Dracunculus medinensis, also known as the African Guinea worm, is the causative agent of dracunculiasis and the focus of the global Guinea Worm Eradication Program (GWEP). Transmission of D. medinensis to humans occurs primarily by drinking water containing cyclopoid copepods infected with third-stage D. medinensis larvae. A common intervention to interrupt transmission and decrease the number of copepods in infected water bodies is the application of the organophosphate larvicide Abate® (temephos). However, the use of alternative compounds to help decrease copepod populations would be beneficial to the GWEP. We compared the immobilization of copepods by three compounds: Abate, Natular® (spinosad), and diflubenzuron. Our results confirm that neither diflubenzuron nor Natular immobilized copepods as quickly or as effectively as Abate. However, doubling or tripling the suggested concentration of Natular resulted in immobilization rates similar to Abate over 72 hours of continuous exposure. Further research on the possible effects of higher concentrations of Natular on the environment and nontarget organisms is necessary to determine whether this compound can be used safely to control the copepod population. Dracunculus medinensis,–,,D. medinensis.,Dracunculiasis (Guinea worm disease) is a neglected tropical disease that historically caused significant morbidity in people living in previously endemic communities. This disease is caused by infection with the parasitic nematode, ® (temephos). Abate was introduced as a mosquito larvicide, but is also effective for controlling D. medinensis transmission because of its high toxicity to copepods and low toxicity to mammals when used in small doses at application sites.,Currently, most water sources in guinea worm endemic countries are treated with the organophosphate larvicide Abate,The Abate formulation currently used by the GWEP is a liquid 50% emulsifiable concentrate. To accurately apply Abate at the appropriate concentration, the volume of water in the targeted water source must be calculated. This can be difficult in some African water bodies due to unfavorable weather conditions (rainy or dry season) or low accessibility, and is impossible in flowing bodies of water.® (spinosad) is a mosquito larvicide that is currently used to control common mosquito vector species in the genera Aedes, Anopheles, and Culex.–Saccharopolyspora spinosa.,,NatularMalacosoma disstria), gypsy moth (Lymantria dispar), and dipteran larvae.–,,,,,,Diflubenzuron is an insect growth regulator (IGR) that is commonly used on forest and field crops to control insects, including the forest tent caterpillar  gene (GenBank accession numbers: MW522586 and MW522587).,Anopheles stephensi) larvae were included in this study as a positive control. All trials were replicated five times and kept at an average room temperature of 21°C. Dissolved oxygen (DO), water temperature, and pH were recorded for all trials.Laboratory-raised copepods  of the ® Mosquito Control Products, St. Charles, IL), and a single component mixture of diflubenzuron in methanol. This Abate formulation was chosen due to its current use in the GWEP, and the other formulations were chosen based on their ease of accessibility and current availability. The first experiment was a sensitivity test directly comparing the effects of all three compounds on copepods. Each test was performed in beakers filled with 1 L of dechlorinated water and 50 adult cyclopoid copepods. The tests were started (0 hours) when the per label application concentration of each compound was added to the beaker , Natular DT Bi-layer tablets  of Natular on copepods. Testing an increased concentration of Abate was determined not necessary because the efficacy of the compound on copepods could not have been improved based on the results from our already completed sensitivity test.carStatistical analyses were performed in R.Sensitivity test section) showed that Abate immobilized more copepods than Natular and diflubenzuron (The sensitivity test (benzuron  when useP < 0.05 (Table 1). Compared with the control, Natular does have significant effect on copepod immobilization, but it was not as effective as Abate (A. stephensi larvae within 24 hours (data not shown).The number of hours post-exposure had a statistically significant effect on the number of copepods immobilized using each chemical treatment, F  = 3.5893, as Abate . Abate aas Abate P < 0.05.Additional testing of Natular concentrations section) indicate that increased concentrations of Natular resulted in almost total immobilization of all 50 copepods after the full 72 hours (P < 0.001 (Table 2). Each