Nevin Manimala

PLoS One. 2023 Jun 2;18(6):e0286599. doi: 10.1371/journal.pone.0286599. eCollection 2023.

ABSTRACT

To reduce the genome sequence representation, restriction site-associated DNA sequencing (RAD-seq) protocols is being widely used either with single-digest or double-digest methods. In this study, we genotyped the sesame population (48 sample size) in a pilot scale to compare single and double-digest RAD-seq (sd and ddRAD-seq) methods. We analysed the resulting short-read data generated from both protocols and assessed their performance impacting the downstream analysis using various parameters. The distinct k-mer count and gene presence absence variation (PAV) showed a significant difference between the sesame samples studied. Additionally, the variant calling from both datasets (sdRAD-seq and ddRAD-seq) exhibits a significant difference between them. The combined variants from both datasets helped in identifying the most diverse samples and possible sub-groups in the sesame population. The most diverse samples identified from each analysis (k-mer, gene PAV, SNP count, Heterozygosity, NJ and PCA) can possibly be representative samples holding major diversity of the small sesame population used in this study. The best possible strategies with suggested inputs for modifications to utilize the RAD-seq strategy efficiently on a large dataset containing thousands of samples to be subjected to molecular analysis like diversity, population structure and core development studies were discussed.

PMID:37267340 | DOI:10.1371/journal.pone.0286599

PLoS One. 2023 Jun 2;18(6):e0286624. doi: 10.1371/journal.pone.0286624. eCollection 2023.

ABSTRACT

Advances in observational and computational assets have led to revolutions in the range and quality of results in many science and engineering settings. However, those advances have led to needs for new research in treating model errors and assessing their impacts. We consider two settings. The first involves physically-based statistical models that are sufficiently manageable to allow incorporation of a stochastic “model error process”. In the second case we consider large-scale models in which incorporation of a model error process and updating its distribution is impractical. Our suggestion is to treat dimension-reduced model output as if it is observational data, with a data model that incorporates a bias component to represent the impacts of model error. We believe that our suggestions are valuable quantitative, yet relatively simple, ways to extract useful information from models while including adjustment for model error. These ideas are illustrated and assessed using an application inspired by a classical oceanographic problem.

PMID:37267337 | DOI:10.1371/journal.pone.0286624

PLoS One. 2023 Jun 2;18(6):e0286250. doi: 10.1371/journal.pone.0286250. eCollection 2023.

ABSTRACT

BACKGROUND: To report a long-term outcome of the novel combined surgical method of complete excision, corneal tattooing, and a sutureless limbal conjunctival autograft for limbal dermoid.

METHODS: All patients who were referred to our clinic for limbal dermoid, and underwent a combined surgery of complete excision, corneal tattooing, and a sutureless limbal conjunctival autograft were retrospectively reviewed. The surgery was performed by one surgeon, and all clinical information was obtained during a seven-year follow up period. In all patients, surgical outcomes of cosmesis, best corrected visual acuity (BCVA), spherical equivalent (SE), and corneal/ocular astigmatism were obtained and compared preoperatively and postoperatively.

RESULTS: During seven years, 24 patients (24 eyes) with limbal dermoid were finally enrolled. The mean age was 10.1±8.9 years old. The surgery resulted in an improved appearing ocular surface in all cases without any complications. There was no statistical difference in BCVA, corneal and ocular astigmatism between preoperatively and postoperatively (p = 0.231, 0.156 and 0.475, respectively). The mean SE was 0.12±3.19D preoperatively, and -0.21±3.02 D postoperatively with statistical significance (p = 0.037). Mean follow up period was 54.50 ± 15.62 months.

CONCLUSIONS: Based on the results of this study, our innovative surgical method which includes complete excision with corneal tattooing and limbal conjunctival autograft can be a simple and safe procedure that achieves long standing cosmesis with limbal dermoids.

PMID:37267334 | DOI:10.1371/journal.pone.0286250

PLoS One. 2023 Jun 2;18(6):e0286018. doi: 10.1371/journal.pone.0286018. eCollection 2023.

