Accelerating Biomedical Discoveries through Rigor and Transparency

Why are clinical trials of deep brain stimulation terminated? An analysis of clinicaltrials.gov

Background

Although deep brain stimulation (DBS) has established uses for patients with movement disorders and epilepsy, it is under consideration for a wide range of neurologic and neuropsychiatric conditions.

Objective

To review successful and unsuccessful DBS clinical trials and identify factors associated with early trial termination.

Methods

The ClinicalTrials.gov database was screened for all studies related to DBS. Information regarding condition of interest, study aim, trial design, trial success, and, if applicable, reason for failure was collected. Trials were compared and logistic regression was utilized to identify independent factors associated with trial termination.

Results

Of 325 identified trials, 79.7% were successful and 20.3% unsuccessful. Patient recruitment, sponsor decision, and device issues were the most cited reasons for termination. 242 trials (74.5%) were interventional with 78.1% successful. There was a statistically significant difference between successful and unsuccessful trials in number of funding sources (p = 0.0375). NIH funding was associated with successful trials while utilization of other funding sources (academic institutions and community organizations) was associated with unsuccessful trials. 83 trials (25.5%) were observational with 84.0% successful; there were no statistically significant differences between successful and unsuccessful observational trials.

Conclusion

One in five clinical trials for DBS were found to be unsuccessful, most commonly due to patient recruitment difficulties. The source of funding was the only factor associated with trial success. As DBS research continues to grow, understanding the current state of clinical trials will help design successful future studies, thereby minimizing futile expenditures of time, cost, and patient engagement.

Twelve years after the ARRIVE guidelines: Animal research has not yet arrived at high standards

The reproducibility crisis across animal studies jeopardizes the credibility of the main findings derived from animal research, even though these findings are critical for informing human studies. To clarify and improve transparency among animal studies, the ARRIVE reporting guidelines were first announced in 2010 and upgraded to version 2.0 in 2020. However, compliance with and awareness of those reporting guidelines has remained suboptimal. Journal editors should encourage the authors to adhere to those guidelines. Authors, editors, referees, and reviewers should be aware of the ARRIVE guideline 2.0 when assessing and evaluating the methodology and findings of animal studies. However, we should also question whether reporting guidelines alone can change a research culture and improve the reproducibility of animal investigations. Reported research may not reflect actual research. Large segments of animal research efforts are wasted because of poor design choices and because of non-publication rather than suboptimal reporting. Better training of the scientific workforce, interventions at improving animal research at the design stage, registration practices, and alignment of the reward system with the publication of rigorous animal research may achieve more than reporting guidelines alone.

Developmental Brain Injury and Social Determinants of Health: Opportunities to Combine Preclinical Models for Mechanistic Insights into Recovery

Epidemiological studies show that social determinants of health are among the strongest factors associated with developmental outcomes after prenatal and perinatal brain injuries, even when controlling for the severity of the initial injury. Elevated socioeconomic status and a higher level of parental education correlate with improved neurologic function after premature birth. Conversely, children experiencing early life adversity have worse outcomes after developmental brain injuries. Animal models have provided vital insight into mechanisms perturbed by developmental brain injuries, which have indicated directions for novel therapeutics or interventions. Animal models have also been used to learn how social environments affect brain maturation through enriched environments and early adverse conditions. We recognize animal models cannot fully recapitulate human social circumstances. However, we posit that mechanistic studies combining models of developmental brain injuries and early life social environments will provide insight into pathways important for recovery. Some studies combining enriched environments with neonatal hypoxic injury models have shown improvements in developmental outcomes, but further studies are needed to understand the mechanisms underlying these improvements. By contrast, there have been more limited studies of the effects of adverse conditions on developmental brain injury extent and recovery. Uncovering the biological underpinnings for early life social experiences has translational relevance, enabling the development of novel strategies to improve outcomes through lifelong treatment. With the emergence of new technologies to analyze subtle molecular and behavioral phenotypes, here we discuss the opportunities for combining animal models of developmental brain injury with social construct models to deconvolute the complex interactions between injury, recovery, and social inequity.

A decade of blood-brain barrier permeability assays: Revisiting old traumatic brain injury rat data for new insights and experimental design

