Biomedical Research Productivity Research Articles

Strategic policy options to improve quality and productivity of biomedical research.

Emerging societal expectations from biomedical research and intensifying international scientific competition are becoming existential matters. Based on a review of pertinent evidence, this article analyzes challenges and formulates public policy recommendations for improving productivity and impact of life sciences. Critical risks include widespread quality defects of research, particularly non-reproducible results, and narrow access to scientifically sound information giving advantage to health misinformation. In funding life sciences, the simultaneous shift to nondemocratic societies is an added challenge. Simply spending more on research will not be enough in the global competition. Considering the pacesetter role of the federal government, five national policy recommendations are put forward: (i) funding projects with comprehensive expectations of reproducibility; (ii) public-private partnerships for contemporaneous quality support in laboratories; (iii) making research institutions accountable for quality control; (iv) supporting new quality filtering standards for scientific journals and repositories, and (v) establishing a new network of centers for scientific health communications.

Enhancing Global Biomedical Research: Educational Strategies for Bridging the Gap between HICs and LMICs

There is a pressing need to address the noticeable disparity in biomedical research output between High-Income Countries (HICs) and Low-Middle Income Countries (LMICs). This imbalance raises urgent concerns about equity and the impact on global health. Despite being home to most of the global population, LMICs face numerous challenges that hinder their ability to contribute significantly to research. This review explores the factors contributing to the disparities and proposes potential solutions to address this global imbalance. A comprehensive strategy is needed to tackle the differences in biomedical research productivity between high-income and low-middle-income nations. Enhancing global partnerships, ensuring fair allocation of resources, and prioritizing the development of research capabilities are crucial measures in nurturing a more diverse and influential worldwide biomedical research landscape. Closing this divide is essential for advancing scientific inclusivity and tackling the health issues economically disadvantaged countries face.

MyoV: a deep learning-based tool for the automated quantification of muscle fibers.

Accurate approaches for quantifying muscle fibers are essential in biomedical research and meat production. In this study, we address the limitations of existing approaches for hematoxylin and eosin-stained muscle fibers by manually and semiautomatically labeling over 660000 muscle fibers to create a large dataset. Subsequently, an automated image segmentation and quantification tool named MyoV is designed using mask regions with convolutional neural networks and a residual network and feature pyramid network as the backbone network. This design enables the tool to allow muscle fiber processing with different sizes and ages. MyoV, which achieves impressive detection rates of 0.93-0.96 and precision levels of 0.91-0.97, exhibits a superior performance in quantification, surpassing both manual methods and commonly employed algorithms and software, particularly for whole slide images (WSIs). Moreover, MyoV is proven as a powerful and suitable tool for various species with different muscle development, including mice, which are a crucial model for muscle disease diagnosis, and agricultural animals, which are a significant meat source for humans. Finally, we integrate this tool into visualization software with functions, such as segmentation, area determination and automatic labeling, allowing seamless processing for over 400000 muscle fibers within a WSI, eliminating the model adjustment and providing researchers with an easy-to-use visual interface to browse functional options and realize muscle fiber quantification from WSIs.

Perspectives in Genome-Editing Techniques for Livestock.

Genome editing of farm animals has undeniable practical applications. It helps to improve production traits, enhances the economic value of livestock, and increases disease resistance. Gene-modified animals are also used for biomedical research and drug production and demonstrate the potential to be used as xenograft donors for humans. The recent discovery of site-specific nucleases that allow precision genome editing of a single-cell embryo (or embryonic stem cells) and the development of new embryological delivery manipulations have revolutionized the transgenesis field. These relatively new approaches have already proven to be efficient and reliable for genome engineering and have wide potential for use in agriculture. A number of advanced methodologies have been tested in laboratory models and might be considered for application in livestock animals. At the same time, these methods must meet the requirements of safety, efficiency and availability of their application for a wide range of farm animals. This review aims at covering a brief history of livestock animal genome engineering and outlines possible future directions to design optimal and cost-effective tools for transgenesis in farm species.

