Accelerating the pace of ecotoxicological assessment using artificial intelligence.
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ABSTRACT:
SUBMITTER: Song R
PROVIDER: S-EPMC8800994 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:By targeting invasive organisms, antibiotics insert themselves into the ancient struggle of the host-pathogen evolutionary arms race. As pathogens evolve tactics for evading antibiotics, therapies decline in efficacy and must be replaced, distinguishing antibiotics from most other forms of drug development. Together with a slow and expensive antibiotic development pipeline, the proliferation of drug-resistant pathogens drives urgent interest in computational methods that promise to expedite candidate discovery. Strides in artificial intelligence (AI) have encouraged its application to multiple dimensions of computer-aided drug design, with increasing application to antibiotic discovery. This review describes AI-facilitated advances in the discovery of both small molecule antibiotics and antimicrobial peptides. Beyond the essential prediction of antimicrobial activity, emphasis is also given to antimicrobial compound representation, determination of drug-likeness traits, antimicrobial resistance, and de novo molecular design. Given the urgency of the antimicrobial resistance crisis, we analyze uptake of open science best practices in AI-driven antibiotic discovery and argue for openness and reproducibility as a means of accelerating preclinical research. Finally, trends in the literature and areas for future inquiry are discussed, as artificially intelligent enhancements to drug discovery at large offer many opportunities for future applications in antibiotic development.
| S-EPMC8429579 | biostudies-literature
Project description:We developed a novel data-driven Artificial Intelligence-enhanced Adaptive Time Stepping algorithm (AI-ATS) that can adapt timestep sizes to underlying biophysical dynamics. We demonstrated its values in solving a complex biophysical problem, at multiple spatiotemporal scales, that describes platelet dynamics in shear blood flow. In order to achieve a significant speedup of this computationally demanding problem, we integrated a framework of novel AI algorithms into the solution of the platelet dynamics equations. Our framework involves recurrent neural network-based autoencoders by the Long Short-Term Memory and the Gated Recurrent Units as the first step for memorizing the dynamic states in long-term dependencies for the input time series, followed by two fully-connected neural networks to optimize timestep sizes and step jumps. The computational efficiency of our AI-ATS is underscored by assessing the accuracy and speed of a multiscale simulation of the platelet with the standard time stepping algorithm (STS). By adapting the timestep size, our AI-ATS guides the omission of multiple redundant time steps without sacrificing significant accuracy of the dynamics. Compared to the STS, our AI-ATS achieved a reduction of 40% unnecessary calculations while bounding the errors of mechanical and thermodynamic properties to 3%.
| S-EPMC9273111 | biostudies-literature
Project description:There are currently no effective biomarkers for diagnosing Parkinson's disease (PD) or tracking its progression. Here, we developed an artificial intelligence (AI) model to detect PD and track its progression from nocturnal breathing signals. The model was evaluated on a large dataset comprising 7,671 individuals, using data from several hospitals in the United States, as well as multiple public datasets. The AI model can detect PD with an area-under-the-curve of 0.90 and 0.85 on held-out and external test sets, respectively. The AI model can also estimate PD severity and progression in accordance with the Movement Disorder Society Unified Parkinson's Disease Rating Scale (R = 0.94, P = 3.6 × 10-25). The AI model uses an attention layer that allows for interpreting its predictions with respect to sleep and electroencephalogram. Moreover, the model can assess PD in the home setting in a touchless manner, by extracting breathing from radio waves that bounce off a person's body during sleep. Our study demonstrates the feasibility of objective, noninvasive, at-home assessment of PD, and also provides initial evidence that this AI model may be useful for risk assessment before clinical diagnosis.
| S-EPMC9556299 | biostudies-literature
Project description:Several scoring systems have been devised to objectively predict survival for patients with intrahepatic cholangiocellular carcinoma (ICC) and support treatment stratification, but they have failed external validation. The aim of the present study was to improve prognostication using an artificial intelligence-based approach. We retrospectively identified 417 patients with ICC who were referred to our tertiary care center between 1997 and 2018. Of these, 293 met the inclusion criteria. Established risk factors served as input nodes for an artificial neural network (ANN). We compared the performance of the trained model to the most widely used conventional scoring system, the Fudan score. Predicting 1-year survival, the ANN reached an area under the ROC curve (AUC) of 0.89 for the training set and 0.80 for the validation set. The AUC of the Fudan score was significantly lower in the validation set (0.77, p < 0.001). In the training set, the Fudan score yielded a lower AUC (0.74) without reaching significance (p = 0.24). Thus, ANNs incorporating a multitude of known risk factors can outperform conventional risk scores, which typically consist of a limited number of parameters. In the future, such artificial intelligence-based approaches have the potential to improve treatment stratification when models trained on large multicenter data are openly available.
