Research Protocol Research Articles

Identification of Potent CHK2 Inhibitors‐Modulators for Therapeutic Application in Cancer: A Machine Learning Integrated Fragment‐Based Drug Design Approach

AbstractThe CHK2 protein regulates the cell division cycle and responds to DNA damage. Additionally, it facilitates the repair of DNA damage and maintains the integrity of its biological processes. Dysregulation of the CHK2 protein is associated with a predisposition to harmful diseases. The current research protocol was designed to identify novel hit molecules as CHK2 inhibitors and disrupt the normal biological function of the CHK2 protein via a fragment‐based drug discovery approach. The protocol involved generating fragments using the MacFrag tool, followed by a chemical similarity search utilizing RDKit to identify fragment molecules analogous to previously established CHK2 inhibitor scaffolds. The bioactive molecules were constructed using the Fragmenstein tool, followed by molecular docking simulations to investigate their binding affinity. In addition, pharmacokinetic properties were analyzed, and a molecular dynamics simulation study was conducted to assess the stability of selected compounds with CHK2 protein. Finally, five novel compounds were identified as excellent CHK2 inhibitors through the FBDD and show good binding interactions at active sites of CHK2 with beneficial ADMET properties. This research work presents novel CHK2 inhibitor molecules that have the potential to be utilized in drug discovery, serving as key leads for future advancements in healthcare industries and sectors.

Macrostructural Brain Abnormalities in Spinal Muscular Atrophy: A Case-Control Study.

Most individuals with spinal muscular atrophy (SMA) on disease-modifying therapies continue to have chronic motor impairment. Insights into brain involvement in SMA may open new pathways for adjunctive therapies to optimize outcomes. We aimed to characterize macrostructural brain abnormalities detected by MRI in individuals with SMA compared with peer controls. We conducted a cross-sectional case-control study of children and adults with a confirmed genetic diagnosis of 5q SMA, and peer controls matched by age and sex. Brain MRIs acquired on a 3T MRI scanner through a standardized research protocol were reviewed to qualitatively assess the presence of macrostructural changes. The primary outcome was the presence of any structural brain anomaly on MRI. In addition, the total volume of each participant's lateral ventricles was quantified by volumetry using MRIcron. Genetic and clinical variables, including SMN2 copy number and motor function (Hammersmith Functional Motor Scale Expanded and Revised Upper Limb Module scores), were then correlated with neuroimaging findings. A total of 42 participants completed the study (mean age 17.4, range 7-40; 67% male). Of the 21 individuals with 5q SMA, 9 (43%) had macrostructural brain abnormalities identified on MRI compared with 2 of 21 (10%) peer controls (odds ratio 7.1, 95% confidence interval 1.4-34.0). In patients with SMA, the most common structural changes were widening of the arachnoid spaces (n = 4) and ventriculomegaly (n = 4). Individuals with SMA had larger median lateral ventricular volume than their normally developing peers (9.3 mL, interquartile range [IQR] 5.5-13.1 vs 5.3 mL, IQR 3.8-9.8; p = 0.034). Structural brain abnormalities were more frequent in those with 2 SMN2 copies (3/5, 60%) compared with 3 or 4 SMN2 copies (4/10, 40% and 2/6, 33% respectively), not reaching significance. We found no association between structural changes and motor function scores. Individuals with SMA have higher rates of macrostructural brain abnormalities than their neurotypical peers, suggesting CNS involvement in SMA. Understanding changes in the brain architecture of the SMA population can inform the development of adjunct therapies targeting the CNS and potentially guide rehabilitation strategies.

Does exposure matter? Association between exposure to clinical trial conduct during training and intent to participate in clinical trials post-training among oncology fellows: An ASCO State of Cancer Care in America study.

