The EQIPD quality system - Assessment and certification procedures.

The EQIPD Quality System was designed with the ultimate mission to provide a framework to ensure the quality and integrity of non-regulated preclinical biomedical research. For research quality to be sustained over time, it is crucial to have continuous improvement mechanisms that routinely monitor the research-related processes and enable solutions for identified issues. The present article is focused on these monitoring and assessment procedures that make the EQIPD Quality System a fully functional 'system' (as opposed to a mere collection of guidelines, work instructions and policies). In this context, a critical instrument are the internal and external assessments of the EQIPD Quality System performance described in detail. The assessment procedures emphasize the unique nature of the EQIPD Quality System being user-friendly, flexible and fit-for-purpose. By undergoing the (voluntary) external EQIPD assessment (leading to the EQIPD certification after all EQIPD core requirements have been implemented), a research unit: (i) secures confidence in the quality of data generated, (ii) ensures continuous improvement of research processes, and (iii) obtains an independent seal of quality communicating commitment to best research practices to the research community.

Eleven strategies for making reproducible research and open science training the norm at research institutions.

Reproducible research and open science practices have the potential to accelerate scientific progress by allowing others to reuse research outputs, and by promoting rigorous research that is more likely to yield trustworthy results. However, these practices are uncommon in many fields, so there is a clear need for training that helps and encourages researchers to integrate reproducible research and open science practices into their daily work. Here, we outline eleven strategies for making training in these practices the norm at research institutions. The strategies, which emerged from a virtual brainstorming event organized in collaboration with the German Reproducibility Network, are concentrated in three areas: (i) adapting research assessment criteria and program requirements; (ii) training; (iii) building communities. We provide a brief overview of each strategy, offer tips for implementation, and provide links to resources. We also highlight the importance of allocating resources and monitoring impact. Our goal is to encourage researchers - in their roles as scientists, supervisors, mentors, instructors, and members of curriculum, hiring or evaluation committees - to think creatively about the many ways they can promote reproducible research and open science practices in their institutions.

As Verified with the Aid of Biotinylated Spermine, the Brain Cannot Take up Polyamines from the Bloodstream Leaving It Solely Dependent on Local Biosynthesis.

The importance of polyamines (PAs) for the central nervous system (CNS) is well known. Less clear, however, is where PAs in the brain are derived from. Principally, there are three possibilities: (i) intake by nutrition, release into the bloodstream, and subsequent uptake from CNS capillaries, (ii) production by parenchymatous organs, such as the liver, and again uptake from CNS capillaries, and (iii) uptake of precursors, such as arginine, from the blood and subsequent local biosynthesis of PAs within the CNS. The present investigation aimed to unequivocally answer the question of whether PAs, especially the higher ones like spermidine (SPD) and spermine (SPM), can or cannot be taken up into the brain from the bloodstream. For this purpose, a biotin-labelled analogue of spermine (B-X-SPM) was synthesized, characterized, and used to visualize its uptake into brain cells following application to acute brain slices, to the intraventricular space, or to the bloodstream. In acute brain slices there is strong uptake of B-X-SPM into protoplasmic and none in fibrous-type astrocytes. It is also taken up by neurons but to a lesser degree. Under in vivo conditions, astrocyte uptake of B-X-SPM from the brain interstitial fluid is also intense after intraventricular application. In contrast, following intracardial injection, there is no uptake from the bloodstream, indicating that the brain is completely dependent on the local synthesis of polyamines.

Is the future of peer review automated?

The rising rate of preprints and publications, combined with persistent inadequate reporting practices and problems with study design and execution, have strained the traditional peer review system. Automated screening tools could potentially enhance peer review by helping authors, journal editors, and reviewers to identify beneficial practices and common problems in preprints or submitted manuscripts. Tools can screen many papers quickly, and may be particularly helpful in assessing compliance with journal policies and with straightforward items in reporting guidelines. However, existing tools cannot understand or interpret the paper in the context of the scientific literature. Tools cannot yet determine whether the methods used are suitable to answer the research question, or whether the data support the authors' conclusions. Editors and peer reviewers are essential for assessing journal fit and the overall quality of a paper, including the experimental design, the soundness of the study's conclusions, potential impact and innovation. Automated screening tools cannot replace peer review, but may aid authors, reviewers, and editors in improving scientific papers. Strategies for responsible use of automated tools in peer review may include setting performance criteria for tools, transparently reporting tool performance and use, and training users to interpret reports.

Introduction to the EQIPD quality system.

While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers, and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e. performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use.

Improving quality of preclinical academic research through auditing: A feasibility study.