concentration of Natular tested immobilized a significantly different number of copepods  did not immobilize copepods as quickly or as effectively as Abate (1 ppm) but did reach complete immobilization of almost all 50 copepods when applied at double (14.28 ppm) or triple (21.42 ppm) the suggested concentration. These results indicate that Natular can be used at higher concentrations to control copepods. Diflubenzuron was not effective at immobilizing copepods; however, the copepods that were tested in this study were adults. Due to diflubenzuron’s specific mechanism of action on the molting process, this compound would likely be more effective on nauplii during their growth to the adult stage. Further testing on cyclopoid nauplii would be needed to conclude if this compound has potential as a possible control intervention of copepod populations in general, which would also be beneficial for the GWEP, as it has been shown to be effective on calanoid and harpacticoid nauplii.,These results further support that Abate is an effective option for chemical control of D. medinensis larvae within copepods. For classical transmission through ingestion of water, the immobilization of these infected copepods makes them unlikely to be ingested or gathered when water is collected. However, it could make it easier for fish or frog transport and paratenic hosts to consume them.,,D. medinensis larvae quickly die after their copepod intermediate host is immobilized.One aspect of copepod control that has not been investigated is the effect of Abate or other compounds on the ,Natular DT tablets were developed to treat drinking water containers for over 60 consecutive days with a slow dissolve rate. However, the use of high concentrations of Natular to control infected copepod populations could have negative effects on other organisms that either live in or consume the water. Using high concentrations in the environment could have a detrimental effect on nontarget invertebrates, as spinosad-based compounds can affect an extensive range of invertebrate species.,The copepods used in this study were collected from Georgia which, although unlikely, may react differently to the compounds tested compared with African copepods. Also, these compounds were tested in water with lower temperatures (20–22°C) than what is normally observed in summer months in Chad, Africa (∼28°C). Of note, spinosad has been shown to have higher efficacy when applied at higher temperatures, so it is possible that effectiveness in the field may be higher than observed in this study.In conclusion, there are still a variety of factors to investigate regarding the use of Natular and diflubenzuron to decrease copepod populations. Our study confirmed the superior performance of Abate in immobilizing copepods. The use of Abate to control copepods remains a critical intervention interrupting the transmission of Guinea-worm. Future research on any possible acquired resistance to applied chemical treatments in Chadian copepod populations would greatly benefit the GWEP.


On day +536, the HHV-8 viral load became undetectable, with an absolute lymphocyte count of 1.06×109/L and the KS disappearance. HHV-8 load in blood detected by mNGS may be used as an early prediction marker for KS, a guide for early withdrawal of immunosuppression, and a tool to monitor KS treatment response in the setting of HSCT, especially in patients with CMV-seropositive or graft failure postengraftment. Through whole-exome sequencing, we explored the molecular mechanism underlying the patient’s longer latency of haematopoietic or immune reconstitution and recurrent infections. Germline mutations in the FANCI and RAD51 genes might impair the patient’s DNA repair ability, leading to a degree of immunodeficiency and tumour susceptibility. We strongly recommended evaluating the clinical history of the donor and investigating whether there were possible germline mutations suspected for immunodeficiency or familial neoplasms. Disseminated visceral KS patients could likely benefit from chemotherapy, especially if the disease appears to be aggressive.Disseminated visceral Kaposi sarcoma (KS) following allogeneic haematopoietic stem cell transplantation (HSCT) is a rare but life-threatening posttransplant complication. A suitable management strategy for disseminated KS involvement in transplant patients is unclear. Here, we reported a patient who developed disseminated visceral KS following HSCT, which was the first detailed report documenting the relationship among KS development, delayed immune reconstitution, and HHV-8 DNA levels by metagenomic next-generation sequencing (mNGS). The HHV-8 viral