Scientific Community Research Articles

First Investigation of Secondary Metabolites from Aspergillus xerophilus Reveals Compounds with Inhibitive Effects against Three Phytopathogenic Fungi of Agrarian Crops.

Fungal secondary metabolites play a highly significant role in crop protection, which is related to their antifungal activity against agriculturally important phytopathogens. In fact, plant diseases caused by fungi including species belonging to the genera of Alternaria, Botrytis, and Fusarium have become increasingly serious affecting crop yield and quality. Hence, there is increasing awareness by the scientific community of the importance of exploiting fungal products for finding new compounds able to inhibit phytopathogens. In this study several drimane-type sesquiterpenes have been detected for the first time as products of Aspergillus xerophilus by GC-MS analysis of the organic extracts obtained from the mycelia and culture filtrates of the fungus grown on two different substrates. Seven pure drimane-type sesquiterpenes were also isolated and identified by spectroscopic methods. The inhibitory effects of the pure compounds have been investigated against three phytopathogenic fungi of agrarian crops (i.e., Botrytis cinerea, Alternaria alternata, and Fusarium oxysporum f. sp. pisi). Among the drimane-type sesquiterpenes isolated in this study, 9,11-dihydroxy-6-oxodrim-7-ene is the most active against the three phytopathogens. Our findings also reveal the high sensitivity of A. alternata to the isolated compounds. These results pave the way for future applications in agriculture of both A. xerophilus and its metabolites.

Twenty years of in vitro nanotoxicology: how AI could make the difference

More than two decades ago, the advent of Nanotechnology has marked the onset of a new and critical field in science and technology, highlighting the importance of multidisciplinary approaches to assess and model the potential human hazard of newly developed advanced materials in the nanoscale, the nanomaterials (NMs). Nanotechnology is, by definition, a multidisciplinary field, that integrates knowledge and techniques from physics, chemistry, biology, materials science, and engineering to manipulate matter at the nanoscale, defined as anything comprised between 1 and 100 nm. The emergence of nanotechnology has undoubtedly led to significant innovations in many fields, from medical diagnostics and targeted drug delivery systems to advanced materials and energy solutions. However, the unique properties of nanomaterials, such as the increased surface to volume ratio, which provides increased reactivity and hence the ability to penetrate biological barriers, have been also considered as potential risk factors for unforeseen toxicological effects, stimulating the scientific community to investigate to which extent this new field of applications could pose a risk to human health and the environment.

A pilot study: Examining cytoskeleton gene expression profiles in Pakistani children with autism spectrum disorder.

Finding effective pharmacological interventions to address the complex array of neurodevelopmental disorders is currently an urgent imperative within the scientific community as these conditions present significant challenges for patients and their families, often impacting cognitive, emotional, and social development. In this study, we aimed to explore non-invasive method to diagnose autism spectrum disorders (ASD) within Pakistan children population and to identify clinical drugs for its treatment. The current report outlines a comprehensive bidirectional investigation showcasing the successful utilization of saliva samples to quantify the expression patterns of profilins (PFN1, 2, and 3); and ERM (ezrin, radixin, and moesin) proteins; and additionally moesin pseudogene 1 and moesin pseudogene 1 antisense (MSNP1AS). Subsequently, these expression profiles were employed to forecast interactions between drugs and genes in children diagnosed with ASD. This study sought to delve into the intricate gene expression profiles using qualitative polymerase chain reaction of profilin isoforms (PFN1, 2, and 3) and ERM genes extracted from saliva samples obtained from children diagnosed with ASD. Through this analysis, we aimed to elucidate potential molecular mechanisms underlying ASD pathogenesis, shedding light on novel biomarkers and therapeutic targets for this complex neurological condition. (n = 22). Subsequently, we implemented a diagnostic model utilizing sparse partial least squares discriminant analysis (sPLS-DA) to predict drugs against our genes of interest. Furthermore, connectivity maps were developed to illustrate the predicted associations of 24 drugs with the genes expression. Our study results showed varied expression profile of cytoskeleton linked genes. Similarly, sPLS-DA model precisely predicted drug to genes response. Sixteen of the examined drugs had significant positive correlations with the expression of the targeted genes whereas eight of the predicted drugs had shown negative correlations. Here we report the role of cytoskeleton linked genes (PFN and ERM) in co-relation to ASD. Furthermore, variable yet significant quantitative expression of these genes successfully predicted drug-gene interactions as shown with the help of connectivity maps that can be used to support the clinical use of these drugs to treat individuals with ASD in future studies.

