Category: Nevin Manimala

Brief Bioinform. 2023 Nov 22;25(1):bbad423. doi: 10.1093/bib/bbad423.

ABSTRACT

Identifying task-relevant structures is important for molecular property prediction. In a graph neural network (GNN), graph pooling can group nodes and hierarchically represent the molecular graph. However, previous pooling methods either drop out node information or lose the connection of the original graph; therefore, it is difficult to identify continuous subtructures. Importantly, they lacked interpretability on molecular graphs. To this end, we proposed a novel Molecular Edge Shrinkage Pooling (MESPool) method, which is based on edges (or chemical bonds). MESPool preserves crucial edges and shrinks others inside the functional groups and is able to search for key structures without breaking the original connection. We compared MESPool with various well-known pooling methods on different benchmarks and showed that MESPool outperforms the previous methods. Furthermore, we explained the rationality of MESPool on some datasets, including a COVID-19 drug dataset.

PMID:38048081 | DOI:10.1093/bib/bbad423

Indian J Pediatr. 2023 Dec 4. doi: 10.1007/s12098-023-04915-z. Online ahead of print.

ABSTRACT

OBJECTIVES: To develop a machine learning algorithm with prognosis data to identify different clinical phenotypes of biliary atresia (BA) and provide instructions for choosing treatment schemes.

METHODS: Six hundred thirty-nine cases of type III BA were retrospectively collected from the Children’s Hospital of Fudan University from Jan 1^st, 2017 to Dec 1^st, 2019 as a training dataset, and a survival-based forward clustering method, which can also be used to predict the subtype of a new patient was developed to identify BA subtypes.

RESULTS: A total of 2 clusters were identified (cluster 1 = 324 and cluster 2 = 315), where cluster 2 had a lower 2 y native liver survival post-Kasai rate. The infant patients in cluster 2 have higher weight, liver, and spleen volume, wider portal vein width, and older operative age; worse coagulation and liver function results; higher grade of liver fibrosis and detection rate of hepatic portal fibrous mass, and higher recent infection detection rate of herpes simplex virus type I. With the proposed prognostic classification system, the authors predicted the subtypes of the 187 cases of type III BA in a testing dataset collected from the whole year of 2020. The p-value computed from the log-rank testing for the Kaplan-Meier survival curves of the predicted two testing groups was 0.0113.

CONCLUSIONS: This classification system would be a convenient tool to choose appropriate treatment and accelerate the choice-making between clinicians and infant patients.

PMID:38047995 | DOI:10.1007/s12098-023-04915-z

Curr Allergy Asthma Rep. 2023 Dec 4. doi: 10.1007/s11882-023-01110-0. Online ahead of print.

ABSTRACT

PURPOSE OF REVIEW: With increasing industrialization, exposure to ambient and wildfire air pollution is projected to increase, necessitating further research to elucidate the complex relationship between exposure and sinonasal disease. This review aims to summarize the role of ambient and wildfire air pollution in chronic rhinosinusitis (CRS) and olfactory dysfunction and provide a perspective on gaps in the literature.

RECENT FINDINGS: Based on an emerging body of evidence, exposure to ambient air pollutants is correlated with the development of chronic rhinosinusitis in healthy individuals and increased symptom severity in CRS patients. Studies have also found a robust relationship between long-term exposure to ambient air pollutants and olfactory dysfunction. Ambient air pollution exposure is increasingly recognized to impact the development and sequelae of sinonasal pathophysiology. Given the rising number of wildfire events and worsening impacts of climate change, further study of the impact of wildfire-related air pollution is a crucial emerging field.

PMID:38047993 | DOI:10.1007/s11882-023-01110-0

Support Care Cancer. 2023 Dec 4;32(1):2. doi: 10.1007/s00520-023-08177-5.

ABSTRACT

PURPOSE: To evaluate the discrepancy and correlation between sleep-wake measures (i.e., time in bed (TIB), total sleep time (TST), sleep onset latency (SOL), wake after sleep onset (WASO), and sleep efficiency (SE%)) reported on sleep diary and measured by actigraphy among cancer survivors with insomnia symptoms; and examine the influences of sociodemographic and clinical variables on these measurement differences.

METHODS: A heterogenous sample of cancer survivors with insomnia symptoms (n = 120; M age = 63.7 ± 10.1; female = 58.3%) was included. Seven consecutive days of sleep diary and actigraphic data were obtained along with information on demographic, sleep, and mental health symptoms. Bland-Altman plot, Pearson correlation coefficient, concordance correlation coefficient, and mixed linear model approach were used to conduct the analysis.