load peaked at 2071 sequence reads with an absolute lymphocyte count of 0.17×10 Kaposi sarcoma (KS) is a vascular tumour characterized by abnormal angioproliferation by immunosuppression and was first described by Moritz Kaposi in 1872. Gamma herpesvirus human herpes virus 8 (HHV-8), also known as Kaposi sarcoma-associated herpes virus (KSHV), was subsequently found to be associated with the development of KS in 1994 . ClinicaUnlike the classic KS form, posttransplant KS (PT-KS) is a rare but often life-threatening posttransplant complication characterized by a rapidly progressive course. The treatment of KS in transplant recipients is particularly complicated because immunosuppression reduces the risk of graft rejection, and when immunosuppressed patients receive chemotherapy, the risk of infection increases. Although PT-KS often occurs after solid organ transplantation  , the freHHV-8 virus loads in blood have been considered to be a predictor of the development of clinical KS. Currently, since there are no validated commercial serology kits, the testing of donors and recipients for HHV-8 is challenging . Since iThis case illustrated the rise and fall of disseminated visceral Kaposi sarcoma coinciding with immunosuppression and reconstitution after HSCT in a 29-year-old Asian patient. Here, we propose that more importance should be attached to the early diagnosis and better understanding of KS after transplantation, especially in recipients who have HHV-8 risk factors such as HLA-mismatched donor allogeneic transplants or those who receive ATG for GVHD prevention. Moreover, our study suggests that routinely performed germline analysis of immunodeficiency-associated mutations might contribute to optimizing alloHSCT from a related donor to avoid delayed haematopoietic or immune reconstitution and disease recurrence after transplantation.A 29-year-old Chinese male patient was admitted to Tongji Hospital in August 2019 due to “skin ecchymosis with low fever for 2 weeks”. The patient was diagnosed with acute myeloid leukaemia AML-M2, t  , -Y, AML1/ETO (+), c-Kit D816Y mutation, indicating a high risk of disease relapse , 16. Aft6/kg CD34+ cells) and peripheral blood mononuclear cells (1.32× 106/kg CD34+ cells) on day +1 (4copies/mL by RT-PCR). As an emerging method of pathogen detection, mNGS in blood on day +13 showed that he was also infected with cytomegalovirus  and herpes simplex virus . Antiviral therapy with ganciclovir was promptly instituted. When he was discharged on day +30, blood tests showed almost normal counts of white blood cells (8.07×109/L), neutrophils (6.13×109/L), lymphocytes (1.08×109/L), and platelets (214×109/L), and haemoglobin levels (108 g/L). Bone marrow biopsy showed normalization of trilineage haematopoiesis and complete donor engraftment of 97.6% by DNA-STR amplification. After discharge, the patient was treated with the immunosuppressants cyclosporine and prednisone for GVHD prevention, antiviral drugs ganciclovir, antifungal prophylaxis (voriconazole), and anti-pneumocystis prophylaxis (sulfamethoxazole), but his oral mucositis persisted (Grade II).In December 2019, the patient underwent allogeneic haploidentical HSCT using a standard dose of the Bu/Cy/AraC/MeCCNU/ATG conditioning regimen  biopsy displayed that marrow hypoplasia and continued leukaemia remission with complete donor engraftment  IgM positive in local hospital, which was alleviated by foscarnet sodium for two weeks and topical medication. On day +122, the patient experienced intermittent epigastric discomfort and progressive emaciation, and multiple dark red or purplish small nodules appeared on his extremities and neck without pain or itch; however, he did not take it seriously, and no special treatment was given. On day +188, the patient’s tongue was scratched by a fishbone when he ate fish. A lingual mass gradually appeared, which affected his eating. On day +218, he was admitted again complaining of dysphagia and polypnea and was unable to eat due to the painful, rapidly growing tongue mass. Physical examination showed an exogenous and lobulated mass (about 4.5 cm × 3.5 cm) on the back of his tongue, with a clear boundary and medium texture  with frequent urination with haematuria. After hydration, alkalization, and antiviral (foscarnet sodium) treatment, his haemorrhagic cystitis was ameliorated. However, on day +326, the patient suffered from severe pneumonia with hypoxemia and secondary sepsis. During this period, the patient’s BM biopsy consistently showed panhypocellularity along with severe pancytopaenia. Until approximately 430 days after alloHSCT, his complete blood count gradually recovered.Given