Parrot optimizer: Algorithm and applications to medical problems

Stochastic optimization methods have gained significant prominence as effective techniques in contemporary research, addressing complex optimization challenges efficiently. This paper introduces the Parrot Optimizer (PO), an efficient optimization method inspired by key behaviors observed in trained Pyrrhura Molinae parrots. The study features qualitative analysis and comprehensive experiments to showcase the distinct characteristics of the Parrot Optimizer in handling various optimization problems. Performance evaluation involves benchmarking the proposed PO on 35 functions, encompassing classical cases and problems from the IEEE CEC 2022 test sets, and comparing it with eight popular algorithms. The results vividly highlight the competitive advantages of the PO in terms of its exploratory and exploitative traits. Furthermore, parameter sensitivity experiments explore the adaptability of the proposed PO under varying configurations. The developed PO demonstrates effectiveness and superiority when applied to engineering design problems. To further extend the assessment to real-world applications, we included the application of PO to disease diagnosis and medical image segmentation problems, which are highly relevant and significant in the medical field. In conclusion, the findings substantiate that the PO is a promising and competitive algorithm, surpassing some existing algorithms in the literature. The supplementary files and open source codes of the proposed Parrot Optimizer (PO) is available at https://aliasgharheidari.com/PO.html and https://github.com/junbolian/PO.

KCNH2A561V Heterozygous Mutation Inhibits KCNH2 Protein Expression via The Activation of UPR Mediated by ATF6

The potassium channel protein KCNH2 is encoded by KCNH2 gene, and there are more than 300 mutations of KCNH2. Unfolded protein response (UPR) is typically initiated in response to an accumulation of unfolded and/or misfolded proteins in the endoplasmic reticulum (ER). The present study aimed to explore the UPR process and the role of activating transcription factor 6 (ATF6) in the abnormal expression of potassium voltage-gated channel subfamily H member 2 (KCNH2)A561V. The wild-type (wt) KCNH2 and A561V mutant KCNH2 was constructed with his-tag. The 293 cells were used and divided into KCNH2wt+KCNH2A561V, KCNH2wt and KCNH2A561V groups. The expression levels of ATF6 and KCNH2 in different groups were detected by Western blotting, reverse transcription-quantitative PCR, immunofluorescence and immuno-coprecipitation assays. The protein types and abundance of immuno-coprecipitation samples were analyzed by mass spectrometry. The proteomic analysis of the mass spectrometry results was carried out by using the reactome database and GO (Gene Ontology) tool. The mRNA expression levels of KCNH2 and ATF6 in the KCNH2wt+KCNH2A561V group were higher compared with the KCNH2A561V group. However, the full-length protein expression of ATF6 was inhibited, indicating that ATF6 was highly activated and a substantial number of ATF6 was sheared in KCNH2wt+KCNH2A561V group compared with control group. Furthermore, A561V-KCNH2 mutation leading to the accumulation of the immature form of KCNH2 (135 kDa bands) in ER, resulting in the reduction of the ratio of 155 kDa/135 kDa. In addition, the abundance of UPR-related proteins in the KCNH2A561V group was higher compared with the KCNH2wt+KCNH2A561V group. The 'cysteine biosynthetic activity' of GO:0019344 process and the 'positive regulation of cytoplasmic translation activity' of GO:2000767 process in the KCNH2A561V group were higher compared with the KCNH2wt+KCNH2A561V group. Hence, co-expression of wild-type and A561V mutant KCNH2 in 293 cells activated the UPR process, which led to the inhibition of protein translation and synthesis, in turn inhibiting the expression of KCNH2. These results provided a theoretical basis for clinical treatment of Long QT syndrome.

An Automated Brain Metastasis Detection and Segmentation System from MRI with a Large Multi-Institutional Dataset

PURPOSE/OBJECTIVE(S)

Developments of automated systems for brain metastasis (BM) detection and segmentation from MRI for assisting early detection and stereotactic radiosurgery (SRS) have been reported but most based upon relatively small datasets from single institutes. This work aims to develop and evaluate a system using a large multi-institutional dataset, and to improve both identification of small/subtle BMs and segmentation accuracy of large BMs.

