Natasha Karp

• Director - Biostatistics at AstraZeneca

For over thirty years, research has highlighted a sex bias in early research, risking the validity of biological knowledge. The first step towards change is effectively challenging misconceptions allowing researchers to perceive sex inclusive research as do-able. Utilising the theory of planned behaviour, we quantified researchers’ intention as a p...

Pilots are small-scale initial experiments that are intended to guide the design of future, larger studies, with a view to increasing their effectiveness. In this statistical primer we highlight five common mistakes that limit the utility of pilot studies and provide practical guidance to avoid such errors and increase their effectiveness. The comm...

Genomic instability arising from defective responses to DNA damage ¹ or mitotic chromosomal imbalances ² can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generatio...

Mutations in SNCA, the gene encoding α-synuclein (αSyn), cause familial Parkinson's disease (PD) and aberrant αSyn is a key pathological hallmark of idiopathic PD. This α-synucleinopathy leads to mitochondrial dysfunction, which may drive dopaminergic neurodegeneration. PARKIN and PINK1, mutated in autosomal recessive PD, regulate the preferential...

A new, interactive framework supports the evaluation of in vivo and ex vivo research proposals from a sex inclusive research perspective delivering a traffic light classification, indicating whether a proposal is appropriate, risky, or insufficient with regards to sex inclusion. This tool is designed for use by researchers, (animal) ethical review...

In recent years, there has been a strong drive to improve the inclusion of animals of both sexes in the design of in vivo research studies, driven by a need to increase sex representation in fundamental biology and drug development. This has resulted in inclusion mandates by funding bodies and journals, alongside numerous published manuscripts high...

Non-clinical rodent safety studies are essential in the development of new medicines to assess for potential adverse effects. Typically, toxicokinetic samples are collected from a satellite group. AstraZeneca implemented repeated microsampling of main study animals as standard in the one-month small molecule regulatory toxicology studies. A retrosp...

[This corrects the article DOI: 10.1371/journal.pbio.3001564.].

In animal experiments, blinding (also known as masking) is a methodological strategy to reduce the risk that scientists, animal care staff, or other staff involved in the research may consciously or subconsciously influence the outcome. Lack of masking has been shown to correlate with an overestimation of treatment efficacy and false positive findi...

In recent years, there has been a strong drive to improve the inclusion of animals of both sex during in vivo research, driven by a need to improve sex representation in fundamental biology and drug development. This has resulted in inclusion mandates by funding bodies and journals, alongside numerous published manuscripts highlighting the issue an...

The credibility of scientific research has been seriously questioned by the widely claimed “reproducibility crisis”. In light of this crisis, there is a growing awareness that the rigorous standardisation of experimental conditions may contribute to poor reproducibility of animal studies. Instead, systematic heterogenisation has been proposed as a...

Growing evidence shows that sex differences impact many facets of human biology. Here we review and discuss the impact of sex on human circadian and sleep physiology, and we uncover a data gap in the field investigating the non-visual effects of light in humans. A virtual workshop on the biomedical implications of sex differences in sleep and circa...

This paper investigates statistical reproducibility of the t -test. We formulate reproducibility as a predictive inference problem and apply the nonparametric predictive inference method. Within our research framework, statistical reproducibility provides inference on the probability that the same test outcome would be reached, if the test were rep...

Within preclinical research, attention has focused on experimental design and how current practices can lead to poor reproducibility. There are numerous decision points when designing experiments. Ethically, when working with animals we need to conduct a harm–benefit analysis to ensure the animal use is justified for the scientific gain. Experiment...

Purpose: Osimertinib is a potent and selective EGFR tyrosine kinase inhibitor (EGFR-TKI) of both sensitizing and T790M resistance mutations. To treat metastatic brain disease, blood-brain barrier (BBB) permeability is considered desirable for increasing clinical efficacy. Experimental design: We examined the level of brain penetration for 16 irr...

In light of the hotly discussed 'reproducibility crisis', a rethinking of current methodologies appears essential. Implementing multi-laboratory designs has been shown to enhance the external validity and hence the reproducibility of findings from animal research. We here aimed at proposing a new experimental strategy that transfers this logic into...

In their correspondence about our recent Perspective article (Reproducibility of animal research in light of biological variation. Nat. Rev. Neurosci. 21, 384–393 (2020)), Richter and von Kortzfleisch support our recommendations for a paradigm shift from rigorous standardization to systematic heterogenization in animal research (It is time for an e...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting is vital to this process; it allows readers to assess the reliability of the findings and repeat or build upon the work of other researchers. The ARRIVE guidelines (Animal Research: Reporting In Vivo Experiments) were developed in 2010 to h...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

Reproducible science requires transparent reporting. The ARRIVE guidelines (Animal Research: Reporting of In Vivo Experiments) were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work ade...