the urgency and complexity of simultaneously controlling the patient’s progressive disseminated KS and his persistent GVHD, the patient’s treatment was adjusted by converting the immunosuppressant cyclosporine to sirolimus  and usinTo determine why the patient’s haematopoietic or immune reconstitution was delayed, WES was performed on the patient’s samples before and after transplantation. Two germline mutations related to delayed immune reconstitution  were detected Figure 3At the last follow-up (+712 days), the patient still received immunosuppressive therapy with low-dose ruxolitinib (5 mg per 3 days) and thalidomide (75 mg qn) to treat mild cutaneous chronic skin rejection (Grade II) , 26. He HHV-8 infection is quite common after HSCT. However, PT-KS, particularly its disseminated visceral form, is a very rare complication, and its relationship with HHV-8 has been reported infrequently , 28. In 9/L on day +242. On day +304, there was a remarkable decrease in skin and tongue lesions coinciding with HHV-8 viral load decreasing to 10 sequence reads. On day +536, the HHV-8 viral load became undetectable, with an absolute lymphocyte count of 1.06×109/L and KS disappearance. HHV-8 infection may be spread through a donor’s latent infection, blood transfusions, or reactivation of the recipient’s previous infection. HHV-8 was found to be negative by mNGS in his haploidentical HLA-matched donor. The origin of HHV-8 infection in our case was unclear since no test was performed on the recipient prior to HSCT. Hence, the screening of donors should be improved to prevent infection with HIV, HHV-8, CMV, and other viruses through transplantation.The presence of HHV-8 has been described as an obligatory diagnostic criterion for KS. Given the variable sensitivity and specificity and lack of standardization, HHV-8 serologic detection was not usually included in pretransplant screening. After HSCT, HHV-8 antibody responses may be damaged owing to immunosuppression. The traditional method RT-PCR has limited sensitivity. Our study indicated that mNGS in blood could provide fast and precise pathogen detection, contributing to the assessment of KS development and guiding treatment decisions dynamically. The HHV-8 viral load peaked at 2071 sequence reads with an absolute lymphocyte count of 0.17×10via vascular endothelial growth factor (VEGF) upregulation. On the contrary, Lupinacci and Delyon et al. reported that mammalian target of rapamycin inhibitors, such as sirolimus, could treat KS in renal transplant recipients based on the capacity of sirolimus to abrogate VEGF-induced tumour proliferation /EBV (HHV-4)/CMV (HHV-5)/KSHV (HHV-8)/BKV infection occurred successively in the patient, which has not been reported previously. Mixed infections of two or three herpesviruses, mostly CMV and EBV infections, have been documented, and other herpesviruses include successive CMV/HHV-8, HHV-6/CMV, and EBV/HHV-7 infections. Cesaro et al. suggested that CMV infection of previously HHV-8-infected human fibroblasts could reactivate the viral lytic cycle of HHV-8 The recurrent HHV-1/CMV/EBV/VZV/HHV-8/BKV infections strongly supported the hypothesis of impaired immunosurveillance in this case. To investigate the mechanism underlying the longer latency of haematopoietic or immune reconstitution, we also performed WES on the patient and his father. Two germline mutations  were detected. FANCI is a well-known pathogenic gene for the Fanconi Anaemia (FA), a progressive bone marrow failure syndrome that affects DNA repair process and increases cancer risk, including AML. RAD51 is a newly identified gene also contributing to FA. Interestingly, the patient in our study had no clinical symptoms that pointed to FA, such as microcephaly, abnormal thumbs, slow growth rate before leukaemia onset. However, germline mutations in the FANCI and RAD51 genes might impair the DNA repair ability, lead to a certain degree of immunodeficiency and tumour susceptibility of the patients, and thereby make the patients sensitive to pathogen infection, ionizing radiation, and other damages . There wAlthough KS is a rare complication of HSCT, it should be given more attention, particularly to recipients of haploidentical HLA-matched alloHSCT who had more intensive immunosuppressive therapy or used ATG to prevent GVHD. HHV-8 DNA detection in blood by mNGS may be used as an early identification marker for KS in the setting of HSCT, especially in patients with CMV seropositivity or graft failure post-engraftment, and may be used as a guide for early withdrawal of immunosuppression and a tool to monitor KS treatment response. This study has a few limitations. This is a