MATERIALS/METHODS

A 3D U-Net system was trained and evaluated to detect and segment intraparenchymal BMs with a size > 2mm using 1856 MRI volumes from 1791 patients treated with SRS from seven institutions (1539 volumes for training, 183 for validation, and 134 for testing). All patients had 3D post-Gd T1w MRI scans pre-SRS. Gross tumor volumes (GTVs) of BMs for SRS were curated by each institute first. Then, additional efforts were spent to create GTVs for the untreated and/or uncontoured BMs, including central reviews by two radiologists, to improve accuracy of ground truth. The training dataset was augmented with synthetic BMs of 3773 MRIs using a 3D generative pipeline. Our system consists of two U-Nets with one using small 3D patches dedicated for detecting small BMs and another using large 3D patches for segmenting large BMs, and a random-forest based fusion module for combining the two network outputs. The first U-Net was trained with 3D patches containing at least one BM < 0.1 cm3. For detection performance, we measured BM-level sensitivity and case-level false-positive (FP) rate. For segmentation performance, we measured BM-level Dice similarity coefficient (DSC) and 95-percentile Hausdorff distance (HD95). We also stratified performances based upon BM sizes.

RESULTS

For 739 BMs in the 134 testing cases, the overall lesion-level sensitivity was 0.870 with an average case-level FP of 1.34±1.92 (95% CI: 1.02-1.67). The sensitivity was >0.969 for the BMs >0.1 cm3, but dropped to 0.755 for the BMs < 0.1 cm3 (Table 1). The average DSC and HD95 for all detected BMs were 0.786 and 1.35mm. The worse performance for BMs > 20 cm3 was caused by a case with 83 cm3 GTV and artifacts in the MRI volume.

CONCLUSION

We achieved excellent detection sensitivity and segmentation accuracy for BMs > 0.1 cm3, and promising performance for small BMs (<0.1cm3) with a controlled FP rate using a large multi-institutional dataset. Clinical utility for assisting early detection and SRS planning will be investigated. Table 1: Per-lesion detection and segmentation performance stratified by individual BM size. N is the number of BMs in each category.

[Analysis of the effect of preventive intervention on occupational exposure of nurses after tumor particle implantation in thoracic surgery]

Objective: To study the effect of preventive intervention on occupational exposure of nurses after tumor particle implantation in thoracic surgery. Methods: In March 2020, 99 nurses who were engaged in postoperative nursing of tumor particle implantation in thoracic surgery department of our hospital from February 2019 to February 2020 were selected as the research objects. According to different preventive interventions, they were divided into observation group (51 cases) and control group (48 cases) . The observation group received preventive intervention, while the control group received routine intervention. The differences of radiation dose, psychological state and abnormal rate of important organ function between the two groups were analyzed. Results: Compared with the control group, the radiation dose of the observation group was significantly less, and the scores of anxiety and depression were lower after the intervention, the difference were statistically significant (P<0.05) . There was no significant difference of the abnormal rate of important organ function between the two groups (P>0.05) . Conclusion: Preventive intervention can reduce the risk of occupational exposure and improve the psychological status of nurses after tumor particle implantation in thoracic surgery.

LINC00641 induces the malignant progression of colorectal carcinoma through the miRNA-424-5p/PLSCR4 feedback loop

OBJECTIVE

To illustrate the role of LINC00641 in inducing the malignant progression of colorectal cancer (CRC) through the miRNA-424-5p/PLSCR4 feedback loop.

PATIENTS AND METHODS

LINC00641 levels in paired CRC and non-tumoral tissues were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Its prognostic potential in CRC was assessed by Kaplan-Meier method. Changes in proliferative and migratory abilities of HCT116 and SW620 cells transfected with si-LINC00641 were evaluated by 5-Ethynyl-2'- deoxyuridine (EdU), cell counting kit-8 (CCK-8) and transwell assay. The feedback loop LINC00641/miRNA-424-5p/PLSCR4 was identified through Dual-Luciferase reporter assay and its involvement in CRC progression was finally explored by rescue experiments.

