Category: Nevin Manimala

J Am Med Inform Assoc. 2023 Apr 22:ocad057. doi: 10.1093/jamia/ocad057. Online ahead of print.

ABSTRACT

OBJECTIVE: Clinical encounter data are heterogeneous and vary greatly from institution to institution. These problems of variance affect interpretability and usability of clinical encounter data for analysis. These problems are magnified when multisite electronic health record (EHR) data are networked together. This article presents a novel, generalizable method for resolving encounter heterogeneity for analysis by combining related atomic encounters into composite “macrovisits.”

MATERIALS AND METHODS: Encounters were composed of data from 75 partner sites harmonized to a common data model as part of the NIH Researching COVID to Enhance Recovery Initiative, a project of the National Covid Cohort Collaborative. Summary statistics were computed for overall and site-level data to assess issues and identify modifications. Two algorithms were developed to refine atomic encounters into cleaner, analyzable longitudinal clinical visits.

RESULTS: Atomic inpatient encounters data were found to be widely disparate between sites in terms of length-of-stay (LOS) and numbers of OMOP CDM measurements per encounter. After aggregating encounters to macrovisits, LOS and measurement variance decreased. A subsequent algorithm to identify hospitalized macrovisits further reduced data variability.

DISCUSSION: Encounters are a complex and heterogeneous component of EHR data and native data issues are not addressed by existing methods. These types of complex and poorly studied issues contribute to the difficulty of deriving value from EHR data, and these types of foundational, large-scale explorations, and developments are necessary to realize the full potential of modern real-world data.

CONCLUSION: This article presents method developments to manipulate and resolve EHR encounter data issues in a generalizable way as a foundation for future research and analysis.

PMID:37087110 | DOI:10.1093/jamia/ocad057

Int Microbiol. 2023 Apr 22. doi: 10.1007/s10123-023-00360-2. Online ahead of print.

ABSTRACT

The aim of this study aimed to examine the existence of a bacterial metagenome in the bone marrow of patients with acute myeloid leukemia (AML). We re-examined whole-genome sequencing data from the bone marrow samples of seven patients with AML, four of whom were remitted after treatment, for metagenomic analysis. After the removal of human reads, unmapped reads were used to profile the species-level composition. We used the metagenomic binning approach to confirm whether the identified taxon was a complete genome of known or novel strains. We observed a unique and novel microbial signature in which Carnobacterium maltaromaticum was the most abundant species in five patients with AML or remission. The complete genome of C. maltaromaticum “BMAML_KR01,” which was observed in all samples, was 100% complete with 8.5% contamination and closely clustered with C. maltaromaticum strains DSM20730 and SF668 based on single nucleotide polymorphism variations. We identified five unique proteins that could contribute to cancer progression and 104 virulent factor proteins in the BMAML_KR01 genome. To our knowledge, this is the first report of a new strain of C. maltaromaticum in patients with AML. The presence of C. maltaromaticum and its new strain in patients indicates an urgent need to validate the existence of this bacterium and evaluate its pathophysiological role.

PMID:37087535 | DOI:10.1007/s10123-023-00360-2

Sci Rep. 2023 Apr 22;13(1):6596. doi: 10.1038/s41598-023-32592-7.

ABSTRACT

Quantum-mimic Optical Coherence Tomography (Qm-OCT) images are cluttered with artefacts – parasitic peaks which emerge as a by-product of the algorithm used in this method. However, the shape and behaviour of an artefact are uniquely related to Group Velocity Dispersion (GVD) of the layer this artefact corresponds to and consequently, the GVD values can be inferred by carefully analysing them. Since for multi-layered objects the number of artefacts is too high to enable layer-specific analysis, we employ a solution based on Machine Learning. We train a neural network with Qm-OCT data as an input and dispersion profiles, i.e. depth distribution of GVD within an A-scan, as an output. By accounting for noise during training, we process experimental data and estimate the GVD values of BK7 and sapphire as well as provide a qualitative GVD value distribution in a grape and cucumber. Compared to other GVD-retrieving methods, our solution does not require user input, automatically provides dispersion values for all the visualised layers and is scalable. We analyse the factors affecting the accuracy of determining GVD: noise in the experimental data as well as general physical limitations of the detection of GVD-induced changes, and suggest possible solutions.

PMID:37087517 | DOI:10.1038/s41598-023-32592-7

Malar J. 2023 Apr 22;22(1):131. doi: 10.1186/s12936-023-04561-y.

ABSTRACT

BACKGROUND: Even though malaria is easily preventable and treatable, it continues to have a devastating impact on people’s health and livelihoods around the world. Sub-Saharan Africa carries a disproportionately high share of the global malaria burden. This study seeks to assess the prevalence, trends and factors associated with malaria in the Shai-Osudoku District Hospital, Ghana.