Transformative agreements, publication venues and Open Access policies at the University of Milan

AbstractStarting from July 2020 at the University of Milan, one of the largest and most important Italian universities, the first transformative agreements with some major international scientific publishers have come into effect. These agreements allow corresponding authors to publish in open access without directly bearing the publication costs. From the perspective of corresponding authors, these agreements could increase the dissemination of their scientific output and, thereby, the impact on the scientific community. However, transformative agreements are part of a rapidly changing publishing market that already includes open access articles in both so‐called ‘Diamond’ and ‘Gold’ journals. The aim of our study is to understand to what extent the positioning of journals in impact rankings, the disciplinary field of the article, together with the career stage of the corresponding author, influence the choice to publish in a journal covered by transformative agreements rather than in other open access or hybrid journals. The results of our investigation draw attention to the importance of rules in Italy governing scientific careers in different disciplinary fields and potential unforeseen effects of policies favouring open access.

We need to rethink the way we identify diamond open access journals in quantitative science studies

Abstract With the announcement of several new diamond open access (OA) related initiatives and the creation of the Global Summit on Diamond Open Access, diamond OA is now at the forefront of the OA movement. However, while working on our recent Quantitative Science Studies publication and datasets, we noticed that temporarily waiving article processing charges (APCs) was a commonly used strategy by big publishers for some of their journals. In the absence of an index of diamond journals, most studies have operationalized the identification of diamond journals as a subset of gold journals that do not charge an APC. While this is a pragmatic approach, we fear that it could undermine the value of the research in understanding what we believe is more commonly understood by diamond OA. This letter discusses the need for bibliometric research to apply more nuance in how it operationalizes diamond OA beyond the absence of APCs. We call on the publishing sector to be more transparent in the costs of publishing. Ultimately, we argue that transparency and a long-term commitment to no-APC publishing are necessary for diamond OA to succeed, and that the research community needs to apply this standard when seeking to understand the model. Peer Review https://www.webofscience.com/api/gateway/wos/peer-review/10.1162/qss_c_00331

Human health risk assessment of heavy metals in residential soil-Houston, Texas.

Human health risk assessment increasingly recognizes the need to integrate participatory-based research, geospatial analysis, and environmental epidemiology, particularly to address contamination concerns in underserved and disadvantaged communities. Here, we demonstrate the combined application of such methods within the Greater Fifth Ward neighborhood in Northeast Houston. In particular, in tandem with community members, we collected soil samples from 193 residential sites using a complete canvassing method from July to November 2021 to characterize contaminant concentrations, focusing on heavy metals and metalloids As, Ba, Cd, Cr, Pb, Se, Ag, and Hg measured using Inductively Coupled Plasma-Mass Spectrometry. Individual heavy metals as well as cumulative cancer and non-cancer risks were calculated for children and adults using the USEPA Regional Soil Screening Levels and benchmarks for specific land uses, such as crop growing. Soils from most sites had low or typical background levels expected in urban areas, but samples from several locations had significantly elevated lead levels (>1200 mg/kg) that warrant additional examination. Geospatial analysis suggested clustering of heavy metal contaminants within one geographic area of the neighborhood. This study highlights how participatory research in underserved environmental justice communities can help characterize current conditions as well as establish priorities for future investigation.

A guide to selecting high-performing antibodies for Rab10 (UniProt ID: P61026) for use in western blot, immunoprecipitation, and immunofluorescence

Rab10 is a small GTPase involved in cargo transport from the trans-Golgi network to the plasma membrane and endocytic recycling back to the cell membrane. It has garnered significant interest in neurodegenerative disease research, particularly due to its phosphorylation by the LRRK2 kinase. This relationship underscores the importance of Rab10 in cellular processes related to disease pathology, specifically Parkinson’s disease. The accessibility of renewable and selective antibodies against Rab10 would advance research efforts, enabling further understanding of its function and implications in disease. Here, we have characterized eight Rab10 commercial antibodies for western blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a larger, collaborative initiative seeking to address antibody reproducibility issues by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs.

