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FEBS Open Bio

Wiley

All preprints, ranked by how well they match FEBS Open Bio's content profile, based on 29 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

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FUNCTIONAL AGEING: A Science-Technology-Society Approach to teach Ageing and Age-related Diseases

Hande, P.; Ng, G.; Rajeev, V.; Selvaraji, S.; Mallilankaraman, K.

2023-05-26 scientific communication and education 10.1101/2023.05.25.538223 medRxiv
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PurposeAgeing is a complex biological process that involves numerous genes and pathways. Experimental studies have identified several of these genes and pathways that that can extend or shorten an individuals lifespan. Understanding these genes and pathways can help develop interventions that improve health and quality of life of older people. Nonetheless, as the global population continues to age, it is essential to comprehend the ageing processs impact on society. Functional age is defined as a combination of chronological, biological, and psychological ages. An educational course called "Functional Ageing" was created for life science students at the National University of Singapore (NUS) during the academic year 2016-2017. The module adopted an interdisciplinary approach based on science-technology-society (STS) methodology and aimed to equip students with the analytical tools needed to assess the ageing process at both the molecular and physiological/functional levels. Ultimately, the module aimed to promote the understanding of ageing processes, particularly functional ageing in a population and its societal impacts. MethodsThis "Functional Ageing" course spanned over 13 weeks, consisting of weekly four-hour sessions that aimed to integrate both biology of ageing and societal perceptions of an ageing population. The first half of the semester covered the molecular processes that govern ageing, while the second half focussed on societal perception, burden of disease, healthy ageing interventions and creating an ageless society. Experimental and epidemiological studies were used to explain the ageing process. Expert guest lecturers were invited throughout the module to share their experiences on the demanding research areas of ageing today, as well as clinical aspects of age-related diseases. In addition, a field visit to a geriatric ward at the mental health organisation was arranged to showcase the countrys approach to dealing with the rising demands of ageing, and to provide experiential learning that can help inculcate a clearer public perception of ageing. ResultsThis 13-week module helped to improve students perception about functional ageing in todays society. After the module, a reflection analysis was conducted to evaluate students perceptions of ageing society. Overall findings garnered have demonstrated that while students generally have a brief understanding of the biological processes of ageing, their perception on how ageing is being manifested in a public health and societal setting is in paucity. However, the routine university-directed feedback survey indicated that the module had a positive impact on students appreciation and comprehension of the interplay between biological and sociological aspects of ageing, thus achieving the learning objectives of the module. ConclusionThe aim of the "Functional ageing" module was to integrate the biology and sociology of ageing to provide a better interdisciplinary understanding of ageing in society. After completing the module, students demonstrated a change in their mindset and attitude towards how their scientific understanding of ageing can be coupled to their public perception of ageing. As ageing populations become more prevalent in many societies, it is crucial that we prepare for an ageing population and develop a positive perception of ageing. Through educational efforts like this course/module, students will exhibit greater awareness of ageing issues, leading to more informed and balanced perceptions.

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Case based learning as a dynamic approach towards learning oral pathology.

Shrestha, A.; Marla, V.; Rimal, J.; Shrestha, S.; Keshwar, S.; Zhimin, J.

2021-04-04 scientific communication and education 10.1101/2021.04.02.438062 medRxiv
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IntroductionOral pathology comprises of extensive teaching-learning of histopathology. Teaching histopathology is always challenging more when numerous histopathology slides are involved. There is lack of interest among the students and also face challenges to correlate with the clinical presentation. For effective learning, need for a method which is interactive and helps create clinico pathological correlation was felt. This study was designed to assess the impact and feasibility of case-based learning in routine teaching among dental students. MethodsA cross sectional study was conducted among 58 undergraduate dental students, wherein a case-based learning method was introduced in the practical classes. Thirty students were randomly selected as case based learning and remaining as conventional group. Multiple paper-based cases on oral cancer was designed and used for the case based learning group of students. A self-designed pre and posttest interventional tools along with post intervention assessment using modified essay question was designed and applied. ResultsSignificant difference in the scores between pre and post intervention questionnaire was observed among the case-based learning group (p<0.0001), however non-significant among the conventional. Similarly, significant difference in the scores of modified essay question was observed between the study groups. Majority of the students among the case-based learning group agreed that it benefitted their personal, professional and communicative skills. The students expressed their enthusiasm in learning with this method and suggested to apply it more often. DiscussionCase-based learning is an effective method and incorporation of it on a regular basis could help favor an effective learning environment.

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Toward pharmacologic therapy for glioblastoma: Identifying inhibitors of very long-chain acyl-CoA synthetase 3 (ACSVL3)

Clay, E. M.; Shi, X.; Kolar, E. A.; Mody, M.; Locke, J. E.; Watkins, P. A.