retrospective case report that lacks basic research. Based on this single case, it is difficult to draw a strong conclusion. Further research is needed to standardize the treatment for HHV-8-associated KS after transplantation. Evaluation of the clinical history of the donor and investigation of whether there are possible germline mutations suspicious for familial neoplasms are strongly recommended.The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.Ethical review and approval was not required for the study on human participants in accordance with the local legislation and institutional requirements. The patients/participants provided their written informed consent to participate in this study. Written informed consent was obtained from the individual(s) for the publication of any potentially identifiable images or data included in this article.Conception and design: KZ, YX. Acquisition of data: KZ, JX, ZS, HS, KS, YX. Analysis and interpretation of data: KZ, KS, YX. Writing, review and/or revision of the manuscript: KZ, KS, YX. Study supervision: KZ, YX. All authors contributed to the article and approved the submitted version.This work was supported by the Natural Science Foundation of China [no. 81873444& 82070213] and the Key Research and Development Program of Hubei Science and Technology Department [2020BCB021].The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.


Mikania micrantha Kunth) is considered as one of top 100 most dangerous invasive species in the world. A fast and accurate detection technology will be needed to identify M. micrantha. It will help to mitigate the extensive ecologic and economic damage on our ecosystems caused by this alien plant. Hyperspectral technology fulfills the above requirement. However, when working with hyperspectral images, preprocessing, dimension reduction, and classifier are fundamental to achieving reliable recognition accuracy and efficiency. The spectral data of M. micrantha were collected using hyperspectral imaging in the spectral range of 450–998 nm. A different combination of preprocessing methods, principal component analysis (for dimension reduction), and three classifiers were used to analyze the collected hyperspectral images. The results showed that a combination of Savitzky-Golay (SG) smoothing, principal component analysis (PCA), and random forest (RF) achieved an accuracy (A) of 88.71%, an average accuracy (AA) of 88.68%, and a Kappa of 0.7740 with an execution time of 9.647 ms. In contrast, the combination of SG, PCA and a support vector machine (SVM) resulted in a weaker performance in terms of A (84.68%), AA(84.66%), and Kappa (0.6934), but with less execution time (1.318 ms). According to the requirements for specific identification accuracy and time cost, SG-PCA-RF and SG-PCA-SVM might represent two promising methods for recognizing M. micrantha in the wild.Mile-a-minute weed ( Mikania micrantha Kunth (M. micrantha), also known as “mile-a-minute,” is one of the world’s 100 most dangerous invasive species , Citrus spp., and sugarcane (Saccharum officinarum L.) infested with M. micrantha ranged from 60 to 70% due to the twining which would block out sunlight  smoothing, SG smoothing, and SNV], a feature selection algorithm (PCA), and classification algorithms  ]  have beeM. micrantha hyperspectral images in the wild. The spectrometer weighs 470 g, uses DC12V power, and can obtain 138 spectral wavebands with a 4-nm sampling interval in the spectrum range of 450 to 998 nm. The collection site was a desolate field of farmland near the Xinnan subway station in Jiulong town, Guangzhou city, China (23°22′29.5′′ north latitude and 13°29′52.9′′ east longitude). The collection time was approximately 9:30 on November 21, 2018; the weather was cloudy. Before image acquisition dark reference (by closing the camera lens) and white reference (using a white plate) images were collected to calibrate the spectrometer according to the following equation:A high-speed imaging spectrograph S185 manufactured by the German company Cubert was used to manually collect the IC is the calibrated image, IR is the raw image, IW is the white reference, and ID is the dark reference.where M. micrantha leaves. Eighteen hyperspectral images were collected over vegetation using the S185 spectrometer and used for this work. Six samples of the eighteen hyperspectral images contained the leaves and flowers of M. micrantha, other plants, and non-plant background are shown in Then the lens of spectrograph were pointed directly toward at the surface of the plant, and manually focused on the middle of M. micrantha and background were manually extracted from hyperspectral