Cajal’s contributions to vestibular research

The Spanish neurohistologist Santiago Ramón y Cajal (1852–1934) is widely regarded as the father of modern Neuroscience. In addition to identifying the individuality of cells in the nervous system (the neuron theory) or the direction followed by nerve impulses (the principle of dynamic polarization), he described numerous details regarding the organization of the different structures of the nervous system. This task was compiled in his magnum opus, “Textura del Sistema Nervioso del Hombre y los Vertebrados,” first published in Spanish between 1899 and 1904, and later revised and updated in French as “Histologie du système nerveux de l’homme et des vertébrés” between 1909 and 1911 for wider distribution among the international scientific community. Some of Cajal’s findings are fundamental to our understanding of the anatomy and histology of the vestibular system. He depicted the nerve endings in the sensory epithelia, the structure of the vestibular nerve and Scarpa ganglion, afferent vestibular fibers, vestibular nuclei, lateral vestibulospinal tract, vestibulocerebellar connections, and the fine structure of the cerebellum. However, most of these pioneering descriptions were published years earlier in Spanish journals with limited circulation. Our study aimed to gather Cajal’s findings on the vestibular system and identify his original publications. After this endeavor, we claim a place for Cajal among the founders of anatomy and histology of the vestibular system.

Minimal invasive extracorporeal circulation: A bibliometric network analysis of the global scientific output.

Minimal Invasive Extracorporeal Circulation (MiECC) has recently emerged as a more 'physiologic' alternative to conventional extracorporeal circulation. However, its adoption is still limited due to lack of robust scientific evidence and ongoing debate about its potential benefits. This bibliometric analysis aims to analyze the scientific articles on MiECC and identify current research domains and existing gaps to be addressed in future studies. Pertinent articles were retrieved from the Web of Science (WOS) database. The search string included 'minimal invasive extracorporeal circulation' and its synonyms. The VOSviewer (version 1.6.17) software was used to conduct comprehensive analyses. Semantic and research networks, bibliographic coupling and journal analysis were performed. Of the 1777 articles identified in WOS, 292 were retrieved. The trend in publications increased from 1991 to date. Most articles focused on transfusion requirements, acute kidney injury, inflammatory markers and cytokines, inflammation and delirium, though the impact of intraoperative optimal fluid and hemodynamic management as far as the occurrence of postoperative complications were poorly addressed. The semantic network analysis found inter-connections between the terms "cardiopulmonary bypass", "inflammatory response", and "cardiac surgery". Perfusion contributed the highest number of published documents. The most extensive research partnerships were between Germany, Greece, Italy, and England. Notwithstanding the scientific community's growing interest in MiECC, crucial topics (i.e., the best anesthetic management and intraoperative need for inotropes, vasopressors and fluids) still require more comprehensive exploration. This investigation may prove to be a useful tool for clinicians, scientists, and students concerning global publication output and for the use of MiECC in cardiac surgery.

The Ethical Responsibilities of Researchers in Light of the Technological Advancement and Artificial Intelligence Methods: A Case Study of Management Ph.D. Researchers at Midocean University

This study aimed to assess the integration, ethical considerations, and governance of artificial intelligence (AI) within the PhD programs at Midocean University. It specifically sought to understand PhD researchers' perceptions and attitudes towards AI and identify areas for enhancement in AI-related policies and educational initiatives. A descriptive analytical approach was adopted, utilizing an electronic questionnaire distributed to 105 PhD researchers, with 54 completing the survey. The questionnaire was designed to measure various aspects of AI usage, ethical concerns, and governance practices. Statistical analysis was conducted to evaluate the relationships between AI awareness, ethical application, and governance perceptions. The findings revealed diverse perceptions of AI among researchers, indicating both opportunities and challenges in AI integration. The statistical analysis confirmed significant correlations between AI awareness and positive perceptions of ethical AI usage. However, the response rate and sample size posed limitations on the generalizability of the results. The study highlights the need for Midocean University to strengthen its AI governance frameworks and expand ethical guidelines to keep pace with technological advancements. Recommendations include enhancing AI-related educational programs, updating AI policies regularly, and promoting interdisciplinary research to foster an informed and ethically aware research community.