2025-07-03 biochemistry 10.1101/2025.07.02.662811 medRxiv
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Brain tumors, in particular glioblastoma multiforme (GBM), are among the most aggressive and difficult to treat human neoplasms. Even with combined surgery, radiation and chemotherapy, the 5-year survival rate for GBM is only [~]7%. Thus, new treatment approaches are needed. We previously found that the fatty acid metabolism enzyme "very long-chain acyl-CoA synthetase 3" (ACSVL3) is overproduced in human glioma tissue and in glioblastoma cell lines such as U87MG cells. These cells exhibited malignant growth properties in culture and were tumorigenic in nude mice. When either knockdown or knockout strategies were used to deplete U87MG cells of ACSVL3, they adopted a more normal growth rate and produced significantly fewer, slower growing tumors in mice. An inhibitor of ACSVL3, if identified, could prove to be a valuable pharmacotherapeutic agent in GBM. Therefore, we sought to identify small molecule compounds that decrease or block the enzyme activity of ACSVL3, as measured by the formation of stearoyl-CoA from the 18-carbon saturated fatty acid stearic acid, a preferred substrate for ACSVL3. We approached this in two ways. First, we tested several compounds that were previously shown to inhibit the activity of a structurally and functionally related enzyme, ACSVL1. Several compounds tested showed inhibition of stearoyl-CoA formation in U87MG cells when added to an in vitro enzyme assay. These included drugs triflupromazine, phenazopyridine, chlorpromazine, emodin, and perphenazine which are approved for treating other conditions. Also inhibitory to stearoyl-CoA production were several compounds from a ChemBridge Corporation library designated CB2, CB5, CB6 and CB 16.2. One caveat regarding interpretation of these results is that in addition to ACSVL3, all cells including U87MG contain other acyl-CoA synthetases capable of using stearic acid as substrate. Therefore, we also measured stearoyl-CoA synthetase activity in ACSVL3-deficient U87MG cells (U87-KO). If a drug or compound is an ACSVL3 inhibitor, it should decrease total conversion of stearate to stearoyl-CoA more in U87MG than in U87-KO cells. By this criterion, most of the tested compounds showed some ACSVL3-specific inhibition. At the screening concentration of 80M drug, CB5 and CB16.2 showed the greatest potency to inhibit ACSVL3 enzyme activity; at 10 M, CB5 still showed significant inhibition but CB16.2 did not. We conclude that these compounds are worthy of further investigation as potential therapeutic agents in GBM, but additional drugs that have greater specificity and are effective at significantly lower concentrations must also be identified. Therefore, our second strategy was to develop a high-throughput library screening assay. For this, we took advantage of the fatty acid transport capability of some ACSVL family members. ACSVL1, when heterologously expressed in COS-1 cells, promotes cellular uptake of the fluorescent fatty acid analog C1-BODIPY-C12; in contrast, overexpressed ACSVL3 does not. We used a domain-swapping strategy to replace the N-terminal 210 amino acids of ACSVL3 with the N-terminal 100 amino acids of ACSVL1, producing ACSVL1/3. Unlike ACSVL3, ACSVL1/3 robustly promoted C1-BODIPY-C12 uptake while retaining the catalytically active C-terminus of ACSVL3. Most of the drugs and compounds that decreased stearoyl-CoA synthetase inhibition also inhibited C1-BODIPY-C12 uptake in a concentration-dependent manner. Catalytically defective ACSVL1/3 mutants lost their ability to promote C1-BODIPY-C12 uptake. Thus, we conclude that chimeric ACSVL1/3 gained the fatty acid transport function of ACSVL1 while retaining the catalytic properties of ACSVL3. A pilot screening study of >1280 drugs from an approved drug library and >880 compounds from a library of drugs predicted to cross the blood-brain barrier detected more than 50 molecules that lowered C1-BODIPY-C12 by more than 3 standard deviations. Although secondary screening will likely exclude many or all of these, our findings support the notion that we have developed a viable method for detecting potential ACSVL3 inhibitors. Further characterization may reveal candidate pharmacologic agents for treatment of GBM and other cancers.

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Precocious hippocampal structural and functional changes in gestational protein-restricted male elderly offspring: an Alzheimer-simile disease model?

Grigoletti-Lima, G. B.; Lopes, M. G.; Franco, A. T. B.; Damico, A. M.; Boer, P. A.; Gontijo, J. A. R.

