Software is at the core of most scientific discoveries today. Therefore, the quality of research results highly depends on the quality of the research software. Rigorous testing, as we know it from software engineering in the industry, could ensure the quality of the research software but it also requires a substantial effort that is often not rewarded in academia. Therefore, this research explores the effects of research software testing integrated into teaching on research software. In an in-vivo experiment, we integrated the engineering of a test suite for a large-scale network simulation as group projects into a course on software testing at the Blekinge Institute of Technology, Sweden, and qualitatively measured the effects of this integration on the research software. We found that the research software benefited from the integration through substantially improved documentation and fewer hardware and software dependencies. However, this integration was effortful and although the student teams developed elegant and thoughtful test suites, no code by students went directly into the research software since we were not able to make the integration back into the research software
This paper presents multi- and interdisciplinary approaches for finding the appropriate AI technologies for research information. Professional research information management (RIM) is becoming increasingly important as an expressly data-driven tool for researchers. It is not only the basis of scientific knowledge processes, but also related to other data. A concept and a process model of the elementary phases from the start of the project to the ongoing operation of the AI methods in the RIM is presented, portraying the implementation of an AI project, meant to enable universities and research institutions to support their researchers in dealing with incorrect and incomplete research information, while it is being stored in their RIMs. Our aim is to show how research information harmonizes with the challenges of data literacy and data quality issues, related to AI, also wanting to underline that any project can be successful if the research institutions and various departments of universities, involved work together and appropriate support is offered to improve research information and data management.
This paper presents a scientometric analysis of research output from the University of Lagos, focusing on the two decades spanning 2004 to 2023. Using bibliometric data retrieved from the Web of Science, we examine trends in publication volume, collaboration patterns, citation impact, and the most prolific authors, departments, and research domains at the university. The study reveals a consistent increase in research productivity, with the highest publication output recorded in 2023. Health Sciences, Engineering, and Social Sciences are identified as dominant fields, reflecting the university's interdisciplinary research strengths. Collaborative efforts, both locally and internationally, show a positive correlation with higher citation impact, with the United States and the United Kingdom being the leading international collaborators. Notably, open-access publications account for a significant portion of the university's research output, enhancing visibility and citation rates. The findings offer valuable insights into the university's research performance over the past two decades, providing a foundation for strategic planning and policy formulation to foster research excellence
The present study attempts to highlight the research output generated in Russia in coronary artery disease (CAD) research during the period 1990-2019 to understand the distribution of research output, top journals for publications, and most prolific authors, authorship pattern, and citation pattern. This study is based on secondary data extracted from the Science Citation Index (SCI), which is an integral component of the Web of Science. Descriptive and inferential statistical techniques were applied in the study. There were 5058 articles by Russian scholars in coronary artery disease during 1990-2019; they preferred to publish in Russian journals. The research contributions were in the form of research articles, meeting abstracts and reviews with a consistent drop in the number of editorial material and article; proceedings paper with time. Co-authorship was the norm in coronary artery disease research, with a steady increase in the number of multi-author documents in recent years.
Modern research heavily relies on software. A significant challenge researchers face is understanding the complex software used in specific research fields. We target two scenarios in this context, namely long onboarding times for newcomers and conference reviewers evaluating replication packages. We hypothesize that both scenarios can be significantly improved when there is a clear link between the paper's ideas and the code that implements them. As a time- and staff-saving approach, we propose an LLM-based automation tool that takes in a paper and the software implementing the paper, and generates a trace mapping between research ideas and their locations in code. Initial experiments have shown that the tool can generate quite useful mappings.
Super-resolution ultrasound (SRUS) technology has overcome the resolution limitations of conventional ultrasound, enabling micrometer-scale imaging of microvasculature. However, due to the nature of imaging principles, three-dimensional reconstruction of microvasculature from SRUS remains an open challenge. We developed microvascular visualization fold (MVis-Fold), an innovative three-dimensional microvascular reconstruction model that integrates a cross-scale network architecture. This model can perform high-fidelity inference and reconstruction of three-dimensional microvascular networks from two-dimensional SRUS images. It precisely calculates key parameters in three-dimensional space that traditional two-dimensional SRUS cannot readily obtain. We validated the model's accuracy and reliability in three-dimensional microvascular reconstruction of solid tumors. This study establishes a foundation for three-dimensional quantitative analysis of microvasculature. It provides new tools and methods for diagnosis and monitoring of various diseases.