RESULTS

LINC00641 was upregulated in CRC tissues, which was an unfavorable factor to the overall survival of CRC. Proliferative and migratory abilities of HCT116 and SW620 cells were inhibited by knockdown of LINC00641. LINC00641 could competitively bind miRNA-424-5p, thereby abolishing its inhibitory effect on PLSCR4 expression. Knockdown of PLSCR4 could inhibit proliferative and migratory abilities of HCT116 and SW620 cells.

CONCLUSIONS

LINC00641 stimulates proliferative and migratory abilities of CRC through the miRNA-424-5p/PLSCR4 feedback loop.

[HIV infection and related factors among men who have sex with men aged 50 and above]

Objectives: To explore the HIV prevalence and related factors among MSM aged 50 and above and provide evidence on the prevention and control of HIV/AIDS. Methods: Based on an MSM social application software Blued 7.1.6, we recruited participants through online convenience sampling to collect demographic variables, behavioral and self-reported HIV infection status, etc. Univariate χ2 test and multivariate logistic regression were used to analyze the related factors of self-reported HIV infection. Results: Self-reported HIV infection rate was 17.6%(126/714) among the participants. In multivariable analysis, participants who got divorced or widowed had a 2.07(95%CI: 1.34-3.21) times greater risk of self-reported HIV-positive than those who were married. Participants unaware of HIV-related knowledge showed a 1.92(95%CI:1.21-3.04) times greater risk of self-reported HIV-positive than those with better HIV-related knowledge. Participants who have ever been diagnosed with sexually transmitted disease (STD) showed a 3.17(95%CI:2.09-4.83) times greater risk of self-reported HIV-positive than those without STD infection history. Conclusion: Our findings indicated that the self-reported HIV infection rate was high among MSM aged 50 and above. Being divorced or widowed, being unaware of HIV-related knowledge and STD infection history was proved related with self-reported HIV infection.

[Role of Orai 1-mediated store-operated calcium entry in the immune function of CD4+ T cells in septic mice]

Objective: To investigate the role of Orai1-mediated store-operated calcium entry in the immune damage of CD4⁺ T cells in septic mice. Methods: Sepsis mouse model was established by cecal ligation and puncture(CLP). Balb/c mice of clean grade were sacrificed 1, 3, and 5 days after operation. Spleen samples were harvested at given intervals. Splenic CD4⁺ T cells were selected by immunomagnetic beads and the expression of Orai1 protein was detected by western blotting, the storage operated calcium entry (SOCE) was detected by flow cytometry, the apoptosis of CD4⁺ T cells was detected by flow cytometry, the proliferation of CD4⁺ T cells was detected by CCK-8, and the IFN-γ and IL-4 were detected by enzyme-linked immunosorbent assay (ELISA). Then the expression of Orai1 protein was regulated to further detect the SOCE and immune function of splenic CD4⁺ T cells in mice. The experiment was divided into 4 groups, sham group, CLP3 group, Orai1 down group (Orai1-down group) and Orai1 up regulation group (Orai1-up group). Results: The relative expression of Orai1 protein in splenic CD4⁺ T cells in sham group was 1.03±0.16. Compared with sham group, Orai1 protein levels in CLP Group were all significantly lower (F=19.64, P=0.000 5). The increased value of splenic CD4⁺ T cells fluorescence intensity in sham group was 494±41. Compared with sham group, the levels of SOCE in CLP Group were all lower (F=30.01, P=0.001). The ratio of early and late apoptosis of CD4⁺ T cells in sham group was 8.7%±1.5%. Compared with sham group, the early and late apoptosis rates of CLP Group were significantly higher (F=32.29, P=0.000 1). The OD of sham group was 0.81±0.10 at 450 nm. Compared with sham group, the proliferation ability of splenic CD4⁺ T cells in CLP Group were significantly decreased (F=7.26, P=0.001 8). Compared with sham group, the secretion of IFN-γ and IL-4 by CD4⁺ T cells and the ratio of IFN-γ/IL-4 in CLP Group were all significantly decreased (F=19.690, 6.183, 11.230, all P<0.05). Compared with CLP3 group, the increased value of fluorescence intensity of CD4⁺ T cells was significantly decreased, the early and late apoptosis ratio of CD4⁺ T cells was significantly increased, the OD450 nm value of CD4⁺ T cells was decreased, the multiplication capacity of splenic CD4⁺ T cells were decreased, the level of IFN-γ and IL-4 secreted by T cells were decreased, and the value of IFN-γ/IL-4 in orai1-down group was decreased (t=4.819, 7.952, 2.988, 28.760, 3.140, 7.670, all P<0.05). However, Orail-up group showed the opposite trend. Conclusion: Orai1-mediated store-operated calcium entry can alleviate the immune dysfunction of CD4⁺ T cells in septic mice.

