Biobanks and biomarkers:Their current and future role in biomedical research

The importance and utility of biobanks has increased exponentially since their inception and creation.Initially used as part of translational research,they now contribute over 40%of data for all cancer research papers in the United States of America and play a crucial role in all aspects of healthcare.Multiple classification systems exist but a simplified approach is to either classify as population-based or disease-oriented entities.Whilst historically publicly funded institutions,there has been a significant increase in industry funded entities across the world which has changed the dynamic of biobanks offering new possibilities but also new challenges.Biobanks face legal questions over data sharing and intellectual property as well as ethical and sustainability questions particularly as the world attempts to move to a low-carbon economy.International collaboration is required to address some of these challenges but this in itself is fraught with complexity and difficulty.This review will examine the current utility of biobanks in the modern healthcare setting as well as the current and future challenges these vital institutions face.

Co-occurrence of Cell Lines, Basal Media and Supplementation in the Biomedical Research Literature

Purpose: The use of in vitro cell culture and experimentation is a cornerstone of biomedical research, however, more attention has recently been given to the potential consequences of using such artificial basal medias and undefined supplements. As a first step towards better understanding and measuring the impact these systems have on experimental results, we use text mining to capture typical research practices and trends around cell culture.Design/methodology/approach: To measure the scale of in vitro cell culture use, we have analyzed a corpus of 94,695 research articles that appear in biomedical research journals published in ScienceDirect from 2000–2018. Central to our investigation is the observation that studies using cell culture describe conditions using the typical sentence structure of cell line, basal media, and supplemented compounds. Here we tag our corpus with a curated list of basal medias and the Cellosaurus ontology using the Aho-Corasick algorithm. We also processed the corpus with Stanford CoreNLP to find nouns that follow the basal media, in an attempt to identify supplements used. Findings: Interestingly, we find that researchers frequently use DMEM even if a cell line's vendor recommends less concentrated media. We see long-tailed distributions for the usage of media and cell lines, with DMEM and RPMI dominating the media, and HEK293, HEK293 T, and HeLa dominating cell lines used. Research limitations: Our analysis was restricted to documents in ScienceDirect, and our text mining method achieved high recall but low precision and mandated manual inspection of many tokens.Practical implications: Our findings document current cell culture practices in the biomedical research community, which can be used as a resource for future experimental design.Originality/value: No other work has taken a text mining approach to surveying cell culture practices in biomedical research.

Auricular Acupuncture and Biomedical Research——A Promising Sino-Austrian Research Cooperation

Treatment by auricular acupuncture has a long history. Ear-acupoint research has been advancing step by step in China and also in Europe. Auricles are rich in nerves, therefore a close relationship with different functions of the human body has been proved by the research teams of the two main authors of this article from China and Austria. In recent years, great progress has been made in the research of regulating human body functions through electroacupuncture at the auricular branch of the vagus nerve, which is part of auricular acupuncture therapy. It is well known that the auricular branch of the vagus nerve is the only peripheral pathway to the cerebral cortex. Studies of the Chinese team on hypertension, diabetes, epilepsy and depression have shown that the mechanism of auricular vagus nerve stimulation （VNS） may be comparable with cervical VNS in terms of pathways. Auricular VNS has a broad clinical application prospect.

The Content of Statistical Requirements for Authors in Biomedical Research Journals

Background：Robust statistical designing,sound statistical analysis,and standardized presentation are important to enhance the quality and transparency of biomedical research.This systematic review was conducted to summarize the statistical reporting requirements introduced by biomedical research journals with an impact factor of 10 or above so that researchers are able to give statistical issues＇ serious considerations not only at the stage of data analysis but also at the stage of methodological design.Methods：Detailed statistical instructions for authors were downloaded from the homepage of each of the included journals or obtained from the editors directly via email.Then,we described the types and numbers of statistical guidelines introduced by different press groups.Items of statistical reporting guideline as well as particular requirements were summarized in frequency,which were grouped into design,method of analysis,and presentation,respectively.Finally,updated statistical guidelines and particular requirements for improvement were summed up.Results：Totally,21 of 23 press groups introduced at least one statistical guideline.More than half of press groups can update their statistical instruction for authors gradually relative to issues of new statistical reporting guidelines.In addition,16 press groups,covering 44 journals,address particular statistical requirements.The most of the particular requirements focused on the performance of statistical analysis and transparency in statistical reporting,including ＂address issues relevant to research design,including participant flow diagram,eligibility criteria,and sample size estimation,＂ and ＂statistical methods and the reasons.＂ Conclusions：Statistical requirements for authors are becoming increasingly perfected.Statistical requirements for authors remind researchers that they should make sufficient consideration not only in regards to statistical methods during the research design,but also standardized statistical reporting,which would be beneficial in providing stronger evidence and making a greater critical appraisal of evidence more accessible.

