Research In Biomedical Sciences Research Articles

Creating cloud platforms for supporting FAIR data management in biomedical research projects.

Biomedical research projects are becoming increasingly complex and require technological solutions that support all phases of the data lifecycle and application of the FAIR principles. At the Berlin Institute of Health (BIH), we have developed and established a flexible and cost-effective approach to building customized cloud platforms for supporting research projects. The approach is based on a microservice architecture and on the management of a portfolio of supported services. On this basis, we created and maintained cloud platforms for several international research projects. In this article, we present our approach and argue that building customized cloud platforms can offer multiple advantages over using multi-project platforms. Our approach is transferable to other research environments and can be easily adapted by other projects and other service providers.

Anti-inflammatory Effect of the Hydroethanolic Extract from Dacryodes kukachkana Leaves in Mice: Role of Macrophage Nitric Oxide

Aims: This study aimed to characterize and evaluate the effect of the hydroethanolic extract from D. kukachkana leaves (HEDkL) in mice models of acute inflammation and in isolated macrophages stimulated with carrageenan, along with possible adverse effects in the central nervous system. Study Design: After characterization of phenolic constituents, HEDkL was injected in the animals 60 min before the administration of inflammatory stimulis. The anti-inflammatory effect of HEDkL was evaluated in the models of paw edema, peritonitis and air pouch and in peritoneal macrophages stimulated with carrageenan in vitro. The per se effect of HEDkL was evaluated for behavioral alterations. Place and Duration of Study: Higher Institute of Biomedical Sciences and Animal Health Research Center, State University of Ceara; Physiopharmacology Laboratory, Federal University of Acre; between March 2021 and March 2023. Methodology: The characterization of phenolic compounds was performed by HPLC-DAD. Swiss mice (25 - 35 g) received HEDkL (25 - 200 mg/kg; per oral) 60 min before carrageenan. Macrophages were incubated with HEDkL (100 - 200 µg/mL) before being stimulated. The anti-inflammatory effect was assessed for edema, hypernociception, vascular permeability, leukocyte infiltrate, oxidative stress and inflammatory. Behavioral alterations (exploratory, anxiolytic, depressant activities) were evaluated in the animals treated with HEDkL (50 mg/kg). Results: The HPLC-DAD revealed the presence of ellagic acid, epicatechin and gallic acid. In the paw edema model, HEDkL (50 mg/kg) inhibited the edema late phase (2 - 5h) by 45% and the activity of the enzyme myeloperoxidase by 48%. In the peritonitis model, HEDkL (50 mg/kg) reduced leukocyte migration (45%), hypernociception (73%), total proteins (20%) and NO2-/NO3- (23%). In the air pouch model, HEDkL (50 mg/kg) reduced the migration of total leukocytes (76%) and neutrophils (88%). In vitro HEDkL (200 µg/mL) reduced by 31% the NO2-/NO3- in the supernatant of macrophages. HEDkL did not alter the animals exploratory, anxiolytic, or depressant behaviors. Conclusion: HEDkL containing flavonoids and phenols presents anti-inflammatory effect in vivo and in vitro involving nitric oxide inhibition, being devoid of behavioral alterations.

Packaging and containerization of computational methods.

Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.