2021-04-07 developmental biology 10.1101/2021.04.07.438796 medRxiv
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BackgroundMaternal undernutrition has been associated with psychiatric and neurological disorders characterized by learning and memory impairment. Considering the lack of evidence for this, we aimed to analyze the effects of gestational protein restriction on learning and memory function later in life. This research associates behavioral findings with hippocampal cell numbers and protein content related to neurodegenerative brain disease. MethodsExperiments were conducted in animals subjected to a low-protein (LP, 6% casein) or regular-protein (NP, 17% casein) diet throughout their pregnancy. Behavioral tests, isolated hippocampal isotropic fractionator cell studies, immunoblotting, and survival lifetime tests were performed. The results confirmed that the birthweight of LP male pups significantly reduced relative to NP male pups and that hippocampal mass increased in 88-week-old LP compared to age-matched NP offspring. We used the Morris water maze proximity measure, which is the sum of 10 distances each second between rat position and location of a hidden platform target, as a suitable test for assessing age-related learning or memory impairment in aged offspring. ResultsThe results showed an increased proximity measure in 87-week-old LP rats (52.6 x 104 {+/-} 10.3 x 104 mm) as compared to NP rats (47.0 x 104 {+/-} 10.6 x 103 mm, p = 0.0007). In addition, LP rats exhibited anxiety-like behaviors compared to NP rats at 48 and 86 weeks of life. Additionally, the estimated neuron number was unaltered in LP rats; however, glial and other cell numbers increased in LP compared to NP rats. Here, we showed unprecedented hippocampal deposition of brain-derived neurotrophic factor, {beta}-amyloid peptide (A{beta}), and tau protein in 88-week-old LP compared to age-matched NP offspring. To date, no predicted studies showed changes in hippocampal neuron and glial cell numbers in maternal protein-restricted elderly offspring. The current data suggest that maternal protein restriction has a high impact on lifespan and brain structure, and function. Conclusionthe gestational protein restriction may accelerate hippocampal function loss, impacting learning/memory performance, and supposedly developing diseases similar to Alzheimers disease (AD) in elderly offspring. Thus, we propose that maternal protein restriction could be a probable, elegant, and novel method for constructing an AD-like model in adult male offspring.

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Assessing Autophagy Flux in Glioblastoma Temozolomide Resistant Cells

Clark, C.; Barzegar-Behrooz, A.; Cordani, M.; Shojaei, S.; Ghavami, S.

2024-08-10 molecular biology 10.1101/2024.08.09.607348 medRxiv
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Autophagy is a critical cellular process involved in the degradation and recycling of cytoplasmic components, playing a dual role in cancer by either promoting cell survival or facilitating cell death. In glioblastoma (GB), autophagy has been implicated in resistance to the chemotherapeutic agent Temozolomide (TMZ). This study presents a novel method to accurately measure autophagy flux in TMZ-resistant glioblastoma cells, combining advanced imaging techniques with biochemical assays. By quantifying key autophagy markers such as LC3-II and SQSTM1, our approach provides detailed insights into the dynamic processes of autophagosome formation and clearance under therapeutic stress. This method not only advances our understanding of autophagy in GB chemoresistance but also has significant implications for the development of autophagy-targeted therapies. The ability to monitor and manipulate autophagy flux in real-time offers a promising avenue for monitoring and understnading TMZ resistance and improving patient outcomes in glioblastoma treatment.

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Gene Editing and Aging: A Bibliometric Analysis of Global Trends and Frontier Themes (2015-2024)

Chen, L.; Li, H.; Zhu, Y.; Zheng, Z.; Wang, J.; Wang, H.; Huang, W.; Luo, Y.

2025-05-02 scientific communication and education 10.1101/2025.05.01.651618 medRxiv
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ObjectiveThe accumulation of DNA damage and mutations is a key contributor to aging. Recent studies have shown that disrupting the Beclin 1-BCL2 autophagy regulatory complex through gene editing can extend lifespan in mice. The precise application of gene editing technologies offers a promising strategy for aging. This study conducted a bibliometric analysis to map the knowledge landscape of gene editing and aging. MethodsWe retrieved publications related to genome editing and aging from the Web of Science Core Collection, covering the period from 2015 to 2024. The data were analyzed using VOSviewer and R package Bibliometrix. These tools enabled us to identify the most productive researchers, journals, institutions, countries and visualized current trends, emerging research hotspots. ResultsA total of 982 publications on genome editing and aging were identified. The United States (n=285) and China (n=214) form a dual-core structure leading global output. Harvard University (n=116) emerged as the most prolific institution. Scientific Reports was the top-publishing journal, with 23 articles in 2024. ZHANG Y (n=12, citations=102, H-index=6) was identified as the most productive author. KIM Es 2017 publication in Nature Communications (TC=494, TC/year=54.9, NTC=9.33) has had a significant and ongoing impact. The analysis indicates that future directions will include CRISPR optimization and AI-assisted genomic analysis. ConclusionThis study presents the first comprehensive bibliometric analysis and visualization of the knowledge structure in gene editing and aging research up to 2024. It offers researchers a detailed overview of current developments, trends, and emerging frontiers in this rapidly evolving domain.

