Biomedical Disciplines Research Articles

A General Perspective of Microbiota in Human Health and Disease

The study of human microbiome is widely perceived to be a young biomedical discipline. Recent studies indicate an association between human microbiome and chronic disease conditions such as diabetes and obesity. An understanding of human microbiome structure and function is important for design and delivery of microbial based therapies especially against immunological and metabolic chronic diseases. In this review, we demonstrate the role human microbiota in health and disease in various anatomic sites and in development of neonate immunity. In particular, the review focuses on the role of placental microbiota in fetoplacental unit receptivity and the effect of early microbiota exposure on neonate immunity development. Additionaly, microbiota impact on health and disease in the gut, lung and skin is explored.

Анализ зарубежного опыта подготовки кадров для фармацевтической отрасли в Евросоюзе

The article is concerned with the system of higher pharmaceutical education in the European Union countries. The analysis has allowed to establish that there is no single curriculum in the training system of pharmaceutical specialists; the curriculum content also has significant differences. For historical reasons, there have been three groups of countries characterized by a different approach to pharmaceutical education: the first group includes countries of Central and Eastern Europe and Scandinavia, where the chemical sciences lie at the root of training of pharmaceutical specialists; the second group is represented by the Franco-Italian-Spanish school, where the priority is given to biomedical disciplines; the third group includes countries, where training is carried out according to the traditions of the English pharmaceutical school. This determines the contradictions in the world practice of training of pharmaceutical personnel. There are significant discrepancies in terms, curricula, academic disciplines, degrees. At the present stage, there have not yet been created any transnational standards for the training of pharmacists, which significantly complicates the training, recognition of diplomas and qualifications at the interstate level.

Использование метода плантографии при изучении медико-биологических дисциплин

The learning process includes a variety of research methods, varying degrees of complexity and importance, which are required by a person in a variety of spheres of life. The article scientifically substantiates the use of a complex method of plantography in the process of teaching biomedical disciplines to determine the functional parameters of the human foot arch. Application of the plantography method in practical classes of the discipline "Human Physiology" will increase interest in learning, since the determination of individual state parameters of the musculoskeletal system will allow students not only to expand the range of knowledge of the physiological profile, but also to develop their skills of research conduct. In the course of our research, the indicators of the condition of students’ foot arch in different modes of loading were identified. The analysis of the results allowed us to determine the so-called "risk group": a group of students who under the influence of the load demonstrated static forms of deformation of the foot arch, while there is a transition of the foot index from one qualitative evaluation zone to another, from "normal" to the category: "flattened", "slightly flattened" and "flat". Therefore, increasing the load on the foot arch leads to a decrease in its springing capabilities. Thus, the data of individual parameters of the foot index obtained by students during the research work in practical classes can contribute to the correct distribution of students in medical groups for physical education. Keywords: plantography, human foot arch, risk groups, research activities.

HNCcorr: combinatorial optimization for neuron identification

We present a combinatorial algorithm for cell detection in two-photon calcium imaging. Calcium imaging is a modern technique used by neuroscientists for recording movies of in-vivo neuronal activity at cellular resolution. The proposed algorithm, named HNCcorr, builds on the combinatorial clustering problem Hochbaum’s Normalized Cut (HNC). HNC is a model that trades off two goals: One goal is that the cluster has low similarity to the remaining objects. The second goal is that the cluster is highly similar to itself. The HNC model is closely related to the Normalized Cut problem of Shi and Malik, a well-known problem in image segmentation. However, whereas Normalized Cut is an NP-hard problem, HNC is solvable in polynomial time. The neuronal cell detection in calcium imaging movies is viewed here as a clustering problem. HNCcorr utilizes HNC to detect cells in these movies as coherent clusters of pixels that are highly distinct from the remaining pixels. HNCcorr guarantees, unlike existing methodologies for cell identification, a globally optimal solution to the underlying optimization problem. Of independent interest is a novel method, named similarity-squared, that is devised here for measuring similarity. In an experimental study on data from the Neurofinder cell identification benchmark, HNCcorr is a top performer. In particular, it achieves a higher average score than two frequently used matrix factorization algorithms. The Python and Matlab implementations of HNCcorr used here are publicly available. The use of HNCcorr demonstrates that combinatorial optimization is a valuable tool for neuroscience and other biomedical disciplines.

Comparing Bibliometric Analysis Using PubMed, Scopus, and Web of Science Databases.