Increased microvascular permeability at the level of the blood-brain barrier (BBB) often leads to vasogenic brain edema following traumatic brain injury (TBI). These pathologic conditions compromise the integrity of the neurovascular unit resulting in severe brain dysfunction. To quantify this permeability and assess ionic equillibrium, preclinical researchers have relied on the use of various molecular weight permeable dyes such as Evans Blue that normally cannot enter the brain parenchyma under homeostatic conditions. Evans Blue, the most cited of the molecular weight dyes, has reported reproducibility issues because of harsh extraction processes, suboptimal detection via absorbance, and wide excitation fluorescence spectra associated with the dye. Our laboratory group transitioned to Alexa Fluor 680, a far-red dye with improved sensitivity compared to Evans Blue and thus improved reproducibility to alleviate this issue. To evaluate our reproducibility and increase the rigor of our experimental design, we retrospectively analyzed our controlled cortical impact (CCI) experiments over the past 10 years to evaluate effect size with larger samples and potential sources of variability. All of our BBB permeability experiments were performed with Male, Sprague Dawley rats weighing between 225 and 300 g. Historically, Sprague Dawleys were randomly divided into treatment groups: SHAM, CCI, and a stem cell-based treatment from years 2007-2020. The assessment of microvascular hyperpermeability were evaluated by comparing the mean at minimum threshold, area at 1 k-2 k, and intensity density obtained from Alexa Fluor 680 permeability data. Studies utilizing Evans Blue were further compared by tip depth, diameter size, and the hemisphere of injury. Statistical evaluation utilizing the G Power software analysis did not yield a significant difference in sample size comparing experimental groups for Evans Blue and Alexa Fluor 680 analyzed brain tissue. Our analysis also demonstrated a trend in that recent studies (years 2018-2020) have yielded more compact sample sizes between experimental groups in Alexa Fluor 680 analyzed rats. This retrospective study further revealed that Alexa Fluor 680 image analysis provides greater sensitivity to BBB permeability following TBI in comparison to Evans Blue. Significant differences in sample size were not detected between Evans Blue and Alexa Fluor 680; there were significant differences found throughout year to year analysis at the lower range of thresholds. SUMMARY STATEMENT: This work provides a comparative analysis of BBB permeability assay techniques after CCI model of injury in rats.

Rigor, Reproducibility, and Transparency in Shared Research Resources: Follow-Up Survey and Recommendations for Improvements

Rigor, reproducibility, and transparency (RR&T) are essential components of all scientific pursuits. Shared research resources, also known as core facilities, are on the frontlines of ensuring robust RR&T practices. The Association of Biomolecular Resource Facilities Committee on Core Rigor and Reproducibility conducted a follow-up survey 4 years after the initial 2017 survey to determine if core facilities have seen a positive impact of new RR&T initiatives (including guidance from the National Institutes of Health, new scientific journal requirements on transparency and data provenance, and educational tools from professional organizations). While there were fewer participants in the most recent survey, the respondents' opinions on the role of core facilities and level of best practices adoption remained the same. Overall, the respondents agreed that procedures should be implemented by core facilities to ensure scientific RR&T. They also indicated that there is a strong correlation between institutions that emphasize RR&T and core customers using this expertise in grant applications and publications. The survey also assessed the impact of the COVID-19 pandemic on core operations and RR&T. The answers to these pandemic-related questions revealed that many of the strategies aimed at increasing efficiencies are also best practices related to RR&T, including the development of standard operating procedures, supply chain management, and cross training. Given the consistent and compelling awareness of the importance of RR&T expressed by core directors in 2017 and 2021 contrasted with the lack of apparent improvements over this time period, the authors recommend an adoption of RR&T statements by all core laboratories. Adhering to the RR&T guidelines will result in more efficient training, better compliance, and improved experimental approaches empowering cores to become "rigor champions."

Transcriptomic-Metabolomic Profiling in Mouse Lung Tissues Reveals Sex- and Strain-Based Differences

Omics analyses are commonly used for identifying pathways and genes responsible for physiologic and pathologic processes. Though sex is considered a biological variable in rigorous assessments of pulmonary responses to oxidant exposures, the contribution of the murine strain is largely ignored. This study utilized an unbiased integrated assessment of high-resolution metabolomic profiling and RNA-sequencing to explore sex- and strain-dependent pathways in adult mouse lungs. The results indicated that strain exhibited a greater influence than sex on pathways associated with inflammatory and oxidant/antioxidant responses and that interaction metabolites more closely resembled those identified as differentially expressed by strain. Metabolite analyses revealed that the components of the glutathione antioxidant pathway were different between strains, specifically in the formation of mixed disulfides. Additionally, selenium metabolites such as selenohomocystiene and selenocystathionine were similarly differentially expressed. Transcriptomic analysis revealed similar findings, as evidenced by differences in glutathione peroxidase, peroxiredoxin, and the inflammatory transcription factors RelA and Jun. In summary, an multi-omics integrated approach identified that murine strain disproportionately impacts baseline expression of antioxidant systems in lung tissues. We speculate that strain-dependent differences contribute to discrepant pulmonary responses in preclincal mouse models, with deleterious effects on clinical translation.