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Benchmarking open access publication rates for the pharmaceutical industry and research-intensive academic institutions

Rees, T. J.; Philippon, V.; Liew, A.; Baronikova, S.; Gattrell, W. T.; Gordon, J.; Koskenkorva, T. S.; Mysore, S.; Osorio, J.; Koder, T. J.

2024-09-16 scientific communication and education 10.1101/2024.09.14.613042 medRxiv
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BackgroundIn biomedical and health sciences, many articles are published open access (OA). OA publication rates continue to grow, especially for pharmaceutical research. Previous analyses of pharmaceutical OA publication rates were labor-intensive and not easily automated. We aimed to create a free, live, online dashboard comparing OA publication rates between pharmaceutical companies and academic institutions. MethodsUsing the Lens - an online platform aggregating full-text content and metadata for over 280 million scholarly works - we built a dashboard showing OA publication rates for medical research articles by authors from the top 40 pharmaceutical companies (pharma) and 40 research-intensive academic institutions (academia). The dashboard details OA rates by model, license and therapy area across three time frames: 12-24 months; 0-12 months; 0-10 years. We downloaded data from the dashboard between 24 July and 4 August 2023 and performed further analysis. ResultsOf the articles published 12-24 months before data extraction, 76.6% by pharma and 69.5% by academia were OA. The most common OA models were gold (pharma, 37%; academia, 41%) and hybrid (pharma, 22%; academia, 11%). Oncology had lower rates of OA articles than other therapy areas. In the 10 years before data extraction, growth in the OA publication rate was generally more rapid for pharmaceutical companies than for academic institutions, regardless of field (change in overall % OA 2013-2023: pharma, 3.1; academia, 1.6). ConclusionsThis dashboard provides novel and regularly updated evidence on the comparative OA publication practices of pharmaceutical companies and academic institutions. In our snapshot analysis, the OA publication rate was higher for pharmaceutical companies than for academic institutions and continues to increase. Notable differences were observed in approaches, in terms of licenses and OA models, which may reflect different institutional practices and circumstances. We encourage others to use this open resource for new research and to report their results.

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ZeptoCTC - Sensitive Protein Analysis of True Single Cell Lysates using Reverse Phase Protein Arrays (RPPA)

Rivandi, M.; Franken, A.; Yang, L.; Abramova, A.; Stamm, N.; Eberhardt, J.; Gierke, B.; Beer, M.; Fehm, T.; Niederacher, D.; Pawlak, M.; Neubauer, H.

2023-09-16 molecular biology 10.1101/2023.09.16.558042 medRxiv
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Circulating Tumor Cells (CTCs) are commonly analyzed through genomic profiling, which does not capture posttranslational and functional alterations of encoded proteins. To address this limitation, we developed ZeptoCTC, a single-cell protein analysis workflow that combines established technologies for single-cell isolation and sensitive Reverse Phase Protein Array (RPPA) analysis to assess multiple protein expression and activation in individual CTCs. The workflow involves single cell labeling, isolation, lysis, and printing of the true single cell lysates onto a ZeptoChip using a modified micromanipulator CellCelectorTM. Subsequently, the printed lysates undergo fluorescence immunoassay RPPA protein detection using a ZeptoReader followed by signal quantification with Image J software. ZeptoCTC was successfully optimized, beginning with the measurement of EpCAM protein expression--a standard marker for CTC detection. As expected, mean fluorescence signals for EpCAM levels were significantly higher in single MCF-7 cells compared to MDA-MB-231 cells. Next, Capivasertib-treated MCF-7 cells exhibited an approximately 2-fold increase in the pAkt/Akt ratio compared to non-treated control cells. This finding was consistent with a co-performed western blot analysis of pooled MCF-7 cells. Application of ZeptoCTC to the analysis of single CTCs derived from a metastasized breast cancer (MBC) patient indicated a significantly higher level of pAkt, accompanied by a corresponding increase in pErk level when compared to patient-matched WBC. Finally, the current workflow successfully indicated the detectable pAkt and Akt signal difference in CTCs from two MBC patients: one with an Akt1 wild-type genotype, and the other harboring approximately 80% Akt1(E17K) mutated CTCs. The mutated CTCs revealed clearly elevated pAkt levels (1.8-fold), along with an even more strongly elevated total Akt (3.4-fold) when compared to the respective signals measured in wild-type CTCs. In conclusion, ZeptoCTC is a highly sensitive method for measuring the expression and phosphorylation of treatment-relevant proteins in key cancer-driving signaling pathways from true single cell samples.