Robotic System for Blood Serum Aliquoting Based on a Neural Network Model of Machine Vision

The quality of the diagnostic information obtained in the course of laboratory studies depends on the accuracy of compliance with the regulations for the necessary work. The process of aliquoting blood serum requires immersing the pipette to different depths depending on the boundary level between blood phases. A vision system can be used to determine this depth during automated aliquoting using various algorithms. As part of the work, two recognition algorithms are synthesized, one of which is based on the use of the HSV color palette, the other is based on the convolutional neural network. In the Python language, software systems have been developed that implement the ability of a vision system to recognize blood in test tubes. The developed methods are supposed to be used for aliquoting biosamples using a delta robot in a multirobotic system, which will increase the productivity of ongoing biomedical research through the use of new technical solutions and principles of intelligent robotics. The visualized results of the work of the considered programs are presented and a comparative analysis of the quality of recognition is carried out.

Optically pumped magnetometer with high spatial resolution magnetic guide for the detection of magnetic droplets in a microfluidic channel

Quantum sensors provide unprecedented magnetic field detection sensitivities, enabling these to extend the common magnetometry range of applications and environments of operation. In this framework, many applications also require high spatial resolution magnetic measurements for biomedical research, environmental monitoring and industrial production. In this regard, optically pumped magnetometers (OPMs) are considered as prominent candidates, but are impaired in size with micrometer scale magnetic particles, e.g. magnetic droplets. In order to address this limitation, here we study the effects of adding a micrometer-to-millimeter magnetic guide to a miniature OPM. This device is applied to detect Fe3O4 magnetic droplets flowing at rates up to 25 drop. s−1 in a microfluidic channel. The computed spatial resolution is 300 µm and the measured signal-to-noise ratio is larger than 15 dB for the different sizes of considered magnetic droplets.

The Diverse Major Histocompatibility Complex Haplotypes of a Common Commercial Chicken Line and Their Effect on Marek's Disease Virus Pathogenesis and Tumorigenesis.

The major histocompatibility complex (MHC) is crucial for appropriate immune responses against invading pathogens. Chickens possess a single predominantly-expressed class I molecule with strong associations between disease resistance and MHC haplotype. For Marek’s disease virus (MDV) infections of chickens, the MHC haplotype is one of the major determinants of genetic resistance and susceptibility. VALO specific pathogen free (SPF) chickens are widely used in biomedical research and vaccine production. While valuable findings originate from MDV infections of VALO SPF chickens, their MHC haplotypes and associated disease resistance remained elusive. In this study, we used several typing systems to show that VALO SPF chickens possess MHC haplotypes that include B9, B9:02, B15, B19 and B21 at various frequencies. Moreover, we associate the MHC haplotypes to MDV-induced disease and lymphoma formation and found that B15 homozygotes had the lowest tumor incidence while B21 homozygotes had the lowest number of organs with tumors. Finally, we found transmission at variable levels to all contact birds except B15/B21 heterozygotes. These data have immediate implications for the use of VALO SPF chickens and eggs in the life sciences and add another piece to the puzzle of the chicken MHC complex and its role in infections with this oncogenic herpesvirus.

MISSIM: An Incremental Learning-Based Model With Applications to the Prediction of miRNA-Disease Association.

In the past few years, the prediction models have shown remarkable performance in most biological correlation prediction tasks. These tasks traditionally use a fixed dataset, and the model, once trained, is deployed as is. These models often encounter training issues such as sensitivity to hyperparameter tuning and "catastrophic forgetting" when adding new data. However, with the development of biomedicine and the accumulation of biological data, new predictive models are required to face the challenge of adapting to change. To this end, we propose a computational approach based on Broad learning system (BLS) to predict potential disease-associated miRNAs that retain the ability to distinguish prior training associations when new data need to be adapted. In particular, we are introducing incremental learning to the field of biological association prediction for the first time and proposed a new method for quantifying sequence similarity. In the performance evaluation, the AUC in the 5-fold cross-validation was 0.9400 +/- 0.0041. To better assess the effectiveness of MISSIM, we compared it with various classifiers and former prediction models. Its performance is superior to the previous method. Besides, the case study on identifying miRNAs associated with breast neoplasms, lung neoplasms and esophageal neoplasms show that 34, 36 and 35 out of the top 40 associations predicted by MISSIM are confirmed by recent biomedical resources. These results provide ample convincing evidence of this approach have potential value and prospect in promoting biomedical research productivity.

Biomedical and health research geography in the Eastern Mediterranean Region.

