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The December 2022 release of the SPARC Portal ( https://sparc.science ) included the first significant update to the anatomical connectivity flatmaps since the portal first launched. These flatmaps provide an interactive and visual map for the display and exploration of the autonomic nervous system of Human, rat, mouse, pig, and cat ( https://sparc.science/maps ). In addition to improved anatomical ‘cartoons’ for all species and adding a female Human map, these maps, for the first time, automatically render the connectivity knowledge directly retrieved from the SPARC Connectivity Knowledge Base of the Autonomic Nervous System (SCKAN; https://sparc.science/resources/6eg3VpJbwQR4B84CjrvmyD ). SCKAN contains explicit knowledge about CNS-ANS-end organ circuitry derived from SPARC data and scientific literature, in a form that supports computational reasoning. Each flatmap consists of a manually drawn base layer for the species-specific anatomical cartoon and a layer of manually drawn tracts for the large nerves. By annotating these drawings with standard reference SPARC vocabularies consistent with SCKAN usage, software tools are then able to semantically map connectivity circuits retrieved from SCKAN to the visual representation on each species’ flatmap. Beyond the interactive visual rendering of the circuitry on the SPARC Portal, the semantic consistency between flatmaps and SCKAN powers further user interface components on the SPARC Portal to surface additional knowledge for each rendered connection. For example, comprehensive links to the literature and/or data supporting a connectivity statement can be retrieved from SCKAN and provided to Portal users. Now that tools are in place to support this automated workflow to generate the flatmaps from SCKAN knowledge, we are continuing to improve the SPARC Portal to visualise new knowledge as it becomes available. NIH Common Fund, NIH Office of the Director, Awards OT3OD025349 and OT2 OD030541 This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

BACKGROUND Improving rigor and transparency measures should lead to improvements in reproducibility across the scientific literature; however, the assessment of measures of transparency tends to be very difficult if performed manually. OBJECTIVE This study addresses the enhancement of the Rigor and Transparency Index (RTI, version 2.0), which attempts to automatically assess the rigor and transparency of journals, institutions, and countries using manuscripts scored on criteria found in reproducibility guidelines (eg, Materials Design, Analysis, and Reporting checklist criteria). METHODS The RTI tracks 27 entity types using natural language processing techniques such as Bidirectional Long Short-term Memory Conditional Random Field–based models and regular expressions; this allowed us to assess over 2 million papers accessed through PubMed Central. RESULTS Between 1997 and 2020 (where data were readily available in our data set), rigor and transparency measures showed general improvement (RTI 2.29 to 4.13), suggesting that authors are taking the need for improved reporting seriously. The top-scoring journals in 2020 were the Journal of Neurochemistry (6.23), British Journal of Pharmacology (6.07), and Nature Neuroscience (5.93). We extracted the institution and country of origin from the author affiliations to expand our analysis beyond journals. Among institutions publishing >1000 papers in 2020 (in the PubMed Central open access set), Capital Medical University (4.75), Yonsei University (4.58), and University of Copenhagen (4.53) were the top performers in terms of RTI. In country-level performance, we found that Ethiopia and Norway consistently topped the RTI charts of countries with 100 or more papers per year. In addition, we tested our assumption that the RTI may serve as a reliable proxy for scientific replicability (ie, a high RTI represents papers containing sufficient information for replication efforts). Using work by the Reproducibility Project: Cancer Biology, we determined that replication papers (RTI 7.61, SD 0.78) scored significantly higher (P CONCLUSIONS These results align with our view that RTI may serve as a reliable proxy for scientific replicability. Unfortunately, RTI measures for journals, institutions, and countries fall short of the replicated paper average. If we consider the RTI of these replication studies as a target for future manuscripts, more work will be needed to ensure that the average manuscript contains sufficient information for replication attempts.