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A review of online learning strategies for biological NMR techniques a survey of educators

Phelan, M. M.

2023-01-19 scientific communication and education 10.1101/2023.01.13.523927 medRxiv
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Disruption to teaching over the pandemic has led to a range of online and digital solutions. Given the utility of software and remote platforms for NMR teaching a UK-based survey for NMR educators in undergraduate and postgraduate teaching was rolled out Spring 2022 in order to establish what online tools and techniques are employed to teach NMR to biological sciences and appraise their relative efficacy. Based on the survey outcomes an overview of the breadth of methods employed as well as their perceived effectiveness is presented with a list of recommendations for common and successful strategies for online (and hybrid) teaching of NMR to the life sciences.

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Development of an undergraduate cell biology laboratory to assess pigmentation and cell size in a zebrafish model of uveal melanoma

Henle, A. M.

2023-09-17 scientific communication and education 10.1101/2023.09.15.558009 medRxiv
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This study outlines a two-week laboratory module for an authentic cell biology undergraduate research experience that uses zebrafish (Danio rerio), a popular model organism for research. Previous research has indicated that course-based undergraduate research experiences such as this one increase student confidence, active learning, and retention. During this research experience, students investigate variations in pigmentation in the caudal fins of wild type and transgenic fish (Tg(mitfa:GNAQQ209L)). The transgenic fish express a hyperactive G protein, GNAQQ209L, under the melanocyte-specific mitfa promoter, offering insights into uveal melanoma, a common eye cancer. Students specifically analyze the black pigmented cells, melanophores, within the caudal fin. We determined that the transgenic zebrafish have increased pigmentation in their caudal fins but smaller melanophores. These results suggest there are more melanophores in the Tg(mitfa:GNAQQ209L) fish compared to the wild type. Future undergraduate research could investigate these cellular differences. This research experience imparts microscopy and image analysis skills and instills the ability to grapple with large datasets, statistical tests, and data interpretation in alignment with biology education principles. Post-lab surveys reveal students attain confidence in the above skills and in handling animals, along with a deeper appreciation for model organism research and its relevance to cancer cell biology.

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When DNA gets in the way in RNA-seq experiments, a sequel

Verwilt, J.; Giraldez, M. D.; Trypsteen, W.; Van Paemel, R.; De Preter, K.; Mestdagh, P.; Vandesompele, J.

2020-09-29 molecular biology 10.1101/2020.09.28.316265 medRxiv
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Using a newly developed method dubbed SILVER-Seq--enabling extracellular RNA sequencing (exRNA-seq) directly from a small volume of human serum or plasma-- Yan et al. recently reported in Current Biology a potential exRNA biomarker for the early diagnosis of Alzheimers disease [1]. After the publication of the initial paper describing the SILVER-Seq method [2], we reported our concern regarding potential DNA contamination in their datasets [3]. Although the authors replied they were able to successfully treat RNA samples with DNase to avoid such contamination, they did not address our observations of the majority of reads without evidence of being derived from RNA, nor documented verified absence of DNA after DNase treatment [4]. To assess whether the newly data generated may suffer from DNA contamination, we downloaded the publicly available sequencing data and evaluated two quality control metrics (i.e., fraction of exonic and splice reads), which were not reported in the paper. We found that both quality metrics were much lower than expected for RNA-seq data (6.28% exonic and 0.478% splice reads), in line with our previous findings on the first SILVER-Seq paper. These observations suggest the data and results presented by Yan et al. are affected by DNA contamination, an issue that may be inherent to the SILVER-Seq technology.

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Benefits of combining individual and small group assessments as an instructional strategy

Arini, G. S.; Almeida, I. d. S.; Torres, B. B.

2024-10-23 scientific communication and education 10.1101/2024.10.21.619510 medRxiv
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Assessment is an essential curricular component despite being often seen only as a performance metric resource. However, its full potential can be harnessed if it is used as a formative instrument. The present study evaluated the benefits of combining individual and group assessments. Students perceptions of this type of strategy, assessed through a Likert scale questionnaire and semi-structured interviews, showed that students acknowledge the benefits of this procedure. We then carried out a dual assessment in an active learning environment. Students were given individual written tests and completed the same test immediately after, but now in a group. The average group scores were higher than the average individual scores, even for students who scored the highest within a group. Put together, these results indicate combining individual and group assessments can be an effective teaching tool in addition to simply measuring student performance.

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Clinical and Molecular Characterization of Glioma Patients: miR-21 Expression as a Prognostic Biomarker in Tissue and Serum

Laghari, A. A.; Sufiyan, S.; Amin, W.; Adnan, U.; Naeem, S.; Abidi, S. H.; Ilyas, S.; Uddin, S.; Bajwa, M. H.; Enam, S. A.; Mughal, N.