ABSTRACT

BACKGROUND: We examined whether information extracted during a visual statistical learning task could be generalised from specific exemplars to semantically similar ones. We then looked at whether performance in autistic people differed to non-autistic people during a visual statistical learning task and specifically examined whether differences in performance between groups occurred when sequential information was presented at a semantic level. We did this by assessing recall performance using a two-alternative forced choice paradigm after presenting participants with a sequence of naturalistic scene images.

METHODS: 125 adult participants (61 participants with an autism diagnosis and 64 non-autistic controls) were presented with a fast serial presentation sequence of images and given a cover task to avoid attention being explicitly drawn to patterns in the underlying sequences. This was followed by a two-alternative forced choice task to assess participants’ implicit recall. Participants were presented with 1 of 3 unique versions of the task, in which the presentation and assessment of statistical regularities was done at either a low feature-based level or a high semantic-based level.

RESULTS: Participants were able to generalise statistical information from specific exemplars to semantically similar ones. There was an overall significant reduction in visual statistical learning in the autistic group but we were unable to determine whether group differences occurred specifically in conditions where the learning of semantic information was required.

CONCLUSIONS: These results provide evidence that participants are able to extract statistical information that is presented at the level of specific exemplars and generalise it to semantically similar contexts. We also showed a modest but statistically significant reduction in recall performance in the autistic participants relative to the non-autistic participants.

PMID:37267333 | DOI:10.1371/journal.pone.0286018

G3 (Bethesda). 2023 Jun 2:jkad104. doi: 10.1093/g3journal/jkad104. Online ahead of print.

ABSTRACT

The large-scale and nonaseptic fermentation of sugarcane feedstocks into fuel ethanol in biorefineries represents a unique ecological niche, in which the yeast Saccharomyces cerevisiae is the predominant organism. Several factors, such as sugarcane variety, process design, and operating and weather conditions, make each of the ∼400 industrial units currently operating in Brazil a unique ecosystem. Here, we track yeast population dynamics in 2 different biorefineries through 2 production seasons (April to November of 2018 and 2019), using a novel statistical framework on a combination of metagenomic and clonal sequencing data. We find that variation from season to season in 1 biorefinery is small compared to the differences between the 2 units. In 1 biorefinery, all lineages present during the entire production period derive from 1 of the starter strains, while in the other, invading lineages took over the population and displaced the starter strain. However, despite the presence of invading lineages and the nonaseptic nature of the process, all yeast clones we isolated are phylogenetically related to other previously sequenced bioethanol yeast strains, indicating a common origin from this industrial niche. Despite the substantial changes observed in yeast populations through time in each biorefinery, key process indicators remained quite stable through both production seasons, suggesting that the process is robust to the details of these population dynamics.

PMID:37267305 | DOI:10.1093/g3journal/jkad104

Int Rev Psychiatry. 2023 May-Jun;35(3-4):242-250. doi: 10.1080/09540261.2023.2186218. Epub 2023 Mar 7.

ABSTRACT

Stigma and discrimination are a major ongoing problem in the field of mental health as these impact on patient outcomes, access to and acceptability of therapeutic interventions, their quality of life, general wellbeing, social inclusion and opportunities. Social stereotypes, culture and prejudices all contribute to continuing discrimination in mental health. Different settings where people function may also be sources of discrimination such as work and educational environments. The lack of knowledge and understanding of mental health/illness by individuals, their families, carers and policymakers as well as the social media reporting also impact on social attitudes to discrimination. It has been also described a relevant impact of stigma among specific social minorities reporting poor mental health such as elderly people, youths, sexual variants, persons with disability. Educational programs, raising awareness trainings and proper public policies may be developed in order to reduce stigma at social level with favourable outcomes for people with mental illness.

PMID:37267024 | DOI:10.1080/09540261.2023.2186218

J Med Internet Res. 2023 Jun 2;25:e47225. doi: 10.2196/47225.

ABSTRACT

BACKGROUND: Social media platforms have been increasingly used to express suicidal thoughts, feelings, and acts, raising public concerns over time. A large body of literature has explored the suicide risks identified by people’s expressions on social media. However, there is not enough evidence to conclude that social media provides public surveillance for suicide without aligning suicide risks detected on social media with actual suicidal behaviors. Corroborating this alignment is a crucial foundation for suicide prevention and intervention through social media and for estimating and predicting suicide in countries with no reliable suicide statistics.