images by Cubeware software  were collected and randomly divided into a training set , a testing set , and a validation set . The labels of M. micrantha consisted of M. micrantha leaves and flowers, and the labels of background included leaves and flowers of other plants, as well as non-plant background. The training, testing, and validation sets were balanced to prevent bias in the classifiers and metrics.The raw spectral data of software , care waM. micrantha and choose the optimal model is illustrated in Five preprocessing methods, one feature selection method and three classifiers were combined and implemented to process and classify extracted raw spectral data, respectively. The framework of the proposed methods to recognize x−4,⋯,x−1,x0, x1,⋯,x4) were selected. Then, the arithmetic mean was computed and assigned to x0. Finally, the window was moved to the next point so that the center of the window traverses the whole raw spectral data. Similar to 9P smoothing, SG smoothing is a filtering method based on least squares polynomial fitting in a moving window. The window size was set as five in this article , average accuracy (AA), the Kappa value  and timeM. micrantha, TN is the number of samples correctly predicted as the background, FP is the number of background samples incorrectly predicted as M. micrantha, and FN is number of M. micrantha samples incorrectly predicted to be the background.where TP is the number of samples correctly predicted to be Also, we summarized the computational time required by each method to recognize the samples in the validation set. All the aforementioned methods were coded and developed in MATLAB R2019a . The CPU of the PC is Intel(R) Core(TM) i7-7700, and the RAM is 16 GB.M. micrantha and background were presented in M. micrantha spectral reflectance is slightly higher than the background in about 450–670 nm range, while parts of M. micrantha have the same reflectance as the background. In about 750–880 nm range, the reflectance of M. micrantha and background are scattered, and the reflectance distribution of the background basically overlapped with that of M. micrantha. The raw spectral data distribution of M. micrantha in the remaining spectral range is almost the same as the background. It indicates that the intra-class differences were more than inter-class differences of M. micrantha and background, and it is a challenging work for M. micrantha identification. In order to be more conducive to the recognition of raw spectral data, five kinds of preprocessing methods were used to eliminate data noise or highlight the distribution law of reflectance with wavelength. The raw spectral data preprocessed using the two smoothing methods are shown in Raw and preprocessed spectral data of M. micrantha and the background through subsequent processing. To determine the most suitable preprocessing method, the next step was to analyze the influence of each preprocessing method combining the dimension reduction and classifiers on the performance of M. micrantha identification.In summary, all the five preprocessing methods can eliminate part of the spectral noise. FD, SD, and SVN can significantly reduce the intra-class differences, however, the inter-class differences were not significantly improved by all pretreatments. Therefore, it is necessary to find the difference in the raw and preprocessed spectral data between Principal component analysis was performed on the raw and preprocessed spectral data. In general, the first and second principal components have the maximum variation of the original data. The first and second principal component scores of 745 samples were depicted as Each of the datasets was clustered and distributed with the origin of the coordinates as the center. k  principal components were also calculated. The raw spectral data, 9P smoothing, and SG smoothing had almost the same curves, and at approximately the first 5 principal components, all curves tended to be smooth and close to 100%. Thus, all the curves are able to fully represent the information contained in the 138-dimensional raw and preprocessed spectral data. Although the contribution rate of the first principal component of the FD was approximately 20% lower than that of the SNV, the FD, and SNV did not have almost the same cumulative contribution rates until the first 18 principal components, where the values are close to 99%. The SD had the lowest contribution rate of the first principal component, and the cumulative contribution rates were not more than 99% until top 40 principal components. Therefore, the first k principal components based on different preprocessing contained most of the