The Shared Core Resource as a Partner in Innovative Scientific Research: Illustration from an Academic Microscopy Imaging Center

Core facilities have a ubiquitous and increasingly valuable presence at research institutions. Although many shared cores were originally created to provide routine services and access to complex and expensive instrumentation for the research community, they are frequently called upon by investigators to design protocols and procedures to help answer complex research questions. For instance, shared microscopy resources are evolving from providing access to and training on complex imaging instruments to developing detailed innovative protocols and experimental strategies, including sample preparation techniques, staining, complex imaging parameters, and high-level image analyses. These approaches require close intellectual collaboration between core staff and research investigators to formulate and coordinate plans for protocol development suited to the research question. Herein, we provide an example of such coordinated collaboration between a shared microscopy facility and a team of scientists and clinician-investigators to approach a complex multiprobe immunostaining, imaging, and image analysis project investigating the tumor microenvironment from human breast cancer samples. Our hope is that this example may be used to convey to institute administrators the critical importance of the intellectual contributions of the scientific staff in core facilities to research endeavors.

Sex as a Biological Variable in Cardiovascular Diseases: JACC Focus Seminar 1/7

Sex and gender influence all aspects of cardiovascular health and disease-including epidemiology, pathophysiology, diagnosis, clinical manifestation, disease progression, and response to treatment-in complex and interrelated ways. Sex-based and gender-based differences have been identified in risk and presentation of cardiovascular diseases (CVDs); however, failure to address sex and gender as key variables in CVD research and reporting and limited understanding of differences have contributed to disparities in risk assessment, prevention, diagnosis, treatment, and outcomes. Improved consideration of both sex and gender in all phases of the biomedical research continuum, along with educational and training curricula focused on the role of sex and gender in CVD, are needed to provide targeted therapies and improve cardiovascular health outcomes for all.

Anesthesia and neurotoxicity study design, execution, and reporting in the nonhuman primate: A systematic review

BACKGROUND

Concern for a role of anesthesia in neurotoxicity in children originated from neonatal rodent and nonhuman primate (NHP) models, yet prospective clinical studies have largely not supported this concern. The goal of this study was to conduct an objective assessment of published NHP study rigor in design, execution, and reporting.

METHODS

A MEDLINE search from 2005 to December 2021 was performed. Inclusion criteria included full-length original studies published in English under peer-reviewed journals. We documented experimental parameters on anesthetic dosing, monitoring, vitals, and experimental outcomes.

RESULTS

Twenty-three manuscripts were included. Critical issues identified in study design included: lack of blinding in data acquisition (57%) and analysis (100%), supratherapeutic (4-12 fold) maintenance dosing in 22% of studies, lack of sample size justification (91%) resulting in a mean (SD) sample size of 6 (3) animals per group. Critical items identified in the conduct and reporting of studies included: documentation of anesthesia provider (0%), electrocardiogram monitoring (35%), arterial monitoring (4%), spontaneous ventilation employed (35%), failed intubations resulting in comingling ventilated and unventilated animals in data analysis, inaccurate reporting of failed intubation, and only 50% reporting on survival. Inconsistencies were noted in drug-related induction of neuroapoptosis and region of occurrence. Further, 67%-100% of behavior outcomes were not significantly different from controls.

CONCLUSIONS

Important deficits in study design, execution, and reporting were identified in neonatal NHP studies. These results raise concern for the validity and reliability of these studies and may explain in part the divergence from results obtained in human neonates.

Validity and reliability of a protocol to establish human critical environmental limits (PSU HEAT Project)

The PSU HEAT protocol has been used to determine critical environmental limits, i.e., those combinations of ambient temperature and humidity above which heat stress becomes uncompensable and core temperature rises continuously. However, no studies have rigorously investigated the reliability and validity of this experimental protocol. Here, we assessed the 1) between-visit reliability and 2) validity of the paradigm. Twelve subjects (5 M/7W; 25 ± 4 yr) completed a progressive heat stress protocol during which they walked on a treadmill (2.2 mph, 3% gradient) in a controllable environmental chamber. After an equilibration period, either dry-bulb temperature (T_db) was increased every 5 min while ambient water vapor pressure (P_a) was held constant (T_crit experiments) or P_a was increased every 5 min while T_db was held constant (P_crit experiments) until an upward inflection in gastrointestinal temperature (T_gi) was observed. For reliability experiments, 11 subjects repeated the same protocol on a different day. For validity experiments, 10 subjects performed a T_crit experiment at their previously determined P_crit or vice versa. The between-visit reliability (intraclass correlation coefficient, ICC) for critical environmental limits was 0.98. Similarly, there was excellent agreement between original and validity trials for T_crit (ICC = 0.95) and P_crit (ICC = 0.96). Furthermore, the wet-bulb temperature at the T_gi inflection point was not different during reliability (P = 0.78) or validity (P = 0.32) trials compared with original trials. These findings support the reliability and validity of this experimental paradigm for the determination of critical environmental limits for maintenance of human heat balance.NEW & NOTEWORTHY The PSU HEAT progressive heat stress protocol has been used to identify critical environmental limits for various populations, clothing ensembles, and metabolic intensities. However, no studies have rigorously investigated the reliability and validity of this experimental model. Here, we demonstrate excellent reliability and validity of the PSU HEAT protocol.