[Baicalin regulates STIM1-mediated calcium overload and reduces apoptosis of cardiomyocytes induced by lipopolysaccharide]

Objective: To investigate the protective effect of Baicalin on apoptosis induced by lipopolysaccharide in H9C2 cardiomyocytes and its possible mechanism. Methods: In order to establish apoptosis model of H9C2 cardiomyocytes, H9C2 cardiomyocytes were cultured and divided into four groups: the control group; the baicalin group was treated with baicalin at the final concentration of 10μmol/L for 12 hours; the LPS group was stimulated with LPS at the final concentration of 1 μg/ml for 6 hours; The LPS+baicalin group was stimulated with LPS at the final concentration of 1 μg/ml for 6 hours within treated with baicalin at the final concentration of 10μmol/L for 12 hours. Collecting cell samples, CCK-8 (The Cell Counting Kit-8) was used to detect cell activity, and Terminal-deoxynucleoitidyl Transferase Mediated Nick End Labeling (TUNEL) was used to detect the expression levels of apoptosis. Laser Scanning Confocal Microscopy was used to detect the expression levels of store-operated calcium entry in H9C2 cardiomyocytes. Western blot was used to detect the protein expression levels of STIM1, cleaved-caspase3, Bax and Bcl-2. Fluorogenic quantitative PCR was used to detect the mRNA expression level of STIM1. Results: Compared with the control group, LPS-induced H9C2 cardiomyocyte survival rate decreased (P<0.05), the expression level of apoptosis increased (P<0.05), the internal flow of calcium increased (P<0.05), the expression levels of cleaved-caspase3, Bax protein levels increased (P<0.05), Bcl-2 protein level decreased (P<0.05), the expression of STIM1 mRNA and protein level increased (P<0.05). Compared with LPS group, the survival rate of H9C2 cardiomyocytes in baicalin intervention group increased (P<0.05), the expression level of apoptosis decreased (P<0.05), the internal flow of calcium decreased (P<0.05), the expression levels of cleaved-caspase3, Bax protein decreased (P<0.05), and the level of Bcl-2 protein increased (P<0.05), the expression of STIM1 mRNA and protein level decreased (P<0.05). Conclusion: Baicalin may alleviate LPS-induced cardiomyocyte apoptosis by alleviating calcium overload, and improve cell survival.

An Adiponectin Receptor Agonist Reduces Type 2 Diabetic Periodontitis

Periodontitis is twice as prevalent in diabetics as in nondiabetics, and type 2 diabetes (T2D)-associated periodontitis is severe in many cases due to the altered and aberrant functions of bone cells in hyperglycemic conditions. Therefore, developing an effective method to halt the disease process, as well as restore and regenerate lost alveolar bone to reserve the natural teeth in diabetics, is critically important. In the current study, we applied a newly discovered adiponectin receptor agonist AdipoRon (APR) in experimental periodontitis in diabetic animal models and demonstrated the underlying molecular mechanisms. We found that when APR systemically quenched the blood sugar level in diet-induced obesity (DIO) diabetic mice, it reduced osteoclast numbers and alveolar bone loss significantly due to APR's inhibition on osteoclast differentiation shown in our in vitro studies. APR also decreased the production of proinflammatory molecules CC chemokine ligand 2 and interleukin 6 in diseased gingival tissues. On the other hand, APR promoted alveolar bone regeneration through enhancing osteogenic differentiation and decreasing stromal cell-derived factor 1 in the bone marrow that facilitates stem cell migration. Same results were achieved by APR treatment of periodontitis induced in adiponectin (APN) knockout mice, indicating the ability of APR to activate the endogenous APN receptors to exert osteoanabolic effects. In summary, our study supports the notion that APR could be used as an effective multipronged approach to target T2D-associated periodontitis.