OBJECTIVE: This study aimed to corroborate whether the suicide risks identified on social media align with actual suicidal behaviors. This aim was achieved by tracking suicide risks detected by 62 million tweets posted in Japan over a 10-year period and assessing the locational and temporal alignment of such suicide risks with actual suicide behaviors recorded in national suicide statistics.

METHODS: This study used a human-in-the-loop approach to identify suicide-risk tweets posted in Japan from January 2013 to December 2022. This approach involved keyword-filtered data mining, data scanning by human efforts, and data refinement via an advanced natural language processing model termed Bidirectional Encoder Representations from Transformers. The tweet-identified suicide risks were then compared with actual suicide records in both temporal and spatial dimensions to validate if they were statistically correlated.

RESULTS: Twitter-identified suicide risks and actual suicide records were temporally correlated by month in the 10 years from 2013 to 2022 (correlation coefficient=0.533; P<.001); this correlation coefficient is higher at 0.652 when we advanced the Twitter-identified suicide risks 1 month earlier to compare with the actual suicide records. These 2 indicators were also spatially correlated by city with a correlation coefficient of 0.699 (P<.001) for the 10-year period. Among the 267 cities with the top quintile of suicide risks identified from both tweets and actual suicide records, 73.5% (n=196) of cities overlapped. In addition, Twitter-identified suicide risks were at a relatively lower level after midnight compared to a higher level in the afternoon, as well as a higher level on Sundays and Saturdays compared to weekdays.

CONCLUSIONS: Social media platforms provide an anonymous space where people express their suicidal thoughts, ideation, and acts. Such expressions can serve as an alternative source to estimating and predicting suicide in countries without reliable suicide statistics. It can also provide real-time tracking of suicide risks, serving as an early warning for suicide. The identification of areas where suicide risks are highly concentrated is crucial for location-based mental health planning, enabling suicide prevention and intervention through social media in a spatially and temporally explicit manner.

PMID:37267022 | DOI:10.2196/47225

Traffic Inj Prev. 2023;24(sup1):S124-S130. doi: 10.1080/15389588.2023.2173521.

ABSTRACT

OBJECTIVES: Automated driving (AD) from SAE level 3 onwards represents a paradigm change from human driver controlling the vehicle to a technical system controlling it. In this light, different regulatory bodies (European Commission, Germany, etc.) have defined guidelines for the operation of such a system. One core principle of these guidelines is that the automated operation needs to be at least as safe as human driving-often referred to as the “positive risk balance.” However, these guidelines are general and do not provide details on what this means in a practical sense. This article discusses a method to demonstrate how positive risk balance can be addressed in practice.

METHODS: Starting from a detailed analysis of corresponding guidelines and a literature review of possible risk assessment frameworks, a comprehensive approach has been developed to consider ethical requirements for the development of AD. This approach covers different development stages. The PrOACT-URL (Problems, Objectives, Alternatives, Consequences, Trade-offs, Uncertainty, Risk attitudes, and Linked decisions) approach was chosen for reporting of the work.

RESULTS: The article will present the approach developed by BMW to ensure that a positive risk balance is achieved for an AD system. The approach is presented per development stage (concept phase, AD development phase, verification and validation phase, post-start of production phase). In the concept phase, the scope is to define how good a human driver is and how good an AD needs to be. In the AD development phase, first the relevant system requirements need to be derived. Monte Carlo experiments in combination with Bayesian networks are applied. The fulfillment of these requirements is checked in the verification phase through simulations and test track and real-world tests. For validation of the risk balance, the impact of AD in terms of traffic safety is derived by means of simulation. In the post-start of production phase, field observation is used.

CONCLUSION: The safety of AD is paramount when it comes to its operation and ensuring trust in this technology. The described approach contributes directly to building this trust by considering the principle of a positive risk balance throughout the development in addition to existing safety standards for advance driver assistance systems, such as ISO 26262, ISO21434 or ISO 21488.

PMID:37267019 | DOI:10.1080/15389588.2023.2173521

Traffic Inj Prev. 2023;24(sup1):S111-S115. doi: 10.1080/15389588.2022.2131403.