179 Clinical and Translational Researchers from Underrepresented Groups Identify the Barriers they Experience

OBJECTIVES/GOALS: Using the NIH’s expanded definition of underrepresented populations in the biomedical, clinical, behavioral and social science research enterprise, we examined the impediments for conducting translational research experienced by those from underrepresented groups. [https://acts.slayte.com/calls/detail/740a13de-316c-11ee-90f4-0e0ce905385c/draft/389221c1-434e-11ee-90f4-0e0ce905385c#_ftn1] #_ftn1 METHODS/STUDY POPULATION: One hundred and ninety-nine people completed a survey distributed to 750 persons who had interacted with our Center’s service cores as users, awardees, mentors, committee members, seminar attendees, and/or participated Center sponsored programming (response rate = 26.5%). The survey addressed barriers to conducting clinical and translational research at the respondent’s institution, awareness of and interest in using specific Advance RI-CTR services, and satisfaction with their institution’s efforts to support clinical and translational research. RESULTS/ANTICIPATED RESULTS: Women reported access to collaboration across institutions as a barrier to clinical and translational research that existed to a great extent (28%) significantly more than men (10%). More than half (53%) of the other underrepresented researchers surveyed identified insufficient grant administration supportas a barrier that occurs to a great extent, compared with 35% of researchers who were not from an underrepresented group. Other barriers reported more frequently among underrepresented researchers included lack of pilot project funding, inadequate space for conducting research, lower access to collaborators across institutions, and difficulty obtaining advice on regulatory issues and commercial development. DISCUSSION/SIGNIFICANCE: Efforts to address the barriers identified by underrepresented groups will include, but not be limited to, improving collaborations across institutions, support for grant administration, and a discussion of plans for the Center to augment and advocate at the partner institutions on behalf of these underrepresented individuals.

Detection and Quantification of Mono-Rhamnolipids and Di-Rhamnolipids Produced by Pseudomonas aeruginosa.

The environmental bacterium Pseudomonas aeruginosa is an opportunistic pathogen with high antibiotic resistance that represents a health hazard. This bacterium produces high levels of biosurfactants known as rhamnolipids (RL), which are molecules with significant biotechnological value but are also associated with virulence traits. In this respect, the detection and quantification of RL may be useful for both biotechnology applications and biomedical research projects. In this article, we demonstrate step-by-step the technique to detect the production of the two forms of RL produced by P. aeruginosa using thin-layer chromatography (TLC): mono-rhamnolipids (mRL), molecules constituted by a dimer of fatty acids (mainly C10-C10) linked to one rhamnose moiety, and di-rhamnolipids (dRL), molecules constituted by a similar fatty acid dimer linked to two rhamnose moieties. Additionally, we present a method to measure the total amount of RL based on the acid hydrolysis of these biosurfactants extracted from a P. aeruginosa culture supernatant and the subsequent detection of the concentration of rhamnose that reacts with orcinol. The combination of both techniques can be used to estimate the approximate concentration of mRL and dRL produced by a specific strain, as exemplified here with the type strains PAO1 (phylogroup 1), PA14 (phylogroup 2), and PA7 (phylogroup 3).

Creating cloud platforms for supporting FAIR data management in biomedical research projects.

Biomedical research projects are becoming increasingly complex and require technological solutions that support all phases of the data lifecycle and application of the FAIR principles. At the Berlin Institute of Health (BIH), we have developed and established a flexible and cost-effective approach to building customized cloud platforms for supporting research projects. The approach is based on a microservice architecture and on the management of a portfolio of supported services. On this basis, we created and maintained cloud platforms for several international research projects. In this article, we present our approach and argue that building customized cloud platforms can offer multiple advantages over using multi-project platforms. Our approach is transferable to other research environments and can be easily adapted by other projects and other service providers.

How to write a “results section” in biomedical scientific research papers?: Critical review

Introduction The “Results section” is a vital organ of a scientific paper, the main reason why readers come and read to find new information in the paper. However, writing the “Results section” demands a rigorous process that discourages many researchers, leaving their work unpublished and uncommunicated in reputable journals. Therefore, this review aims to describe the content, structure, and key standards of writing the “results section” and suggest practical recommendations to reduce common errors in writing the “results section” of manuscripts. Methods We searched the literature using search terms in the PubMed database. We also traditionally searched for literature from “Google Scholars”, “Google”, and “Websites”. We narrated and summarized finding sections as the content, structure, writing and presenting of data, logical flow of, and advised on the writing of the “results section” of the scientific paper. Result The review suggests guidelines for writing the content and organization, techniques of tabular, and graphical presentation of data in the “results section”. The review also suggests experiences on how to effectively present data in numbers such as percentages, statistical measures such as p-values, and other advanced forms of statistics, Finally, the review recommends relevant points to keep language brevity and logical flow in writing the “results section” of a scientific paper. Conclusions Writing a result section of a scientific paper requires practice and it must be concisely written, logically structured, and supported by a good journal-specific standard to be published.

