore, the patients’ individual sensory phenotype (ie, cluster) was determined using laboratory QST, to select bedside-QST parameters most indicative for a correct cluster allocation. Results: The bedside-QST parameters “loss of cold perception to 22˚C metal,” “hypersensitivity towards 45˚C metal,” “loss of tactile perception to Q-tip and 0.7 mm CMS hair,” as well as “the allodynia sum score” indicated good sensitivity and specificity (ie, ≳70%). Results of interrater variability indicated that training is necessary for individual parameters (ie, CMS 0.7). For the cluster assessment, the respective bedside quantitative sensory testing (QST) parameter combination indicated the following agreements as compared to laboratory QST stratification: excellent for “sensory loss” (area under the curve [AUC] 5 0.91), good for “thermal hyperalgesia” (AUC 5 0.83), and fair for “mechanical hyperalgesia” (AUC 5 0.75). Conclusion: This study presents a selection of bedside parameters to identify the individual sensory phenotype as cost and time efficient as possible

Protocol for a systematic review of guidelines for rigour in the design, conduct and analysis of biomedical experiments involving laboratory animals

Objective: Within the last years, there has been growing awareness of the negative repercussions of unstandardized planning, conduct and reporting of preclinical and biomedical research. Several initiatives have set the aim of increasing validity and reliability in reporting of studies and publications, and publishers have formed similar groups. Additionally, several groups of experts across the biomedical spectrum have published experience and opinion-based guidelines and guidance on potential standardized reporting. While all these guidelines cover reporting of experiments, an important step prior to this should be rigours planning and conduction of studies. The aim of this systematic review is to identify and harmonize existing experimental design, conduct and analysis guidelines relating to internal validity and reproducibility of preclinical animal research. The review will also identify literature describing risks of bias pertaining to the design, conduct and analysis of preclinical biomedical research. Search strategy: PubMed, Embase and Web of Science will be searched systematically to identify guidelines published in English language in peer-reviewed journals before January 2018 (box 1). All articles or systematic reviews in English language that describe or review guidelines on the internal validity and reproducibility of animal studies will be included. Google search for guidelines published on the websites of major funders and professional organisations can be found in (Box 2). Screening and annotation: Unique references will be screened in two phases: screening for eligibility based on title and abstract, followed by screening for definitive inclusion based on full text. Screening will be performed in SyRF (http://syrf.org.uk). Each reference will be randomly presented to two independent reviewers. Disagreements between reviewers will be resolved by additional screening of the reference by a third, senior researcher. Data management and reporting: All data, including extracted text and guidelines, will be stored in the SyRF platform. Elements of the included guidelines will be identified using a standardized extraction form. Reporting will follow the PRISMA guidelines as far as applicable

Analysis of sloppiness in model simulations: unveiling parameter uncertainty when mathematical models are fitted to data

This work introduces a Bayesian approach to assess the sensitivity of model outputs to changes in parameter values, constrained by the combination of prior beliefs and data. This novel approach identifies stiff parameter combinations that strongly affect the quality of the model-data fit while simultaneously revealing which of these key parameter combinations are informed primarily from the data or are also substantively influenced by the priors. We focus on the very common context in complex systems where the amount and quality of data are low compared to the number of model parameters to be collectively estimated, and showcase the benefits of our technique for applications in biochemistry, ecology, and cardiac electrophysiology. We also show how stiff parameter combinations, once identified, uncover controlling mechanisms underlying the system being modeled and inform which of the model parameters need to be prioritized in future experiments for improved parameter inference from collective model-data fitting