IL6 derived from cancer-associated fibroblasts promotes chemoresistance via CXCR7 in esophageal squamous cell carcinoma

Various factors and cellular components in the tumor microenvironment are key drivers associated with drug resistance in many cancers. Here, we analyzed the factors and molecular mechanisms involved in chemoresistance in patients with esophageal squamous cell carcinoma (ESCC). We found that interleukin 6 (IL6) derived mainly from cancer-associated fibroblasts played the most important role in chemoresistance by upregulating C-X-C motif chemokine receptor 7 (CXCR7) expression through signal transducer and activator of transcription 3/nuclear factor-κB pathway. CXCR7 knockdown resulted in the inhibition of IL6-induced proliferation and chemoresistance. In addition, CXCR7 silencing significantly decreased gene expression associated with stemness, chemoresistance and epithelial-mesenchymal transition and suppressed the proliferation ability of ESCC cells in three-dimensional culture systems and angiogenesis assay. In clinical samples, ESCC patients with high expression of CXCR7 and IL6 presented a significantly worse overall survival and progression-free survival upon receiving cisplatin after operation. These results suggest that the IL6-CXCR7 axis may provide a promising target for the treatment of ESCC.

Cortical Potential Imaging of Brain Electrical Activity by Means of Parametric Projection Filter

Objectives: The objective of this study was to explore suitable spatial filters for inverse estimation of cortical potentials from the scalp electroencephalogram. The effect of incorporating noise covariance into inverse procedures was examined by computer simulations and tested in human experiment.

Methods: The parametric projection filter, which allows inverse estimation with the presence of information on the noise, was applied to an inhomogeneous three-concentric-sphere model under various noise conditions in order to estimate the cortical potentials from the scalp potentials. The method for determining the optimum regularization parameter, which can be applied for parametric inverse techniques, is also discussed.

Results: Human visual evoked potential experiment was carried out to examine the performance of the proposed restoration method. The parametric projection filter gave more localized inverse solution of cortical potential distribution than the truncated SVD and Tikhonov regularization.

Conclusion: The present simulation results suggest that incorporation of information on the noise covariance allows better estimation of cortical potentials, than inverse solutions without knowledge about the noise covariance, when the correlation between the signal and noise is low.

Mechanism of iodine release from iodoapatite in aqueous solution

Incongruent release of iodine from iodoapatite (Pb₅(VO₄)₃I) for immobilization of¹²⁹iodine, controlled by exchange of iodide and hydroxide in solution.

Are we making good use of our public resources? The false-positive rate of screening by fundus photography for diabetic macular oedema

INTRODUCTION

A large proportion of patients diagnosed with diabetic maculopathy using fundus photography and hence referred to specialist clinics following the current screening guidelines adopted in Hong Kong and United Kingdom are found to be false-positive, implying that they did not have macular oedema. This study aimed to evaluate the false-positive rate of diabetic maculopathy screening using the objective optical coherence tomography scan.

METHODS

This was a cross-sectional observational study. Consecutive diabetic patients from the Hong Kong West Cluster Diabetic Retinopathy Screening Programme with fundus photographs graded R1M1 were recruited between October 2011 and June 2013. Spectral-domain optical coherence tomography imaging was performed. Central macular thickness of ≥300 μm and/or the presence of optical coherence tomography signs of diabetic macular oedema were used to define the presence of diabetic macular oedema. Patients with conditions other than diabetes that might affect macular thickness were excluded. The mean central macular thickness in various subgroups of R1M1 patients was calculated and the proportion of subjects with central macular thickness of ≥300 μm was used to assess the false-positive rate of this screening strategy.