Streamlining statistical reproducibility: NHLBI ORCHID clinical trial results reproduction

Reproducibility in medical research has been a long-standing issue. More recently, the COVID-19 pandemic has publicly underlined this fact as the retraction of several studies reached out to general media audiences. A significant number of these retractions occurred after in-depth scrutiny of the methodology and results by the scientific community. Consequently, these retractions have undermined confidence in the peer-review process, which is not considered sufficiently reliable to generate trust in the published results. This partly stems from opacity in published results, the practical implementation of the statistical analysis often remaining undisclosed. We present a workflow that uses a combination of informatics tools to foster statistical reproducibility: an open-source programming language, Jupyter Notebook, cloud-based data repository, and an application programming interface can streamline an analysis and help to kick-start new analyses. We illustrate this principle by (1) reproducing the results of the ORCHID clinical trial, which evaluated the efficacy of hydroxychloroquine in COVID-19 patients, and (2) expanding on the analyses conducted in the original trial by investigating the association of premedication with biological laboratory results. Such workflows will be encouraged for future publications from National Heart, Lung, and Blood Institute-funded studies.

The COVID-19 pandemic has seen several articles published in high-profile journals being retracted. These retractions undermined even more confidence in the peer-review process, which is not considered sufficiently reliable to generate trust in the published results. A significant number of these retractions occurred after in-depth scrutiny of the methodology and results by the scientific community. This partly stems from opacity in published results, the practical implementation of the statistical analysis often remaining undisclosed. This article presents a simple workflow that leverages a combination of preexisting and newly developed biomedical informatics tools to promote transparent statistical analysis in biomedical research, which relies on the National Heart, Lung, and Blood Institute (NHLBI) BioData Catalyst platform. By streamlining access to data and analysis source code, it eases results reproduction and accelerates supplemental analyses. Such workflows will be encouraged for future publications from NHLBI-funded studies. We illustrate it by reproducing the results of the ORCHID clinical trial, which evaluated the efficacy of hydroxychloroquine in COVID-19 patients.

Preclinical Research Reporting in Shock: Room for Improvement

ABSTRACT

The ARRIVE (Animals in Research: Reporting In Vivo Experiments) guidelines were endorsed by the Shock Society in 2012, but to date there has been no systematic evaluation of research reporting quality for Shock. We systematically assessed 100 randomly selected animal-based research articles published between 2014 and 2018 for reporting quality and statistical practice, compared with 40 pre-ARRIVE studies. More than half of surveyed papers omitted verifiable ethical oversight information and basic animal descriptive information. Few papers reported best-practice methods, such as sample size justification (10%), randomization (43%), randomization method (7%), blinding (23%). Only one paper reported effect sizes to interpret study results. Most troubling was inadequate reporting of welfare-related information (anesthesia, analgesia, humane endpoints, euthanasia). Almost a decade after ARRIVE endorsement, our findings show that reporting deficiencies have persisted with little sign of correction. There is a clear need for investigators to increase transparency of research methods reporting, and drastically improve skills in experimental design. Improvement in standards and greater attention paid to reporting will lead to improvement in reproducibility, replicability, and research quality. It is incumbent upon the research community to improve reporting practices; accurate and transparent reporting is integral to producing rigorous and ethical science.

Auricular Vagus Neuromodulation-A Systematic Review on Quality of Evidence and Clinical Effects

Background: The auricular branch of the vagus nerve runs superficially, which makes it a favorable target for non-invasive stimulation techniques to modulate vagal activity. For this reason, there have been many early-stage clinical trials on a diverse range of conditions. These trials often report conflicting results for the same indication. Methods: Using the Cochrane Risk of Bias tool we conducted a systematic review of auricular vagus nerve stimulation (aVNS) randomized controlled trials (RCTs) to identify the factors that led to these conflicting results. The majority of aVNS studies were assessed as having "some" or "high" risk of bias, which makes it difficult to interpret their results in a broader context. Results: There is evidence of a modest decrease in heart rate during higher stimulation dosages, sometimes at above the level of sensory discomfort. Findings on heart rate variability conflict between studies and are hindered by trial design, including inappropriate washout periods, and multiple methods used to quantify heart rate variability. There is early-stage evidence to suggest aVNS may reduce circulating levels and endotoxin-induced levels of inflammatory markers. Studies on epilepsy reached primary endpoints similar to previous RCTs testing implantable vagus nerve stimulation therapy. Preliminary evidence shows that aVNS ameliorated pathological pain but not evoked pain. Discussion: Based on results of the Cochrane analysis we list common improvements for the reporting of results, which can be implemented immediately to improve the quality of evidence. In the long term, existing data from aVNS studies and salient lessons from drug development highlight the need for direct measures of local neural target engagement. Direct measures of neural activity around the electrode will provide data for the optimization of electrode design, placement, and stimulation waveform parameters to improve on-target engagement and minimize off-target activation. Furthermore, direct measures of target engagement, along with consistent evaluation of blinding success, must be used to improve the design of controls-a major source of concern identified in the Cochrane analysis. The need for direct measures of neural target engagement and consistent evaluation of blinding success is applicable to the development of other paresthesia-inducing neuromodulation therapies and their control designs.