Molecular epigenetics: dawn of a new era of biomedical research

At about the same time in 1940s when Erwin Schrdinger published his famous little book What Is Life, which sparked the birth of molecular biology, the term epigenetics was coined by the English biologist Conrad Waddington. The concept of epi-inheritance can be traced back to French naturalist Jean-Baptiste Lamarck’s idea of "inheritance

Data analysis guidelines for single‑cell RNA‑seq in biomedical studies and clinical applications

The application of single-cell RNA sequencing(scRNA-seq)in biomedical research has advanced our understanding of the pathogenesis of disease and provided valuable insights into new diagnostic and therapeutic strategies.With the expansion of capacity for high-throughput scRNA-seq,including clinical samples,the analysis of these huge volumes of data has become a daunting prospect for researchers entering this field.Here,we review the workflow for typical scRNA-seq data analysis,covering raw data processing and quality control,basic data analysis applicable for almost all scRNA-seq data sets,and advanced data analysis that should be tailored to specific scientific questions.While summarizing the current methods for each analysis step,we also provide an online repository of software and wrapped-up scripts to support the implementation.Recommendations and caveats are pointed out for some specific analysis tasks and approaches.We hope this resource will be helpful to researchers engaging with scRNA-seq,in particular for emerging clinical applications.

Artificial Intelligence in Healthcare:Review and Prediction Case Studies

Artificial intelligence(AI)has been developing rapidly in recent years in terms of software algorithms,hardware implementation,and applications in a vast number of areas.In this review,we summarize the latest developments of applications of AI in biomedicine,including disease diagnostics,living assistance,biomedical information processing,and biomedical research.The aim of this review is to keep track of new scientific accomplishments,to understand the availability of technologies,to appreciate the tremendous potential of AI in biomedicine,and to provide researchers in related fields with inspiration.It can be asserted that,just like AI itself,the application of AI in biomedicine is still in its early stage.New progress and breakthroughs will continue to push the frontier and widen the scope of AI application,and fast developments are envisioned in the near future.Two case studies are provided to illustrate the prediction of epileptic seizure occurrences and the filling of a dysfunctional urinary bladder.

Statistical testing and distribution for lead chloride toxicity

Dear Sir, Graca et al.[1]provided an interesting investigationon the toxicity of lead chloride and sperm developmentin mice.However, I would like to make a comment onthe statistical analysis presented.Table 1 and its resultsSuggest that a comparison of treated(experlment) andcontrol mice were undertaken using the t-test.The au-

Dissecting Cohen

Readers of The New England Journal of Medicine may be excused for thinking that there is a good case for, and nogood case against, the use of animals in biomedical research. In October 1986, philosopher Carl Cohen, who is knownfor his principled positions on affirmative action and other issues, published an article in that journal in which heclaimed that there are (only) two kinds of argument against the use of animals in biomedical research. After examiningboth arguments, Cohen concluded that they “deserve definitive dismissal.” In this article, I show that both of Cohen’sattempted refutations fail. Not only has he not laid a glove on the arguments in question;his discussion betrays afundamental misunderstanding of the arguments that he so cavalierly dismisses. Readers of Cohen’s article owe it tothemselves—and, more importantly, to the animals whose use as research subjects Cohen defends—to take anotherlook at the issue.

