Evaluating and extending the Informed Consent Ontology for representing permissions from the clinical domain

The purpose of this study was to evaluate, revise, and extend the Informed Consent Ontology (ICO) for expressing clinical permissions, including reuse of residual clinical biospecimens and health data. This study followed a formative evaluation design and used a bottom-up modeling approach. Data were collected from the literature on US federal regulations and a study of clinical consent forms. Eleven federal regulations and fifteen permission-sentences from clinical consent forms were iteratively modeled to identify entities and their relationships, followed by community reflection and negotiation based on a series of predetermined evaluation questions. ICO included fifty-two classes and twelve object properties necessary when modeling, demonstrating appropriateness of extending ICO for the clinical domain. Twenty-six additional classes were imported into ICO from other ontologies, and twelve new classes were recommended for development. This work addresses a critical gap in formally representing permissions clinical permissions, including reuse of residual clinical biospecimens and health data. It makes missing content available to the OBO Foundry, enabling use alongside other widely-adopted biomedical ontologies. ICO serves as a machine-interpretable and interoperable tool for responsible reuse of residual clinical biospecimens and health data at scale.

Characterizing the genetic basis of trait evolution in the Mexican cavefish

Evolution in response to a change in ecology often coincides with various morphological, physiological, and behavioral traits. For most organisms little is known about the genetic and functional relationship between evolutionarily derived traits, representing a critical gap in our understanding of adaptation The Mexican tetra, Astyanax mexicanus, consists of largely independent populations of fish that inhabit at least 30 caves in Northeast Mexico, and a surface fish population, that inhabits the rivers of Mexico and Southern Texas. The recent application of molecular genetic approaches combined with behavioral phenotyping have established A. mexicanus as a model for studying the evolution of complex traits. Cave populations of A. mexicanus are interfertile with surface populations and have evolved numerous traits including eye degeneration, insomnia, albinism and enhanced mechanosensory function. The infertility of different populations from the same species provides a unique opportunity to define the genetic relationship between evolved traits and assess the co-evolution of behavioral and morphological traits with one another. To define the relationships between morphological and behavioral traits, we developed a pipeline to test individual fish for multiple traits. This pipeline confirmed differences in locomotor activity, prey capture, and startle reflex between surface and cavefish populations. To measure the relationship between traits, individual F2 hybrid fish were characterized for locomotor behavior, prey-capture behavior, startle reflex and morphological attributes. Analysis revealed an association between body length and slower escape reflex, suggesting a trade-off between increased size and predator avoidance in cavefish. Overall, there were few associations between individual behavioral traits, or behavioral and morphological traits, suggesting independent genetic changes underlie the evolution of behavioral and morphological traits. Taken together, this approach provides a novel system to identify genes that underlie naturally occurring genetic variation in morphological and behavioral traits.

An alternative model of gravitational forces in nature using the combined effects of repulsion and attraction forces on gaseous molecules

Laboratory experiments and natural phenomena investigations in this research series experimentally revealed the existence of gravitational repulsion force dependent on thermal energy content, pervading our surroundings both microscopically and macroscopically. This paper presents an alternative mathematical model of both gravitational repulsion and attraction forces between two gaseous molecules, validated by experimental data. The model is self-standing and independent of existing models built on idealistic assumptions. While existing models considered gravitational interaction as a single force, the presented experimental model considers it the resultant of two distinct forces: gravitational repulsion and attraction. When established experimental data on nitrogen, hydrogen, oxygen, water vapor, carbon monoxide and carbon dioxide were applied, the model performed, both analytically and experimentally: (1) confirming the existence of both gravitational repulsion and attraction forces among gas molecules, (2) demonstrating that the two forces follow Inverse-Cube relationship with the distance between molecules, (3) revealing that repulsion force is linearly proportional to the absolute temperature, thus filling the critical gap between energy and fundamental forces. Orders of magnitude of gravitational repulsion and attraction forces are very large compared to the gravitational force between gas molecules calculated according to the classical theory, enabling manipulation to achieve hitherto unknown outcomes and developments.