69 Background: Clinical trials are part of standard cancer care. Yet, a quarter of oncology fellows in a 2023 survey reported feeling underprepared to conduct research after training and nearly half did not identify research as important to their practice. In a 2024 survey, we explore the impact of exposure to research activities in fellowship on intentions to conduct research post-training. Methods: Fellows who took the 2024 ASCO Medical Oncology In-Training Exam (ITE) were invited to an optional IRB-exempted post-exam survey to measure (1) research exposure during training and (2) anticipated research participation once in practice. Responses of moderate and great amount are combined as frequent (vs. never, rarely, occasionally as not frequent). Rates of frequent research engagement in future practice are compared by frequent/not frequent research exposure during fellowship, expected practice setting, and program year using chi-squared analysis. Results: Of the 1884 US medical oncology fellows taking the ITE, 1491 (79%) participated in this study, 33% 1st year, 37% 2nd year, 39% 3rd year. 891 (60%) expect their first post-training role to be in academics, 527 (35%) in a non-academic practice, and 67 (5%) in other settings. Anticipated engagement in enrollment and management of participants on clinical trials post-training was associated with exposure to those activities in fellowship and with expected practice setting. Overall, 827 (63%) anticipate frequent participation in research once in practice. 531 (76%) of 701 with frequent exposure in training compared to 296 (37%) of 790 with not frequent exposure anticipate frequent participation in practice (p<0.001). 610 (78%) of fellows expecting to practice in an academic setting vs. 192 (40%) in a non-academic setting anticipate frequent future participation in practice (p<0.001). For research leadership activities (writing clinical research protocols, applying for clinical research grants, serving as principal investigator), 622 (49%) anticipate frequent participation once in practice. 390 (79%) of 519 with frequent vs. 229 (29%) of 855 with not frequent exposure to leadership activities during fellowship anticipate frequent future engagement (p<0.001). 523 (67%) of fellows expecting to practice in an academic setting vs. 76 (16%) in a non-academic setting anticipate frequent leadership engagement after training (p<0.001). Anticipated future participation did not vary by program year for either type of research activity. Conclusions: Findings show an urgent need to increase exposure to research during fellowship training to improve participation in clinical trials by practicing oncologists. This is a critical component of improving patient access to research.

Metabolomic signature identifies HDL and apolipoproteins as potential biomarker for systemic sclerosis with interstitial lung disease

BackgroundHigh-density lipoproteins (HDL) affect endothelial functions such as the expression of endothelial cell adhesion molecules and exert anti-apoptotic/-thrombotic functionalities. Therefore, profound analysis of lipoproteins may unveil biomarkers for (micro-)vasculopathy in systemic sclerosis (SSc) and mortality determining disease manifestations like interstitial lung disease (SSc-ILD). Because nuclear magnetic resonance (NMR) spectroscopy provides a wide range of lipoprotein parameters beyond the capabilities of classical analyses it has been used herein to examine lipoprotein profiles in SSc. MethodsTo detect the metabolic and lipidomic profile serum samples from clinically well-characterized SSc patients (n = 100) and age-and sex-matched healthy controls (n = 40) were analyzed by 1H NMR spectroscopy using Bruker's in-vitro diagnostic research (IVDr) protocol. Statistical analyses were performed to validate significant findings and to search for associations between lipoproteins and clinical phenotypes. ResultsPatients with SSc-ILD and lung fibrosis displayed reduced HDL levels. Furthermore, a reduction in apolipoprotein A1 + A2 and its HDL fractions reflected a distinct lipoprotein profile for SSc-ILD patients. This association was independent of potential clinical confounders for dyslipidemia. Notably, in SSc-ILD HDL levels correlate with FVC (forced vital capacity), DLCO (diffusion capacity of the lungs for carbon monoxide), and the modified Rodnan-Skin-Score. ConclusionThese results suggest HDL and its lipoproteins may be considered as potential new biomarkers for SSc-ILD. Immune-mediated HDL effects on the endothelium facilitate microvasculopathy - one of the pathophysiological hallmarks in SSc. Therefore, a closer prospective evaluation of the capability of HDL-determination and its lipoproteins regarding a more individualized evaluation of SSc-ILD is warranted.

