Scientific Community Research Articles

Development of an Educational Website for Patients With Cancer and Preexisting Autoimmune Diseases Considering Immune Checkpoint Blockers: Usability and Acceptability Study.

Patients with cancer and an underlying autoimmune disease who are considering immune checkpoint blockers (ICBs) need to know about the benefits and risks of severe immune-related adverse events and flares of the autoimmune condition. This study aims to develop and alpha test an educational website for patients with cancer. Learning topics, images, and website architecture (including flow and requirements) were developed and iteratively reviewed by members of a community scientist program, a patient advisory group, and content experts. Alpha testing was performed, measuring the site's usability using the Suitability Assessment of Materials and its acceptability using the Ottawa Acceptability Measure. The website included a home page; general information about ICBs; comprehensive modules on the benefits and risks of ICBs for patients with cancer and preexisting autoimmune diseases; general wellness information; and features such as a quiz, additional resources, and a glossary. For the alpha testing, 9 users assessed the newly developed website. Patient reviewers (n=5) had rheumatoid arthritis, Crohn disease, Sjogren syndrome, or vasculitis. Health care provider reviewers (n=4) were medical oncologists or rheumatologists. The median Suitability Assessment of Materials rating was 75 (IQR 70-79; range 0-100) for patients versus 66 (IQR 57-72; range 0-100) for providers (scores ≥70 indicate no substantial changes needed). Recommendations for improvement, mostly involving navigation and accessibility, were addressed. All participants expressed that the website was acceptable and balanced in terms of discussion of benefits and harms. Because half (2/4, 50%) of the providers suggested we increase the amount of information, we extended the content on the impact of having an autoimmune disease when considering ICB treatment, the probability of flares, and the management of flares in this context. The feedback led to minor revisions to enhance readability, navigation, and accessibility, ensuring the website's suitability as a decision-making aid. The newly developed website could become a supporting tool to facilitate patient-physician discussion regarding ICBs.

Emerging concepts and success stories in type 1 diabetes research: a roadmap for a bright future.

Type 1 diabetes treatment stands at a crucial and exciting crossroad since the 2022 U.S. Food and Drug Administration (FDA) approval of teplizumab to delay disease development. In this Perspective article, we discuss four major conceptual and practical issues that emerged as key to further advance type 1 diabetes research and therapies. First, collaborative networks leveraging the synergy between the type 1 diabetes research and care community members are key to fostering innovation, know-how and translation into the clinical arena worldwide. Second, recent clinical trials in presymptomatic stage 2 and recent-onset stage 3 disease have shown the promise, and potential pitfalls, of using immunomodulatory and/or beta-cell protective agents to achieve sustained remission or prevention. Third, the increasingly appreciated heterogeneity of clinical, immunological, and metabolic phenotypes and disease trajectories is of critical importance to advance the decision-making process for tailored type 1 diabetes care and therapy. Fourth, the clinical benefits of early diagnosis of beta-cell autoimmunity warrant consideration of general population screening for islet autoantibodies, which requires further efforts to address the technical, organizational and ethical challenges inherent to a sustainable program. Efforts are underway to integrate these four concepts into the future directions of type 1 diabetes research and therapy.

Сравнително проучване на морфологичните качества и люпимостта на яйцата от чисти линии и кръстоски от общоползвателно и яйценосно направление

During the recent decades, the scientific community turned its attention towards the dual purpose lines and crosses that might offer a suitable solution for two problems in poultry breeding - the use of male chickens for meat and the use of female chickens for rearing in alternative types of systems for egg production. Hence, a study with four groups of birds: a dual purpose cross „Salmon“, a dual purpose purebred line „BB“, a laying line „L“ and a laying hybrid line „ISA-Brown“ was conducted. The aim was to compare the morphological traits, as well as the fertility and the hatchability of the eggs, obtained from „ISA-Brown“, compared to the dual purpose „Salmon“ reared at IAS-Kostinbrod, and the local dual purpose and laying lines involved in its creation. As a result of the conducted research, we can conclude that the selection for high performance, larger eggs and the presence of heterosis in hybrids has to some extent a positive influence on most of the morphological traits determining the quality of the eggs produced. In addition, negative consequences for their hatchability, embryo survival and some morphological parameters such as increased width of the egg and increased diameter of the yolk were also observed. On the other hand, in the stock hybrids, compared to the purebred lines and the dual purpose crosses, this can also be considered as a sign of deterioration of the nutritional quality of the eggs.