Literature databases (i.e., PubMed, Scopus, and Web of Science) differ in terms of their coverage, focus, and the tool they provide. PubMed focuses mainly on life sciences and biomedical disciplines, whereas Scopus and Web of Science are multidisciplinary. The protocol described in the current study was used to search for publications from Jordanian authors in the years 2013-2017. In this protocol, how to use each database to conduct this type of search is explained in detail. A Scopus search resulted in the highest number of documents (11,444 documents), followed by a Web of Science search (10,943 documents). PubMed resulted in a smaller number of documents due to its narrower scope and coverage (4,363 documents). The results also show a yearly trend in: (1) the number of publications, (2) the disciplines that have the most publications, (3) the countries of collaboration, and (4) the number of open access publications. In contrast, PubMed has a sophisticated keyword optimization service (i.e., Medical Subject Heading, or MeSH), while both Scopus and Web of Science provide search analysis tools that can produce representative figures. Finally, the features of each database are explained in detail and several indices that can be extracted using the search results are provided. This study provides a base for using literature databases for bibliometric analysis.

Relating the small world coefficient to the entropy of 2D networks and applications in neuromorphic engineering

The study of networks pervades science. The techniques of networks are recently being applied to biomedical disciplines, where the complexity of biomedical systems requires new schemes that can process elevated volumes of data with high efficiency. Artificial neural networks, on which much of artificial intelligence relies, are statistical models partially modeled on biological neural networks. They are capable of modeling and processing nonlinear relationships between inputs and outputs in parallel—in opposition to deterministic models and classical computation schemes, which perform tasks in linear sequences of calculations and may fail to keep up with the challenges of complex biological systems. For these biological or bio-inspired systems, the performance of the networks depends on their topological characteristics. Here, we generated a large number of configurations of points in a plane, in which the entropy s of the configurations was varied over large intervals. Then, we connected points using the Waxman model to obtain the corresponding networks. In correlating the entropy (s) to the small-world coefficient () of those networks, we found that SW varies hyperbolically with s as SW = 0.88 + 0.28/s, where s is expressed in millibits per node. Since the entropy of a distribution of points depends in turn on the density of those points in the plane, such a relationship suggests that the distribution of mass () in a complex system determines the topological characteristics () of that system. The small-world-ness of the system, in turn, determines its information efficiency. These findings may have implications in neuromorphic engineering, where chips modeled on biological brains may lead to machines that are able, as for some examples, to diagnose diseases, develop drugs and drug delivery systems faster, design personalized treatments targeted to patient’s needs.

Perspectives From Authors and Editors in the Biomedical Disciplines on Predatory Journals: Survey Study.

BackgroundPredatory journals fail to fulfill the tenets of biomedical publication: peer review, circulation, and access in perpetuity. Despite increasing attention in the lay and scientific press, no studies have directly assessed the perceptions of the authors or editors involved.ObjectiveOur objective was to understand the motivation of authors in sending their work to potentially predatory journals. Moreover, we aimed to understand the perspective of journal editors at journals cited as potentially predatory.MethodsPotential online predatory journals were randomly selected among 350 publishers and their 2204 biomedical journals. Author and editor email information was valid for 2227 total potential participants. A survey for authors and editors was created in an iterative fashion and distributed. Surveys assessed attitudes and knowledge about predatory publishing. Narrative comments were invited.ResultsA total of 249 complete survey responses were analyzed. A total of 40% of editors (17/43) surveyed were not aware that they were listed as an editor for the particular journal in question. A total of 21.8% of authors (45/206) confirmed a lack of peer review. Whereas 77% (33/43) of all surveyed editors were at least somewhat familiar with predatory journals, only 33.0% of authors (68/206) were somewhat familiar with them (P<.001). Only 26.2% of authors (54/206) were aware of Beall’s list of predatory journals versus 49% (21/43) of editors (P<.001). A total of 30.1% of authors (62/206) believed their publication was published in a predatory journal. After defining predatory publishing, 87.9% of authors (181/206) surveyed would not publish in the same journal in the future.ConclusionsAuthors publishing in suspected predatory journals are alarmingly uninformed in terms of predatory journal quality and practices. Editors’ increased familiarity with predatory publishing did little to prevent their unwitting listing as editors. Some suspected predatory journals did provide services akin to open access publication. Education, research mentorship, and a realignment of research incentives may decrease the impact of predatory publishing.

Eine kurze Einführung in die Chronobiologie A short introduction to Chronobiology.