Open Transparent Communication about Animals in Laboratories: Dialog for Multiple Voices and Multiple Audiences

In this article, I offer insights and proposals to the current movement for increased openness and transparency about animal use in laboratories. Increased transparency cannot be total transparency-as no story or picture can ever be complete. When research advocates share their stories, they must decide which words and pictures to edit out. I ask here: Who of the listening "public" gets a chance to revisit this editing, and find the information that is important to them? To the extent that (what I call) the "new openness" attempts to speak to a "lay public" and exclude animal activists, I suggest that refinement-focused animal protectionists deserve enhanced avenues of openness and inclusion-which some research advocates might fear giving to more extreme activists and which a less invested "lay public" may not want or need. I conclude with some specific examples and suggestions to not just invite inquiry from animal advocates, but to bring them in as witnesses and participants, to learn from and incorporate their concerns, priorities, expertise, and suggestions. This can bring a diversity of ideas and values that could improve the quality of science, the credibility of animal researchers, and the welfare of the animals in laboratories.

CORP: Standardizing methodology for assessing spontaneous baroreflex control of muscle sympathetic nerve activity in humans

The use of spontaneous bursts of muscle sympathetic nerve activity (MSNA) to assess arterial baroreflex control of sympathetic nerve activity has seen increased utility in studies of both health and disease. However, methods used for analyzing spontaneous MSNA baroreflex sensitivity are highly variable across published studies. Therefore, we sought to comprehensively examine methods of producing linear regression slopes to quantify spontaneous MSNA baroreflex sensitivity in a large cohort of subjects (n = 150) to support a standardized procedure for analysis that would allow for consistent and comparable results across laboratories. The primary results demonstrated that 1) consistency of linear regression slopes was considerably improved when the correlation coefficient was above -0.70, which is more stringent compared with commonly reported criterion of -0.50, 2) longer recording durations increased the percentage of linear regressions producing correlation coefficients above -0.70 (1 min = 15%, 2 min = 28%, 5 min = 53%, 10 min = 67%, P < 0.001) and reaching statistical significance (1 min = 40%, 2 min = 69%, 5 min = 78%, 10 min = 89%, P < 0.001), 3) correlation coefficients were improved with 3-mmHg versus 1-mmHg and 2-mmHg diastolic blood pressure (BP) bin size, and 4) linear regression slopes were reduced when the acquired BP signal was not properly aligned with the cardiac cycle triggering the burst of MSNA. In summary, these results support the use of baseline recording durations of 10 min, a correlation coefficient above -0.70 for reliable linear regressions, 3-mmHg bin size, and importance of properly time-aligning MSNA and diastolic BP. Together, these findings provide best practices for determining spontaneous MSNA baroreflex sensitivity under resting conditions for improved rigor and reproducibility of results.

Rethinking animal models of sepsis - working towards improved clinical translation whilst integrating the 3Rs

Sepsis is a major worldwide healthcare issue with unmet clinical need. Despite extensive animal research in this area, successful clinical translation has been largely unsuccessful.

We propose one reason for this is that, sometimes, the experimental question is misdirected or unrealistic expectations are being made of the animal model.

As sepsis models can lead to a rapid and substantial suffering – it is essential that we continually review experimental approaches and undertake a full harm:benefit impact assessment for each study. In some instances, this may require refinement of existing sepsis models. In other cases, it may be replacement to a different experimental system altogether, answering a mechanistic question whilst aligning with the principles of reduction, refinement and replacement (3Rs).

We discuss making better use of patient data to identify potentially useful therapeutic targets which can subsequently be validated in preclinical systems. This may be achieved through greater use of construct validity models, from which mechanistic conclusions are drawn. We argue that such models could provide equally useful scientific data as face validity models, but with an improved 3Rs impact. Indeed, construct validity models may not require sepsis to be modelled, per se. We propose that approaches that could support and refine clinical translation of research findings, whilst reducing the overall welfare burden on research animals.