How much can we rely on whether what was reported in a study was actually done? Systematic and independent examination of records, documents and processes through audits are a central element of quality management systems. In the context of current concerns about the robustness and reproducibility of experimental biomedical research audits have been suggested as a remedy a number of times. However, audits are resource intense and time consuming, and due to their very nature may be perceived as inquisition. Consequently, there is very little experience or literature on auditing and assessments in the complex preclinical biomedical research environment. To gain some insight into which audit approaches might best suit biomedical research in academia, in this study we have applied a number of them in a typical academic neuroscience environment consisting of twelve research groups with about 100 researchers, students and technicians, utilizing the full gamut of state-of-the-art methodology. Several types of assessments and internal as well as external audits (including the novel format of a peer audit) were systematically explored by a team of quality management specialists. An experimental design template was developed (and is provided here) that takes into account and mitigates difficulties, risks and systematic errors that may occur during the course of a study. All audits were performed according to a pre-defined workflow developed by us. Outcomes were assessed qualitatively. We asked for feedback from participating employees in every final discussion of an audit and documented this in the audit reports. Based on these reports follow-up audits were improved. We conclude that several realistic options for auditing exist which have the potential to improve preclinical biomedical research in academia, and have listed specific recommendations regarding their benefits and provided practical resources for their implementation (e.g. study design and audit templates, audit workflow).

fiddle: a tool to combat publication bias by getting research out of the file drawer and into the scientific community.

Statistically significant findings are more likely to be published than non-significant or null findings, leaving scientists and healthcare personnel to make decisions based on distorted scientific evidence. Continuously expanding ´file drawers' of unpublished data from well-designed experiments waste resources creates problems for researchers, the scientific community and the public. There is limited awareness of the negative impact that publication bias and selective reporting have on the scientific literature. Alternative publication formats have recently been introduced that make it easier to publish research that is difficult to publish in traditional peer reviewed journals. These include micropublications, data repositories, data journals, preprints, publishing platforms, and journals focusing on null or neutral results. While these alternative formats have the potential to reduce publication bias, many scientists are unaware that these formats exist and don't know how to use them. Our open source file drawer data liberation effort (fiddle) tool (RRID:SCR_017327 available at: http://s-quest.bihealth.org/fiddle/) is a match-making Shiny app designed to help biomedical researchers to identify the most appropriate publication format for their data. Users can search for a publication format that meets their needs, compare and contrast different publication formats, and find links to publishing platforms. This tool will assist scientists in getting otherwise inaccessible, hidden data out of the file drawer into the scientific community and literature. We briefly highlight essential details that should be included to ensure reporting quality, which will allow others to use and benefit from research published in these new formats.

Quality in Non-GxP Research Environment.

There has been increasing evidence in recent years that research in life sciences is lacking in reproducibility and data quality. This raises the need for effective systems to improve data integrity in the evolving non-GxP research environment. This chapter describes the critical elements that need to be considered to ensure a successful implementation of research quality standards in both industry and academia. The quality standard proposed is founded on data integrity principles and good research practices and contains basic quality system elements, which are common to most laboratories. Here, we propose a pragmatic and risk-based quality system and associated assessment process to ensure reproducibility and data quality of experimental results while making best use of the resources.

Atlas registration for edema-corrected MRI lesion volume in mouse stroke models.

Lesion volume measurements with magnetic resonance imaging are widely used to assess outcome in rodent models of stroke. In this study, we improved a mathematical framework to correct lesion size for edema which is based on manual delineation of the lesion and hemispheres. Furthermore, a novel MATLAB toolbox to register mouse brain MR images to the Allen brain atlas is presented. Its capability to calculate edema-corrected lesion size was compared to the manual approach. Automated image registration performed equally well in in a mouse middle cerebral artery occlusion model (Pearson r = 0.976, p = 2.265e-11). Information encapsulated in the registration was used to generate maps of edema induced tissue volume changes. These showed discrepancies to simplified tissue models underlying the manual approach. The presented techniques provide biologically more meaningful, voxel-wise biomarkers of vasogenic edema after stroke.

Agmatine modulates spontaneous activity in neurons of the rat medial habenular complex-a relevant mechanism in the pathophysiology and treatment of depression?