Chronobiology is a thriving research field that spans all biomedical disciplines ranging from molecular biology and metabolism to psychology and internal medicine. Circadian rhythms are generated at the molecular level in practically all cells of the body. This ensemble of clocks forms the "circadian system" that coordinates every aspect of our biology on a daily basis-from the cells, tissues and organs up to the concerted regulation of metabolism or higher functions like sleep-wake behaviour, immune responses or cognition. With the help of a "master clock" in the brain, the mammalian circadian system actively synchronises (entrains) to light and darkness via the eyes. Industrialisation and urbanisation have drastically changed the way we expose ourselves to light and darkness and consequently how our clocks entrain. These changes led to the modern syndrome of social jetlag, a misalignment between circadian and social time. In most of us, the circadian clock is so delayed that we have to interrupt our natural sleep with an alarm clock to be awake for work/school schedules. Shift-workers suffer from the most extreme form of social jetlag. A growing body of studies show that this misalignment is associated with health deficits including various metabolic, cardiovascular and psychiatric syndromes and even increased cancer risks.

Infant feeding: a selective review and research needs

Growth faltering starting in infancy can be considered the onset of malnutrition. Infant feeding practices as well as a high prevalence of infectious diseases are causal in this process. While general recommendations on infant feeding are useful as guidelines, it is futile to attempt univorm recommendations as good feeding practices are bound to differ by community.&#x0D; It is felt that the biomedical and social science discipline should investigate the factors influencing infant feeding as well as the consequences of habitual practices on infant health and survival.

Three-Dimensional Microwave-Induced Thermoacoustic Imaging Based on Compressive Sensing Using an Analytically Constructed Dictionary

Microwave-induced thermoacoustic imaging (MITAI) has found diversified applications in biomedical related disciplines and holds the potential to serve as an auxiliary measure for diagnosis and treatment in clinics. Conventional imaging algorithms for MITAI, for example, back-projection (BP), require exceedingly intensive sampling of thermoacoustic signals stemming from a sample under test, and thus, suffer from deficiencies such as low time efficiency, high system cost, and more microwave radiation received by patients. Combining compressive sensing (CS) and MITAI, referred to as CS-MITAI, is promising to address the problem. Reported experiments in two dimensions and simulations in three dimensions (3D) have proved that the CS-MITAI approach can reliably reconstruct images with much fewer measurements than the BP algorithm. However, there is a pressing need for the experimental validation of the CS-MITAI technique in a real three-dimensional (3-D) environment, which has profound implications for its practical applications and further improvement. This article experimentally investigates the 3-D CS-MITAI technique by imaging a sample with 3-D features. Establishment of a dictionary is crucial for the successful implementation of the 3-D CS-MITAI approach. An analytical method is proposed to build the dictionary with much higher efficiency than other reported measures, and its detailed derivation is provided. In addition, modeling work and parametric studies are performed to explore the robustness of the 3-D CS-MITAI mechanism in dealing with different cases. Both simulation and experimental results show that the 3-D CS-MITAI modality can offer comparable imaging quality as the BP method but requires 200 and 68 times fewer measurements, respectively.

Vibration‐Induced Emission (VIE) of N,N′‐Disubstituted‐Dihydribenzo[a,c]phenazines: Fundamental Understanding and Emerging Applications

AbstractOrganic fluorophores with dual‐emission and large Stokes shifts are attracting great attention due to their importance in fundamental research and technique applications. This Progress Report gives an account on how a novel luminescence mechanism termed vibration‐induced emission (VIE) is established. The VIE mechanism is coined for the rationalization of an alterable dual emission of V‐shaped N,N′‐disubstituded‐dihydribenzo[a,c]phenazines (DHPs), which are originated from a bent‐to‐planar vibration and the reverse in the excited state. The validation of the VIE mechanism is highlighted, such as the work reporting the utilization of chemically‐locked strategy to snapshot the excited‐state planarization of DHPs, and the application of the approach of steric hindrance‐induced planarization to tune the ground‐state geometry of DHPs. Moreover, the emerging applications of this VIE concept in photoelectric and biomedical disciplines are summarized. Additionally, further development of the VIE systems as well as the remaining challenges are prospected. This report could arouse wide interest from various fields to the specific area of VIE, which would not only broaden the VIE territory but also enlarge the scope of advanced functional materials.

Is ‘decolonisation’ a legitimate and appropriate value in biomedical research and teaching?

This article investigates the claim that decolonisation is an appropriate and legitimate value in the process of current-day biomedical research, particularly in Africa. Can we expect that the nature and effects of the decolonisation of research will be comparable and similar for all scientific disciplines (obviously including the biomedical disciplines), or does the claim to significant differences between the ‘natural’ and ‘human’ sciences have notable implications for our understanding of both the nature and the effects of decolonisation, as well as for our understanding of the biomedical disciplines themselves? In this article I firstly analyse the notion of decolonisation. Secondly, I investigate the legitimacy of holding and maintaining a conceptual difference between the natural and the human sciences. I do this in conversation with Charles Taylor and Jurgen Habermas, who have produced invaluable contributions in this regard. Thirdly, I apply these insights to the question as to whether the decolonialist project (the general legitimacy of which I accept) is equally applicable to both the natural and the human sciences in their traditional formats. Finally, I discuss the relevance of this debate for both the nature of the biomedical sciences and the question as to the extent to which the biomedical sciences can and ought to be successfully decolonised – a question that is answered in the affirmative.