Debiasing large language models: research opportunities*

ABSTRACT Large language models (LLMs) are powerful decision-making tools widely adopted in healthcare, finance, and transportation. Embracing the opportunities and innovations of LLMs is inevitable. However, LLMs inherit stereotypes, misrepresentations, discrimination, and societies' biases from various sources–including training data, algorithm design, and user interactions–resulting in concerns about equality, diversity, and fairness. The bias problem has triggered increased research towards defining, detecting and quantifying bias and developing debiasing techniques. The predominant focus in tackling the bias problem is skewed towards resource-rich regions such as the US and Europe, resulting in a scarcity of research in other societies. As a small country with a unique history, culture and social composition, there is an opportunity for Aotearoa New Zealand's (NZ) research community to address this inadequacy. This paper presents an experimental evaluation of existing bias metrics and debiasing techniques in the NZ context. Research gaps derived from the study and a literature review are outlined, current and ongoing research in this space are discussed, and the suggested scope of research opportunities for NZ are presented.

The harms of promoting the lab leak hypothesis for SARS-CoV-2 origins without evidence.

Science is humanity's best insurance against threats from nature, but it is a fragile enterprise that must be nourished and protected. The preponderance of scientific evidence indicates a natural origin for SARS-CoV-2. Yet, the theory that SARS-CoV-2 was engineered in and escaped from a lab dominates media attention, even in the absence of strong evidence. We discuss how the resulting anti-science movement puts the research community, scientific research, and pandemic preparedness at risk.

The Pico Balloon Archive: Establishing the First Super Pressure Balloon Satellite Network for Atmospheric Research

Abstract We present the Pico Balloon Archive (PBA), a specialized platform for archiving, visualizing, and verifying data from pico balloons— lightweight, super pressure balloons capable of operating in the upper troposphere and lower stratosphere for durations ranging from weeks to years. With a latitudinal range from 88.77°S to 89.60°N and data collection ongoing since 2021, the PBA stands as the most spatially extensive repository for super pressure balloons to date. It offers a centralized, user-friendly online portal (http://picoballoonarchive.org) for data access, featuring a summary of flight details, downloadable raw data, and individual flight visualizations. In this study, we validate the PBA’s wind speed and direction calculations against the Integrated Radiosonde Archive (IGRA), showing strong correlations (r2 = 0.66 and 0.78 for wind speed and direction, respectively). We also highlight the PBA’s effectiveness in charting global atmospheric circulation and the capacity of certain balloons to traverse hemispheres, a feat made possible by unique stratospheric dynamics. Furthermore, we demonstrate the PBA’s effectiveness in validating Numerical Weather Prediction (NWP) Lagrangian trajectories, quantifying errors based on model initialization latitude. This continuously updated super pressure balloon network is poised to significantly aid the atmospheric science community, facilitating a deeper understanding of global atmospheric processes.

Computational Screening of FDA‐Approved Hepatitis C Drugs for Inhibition of VEGFR2 in Liver Cancer

AbstractLiver cancer (LC) is one of the most common tumours and the leading cause of cancer‐related death globally. Amidst the problems associated with existing treatments, such as hepatotoxicity, recurrence, drug resistance, and other adverse effects, researchers are under pressure to find alternatives. Towards a comprehensive rationalisation of the search for new anti‐LC drugs among approved ones, we employed an in‐silico approach to accelerate the selection of the most efficacious LC drugs. The FDA‐approved hepatitis C virus (HCV) drugs were docked with the LC protein using the AutoDock Vina software. Compared to the control compound, two FDA‐approved HCV drugs (DB09102 and DB09027) were selected based on their binding energies and interactions with the target protein, which showed comparable binding energies. Furthermore, these compounds were then subjected to molecular dynamic simulation, principle component analysis, and MMGBSA using the AMBER20 software, and the results showed stable complexes compared to the control complex. All things considered, this study will help the scientific community and society find a novel drug to treat LC.

Next-Gen Therapeutics: Pioneering Drug Discovery with iPSCs, Genomics, AI, and Clinical Trials in a Dish.