Screening tools for autism in culturally and linguistically diverse paediatric populations: a systematic review

BackgroundAutism Spectrum Disorder (ASD) has varying prevalence rates worldwide, often higher in culturally diverse populations. Cultural differences can affect autism symptom recognition. Language barriers and differing healthcare attitudes may delay diagnosis and intervention. Most autism screening tools were developed in Western, predominantly Caucasian populations, and their appropriateness in culturally and linguistically diverse (CALD) contexts remains uncertain. There is a lack of comprehensive data on the accuracy of these tools in identifying autism in culturally and linguistically diverse groups. Consequently, it is unclear whether current screening tools are culturally sensitive and appropriate.MethodsA research protocol was registered in PROSPERO (CRD42022367308). A comprehensive search of literature published from inception to October 2022 was conducted using the following databases: PubMed, Medline Complete, Scopus, PsychInfo and CINAHL Complete. The articles were screened using pre-determined inclusion and exclusion criteria. Data extracted included participant demographics, screening tool psychometric properties (validity, reliability, accuracy) and acceptability. A narrative synthesis approach was used.ResultsFrom the initial retrieval of 2310 citations, 51 articles were included for analysis. The studies were conducted in 32 different countries with screening tools in the following languages: Chinese, Spanish, Korean, Turkish, Arabic, Kurdish, Persian, Serbian, Italian, French, Sinhala, Taiwanese, Finnish, Northern Soho, Albanian, German, Japanese, Vietnamese, Farsi, Greek and English. There was no data on acceptability of the screening tools in CALD populations. Validity, reliability, and accuracy ranged from poor to excellent with consistently high performance by screening tools devised within the populations they are intended for.ConclusionsThe review evaluated autism screening tools in culturally diverse populations, with a focus on validity, reliability, and acceptability. It highlighted variations in the effectiveness of these tools across different cultures, with high performance by tools devised specifically for the intended population, emphasizing the need for culturally sensitive screening tools. Further research is needed to improve culturally specific, reliable autism screening tools for equitable assessment and intervention in diverse communities.

Antibody–drug conjugates and immune checkpoint inhibitors in cancer treatment: a systematic review and meta-analysis

Although antibody–drug conjugate (ADC) or immune checkpoint inhibitors (ICIs) alone fosters hope for the treatment of cancer, the effect of single drug treatment is limited and the safety profile of ADC and ICI therapy remains unclear. This meta-analysis aimed to examine the efficacy and safety of the combination of ADC and ICI therapy. This study type is a systematic review and meta-analysis. Literature retrieval was carried out through PubMed, Embase, Cochrane from inception to Jun. 5, 2024. Then, after data extraction, overall response rate (ORR) and adverse effects (AEs) were used to study its efficiency and safety. Publication bias was also calculated through Funnel plot, Begg's Test and Egger's test. Heterogeneity was investigated through subgroup and sensitivity analysis. The research protocol was registered with the PROSPERO (CRD42023375601). A total of 12 eligible clinical studies with 584 patients were included. The pooled ORR was 58% (95%CI 46%, 70%). Subgroup analysis showed an ORR of 77% (95%CI 63%, 91%) in classical Hodgkin lymphoma (cHL) and an ORR of 73% (95%CI 56%, 90%) in non-Hodgkin lymphoma (NHL). The most common AEs was peripheral neuropathy (38.0%). Meanwhile, AEs on skin (13.1–20.0%) and digestive system (9.0–36.0%) was hard be overlooked. ADC + ICI therapy may be recommended in cancer treatment, especially in cHL and NHL. However, strategies to manage toxicities warranted further exploration.

Public Perspectives on Consent for and Governance of Biobanking in Japan.