Accurate wisdom of the crowd from unsupervised dimension reduction

Wisdom of the crowd, the collective intelligence from responses of multiple human or machine individuals to the same questions, can be more accurate than each individual and improve social decision-making and prediction accuracy. Crowd wisdom estimates each individual’s error level and minimizes the overall error in the crowd consensus. However, with problem-specific models mostly concerning binary (yes/no) predictions, crowd wisdom remains overlooked in biomedical disciplines. Here we show, in real-world examples of transcription factor target prediction and skin cancer diagnosis, and with simulated data, that the crowd wisdom problem is analogous to one-dimensional unsupervised dimension reduction in machine learning. This provides a natural class of generalized, accurate and mature crowd wisdom solutions, such as PCA and Isomap, that can handle binary and also continuous responses, like confidence levels. They even outperform supervised-learning-based collective intelligence that is calibrated on historical performance of individuals, e.g. random forest. This study unifies crowd wisdom and unsupervised dimension reduction, and extends its applications to continuous data. As the scales of data acquisition and processing rapidly increase, especially in high-throughput sequencing and imaging, crowd wisdom can provide accurate predictions by combining multiple datasets and/or analytical methods.

Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1.

CRISPR-Cas gene editing holds substantial promise in many biomedical disciplines and basic research. Due to the important functional implications of non-histone chromosomal protein HMG-14 (HMGN1) in regulating chromatin structure and tumor immunity, gene knockout of HMGN1 is performed by CRISPR in cancer cells and the following proteomic regulation events are studied. In particular, DIA mass spectrometry (DIA-MS) is utilized, and more than 6200 proteins (protein- FDR 1%) and more than 82000 peptide precursors are reproducibly measured in the single MS shots of 2 h. HMGN1 protein deletion is confidently verified by DIA-MS in all of the clone- and dish- replicates following CRISPR. Statistical analysis reveals 147 proteins change their expressions significantly after HMGN1 knockout. Functional annotation and enrichment analysis indicate the deletion of HMGN1 induces histone inactivation, various stress pathways, remodeling of extracellular proteomes, cell proliferation, as well as immune regulation processes such as complement and coagulation cascade and interferon alpha/ gamma response in cancer cells. These results shed new lights on the cellular functions of HMGN1. It is suggested that DIA-MS can be reliably used as a rapid, robust, and cost-effective proteomic-screening tool to assess the outcome of the CRISPR experiments.

Massive volumetric imaging of cleared tissue: The necessary tools to be successful.

Recent technological innovations in high-speed microscopes, tissue clearing methods, optics and computation have made it possible to image enormous biologic volumes. These techniques are applicable to a broad range of biomedical disciplines and are becoming a necessary tool for exploring biologic systems that extend beyond cellular microenvironments to entire organs and organisms. Here we broadly discuss the tool sets that are available for cleared tissue imaging and how various choices may influence the planning and feasibility of an experiment.

CRISPR/Cas9 as a tool to dissect cancer mutations.

The CRISPR/Cas9 system is transforming many biomedical disciplines, including cancer research. Through its flexible programmability and efficiency to induce DNA double strand breaks it has become straightforward to introduce cancer mutations into cells in vitro and/or in vivo. However, not all mutations contribute equally to tumorigenesis and distinguishing essential mutations for tumor growth and survival from biologically inert mutations is cumbersome. Here we present a method to screen for the functional relevance of mutations in high throughput in established cancer cell lines. We employ the CRISPR/Cas9 system to probe cancer vulnerabilities in a colorectal carcinoma cell line in an attempt to identify novel cancer driver mutations. We designed 100 high quality sgRNAs that are able to specifically cleave mutations present in the colorectal carcinoma cell line RKO. An all-in-one lentiviral library harboring these sgRNAs was then generated and used in a pooled screen to probe possible growth dependencies on these mutations. Genomic DNA at different time points were collected, the sgRNA cassettes were PCR amplified, purified and sgRNA counts were quantified by means of deep sequencing. The analysis revealed two sgRNAs targeting the same mutation (UTP14A: S99delS) to be depleted over time in RKO cells. Validation and characterization confirmed that the inactivation of this mutation impairs cell growth, nominating UTP14A: S99delS as a putative driver mutation in RKO cells. Overall, our approach demonstrates that the CRISPR/Cas9 system is a powerful tool to functionally dissect cancer mutations at large-scale.

