Newborn Skin Maturity Medical Device Validation for Gestational Age Prediction: Clinical Trial.

BACKGROUND: Early access to antenatal care and high-cost technologies for pregnancy dating challenge early neonatal risk assessment at birth in resource-constrained settings. To overcome the absence or inaccuracy of postnatal gestational age (GA), we developed a new medical device to assess GA based on the photobiological properties of newborns' skin and predictive models. OBJECTIVE: This study aims to validate a device that uses the photobiological model of skin maturity adjusted to the clinical data to detect GA and establish its accuracy in discriminating preterm newborns. METHODS: A multicenter, single-blinded, and single-arm intention-to-diagnosis clinical trial evaluated the accuracy of a novel device for the detection of GA and preterm newborns. The first-trimester ultrasound, a second comparator ultrasound, and data regarding the last menstrual period (LMP) from antenatal reports were used as references for GA at birth. The new test for validation was performed using a portable multiband reflectance photometer device that assessed the skin maturity of newborns and used machine learning models to predict GA, adjusted for birth weight and antenatal corticosteroid therapy exposure. RESULTS: The study group comprised 702 pregnant women who gave birth to 781 newborns, of which 366 (46.9%) were preterm newborns. As the primary outcome, the GA as predicted by the new test was in line with the reference GA that was calculated by using the intraclass correlation coefficient (0.969, 95% CI 0.964-0.973). The paired difference between predicted and reference GAs was -1.34 days, with Bland-Altman limits of -21.2 to 18.4 days. As a secondary outcome, the new test achieved 66.6% (95% CI 62.9%-70.1%) agreement with the reference GA within an error of 1 week. This agreement was similar to that of comparator-LMP-GAs (64.1%, 95% CI 60.7%-67.5%). The discrimination between preterm and term newborns via the device had a similar area under the receiver operating characteristic curve (0.970, 95% CI 0.959-0.981) compared with that for comparator-LMP-GAs (0.957, 95% CI 0.941-0.974). In newborns with absent or unreliable LMPs (n=451), the intent-to-discriminate analysis showed correct preterm versus term classifications with the new test, which achieved an accuracy of 89.6% (95% CI 86.4%-92.2%), while the accuracy for comparator-LMP-GA was 69.6% (95% CI 65.3%-73.7%). CONCLUSIONS: The assessment of newborn's skin maturity (adjusted by learning models) promises accurate pregnancy dating at birth, even without the antenatal ultrasound reference. Thus, the novel device could add value to the set of clinical parameters that direct the delivery of neonatal care in birth scenarios where GA is unknown or unreliable. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.1136/bmjopen-2018-027442.

GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.

Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/.

Factors Associated With Weight Change in Online Weight Management Communities: A Case Study in the LoseIt Reddit Community.

BACKGROUND: Recent research has shown that of the 72% of American Internet users who have looked for health information online, 22% have searched for help to lose or control weight. This demand for information has given rise to many online weight management communities, where users support one another throughout their weight loss process. Whether and how user engagement in online communities relates to weight change is not totally understood. OBJECTIVE: We investigated the activity behavior and analyze the semantic content of the messages of active users in LoseIt (r/loseit), a weight management community of the online social network Reddit. We then explored whether these features are associated with weight loss in this online social network. METHODS: A data collection tool was used to collect English posts, comments, and other public metadata of active users (ie, users with at least one post or comment) on LoseIt from August 2010 to November 2014. Analyses of frequency and intensity of user interaction in the community were performed together with a semantic analysis of the messages, done by a latent Dirichlet allocation method. The association between weight loss and online user activity patterns, the semantics of the messages, and real-world variables was found by a linear regression model using 30-day weight change as the dependent variable. RESULTS: We collected posts and comments of 107,886 unique users. Among these, 101,003 (93.62%) wrote at least one comment and 38,981 (36.13%) wrote at least one post. Median percentage of days online was 3.81 (IQR 9.51). The 10 most-discussed semantic topics on posts were related to healthy food, clothing, calorie counting, workouts, looks, habits, support, and unhealthy food. In the subset of 754 users who had gender, age, and 30-day weight change data available, women were predominant and 92.9% (701/754) lost weight. Female gender, body mass index (BMI) at baseline, high levels of online activity, the number of upvotes received per post, and topics discussed within the community were independently associated with weight change. CONCLUSIONS: Our findings suggest that among active users of a weight management community, self-declaration of higher BMI levels (which may represent greater dissatisfaction with excess weight), high online activity, and engagement in discussions that might provide social support are associated with greater weight loss. These findings have the potential to aid health professionals to assist patients in online interventions by focusing efforts on increasing engagement and/or starting discussions on topics of higher impact on weight change.