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Context- dependent biological variation presents a unique challenge to the reproducibility of results in experimental animal research, because organisms’ responses to experimental treatments can vary with both genotype and environmental conditions. In March 2019, experts in animal biology, experimental design and statistics convened in Blonay, Swit...

Phenotypic plasticity, the ability of a living organism to respond to the environment, can lead to conclusions from experiments that are idiosyncratic to a particular environment. The level of environmental responsiveness can result in difficulties in reproducing studies from the same institute with the same standardised environment. Here we presen...

By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation (http://www.immunophenotype.org). Specifically, high-throughput phenotyping of 530 unique mouse gene knockouts identified 140 monogenic ‘hits’, of...

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translate...

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translate...

In many areas of biological research, hypotheses are tested in a sequential manner, without having access to future P-values or even the number of hypotheses to be tested. A key setting where this online hypothesis testing occurs is in the context of publicly available data repositories, where the family of hypotheses to be tested is continually gr...

Improving the reproducibility of biomedical research is a major challenge. Transparent and accurate reporting are vital to this process; it allows readers to assess the reliability of the findings, and repeat or build upon the work of other researchers. The NC3Rs developed the ARRIVE guidelines in 2010 to help authors and journals identify the mini...

Reproducible science requires transparent reporting. The ARRIVE guidelines were originally developed in 2010 to improve the reporting of animal research. They consist of a checklist of information to include in publications describing in vivo experiments to enable others to scrutinise the work adequately, evaluate its methodological rigour, and rep...

By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation. Specifically, high-throughput phenotyping of 530 knockout mouse lines identified 140 monogenic "hits" (>25%), most of which had never hitherto bee...

Background The ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines are widely endorsed but compliance is limited. We sought to determine whether journal-requested completion of an ARRIVE checklist improves full compliance with the guidelines. Methods In a randomised controlled trial, manuscripts reporting in vivo animal research...

Background: Evaluation of the effects of candidate drugs on the nervous system in preclinical safety pharmacology studies utilises a global neurobehavioral assessment, usually in the rat. This either takes the form of the functional observational battery (FOB) or modified Irwin Test, both of which evaluate effects across 4 functional domains: auto...

Aim: Microsampling in preclinical pharmacokinetics (PK) studies is currently widely adopted across the pharmaceutical industry. Materials & methods: The European Bioanalysis Forum liquid microsampling consortium member companies assessed the accuracy and precision of handheld pipettes and microcapillaries at volumes of less than 10 μl. The followin...

[This corrects the article DOI: 10.1038/s42003-018-0226-0.]. Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for a...

The whipworm Trichuris trichiura is a soil-transmitted helminth that dwells in the epithelium of the caecum and proximal colon of their hosts causing the human disease, trichuriasis. Trichuriasis is characterized by colitis attributed to the inflammatory response elicited by the parasite while tunnelling through intestinal epithelial cells (IECs)....

IL-22 and IL-28 signalling are dispensable in responses to high dose T. muris infections. Antibody (IgG1 and IgG2a/c) titres of T. muris-infected, six to ten-wk-old female WT and (A) Il22-/-, (B) Il22ra-/- and (C) Il28ra-/- mice after 32 days of high dose infection (400 eggs). No differences in worm expulsion were observed at this time point. Data...

IL-22 and IL-28 signalling are dispensable in responses to high dose T. muris infections. Antibody (IgG1 and IgG2a/c) titres of T. muris-infected, six to ten-wk-old female WT and (A) Il22-/-, (B) Il22ra-/- and (C) Il28ra-/- mice after 21 days of high dose infection (400 eggs). No differences in worm expulsion were observed at this time point. Data...

IL-22 and IL-28 signalling are dispensable in responses to low dose T. muris infections. Worm burden and antibody (IgG1 and IgG2a/c) titres of T. muris-infected, six to ten-wk-old female WT and (A) Il22-/-, (B) Il22ra-/- and (C) Il28ra-/- mice after 35 days of low dose infection (20–25 eggs). Data from two independent replicas. Median and interquar...

Caecal dysbiosis upon whipworm infection and defective IL-10Rα signalling is associated with expanded populations of pathobionts. Caecal microbial community structure at the operational taxonomic unit (OTU) level of co-housed uninfected and T. muris-infected (high dose, 400 eggs) six-wk-old female and male littermate WT and Il10ra-/- mice at day of...

IL-10Rβ signalling in haematopoietic cells is essential to control immunopathology leading to reduced survival during whipworm infections. Survival curves, worm burdens and representative H&E histological images of T. muris-infected (high dose, 400 eggs) ten-wk-old female and male irradiated (A, B) WT and (C, D) Il10rb-/- mice reconstituted with th...

