The Neuroscience Experiments System (NES)-A Software Tool to Manage Experimental Data and Its Provenance

Provenance Information for Biomedical Data and Workflows: Scoping Review

BACKGROUND

The record of the origin and the history of data, known as provenance, holds importance. Provenance information leads to higher interpretability of scientific results and enables reliable collaboration and data sharing. However, the lack of comprehensive evidence on provenance approaches hinders the uptake of good scientific practice in clinical research.

OBJECTIVE

This scoping review aims to identify approaches and criteria for provenance tracking in the biomedical domain. We reviewed the state-of-the-art frameworks, associated artifacts, and methodologies for provenance tracking.

METHODS

This scoping review followed the methodological framework developed by Arksey and O'Malley. We searched the PubMed and Web of Science databases for English-language articles published from 2006 to 2022. Title and abstract screening were carried out by 4 independent reviewers using the Rayyan screening tool. A majority vote was required for consent on the eligibility of papers based on the defined inclusion and exclusion criteria. Full-text reading and screening were performed independently by 2 reviewers, and information was extracted into a pretested template for the 5 research questions. Disagreements were resolved by a domain expert. The study protocol has previously been published.

RESULTS

The search resulted in a total of 764 papers. Of 624 identified, deduplicated papers, 66 (10.6%) studies fulfilled the inclusion criteria. We identified diverse provenance-tracking approaches ranging from practical provenance processing and managing to theoretical frameworks distinguishing diverse concepts and details of data and metadata models, provenance components, and notations. A substantial majority investigated underlying requirements to varying extents and validation intensities but lacked completeness in provenance coverage. Mostly, cited requirements concerned the knowledge about data integrity and reproducibility. Moreover, these revolved around robust data quality assessments, consistent policies for sensitive data protection, improved user interfaces, and automated ontology development. We found that different stakeholder groups benefit from the availability of provenance information. Thereby, we recognized that the term provenance is subjected to an evolutionary and technical process with multifaceted meanings and roles. Challenges included organizational and technical issues linked to data annotation, provenance modeling, and performance, amplified by subsequent matters such as enhanced provenance information and quality principles.

CONCLUSIONS

As data volumes grow and computing power increases, the challenge of scaling provenance systems to handle data efficiently and assist complex queries intensifies, necessitating automated and scalable solutions. With rising legal and scientific demands, there is an urgent need for greater transparency in implementing provenance systems in research projects, despite the challenges of unresolved granularity and knowledge bottlenecks. We believe that our recommendations enable quality and guide the implementation of auditable and measurable provenance approaches as well as solutions in the daily tasks of biomedical scientists.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR2-10.2196/31750.

Plasticity of face-hand sensorimotor circuits after a traumatic brachial plexus injury

Background

Interactions between the somatosensory and motor cortices are of fundamental importance for motor control. Although physically distant, face and hand representations are side by side in the sensorimotor cortex and interact functionally. Traumatic brachial plexus injury (TBPI) interferes with upper limb sensorimotor function, causes bilateral cortical reorganization, and is associated with chronic pain. Thus, TBPI may affect sensorimotor interactions between face and hand representations.

Objective

The aim of this study was to investigate changes in hand-hand and face-hand sensorimotor integration in TBPI patients using an afferent inhibition (AI) paradigm.

Method

The experimental design consisted of electrical stimulation (ES) applied to the hand or face followed by transcranial magnetic stimulation (TMS) to the primary motor cortex to activate a hand muscle representation. In the AI paradigm, the motor evoked potential (MEP) in a target muscle is significantly reduced when preceded by an ES at short-latency (SAI) or long-latency (LAI) interstimulus intervals. We tested 18 healthy adults (control group, CG), evaluated on the dominant upper limb, and nine TBPI patients, evaluated on the injured or the uninjured limb. A detailed clinical evaluation complemented the physiological investigation.

Results

Although hand-hand SAI was present in both the CG and the TBPI groups, hand-hand LAI was present in the CG only. Moreover, less AI was observed in TBPI patients than the CG both for face-hand SAI and LAI.

Conclusion

Our results indicate that sensorimotor integration involving both hand and face sensorimotor representations is affected by TBPI.

Natural product-based pharmacological studies for neurological disorders

Central nervous system (CNS) disorders and diseases are expected to rise sharply in the coming years, partly because of the world's aging population. Medicines for the treatment of the CNS have not been successfully made. Inadequate knowledge about the brain, pharmacokinetic and dynamic errors in preclinical studies, challenges with clinical trial design, complexity and variety of human brain illnesses, and variations in species are some potential scenarios. Neurodegenerative diseases (NDDs) are multifaceted and lack identifiable etiological components, and the drugs developed to treat them did not meet the requirements of those who anticipated treatments. Therefore, there is a great demand for safe and effective natural therapeutic adjuvants. For the treatment of NDDs and other memory-related problems, many herbal and natural items have been used in the Ayurvedic medical system. Anxiety, depression, Parkinson's, and Alzheimer's diseases (AD), as well as a plethora of other neuropsychiatric disorders, may benefit from the use of plant and food-derived chemicals that have antidepressant or antiepileptic properties. We have summarized the present level of knowledge about natural products based on topological evidence, bioinformatics analysis, and translational research in this review. We have also highlighted some clinical research or investigation that will help us select natural products for the treatment of neurological conditions. In the present review, we have explored the potential efficacy of phytoconstituents against neurological diseases. Various evidence-based studies and extensive recent investigations have been included, which will help pharmacologists reduce the progression of neuronal disease.