| S-EPMC8150393 | biostudies-literature
Project description:Backgroundrequires training and validation to standards expected of humans. We developed an online platform and established the Unity Collaborative to build a dataset of expertise from 17 hospitals for training, validation, and standardization of such techniques.MethodsThe training dataset consisted of 2056 individual frames drawn at random from 1265 parasternal long-axis video-loops of patients undergoing clinical echocardiography in 2015 to 2016. Nine experts labeled these images using our online platform. From this, we trained a convolutional neural network to identify keypoints. Subsequently, 13 experts labeled a validation dataset of the end-systolic and end-diastolic frame from 100 new video-loops, twice each. The 26-opinion consensus was used as the reference standard. The primary outcome was precision SD, the SD of the differences between AI measurement and expert consensus.ResultsIn the validation dataset, the AI's precision SD for left ventricular internal dimension was 3.5 mm. For context, precision SD of individual expert measurements against the expert consensus was 4.4 mm. Intraclass correlation coefficient between AI and expert consensus was 0.926 (95% CI, 0.904-0.944), compared with 0.817 (0.778-0.954) between individual experts and expert consensus. For interventricular septum thickness, precision SD was 1.8 mm for AI (intraclass correlation coefficient, 0.809; 0.729-0.967), versus 2.0 mm for individuals (intraclass correlation coefficient, 0.641; 0.568-0.716). For posterior wall thickness, precision SD was 1.4 mm for AI (intraclass correlation coefficient, 0.535 [95% CI, 0.379-0.661]), versus 2.2 mm for individuals (0.366 [0.288-0.462]). We present all images and annotations. This highlights challenging cases, including poor image quality and tapered ventricles.ConclusionsExperts at multiple institutions successfully cooperated to build a collaborative AI. This performed as well as individual experts. Future echocardiographic AI research should use a consensus of experts as a reference. Our collaborative welcomes new partners who share our commitment to publish all methods, code, annotations, and results openly.
| S-EPMC8136463 | biostudies-literature
Project description:BackgroundMajority of research and commercial efforts have focussed on use of artificial intelligence (AI) for fracture detection in adults, despite the greater long-term clinical and medicolegal implications of missed fractures in children. The objective of this study was to assess the available literature regarding diagnostic performance of AI tools for paediatric fracture assessment on imaging, and where available, how this compares with the performance of human readers.Materials and methodsMEDLINE, Embase and Cochrane Library databases were queried for studies published between 1 January 2011 and 2021 using terms related to 'fracture', 'artificial intelligence', 'imaging' and 'children'. Risk of bias was assessed using a modified QUADAS-2 tool. Descriptive statistics for diagnostic accuracies were collated.ResultsNine eligible articles from 362 publications were included, with most (8/9) evaluating fracture detection on radiographs, with the elbow being the most common body part. Nearly all articles used data derived from a single institution, and used deep learning methodology with only a few (2/9) performing external validation. Accuracy rates generated by AI ranged from 88.8 to 97.9%. In two of the three articles where AI performance was compared to human readers, sensitivity rates for AI were marginally higher, but this was not statistically significant.ConclusionsWide heterogeneity in the literature with limited information on algorithm performance on external datasets makes it difficult to understand how such tools may generalise to a wider paediatric population. Further research using a multicentric dataset with real-world evaluation would help to better understand the impact of these tools.
| S-EPMC9166920 | biostudies-literature
Project description:IntroductionThe detection and monitoring of electrolyte imbalance is essential for appropriate management of many metabolic diseases; however, there is no tool that detects such imbalances reliably and noninvasively. In this study, we developed a deep learning model (DLM) using electrocardiography (ECG) for detecting electrolyte imbalance and validated its performance in a multicenter study.Methods and resultsThis retrospective cohort study included two hospitals: 92,140 patients who underwent a laboratory electrolyte examination and an ECG within 30 min were included in this study. A DLM was developed using 83,449 ECGs of 48,356 patients; the internal validation included 12,091 ECGs of 12,091 patients. We conducted an external validation with 31,693 ECGs of 31,693 patients from another hospital, and the result was electrolyte imbalance detection. During internal, the area under the receiving operating characteristic curve (AUC) of a DLM using a 12-lead ECG for detecting hyperkalemia, hypokalemia, hypernatremia, hyponatremia, hypercalcemia, and hypocalcemia were 0.945, 0.866, 0.944, 0.885, 0.905, and 0.901, respectively. The values during external validation of the AUC of hyperkalemia, hypokalemia, hypernatremia, hyponatremia, hypercalcemia, and hypocalcemia were 0.873, 0.857, 0.839, 0.856, 0.831, and 0.813 respectively. The DLM helped to visualize the important ECG region for detecting each electrolyte imbalance, and it showed how the P wave, QRS complex, or T wave differs in importance in detecting each electrolyte imbalance.ConclusionThe proposed DLM demonstrated high performance in detecting electrolyte imbalance. These results suggest that a DLM can be used for detecting and monitoring electrolyte imbalance using ECG on a daily basis.