Supplemental Experimental Procedures. Extended information on housing and husbandry of mice and microbiota analysis is provided in this file. (DOCX)

Isolation and identification by 16S rRNA gene sequencing of systemic bacterial isolates in T. muris-infected WT and Il10ra-/- mice. A-E indicate independent experiments with similar outcome. In each experiment, Il10ra-/- animals showing significant signs of morbidity were examined for bacterial breakthrough in the livers. Isolates from non-selectiv...

IL-10 family of cytokines and their receptors. Schematic illustration showing IL-10 family of cytokines that share the IL-10Rβ chain as a subunit of their receptors. Highlighted in bold are the molecules for which mutant mice were available and used for experiments. (TIF)

Inflammatory systemic responses upon T. muris infection of defective IL-10 signalling mice. IL-6 and TNF-α concentrations in plasma of T. muris-infected (high dose, 400 eggs), six-wk-old female and male littermate WT and (A) Il10-/- and (B) Il10rb-/- mice. (A) Data from two independent replicas. WT n = 7. Il10-/- n = 7. Median and interquartile ran...

Caecal dysbiosis upon whipworm infection and defective IL-10 signalling is associated with expanded populations of pathobionts. Caecal microbial community structure at the operational taxonomic unit (OTU) level of co-housed uninfected and T. muris-infected (high dose, 400 eggs) six-wk-old female and male littermate WT and Il10-/- mice at day of cul...

Caecal dysbiosis upon whipworm infection and defective IL-10Rβ signalling is associated with expanded populations of pathobionts. Caecal microbial community structure at the operational taxonomic unit (OTU) level of co-housed uninfected and T. muris-infected (high dose, 400 eggs) six-wk-old female and male littermate WT and Il10rb-/- mice at day of...

Extend of microbiota colonization by pathobionts correlates with reduced survival and liver disease of whipworm-infected IL-10 signalling-deficient mice. (A) The degree of colonization by Enterococcus and Enterobacteriaceae (percentage of abundance from total microbiota) among IL-10 signalling-deficient mice showing a severe or mild phenotype upon...

Integrated Data Analysis estimates of the effect of genotype (WT or Il10-/-) after accounting for infection on plasma chemistry parameters. The effect of genotype on plasma chemistry parameters for both infected and non-infected animals was explored using an Integrated Data Analysis. A complex regression model was fitted to account for various sour...

Integrated Data Analysis estimates of the effect of genotype (WT or Il10ra-/-) after accounting for infection on plasma chemistry parameters. The effect of genotype on plasma chemistry parameters for both infected and non-infected animals was explored using an Integrated Data Analysis. A complex regression model was fitted to account for various so...

Whipworm infection of IL-10 signalling-deficient mice results in loss of goblet cells in caecal epithelium. Representative images of PAS staining on caecum sections of T. muris-infected (high dose, 400 eggs) (A) WT, (B) Il10-/-, C) Il10ra-/- and (D) Il10rb-/- mice upon culling. Infected WT mice present goblet cell hyperplasia while infected IL-10 s...

3i consortium authors. List of The 3i consortium authors and their affiliations. (XLSX)

Integrated Data Analysis estimates of the effect of genotype (WT or Il10rb-/-) after accounting for infection on plasma chemistry parameters. The effect of genotype on plasma chemistry parameters for both infected and non-infected animals was explored using an Integrated Data Analysis. A complex regression model was fitted to account for various so...

Isolation and identification by 16S rRNA gene sequencing of systemic bacterial isolates in T. muris-infected WT and Il10rb-/- mice. A-E indicate independent experiments with similar outcome. In each experiment, Il10rb-/- animals showing significant signs of morbidity were examined for bacterial breakthrough in the livers. Isolates from non-selectiv...

Defective IL-10 signalling results in liver immunopathology characterised by foamy macrophages upon whipworm infection. Liver histopathology of uninfected and T. muris-infected (high dose, 400 eggs) (A) WT, (B) Il10-/-, (C) Il10ra-/- and (D) Il10rb-/- mice upon culling. Sections stained with H&E. Uninfected WT and mutant mice show no lesions. Upon...

Liver disease upon defects on IL-10 signalling during T. muris infection is reflected in plasma chemistry changes. Percentage change of plasma chemistry parameters upon culling of T. muris-infected (high dose, 400 eggs), six-wk-old female and male littermate WT and (A) Il10-/-, (B) Il10ra-/-, (C) Il10rb-/- mice. The infection status effect on each...

Lack of IL-10Ra on IECs does not impact worm expulsion and immune responses during T. muris infections. Antibody (IgG1, IgG2a/c and IgE) titers of T. muris-infected (high dose, 400 eggs) six-wk-old female and male littermates Il10ra+/+ Vilcre/+, Il10rafl/fl Vil+/+ and Il10rafl/fl Vilcre/+ mice after (A) 20 days (n = 16 mice for each group) and (B)...