Starting from macroscopic and microscopic facts of cerebellar histology, we propose a new functional interpretation that may elucidate the role of the cerebellum in movement control. The idea is that the cerebellum is a large collection of individual lines (Eccles's "beams": Eccles et al. 1967a) that respond specifically to certain sequences of events in the input and in turn produce sequences of signals in the output. We believe that the sequence-in/sequence-out mode of operation is as typical for the cerebellar cortex as the transformation of sets into sets of active neurons is typical for the cerebral cortex, and that both the histological differences between the two and their reciprocal functional interactions become understandable in the light of this dichotomy. The response of Purkinje cells to sequences of stimuli in the mossy fiber system was shown experimentally by Heck on surviving slices of rat and guinea pig cerebellum. Sequential activation of a row of eleven stimulating electrodes in the granular layer, imitating a "movement" of the stimuli along the folium, produces a powerful volley in the parallel fibers that strongly excites Purkinje cells, as evidenced by intracellular recording. The volley, or "tidal wave," has maximal amplitude when the stimulus moves toward the recording site at the speed of conduction in parallel fibers, and much smaller amplitudes for lower or higher "velocities." The succession of stimuli has no effect when they "move" in the opposite direction. Synchronous activation of the stimulus electrodes also had hardly any effect. We believe that the sequences of mossy fiber activation that normally produce this effect in the intact cerebellum are a combination of motor planning relayed to the cerebellum by the cerebral cortex, and information about ongoing movement, reaching the cerebellum from the spinal cord. The output elicited by the specific sequence to which a "beam" is tuned may well be a succession of well timed inhibitory volleys "sculpting" the motor sequences so as to adapt them to the complicated requirements of the physics of a multijointed system.

We report a new Web-based resource (LAMHDI) integrating information about animal models for human disease research. This NCRR supported resource provides a simple interface to existing animal model information for the biomedical research community. It provides more efficient access to animal model information, better categorizes and organizes existing data, facilitates interactions between researchers and resource providers, and promotes broader and more applicable use of animal models for human disease research. Approach Phase 1: A first-generation prototype is available at www.LAMHDI.org. This portal provides searchable access to existing mouse and zebrafish databases through an integrated search engine, as well as linked access to information about a variety of other species including nonhuman primates and rats. The portal also allows researchers to contribute data on animal models, thereby extending the impact of existing information through direct posting by the research community. Phase 2: The second generation will add extensive new information for additional animal model species and will increase the depth and connectivity of the data through development of semantic datastores. A sophisticated software architecture will support intelligent relational searches across diverse datasets to highlight associations between diseases, animal models, and biologic pathways.

This chapter reviews evidence demonstrating the essential role of the cerebellum and its associated circuitry in the learning and memory of classical conditioning of discrete behavioral responses (e.g., eyeblink, limb flexion, head turn). It now seems conclusive that the memory traces for this basic category of associative learning are formed and stored in the cerebellum. Lesion, neuronal recording, electrical microstimulation, and anatomical procedures have been used to identify the essential conditioned stimulus (CS) circuit, including the pontine mossy fiber projections to the cerebellum; the essential unconditioned stimulus (US) reinforcing or teaching circuit, including neurons in the inferior olive (dorsal accessory olive) projecting to the cerebellum as climbing fibers; and the essential conditioned response (CR) circuit, including the interpositus nucleus, its projection via the superior cerebellar peduncle to the magnocellular red nucleus, and rubral projections to premotor and motor nuclei. Each major component of the eyeblink CR circuit was reversibly inactivated both in trained animals and over the course of training. In all cases in trained animals, inactivation abolished the CR (and the UR as well when motor nuclei were inactivated). When animals were trained during inactivation (and not exhibiting CRs) and then tested without inactivation, animals with inactivation of the motor nuclei, red nucleus, and superior peduncle had fully learned, whereas animals with inactivation of a very localized region of the cerebellum (anterior interpositus and overlying cortex) had not learned at all. Consequently, the memory traces are formed and stored in the cerebellum. Several alternative possibilities are considered and ruled out. Both the cerebellar cortex and the interpositus nucleus are involved in the memory storage process, suggesting that a phenomenon-like long-term depression (LTD) is involved in the cerebellar cortex and long-term potentiation (LTP) is involved in the interpositus. The experimental findings reviewed in this chapter provide perhaps the first conclusive evidence for the localization of a basic form of memory storage to a particular brain region, namely the cerebellum, and indicate that the cerebellum is indeed a cognitive machine.