Micro- and Macroenvironmental Conditions and Stability of Terrestrial Models

Environmental variables can have profound effects on the biological responses of research animals and the outcomes of experiments dependent on them. Some of these influences are both predictable and unpredictable in effect, many are challenging to standardize, and all are influenced by the planning and conduct of experiments and the design and operation of the vivarium. Others are not yet known. Within the immediate environment where the research animal resides, in the vivarium and in transit, the most notable of these factors are ambient temperature, relative humidity, gaseous pollutant by-products of animal metabolism and physiology, dust and particulates, barometric pressure, electromagnetic fields, and illumination. Ambient temperatures in the animal housing environment, in particular those experienced by rodents below the thermoneutral zone, may introduce degrees of stress and thermoregulatory compensative responses that may complicate or invalidate study measurements across a broad array of disciplines. Other factors may have more subtle and specific effects. It is incumbent on scientists designing and executing experiments and staff responsible for animal husbandry to be aware of, understand, measure, systematically record, control, and account for the impact of these factors on sensitive animal model systems to ensure the quality and reproducibility of scientific studies.

Facility-dependent metabolic phenotype and gut bacterial composition in CD-1 mice from a single vendor: A brief report

Utilization of murine models remains a valuable tool in biomedical research, yet, disease phenotype of mice across studies can vary considerably. With advances in next generation sequencing, it is increasingly recognized that inconsistencies in host phenotype can be attributed, at least in part, to differences in gut bacterial composition. Research with inbred murine strains demonstrates that housing conditions play a significant role in variations of gut bacterial composition, however, few studies have assessed whether observed variation influences host phenotype in response to an intervention. Our study initially sought to examine the effects of a long-term (9-months) dietary intervention (i.e., diets with distinct fatty acid compositions) on the metabolic health, in particular glucose homeostasis, of genetically-outbred male and female CD-1 mice. Yet, mice were shipped from two different husbandry facilities of the same commercial vendor (Cohort A and B, respectively), and we observed throughout the study that diet, sex, and aging differentially influenced the metabolic phenotype of mice depending on their husbandry facility of origin. Examination of the colonic bacteria of mice revealed distinct bacterial compositions, including 23 differentially abundant genera and an enhanced alpha diversity in mice of Cohort B compared to Cohort A. We also observed that a distinct metabolic phenotype was linked with these differentially abundant bacteria and indices of alpha diversity. Our findings support that metabolic phenotypic variation of mice of the same strain but shipped from different husbandry facilities may be influenced by their colonic bacterial community structure. Our work is an important precautionary note for future research of metabolic diseases via mouse models, particularly those that seek to examine factors such diet, sex, and aging.

Reproducibility of the neurocardiovascular responses to common laboratory-based sympathoexcitatory stimuli in young adults

The magnitude of blood pressure (BP) and muscle sympathetic nerve activity (MSNA) responses to laboratory stressors is commonly used to compare neurocardiovascular responsiveness between groups and conditions. However, no studies have rigorously examined the reproducibility of BP and MSNA responsiveness. Here, we assess the within-visit reproducibility of BP (finger photoplethysmography) and MSNA (microneurography) responses to isometric handgrip (HG) and postexercise ischemia (PEI) in young healthy adults (n = 30). In a subset (n = 21), we also examined the between-visit reproducibility of responsiveness to HG, PEI, and the cold pressor test (CPT). Intraclass correlation coefficients (ICCs) were used as a primary reproducibility measure (e.g., ICC >0.75 is considered very good). Within a visit, the increase in mean arterial pressure during HG [ICC = 0.85 (0.69-0.93); P < 0.001] and PEI [ICC = 0.85 (0.69-0.93); P < 0.001] demonstrated very good reproducibility. Furthermore, the between-visit reproducibility of the pressor response to HG [ICC = 0.85 (0.62-0.94); P < 0.001], PEI [ICC = 0.84 (CI = 0.58-0.94); P < 0.001], and the CPT [ICC = 0.89 (0.72-0.95) P < 0.001]) were also very good. However, there was greater variability in both the within- [HG: ICC = 0.58 (-0.22-0.85), P = 0.001; PEI: ICC = 0.33 (-0.24-0.69), P = 0.042] and between-visit reproducibility of MSNA responsiveness [HG: ICC = 0.87 (0.53-0.96), P = 0.001; PEI: ICC = 0.24 (-0.62-0.78), P = 0.27; CPT: ICC = 0.77 (0.29-0.93), P = 0.007]. The magnitude of the BP response to several standard laboratory stimuli was very good, whereas the variability of the MSNA response to these perturbations was generally less consistent, particularly during PEI. These data provide novel insight for both study design and data interpretation when comparing neurocardiovascular responsiveness between different conditions, groups, or studies, as well as before and after interventions/treatments.NEW & NOTEWORTHY The magnitude of the increases in blood pressure and muscle sympathetic nerve activity in response to sympathoexcitatory stimuli such as static handgrip, postexercise ischemia, and the cold pressor test are commonly used to assess neurocardiovascular responsiveness. However, limited studies have comprehensively examined the reproducibility of these responses. We demonstrate that the reproducibility of the pressor response to these perturbations was very good within an individual, whereas the reproducibility of the MSNA response was less consistent.