GASS: identifying enzyme active sites with genetic algorithms.

MOTIVATION: Currently, 25% of proteins annotated in Pfam have their function unknown. One way of predicting proteins function is by looking at their active site, which has two main parts: the catalytic site and the substrate binding site. The active site is more conserved than the other residues of the protein and can be a rich source of information for protein function prediction. This article presents a new heuristic method, named genetic active site search (GASS), which searches for given active site 3D templates in unknown proteins. The method can perform non-exact amino acid matches (conservative mutations), is able to find amino acids in different chains and does not impose any restrictions on the active site size. RESULTS: GASS results were compared with those catalogued in the catalytic site atlas (CSA) in four different datasets and compared with two other methods: amino acid pattern search for substructures and motif and catalytic site identification. The results show GASS can correctly identify >90% of the templates searched. Experiments were also run using data from the substrate binding sites prediction competition CASP 10, and GASS is ranked fourth among the 18 methods considered.

Genetic algorithms coupled with quantum mechanics for refinement of force fields for RNA simulation: a case study of glycosidic torsions in the canonical ribonucleosides.

We report the use of genetic algorithms (GA) as a method to refine force field parameters in order to determine RNA energy. Quantum-mechanical (QM) calculations are carried out for the isolated canonical ribonucleosides (adenosine, guanosine, cytidine and uridine) that are taken as reference data. In this particular study, the dihedral and electrostatic energies are reparametrized in order to test the proposed approach, i.e., GA coupled with QM calculations. Overall, RMSE comparison with recent published results for ribonucleosides energies shows an improvement, on average, of 50%. Finally, the new reparametrized potential energy function is used to determine the spatial structure of RNA (PDB code ) that was not taken into account in the parametrization process. This structure was improved about 82% comparable with previously published results.

Respiratory distress syndrome prediction at birth by optical skin maturity assessment and machine learning models for limited-resource settings: a development and validation study.

Background: A handheld optical device was developed to evaluate a newborn's skin maturity by assessing the photobiological properties of the tissue and processing it with other variables to predict early neonatal prognosis related to prematurity. This study assessed the device's ability to predict respiratory distress syndrome (RDS). Methods: To assess the device's utility we enrolled newborns at childbirth in six urban perinatal centers from two multicenter single-blinded clinical trials. All newborns had inpatient follow-up until 72 h of life. We trained supervised machine learning models with data from 780 newborns in a Brazilian trial and provided external validation with data from 305 low-birth-weight newborns from another trial that assessed Brazilian and Mozambican newborns. The index test measured skin optical reflection with an optical sensor and adjusted acquired values with clinical variables such as birth weight and prenatal corticoid exposition for lung maturity, maternal diabetes, and hypertensive disturbances. The performance of the models was evaluated using intrasample k-parts cross-validation and external validation in an independent sample. Results: Models adjusting three predictors (skin reflection, birth weight, and antenatal corticoid exposure) or five predictors had a similar performance, including or not maternal diabetes and hypertensive diseases. The best global accuracy was 89.7 (95% CI: 87.4 to 91.8, with a high sensitivity of 85.6% (80.2 to 90.0) and specificity of 91.3% (95% CI: 88.7 to 93.5). The test correctly discriminated RDS newborns in external validation, with 82.3% (95% CI: 77.5 to 86.4) accuracy. Our findings demonstrate a new way to assess a newborn's lung maturity, providing potential opportunities for earlier and more effective care. Trial registration: RBR-3f5bm5 (online access: http://www.ensaiosclinicos.gov.br/rg/RBR-3f5bm5/), and RBR-33mjf (online access: https://ensaiosclinicos.gov.br/rg/RBR-33rnjf/).

Gestational age assessed by optical skin reflection in low-birth-weight newborns: Applications in classification at birth.