Integrated Data Analysis estimates of the effect of genotype (WT or KO) as a function of infection on plasma chemistry parameters. The effect of genotype on plasma chemistry parameters for both infected and non-infected animals was explored using an Integrated Data Analysis. A complex regression model was fitted to account for various sources of va...

Isolation and identification by 16S rRNA gene sequencing of systemic bacterial isolates in T. muris-infected WT and Il10-/- mice. A-E indicate independent experiments with similar outcome. In each experiment, Il10-/- animals showing significant signs of morbidity were examined for bacterial breakthrough in the livers. Isolates from non-selective cu...

Despite advances in next generation sequencing technologies, determining the genetic basis of ocular disease remains a major challenge due to the limited access and prohibitive cost of human forward genetics. Thus, less than 4,000 genes currently have available phenotype information for any organ system. Here we report the ophthalmic findings from...

There has been a revolution within clinical trials to include females in the research pipeline. However, there has been limited change in the preclinical arena; yet the research here lays the ground work for the subsequent clinical trials. Sex bias has been highlighted as one of the contributing factors to the poor translation and replicability iss...

The high attrition rate of preclinical agents entering oncology clinical trials has been associated with poor understanding of the heterogeneous patient response arising from limitations in the pre-clinical pipeline with cancer models. PDX models have been shown to better recapitulate the patient drug response. However, the platform of evidence gen...

Although next-generation sequencing has revolutionized the ability to associate variants with human diseases, diagnostic rates and development of new therapies are still limited by a lack of knowledge of the functions and pathobiological mechanisms of most genes. To address this challenge, the International Mouse Phenotyping Consortium is creating...

The ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines are widely endorsed but compliance is limited. We sought to determine whether journal-requested completion of an ARRIVE checklist improves full compliance with the guidelines. In a randomised controlled trial, manuscripts reporting in vivo animal research submitted to PLOS ON...

The whipworm Trichuris trichiura is a soil-transmitted helminth that dwells in the epithelium of the caecum and proximal colon of their hosts causing the human disease, trichuriasis. Trichuriasis is characterized by colitis attributed to the inflammatory response elicited by the parasite while tunnelling through intestinal epithelial cells (IECs)....

In 2010, the NC3Rs published the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines to improve the reporting of animal research. Despite considerable levels of support from the scientific community, the impact on the quality of reporting in animal research publications has been limited. This position paper highlights the strategy...

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare, but devastating genetic disease characterized by segmental premature aging, with cardiovascular disease being the main cause of death. Cells from HGPS patients accumulate progerin, a permanently farnesylated, toxic form of Lamin A, disrupting the nuclear shape and chromatin organization, leadin...

Background: The ActualHCA™ system continuously monitors the activity, temperature and behaviour of group-housed rats without invasive surgery. The system was validated to detect the contrasting effects of sedative and stimulant test agents (chlorpromazine, clonidine and amphetamine), and compared with the modified Irwin test (mIT) with rectal temp...

Translational failures and replication issues of published research are undermining preclinical research and, if the outcomes are questionable, raise ethical implications over the continued use of animals. Standardization of procedures, environmental conditions, and genetic background has traditionally been proposed as the gold standard approach, a...

Hutchinson-Gilford Progeria Syndrome (HGPS) is a rare but devastating genetic disease characterized by segmental premature aging, with cardiovascular disease being the main cause of death. Cells from HGPS patients accumulate progerin, a permanently farnesylated, toxic form of Lamin A, disrupting nuclear shape and chromatin organization, leading to...

The scientific community is increasingly concerned with the proportion of published "discoveries" that are not replicated in subsequent studies. The field of rodent behavioral phenotyping was one of the first to raise this concern, and to relate it to other methodological issues: the complex interaction between genotype and environment; the definit...

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been id...

We describe a sensitive, robust, high-throughput method for quantifying the ability of metastatic tumor cells to colonize a secondary organ. Metastasis is the leading cause of death in cancer patients, and successful colonization of the secondary organ is the rate-limiting step in the metastatic process; thus, experimental methods that can be used...

Addressing the common problems that researchers encounter when designing and analysing animal experiments will improve the reliability of in vivo research. In this article, the Experimental Design Assistant (EDA) is introduced. The EDA is a web-based tool that guides the in vivo researcher through the experimental design and analysis process, provi...

Measuring the activity and temperature of rats is commonly required in biomedical research. Conventional approaches necessitate single housing, which affects their behavior and wellbeing. We have used a subcutaneous radiofrequency identification (RFID) transponder to measure ambulatory activity and temperature of individual rats when group-housed i...