Creating cloud platforms for supporting FAIR data management in biomedical research projects.

Biomedical research projects are becoming increasingly complex and require technological solutions that support all phases of the data lifecycle and application of the FAIR principles. At the Berlin Institute of Health (BIH), we have developed and established a flexible and cost-effective approach to building customized cloud platforms for supporting research projects. The approach is based on a microservice architecture and on the management of a portfolio of supported services. On this basis, we created and maintained cloud platforms for several international research projects. In this article, we present our approach and argue that building customized cloud platforms can offer multiple advantages over using multi-project platforms. Our approach is transferable to other research environments and can be easily adapted by other projects and other service providers.

Scientific misconduct: A cross-sectional study of the perceptions, attitudes and experiences of Spanish researchers

ABSTRACT This study sought to identify the perceptions, attitudes and experiences of Spanish researchers regarding different aspects relating to scientific misconduct, both overall and by gender, years of research experience, and type of research institution. This is a cross-sectional study based on an anonymous online survey, targeting researchers in the field of biomedicine. The survey comprised a first block (13 questions) covering sociodemographic data, and a second block (14 questions) covering researchers’ perceptions, attitudes and experiences. A descriptive analysis was performed. 403 researchers answered the survey: 51.1% (n = 205) women, median age 45 years. The observed frequency of scientific misconduct was 78.8%. Additionally, 43.3% of researchers acknowledged having intentionally engaged in some type of scientific misconduct (self-reported frequency). The most frequent type of scientific misconduct was false authorship. The most frequent types of both observed and self-reported scientific misconduct did not appear to differ by years of experience but did differ by gender and type of research institution. In conclusion, there is a high frequency of scientific misconduct among Spanish biomedical science researchers as 4 of 10 researchers recognized that took part in any type of scientific misconduct. There are differences between the most frequent types of misconduct according to different characteristics, mainly type of institution.

Multisectoral Collaborations to Increase Recruitment and Retention of Diverse Older Adults in Biomedical Research.

Older adults, especially minoritized racial-ethnic groups, are historically underrepresented in biomedical research. This study summarizes the development and assesses the impact of a review board involving a multisectoral group of stakeholders with the goal of increasing the diversity of older adults in biomedical research. A 25-member board of community members, caregivers, researchers, and clinicians from Upstate New York reviewed 3 projects presented by researchers, clinician-scientists, and a pharmaceutical company between January and December 2022. For each biomedical research project, the reviews provided guidance to increase the recruitment and retention of diverse older adults engaged in the study. Review board members and presenters completed surveys to provide feedback on their experience in this collaboration. There was consistent positive feedback from all members and presenters. From member surveys, feedback trended positive in meetings throughout the year. Community members and caregivers initially indicated discomfort in expressing their views; however, these concerns subsided over time. Presenters had a very positive experience in the review board's impact on their recruitment strategy and study design, and therefore very likely to use this service again. Recommendations were made to adjust membership criteria, presentation format, and funding to sustain this effort. Lack of diversity for older adults represented in biomedical research contributes to ethical and generalizability ramifications. The positive feedback from all stakeholders in our multisectoral board of community members, caregivers, researchers, and clinicians offers a promising structure for developing similar strategies to increase diversity within and beyond biomedical aging research in other communities.