This scientometric study analyzes Avian Influenza research from 2014 to 2023 using bibliographic data from the Web of Science database. We examined publication trends, sources, authorship, collaborative networks, document types, and geographical distribution to gain insights into the global research landscape. Results reveal a steady increase in publications, with high contributions from Chinese and American institutions. Journals such as PLoS One and the Journal of Virology published the highest number of studies, indicating their influence in this field. The most prolific institutions include the Chinese Academy of Sciences and the University of Hong Kong, while the College of Veterinary Medicine at South China Agricultural University emerged as the most productive department. China and the USA lead in publication volume, though developed nations like the United Kingdom and Germany exhibit a higher rate of international collaboration. "Articles" are the most common document type, constituting 84.6% of the total, while "Reviews" account for 7.6%. This study provides a comprehensive view of global trends in Avian Influenza research, emphasizing the need for collaborative efforts ac
Today, scientific research is increasingly data-centric and compute-intensive, relying on data and models across distributed sources. However, it still faces challenges in the traditional cooperation mode, due to the high storage and computing cost, geo-location barriers, and local confidentiality regulations. The Jupyter environment has recently emerged and evolved as a vital virtual research environment for scientific computing, which researchers can use to scale computational analyses up to larger datasets and high-performance computing resources. Nevertheless, existing approaches lack robust support of a decentralized cooperation mode to unlock the full potential of decentralized collaborative scientific research, e.g., seamlessly secure data sharing. In this work, we change the basic structure and legacy norms of current research environments via the seamless integration of Jupyter with Ethereum blockchain capabilities. As such, it creates a Decentralized Virtual Research Environment (D-VRE) from private computational notebooks to decentralized collaborative research ecosystem. We propose a novel architecture for the D-VRE and prototype some essential D-VRE elements for enabli
Drawing on 1,178 safety and reliability papers from 9,439 generative AI papers (January 2020 - March 2025), we compare research outputs of leading AI companies (Anthropic, Google DeepMind, Meta, Microsoft, and OpenAI) and AI universities (CMU, MIT, NYU, Stanford, UC Berkeley, and University of Washington). We find that corporate AI research increasingly concentrates on pre-deployment areas -- model alignment and testing & evaluation -- while attention to deployment-stage issues such as model bias has waned. Significant research gaps exist in high-risk deployment domains, including healthcare, finance, misinformation, persuasive and addictive features, hallucinations, and copyright. Without improved observability into deployed AI, growing corporate concentration could deepen knowledge deficits. We recommend expanding external researcher access to deployment data and systematic observability of in-market AI behaviors.
The relationship between measures of stenosis and microvascular resistance is of importance due to medical decisions being based on these values. This research investigates the impact of varying microvascular resistance on fractional flow reserve (FFR) and hyperaemic stenosis resistance (hSR). Microvascular resistance is classified using hyperaemic microvascular resistance (hMR). Additionally, hMR using the upstream pressure value (hMRPa) has also been calculated and is compared to hMR measured conventionally. Tests were conducted at three different degrees of stenosis (quantified by percent area) in a coronary flow circuit with varying downstream resistance to simulate the microvasculature. Pressure and flow values are recorded across the stenosed section, allowing for calculation of the diagnostic indexes. Results indicate that for a constant degree of stenosis, FFR would increase with increasing microvascular resistance while hSR would remain almost constant. hMRPa was found to approach hMR as the stenosis severity decreased, and the pressure gradient decreased. In the results shown here, with sufficiently high downstream resistance, an 84% stenosis could produce an FFR value ov
Research is facing a reproducibility crisis, in which the results and findings of many studies are difficult or even impossible to reproduce. This is also the case in machine learning (ML) and artificial intelligence (AI) research. Often, this is the case due to unpublished data and/or source-code, and due to sensitivity to ML training conditions. Although different solutions to address this issue are discussed in the research community such as using ML platforms, the level of reproducibility in ML-driven research is not increasing substantially. Therefore, in this mini survey, we review the literature on reproducibility in ML-driven research with three main aims: (i) reflect on the current situation of ML reproducibility in various research fields, (ii) identify reproducibility issues and barriers that exist in these research fields applying ML, and (iii) identify potential drivers such as tools, practices, and interventions that support ML reproducibility. With this, we hope to contribute to decisions on the viability of different solutions for supporting ML reproducibility.