Through strengthened biobank governance, broad consent has been widely accepted as a means to replace donors' discretion based on the information of individual research protocols. Trust and other ethical and social notions, such as reciprocity and solidarity, are key concepts that support biobank governance. The types of allowed broad consent are several; however, they remain unclear, and whether these ethical and social notions are associated with public attitudes toward the consent model is not fully understood. This quantitative study examined two hypotheses: narrower and limited broad consent are more accepted by the public, and acceptance rates for broad consent increase with established measures related to biobank governance. This analysis supported both hypotheses, implying that the limited type of broad consent should be considered an important option, and that a specific type of governance is critical in promoting trust, reciprocity, and solidarity between biobanks and the public.

Hair cortisol sampling as a measure of physiological stress in youth with acute musculoskeletal pain

Stress physiology contributes to health outcomes. Hair cortisol concentration (HCC) is an objective measure of cumulative cortisol secretion associated with health, including pain. The aim of the current study was to describe associations between pre-injury stress physiology (as measured by HCC), acute pain characteristics and relevant demographic factors (i.e., BMI, age, sex, days since injury) in youth with an acute musculoskeletal (MSK) injury. Participants were 58 youth aged 11 to 17 with acute MSK pain. Participants completed self-report measures assessing pain intensity, pain catastrophizing, and pain interference. Hair was collected within 1 month after injury using hair cortisol collection procedures adapted from published research protocols. Correlations examining associations among HCC values and clinical/demographic factors revealed that higher HCC was associated with lower body mass index (BMI) and male sex. HCC was not associated with pain variables or age. Additional research is needed to clarify the relation between HCC and psychosocial variables to aid researchers in studying the role of pre-injury stress in acute MSK injury and pain recovery in youth.

From the Bio-Psycho-Social Model to the Development of a Clinical-Forensic Assessment Tool for Chronic Pain in Victims of Violence: A Research Protocol.

Violence against women impacts a minimum of 35% of the global female population, encompassing sexual, physical, and psychological forms. Perpetrators of this violence include partners, family members, or strangers. Its ramifications are substantial, evident in the prevalence of chronic pain reported by between 48% and 84% of women who have experienced abuse, with an odds ratio of 2.08. Notably associated diagnoses include pelvic/vaginal pain, fibromyalgia, irritable bowel syndrome/bowel symptoms, abdominal pain, migraine/headache, and back and neck pain. These diagnoses significantly limit a woman's ability to participate in daily activities, such as exercising or working, leading to genuine disability. Despite substantial evidence, the precise cause and etiology of these conditions remain unclear. Adhering to the bio-psycho-social model, it is conceivable that chronic pain in victims of violence cannot be attributed to a single factor alone, but rather to a combination of all three: biological, psychological, and social factors. Uncovering these factors could have significant clinical and legal implications. On one hand, it would be possible to conduct screenings to avoid developing chronic pain. and guide individuals toward the correct treatment. On the other hand, victims could seek compensation for chronic pain resulting from violence. Considering the limited knowledge about the causes of chronic pain and the absence of tools to identify risk factors or a set of tests for evaluating victims of violence, the goal of the research described in this project protocol is to pinpoint the specific contributing factors for chronic pain due to violence victimization. Additionally, it aims to devise a comprehensive protocol for assessing these factors in forensic science.

Antibacterial and therapeutic potential of historic deposits of silesian healing clay – terra sigillataSilesiaca