Quality evaluation tool for animal experiments and the usage specifications

The animal experiment is the best method for therapeutic efficacy testing of various treatment methods before clinical application and serves as an irreplaceable “live reagent” and “live precise instrument,” thus playing a vital role in biomedical science research. However, there were significant differences between the results of animal experiments and clinical efficacy in previous findings that are hard to ignore, especially in cerebrovascular accident research due to the unsatisfactory specification of animal experiments. Accordingly, more prescriptive and standard tools are required for evaluating the quality of animal experiments. This study will introduce the current commonly used quality evaluation tools for animal experiments.

Evaluation of an 8-week high school science communication course designed to read, write, and present scientific research.

The development of science writing and presentation skills are necessary for a successful science career. Too often these skills are not included in pre- or postsecondary STEM education, leading to a disconnect between high schoolers' expectations for college preparedness and the skills needed to succeed in college. The Young Scientist Program (YSP) Summer Focus recruits high school students from historically marginalized backgrounds to participate in eight-week summer internships at Washington University in St. Louis. Students conduct hands-on biomedical research projects under the mentorship of Washington University scientists (graduate students, post-doctorates, lab staff). Here, we present the curriculum for a science communication course that accompanies this early research experience. The course is designed to strengthen students' communication skills (critical reading, writing, presenting, and peer review) through a combination of weekly lectures and active learning methods. It prepares students for the capstone of their summer internship: writing a scientific paper and presenting their results at a closing symposium. We administered pre- and post-program surveys to four Summer Focus cohorts to determine whether the course met its learning objectives. We found significant improvements in students' self-confidence in reading, interpreting, and communicating scientific data. Thus, this course provides a successful model for introducing science literacy and communication skills that are necessary for any career in STEM. We provide a detailed outline of the course structure and content so that this training could be incorporated into any undergraduate and graduate research programs.

Unmasking the Adverse Impacts of Sex Bias on Science and Research Animal Welfare.

Sex bias in biomedical and natural science research has been prevalent for decades. In many cases, the female estrous cycle was thought to be too complex an issue to model for, and it was thought to be simpler to only use males in studies. At times, particularly when studying efficacy and safety of new therapeutics, this sex bias has resulted in over- and under-medication with associated deleterious side effects in women. Many sex differences have been recognized that are unrelated to hormonal variation occurring during the estrous cycle. Sex bias also creates animal welfare challenges related to animal over-production and wastage, insufficient consideration of welfare (and scientific) impact related to differential housing of male vs female animals within research facilities, and a lack of understanding regarding differential requirements for pain recognition and alleviation in male versus female animals. Although many funding and government agencies require both sexes to be studied in biomedical research, many disparities remain in practice. This requires further enforcement of expectations by the Institutional Animal Care and Use Committee when reviewing protocols, research groups when writing grants, planning studies, and conducting research, and scientific journals and reviewers to ensure that sex bias policies are enforced.

Simple models for neuroscience research discoveries: how often are these models used in Africa?

Background: Simple animal model systems such as Drosophila, Caenorhabditis Elegans and Zebrafish have enabled numerous breakthroughs in understanding human health and disease. Owing to their cheap maintenance cost, adopting these model systems will improve research in Africa. However, the extent to which these models are used across Africa is unknown. This study aimed to identify how often these models are used in Africa. Methods: We downloaded all the PUBMED-indexed publications from the year 2000 to 2021 that have an African affiliation and have mentioned Drosophila, C. elegans or Zebrafish. We manually curated the information on the experimental use of these model systems, author affiliations and details of funding from research publications. Descriptive statistics was used to describe the major hotspots for the use of the model systems and funders, and the pattern of local and international collaborations. Results: Of the 1851 publications in which at least one of the models was mentioned, only 168 used at least one for the actual investigation. With an average of 21 articles per country, South Africa, Nigeria, Kenya, Egypt, Morocco, and Tunisia contributed 75% of these studies. The remaining 25% were contributed by seven other countries. Analysis of funding information revealed that 24.4% of the studies were exclusively locally funded, 28.57% exclusively internationally funded, 15.5% received both local and international funding, and the rest (31.5%) were unfunded, revealing that there is satisfactory access to funds for simple animal model studies, especially from external funders. By analysing the pattern of collaborations, we show that collaborations with researchers from other continents predominate over intra-Africa collbaorations. Conclusions: Our work provides data on the current state of research using simple model systems in African laboratories and argues that incorporating these models will advance biomedical science research in Africa.