METHODS: A cross-sectional study was conducted to determine the prevalence, trend, and factors associated with malaria in the Shai-Osudoku District Hospital; a 10-month secondary data was extracted from February to November 2020. The extracted data were entered into Epi Data version 6 and analysed using STATA version 16. Descriptive analysis was performed to determine the prevalence, trend and socio-demographic characteristics of study participants. Simple logistic regression at a 95% confidence level was performed to investigate socio-demographic factors associated with malaria infection. Tables and charts with summary statistics were used to present the results.

RESULTS: Secondary data from 3896 individuals were included in the study. The age of the participants range from 0.8 to 101 years with a mean age of 32.5. The estimated prevalence of malaria during the study period is 20.9%. A majority (79.1%) of the participants who presented signs and symptoms of malaria were negative after testing. The prevalence of malaria cases increased progressively from 6.7 to 55.4% across the ten months. The simple logistic regression at a 95% confidence level revealed that age group, sex, residential status, religion, occupation and marital status were statistically significantly associated with malaria. The results shows that persons who tested positive for malaria were mostly treated with artemether-lumefantrine (46.1%), some malaria positive cases were given artesunate injection (11.6%), dihydroartemisinin-piperaquine (16.2%) and oral artemether-lumefantrine (6.5%). Surprisingly 19.6% of the malaria-positive cases were not given any form of malaria medication.

CONCLUSION: Factors found to influence malaria infection in the Shai-Osudoku District Hospital include participant’s age, sex, residential status, religious affiliation occupation and marital status. The findings of this study showed that malaria remains a serious public health problem in the Shai Osudoku District Hospital. The information obtained from this study can guide the implementation of malaria prevention, control and elimination strategies in Ghana.

PMID:37087510 | DOI:10.1186/s12936-023-04561-y

BMC Oral Health. 2023 Apr 22;23(1):236. doi: 10.1186/s12903-023-02942-y.

ABSTRACT

BACKGROUND: Dentists started to follow the era of using single-shade resin composite restorations to avoid color shade selection. Our study was done to evaluate and compare the color stability of two single-shade resin composite materials.

METHODS: Sixty samples were randomly allocated into two main groups (n = 30) according to the composite resin used: Group O: (Omnichroma) samples and Group V: (Venus Peral) samples. Each group was then divided into two subgroups (n = 15): group O1 and V1: samples immersed in coffee. Group O2 and V2: samples immersed in distilled water. Color changes (ΔE) and roughness values (Ra) were evaluated at baseline, first, and 14^th days of immersion. The color change was assessed using Vita Easyshade V, while surface roughness was assessed using a profilometer and Atomic Force Microscope (AFM). Data were collected and statistically analyzed using two-way variance analysis (ANOVA) and Tukey’s post-hoc test (p < 0.05).

RESULTS: Group O1 and V1 recorded the highest ΔE₀₀ (P = 0.002, 0.0001, respectively) and Ra values (P < 0.001) with no significant difference between both materials at 14 days.

CONCLUSION: Single shade resin composite with innovative chromatic material technology has dramatic color change and surface roughness that sacrifice esthetic success.

PMID:37087507 | DOI:10.1186/s12903-023-02942-y

Int J Cardiol. 2023 Apr 20:S0167-5273(23)00587-9. doi: 10.1016/j.ijcard.2023.04.033. Online ahead of print.

NO ABSTRACT

PMID:37087054 | DOI:10.1016/j.ijcard.2023.04.033

J Theor Biol. 2023 Apr 20:111497. doi: 10.1016/j.jtbi.2023.111497. Online ahead of print.

ABSTRACT

Recent evidence suggests that nongenetic (epigenetic) mechanisms play an important role at all stages of cancer evolution. In many cancers, these mechanisms have been observed to induce dynamic switching between two or more cell states, which commonly show differential responses to drug treatments. To understand how these cancers evolve over time, and how they respond to treatment, we need to understand the state-dependent rates of cell proliferation and phenotypic switching. In this work, we propose a rigorous statistical framework for estimating these parameters, using data from commonly performed cell line experiments, where phenotypes are sorted and expanded in culture. The framework explicitly models the stochastic dynamics of cell division, cell death and phenotypic switching, and it provides likelihood-based confidence intervals for the model parameters. The input data can be either the fraction of cells or the number of cells in each state at one or more time points. Through a combination of theoretical analysis and numerical simulations, we show that when cell fraction data is used, the rates of switching may be the only parameters that can be estimated accurately. On the other hand, using cell number data enables accurate estimation of the net division rate for each phenotype, and it can even enable estimation of the state-dependent rates of cell division and cell death. We conclude by applying our framework to a publicly available dataset.