Measuring scientific outputs allows for objective evaluation of established health research systems and ranking countries according to scientific achievements. To our knowledge, attempts for systematic mapping health research output in the Eastern Mediterranean Region (EMR) are limited. We aimed to conduct a detailed bibliometric analysis of EMR biomedical and health research productivity during the period 2004-2013, considering country of first author. We applied an improved PubMed search strategy to obtain precise data on EMR research productivity, limiting articles to reviews, original research and case reports. Data were normalized to global research output, represented by total articles indexed in PubMed per year from 2004-2013, according to population size of each country. Second order polynomial trend lines were calculated and comparing 5-year periods: 2004-2008 with 2009-2013. Inspecting overall raw data, a clear increasing trend is observed. Regional share of global health related research ranged from 0.85-2.36% of total PubMed indexed publications during the study period. Five countries contributed to 80% of all published articles during study period; i.e., Islamic Republic of Iran (39%), Egypt (14%), Saudi Arabia (11%), Tunisia, and Pakistan (8% each). Overall, 2.35 articles are published per 100 000 population per year. While Kuwait maintained the highest per capita publication (followed by Tunisia, Lebanon, Qatar and Islamic Republic of Iran), Qatar, Islamic Republic of Iran and Saudi Arabia demonstrated the highest "per capita" population growth in publications. Three academic institutions accounted for over 10% of all publications that were led by an investigator from the Region. Collectively, most prolific 25 EMR institutions published 44% of all published biomedical and health research in the EMR. The overall global share of EMR health research publication is smaller than its global share of population or wealth. Biomedical and health research needs greater encouragement and supporting many EMR countries and/or institutions, especially those found to be least prolific in our analysis. The increase in academic publication on health has been more prominent in a few countries only. It is anticipated that the concentration of biomedical and health research in EMR academic institutions would help in translating knowledge into public health outcomes, if more suitable conditions are provided.

BIOMEDICAL PUBLICATIONS PRODUCTIVITY OF ORAL AND DENTAL MEDICINE FROM LIBYA (PUBMED 2003-2013)

The purpose of this short communication study was to investigation the trends of biomedical publications productivity of oral and dentistry field from Libya using the most popular biomedical search engine PubMed with focus on Libyan academic institutions. This search was performed on articles that were related to dentistry and oral medicine using the affiliation of Libya for the period 2003-2013. A total of 358 biomedical published articles were retrieved of which only 40 were related to oral and dentistry medicine. In conclusion, this investigation shows a very low productivity and weak distribution of biomedical research in oral and dentistry medicine productivity throughout Libya.

Biomedical research productivity and economic crisis in Greece: a 22-year study

This article aims to study the effect of the current financial crisis (2010–2017) on biomedical productivity and impact of Greece-affiliated investigators. PubMed, Scopus and Web of Science were searched for articles published in biomedical journals with at least one Greek affiliation during the period 1995–2016 (date of last search October 19, 2017). The impact of Greek articles was the citations received by published articles during the first 2 years following the year of publication adjusted to the number of Greek and global articles. A discrepancy in the absolute article productivity between the databases was observed: a mean annual increase before the crisis was observed in all databases, while after the crisis the increase persisted in PubMed, in Scopus a decline was observed and in the Web of Science a smaller increase was observed. The changes in relative productivity were similar for both study periods in all databases (increasing before and decreasing after crisis, p < 0.001 for trend in both periods). A continuous increase in total citations in both periods was observed (mean 2347 ± 1622 before and 2627 ± 3374 after the crisis). A continuous increase in the impact indices following adjustment for Greek (mean annual increase 0.27 ± 0.30 before to 0.37 ± 0.62 during the crisis, p = 0.58) and global productivity (mean annual increase from 0.0024 ± 0.0018 to 0.0007 ± 0.004, p = 0.95) was observed throughout the study period. In conclusion, the decline observed in the relative productivity of Greek affiliated articles during crisis compared to the period before was not reflected in their impact.

A Natural Language Interface for Dissemination of Reproducible Biomedical Data Science.

Computational tools in the form of software packages are burgeoning in the field of medical imaging and biomedical research. These tools enable biomedical researchers to analyze a variety of data using modern machine learning and statistical analysis techniques. While these publicly available software packages are a great step towards a multiplicative increase in the biomedical research productivity, there are still many open issues related to validation and reproducibility of the results. A key gap is that while scientists can validate domain insights that are implicit in the analysis, the analysis itself is coded in a programming language and that domain scientist may not be a programmer. Thus, there is no/limited direct validation of the program that carries out the desired analysis. We propose a novel solution, building upon recent successes in natural language understanding, to address this problem. Our platform allows researchers to perform, share, reproduce and interpret the analysis pipelines and results via natural language. While this approach still requires users to have a conceptual understanding of the techniques, it removes the burden of programming syntax and thus lowers the barriers to advanced and reproducible neuroimaging and biomedical research.