Mass spectrometry as a lens into molecular human nutrition and health.

Mass spectrometry (MS) has developed over the last decades into the most informative and versatile analytical technology in molecular and structural biology (). The platform enables discovery, identification, and characterisation of non-volatile biomolecules, such as proteins, peptides, DNA, RNA, nutrients, metabolites, and lipids at both speed and scale and can elucidate their interactions and effects. The versatility, robustness, and throughput have rendered MS a major research and development platform in molecular human health and biomedical science. More recently, MS has also been established as the central tool for 'Molecular Nutrition', enabling comprehensive and rapid identification and characterisation of macro- and micronutrients, bioactives, and other food compounds. 'Molecular Nutrition' thereby helps understand bioaccessibility, bioavailability, and bioefficacy of macro- and micronutrients and related health effects. Hence, MS provides a lens through which the fate of nutrients can be monitored along digestion via absorption to metabolism. This in turn provides the bioanalytical foundation for 'Personalised Nutrition' or 'Precision Nutrition' in which design and development of diets and nutritional products is tailored towards consumer and patient groups sharing similar genetic and environmental predisposition, health/disease conditions and lifestyles, and/or objectives of performance and wellbeing. The next level of integrated nutrition science is now being built as 'Systems Nutrition' where public and personal health data are correlated with life condition and lifestyle factors, to establish directional relationships between nutrition, lifestyle, environment, and health, eventually translating into science-based public and personal heath recommendations and actions. This account provides a condensed summary of the contributions of MS to a precise, quantitative, and comprehensive nutrition and health science and sketches an outlook on its future role in this fascinating and relevant field.

Assessment of diversity-based approaches used by American Universities to increase recruitment and retention of biomedical sciences research faculty members: A scoping review protocol.

Diversity enriches the educational experience by improving intellectual engagement, self-motivation, citizenship, cultural engagement, and academic skills like critical thinking, problem-solving, and writing for students of all races. Faculty role models from similar backgrounds are essential for students from traditionally underrepresented groups as it sends a powerful message of support, belonging, and the confidence to pursue higher education. However, in the biomedical sciences, the percentage of historically underrepresented tenure-track faculty is far lower than that of their white colleagues. For this to change, a strong strategic plan and commitment from the university are imperative. This scoping review will assess the size and scope of available peer-reviewed research literature on diversity programs that aim to increase the recruitment and retention of biomedical sciences research faculty and are implemented and evaluated at American Universities. The information provided in this scoping review will help universities identify novel, successful diversity-based approaches for recruiting and retaining biomedical science faculty that might suit their own unique academic and geographic needs and be incorporated into their diversity initiatives and policies. The review follows the Population-Concept-Context methodology for Joanna Briggs Institution Scoping Reviews. Relevant peer-reviewed studies published in English between June 1, 2012, to June 1, 2022, will be identified from the following electronic databases; MEDLINE (PubMed), Scopus (Elsevier), EMBASE (Elsevier), CINAHL (EBSCO), and ERIC (EBSCO). The search strings using the key variables "biomedical research faculty," "recruitment/retention," "diversity/ minority/ underrepresented, and "mentoring" will be conducted using Boolean logic. Two independent reviewers will conduct all title and abstract screening, followed by a full article screening and data extraction. Due to the possible heterogeneity of the studies, we hope to use either a narrative analysis and/or descriptive figures/tables to depict the results.