Ethnopharmacological relevanceThe increasing evolution of pathogen resistance is a global problem that requires novel solutions. Recently, an increased interest in ethnomedicinal sources can be observed in the derivation of new medicines. The return to traditional medicinal formulations handed down for generations is being followed, but it is necessary to revise them again, taking into account the generally accepted research protocol. Aim of the studyWe aimed to evaluate the antimicrobial potential of historical deposits of Silesian healing clay (SHC), used in ethnomedicine against Gram-positive bacteria and to assess their biological activity using a primary dermal fibroblast line (NHDF) and a model monocyte line (THP1). Materials and methodsInformation on medicinal clay deposits that occur in Silesia and are traditionally used in ethnomedicine or ancient medicine and known as terra sigillata Silesiaca or SHC, was selected on available source materials and old prints and maps from the archives of the Polish Geological Institute (Wrocław, Poland). Subsequently, their places of occurrence were identified and traced in the field by taking three deposits from the Silesia territory: Upper Silesia (D1), Opole Silesia (D2), and Lower Silesian (D3) Voivodeships for analysis. Their basic parameters and antimicrobial efficacy against pathogenic bacteria, Gram-positive streptococci and staphylococci, including methicillin-resistant strains, were examined. The study evaluated the effects of clays on growth and vitality using a primary dermal fibroblast line (NHDF) and a monocytic line (THP1). Studies were performed on a cell culture model to determine the effects on tissue regeneration (fibroblasts) and anti-inflammatory effects (monocytes). The study attempted to identify the mechanism of antimicrobial action, especially the textural characteristics and geochemical composition, as well as the environmental reaction (pH). ResultsSHCs were classified into the following textural classes: clay loam (D1), clay (D2), and sand (D3). The tested deposits have antimicrobial properties that reduce the bacterial population (104 CFU) compared to the control (108 CFU). The antimicrobial effect depends on the type of clay and the species or strain of bacteria used. In-house studies clearly showed that Staphylococcus aureus Pcm 2054 and Staphylococcus epidermidis MRSE ATCC 2538 cells were completely adsorbed by clay minerals from clay D3.13. Furthermore, 10% leachates also showed an antimicrobial effect, as a reduction in bacterial populations was observed ranging from 91 to 100%. The results showed stimulation of fibroblast culture proliferation and inhibition of the growth of inflammatory cells (monocytes). ConclusionSHCs tested have antimicrobial potential, in particular D2.7, D2.11, and D3.13. The D3.13 deposit had a bactericidal effect against the staphylococci tested. Aqueous solutions of clays also showed bacteriostatic effect. The results obtained in cell culture model tests indicate properties that modulate the healing process – stimulation of fibroblast growth (NHDF line) and inhibition of monocyte growth (THP1 line).

Rare diseases, trends and challenges for scientific advances: a snapshot of a decade of research in Brazil

Brazil is home to around 13 million rare disease patients, which represents a significant challenge for biomedical research and public health. This descriptive and exploratory study analyzed research protocols on rare diseases submitted to Plataforma Brasil between 2013 and 2023, with the aim of identifying trends, challenges and opportunities for scientific progress in this area. The research evaluated variables such as the number of studies submitted and approved, sample characteristics, type of study, experimental design, research phase, participation in international networks, and epidemiological data (ICD). The results indicate a substantial increase in the number of protocols submitted over the period analyzed, with an average approval rate of 87.26%. Most of the studies were conducted in public institutions, highlighting the fundamental role of the public sector in rare disease research in Brazil. These findings suggest a growing investment and interest in research in this area, which could boost the development of new therapies and interventions, as well as supporting the formulation of more effective public policies to meet the needs of patients with rare diseases.

Evaluation of learning in emergency medicine: An umbrella IRB protocol for education outcomes research.

Evaluation of learning in emergency medicine: An umbrella IRB protocol for education outcomes research.