Predicting protein synergistic effect in Arabidopsis using epigenome profiling

Histone modifications can regulate transcription epigenetically by marking specific genomic loci, which can be mapped using chromatin immunoprecipitation sequencing (ChIP-seq). Here we present QHistone, a predictive database of 1534 ChIP-seqs from 27 histone modifications in Arabidopsis, offering three key functionalities. Firstly, QHistone employs machine learning to predict the epigenomic profile of a query protein, characterized by its most associated histone modifications, and uses these modifications to infer the protein’s role in transcriptional regulation. Secondly, it predicts synergistic regulatory activities between two proteins by comparing their profiles. Lastly, it detects previously unexplored co-regulating protein pairs by screening all known proteins. QHistone accurately identifies histone modifications associated with specific known proteins, and allows users to computationally validate their results using gene expression data from various plant tissues. These functions demonstrate an useful approach to utilizing epigenome data for gene regulation analysis, making QHistone a valuable resource for the scientific community (https://qhistone.paoyang.ipmb.sinica.edu.tw).

An evaluation of trends for mesothelioma mortality in American women: Addressing the content of a recent Morbidity and Mortality Weekly Report (MMWR).

Mesothelioma is a fatal disease that has historically been associated with exposure to airborne asbestos. Because occupational asbestos exposures dropped dramatically in the late 1960s and early 1970s, far fewer cases of mesothelioma today are due to these fibers but, instead, are usually a result of the aging process or genetic predisposition. In May of 2022, a Morbidity and Mortality Weekly Report (MMWR) was issued by the Centers for Disease Control and Prevention (CDC) regarding malignant mesothelioma incidence in women from 1999 to 2020. While this MMWR alerted citizens to the continued presence of the disease, after reading this article one might have thought that the CDC was suggesting that the disease was increasing in women due to asbestos exposures (which it is not). In the present analysis, we investigate several factors related to the interpretation of epidemiological data for mesothelioma, including the role of asbestos as a risk factor over time. The authors conducted a review of the scientific community's understanding of mesothelioma incidence and asbestos exposures amongst women, as well as an investigation of the methods and references in the MMWR article. Although various articles have recently discussed the incidence of both peritoneal and pleural mesothelioma in women, it is fortunate that the age-adjusted rates for mesothelioma have remained flat (neither increased nor decreased significantly) in women for the past 50 years. Incredibly few women in the U. S. have had appreciable cumulative exposures to any type of asbestos (chrysotile, amosite, or crocidolite) in the workplace or from the ambient environment, especially since about 1965-1970. In this paper, we highlight six factors that should be considered when evaluating the incidence of mesothelioma amongst American women in the current era. Without sufficient consideration of these factors, improper conclusions have been drawn over the past several years.

Leveraging a new data resource to define the response of C. neoformans to environmental signals: How host-like signals drive gene expression and capsule expansion in Cryptococcus neoformans.

Cryptococcus neoformans is an opportunistic fungal pathogen with a polysaccharide capsule that becomes greatly enlarged in the mammalian host and during in vitro growth under host-like conditions. To understand how individual environmental signals affect capsule size and gene expression, we grew cells in all combinations of five signals implicated in capsule size and systematically measured cell and capsule sizes. We also sampled these cultures over time and performed RNA-Seq in quadruplicate, yielding 881 RNA-Seq samples. Analysis of the resulting data sets showed that capsule induction in tissue culture medium, typically used to represent host-like conditions, requires the presence of either CO2 or exogenous cyclic AMP (cAMP). Surprisingly, adding either of these pushes overall gene expression in the opposite direction from tissue culture media alone, even though both are required for capsule development. Another unexpected finding was that rich medium blocks capsule growth completely. Statistical analysis further revealed many genes whose expression is associated with capsule thickness; deletion of one of these significantly reduced capsule size. Beyond illuminating capsule induction, our massive, uniformly collected dataset will be a significant resource for the research community.