The dorsal diencephalic conduction system connects limbic forebrain structures to monaminergic mesencephalic nuclei via a distinct relay station, the habenular complexes. Both habenular nuclei, the lateral as well as the medial nucleus, are considered to play a prominent role in mental disorders like major depression. Herein, we investigate the effect of the polyamine agmatine on the electrical activity of neurons within the medial habenula in rat. We present evidence that agmatine strongly decreases spontaneous action potential firing of medial habenular neurons by activating I1-type imidazoline receptors. Additionally, we compare the expression patterns of agmatinase, an enzyme capable of inactivating agmatine, in rat and human habenula. In the medial habenula of both species, agmatinase is similarly distributed and observed in neurons and, in particular, in distinct neuropil areas. The putative relevance of these findings in the context of depression is discussed. It is concluded that increased activity of the agmatinergic system in the medial habenula may strengthen midbrain dopaminergic activity. Consequently, the habenular-interpeduncular axis may be dysregulated in patients with major depression.

Anterior and posterior parts of the rat ventral tegmental area and the rostromedial tegmental nucleus receive topographically distinct afferents from the lateral habenular complex.

That activation of the reward system involves increased activity of dopaminergic (DA) neurons in the ventral tegmental area (VTA) is widely accepted. In contrast, the lateral habenular complex (LHb), which is known as the center of the anti-reward system, directly and indirectly inhibits DA neurons in the VTA. The VTA, however, is not a homogenous entity. Instead, it displays major functional differences between its anterior (aVTA) and posterior (pVTA) regions. It is not precisely known, whether habenular input to the aVTA, pVTA, and the newly recognized rostromedial tegmental nucleus (RMTg) are similarly or differently organized. Consequently, the present investigation addressed the connections between LHb and aVTA, pVTA, and RMTg using retrograde and anterograde tracing techniques in the rat. Our experiments disclosed strictly reciprocal and conspicuously focal interconnections between LHbM (LHbMPc/LHbMC) and PN, as well as between RLi and LHbLO. In addition, we found that LHb inputs to the aVTA are dorsoventrally ordered. Dorsal parts of the aVTA receive afferents from LHbL and LHbM, whereas ventral parts of the aVTA are preferentially targeted by the LHbM. LHb afferents to the pVTA are distinct from those to the RMTg, given that the RMTg is primarily innervated from the LHbL, whereas pVTA receives afferents from LHbM and LHbL. These data indicate the existence of two separate pathways from the LHb to the VTA, a direct and an indirect one, which may subserve distinct biological functions.

Interaction of ARC and Daxx: A Novel Endogenous Target to Preserve Motor Function and Cell Loss after Focal Brain Ischemia in Mice.

UNLABELLED: The aim of this study was to explore the signaling and neuroprotective effect of transactivator of transcription (TAT) protein transduction of the apoptosis repressor with CARD (ARC) in in vitro and in vivo models of cerebral ischemia in mice. In mice, transient focal cerebral ischemia reduced endogenous ARC protein in neurons in the ischemic striatum at early reperfusion time points, and in primary neuronal cultures, RNA interference resulted in greater neuronal susceptibility to oxygen glucose deprivation (OGD). TAT.ARC protein delivery led to a dose-dependent better survival after OGD. Infarct sizes 72 h after 60 min middle cerebral artery occlusion (MCAo) were on average 30 ± 8% (mean ± SD; p = 0.005; T2-weighted MRI) smaller in TAT.ARC-treated mice (1 µg intraventricularly during MCAo) compared with controls. TAT.ARC-treated mice showed better performance in the pole test compared with TAT.ß-Gal-treated controls. Importantly, post-stroke treatment (3 h after MCAo) was still effective in affording reduced lesion volume by 20 ± 7% (mean ± SD; p < 0.05) and better functional outcome compared with controls. Delayed treatment in mice subjected to 30 min MCAo led to sustained neuroprotection and functional behavior benefits for at least 28 d. Functionally, TAT.ARC treatment inhibited DAXX-ASK1-JNK signaling in the ischemic brain. ARC interacts with DAXX in a CARD-dependent manner to block DAXX trafficking and ASK1-JNK activation. Our work identifies for the first time ARC-DAXX binding to block ASK1-JNK activation as an ARC-specific endogenous mechanism that interferes with neuronal cell death and ischemic brain injury. Delayed delivery of TAT.ARC may present a promising target for stroke therapy. SIGNIFICANCE STATEMENT: Up to now, the only successful pharmacological target of human ischemic stroke is thrombolysis. Neuroprotective pharmacological strategies are needed to accompany therapies aiming to achieve reperfusion. We describe that apoptosis repressor with CARD (ARC) interacts and inhibits DAXX and proximal signals of cell death. In a murine stroke model mimicking human malignant infarction in the territory of the middle cerebral artery, TAT.ARC salvages brain tissue when given during occlusion or 3 h delayed with sustained functional benefits (28 d). This is a promising novel therapeutic approach because it appears to be effective in a model producing severe injury by interfering with an array of proximal signals and effectors of the ischemic cascade, upstream of JNK, caspases, and BIM and BAX activation.