Co-producing and co-assessing a new service solution for enhancing health and social care integration: a participatory research protocol

BackgroundThis paper describes a study protocol for co-producing and co-assessing a new sustainable and scalable service solution that enhances health and social integration by involving providers and volunteers delivering services for elderly people in the province of Cremona (Italy), where the elderly population will reach 27% in 2023.MethodsThis upcoming study involves mixed-method participatory research and is structured in three study phases and related objectives. First, it will co-produce a new, accessible and sustainable service solution using an iterative design and management method, Plan-Do-Check-Act by involving professionals and volunteers of a heterogeneous group of health, social and third sector organizations located in the city of Cremona (Italy). Second, the study protocol will co-assess the outcomes of the new service solution using a mixed-method approach for measuring the outcomes on: professionals and volunteers (micro level) and their health, social and third sector organizations (meso level). Third, this study will co-investigate the scalability of the new solution promoting health and social integration in other similar urban areas of the Province of Cremona via the Intervention Scalability Assessment Tool (macro level). The data will be collected through the analysis of official documents, websites, policies and participatory workshops.DiscussionThis protocol proposes an innovative intervention, a novel participatory approach, and an unexplored scalability assessment tool in the context of health and social care integration. This study aims to support professionals from health and social care service providers and volunteers from third-sector organizations to collaborate and integrate each other’s resources. In doing so, the participatory approach will facilitate the co-creation of an effective response to the need of health and social integration, and the development of trustful relationships between health and social care service providers. Moreover, the adoption of Plan-Do-Check-Act and Intervention Scalability Assessment Tool will ensure the quality, scalability and sustainability of the new service solution in other settings.

Human Rights in Science: Observations From Ethics Committees on Medical Research Protocols

Objective: To determine the frequency with which Research Ethics Committees (RECs) identify breaches of ethical principles in research protocols. Theoretical Framework: Ethical principles in human research are established in the Nuremberg Code (informed consent and the common good), the Declaration of Helsinki (protection of vulnerable groups), and the Belmont Report (autonomy, beneficence, and justice). These principles are monitored by RECs to protect participants and ensure fairness in resource use. Informed consent ensures autonomy and the integrity of the research. Method: Searches were conducted in PubMed, Scopus, and Google Scholar up to November 30, 2023. A meta-analysis of single proportions was performed. PROSPERO Registration: CRD42021291893 Results and Discussion: Nine publications were reviewed, revealing violations of the principle of justice in up to 100% of protocols. In Latin America, violations were observed in 9% (95% CI: 7-12) of protocols, while in Europe, the rate was 15% (95% CI: 9-24). Autonomy was observed in 26% (95% CI: 20-33) of protocols, with 17% (95% CI: 13-22) in experimental studies. Observations on beneficence varied between 41.17% and 77.38%. Protocol-specific observations ranged between 5.26% and 27.11%, showing regional disparities among study types. RECs must ensure thorough evaluations to uphold autonomy and maximize benefits for participants. Research Implications: Provide a foundation for future investigations on the work of RECs, the implementation of ethical principles, and equity in research. Originality/Value: The publication of observations on ethical principles made by the Research Ethics Committees is essential for drafting new research protocols.

Transplacental Transmission of SARS-CoV-2: A Narrative Review.

Background and Objectives: The study aims to explore the potential for transplacental transmission of SARS-CoV-2, focusing on its pathophysiology, placental defense mechanisms, and the clinical implications for maternal and neonatal health. Materials and Methods: A comprehensive review of the current literature was conducted, analyzing studies on SARS-CoV-2 infection in pregnancy, the expression of key viral receptors (ACE2 and TMPRSS2) in placental cells, and the immune responses involved in placental defense. The review also examined the clinical outcomes related to maternal and neonatal health, including adverse pregnancy outcomes and neonatal infection. Results: The expression of ACE2 and TMPRSS2 in the placenta supports the biological plausibility of SARS-CoV-2 transplacental transmission. Histopathological findings from the infected placentas reveal inflammation, vascular changes, and the evidence of viral particles in placental tissues. Clinical reports indicate an increased risk of preterm birth, intrauterine growth restriction, and neonatal infection in pregnancies affected by COVID-19. However, the frequency and mechanisms of vertical transmission remain variable across studies, highlighting the need for standardized research protocols. Conclusions: SARS-CoV-2 can potentially infect placental cells, leading to adverse pregnancy outcomes and neonatal infection. While evidence of transplacental transmission has been documented, the risk and mechanisms are not fully understood. Ongoing research is essential to clarify these aspects and inform obstetric care practices to improve maternal and neonatal outcomes during the COVID-19 pandemic.