Development of an Eastern Mediterranean Region search strategy for biomedical citations indexed in PubMed.

PubMed, a 'barrier-free' bibliographic database covering biomedical and health disciplines, has been successfully used to identify a multitude of indicators that assist in analyzing global trends for biomedical research productivity. The current study represents an original attempt to develop and optimize an Eastern Mediterranean Region (EMR) search strategy in PubMed to pave the way for subsequent descriptive analyses. The refined EMR search strategy contains elaborate syntaxes which facilitate controlling the search process and maintaining a proper balance between sensitivity and precision of the obtained results. Country-specific citation data were manually scanned for false positive publications. Our results indicate that publication productivity increased nearly five-fold in the EMR from 2004 to 2013. Five countries (Islamic Republic of Iran, Egypt, Saudi Arabia, Tunisia and Pakistan; in order of total publications) contributed to 80% of all EMR publications during this period. Each of the remaining 17 EMR countries contributed less than 4%. We believe that the methodology presented in this study can be used in conjunction with other metrics to extract invaluable indicators to describe EMR health research systems.

An evolving research culture: Analysis of biomedical publications from Libya, 2003–13

Understanding the publication output of a country’s biomedical research can provide information for strengthening its policies, economy, and educational systems. Yet, this is the first bibliometric study to date to analyze and provide an in-depth discussion of the biomedical research productivity from Libyan academic institutions. The biomedical research productivity of higher education institutes and affiliated hospitals from Libya, with a focus on the higher education sector, was analyzed and discussed for the period of 2003–13 using the PubMed database. A questionnaire online survey was also developed to obtain opinions of Libyan scientists on productivity status and quality of research output. A total of 345 peer-reviewed articles were included in the analysis and were authored by researchers in the cities of Benghazi (32%), Tripoli (29%), Al-Zawiya (9%), Al-Bayda (8%), Sabha (3%), Misrata (3%), and Al-Khoms (1%). The papers included co-authors and/or corresponding authors from over 40 other countries were published in 179 journals covering a broad range of biomedical topics. Questionnaire (44% response rate) indicated research is largely self-funded. Information along with accurate, comprehensive, and transparent metrics can be applied to aid governmental and nongovernmental institutions to develop stable infrastructures for academic communities to achieve effective research performance and innovation.

Filovirus Research: How it Began.

The first reported filovirus outbreak occurred in August 1967, when laboratory workers in Marburg and Frankfurt, Germany, and Belgrade, Yugoslavia (now Serbia) became infected with an unknown highly pathogenic agent. The disease was characterized by high fever, malaise, rash, hemorrhagic and tetanic manifestations, and high lethality, amounting to 25%. The disease was introduced to Europe by grivets (Chlorocebus aethiops), which were used for biomedical research and vaccine production. The causative agent, Marburg virus, was isolated and identified by scientists of the University of Marburg, Germany in cooperation with specialists for viral electron microscopy at the Bernhard Nocht Institute in Hamburg, Germany. In this chapter, Dr. Slenczka, who was involved in the first isolation of Marburg virus in 1967, describes the desperate hunt of the causative agent of this first filovirus disease outbreak in the center of Europe, its successful isolation, the likely route of transmission from a monkey trading station to vaccine production facilities in Germany and Yugoslavia, and the consequences of this outbreak, including a shortage in the production of poliomyelitis vaccine In addition, this chapter provides insight into some of the peculiarities of filovirus infection, such as sexual virus transmission several months after recovery and the role of Ca2+-loss in Marburg virus pathogenesis, which were already observed during this first well-documented Marburg virus disease outbreak.

Leveraging Industry‐Academia Collaborations in Adaptive Biomedical Innovation

Despite the rapid pace of biomedical innovation, research and development (R&D) productivity in the pharmaceutical industry has not improved broadly. Increasingly, firms need to leverage new approaches to product development and commercial execution, while maintaining adaptability to rapid changes in the marketplace and in biomedical science. Firms are also seeking ways to capture some of the talent, infrastructure, and innovation that depends on federal R&D investment. As a result, a major transition to external innovation is taking place across the industry. One example of these external innovation initiatives is the Sanofi-MIT Partnership, which provided seed funding to MIT investigators to develop novel solutions and approaches in areas of interest to Sanofi. These projects were highly collaborative, with information and materials flowing both ways. The relatively small amount of funding and short time frame of the awards built an adaptable and flexible process to advance translational science.