Microarray analysis of transcripts with elevated expressions in the rat medial or lateral habenula suggest fast GABAergic excitation in the medial habenula and habenular involvement in the regulation of feeding and energy balance.

In vertebrates the "anti-reward-system" mainly is represented by the habenula and its medial (MHb) and especially lateral (LHb) complexes. Considerable knowledge has accumulated concerning subnuclear structures and connectivities of MHb and LHb subnuclei. The present investigation aimed to obtain novel information, whether MHb or LHb or their subnuclei display field-characteristic gene products, which may shed light on biological functions of these areas. Unfortunately this was not the case. Microarray analysis of mRNAs in microdissected habenular and thalamic control areas yielded expression values of 17,745 RNAs representing protein-coding genes, to which annotated gene names could be assigned. High relative values of genes with known expression in MHb, LHb or thalamus in the corresponding areas indicated a high precision of the microdissection procedure. Note that the present report emphasizes differences between and not absolute expression values in the selected regions. The present investigation disclosed that the LHb genetically is much closer related to the thalamus as compared to the MHb. The results presented here focuse on gene transcripts related to major transmitter systems, catecholamines and neuropeptides. Quite surprisingly, our data indicate potentially inhibitory effects of acetylcholine and glutamate in the habenula. In addition, the absence of the K-Cl co-transporter 2 supports a largely excitatory role of GABAergic transmission especially in the MHb. Furthermore, several G-protein related receptors (Gpr83, Gpr139, Gpr149, Gpr151, Gpr158) and many neuropeptides related to feeding are differentially expressed in the habenular region, indicating that its involvement in the regulation of food consumption and energy expenditure may have been underestimated so far.

Hypothalamic, thalamic and hippocampal lesions in the mouse MCAO model: Potential involvement of deep cerebral arteries?

Intraluminal monofilament occlusion of the middle cerebral artery (MCAO) in mice is the most used rodent model to study the pathophysiology of stroke. However, this model often shows brain damage in regions not supplied by the MCA such as the hypothalamus, hippocampus and thalamus. Several studies have suggested some explanations on these localized infarcts. We aim to provide an alternative explanation which could allow each experimenter to better grasp the MCAO model. We propose that the MCA occlusion by the monofilament also occludes deep and small cerebral arteries arising directly from the internal carotid artery, proximally to the origin of MCA. Then, drawbacks and pitfalls of the MCAO model must be appreciated and the almost systematic risk of inducing lesions in some unwanted territories for neuroanatomical reasons, i.e. vascular connections between deep arteries and hypothalamic, thalamic and hippocampal areas in rodents has to be integrated.

A glutamatergic projection from the lateral hypothalamus targets VTA-projecting neurons in the lateral habenula of the rat.

Homeostasis describes the fundamental biological ability of individuals to maintain stable internal conditions in a changing environment. Homeostatic reactions include internal adjustments as well as behavioral responses. In vertebrates, behavioral responses are induced by the reward system. This system originates in the ventral tegmental area (VTA) and leads to increased dopamine levels in the forebrain whenever activated. A major inhibitor of VTA activity is the lateral habenula (LHb). This epithalamic structure is able to almost completely suppress dopamine release, either directly or via the rostromedial tegmental nucleus (RMTg), when rewarding expectations are not met. A major input to the LHb arises from the lateral hypothalamic area (LHA), an important regulator of the homeostatic system. Currently, little is known about the effects of the strong hypothalamic projection on the activity of LHb neurons. In the present study, we analyze neurotransmitters and cellular targets of the LHA-LHb projection in the rat. Therefore, anterograde tracing from the LHA was combined with the visualization of neurotransmitters in the LHb. These experiments revealed a mainly glutamatergic projection, probably exerting excitatory effects on the targeted LHb cells. These cellular targets were analyzed in a second step. Anterograde tracing from the LHA in combination with retrograde tracing from the VTA/RMTg region revealed that LHb neurons projecting to the VTA/RMTg region are densely targeted by the LHA projection. Visualization of synaptophysin at these contact sites indicates that the contact sites indeed are synapses. Taken together, the present study describes a strong mainly glutamatergic projection from the LHA that targets VTA/RMTg-projecting neurons in the LHb. These findings emphasize the potential role of the LHb as direct link between homeostatic areas and reward circuitries, which may be important for the control of homeostatic behaviors.

Evidence for transcriptional factor dysregulation in the dorsal raphe nucleus of patients with major depressive disorder.