Research protocol for bridging research, accurate information and dialogue (BRAID)-clinical trials: a mixed-methods study of a community-based intervention to improve trust and diversify participation in clinical trials.

Cultural beliefs, personal experiences, and historic abuses within the healthcare system-rooted in structural racism-all contribute to community distrust in science and medicine. This lack of trust, particularly within underserved communities, contributes to decreased participation in clinical trials and a lack of representation in the data. Open dialogue about community concerns and experiences related to research participation and medical care processes can help build trust and change attitudes and behaviors that affect community health. This protocol outlines an approach to increase trust in science and clinical trials among communities in the Bronx, New York that are typically underrepresented in research data. Bridging Research, Accurate Information and Dialogue (BRAID) is a two-phased, evidence-based community engagement model that creates safe spaces for bilateral dialogues between trusted community messengers, and clinicians and scientists. The team will conduct a series of BRAID Conversation Circles on the topic of clinical trials with local trusted community messengers. Participants will be members of the community who are perceived as "trusted messengers" and can represent the community's voice because they have insight into "what matters" locally. Conversation Circles will be audiotaped, transcribed, and analyzed to identify emergent challenges and opportunities surrounding clinical trial participation. These key themes will subsequently inform the codesign and co-creation of tailored messages and outreach efforts that community participants can disseminate downstream to their social networks. Surveys will be administered to all participants before and after each Conversation Circle to understand participants experience and evaluate changes in knowledge and attitudes about clinical trials, including protections for research participants the advantages of having diverse representation. Changes in motivation and readiness to share accurate clinical trial information downstream will also be assessed. Lastly, we will measure participants dissemination of codesigned science messages through their social networks by tracking participant specific resource URLs of materials and videos posted on a BRAID website. This protocol will assess the effectiveness and adoptability of an innovative CBPR model that can be applied to a wide range of public health issues and has the potential to navigate the ever-changing needs of the communities that surround health systems.

Celiac disease gut microbiome studies in the third millennium: reviewing the findings and gaps of available literature.

Celiac disease is an autoimmune enteropathy caused by the ingestion of minute amounts of gluten in a subset of genetically predisposed individuals. Its onset occurs at different ages and with variable symptoms. The gut microbiome may contribute to this variability. This review aims to provide an overview of the available research on celiac disease gut microbiome and identify the knowledge gap that could guide future studies. Following the guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-analysis extension for Scoping Reviews (PRISMA-ScR), four electronic databases were searched for literature from January 2000 to July 2023 addressing celiac disease gut microbiome characterization using next-generation sequencing (NGS) approaches. From the 489 publications retrieved, 48 publications were selected and analyzed, focusing on sample characterization (patients, controls, and tissues) and methodologies used for NGS microbiome analysis and characterization. The majority of the selected publications regarded children and adults, and four were randomized clinical trials. The number of participants per study greatly varied and was typically low. Feces were the most frequently tested sample matrix, and duodenal samples were analyzed in one-third of the studies. Incomplete and diverse information on the methodological approaches and gut microbiome results was broadly observed. While similar trends regarding the relative abundance of some phyla, such as Pseudomonadota (former Proteobacteria), were detected in some studies, others contradicted those results. The observed high variability of technical approaches and possibly low power and sample sizes may prevent reaching a consensus on celiac disease gut microbiome composition. Standardization of research protocols to allow reproducibility and comparability is required, as interdisciplinary collaborations to further data analysis, interpretation, and, more importantly, health outcome prediction or improvement.