PMID:37087049 | DOI:10.1016/j.jtbi.2023.111497

World Neurosurg. 2023 Apr 20:S1878-8750(23)00546-6. doi: 10.1016/j.wneu.2023.04.062. Online ahead of print.

ABSTRACT

BACKGROUND: The aim of this study was to investigate the effect of burr hole width on postoperative chronic subdural hematoma thickness and midline shift radiologically.

METHODS: The files of 92 patients who were operated after diagnosis of Chronic Subdural Hematoma between April 1, 2015 and July 1, 2021 were reviewed retrospectively. Preoperative and postoperative computerized tomography (CT) scans were scrutinized and the thickness of hematoma and midline shift and the diameters of two burr holes opened were measured and recorded. The correlation between burr hole diameter width and chronic subdural hematoma thickness in postoperative CT and improvement in midline shift was investigated statistically.

RESULTS: When the CT scans performed on the postoperative 1^st day and postoperative 1^st month were examined, it was determined that the preoperative hematoma thickness and midline shift were significantly reduced (p<0.001). A positive significant correlation was found between the improvement of the midline shift, the posterior burr hole diameter and the anterior-posterior burr hole arithmetic mean (p<0.001; p=0.029, respectively).

CONCLUSION: Having examined the current surgical treatment techniques in the treatment of chronic subdural hematoma, we found that an increase in the width of burr hole craniotomies (BHC), especially the posterior BHC, contributed to the improvement in midline shift.

PMID:37087033 | DOI:10.1016/j.wneu.2023.04.062

Mol Phylogenet Evol. 2023 Apr 20:107797. doi: 10.1016/j.ympev.2023.107797. Online ahead of print.

ABSTRACT

Pleione is an orchid endemically distributed in high mountain areas across the Hengduan Mountains (HDM), Himalayas, Southeast Asia and South of China. The unique flower shapes, rich colors and immense medicinal importance of Pleione are valuable ornamental and economic resources. However, the phylogenetic relationships and evolutionary history of the genus have not yet been comprehensively resolved. Here, the evolutionary history of Pleione was investigated using single-copy gene single nucleotide polymorphisms and chloroplast genome datasets. The data revealed that Pleione could be divided into five clades. Discordance in topology between the two phylogenetic trees and network and D-statistic analyses indicated the occurrence of reticulate evolution in the genus. The evolution could be attributed to introgression and incomplete lineage sorting. Ancestral area reconstruction suggested that Pleione was originated from the HDM. Uplifting of the HDM drove rapid diversification by creating conditions favoring rapid speciation. This coincided with two periods of consolidation of the Asian monsoon climate, which caused the first rapid diversification of Pleione from 8.87 to 7.83 Mya, and a second rapid diversification started at around 4.05 Mya to Pleistocene. The interaction between Pleione and climate changes, especially the monsoons, led to the current distribution pattern and shaped the dormancy characteristic of the different clades. In addition to revealing the evolutionary relationship of Pleione with orogeny and climate changes, the findings of this study provide insights into the speciation and diversification mechanisms of plants in the East Asian flora.

PMID:37086913 | DOI:10.1016/j.ympev.2023.107797

J Stomatol Oral Maxillofac Surg. 2023 Apr 20:101476. doi: 10.1016/j.jormas.2023.101476. Online ahead of print.

ABSTRACT

BACKGROUND: The aim of this study is to compare wound healing and vestibular depth gain in individuals undergoing vestibule deepening surgery using diode laser and conventional technique and to further investigate the possible wound healing effect of low-level laser therapy (LLLT).

MATERIAL AND METHODS: 52 systemically healthy individuals with insufficient vestibular depth in the region of teeth 33-43 in the lower jaw were included. Following nonsurgical periodontal treatment, patients were divided into four groups as follows: a) diode laser (L); b) diode laser + LLLT; c) conventional surgery and d) conventional surgery + LLLT. Vestibular depth and horizontal wound size measurements of the individuals were recorded using digital calipers. Reepithelization was evaluated via an image analysis program.

RESULTS: Vestibular depth measurements were found to be higher in the conventional surgery groups compared to that of diode laser groups after the operation, while the results were not statistically different between groups (p >0.05). Reepithelization area did not differ between groups in the evaluated time periods (p >0,05). On the other hand, horizontal wound shrinkage was significantly higher in the conventional surgery group than that of diode laser.

CONCLUSIONS: Within the limits of this study, both methods yielded in vestibule depth gain. On the other hand, LLLT did not have an additional positive effect on mucosal wound healing. As a clinical relevance, the results are valuable for clinicians in terms of showing that suturing of the mucosal flap formed following vestibule deepening should not be necessary in laser assisted surgery for attaining more vestibule depth.

PMID:37086896 | DOI:10.1016/j.jormas.2023.101476