RESULTS: Self-reported TIB, SOL, and WASO were longer than measured by actigraphy (TIB: 8.6 min. (95% CI, 3.7, 13.5; p < .001); SOL: 14.8 min. (95% CI, 9.4, 20.2; p < .0001); and WASO: 20.7 min. (95% CI, 9.4, 20.2; p < .0001), respectively); and self-reported TST and SE% were shorter than measured by actigraphy (TST: 6.8 min. (95% CI, -18.7, 5.13); and SE%: 0.7% (95%CI, -3.0, 2.0), respectively), but were not statistically significant. Sex, higher insomnia severity, and poor sleep quality were associated with discrepancy between several sleep-wake measures.

CONCLUSION: Subjective and objective sleep-wake measures may present discrepant finding among cancer survivors with symptoms of insomnia. Future research is needed to validate appropriate sleep-wake assessment, and better understand factors that influence the discrepancy that exists between measures among this population.

CLINICAL TRIAL REGISTRATION: Clinical trials identifier: NCT03810365. Date of registration: January 14, 2019.

PMID:38047967 | DOI:10.1007/s00520-023-08177-5

Eur J Pediatr. 2023 Dec 4. doi: 10.1007/s00431-023-05346-w. Online ahead of print.

NO ABSTRACT

PMID:38047960 | DOI:10.1007/s00431-023-05346-w

Parasitol Res. 2023 Dec 4;123(1):2. doi: 10.1007/s00436-023-08024-w.

ABSTRACT

Trypanosoma evansi infects domestic animals, causing a debilitating and occasionally fatal disease. The disease leads to significant economic losses to farmers and poses a substantial impediment to the growth of livestock production in developing nations, including India. Considering the challenges associated with managing this infection, there is an urgent need to enhance our understanding of the molecular and genetic diversity of T. evansi. Therefore, this study was planned to analyze the genetic diversity of T. evansi using available internal transcribed spacer-1 (ITS-1) gene sequences from India and compare them with sequences from around the globe. Blood samples used in this study were collected from naturally infected animals including dogs, cattle, and buffaloes in the Indian state of Madhya Pradesh. Using the ITS-1 gene, we amplified a 540 base pairs (bp) segment using polymerase chain reaction (PCR), sequenced it, and identified intra-specific variations. Phylogenetic analysis of 90 sequences, including 27 from India, revealed three distinct clusters with high bootstrap support values. A haplotype network analysis identified 34 haplotypes, with H7 being the most prevalent, indicating a complex evolutionary history involving multiple countries. The genetic analysis of the Indian population revealed distinct characteristics. Despite low nucleotide diversity, there was high haplotype diversity in comparison to other populations. Tajima’s D, Fu and Li’s D, and Fu and Li’s F exhibited non-significant negative values, indicating potential stability. Additionally, the slightly positive values in Fu’s Fs, Raggedness (r), and Ramos-Onsins and Rozas (R2) statistics suggested a lack of recent significant selective pressures or population expansions. Furthermore, the presence of genetic differentiation and gene flow among T. evansi populations highlighted ongoing evolutionary processes. These findings collectively depicted a complex genetic landscape, suggesting both stability and ongoing evolutionary dynamics within the Indian population of T. evansi. The findings of this study are important for understanding the evolutionary history and population dynamics of T. evansi, and they may help us develop effective control strategies.

PMID:38047956 | DOI:10.1007/s00436-023-08024-w

Cancer Sci. 2023 Dec 4. doi: 10.1111/cas.16021. Online ahead of print.

ABSTRACT

Due to the scarcity of large-sized prospective databases, the Japanese Joint Committee for Lung Cancer Registry conducted a nationwide prospective registry for newly diagnosed and untreated pleural mesothelioma. All new cases diagnosed pathologically as any subtype of pleural mesothelioma in Japan during the period between April 1, 2017, to March 31, 2019, were included before treatment. Data on survival were collected in April 2021. The eligible 346 patients (285 men [82.3%]; 61 women [17.7%]; median age, 71.0 years [range, 44-88]) were included for analysis. Among these patients, 138 (39.9%) underwent surgery, 164 (47.4%) underwent non-surgical therapy, and the remaining 44 (12.7%) underwent best supportive care. The median overall survival for all 346 patients was 19.0 months. Survival rates at 1, 2, and 3 years for all patients were, 62.8%, 42.3%, and 26.5%, respectively. Median overall survival was significantly different among patients undergoing surgery, non-surgical treatment, and best supportive care (32.2 months vs. 14.0 months vs. 3.8 months, p < 0.001). The median overall survival of patients undergoing pleurectomy/decortication and extrapleural pneumonectomy was 41.8 months and 25.0 months, respectively. Macroscopic complete resection resulted in longer overall survival than R2 resection and partial pleurectomy/exploratory thoracotomy (41.8 months vs. 32.2 months vs. 16.8 months, p < 0.001). Tumor shape, maximum tumor thickness, and sum of three level thickness were significant prognostic factors. The data in the prospective database would serve as a valuable reference for clinical practice and further studies for pleural mesothelioma.