In the high-stakes arena of drug discovery, the journey from bench to bedside is hindered by a daunting 92% failure rate, primarily due to unpredicted toxicities and inadequate therapeutic efficacy in clinical trials. The FDA Modernization Act 2.0 heralds a transformative approach, advocating for the integration of alternative methods to conventional animal testing, including cell-based assays that employ human induced pluripotent stem cell (iPSC)-derived organoids, and organ-on-a-chip technologies, in conjunction with sophisticated artificial intelligence (AI) methodologies. Our review explores the innovative capacity of iPSC-derived clinical trial in a dish models designed for cardiovascular disease research. We also highlight how integrating iPSC technology with AI can accelerate the identification of viable therapeutic candidates, streamline drug screening, and pave the way toward more personalized medicine. Through this, we provide a comprehensive overview of the current landscape and future implications of iPSC and AI applications being navigated by the research community and pharmaceutical industry.

A transdisciplinary co‐conceptualisation of marine identity

Abstract Challenge 10 of the United Nations Decade of Ocean Science for Sustainable Development (2021–2030) calls for the restoration of society's relationship with the ocean. Research suggests that the relationship people have with marine environments can influence their depth of engagement in marine citizenship action, and the important role for ‘marine identity’ in driving that action. Although identity is well‐researched, marine identity is a concept novel to academia and a baseline understanding is required, both to grasp the scope of the concept, and to support research into its role in transforming the human‐ocean relationship. Here, a transdisciplinary study, endorsed as a UN Ocean Decade Activity and by the EU Mission Ocean & Waters, brought together a multinational community of marine researchers and practitioners to co‐produce a baseline conceptualisation of marine identity, drawing on photovoice and deliberative methodology. This paper presents the findings of the co‐production process and offers a first introduction in the literature of the multiple variations and formations of marine identity. We find marine identity to be a complex and multidimensional concept, suffused with individual experiences and understandings of the marine environment, based on social and cultural understandings of the ocean, contemporarily and historically. We present real‐world examples of marine identity to illustrate key themes that were developed through co‐production. Policy implications: We propose marine identity as a catalyst for understanding existing multifaceted and caring relationships with the ocean, as well as the restoration of society's relationship with the ocean. Marine identity research should, therefore, be prioritised in research seeking to contribute to the UN Ocean Decade Challenge 10, as this will support integration of non‐material values of the ocean into marine planning processes and policy making, enabling effective responses to Challenge 10's emphasis on integrating traditional/cultural ways of knowing and valuing the marine environment, through diverse marine identities. We welcome research efforts that will further develop the marine identity concept and empirically investigate the relationships between marine identity, marine citizenship, and people's relationships with the ocean. Read the free Plain Language Summary for this article on the Journal blog.

To Harmonize or to Hinder... Do We Need Two Sets of European Guidelines in 2024?

Hypertension control remains a significant challenge globally.1 Even in Europe, a region that has produced some of the best science on managing hypertension, the control rates of hypertension is poor, ranging between ~20% and 40% for most countries.2 If this was a simple issue to solve, one could ask - what do we need to ensure that the 60% to 80% of people with hypertension who are at high risk of a stroke, heart attack and other consequences, are not left behind? The first logical response would be that the ~500,000 general practitioners (GPs) in Europe3 should be clear on what the best approach is to diagnose and manage patients with hypertension. With the workload of GPs ever increasing, this guidance should be as simple and clear as possible. In 2018 the European Society of Cardiology (ESC) and the European Society of Hypertension (ESH) collaborated to develop a unified guideline for managing hypertension in Europe. These 2018 ESC/ESH Guidelines were well received by the scientific community to judge from the >7,1004 and >2,1005 citations (Scopus) in the two journals in which it was copublished. However, more recently these organizations developed two independent guidelines in 2023 and 2024. The 2024 ESC guidelines have had the benefit of new evidence published since the 2023 ESH guidelines, which have been incorporated into the 2024 ESC guidelines. Most importantly, though, is that the real-world impact of the 2018 guidelines on improving hypertension control rates is not clear. To make new guidelines more relevant, and to make sure they are implemented, guideline developers have become much more vigilant in including GPs and end users on guideline committees and liaising closely with patients in ensuring the implementation of new guidelines are feasible and acceptable for implementation by both providers and patients. [see the full article for more].

