Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over.
Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over.
Project description:We live in interesting times. Portents of impending catastrophe pervade the literature, calling us to action in the face of unmanageable volumes of scientific data. But it isn't so much data generation per se, but the systematic burial of the knowledge embodied in those data that poses the problem: there is so much information available that we simply no longer know what we know, and finding what we want is hard - too hard. The knowledge we seek is often fragmentary and disconnected, spread thinly across thousands of databases and millions of articles in thousands of journals. The intellectual energy required to search this array of data-archives, and the time and money this wastes, has led several researchers to challenge the methods by which we traditionally commit newly acquired facts and knowledge to the scientific record. We present some of these initiatives here - a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment. With their promises to provide new ways of interacting with the literature, and new and more powerful tools to access and extract the knowledge sequestered within it, we ask what advances they make and what obstacles to progress still exist? We explore these questions, and, as you read on, we invite you to engage in an experiment with us, a real-time test of a new technology to rescue data from the dormant pages of published documents. We ask you, please, to read the instructions carefully. The time has come: you may turn over your papers...
Project description:Although oceans provide critical ecosystem services and support the most abundant populations on earth, the extent of damage impacting oceans and the diversity of strategies to protect them is disconcertingly, and disproportionately, understudied. While conventional modes of conservation have made strides in mitigating impacts of human activities on ocean ecosystems, those strategies alone cannot completely stem the tide of mounting threats. Biotechnology and genomic research should be harnessed and developed within conservation frameworks to foster the persistence of viable ocean ecosystems. This document distills the results of a targeted survey, the Ocean Genomics Horizon Scan, which assessed opportunities to bring novel genetic rescue tools to marine conservation. From this Horizon Scan, we have identified how novel approaches from synthetic biology and genomics can alleviate major marine threats. While ethical frameworks for biotechnological interventions are necessary for effective and responsible practice, here we primarily assessed technological and social factors directly affecting technical development and deployment of biotechnology interventions for marine conservation. Genetic insight can greatly enhance established conservation methods, but the severity of many threats may demand genomic intervention. While intervention is controversial, for many marine areas the cost of inaction is too high to allow controversy to be a barrier to conserving viable ecosystems. Here, we offer a set of recommendations for engagement and program development to deploy genetic rescue safely and responsibly.
Project description:IntroductionArtificial Intelligence tools are being introduced in almost every field of human life, including medical sciences and medical education, among scepticism and enthusiasm.Research questionto assess how a generative language tool (Generative Pretrained Transformer 3.5, ChatGPT) performs at both generating questions and answering a neurosurgical residents' written exam. Namely, to assess how ChatGPT generates questions, how it answers human-generated questions, how residents answer AI-generated questions and how AI answers its self-generated question.Materials and methods50 questions were included in the written exam, 46 questions were generated by humans (senior staff members) and 4 were generated by ChatGPT. 11 participants took the exam (ChatGPT and 10 residents). Questions were both open-ended and multiple-choice.8 questions were not submitted to ChatGPT since they contained images or schematic drawings to interpret.Resultsformulating requests to ChatGPT required an iterative process to precise both questions and answers. Chat GPT scored among the lowest ranks (9/11) among all the participants). There was no difference in response rate for residents' between human-generated vs AI-generated questions that could have been attributed to less clarity of the question. ChatGPT answered correctly to all its self-generated questions.Discussion and conclusionsAI is a promising and powerful tool for medical education and for specific medical purposes, which need to be further determined. To request AI to generate logical and sound questions, that request must be formulated as precise as possible, framing the content, the type of question and its correct answers.
Project description:Abandoned, lost, or otherwise discarded fishing gear (ALDFG) is a major contributor to ocean pollution, with extensive social, economic, and environmental impacts. However, quantitative ALDFG estimates are dated and limited in scope. To provide current global estimates, we interviewed fishers around the world about how much fishing gear they lose annually and multiplied reported losses by global fishing effort data. We estimate that nearly 2% of all fishing gear, comprising 2963 km2 of gillnets, 75,049 km2 of purse seine nets, 218 km2 of trawl nets, 739,583 km of longline mainlines, and more than 25 million pots and traps are lost to the ocean annually. These estimates represent critical baselines that can inform solutions targeted to ALDFG reduction strategies.
Project description:Regular and long-term monitoring of coastal areas is a prerequisite to avoiding or mitigating the impacts of climate and human-driven hazards. In Africa, where populations and infrastructures are particularly exposed to risk, there is an urgent need to establish coastal monitoring, as observations are generally scarce. Measurement campaigns and very high-resolution satellite imagery are costly, while freely available satellite observations have temporal and spatial resolutions that are not suited to capture the event scale. To address the gap, a network of low-cost, multi-variable, shore-based video camera systems has been installed along the African coasts. Here, we present this network and its principle of sharing data, methods, and results obtained, building toward the implementation of a common integrated coastal management policy between countries. Further, we list new contributions to the understanding of still poorly documented African beaches' evolution, waves, and sea level impacts. This network is a solid platform for the development of inter-disciplinary observations for resources and ecology (such as fisheries, and sargassum landing), erosion and flooding, early warning systems during extreme events, and science-based coastal infrastructure management for sustainable future coasts.