Enhancing Equity in Clinical Research: A Multifaceted Proposal for Spondyloarthritis.

Clinical research advances medical knowledge and improves healthcare outcomes. However, disparities in research participation hinder progress. The Unmet Research Needs in Spondyloarthritis Conference IV highlighted critical insights and strategies to enhance equity in clinical research. Talks focused on engaging underrepresented communities and addressing disparities in rheumatic diseases, particularly spondyloarthritis (SpA), to ensure research results are generalizable and inclusive. Disparities in SpA management, such as greater back pain severity among Black and Hispanic Americans and sex-based differences in pain management, emphasize the need for equitable research. Dr. Elizabeth Ferucci discussed the racial disparities in rheumatologic care, highlighting the importance of early access to rheumatologists and culturally informed primary care to improve outcomes. Dr. Hani El-Gabalawy's talk on engaging Indigenous communities stressed the importance of community consent and reciprocal benefits. Dr. Sarfaraz Hasni's presentation on mitigating disparities in research participation underscored the need for inclusive practices and strategies to promote diverse representation. Finally, Dr. Edith Williams emphasized institutional approaches to fostering equity, including diverse recruitment practices and institutional review board alignment with diversity priorities. Strategies to enhance equity in clinical research include community engagement, addressing logistical barriers to participation, and ensuring diverse research teams. These approaches can dismantle barriers for underrepresented communities, making research more accessible and reflective of the broader population. The SpA research community must commit to creating structures that foster inclusivity, ensuring medical advancements benefit all populations, especially historically underrepresented groups. The principles and strategies proposed serve as a roadmap for achieving equity in SpA research.

Animal researchers' views on the publication of negative results and subsequent policy adoptions.

For over a decade, the non-publication of negative results from preclinical studies has been identified as a significant concern in biomedical research. Such underreporting is considered a contributor to the reproducibility crisis in the field and has been recognized by significant journals such as Science and Nature. In response to the consistently high non-publication rates of preclinical animal research in Europe, a survey was conducted among the biomedical research community to gather their views on publishing negative results. Using the EUSurvey platform, over 200 researchers directly working with animals were surveyed. The study aimed to understand the frequency of negative results, the reasons behind their non-publication, and the perceived pros and cons of making such results public. Insights from the survey could guide steps toward promoting transparency in science, refining research methodologies, reducing animal usage in experiments and minimizing research waste.

Enhancing Few-Shot Out-of-Distribution Detection with Pre-Trained Model Features.

Ensuring the reliability of open-world intelligent systems heavily relies on effective out-of-distribution (OOD) detection. Despite notable successes in existing OOD detection methods, their performance in scenarios with limited training samples is still suboptimal. Therefore, we first construct a comprehensive few-shot OOD detection benchmark in this paper. Remarkably, our investigation reveals that Parameter-Efficient Fine-Tuning (PEFT) techniques, such as visual prompt tuning and visual adapter tuning, outperform traditional methods like fully fine-tuning and linear probing tuning in few-shot OOD detection. Considering that some valuable information from the pre-trained model, which is conducive to OOD detection, may be lost during the fine-tuning process, we reutilize features from the pre-trained models to mitigate this issue. Specifically, we first propose a training-free approach, termed uncertainty score ensemble (USE). This method integrates feature-matching scores to enhance existing OOD detection methods, significantly narrowing the gap between traditional fine-tuning and PEFT techniques. However, due to its training-free property, this method is unable to improve in-distribution accuracy. To this end, we further propose a method called Domain-Specific and General Knowledge Fusion (DSGF) to improve few-shot OOD detection performance and ID accuracy under different fine-tuning paradigms. Experiment results demonstrate that DSGF enhances few-shot OOD detection across different fine-tuning strategies, shot settings, and OOD detection methods. We believe our work can provide the research community with a novel path to leveraging large-scale visual pre-trained models for addressing FS-OOD detection. The code will be released.