PMID:38047872 | DOI:10.1111/cas.16021

Chimia (Aarau). 2023 Feb 22;77(1-2):7-16. doi: 10.2533/chimia.2023.7.

ABSTRACT

Accelerating R&D is essential to address some of the challenges humanity is currently facing, such as achieving the global sustainability goals. Today’s Edisonian approach of trial-and-error still prevalent in R&D labs takes up to two decades of fundamental and applied research for new materials to reach the market. Turning around this situation calls for strategies to upgrade R&D and expedite innovation. By conducting smart experiment planning that is data-driven and guided by AI/ML, researchers can more efficiently search through the complex – often constrained – space of possible experiments and find or hit the global optima much faster than with the current approaches. Moreover, with digitized data management, researchers will be able to maximize the utility of their data in the short and long terms with the aid of statistics, ML and visualization tools. In what follows, we describe a framework and lay out the key technologies to accelerate R&D and optimize experiment planning.

PMID:38047848 | DOI:10.2533/chimia.2023.7

Chem Res Toxicol. 2023 Dec 4. doi: 10.1021/acs.chemrestox.3c00238. Online ahead of print.

ABSTRACT

Read-across (RA) and quantitative structure-activity relationship (QSAR) are two alternative methods commonly used to fill data gaps in chemical registrations. These approaches use physicochemical properties or molecular fingerprints of source substances to predict the properties of unknown substances that have similar chemical structures or physicochemical properties. Research on RA and QSAR is essential to minimize the time, money, and animal testing needed to determine biological properties that are not currently known. This study developed a stacked ensemble quantitative read-across structure-activity relationship algorithm (enQRASAR) for predicting skin irritation toxicity based on negative log cell viability inhibition concentration at 50% (pIC50) against skin keratinocytes as the end point. The goodness-of-fit and predictability of this algorithm were validated using leave-one-out cross-validation and external test data sets. The results obtained were statistically reliable in terms of goodness-of-fit, robustness, and predictability metrics. Additionally, the developed model demonstrated a low prediction error when predicting FDA-approved drugs. These results confirm that the enQRASAR algorithm can be used to predict skin cytotoxicity of chemicals. Therefore, this model was publicly available to further facilitate toxicity predictions of unknown compounds in chemical registrations.

PMID:38047785 | DOI:10.1021/acs.chemrestox.3c00238

Pain. 2023 Nov 30. doi: 10.1097/j.pain.0000000000003126. Online ahead of print.

ABSTRACT

Pain neuroscience education (PNE) has shown promising results in the management of patients with chronic spinal pain (CSP). However, no previous review has determined the optimal dose of PNE added to an exercise programme to achieve clinically relevant improvements. The aim was to determine the dose-response association between PNE added to an exercise programme and improvements in pain intensity and disability in patients with CSP. A systematic search of PubMed/MEDLINE, Embase, Web of Science, Scopus, and the Cochrane Library was conducted from inception to April 19, 2023. The exposure variable (dosage) was the total minutes of PNE. Outcome measures included pain intensity, disability, quality of life, pressure pain thresholds, and central sensitization inventory. Data extraction, risk-of-bias assessment, and certainty of evidence were performed by 2 independent reviewers. The dose-response relationship was assessed using a restricted cubic spline model. Twenty-six randomised controlled trials with 1852 patients were included. Meta-analysis revealed a statistically significant effect in favour of PNE on pain intensity and disability. In addition, a dose of 200 and 150 minutes of PNE added to an exercise programme was estimated to exceed the minimum clinically important difference described in the literature for pain intensity (-2.61 points, 95% CI = -3.12 to -2.10) and disability (-6.84 points, 95% CI = -7.98 to -5.70), respectively. The pooled effect of the isolated exercise was small. These findings may be useful in optimising the most appropriate PNE dose to achieve clinically relevant improvements in patients with CSP.

PMID:38047772 | DOI:10.1097/j.pain.0000000000003126