Securing Aggregate Queries for DNA Databases

Abstract: This paper addresses the problem of sharing person-specific genomic sequences without violating the privacy of their data subjects to support large- scale biomedical research projects. The proposed method builds on the framework but extends the results in a number of ways. One improvement is that our scheme is deterministic, with zero probability of a wrong answer. We also provide a new operating point in the space-time tradeoff, by offering a scheme that is twice as fast as theirs but uses twice the storage space. This point is motivated by the fact that storage is cheaper than computation in current cloud computing pricing plans. Moreover, our encoding of the data makes it possible for us to handle a richer set of queries than exact matching between the query and each sequence of the database, including: (i) counting the number of matches between the query symbols and a sequence; (ii) logical OR matches where a query symbol is allowed to match a subset of the alphabet thereby making it possible to handle a "not equal to" requirement for a query symbol (iii) support f for the extended alphabet of nucleotide base codes that encompasses ambiguities in DNA sequences (iv) queries that specify the number of occurrences of each kind of symbol in the specified sequence positions (v) a threshold query whose answer is 'yes' if the number of matches exceeds a queryspecified threshold. (vi) For all query types we can hide the answers from the decrypting server, so that only the client learns the answer. (vii) In all cases, the client deterministically learns only the query's answer, except for query type (v) where we quantify the (very small) statistical leakage to the client of the actual count.

Knowledge-integrated research is more disruptive when supported by homogeneous funding sources: a case of US federally funded research in biomedical and life sciences

Knowledge-integrated research is more disruptive when supported by homogeneous funding sources: a case of US federally funded research in biomedical and life sciences

Plant-Derived Exosome-like Nanoparticles for Biomedical Applications and Regenerative Therapy.

Plant-derived exosome-like nanoparticles (PDENs) comprise various bioactive biomolecules. As an alternative cell-free therapeutic approach, they have the potential to deliver nano-bioactive compounds to the human body, and thus lead to various anti-inflammatory, antioxidant, and anti-tumor benefits. Moreover, it is known that Indonesia is one of the herbal centers of the world, with an abundance of unexplored sources of PDENs. This encouraged further research in biomedical science to develop natural richness in plants as a source for human welfare. This study aims to verify the potential of PDENs for biomedical purposes, especially for regenerative therapy applications, by collecting and analyzing data from the latest relevant research and developments.

DECIPHERING THE ROLE OF GENE EDITING: RETORT FOR PERPLEXED UNHEALTHY AND DISEASED CONDITIONS

A breakthrough approach that unleashed the function of bacterial nucleases and the engineered ones has prompted the Creation of innovative gene editing technologies and procedures. In practically all eukaryotic cells, puzzled unclear Situations can be resolved by directly addressing certain genomic sequences and modifying them for use in various tactics. This expanding field of research has made this possibility possible. The ability to detect unique phenomena linked to the Genetic and epigenetic variables driving the development of disease have been enhanced through genome editing. It has majorly promoted the way for creating more precise cellular and animal models for elucidating pathological pathways and has shown remarkable potential in varying fields such as biotechnology, crop engineering, and biomedical science research Is under way. The creation of sophisticated methods based on nucleases, such as those connected to the CRISPR system, such as zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), and CRISPR-Cas-Associated nucleases, has greatly enhanced their practical utility in designing most promising biotechniques. Surprisingly, The applications of genome editing are leading to a variety of therapeutic and therapy options. This review will focus on Some applications and research that have revealed their implementation and strategies. Keywords: Epigenetic, Biotechnology, CRISPR, ZFN, TALENs, Nucleases. Cite this article- Shweta Sharma, Parul Singh, AkshitaTiwari, Faizan ul Haque, Vijaylaxmi Tripathi, Nupur Raghav, Shweta Sharma, Priyambada Kumari, 2023, “Deciphering the Role of Gene Editing: Retort for Perplexed Unhealthy and Diseased Conditions” journal of Science Innovations and Nature of Earth, Vol. 3(1), page- 46-51 www.doi.org/10.59436/https://jsiane.com/archives3/12/73