Virtue Ethics and Laboratory Animal Research

This article appeals to virtue ethics to help guide laboratory animal research by considering the role of character and flourishing in these practices. Philosophical approaches to animal research ethics have typically focused on animal rights or on the promotion of welfare for all affected, while animal research itself has been guided in its practice by the 3Rs (reduction, refinement, replacement). These different approaches have sometimes led to an impasse in debates over animal research where the philosophical approaches are focused on whether or when animal studies are justifiable, while the 3Rs assume a general justification for animal work but aim to reduce harm to sentient animals and increase their welfare in laboratory spaces. Missing in this exchange is a moral framework that neither assumes nor rejects the justifiability of animal research and focuses instead on the habits and structures of that work. I shall propose a place for virtue ethics in laboratory animal research by considering examples of relevant character traits, the moral significance of human-animal bonds, mentorship in the laboratory, and the importance of animals flourishing beyond mere welfare.

Neuroethics: Fostering Collaborations to Enable Neuroscientific Discovery

The NIH-funded Brain Research through Advancing Innovative Neurotechnologies^® (BRAIN) Initiative has led to significant advances in what we know about the functions and capacities of the brain. This multifaceted and expansive effort supports a range of experimentation from cells to circuits, and its outputs promise to ease suffering from various neurological injuries, diseases, and neuropsychiatric conditions. At the midway point of the 10-year BRAIN Initiative, we pause to consider how these studies, and neuroscience research more broadly, may bear on human characteristics and moral concepts such as identity, agency, and others. This midway point also offers us an opportunity to evaluate the sociology and impacts of BRAIN Initiative-funded investigations to ensure that ethical standards of fairness and justice pervade the scientific process itself. Neuroethics inquiry provides a mechanism to invite relevant, novel expertise from the wide array of disciplines that intersect with biomedicine in neuroscience research. As the BRAIN Initiative and the broader field of neuroscience proceed, neuroethics serves as a central component of neuroscience inquiry to i) foster necessary and beneficial collaborations for responsible discovery; ii) ensure a rigorous, reproducible, and representative neuroscience research process; and iii) explore the unique nature of study of the human brain through accurate and representative models of its function and dysfunction.

Reporting animal research: Explanation and elaboration for the ARRIVE guidelines 2.0

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 help authors and journals identify the minimum information necessary to report in publications describing in vivo experiments. Despite widespread endorsement by the scientific community, the impact of ARRIVE on the transparency of reporting in animal research publications has been limited. We have revised the ARRIVE guidelines to update them and facilitate their use in practice. The revised guidelines are published alongside this paper. This explanation and elaboration document was developed as part of the revision. It provides further information about each of the 21 items in ARRIVE 2.0, including the rationale and supporting evidence for their inclusion in the guidelines, elaboration of details to report, and examples of good reporting from the published literature. This document also covers advice and best practice in the design and conduct of animal studies to support researchers in improving standards from the start of the experimental design process through to publication.

Standard Proteoforms and Their Complexes for Native Mass Spectrometry

Native mass spectrometry (nMS) is a technique growing at the interface of analytical chemistry, structural biology, and proteomics that enables the detection and partial characterization of non-covalent protein assemblies. Currently, the standardization and dissemination of nMS is hampered by technical challenges associated with instrument operation, benchmarking, and optimization over time. Here, we provide a standard operating procedure for acquiring high-quality native mass spectra of 30-300 kDa proteins using an Orbitrap mass spectrometer. By describing reproducible sample preparation, loading, ionization, and nMS analysis, we forward two proteoforms and three complexes as possible standards to advance training and longitudinal assessment of instrument performance. Spectral data for five standards can guide assessment of instrument parameters, data production, and data analysis. By introducing this set of standards and protocols, we aim to help normalize native mass spectrometry practices across labs and provide benchmarks for reproducibility and high-quality data production in the years ahead. Graphical abstract.

Rat Strain and Housing Conditions Alter Oxidative Stress and Hormone Responses to Chronic Intermittent Hypoxia

Sleep apnea has been associated with elevated risk for metabolic, cognitive, and cardiovascular disorders. Further, the role of hypothalamic–pituitary–adrenal (HPA) activation in sleep apnea has been controversial in human studies. Chronic intermittent hypoxia (CIH) is a rodent model, which mimics the hypoxemia experienced by patients with sleep apnea. Most studies of CIH in rats have been conducted in the Sprague Dawley rat strain. Previously published literature suggests different strains of rats exhibit various responses to disease models, and these effects can be further modulated by the housing conditions experienced by each strain. This variability in response is similar to what has been observed in clinical populations, especially with respect to the HPA system. To investigate if strain or housing (individual or pair-housed) can affect the results of CIH (AHI 8 or 10) treatment, we exposed individual and pair-housed Sprague Dawley and Long-Evans male rats to 7 days of CIH treatment. This was followed by biochemical analysis of circulating hormones, oxidative stress, and neurodegenerative markers. Both strain and housing conditions altered oxidative stress generation, hyperphosphorylated tau protein (tau tangles), circulating corticosterone and adrenocorticotropic hormone (ACTH), and weight metrics. Specifically, pair-housed Long-Evans rats were the most sensitive to CIH, which showed a significant association between oxidative stress generation and HPA activation under conditions of AHI of 8. These results suggest both strain and housing conditions can affect the outcomes of CIH.