Microvascular imaging has advanced significantly with ultrafast data acquisition and improved clutter filtering, enhancing the sensitivity of power Doppler imaging to small vessels. However, the image quality remains limited by spatial resolution and elevated background noise, both of which impede visualization and accurate quantification. To address these limitations, this study proposes a high-resolution cross-correlation Power Doppler (HR-XPD) method that integrates spatial radiality weighting with Doppler signal coherence analysis, thereby enhancing spatial resolution while suppressing artifacts and background noise. Quantitative evaluations in simulation and in vivo experiments on healthy human liver, transplanted human kidney, and pig kidney demonstrated that HR-XPD significantly improves microvascular resolvability and contrast compared to conventional PD. In vivo results showed up to a 2 to 3-fold enhancement in spatial resolution and an increase in contrast by up to 20 dB. High-resolution vascular details were clearly depicted within a short acquisition time of only 0.3 s-1.2 s without the use of contrast agents. These findings indicate that HR-XPD provides an effective, c
Ultrasound microvascular imaging (UMI) is often hindered by low signal-to-noise ratio (SNR), especially in contrast-free or deep tissue scenarios, which impairs subsequent vascular quantification and reliable disease diagnosis. To address this challenge, we propose Half-Angle-to-Half-Angle (HA2HA), a self-supervised denoising framework specifically designed for UMI. HA2HA constructs training pairs from complementary angular subsets of beamformed radio-frequency (RF) blood flow data, across which vascular signals remain consistent while noise varies. HA2HA was trained using in-vivo contrast-free pig kidney data and validated across diverse datasets, including contrast-free and contrast-enhanced data from pig kidneys, as well as human liver and kidney. An improvement exceeding 15 dB in both contrast-to-noise ratio (CNR) and SNR was observed, indicating a substantial enhancement in image quality. In addition to power Doppler imaging, denoising directly in the RF domain is also beneficial for other downstream processing such as color Doppler imaging (CDI). CDI results of human liver derived from the HA2HA-denoised signals exhibited improved microvascular flow visualization, with a supp
Super-resolution ultrasound (SRUS) visualises microvasculature beyond the ultrasound diffraction limit (wavelength($λ$)/2) by localising and tracking spatially isolated microbubble contrast agents. SRUS phantoms typically consist of simple tube structures, where diameter channels below 100 $μ$m are not available. Furthermore, these phantoms are generally fragile and unstable, have limited ground truth validation, and their simple structure limits the evaluation of SRUS algorithms. To aid SRUS development, robust and durable phantoms with known and physiologically relevant microvasculature are needed for repeatable SRUS testing. This work proposes a method to fabricate durable microvascular phantoms that allow optical gauging for SRUS validation. The methodology used a microvasculature negative print embedded in a Polydimethylsiloxane to fabricate a microvascular phantom. Branching microvascular phantoms with variable microvascular density were demonstrated with optically validated vessel diameters down to $\sim$ 60 $μ$m ($λ$/5.8; $λ$ =$\sim$ 350 $μ$m). SRUS imaging was performed and validated with optical measurements. The average SRUS error was 15.61 $μ$m ($λ$/22) with a standard
Blood coagulation is governed by tightly regulated reaction networks that unfold within a flowing, heterogeneous microvascular environment. Reduced kinetic models of the intrinsic and extrinsic pathways have seen limited in vitro validation, and their behavior within spatially resolved flow fields remains largely unexplored. Here, we embed two established reduced networks into a recently proposed mesoscale particle-based framework that resolves fluid momentum transport alongside multispecies advection-diffusion-reaction dynamics. We investigate the initiation phase of coagulation by simulating thrombin formation in microvascular geometries and in vitro assays, and we assess the framework's ability to reproduce thrombin generation curves (TGCs) under physiologically relevant conditions. We further examine how variations in fibrinogen levels - an important determinant of clot structure and a biomarker for inflammation and thrombosis - affect thrombin and fibrin formation. Overall, this study provides a unified computational approach for analysing how biochemical kinetics interact with transport processes, offering insights relevant to thrombosis modeling and blood diagnostics.