Introduction: A new medical device was previously developed to estimate gestational age (GA) at birth by processing a machine learning algorithm on the light scatter signal acquired on the newborn's skin. The study aims to validate GA calculated by the new device (test), comparing the result with the best available GA in newborns with low birth weight (LBW). Methods: We conducted a multicenter, non-randomized, and single-blinded clinical trial in three urban referral centers for perinatal care in Brazil and Mozambique. LBW newborns with a GA over 24 weeks and weighing between 500 and 2,500 g were recruited in the first 24 h of life. All pregnancies had a GA calculated by obstetric ultrasound before 24 weeks or by reliable last menstrual period (LMP). The primary endpoint was the agreement between the GA calculated by the new device (test) and the best available clinical GA, with 95% confidence limits. In addition, we assessed the accuracy of using the test in the classification of preterm and SGA. Prematurity was childbirth before 37 gestational weeks. The growth standard curve was Intergrowth-21st, with the 10th percentile being the limit for classifying SGA. Results: Among 305 evaluated newborns, 234 (76.7%) were premature, and 139 (45.6%) were SGA. The intraclass correlation coefficient between GA by the test and reference GA was 0.829 (95% CI: 0.785-0.863). However, the new device (test) underestimated the reference GA by an average of 2.8 days (95% limits of agreement: -40.6 to 31.2 days). Its use in classifying preterm or term newborns revealed an accuracy of 78.4% (95% CI: 73.3-81.6), with high sensitivity (96.2%; 95% CI: 92.8-98.2). The accuracy of classifying SGA newborns using GA calculated by the test was 62.3% (95% CI: 56.6-67.8). Discussion: The new device (test) was able to assess GA at birth in LBW newborns, with a high agreement with the best available GA as a reference. The GA estimated by the device (test), when used to classify newborns on the first day of life, was useful in identifying premature infants but not when applied to identify SGA infants, considering current algohrithm. Nonetheless, the new device (test) has the potential to provide important information in places where the GA is unknown or inaccurate.

Political polarization on Twitter during the COVID-19 pandemic: a case study in Brazil.

The debate over the COVID-19 pandemic is constantly trending at online conversations since its beginning in 2019. The discussions in many social media platforms is related not only to health aspects of the disease, but also public policies and non-pharmacological measures to mitigate the spreading of the virus and propose alternative treatments. Divergent opinions regarding these measures are leading to heated discussions and polarization. Particularly in highly politically polarized countries, users tend to be divided in those in-favor or against government policies. In this work we present a computational method to analyze Twitter data and: (i) identify users with a high probability of being bots using only COVID-19 related messages; (ii) quantify the political polarization of the Brazilian general public in the context of the COVID-19 pandemic; (iii) analyze how bots tweet and affect political polarization. We collected over 100 million tweets from 26 April 2020 to 3 January 2021, and observed in general a highly polarized population (with polarization index varying from 0.57 to 0.86), which focuses on very different topics of discussions over the most polarized weeks-but all related to government and health-related events.

Counterfactual inference with latent variable and its application in mental health care.

This paper deals with the problem of modeling counterfactual reasoning in scenarios where, apart from the observed endogenous variables, we have a latent variable that affects the outcomes and, consequently, the results of counterfactuals queries. This is a common setup in healthcare problems, including mental health. We propose a new framework where the aforementioned problem is modeled as a multivariate regression and the counterfactual model accounts for both observed and a latent variable, where the latter represents what we call the patient individuality factor ( φ ). In mental health, focusing on individuals is paramount, as past experiences can change how people see or deal with situations, but individuality cannot be directly measured. To the best of our knowledge, this is the first counterfactual approach that considers both observational and latent variables to provide deterministic answers to counterfactual queries, such as: what if I change the social support of a patient, to what extent can I change his/her anxiety? The framework combines concepts from deep representation learning and causal inference to infer the value of φ and capture both non-linear and multiplicative effects of causal variables. Experiments are performed with both synthetic and real-world datasets, where we predict how changes in people's actions may lead to different outcomes in terms of symptoms of mental illness and quality of life. Results show the model learns the individually factor with errors lower than 0.05 and answers counterfactual queries that are supported by the medical literature. The model has the potential to recommend small changes in people's lives that may completely change their relationship with mental illness.

Social Determinants in Self-Protective Behavior Related to COVID-19: Association Rule-Mining Study.