Acknowledgments

Epilepsy is the most common neurological disorder of the brain that affects people worldwide at any age from newborn to adult. It is characterized by recurrent seizures, which are brief episodes of signs or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. The electroencephalogram, or EEG, is a physiological method to measure and record the electrical

Bridging the Gap:Integration of Artificial Intelligence with Organ-on-Chip(AI-OoC)

.Organ-on-Chip(OoC)has emerged as a revolutionary approach to emulate human organ function-ality in vitro,offering unparalleled insights into physiological processes and disease modeling.The integration of artificial intelligence(AI)with OoC platforms presents a transformative synergy,combining the precision of microscale organ replication with the analytical prowess of intelligent algorithms,is emerging as a transforma-tive force in harnessing the full potential of OoC.This perspective investigates the multifaceted implications of integrating AI with OoC,examining its impact on biomedical research,acknowledging the synergistic po-tential that arises from combining the precision of microscale organ replication with the analytical capabilities of intelligent algorithms,and fostering a future where the intricate workings of the technology and biology.

Mixed methods research in complementary and alternative medicine:a scoping review

OBJECTIVE:To update the current characteristics about the scope and quality of mixed methods research(MMR)in complementary and alternative medicine(CAM)after nearly 10 years.METHODS:A 5-stage approach for conducting a scoping review was adopted.Articles published on the top 10 journals in CAM with the highest impact factor in 2020 were screened for MMR.Information of included articles were extracted,and then synthesized to illustrate the current state.Methodological quality was evaluated according to the Mixed Method Appraisal Tool(MMAT)2018 version.RESULTS:A total of 55(55/2991,2%)articles using mixed methods were retrieved,including 17 medical studies and 38 ethnobotanical studies.We performed an in-depth analysis on the 17 medical studies,which studied cancer,stress,pain,fatigue,exercises,mindfulness intervention,herbal medicine use,art and acupuncture.Thirteen pilot studies applied MMR to evaluate the feasibility of interventions or programs(13/17,76%);phenomenology was inferred as the most common philosophical assumptions(13/17,76%);the most applied type of MMR was convergent design(16/17,94%);integration often took place at integration(12/17,71%).Among the 16 eligible studies for quality appraisal,majority were rated as good(14/16,88%),whereas two studies were rated as poorly described.Primarily,a poor rating was due to incomplete reporting of data analysis and citations in qualitative components;lack of confounder controlling and the sampling strategy in quantitative components;poor description of integration and justification for mixed methods.Comparing with the previous review,fewer MMR were published in 2020 in CAM,but the proportion of studies that clearly reported MMR has increased by 4 times(4%→15%).CONCLUSION:CAM researchers need to realize the benefits that MMR can have on conducting further health care research.Our findings highlight that applying MMR will be helpful to understand the complex dynamics and interdisciplinary nature of complex intervention.In addition,addressing a standardized reporting criteria for MMR is recommended.

Kidney organoids as a promising tool in nephrology

Kidney disease has become a global public health problem affecting over 750 million people worldwide and imposing a heavy economic burden on patients.The complex architecture of the human kidney makes it very difficult to study the pathophysiology of renal diseases in vitro and to develop effective therapeutic options for patients.Even though cell lines and animal models have enriched our understanding,they fail to recapitulate key aspects of human kidney development and renal disease at cellular and functional levels.Organoids can be derived from either pluripotent stem cells or adult stem cells by strictly regulating key signalling pathways.Today,these self-differentiated organoids represent a promising technology to further understand the human kidney,one of the most complex organs,in an unprecedented way.The newly established protocols improved by organ-on-chip and coculture with immune cells will push kidney organoids towards the next generation.Herein,we focus on recent achievements in the application of kidney organoids in disease modelling,nephrotoxic testing,precision medicine,biobanking,and regenerative therapy,followed by discussions of novel strategies to improve their utility for biomedical research.The applications we discuss may help to provide new ideas in clinical fields.

PETG:Applications in Modern Medicine

Polyethylene terephthalate glycol,PETG,is a miscible,transparent thermoplastic known to have strong tensile properties,high ductility,as well as resistance to heat and chemical insults.PETG may be manufactured in several ways,most notably 3D printing modalities.As such,PETG has emerged as a viable biomaterial for a variety of medical applications such as tissue engineering,dentistry,optometry,vascular health,cardiology,orthopedics,neurology,gynecology,and surgery.PETG also serves a valuable role in biomedical research and engineering by offering improvements in cell studies,drug carriers,and anti-bacterial measures.Further medical research and innovation utilizing PETG will better characterize its value as an inexpensive and versatile biomaterial.