2024-11-21 molecular biology 10.1101/2024.11.20.624501 medRxiv
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BackgroundGlioma remains challenging due to high recurrence rates and resistance to treatment. Diagnosis and follow-up in resource-constrained regions often leads to significant patient attrition. Serum microRNA (miRNA) expression profiles, which have been shown to correlate with tissue expression profiles, are detectable in peripheral blood samples, providing a promising avenue for non-invasive and repeatable liquid biopsies. miR-21 shows promise in many populations; however, there is a dearth of data from our region. MethodologyWe collected 90 tumor tissues, 42 pre- and post-operative serum samples from glioma patients, and included 10 normal tissue adjacent to the tumor (NATs) along with serum samples from 8 healthy individuals and analyzed for miR-21 expression through RT-qPCR. Shapiro Wilk test was applied to calculate data distribution, ANOVA, Fishers exact, and Wilcox test, along with pairwise Students t-test, were applied to determine the differences in gene expression. The expression level of miR-21 was assessed for correlation with Kaplan-Meier survival curves and different molecular markers (IDH, Ki-67, ATRX and p53). The quantitative hazard ratio was determined using Cox regression analysis. ResultsmiR-21 expression in tissue increased with the mean log fold expression 0.101 (median fold = 2.35) in grade 2, 1.00 (median fold = 7.49) in grade 3 and 1.53 (median fold = 26.0) in grade 4 for glioma patients. The expression level showed significant difference between control tissue and grade 4 patients along with significant inter-comparison between grade 1 and grade 4, as well as grade 2 and grade 4.A significant elevated expression of miR-21 has been noticed in patients above 50 years of age. Similarly, in serum samples a significant decline in miR-21 expression was observed in post-operative samples as compared to pre-operative samples mean log fold in grade 2 is 1.30 (11.6-fold), grade 3 is 1.08 (15.3-fold) and grade 4 is 0.749 (13.2-fold). Furthermore, there was positive correlation of miR-21 expression with tumor volume. IDH-wildtype and high Ki-67 expression in gliomas showed significant upregulation of miR-21 compared to IDH-mutant and low Ki-67 respectively. Patients with low miR-21 expression had significantly longer overall survival (OS) than patients with high miR-21 expression. Quantitative hazard analysis indicates that patients in the high expression group have a 3.4 times higher risk of mortality (95% CI: 1.6-7.1), in comparison to patients in the low expression group with AUC of 0.742 (all p <0.05). ConclusionThis study demonstrates the potential of microRNA 21 as a serum biomarker for early, cost-effective diagnosis of glioma. Furthermore, it may inform the development of targeted treatment strategies for various glioma grades, particularly in our population.

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AuthormetriX: Automated Calculation of Individual Authors' Non-Inflationary Credit-Allocation Schemas' and Collaboration Metrics from a Scopus Corpus

Adeosun, S. O.

2025-01-20 scientific communication and education 10.1101/2025.01.19.633820 medRxiv
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BackgroundPublication count is the currency in academia, but the most widely used whole count method is considered unfair and inflationary. Several non-inflationary author credit-allocation schemas (NIACAS) have been proposed, but none is widely adopted in practice (e.g., in evaluating faculty scholarly productivity) or in bibliometric research. This low adoption and implementation rate may be due to the complexity in operationalizing the schemas. AimTo develop an application that automates the calculation of individual authors scholarly output metrics based on multiple NIACAS. MethodPublished formulas of NIACAS were written as Python functions wrapped in a Streamlit user interface that takes .csv files of the relevant corpus, and a list of authors Scopus IDs as inputs. The functions calculate the authors output metrics based on NIACAS including first- and last-author straight counts, arithmetic, golden share, and multiple variations of fractional, geometric, and harmonic schemas. Collaboration metrics are also calculated. Secondary features include modelers for author counts and schemas. In a use-case, absolute rank displacement (ARD) and actual contribution proportions (ACP) were compared between highly cited clinical medicine researchers and high h-index pharmacy practice faculty populations. ResultsAuthormetriX accurately calculates individual authors aggregate scholarly output based on 14 NIACAS, from the file inputs. There were schema and population differences in ACP, but only schema differences in ARD within the populations studied. ConclusionsAuthormetriX simplifies the implementation of non-inflationary author credit-allocation schemas and will facilitate their broader adoption in practice and bibliometric research. AuthormetriX is freely available at https://sadeosun-a-uthormetrix-v1.streamlit.app/.

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Observation of the Transport and Removal of Lipofuscin from the Mouse Myocardium using Transmission Electron Microscope

Wang, L.; Xiao, C.-Y.; Li, J.-H.; Tang, G.-C.; Xiao, S.-S.