Charting the Future of the Global Anesthesia Research Community: The Vision of the International Anesthesia Research Society.

Charting the Future of the Global Anesthesia Research Community: The Vision of the International Anesthesia Research Society.

Exploring the Feasibility of Social Skills Programs for Autistic Youth Through Virtual Reality.

Many autistic individuals may desire support and services primarily in the areas of adaptive functioning and social well-being throughout their lifetime. There is a need for community-informed and person-centered social programs targeted for autistic adolescents and adults. New technology, such as virtual reality (VR), is being researched to assess the feasibility of providing therapeutic services to autistic individuals. This qualitative study aims to better understand and explore the perceptions of parents and autistic adolescents regarding social development and thoughts around social skills interventions delivered through technologies such as VR. Eight autistic adolescents between the ages of 12 to 17, and five parents participated across five focus groups. The focus group interviews were semi-structured, and qualitative data analysis was conducted through an open thematic approach and inductive coding process. Seven primary themes with sub-themes were identified throughout the focus group interview discussions: Social Skills of the participating autistic adolescents as reported by their parents and by self-report, Family Dynamics affecting social relationships within the family, Social Skills Goals both groups hoped to develop and improve, the existence and quality of In-Person vs. Online Friendships, Experience/Comfort With Technology, Openness to Virtual Environments, and Concerns for Virtual Environments. Researchers identified these themes across both parent and adolescent focus groups. This study provides guidance to the research community on investigating different innovative approaches for offering a social program that is supported by autistic individuals.

Contemporary Methods and Novel Approaches in the Identification and Quantification of Foodborne Pathogens

Foodborne pathogens are a continuous problem attracting the attention of public health institutions, microbiologists and food producers globally. The scientific community has therefore been focused for years on finding “new” and “better” methods, all in an effort to detect foodborne pathogens in the timeliest manner possible. It should be emphasized that the development of molecular genetics – the use of genetic information of biological macromolecules in routine testing in particular – has led to a revolutionary turn in biological science research. Almost all procedures detect different bacterial genetic footprint or biomarkers, which makes bacterial isolation unnecessary. However, these recent studies of “fast microbiological methods”, which require only a fewhours, rather than a few days, have not supplanted the classic way of microbiological food testing, i.e. the classic microbiological methods and the gold standard. The new methods are therefore faced with high requirements such as great detection limits, speed of analysis, relatively low costs and high sensitivity to identify various foodborne pathogens. Some of them provide the possibility of monitoring the pathogens, which is an important part of establishing a pathogen control network in the agri-food production chain at the international level. In this comprehensive literature review the authors present and review identification and quantification methodswith emphasis on the most important EU foodborne pathogens (Salmonella, Campylobacter, Escherichiacoli – STEC, Yersinia and Listeria). Methods have been divided into two large groups – Contemporary methods (Immunoassays and Polymerase Chain Reaction) and Novel approach methods (Biosensors, Bacterial typing, and Omics), and assessed by their functionality, advantages and disadvantages.

The Otoacoustic Emissions in the Universal Neonatal Hearing Screening: An Update on the European Data (2004 to 2024)