| S-EPMC8164149 | biostudies-literature
Project description:ObjectivesTo study whether a trained convolutional neural network (CNN) can be of assistance to radiologists in differentiating Coronavirus disease (COVID)-positive from COVID-negative patients using chest X-ray (CXR) through an ambispective clinical study. To identify subgroups of patients where artificial intelligence (AI) can be of particular value and analyse what imaging features may have contributed to the performance of AI by means of visualisation techniques.MethodsCXR of 487 patients were classified into [4] categories-normal, classical COVID, indeterminate, and non-COVID by consensus opinion of 2 radiologists. CXR which were classified as "normal" and "indeterminate" were then subjected to analysis by AI, and final categorisation provided as guided by prediction of the network. Precision and recall of the radiologist alone and radiologist assisted by AI were calculated in comparison to reverse transcriptase-polymerase chain reaction (RT-PCR) as the gold standard. Attention maps of the CNN were analysed to understand regions in the CXR important to the AI algorithm in making a prediction.ResultsThe precision of radiologists improved from 65.9 to 81.9% and recall improved from 17.5 to 71.75 when assistance with AI was provided. AI showed 92% accuracy in classifying "normal" CXR into COVID or non-COVID. Analysis of attention maps revealed attention on the cardiac shadow in these "normal" radiographs.ConclusionThis study shows how deployment of an AI algorithm can complement a human expert in the determination of COVID status. Analysis of the detected features suggests possible subtle cardiac changes, laying ground for further investigative studies into possible cardiac changes.Key points• Through an ambispective clinical study, we show how assistance with an AI algorithm can improve recall (sensitivity) and precision (positive predictive value) of radiologists in assessing CXR for possible COVID in comparison to RT-PCR. • We show that AI achieves the best results in images classified as "normal" by radiologists. We conjecture that possible subtle cardiac in the CXR, imperceptible to the human eye, may have contributed to this prediction. • The reported results may pave the way for a human computer collaboration whereby the expert with some help from the AI algorithm achieves higher accuracy in predicting COVID status on CXR than previously thought possible when considering either alone.
| S-EPMC7816060 | biostudies-literature
Project description:Abnormal torsion of the lower limbs may adversely affect joint health. This study developed and validated a deep learning-based method for automatic measurement of femoral and tibial torsion on MRI. Axial T2-weighted sequences acquired of the hips, knees, and ankles of 93 patients (mean age, 13 ± 5 years; 52 males) were included and allocated to training (n = 60), validation (n = 9), and test sets (n = 24). A U-net convolutional neural network was trained to segment both femur and tibia, identify osseous anatomic landmarks, define pertinent reference lines, and quantify femoral and tibial torsion. Manual measurements by two radiologists provided the reference standard. Inter-reader comparisons were performed using repeated-measures ANOVA, Pearson's r, and the intraclass correlation coefficient (ICC). Mean Sørensen-Dice coefficients for segmentation accuracy ranged between 0.89 and 0.93 and erroneous segmentations were scarce. Ranges of torsion as measured by both readers and the algorithm on the same axial image were 15.8°-18.0° (femur) and 33.9°-35.2° (tibia). Correlation coefficients (ranges, .968 ≤ r ≤ .984 [femur]; .867 ≤ r ≤ .904 [tibia]) and ICCs (ranges, .963 ≤ ICC ≤ .974 [femur]; .867 ≤ ICC ≤ .894 [tibia]) indicated excellent inter-reader agreement. Algorithm-based analysis was faster than manual analysis (7 vs 207 vs 230 s, p < .001). In conclusion, fully automatic measurement of torsional alignment is accurate, reliable, and sufficiently fast for clinical workflows.
| S-EPMC8636587 | biostudies-literature
Project description:The present work aimed to predict the fate of two pesticides, copper (Cu) and glyphosate in a Mediterranean basin with an intermittent river and to assess the ecotoxicological risk related to their presence in water bodies coupling field measurements of streamflow and pesticide concentrations, and an eco-hydrological model. The Soil and Water Assessment Tool (SWAT) model was calibrated and, subsequently used to assess predicted environmental concentrations of pesticides in surface waters. The ecotoxicological risk related to the presence of Cu and glyphosate in surface water was assessed at the reach scale by using the Toxicity to Exposure Ratio approach (TER). Measurements of glyphosate concentrations (< 0.5 μg l-1) exceeded the maximum European threshold of environmental quality standards for pesticides (EQS) of 0.1 μg l-1. High concentrations of glyphosate were predicted in the wet season and in September, when glyphosate is mostly used in vineyards and olive grove productions. Acute risk (TER < 100) associated with the presence of glyphosate was detected for several reaches. High concentrations of Cu (< 6.5 μg l-1), mainly used as a fungicide in vineyards, were predicted in several river reaches. The results of the ecotoxicological risk assessment revealed that November and January were the critical months during which most of the river reaches showed a chronic risk associated with the presence of Cu.
| S-EPMC10944508 | biostudies-literature