2020-03-10 physiology 10.1101/2020.03.10.985507 medRxiv
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This study was performed to investigate whether the lipofuscin formed within cardiomyocytes can be excluded by the myocardial tissue. We have provided indicators that can be used for future studies on anti-aging interventions. In the present study, the heart of a 5-month-old BALB/c mouse was obtained for resin embedding and ultra-thin sectioning. The specimens were observed under a Hitach 7500 transmission electron microscope, and the images were acquired using an XR401 side-insertion device. Lipofuscin granules are found abundantly in myocardial cells. Cardiomyocytes can excrete lipofuscin granules into the myocardial interstitium using capsule-like protrusions that are formed on the sarcolemma. These granules enter the myocardial interstitium and can be de-aggregated to form "membrane-like garbage", which can pass from the myocardial stroma into the lumen of the vessel through its walls in the form of soluble fine particles through diffusion or endocytosis of capillaries. Smaller lipofuscin granules can pass through the walls of the vessels and enter the blood vessel lumen through the active transport function of the capillary endothelial cells. When the extended cytoplasmic end of macrophages and fibroblasts fuse with the endothelial cells, the lipofuscin granules or clumps found in the cells of the myocardial interstitium are transported to the capillary walls, and then, they are released into the lumen of the blood vessel by the endothelial cells. The myocardial tissues of mice have the ability to eliminate the lipofuscin produced in the cardiomyocytes into the myocardial blood circulation. Although there are several mechanisms through which the myocardial tissues release lipofuscin into the bloodstream, it is mainly carried out in the form of small, fine, soluble, continuous transport.

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The Need for Sustainable Leadership in Academia - a German Case Study

Haage, V. C.; Voss, L.; Nguyen, D.; Eggert, F.

2021-02-17 scientific communication and education 10.1101/2021.02.17.431650 medRxiv
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Academic leaders are selected based on their publication record, citation index and acquisition of third party funding. However, heading a successful research team, also requires leadership skills. Despite the clear need, leadership development has been systematically neglected in the present academic system. At the same time, growing evidence suggests that leadership styles of academic supervisors can dramatically affect the mental health of academic employees as well as drive highly skilled researchers out of academia. Here, we assessed the current state of academic leadership in the German academic system by surveying 368 participants currently employed in academia in Germany. We report that 64% of current academic leaders did not feel prepared for their current position while 86% of participants expressed their interest in leadership development programs offered by their research institutions. Our results highlight the demand for leadership development programs in German academic institutions to ensure a more efficient academic system.

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Diversity of Abeta aggregates produced in a gut-based Drosophila model of Alzheimer's disease

Elovsson, G.; Klingstedt, T.; Nilsson, K. P. R.; Brorsson, A.-C.

2024-11-20 molecular biology 10.1101/2024.11.19.624423 medRxiv
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Alzheimers disease (AD) is a neurodegenerative disease manifested by memory loss and premature death. One major histopathological hallmark of AD is the amyloid plaques formed by aggregates of the amyloid-beta (Abeta) peptide and the Abeta aggregation process results in amyloid fibrils with different structures. Herein, we investigate the heterogeneity of Abeta aggregates produced by Drosophila melanogaster expressing the Abeta1-42 peptide with the Arctic mutation E22G (Arctic flies) or a dimeric construct of Abeta1-42 (T22Abeta1-42 flies) in the digestive tract. Staining of the gut of the flies using luminescent conjugated oligothiophenes (LCOs) revealed that the amount of Abeta aggregates increased in both genotypes with age. The LCOs also exhibited distinct staining patterns in the flies. The expression of T22Abeta1-42 resulted in a heavier Abeta load compared to Abeta1-42 with the Arctic mutation. Since the genotypes have similar median survival times, the result indicates that the toxicity of the combined number of aggregates in the Arctic flies is higher compared to the T22Abeta1-42 flies. Stability measurements showed that the most accumulated Abeta species in the Arctic and the T22Abeta1-42 flies were found in the 4 M and 5 M Gua-HCl-fraction, respectively. This indicates that prefibrillar Abeta aggregates constitute the toxic species in Arctic flies while the cause of death in T22Abeta1-42 flies might be the massive load of insoluble aggregates. The study shows that even though the different Abeta peptides resulted in an equal reduction of the lifespan, they formed an array of different aggregates confirming the heterogeneity of this process. Overall, our findings support that distinct Abeta aggregates can exhibit different pathological effects, and we foresee that our Drosophila models can potentially aid in identifying anti-Abeta agents targeting different types of aggregated Abeta species.

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The Intergenerational Classroom: A Case Study Integrating Undergraduate and Lifelong Learning Curricula for Biology Education

Earles, J.; Robbins, K.; Stanhope, B.; Keene, A. C.