Background: The reported data on European universal neonatal hearing screening (UNHS) practices tend to be scarce, despite the fact that the European Union project, EUScreen, collected unofficial data from 38 collaborating European institutions. The objectives of this systematic review were as follows: (a) to identify the most recent (in a 20-year span) literature information about UNHS programs in Europe and (b) to provide data on the procedures used to assess the population, the intervention policies, and on the estimated prevalence of congenital hearing loss with emphasis on the bilateral hearing loss cases. Methods: Queries were conducted via the Pubmed, Scopus and Google Scholar databases for the time period of 2004–2024. The Mesh terms used were “OAE”, “Universal Neonatal Hearing Screening”, “congenital hearing loss” and “well babies”. Only research articles and review papers of European origin were considered good candidates. The standard English language filter was not used, in order to identify information from non-English-speaking scientific communities and groups. Results: Very few data and reports were identified in the literature search. Eleven manuscripts were identified corresponding to eight UNHS programs. Except in Poland, most of the data refer to regional and not national programs. The screening coverage estimates of all programs exceed 90%; infants were mostly assessed by a three-stage protocol (TEOAE + TEOAE + AABR), followed by a clinical ABR test. The average prevalence (i.e., from well babies AND NICU infants) of bilateral hearing loss ranged from 0.5 to 20.94 per 1000 (Zurich sample). Infants presenting unilateral or bilateral hearing losses were first rehabilitated by hearing aids and consequently (>15 mo) by cochlear implants. Conclusions: Even though UNHS programs are well-established clinical practices in the European States, the amount of information in the literature about these programs is surprising low. The existing data in the timespan 2004–2024 corroborate the international UNHS data in terms of coverage and bilateral hearing loss prevalence, but there is a strong need to supplement the existing information with the latest developments, especially in the area of hearing loss rehabilitation.

Wine industry by-products as a source of active ingredients for topical applications

AbstractThe wine industry is responsible for a considerable amount of waste produced by agricultural activities worldwide, which impacts both the economic sector and the environment through pollution and ecosystem imbalance. There are several examples of by-products generated during the winemaking process, such as grape pomace, vine leaves, grape stalks, or wine lees. These can be recovered and reused by the cosmetic industry, which is actively seeking natural and greener products. There are active ingredients that come from by-products that have relevant bioactive properties such as antioxidant, antiaging, anti-hyperpigmentation, or cellular protection. Therefore, the use of by-products from the wine industry as a source of active ingredients for topical application has attracted attention from the scientific community, overcoming some of the drawbacks of the winemaking process. Further research into extraction processes and methods is essential, as they directly influence the quality and quantity of recovered active ingredients. While current cosmetic products on the market undergo safety and cytotoxicity testing, it is important to evaluate the effects of pesticide treatments applied before pruning and the toxicity of the by-products to ensure the safety of future formulations. This review addresses a critical discussion on this subject, assessing the potential benefits of their use in topical formulations. Graphical Abstract

Potential and challenges of clinical high-dimensional flow cytometry: A call to action.

Clinical biomarker strategies increasingly integrate translational research to gain new insights into disease mechanisms or to define better biomarkers in clinical trials. High-dimensional flow cytometry (HDFCM) holds the promise to enhance the exploratory potential beyond traditional, targeted biomarker strategies. However, the increased complexity of HDFCM poses several challenges, which need to be addressed in order to fully leverage its potential and to align with current regulatory requirements in clinical flow cytometry. These challenges include among others extended timelines for assay development and validation, the necessity for extensive knowledge in HDFCM, and sophisticated data analysis strategies. However, no guidelines exist on how to manage such challenges in adopting clinical HDFCM. Our CYTO 2024 workshop "Potential and challenges of clinical high-dimensional flow cytometry" aimed to find consensus across the pharmaceutical industry and broader scientific community on the overall benefits and most urgent challenges of HDFCM in clinical trials. Here, we summarize the insights we gained from our workshop. While this report does not provide a blueprint, it is a first step in defining and summarizing the most pressing challenges in implementing HDFCM in clinical trials. Furthermore, we compile current efforts with the goal to overcome some of these challenges. As such we bring the scientific community and health authorities together to build solutions, which will accelerate and simplify the full adoption of HDFCM in clinical trials.