Monosomy X in isogenic human iPSC-derived trophoblast model impacts expression modules preserved in human placenta

Mammalian sex chromosomes encode homologous X/Y gene pairs that were retained on the male Y and escape X chromosome inactivation (XCI) in females. Inferred to reflect X/Y-pair dosage sensitivity, monosomy X is a leading cause of miscarriage in humans with near full penetrance. This phenotype is shared with many other mammals but not the mouse, which offers sophisticated genetic tools to generate sex chromosomal aneuploidy but also tolerates its developmental impact. To address this critical gap, we generated X-monosomic human induced pluripotent stem cells (hiPSCs) alongside otherwise isogenic euploid controls from male and female mosaic samples. Phased genomic variants of these hiPSC panels enable systematic investigation of X/Y dosage-sensitive features using in vitro models of human development. Here, we demonstrate the utility of these validated hiPSC lines to test how X/Y-linked gene dosage impacts a widely-used model for the human syncytiotrophoblast. While these isogenic panels trigger a GATA2/3 and TFAP2A/C -driven trophoblast gene circuit irrespective of karyotype, differential expression implicates monosomy X in altered levels of placental genes, and in secretion of placental growth factor (PlGF) and human chorionic gonadotropin (hCG). Remarkably, weighted gene co-expression network modules that significantly reflect these changes are also preserved in first-trimester chorionic villi and term placenta. Our results suggest monosomy X may skew trophoblast cell type composition, and that the pseudoautosomal region likely plays a key role in these changes, which may facilitate prioritization of haploinsufficient drivers of 45,X extra-embryonic phenotypes.

Behavior change techniques utilized in Canadian online smoking cessation programs: A content analysis (Preprint)

BACKGROUND Smoking rates in Canada remain unacceptably high, and cessation rates have stalled in recent years. Online cessation programs, touted for their ability to reach many different populations anytime, have shown promise in their efficacy. The Government of Canada has therefore funded provincial and national smoking cessation websites across the country. However, little is known about the behavior change techniques (BCTs) that underpin the content of these websites, which is key to establishing the quality of the websites, as well as a way forward for evaluation. OBJECTIVE The purpose of this study, therefore, was to apply the BCTTv1 taxonomy to Canadian provincial and federal websites and determine which BCTs they use. METHODS A total of 12 government-funded websites across Canada were included for analysis. Using deductive content analysis, and through training in applying the BCTTv1 taxonomy, the website content was coded according to the 93 BCTs across the 16 BCT categories. RESULTS Of the 16 BCT categories, 14 were present within the websites. The most widely represented BCT categories (used in all 12 websites) included: 1. Goals and planning, 3. Social support, 5. Natural consequences, and 11. Regulation. The most saturated BCT categories (those most heavily used) included: 10. Reward and threat, 12. Antecedents, 1. Goals and planning, and 5. Natural consequences. Implementation of BCTs within these categories varied across the sites. CONCLUSIONS This study addresses a critical gap in knowledge around the behavior change techniques that underpin government-funded smoking cessation websites in Canada. The findings offer programmers and researchers with tangible directions for prioritizing and enhancing provincial and national smoking cessation programs, and an evaluation framework to assess smoking cessation outcomes in relation to the web-based content.

The CORE (Consensus on Relevant Elements) Approach to Determining Initial Core Components of an Innovation

Identifying an intervention's core components is indispensable to gauging whether an intervention is implemented with fidelity and/or is modified; it is often a multi-stage process, starting with the first stage of identifying an initial set of core components that are gradually refined. This first stage of identifying initial core components has not been thoroughly examined. Without a clear set of steps to follow, interventions may vary in the rigor and thought applied to identifying their initial core components. We devised the CORE (Consensus on Relevant Elements) approach to synthesize opinions of intervention developers/implementers to identify an intervention's initial core components, particularly applicable to innovative interventions. We applied CORE to a peer-based intervention that aids military veterans with post-incarceration community reintegration. Our CORE application involved four intervention developers/implementers and two moderators to facilitate the seven CORE steps. Our CORE application had two iterations, moving through Steps 1 (individual core component suggestions) through 7 (group discussion for consensus), then repeating Steps 4 (consolidation of component definitions) through 7. This resulted in 18 consensus-reached initial core components of the peer-based intervention, down from the 60 that the developers/implementers individually suggested at Step 1. Removed components were deemed to not threaten the intervention's effectiveness even if absent. CORE contributes to filling a critical gap regarding identifying an intervention's initial core components (so that the identified components can be subsequently refined), by providing concrete steps for synthesizing the knowledge of an intervention's developers/implementers. Future research should examine CORE's utility across various interventions and implementation settings.