Project description:Certain members of the Arenaviridae family are category A agents capable of causing severe hemorrhagic fevers in humans. Specific antiviral treatments do not exist, and the only commonly used drug, ribavirin, has limited efficacy and can cause severe side effects. The discovery and development of new antivirals are inhibited by the biohazardous nature of the viruses, making them a relatively poorly understood group of human pathogens. We therefore adapted a reverse-genetics minigenome (MG) rescue system based on Junin virus, the causative agent of Argentine hemorrhagic fever, for high-throughput screening (HTS). The MG rescue system recapitulates all stages of the virus life cycle and enables screening of small-molecule libraries under biosafety containment level 2 (BSL2) conditions. The HTS resulted in the identification of four candidate compounds with potent activity against a broad panel of arenaviruses, three of which were completely novel. The target for all 4 compounds was the stage of viral entry, which positions the compounds as potentially important leads for future development.The arenavirus family includes several members that are highly pathogenic, causing acute viral hemorrhagic fevers with high mortality rates. No specific effective treatments exist, and although a vaccine is available for Junin virus, the causative agent of Argentine hemorrhagic fever, it is licensed for use only in areas where Argentine hemorrhagic fever is endemic. For these reasons, it is important to identify specific compounds that could be developed as antivirals against these deadly viruses.
Project description:Thousands of people are reported lost in the wilderness in the United States every year and locating these missing individuals as rapidly as possible depends on coordinated search and rescue (SAR) operations. As time passes, the search area grows, survival rate decreases, and searchers are faced with an increasingly daunting task of searching large areas in a short amount of time. To optimize the search process, mathematical models of lost person behavior with respect to landscape can be used in conjunction with current SAR practices. In this paper, we introduce an agent-based model of lost person behavior which allows agents to move on known landscapes with behavior defined as independent realizations of a random variable. The behavior random variable selects from a distribution of six known lost person reorientation strategies to simulate the agent's trajectory. We systematically simulate a range of possible behavior distributions and find a best-fit behavioral profile for a hiker with the International Search and Rescue Incident Database. We validate these results with a leave-one-out analysis. This work represents the first time-discrete model of lost person dynamics validated with data from real SAR incidents and has the potential to improve current methods for wilderness SAR.
Project description:The dispersal of larvae and their settlement to suitable habitat is fundamental to the replenishment of marine populations and the communities in which they live. Sound plays an important role in this process because for larvae of various species, it acts as an orientational cue towards suitable settlement habitat. Because marine sounds are largely of biological origin, they not only carry information about the location of potential habitat, but also information about the quality of habitat. While ocean acidification is known to affect a wide range of marine organisms and processes, its effect on marine soundscapes and its reception by navigating oceanic larvae remains unknown. Here, we show that ocean acidification causes a switch in role of present-day soundscapes from attractor to repellent in the auditory preferences in a temperate larval fish. Using natural CO2 vents as analogues of future ocean conditions, we further reveal that ocean acidification can impact marine soundscapes by profoundly diminishing their biological sound production. An altered soundscape poorer in biological cues indirectly penalizes oceanic larvae at settlement stage because both control and CO2-treated fish larvae showed lack of any response to such future soundscapes. These indirect and direct effects of ocean acidification put at risk the complex processes of larval dispersal and settlement.
Project description:Two studies investigated the effect of trait Emotional Intelligence (trait EI) on people's motivation to help. In Study 1, we developed a new computer-based paradigm that tested participants' motivation to help by measuring their performance on a task in which they could gain a hypothetical amount of money to help children in need. Crucially, we manipulated participants' perceived efficacy by informing them that they had been either able to save the children (positive feedback) or unable to save the children (negative feedback). We measured trait EI using the Trait Emotional Intelligence Questionnaire-Short Form (TEIQue-SF) and assessed participants' affective reactions during the experiment using the PANAS-X. Results showed that high and low trait EI participants performed differently after the presentation of feedback on their ineffectiveness in helping others in need. Both groups showed increasing negative affective states during the experiment when the feedback was negative; however, high trait EI participants better managed their affective reactions, modulating the impact of their emotions on performance and maintaining a high level of motivation to help. In Study 2, we used a similar computerized task and tested a control situation to explore the effect of trait EI on participants' behavior when facing failure or success in a scenario unrelated to helping others in need. No effect of feedback emerged on participants' emotional states in the second study. Taken together our results show that trait EI influences the impact of success and failure on behavior only in affect-rich situation like those in which people are asked to help others in need.
Project description:The ocean is experiencing unprecedented rapid change, and visually monitoring marine biota at the spatiotemporal scales needed for responsible stewardship is a formidable task. As baselines are sought by the research community, the volume and rate of this required data collection rapidly outpaces our abilities to process and analyze them. Recent advances in machine learning enables fast, sophisticated analysis of visual data, but have had limited success in the ocean due to lack of data standardization, insufficient formatting, and demand for large, labeled datasets. To address this need, we built FathomNet, an open-source image database that standardizes and aggregates expertly curated labeled data. FathomNet has been seeded with existing iconic and non-iconic imagery of marine animals, underwater equipment, debris, and other concepts, and allows for future contributions from distributed data sources. We demonstrate how FathomNet data can be used to train and deploy models on other institutional video to reduce annotation effort, and enable automated tracking of underwater concepts when integrated with robotic vehicles. As FathomNet continues to grow and incorporate more labeled data from the community, we can accelerate the processing of visual data to achieve a healthy and sustainable global ocean.