The translation of transformative policy ambitions in funding research for climate change

Abstract This paper addresses how research and innovation (R&I) policy responds to global challenges, which demand fundamental transformations of societies and economies. The paper presents the case of a transnational, European funding call (SOLSTICE) for climate change research led by social sciences and humanities. Both the development of SOLSTICE and the research community’s responses are analysed in relation to the transformative R&I policy literature, identifying potential future avenues for improving the transformative outcomes of this type of funding. The study concludes that unlocking the value of transformative R&I policy concepts and approaches depends on wide stakeholder engagement in the funding instrument design phase and an active and sustained focus on achieving societal outcomes during project implementation. In addition, barriers to the effectiveness of (European) transnational funding programmes are identified, particularly when policies target community-level socio-technical transitions to address global challenges.

CoFFEE: a codec-based forensic feature extraction and evaluation software for H.264 videos

The forensic analysis of digital videos is becoming increasingly relevant to deal with forensic cases, propaganda, and fake news. The research community has developed numerous forensic tools to address various challenges, such as integrity verification, manipulation detection, and source characterization. Each tool exploits characteristic traces to reconstruct the video life-cycle. Among these traces, a significant source of information is provided by the specific way in which the video has been encoded. While several tools are available to analyze codec-related information for images, a similar approach has been overlooked for videos, since video codecs are extremely complex and involve the analysis of a huge amount of data. In this paper, we present a new tool designed for extracting and parsing a plethora of video compression information from H.264 encoded files, including macroblocks structure, prediction residuals, and motion vectors. We demonstrate how the extracted features can be effectively exploited to address various forensic tasks, such as social network identification, source characterization, and double compression detection. We provide a detailed description of the developed software, which is released free of charge to enable its use by the research community to create new tools for forensic analysis of video files.

Examining the healthy human microbiome concept.

Human microbiomes are essential to health throughout the lifespan and are increasingly recognized and studied for their roles in metabolic, immunological and neurological processes. Although the full complexity of these microbial communities is not fully understood, their clinical and industrial exploitation is well advanced and expanding, needing greater oversight guided by a consensus from the research community. One of the most controversial issues in microbiome research is the definition of a 'healthy' human microbiome. This concept is complicated by the microbial variability over different spatial and temporal scales along with the challenge of applying a unified definition to the spectrum of healthy microbiome configurations. In this Perspective, we examine the progress made and the key gaps that remain to be addressed to fully harness the benefits of the human microbiome. We propose a road map to expand our knowledge of the microbiome-health relationship, incorporating epidemiological approaches informed by the unique ecological characteristics of these communities.

The Understanding America Study (UAS)

PurposeThe Understanding America Study (UAS) is a probability-based Internet panel housed at the Center for Economic and Social Research at the University of Southern California (USC). The UAS serves as...

Equitable community-based participatory research engagement with communities of color drives All of Us Wisconsin genomic research priorities.

The NIH All of Us Research Program aims to advance personalized medicine by not only linking patient records, surveys, and genomic data but also engaging with participants, particularly from groups traditionally underrepresented in biomedical research (UBR). This study details how the dialogue between scientists and community members, including many from communities of color, shaped local research priorities. We recruited area quantitative, basic, and clinical scientists as well as community members from our Community and Participant Advisory Boards with a predetermined interest in All of Us research as members of a Special Interest Group (SIG). An expert community engagement scientist facilitated 6 SIG meetings over the year, explicitly fostering openness and flexibility during conversations. We qualitatively analyzed discussions using a social movement framework tailored for community-based participatory research (CBPR) mobilization. The SIG evolved through CBPR stages of emergence, coalescence, momentum, and maintenance/integration. Researchers prioritized community needs above personal academic interests while community members kept discussions focused on tangible return of value to communities. One key outcome includes SIG-driven shifts in programmatic and research priorities of the All of Us Research Program in Southeastern Wisconsin. One major challenge was building equitable conversations that balanced scientific rigor and community understanding. Our approach allowed for a rich dialogue to emerge. Points of connection and disconnection between community members and scientists offered important guidance for emerging areas of genomic inquiry. Our study presents a robust foundation for future efforts to engage diverse communities in CBPR, particularly on healthcare concerns affecting UBR communities.