BACKGROUND: Human behavior is crucial in health outcomes. Particularly, individual behavior is a determinant of the success of measures to overcome critical conditions, such as a pandemic. In addition to intrinsic public health challenges associated with COVID-19, in many countries, some individuals decided not to get vaccinated, streets were crowded, parties were happening, and businesses struggling to survive were partially open, despite lockdown or stay-at-home instructions. These behaviors contrast with the instructions for potential benefits associated with social distancing, use of masks, and vaccination to manage collective and individual risks. OBJECTIVE: Considering that human behavior is a result of individuals' social and economic conditions, we investigated the social and working characteristics associated with reports of appropriate protective behavior in Brazil. METHODS: We analyzed data from a large web survey of individuals reporting their behavior during the pandemic. We selected 3 common self-care measures: use of protective masks, distancing by at least 1 m when out of the house, and handwashing or use of alcohol, combined with assessment of the social context of respondents. We measured the frequency of the use of these self-protective measures. Using a frequent pattern-mining perspective, we generated association rules from a set of answers to questions that co-occur with at least a given frequency, identifying the pattern of characteristics of the groups divided according to protective behavior reports. RESULTS: The rationale was to identify a pool of working and social characteristics that might have better adhesion to behaviors and self-care measures, showing these are more socially determined than previously thought. We identified common patterns of socioeconomic and working determinants of compliance with protective self-care measures. Data mining showed that social determinants might be important to shape behavior in different stages of the pandemic. CONCLUSIONS: Identification of context determinants might be helpful to identify unexpected facilitators and constraints to fully follow public policies. The context of diseases contributes to psychological and physical health outcomes, and context understanding might change the approach to a disease. Hidden social determinants might change protective behavior, and social determinants of protective behavior related to COVID-19 are related to work and economic conditions. TRIAL REGISTRATION: Not applicable.

Towards automatic diagnosis of rheumatic heart disease on echocardiographic exams through video-based deep learning.

OBJECTIVE: Rheumatic heart disease (RHD) affects an estimated 39 million people worldwide and is the most common acquired heart disease in children and young adults. Echocardiograms are the gold standard for diagnosis of RHD, but there is a shortage of skilled experts to allow widespread screenings for early detection and prevention of the disease progress. We propose an automated RHD diagnosis system that can help bridge this gap. MATERIALS AND METHODS: Experiments were conducted on a dataset with 11 646 echocardiography videos from 912 exams, obtained during screenings in underdeveloped areas of Brazil and Uganda. We address the challenges of RHD identification with a 3D convolutional neural network (C3D), comparing its performance with a 2D convolutional neural network (VGG16) that is commonly used in the echocardiogram literature. We also propose a supervised aggregation technique to combine video predictions into a single exam diagnosis. RESULTS: The proposed approach obtained an accuracy of 72.77% for exam diagnosis. The results for the C3D were significantly better than the ones obtained by the VGG16 network for videos, showing the importance of considering the temporal information during the diagnostic. The proposed aggregation model showed significantly better accuracy than the majority voting strategy and also appears to be capable of capturing underlying biases in the neural network output distribution, balancing them for a more correct diagnosis. CONCLUSION: Automatic diagnosis of echo-detected RHD is feasible and, with further research, has the potential to reduce the workload of experts, enabling the implementation of more widespread screening programs worldwide.

Predicting post-synaptic activity in proteins with data mining.

The bioinformatics problem being addressed in this paper is to predict whether or not a protein has post-synaptic activity. This problem is of great intrinsic interest because proteins with post-synaptic activities are connected with functioning of the nervous system. Indeed, many proteins having post-synaptic activity have been functionally characterized by biochemical, immunological and proteomic exercises. They represent a wide variety of proteins with functions in extracellular signal reception and propagation through intracellular apparatuses, cell adhesion molecules and scaffolding proteins that link them in a web. The challenge is to automatically discover features of the primary sequences of proteins that typically occur in proteins with post-synaptic activity but rarely (or never) occur in proteins without post-synaptic activity, and vice-versa. In this context, we used data mining to automatically discover classification rules that predict whether or not a protein has post-synaptic activity. The discovered rules were analysed with respect to their predictive accuracy (generalization ability) and with respect to their interestingness to biologists (in the sense of representing novel, unexpected knowledge).