The production of knowledge has become increasingly a global endeavor. Yet, location related factors, such as local working environment and national policy designs, may continue to affect what kind of science is being pursued. Here we examine the geography of the production of creative science by country, through the lens of novelty and atypicality proposed in Uzzi et al. (2013). We quantify a country's representativeness in novel and atypical science, finding persistent differences in propensity to generate creative works, even among developed countries that are large producers in science. We further cluster countries based on how their tendency to publish novel science changes over time, identifying one group of emerging countries. Our analyses point out the recent emergence of China not only as a large producer in science but also as a leader that disproportionately produces more novel and atypical research. Discipline specific analysis indicates that China's over-production of atypical science is limited to a few disciplines, especially its most prolific ones like materials science and chemistry.
The simulation of microcirculatory blood flow in realistic vascular architectures poses significant challenges due to the multiscale nature of the problem and the topological complexity of capillary networks. In this work, we propose a novel deep learning-based reduced-order modeling strategy, leveraging Graph Neural Networks (GNNs) trained on synthetic microvascular graphs to approximate hemodynamic quantities on anatomically realistic domains. Our method combines algorithms for synthetic vascular generation with a physics-informed training procedure that integrates graph topological information and local flow dynamics. To ensure the physical reliability of the learned surrogates, we incorporate a physics-informed loss functional derived from the governing equations, allowing enforcement of mass conservation and rheological constraints. The resulting GNN architecture demonstrates robust generalization capabilities across diverse network configurations. The GNN formulation is validated on benchmark problems with linear and nonlinear rheology, showing accurate pressure and velocity field reconstruction with substantial computational gains over full-order solvers. The methodology sho
Cardiovascular disease (CVD) remains the leading global cause of mortality, yet current risk stratification methods often fail to detect early, subclinical changes. Previous studies have generally not integrated retinal microvasculature characteristics with comprehensive serum lipidomic profiles as potential indicators of CVD risk. In this study, an innovative imaging omics framework was introduced, combining retinal microvascular traits derived through deep learning based image processing with serum lipidomic data to highlight asymptomatic biomarkers of cardiovascular risk beyond the conventional lipid panel. This represents the first large scale, covariate adjusted and stratified correlation analysis conducted in a healthy population, which is essential for identifying early indicators of disease. Retinal phenotypes were quantified using automated image analysis tools, while serum lipid profiling was performed by Ultra High Performance Liquid Chromatography Electrospray ionization High resolution mass spectrometry (UHPLC ESI HRMS). Strong, age- and sex-independent correlations were established, particularly between average artery width, vessel density, and lipid subclasses such a
This article presents a partial differential equation (PDE) of Keller-Segel (KS) type that reproduces patterns commonly observed during the growth of brain microvasculature. We provide mathematical insights into the mechanisms underlying the emergence of these patterns. In addition, we derive a data-driven equation that ensures a consistent temporal evolution of the chemoattractant associated with the observed microvascular dynamics. Beyond numerical simulations, the aim of this study is to advance a comprehensive mathematical modeling framework, spanning blood flow in cerebral arterial networks to biochemical processes, in order to better understand how vascular impairments may contribute to neurodegenerative diseases.
Continuous monitoring and in-situ assessment of microvascular connectivity have significant implications for culturing vascularized organoids and optimizing the therapeutic strategies. However, commonly used methods for vascular connectivity assessment heavily rely on fluorescent labels that may either raise biocompatibility concerns or interrupt the normal cell growth process. To address this issue, a Vessel Connectivity Network (VC-Net) was developed for label-free assessment of vascular connectivity. To validate the VC-Net, microvascular networks (MVNs) were cultured in vitro and their microscopic images were acquired at different culturing conditions as a training dataset. The VC-Net employs a Vessel Queue Contrastive Learning (VQCL) method and a class imbalance algorithm to address the issues of limited sample size, indistinctive class features and imbalanced class distribution in the dataset. The VC-Net successfully evaluated the vascular connectivity with no significant deviation from that by fluorescence imaging. In addition, the proposed VC-Net successfully differentiated the connectivity characteristics between normal and tumor-related MVNs. In comparison with those cultu