2025-07-25 scientific communication and education 10.1101/2025.07.23.666467 medRxiv
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According to the US Census Bureau (2019) there are approximately 95 million people in the US 55 years of age and older, and that number is expected to increase dramatically in the next decade. This growing population results in an increasing need for STEM learning opportunities for older adults. This need is partially met by lifelong learning communities across the country that offer non-degree programs on a broad range of topics. While many of these programs are located on a college campus, there are few opportunities for interaction between lifelong learners and students in degree-oriented programs. To improve access to STEM education for lifelong learners, we generated an intergenerational classroom composed of lifelong learners and undergraduate students. The semester-long course focused on the biography and medical writings of the late neurologist Oliver Sacks. Our analysis revealed a high level of satisfaction from both undergraduate students and lifelong learners. Both groups overwhelmingly found the intergenerational format beneficial to learning. Furthermore, self-assessments revealed that students felt more positively about intergenerational interactions following completion of the course. Overall, this course provides a framework for increasing access to STEM for the growing older adult population and fostering positive intergenerational interactions. This model could be readily implemented across the country given the abundance of lifelong learning programs currently affiliated with colleges and universities.

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Biophysical characterization of the human K0513 protein

Nemukondeni, N.; Arowolo, A.; Shonhai, A.; Zininga, T.; Burger, A.

2020-06-18 biochemistry 10.1101/2020.06.18.158949 medRxiv
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Glioblastoma multiforme (GBM) is an aggressive grade IV primary malignant tumour which accounts for 78 % of all brain tumours. K0513 is a GBM biomarker that is upregulated in the invasive phenotype. K0513 is expressed ubiquitously and is reportedly enriched in the cerebral cortex of the brain. K0513 is further implicated in signalling pathways involving neuroplasticity, cytoskeletal regulation and apoptosis. The protein encoded by K0513 is a prospective biomarker for pancreatic cancer prognosis. However, the gene product of K0153 is not well characterised. This study focused on structure-function characterisation of human K0513 protein. To this end, we employed bioinformatics analysis and biophysical approaches to characterize the protein. In silico structural characterisation of the human K0513 protein suggests the presence of a SET binding factor 2 (SBF2) domain and a transmembrane region. The SBF2 domain is found in the Myotubularin-related protein 13 (MTMR13), which may function as a nucleotide exchange factor for the RAS-associated GTPase, Rab28. K0513 was predicted to interact with RAS-associated GTPase, Rab3a. Secondary structure prediction revealed K0513 to be predominantly -helical in nature. The predicted three-dimensional model of K0513 showed a globular fold, suggesting that the protein is water-soluble. K0513 was heterologously expressed in E. coli XL1-Blue cells and subsequent purification yielded 80 % soluble protein. Biophysical characterisation using tryptophan-based fluorescence spectroscopy and limited proteolysis showed the conformation of K0513 is mostly unperturbed in the presence of nucleotides. Interestingly, K0513 was detected in lung carcinoma, fibrosarcoma and cervical adenocarcinoma cells, supporting its possible role in cancer signalling pathways.

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Characterization of the intraspecies chimeric mouse brain at embryonic day 12.5

Strell, P.; Waldron, M. A.; Johnson, S.; Shetty, A. V.; Crane, A.; Steer, C.; Low, W. C.

2025-04-02 developmental biology 10.1101/2025.03.31.646380 medRxiv
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Incidence of neurodegenerative diseases such as Alzheimers, Parkinsons, Huntingtons, and amyotrophic lateral sclerosis have increased dramatically as life expectancy at birth has risen year-over-year and the population ages. Neurological changes within the central nervous system, specifically the brain, include cell loss and deterioration that impact motor function, memory, executive function, and mood. Available treatments are limited and often only address symptomatic manifestations of the disease rather than disease progression. Cell transplantation therapy has shown promise for treating neurodegenerative diseases, but a source of autologous cells is required. Blastocyst complementation provides an innovative method for generating those autologous neural cells. By injecting mouse induced pluripotent stem cells (iPSCs) into a wild type (WT) mouse blastocyst, we generated a chimeric mouse brain derived of both donor and host neuronal and non-neuronal cells. An embryonic day 12.5 (E12.5), automated image analysis of mouse-mouse chimeric brains showed the presence of GFP-labeled donor-derived dopaminergic and serotonergic neuronal precursors. GFP-labeled donor-derived cholinergic precursor neurons and non-neuronal microglia-like and macrophage-like cells were also observed using more conventional imaging analysis software. This work demonstrates that the generation of mouse-mouse chimeric neural cells is possible; and that characterization of early neuronal and non-neuronal precursors provides a first step towards utilizing these cells for cell transplantation therapies for neurodegenerative diseases.