Deep learning for detecting distresses in buildings and pavements: a critical gap analysis

Purpose The massive number of pavements and buildings coupled with the limited inspection resources, both monetary and human, to detect distresses and recommend maintenance actions lead to rapid deterioration, decreased service life, lower level of service and increased community disruption. Therefore, this paper aims at providing a state-of-the-art review of the literature with respect to deep learning techniques for detecting distress in both pavements and buildings; research advancements per asset/structure type; and future recommendations in deep learning applications for distress detection. Design/methodology/approach A critical analysis was conducted on 181 papers of deep learning-based cracks detection. A structured analysis was adopted so that major articles were analyzed according to their focus of study, used methods, findings and limitations. Findings The utilization of deep learning to detect pavement cracks is advanced compared to assess and evaluate the structural health of buildings. There is a need for studies that compare different convolutional neural network models to foster the development of an integrated solution that considers the data collection method. Further research is required to examine the setup, implementation and running costs, frequency of capturing data and deep learning tool. In conclusion, the future of applying deep learning algorithms in lieu of manual inspection for detecting distresses has shown promising results. Practical implications The availability of previous research and the required improvements in the proposed computational tools and models (e.g. artificial intelligence, deep learning, etc.) are triggering researchers and practitioners to enhance the distresses’ inspection process and make better use of their limited resources. Originality/value A critical and structured analysis of deep learning-based crack detection for pavement and buildings is conducted for the first time to enable novice researchers to highlight the knowledge gap in each article, as well as building a knowledge base from the findings of other research to support developing future workable solutions.

Potential Applications of Nanotechnology in Agriculture: A Smart Tool for Sustainable Agriculture

Most of the early uses of nanotechnology have come from material sciences, although applications in agriculture are still expanding. Due to a few comprehensive reviews, we described application of nanomaterials along with their fate in soil and interaction with soil and plant system. From synthesis to metabolism, nano-fertilizers like zinc, silver, selenium, titanium oxide have enhanced the physio-chemical characteristics of crop plants in every manner conceivable. On the other hand, it has the potential to minimize pesticide use by boosting reactivity and surface area of nanoparticles. Nanotechnology in pesticides will, without a doubt, replace the current way of pesticide application because of its efficacy. Nano-based approaches can readily overcome the constraints of conventional soil remediation technologies. While soil nanomaterials mobility has been investigated in a limited number of research studies, it’s likely the most critical gap in knowing the real risk of their transport. As well as enhancing plant nutrient absorption, nanomaterials may also be used to regulate soil microbial activity and stimulate plant defenses. When it comes to shipping food, nanotechnology has made things easier by extending the shelf life of most foods. While it offers tremendous potential for agricultural applications, the health effects of nanoparticles on plants, animals, and humans must be thoroughly investigated.

Finding your scientific story by writing backwards

To succeed, a scientist must write well. Substantial guidance exists on writing papers that follow the classic Introduction, Methods, Results, and Discussion (IMRaD) structure. Here, we fill a critical gap in this pedagogical canon. We offer guidance on developing a good scientific story. This valuable—yet often poorly achieved—skill can increase the impact of a study and its likelihood of acceptance. A scientific story goes beyond presenting information. It is a cohesive narrative that engages the reader by presenting and solving a problem, with a beginning, middle, and end. To create this narrative structure, we urge writers to consider starting at the end of their study, starting with writing their main conclusions, which provide the basis of the Discussion, and then work backwards: Results → Methods → refine the Discussion → Introduction → Abstract → Title. In this brief and informal editorial, we offer guidance to a wide audience, ranging from upper-level undergraduates (who have just conducted their first research project) to senior scientists (who may benefit from re-thinking their approach to writing). To do so, we provide specific instruction, examples, and a guide to the literature on how to “write backwards”, linking scientific storytelling to the IMRaD structure.

Smoking Protective and Risk Factors Among Transgender and Gender-Expansive Individuals (Project SPRING): Qualitative Study Using Digital Photovoice

Background Transgender and gender-expansive (TGE) adults are twice as likely to smoke cigarettes than cisgender individuals. There is a critical gap in research on effective and culturally sensitive approaches to reduce smoking prevalence among TGE adults. Objective This study aims to qualitatively examine the risk and protective factors of cigarette smoking among TGE adults through real-world exemplars. Methods We conducted a digital photovoice study among a purposeful sample of 47 TGE adults aged ≥18 years and currently smoking in the United States (March 2019-April 2020). Participants uploaded photos daily that depicted smoking risk and protective factors they experienced over 21 days on either private Facebook or Instagram groups. Next, we conducted separate focus group discussions to explore the experiences of these factors among a subset of participants from each group. We analyzed participants’ photos, captions, and focus group transcripts and generated themes associated with smoking risk and protective factors. Results We identified 6 major themes of risk and protective factors of smoking among TGE individuals: experience of stress, gender affirmation, health consciousness, social influences, routine behaviors, and environmental cues. We describe and illustrate each theme using exemplar photos and quotes. Conclusions The findings of this study will inform future community-engaged research to develop culturally tailored interventions to reduce smoking prevalence among TGE individuals.