Research Methodology and Biostatistics Series III - Medical Research Protocol

Research Methodology and Biostatistics Series III - Medical Research Protocol

Real-world phenotyping and risk assessment of childhood asthma burden using national registries

BackgroundPhenotype classification contributes to risk assessment of asthma. Previous studies have applied this concept primarily to adult populations and in the setting of research protocol assessments which may not be applicable to clinical settings. ObjectiveExploring the value of routinely collected clinical data for phenotype classification and risk assessment of childhood asthma. MethodsUsing hospital and laboratory data, 29,851 children in a Danish nationwide database aged 2–17 years with ICS-treated asthma in 2015 followed for two years (730 days) were classified to have T2 (elevated blood eosinophils (>300 cells/μL) and/or elevated total- or specific-IgE), and/or non-T2 risk factors (in utero tobacco exposure and/or severe viral infections). Logistic regression was applied to quantify associations of risk factors with asthma severity, control, and exacerbation risk. ResultsIn a complete case analysis, 85.8 % children had at least one T2 risk factor and 29.3 % had mixed T2/non-T2 risk factors. Elevated blood eosinophils and total/specific IgE were associated with exacerbations (ORs 1.55 (1.38–1.73) and 1.41 (1.20–1.66) and higher asthma severity (1.42 (1.24–1.63) and 1.31 (1.08–1.60)), respectively.Dose-dependency was observed between blood eosinophil counts, total IgE levels, and risk of adverse outcomes. Furthermore, accumulation of risk factors demonstrated an increasing risk, with children with all four risk factors having a high risk of any adverse asthma-related outcome (OR 3.13 (2.03–4.82) ConclusionAsthma phenotypic markers defined in research protocols can be reliably applied in real-world settings by utilizing data collected during routine clinical care and enable better classification of risk of adverse asthma outcomes.

451 Establishing producer research sites for the development of beef and bison climate-smart agriculture

Abstract Greenhouse gas (GHG) emissions and livestock production are topics that are increasingly intertwined. While livestock production is frequently presented as harmful to the environment, this perception fails to consider the carbon sequestration that takes place in livestock grazing systems and the role that grazing ruminants have in maintaining healthy grassland ecosystems. Grazing lands, which are often unsuited to row crop agriculture, are estimated to account for 25% of the global soil sequestration potential for soil carbon storage. Grazing livestock producers are often overlooked in the GHG reduction conversation, despite over 70% of beef GHG emissions being attributed to the cow-calf sector, which is primarily grazing. Furthermore, there is a relative lack of data surrounding the implementation of climate-smart agriculture practices on grazing operations and a lack of cost-effective methods to measure carbon/GHG sinks and sources on these landscapes. The potential climate benefits are considerable, with nearly 940 million acres of rangelands in the U.S. supporting forage-based livestock production. South Dakota State University recently received funding to support a large-scale climate-smart project focused on grazing beef and bison. For this project, we are utilizing the Cottonwood Field Station that has over 80 yr of historical grazing data, along with six grazing beef and bison ranching operations in the Northern Great Plains. The work on these ranches will focus on measuring and monitoring the impacts of climate-smart NRCS land practices, including cover crops, improved pasture and range seedings, prescribed grazing, and prescribed burning. A significant focus will be extensive, annual soil sampling across these operations to continuously monitor changes in soil organic carbon, bulk density, texture, pH, and soil microbiome community profiles. Each operation will have GreenFeed methane pasture units deployed for 5 yr to monitor changes in beef cattle and bison methane emissions in response to climate-smart practice adoption. We are also assessing biodiversity pre and post climate-smart practice adoption, as biodiversity improvements may be one of the most overlooked and yet most important responses to climate-smart land practice implementation. Over the duration of this project, a large-scale, comprehensive data collection will be achieved and used to refine GHG and carbon sequestration estimates associated with range livestock systems. Data resulting from this project will be used to inform research protocols and prediction models, fill knowledge gaps, and shape science-based discussions and marketing strategies for climate-smart agricultural commodities.