ABSTRACT

OBJECTIVE: The first automatic emergency braking (AEB) system was presented in 2003 and aimed to mitigate or reduce rear-end crashes. Since then, several AEB systems aimed to reduce other collision types have been introduced and studies have shown that they reduce crash risks. The aim with this study was to evaluate crash reductions of cars fitted with AEB systems with pedestrian detection and those with bicyclist detection.

METHODS: The study is based on the Swedish Traffic Accident Data Acquisition that includes road traffic accidents reported by the police and by emergency hospitals. Crashes occurring between 2015 and 2020 and with cars from model years 2015 to 2020 were included. The statistical analysis used odds ratio calculations with an induced exposure approach where the outcomes of sensitive and nonsensitive crashes were studied. The sensitive crashes were hit pedestrians and bicyclists, respectively. The nonsensitive crash type in both comparisons was struck vehicles in rear-end crashes. Evaluations were also made for different light and weather conditions and for high and low speed roads.

RESULTS: Seven hundred and twelve hit pedestrians and 1,105 hit bicyclists were included, and the nonsensitive crashes consisted of 1,978 vehicles. The overall reduction on crash risk for AEB with pedestrian detection was 8% (±15%; ns) and for AEB with bicyclist detection it was 21% (±17%). When separating for light conditions, no reduction in crash risk for AEB with pedestrian detection nor for AEB with bicyclist detection could be seen in darkness. However, in daylight and twilight conditions, AEB with pedestrian detection reduced pedestrian crash risk by 18% (±19%; ns) and AEB with bicyclist detection reduced bicyclist crash risk by 23% (±19%). No significant reductions could be seen when separating for weather conditions except for a 53% (±31%) reduction for bicyclists in rain, fog, and snowfall. A larger reduction on high-speed roads (50-120 km/h) compared with low-speed roads (10-40 km/h) was also found.

CONCLUSIONS: AEB systems with bicyclist detection were found to reduce the numbers of hit bicyclists, especially in daylight and twilight conditions. In darkness, no reduction for hit pedestrians or bicyclists was found.

PMID:37267014 | DOI:10.1080/15389588.2022.2131403

Traffic Inj Prev. 2023;24(sup1):S9-S15. doi: 10.1080/15389588.2022.2157209.

ABSTRACT

OBJECTIVE: The objectives of this study were to evaluate computationally efficient small female (54.1 kg, 149.9 cm) and midsize male (78.4 kg, 174.9 cm) models with active muscles using volunteer sled test data in a frontal-oblique loading direction and check their response in crash mitigating maneuvers using field test data.

METHODS: The Global Human Body Models Consortium small female (F05-OS+Active) and midsize male (M50-OS+Active) simplified occupant models with active musculature were used in this study. The data from a total of 48 previously published sled test experiments were used to simulate a total of 16 simulations. The experimental study recorded occupant responses of six small female and six midsize male volunteers (n = 12 total) in two muscle conditions (relaxed and braced) at two acceleration pulses representing pre-crash braking (1.0 g) and a low-speed impact (2.5 g). Each model’s kinematics and reaction forces were compared with experimental data. Along with sled test simulations, both of these models were simulated in abrupt braking, lane change, and turn and brake events using literature data. A total of 36 field test simulations were carried out. A CORA analysis was carried out using reaction load and displacement time-history data for sled test simulations and head CG displacement time-history was used for field test simulations.

RESULTS: The occupant peak forward and lateral excursion results of both active models reasonably matched the volunteer data in the low-speed sled test simulations for both pulse severities. The differences between the active and control models were statistically significant (p-value < 0.05) based on the results of Wilcoxon signed-rank tests using peak forward and lateral excursion data. The average CORA scores calculated for the sled test (sled test: M50-OS+Active= 0.543, male control= 0.471, F05-OS+Active= 0.621, female control= 0.505) and field test (M50-OS+Active= 0.836, male control= 0.466, F05-OS+Active= 0.832, female control= 0.787) simulations were higher for active models than control.

CONCLUSIONS: The responses of the F05-OS+Active and M50-OS+Active models were better than control models based on overall CORA scores calculated using both sled and field tests. The results highlight their ability to predict occupant kinematics in crash-mitigating maneuvers and low-speed impacts in the frontal, lateral and frontal-oblique directions.

PMID:37267011 | DOI:10.1080/15389588.2022.2157209