Assembled genome of an Ethiopian Plasmodium vivax isolate generated using GridION long-read technology.

Plasmodium vivax causes ~20% of malaria cases in Ethiopia. Here, we report a long-read genome assembly generated from an individual collected in 2022. P. vivax is genetically diverse across endemic regions; thus, the genome assembly of an African isolate is an important resource for the malaria research community.

Health text simplification: An annotated corpus for digestive cancer education and novel strategies for reinforcement learning

Objective:The reading level of health educational materials significantly influences the understandability and accessibility of the information, particularly for minoritized populations. Many patient educational resources surpass widely accepted standards for reading level and complexity. There is a critical need for high-performing text simplification models for health information to enhance dissemination and literacy. This need is particularly acute in cancer education, where effective prevention and screening education can substantially reduce morbidity and mortality. Methods:We introduce Simplified Digestive Cancer (SimpleDC), a parallel corpus of cancer education materials tailored for health text simplification research, comprising educational content from the American Cancer Society, Centers for Disease Control and Prevention, and National Cancer Institute. The corpus includes 31 web pages with the corresponding manually simplified versions. It consists of 1183 annotated sentence pairs (361 train, 294 development, and 528 test). Utilizing SimpleDC and the existing Med-EASi corpus, we explore Large Language Model (LLM)-based simplification methods, including fine-tuning, reinforcement learning (RL), reinforcement learning with human feedback (RLHF), domain adaptation, and prompt-based approaches. Our experimentation encompasses Llama 2, Llama 3, and GPT-4. We introduce a novel RLHF reward function featuring a lightweight model adept at distinguishing between original and simplified texts when enables training on unlabeled data. Results:Fine-tuned Llama models demonstrated high performance across various metrics. Our RLHF reward function outperformed existing RL text simplification reward functions. The results underscore that RL/RLHF can achieve performance comparable to fine-tuning and improve the performance of fine-tuned models. Additionally, these methods effectively adapt out-of-domain text simplification models to a target domain. The best-performing RL-enhanced Llama models outperformed GPT-4 in both automatic metrics and manual evaluation by subject matter experts. Conclusion:The newly developed SimpleDC corpus will serve as a valuable asset to the research community, particularly in patient education simplification. The RL/RLHF methodologies presented herein enable effective training of simplification models on unlabeled text and the utilization of out-of-domain simplification corpora.

Diatom silicon isotope ratios in Quaternary research: Where do we stand?

Silicon stable isotope ratios (expressed as δ30Si) in biogenic silica have been widely used as a proxy for past and present biogeochemical cycling in both marine and lacustrine settings, in particular for nutrient utilization reconstructions. Yet an analysis of publication trends suggests a significant decline in the application of δ30Si to Quaternary science questions in the last five years. At the same time as δ30Si proxy applications have decreased, we are learning more about its complexities: an expanding body of work is highlighting biases, caveats or complications involved in the application of δ30Si-based approaches to the sediment record. These include the demonstration of species-specific silicon isotope fractionation factors (i.e. ‘vital effects’) or the potential for Fe or other trace metals to influence silicon isotope fractionation. Others have inferred the potential of biogenic silica dissolution to alter an initial δ30Si value, or questioned the preservation of the initial δ30Si through early diagenetic processes more generally. Another challenge receiving more attention is centered around deconvolving a δ30Si-value into a signal reflecting biological productivity and a signal reflecting changes in the δ30Si of dissolved silicon driven by whole-system and/or circulation changes. Finally, a number of studies focus on analytical difficulties, especially during sample preparation related to achieving and demonstrating a contaminant free biogenic silica. These challenges lead us to posit that the Quaternary science community is moving away from silicon isotope proxies because they are losing confidence in their reliability and usefulness. Here, focusing on the diatoms – the dominant biosilicifiers in both lakes and the ocean – we synthesize progress in understanding nuances and caveats of δ30Si-based proxies in order to answer whether the fall-off in δ30Si-based Quaternary research is warranted. We suggest that with some simple steps that can be readily implemented, and with the closing of key knowledge gaps, there is no reason to believe silicon isotopes do not have a promising future in the Quaternary sciences.