Extensive evidence implicates dysfunction in serotonin (5-HT) signaling in the etiology of major depressive disorder (MDD). Dorsal raphe nucleus (DR) is a major source of serotonin in the brain, and previous studies have reported within it alterations in 5-HT-related gene expression, protein levels, receptor binding, and morphological organization in mood disorders. In the present study, we utilized in situ hybridization-guided laser capture microdissection to harvest tissue samples from the middle-caudal subregion of the human DR post-mortem from MDD patients and from psychiatrically normal comparison subjects. Extracted RNA was prepared for gene expression profiling, and subsequent confirmation of select targets with quantitative real-time PCR. Our data indicate expression changes in functional gene families that regulate: (1) cellular stress and energy balance, (2) intracellular signaling and transcriptional regulation, and (3) cell proliferation and connectivity. The greatest changes in expression were observed among transcriptional regulators, including downregulation in the expression of TOB1, EGR1, and NR4A2 and their downstream targets. Previous studies have implicated these gene products in the regulation of functional domains impacted by MDD, including cognitive function, affective regulation, and emotional memory formation. These observations indicate altered function of several transcriptional regulators and their downstream targets, which may lead to the dysregulation of multiple cellular functions that contribute to the pathophysiology of MDD. Future studies will require single cell analyses in the DR to determine potential impact of these changes on its cellular functions and related circuits.

Individual neurons in the rat lateral habenular complex project mostly to the dopaminergic ventral tegmental area or to the serotonergic raphe nuclei.

The lateral habenular complex (LHb) is a bilateral epithalamic brain structure involved in the modulation of ascending monoamine systems in response to afferents from limbic regions and basal ganglia. The LHb is implicated in various biological functions, such as reward, sleep-wake cycle, feeding, pain processing, and memory formation. The modulatory role of the LHb is partially assumed by putative spontaneously active LHb neurons projecting to the dopaminergic ventral tegmental area (VTA) and to the serotonergic median (MnR) and dorsal raphe nuclei (DR). All four nuclei form a complex and coordinated network to evoke appropriate responses to reward-related stimuli. At present it is not known whether individual LHb neurons project to only one or to more than one monoaminergic nucleus. To answer this question, we made dual injections of two different retrograde tracers into the rat VTA and either DR or MnR. Tracers were visualized by immunohistochemistry. In coronal sections, the different retrogradly labeled habenular neurons were quantified and assigned to the corresponding habenular subnuclei. Our results show that 1) the distribution of neurons in the LHb projecting to the three monoamine nuclei is similar and exhibits a great overlap, 2) the vast majority of LHb projection neurons target one monoaminergic nucleus only, and 3) very few, heterogeneously distributed LHb neurons project to both dopaminergic and serotonergic nuclei. These results imply that the LHb forms both separate and interconnected circuits with each monoaminergic nucleus, permitting the LHb to modulate its output to different monoamine systems either independently or jointly.

Inborn differences in environmental reactivity predict divergent diurnal behavioral, endocrine, and gene expression rhythms.

Circadian dysfunction has long been implicated in the etiology of mood disorders. The gene Clock and related molecules (e.g. Per1, Per2) represent key regulators of circadian rhythmicity, and their targeted disruption in mutant mice produces potentiated reward drive, novelty-seeking, impulsivity, disrupted sleep, reduced depression and anxiety - a behavioral profile highly reminiscent of our selectively bred high responder (bHR) rats compared to bred low responders (bLRs). The current study evaluated potential diurnal bHR-bLR differences in behavior, gene expression, and neuroendocrinology. Relative to bHRs, bLRs showed diminished homecage locomotion during the dark (but not light) phase and a delayed corticosterone peak. In situ hybridizations in hypothalamus, amygdala, and hippocampus at Zeitgeber Time (ZT)2 and ZT14 revealed distinct bHR-bLR day-night gene expression fluctuations. bHRs exhibited altered day-night patterns of corticotrophin releasing hormone (CRH) and arginine vasopression (AVP) mRNA in the hypothalamus, and perturbed hippocampal MR:GR ratios relative to bLR rats. bHR-bLR rats showed disparate day-night Clock expression in the suprachiasmatic nucleus, a master circadian oscillator, with bHRs showing higher levels at ZT14 versus ZT2 and bLRs showing the opposite pattern. Clock, Per1 and Per2 were assessed in the substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) since disruption of these genes induces "bHR-like" behavior in mutant mice. Clock and Per1 did not differ between strains, but there were robust Per2 differences, with bHRs having reduced Per2 in VTA and SNc. These findings resonate with earlier work demonstrating that perturbation of Clock and related molecules contributes to disturbances of emotional and addictive behaviors.