Peculiarities of teaching foreign students at the Department of the normal physiology of Vinnytsia National Pirogov’ Memorial Medical University

The features of teaching normal physiology in the medical university of English-speaking students of the medical faculty are presented. It reveals the methodological approaches to the organization of teaching foreign students in the course of their receiving higher education in Ukrainian universities, discusses the basic principles and content of the organization of the educational process, taking into account the specifics of the contingent of students. Topical issues of organizing the process of teaching foreign students to medical specialities are considered. The private experience of teaching normal physiology in English to foreign students by teachers of our department is summarized. The analysis of factors affecting the effectiveness of the learning process was carried out. The features of the organization of this process are considered on the example of Vinnitsa national Pirogov’ memorial medical university. Detailed problem analysis will help to systematize and optimize the teaching and examination of knowledge of this kind of students. The use of innovative technologies in the teaching of foreign students can solve a number of both instructional and extracurricular tasks stay of foreign students in Ukraine; and it is the most optimal system of teaching biomedical disciplines in medical high school. A number of reasons are given that reduce the intensity of teaching to foreign students, the main ones being the different level of their linguistic training and educational base, lack of motivation, difficulty with discipline.

Strategic Talent Management: Implementation and Impact of a Leadership Development Program in Radiology

The rapidity of change and increasing complexity of the academic medical center environment require a talented and engaged workforce with competencies in adaptability, capacity for working in empowered and diverse interprofessional teams, and self-efficacy. Radiology—a crosscutting field that interfaces with most other biomedical disciplines and that is often at the forefront of technological disruption—is a potentially ideal venue to focus professional and leadership development to create positive organizational value. In this report, we detail the design of and 9-year experience with a departmental leadership academy at a large academic center intended to foster team-based skills in early to midcareer faculty and staff. Over the past decade, 100 participants have completed the program with 80% retention, substantial professional growth, and increased capacity for mentoring others. This in-house, customized leadership development program is aligned with our strategic and cultural imperative to promote nimble, engaged, and empowered teams in a diverse and inclusive setting.

Transforming a cookbook undergraduate microbiology laboratory to inquiry based using a semester-long PBL case study.

Microbial physiology is a basic course taught throughout biomedical science disciplines. Students study the structure, growth, and metabolism of microorganisms and often find it difficult to learn the information, usually because they fail to see the wider applications. The current microbiology laboratory series describes how to transform a "cookbook" undergraduate laboratory to an inquiry-based one by incorporating problem-based learning. The students use a food poisoning case study that develops over a series of seven experiments and take on the role of the microbiology technician who is responsible for coming up with the answer and submitting a report to a clinician. The case provides coherence to the sessions, and the students are given the opportunity to learn about, and practice, common techniques they would encounter in a clinical microbiology laboratory. Those include the aseptic method, cultivation of bacteria, quantification of bacteria in culture, isolation of pure culture, morphological observation by light microscopy, Gram staining, the use of selective and differential media, and the effectiveness of a variety of antimicrobials and antibiotics. This laboratory series has been designed so that it can be implemented in any setting, using simple materials and inexpensive, nonspecialized equipment. The experiments are carried out in small groups, and a facilitator may tutor up to two groups of 10 students at a time. The current method has been successfully implemented for the past 2 yr, and the students demonstrated greater motivation in learning and understanding.

Sex still matters: has the prevalence of male-only studies of drug effects on rodent behaviour changed during the past decade?

During the past 10 years, for a number of biomedical disciplines, including behavioural pharmacology, there have been appeals to include both sexes in animal studies of processes that are not sex specific. In 2007, a survey of experimental studies of drug or other chemical effects on rodent behaviour, published in five prominent journals over 20 months (February 2005 to September 2006, inclusive), revealed that 85% of these conducted with rats and 78% of these conducted with mice involved males only. This was in spite of the evidence of sex differences in responsiveness to an increasing number of compounds. To see if the situation has improved, the survey was repeated with the same journals for a comparable period namely, February 2016 to September 2017 (inclusive). Even though there have been repeated appeals for biomedical research that is not sex specific to involve both sexes, it was apparent that little has changed since 2005-2006, as 82% of rat and 75% of mouse studies were again conducted with males only. However, there was an increase in studies with mice, which may be owing to a greater interest in genetic factors. The male-only situation could be rectified by appropriate funding agencies and journals that publish behavioural pharmacological research insisting that both sexes must be included in research that is not sex specific along with valid scientific justification for single-sex studies, as now typifies some other disciplines.