Translation of combination nanodrugs into nanomedicines: lessons learned and future outlook

The concept of nanomedicine is not new. For instance, some nanocrystals and colloidal drug molecules are marketed that improve pharmacokinetic characteristics of single-agent therapeutics. For the past two decades, the number of research publications on single-agent nanoformulations has grown exponentially. However, formulations advancing to pre-clinical and clinical evaluations that lead to therapeutic products has been limited. Chronic diseases such as cancer and HIV/AIDS require drug combinations, not single agents, for durable therapeutic responses. Therefore, development and clinical translation of drug combination nanoformulations could play a significant role in improving human health. Successful translation of promising concepts into pre-clinical and clinical studies requires early considerations of the physical compatibility, pharmacological synergy, as well as pharmaceutical characteristics (e.g. stability, scalability and pharmacokinetics). With this approach and robust manufacturing processes in place, some drug-combination nanoparticles have progressed to non-human primate and human studies. In this article, we discuss the rationale and role of drug-combination nanoparticles, the pre-clinical and clinical research progress made to date and the key challenges for successful clinical translation. Finally, we offer insight to accelerate clinical translation through leveraging robust nanoplatform technologies to enable implementation of personalised and precision medicine.

Bridging the Gap between Reproducibility and Translation: Data Resources and Approaches

Animal research has constituted a fundamental means to achieve groundbreaking therapies for human disease. However, for complex diseases, promising preclinical results have failed to translate to the clinic. Reasons for this disparity are multifactorial. These include the challenges inherent in modeling complex disease in animals, as well issues of study design, reproducibility and operational norms within the biomedical research enterprise. In this issue, we explore the range of information resources available for the comparative study of disease, as well as challenges to the ultimate translation of preclinical findings. Genomics resources in support of translational research are described for zebrafish, mice, rats and non-human primates. The utility of transcriptomics to explore the temporal basis of lesion development in toxicologic pathology is reviewed. Integration of the ever-increasing volume of text-based and bioinformatics data is a significant challenge, and in this issue, informatics resources and general text mining methodologies to explore and aggregate text data are described. Finally, factors contributing to both reproducibility and translatability are examined. Guidelines designed to address reproducibility are essential to improving individual studies. To this end, a viewpoint from the National Institutes of Health on measures needed to enhance rigor and reproducibility is given, as well as an overview of the role of the Institutional Animal Care and Use Committee in this regard. The challenge of improving generalizability of animal experiments so that their findings can be more frequently extended to the intended human population remains. Reasons why models that replicate key aspects of human disease fail to be predictive in humans are explored in two fields in which translation has been a challenge: sepsis and neurodegeneration.

Nonhuman Primates and Translational Research: Progress, Opportunities, and Challenges

Nonhuman primates (NHPs) are the closest animal models to humans regarding genetics, physiology and behavior. Therefore, NHPs are usually a critical component in translational research projects aimed at developing therapeutics, vaccines, devices or other interventions aimed at preventing, curing or ameliorating human disease. NHPs are often used in conjunction with other animal models, such as rodents, and results obtained using NHPs must often be used as the final criterion for establishing the potential efficacy of a pharmaceutical or vaccine before transition to human clinical trails. In some cases, NHPs may be the only relevant animal models for a particlular translational study. This issue of the ILAR journal brings together, in one place, articles that discuss the use of NHP models for studying human diseases that are highly prevalent and that cause extraordinary human suffering and financial and social burdens. Topics covered in detail include: tuberculosis; viral hepatitis; HIV/AIDS; neurodegenerative disorders; Substance abuse disorders; vision and prevention of blindness; disorder associated with psychosocial processes, such as anxiety, depression and loneliness; cardiovascular disease; metabolic disease, such as obesity and metabolic syndrome; respiratory disease; and female reproduction, prenatal development and women's health. Proper husbandry of NHPs that reduces stress and maintains animal health is critical for the development of NHP models. This issue of the journal includes a review of procedures for environmental enrichment, which helps assure animal health and wellbeing. Taken together, these articles provide detailed reviews of the use of NHP models for translational investigations and discuss successes, limitations, challenges and opportunities associated with this research.