RESULTS

A total of 491 patients were recruited during the study period. Of the 352 who were eligible for analysis, 44.0%, 17.0%, and 38.9% were graded as M1 due to the presence of foveal 'haemorrhages', 'exudates', or 'haemorrhages and exudates', respectively. The mean (±standard deviation) central macular thickness was 265.1±55.4 μm. Only 13.4% (95% confidence interval, 9.8%-17.0%) of eyes had a central macular thickness of ≥300 μm, and 42.9% (95% confidence interval, 37.7%-48.1%) of eyes had at least one optical coherence tomography sign of diabetic macular oedema. For patients with retinal haemorrhages only, 9.0% (95% confidence interval, 4.5%-13.5%) had a central macular thickness of ≥300 μm; 23.2% (95% confidence interval, 16.6%-29.9%) had at least one optical coherence tomography sign of diabetic macular oedema. The false-positive rate of the current screening strategy for diabetic macular oedema was 86.6%.

CONCLUSION

The high false-positive rate of the current diabetic macular oedema screening adopted by the United Kingdom and Hong Kong may lead to unnecessary psychological stress for patients and place a financial burden on the health care system. A better way of screening is urgently needed. Performing additional spectral-domain optical coherence tomography scans on selected patients fulfils this need.

Optimization of polarizer azimuth in improving signal-to-noise ratio in Kerr microscopy

The magneto optical Kerr effect (MOKE) is a widely used technique in magnetic domain imaging for its high surface sensitivity and external magnetic compatibility. Optimization of Kerr microscopy will improve the detecting sensitivity and provide high-quality domain images. In this work, we provide a method to optimize the polarizer azimuth in improving the signal-to-noise ratio (S/N) in longitudinal Kerr microscopy with the generalized magneto optical ellipsometry. Detailed analysis of the MOKE signal and the noise components are provided to study the optimum polarizer and analyzer azimuth combinations. Results show that, for a fixed polarizer angle 1°, the laser intensity noise and the shot noise, which vary with the input laser power, have a similar amplitude and decline with the analyzer azimuth increasing. When the analyzer is set at the extinction place, the Johnson noise plays a dominate role in the total noise. Then, the S/N values are calculated to find the optimum polarizer and analyzer azimuth. Results show that the optimum polarizer and analyzer azimuth combination for Permalloy is (18.35°, 68.35°) under an incident angle of 45°. After that, the S/N of 200 nm Permalloy at different analyzer angles with the polarizer azimuth set at 18.35° is measured to verify the validity of the simulation results. At last, the S/N at different incident angles is calculated. Results show that the optimum incident angle of 200 nm Permalloy film to improve the S/N is 70.35° under the polarizer and analyzer angles set at the optimal combinations (18.35°, 68.35°).

Multispecies coexistence of trees in tropical forests: spatial signals of topographic niche differentiation increase with environmental heterogeneity

Neutral and niche theories give contrasting explanations for the maintenance of tropical tree species diversity. Both have some empirical support, but methods to disentangle their effects have not yet been developed. We applied a statistical measure of spatial structure to data from 14 large tropical forest plots to test a prediction of niche theory that is incompatible with neutral theory: that species in heterogeneous environments should separate out in space according to their niche preferences. We chose plots across a range of topographic heterogeneity, and tested whether pairwise spatial associations among species were more variable in more heterogeneous sites. We found strong support for this prediction, based on a strong positive relationship between variance in the spatial structure of species pairs and topographic heterogeneity across sites. We interpret this pattern as evidence of pervasive niche differentiation, which increases in importance with increasing environmental heterogeneity.

Physical activity for children in special school environment

1. We assessed children's physical activity (PA) in structured (physical education) and unstructured (recess, lunch, before and after school) periods in special schools and examined its association with modifiable area contextual characteristics. 2. Children with disabilities were not highly active, but were more active during recess and lunch periods than at other times including physical education classes. 3. Areas were often not accessible during unstructured settings. Children were more active in areas when supervision and organised activities were provided. 4. Providing an interactive game during free play did not significantly increase group's PA. 5. Children's PA accrual is influenced by contextual characteristics of the school environment. There is a need to make areas more accessible and to use social marketing and programming to attract more users. School and health professionals should modify contextual characteristics by providing more direct supervision and organised activities during free play.