The world of biomedical apps: their uses, limitations, and potential

Many significant biomedical discoveries of old were made in the private property of famous scientists e.g. Leeuwenhoek and Archimedes. Today, discoveries are made in brightly-lit, hi-tech, ergonomic buildings that house research institutes. While such development is advantageous in many aspects, the spatial restriction of research into well-organized structures may delay and limit the spontaneity necessary for discoveries. The smartphone and peripheral mobile devices have the potential to not only increase the productivity and mobility of biomedical research, but also restore some freedom from spatial constraints. One possible way this can occur is the development of a mobile biomedical lab that allows researchers to carry out core research processes ‘on-the-go’ without being spatially restrained within a building or availability of equipment. For this exciting prospect, we surveyed the Google and Apple app stores, discussing the limitations and the potential of this area. Based on the developments, it appears to be just a matter of time before the majority of biomedical labs processes and equipment become mobile, centred on the smartphone and peripheral devices.

Biomedical research productivity in dentistry and oral medicine from Libya: A bibliometric analysis

Biomedical research productivity from under developed regions and low income countries are generally low. This has been attributed to multiple reasons even in those relatively rich countries such as Libya. The volume and trends of biomedical publication productivity in the oral medicine and dentistry from Libya was investigated using “PubMed” database with a focus contributions from on Libyan academic institutions. A low quantity and quality of dental and oral research productivity was detected in Libya not matching the wealth of this small nation. Poor distribution of this productivity throughout the geographical landscape of Libya was also evident. Libyan biomedical research infrastructure requires reforms and funding.

Medical and biomedical research productivity from the Kingdom of Saudi Arabia (2008-2012).

Background:Biomedical publications from a country mirror the standard of Medical Education and practice in that country. It is important that the performance of the health profession is occasionally documented.Aims:This study aimed to analyze the quantity and quality of biomedical publications from the Kingdom of Saudi Arabia (KSA) in international journals indexed in PubMed between 2008 and 2012.Materials and Methods:PubMed was searched for publications associated with KSA from 2008 to 2012. The search was limited to medical and biomedical subjects. Results were saved in a text file and later checked carefully to exclude false positive errors. The quality of the publication was assessed using Journal Citation Report 2012.Results:Biomedical research production in KSA in those 5 years showed a clear linear progression. Riyadh was the main hub of medical and biomedical research activity. Most of the publications (40.9%) originated from King Saud University (KSU). About half of the articles were published in journals with an Impact Factor (IF) of < 1, one-fourth in journals with no IF, and the remaining one-fourth in journals with a high IF (≥1).Conclusion:This study revealed that research activity in KSA is increasing. However, there is an increasing trend of publishing in local journals with a low IF. More effort is required to promote medical research in Saudi Arabia.

Microtexturing of the Conductive PEDOT:PSS Polymer for Superhydrophobic Organic Electrochemical Transistors

Superhydrophobic surfaces are bioinspired, nanotechnology artifacts, which feature a reduced friction coefficient, whereby they can be used for a number of very practical applications including, on the medical side, the manipulation of biological solutions. In this work, we integrated superhydrophobic patterns with the conducting polymer PEDOT:PSS, one of the most used polymers in organic electronics because highly sensitive to ionized species in solution. In doing so, we combined geometry and materials science to obtain an advanced device where, on account of the superhydrophobicity of the system, the solutions of interest can be manipulated and, on account of the conductive PEDOT:PSS polymer, the charged molecules dispersed inside can be quantitatively measured. This original substrate preparation allowed to perform electrochemical measurements on ionized species in solution with decreasing concentration down to 10−7 molar. Moreover, it was demonstrated the ability of the device of realizing specific, combined time and space resolved analysis of the sample. Collectively, these results demonstrate how a tight, interweaving integration of different disciplines can provide realistic tools for the detection of pathologies. The scheme here introduced offers breakthrough capabilities that are expected to radically improve both the pace and the productivity of biomedical research, creating an access revolution.