information. To achieve accurate M. micrantha identification, the first k principal components were selected as the input of the classification model. However, the k values were dependent on the preprocessing and classification algorithms combined with PCA.As shown in k  principal components, which were generated by employing PCA on raw and preprocessed spectral data. The recognition accuracies of the first k principal components are shown in Among the 745 samples, 496 samples were used to train the models, and 125 samples were used to test the trained models. The SVM, the BPNN, and the RF were separately trained based on the first k > 10, the accuracies of the adjacent first k principal components fluctuated within the smallest range. The SVM was the second most accurate; its accuracy first increased and then decreased with the increase of k. The BPNN did not achieve good results, and the accuracies of adjacent k fluctuated within a large range, although the accuracy was higher than that of the SVM as the k increased to a certain degree. Using the same classification method, the accuracies of SG-PCA-RF, FD-PCA-RF, and SD-PCA-RF methods were more significantly improved than the accuracy of OR-PCA-RF, but 9P-PCA-RF did not achieve much improvement except for when the first k principal component was between 70 and 80. The accuracy of SNV-PCA-RF improved as the k increased, but there was little benefit in terms of dimension reduction. In k between 10 and 20, and the accuracies of SD-PCA-RF were higher than those of SG-PCA-RF and FD-PCA-RF. In addition, compared with OR-PCA-SVM, the combinations of the other preprocessing methods with PCA and SVM did not improve accuracy obviously. And the k values corresponding to the maximum accuracy of the other combination methods were higher than that of OR-PCA-SVM, such as 9P-PCA-SVM, SG-PCA-SVM, and FD-PCA-SVM. For the BPNN algorithm, 9P smoothing and SG smoothing improved the accuracy and reduced the dimensions, while the k values corresponding to the maximum accuracy were located at between 1 and 10. However, the accuracy of other preprocessing methods was lower than the raw, thereby having even negative effects.The results showed that the accuracy of the RF was significantly higher than the other two methods. When k principal components corresponding to the maximum accuracy of each combination method were separately confirmed to reduce the dimensions  and SG-PCA-SVM  algorithms outperformed other methods for The recognition methods based on convolutional neural network (CNN) are very popular at present, however, it does not mean that these methods are applicable to all researches. M. micrantha in a small field. The image samples used were hyperspectral images taken with a handheld spectrometer. In the future research, the hyperspectral images of other invasive plants will be collected to verify the generalization performance of the proposed method. In addition, the images acquired by the handheld spectrometer were mainly used to study the hyperspectral image data processing method, which can save time and cost on the basis of ensuring the reliability of the data. In practical applications, it is often necessary to identify invasive plants in a wide range, which requires the hyperspectral imager to be mounted on the UAV for image acquisition. Our study provides a reliable reference for hyperspectral image data processing of M. micrantha.The main work of this research was to complete the identification of M. micrantha recognition based on hyperspectral technology, five preprocessing methods, one dimension reduction method, and three classifiers were separately combined to process the hyperspectral image data of M. micrantha. It was demonstrated that SG smoothing could eliminate the interference of high-frequency noise in raw spectral data and improved the spectral signal-to-noise ratio. Importantly, PCA reduced the dimensions of the feature set and kept most of the dataset information. Additionally, PCA improved the accuracy and calculation efficiency of the algorithm to some extent. In our study, the recognition accuracy and time after PCA dimension reduction were universally better than those without PCA processing. Finally, the dataset after dimension reduction was classified by classifiers, proving that RF had the most accurate and consistent result in our dataset, while SVM had the shortest execution time. In subsequent studies, SG-PCA-RF and SG-PCA-SVM algorithms, which performed well in this study, will be tested in the hyperspectral images of other invasive plants obtained by UAV.In this study, to determine the best methods for The raw data supporting the conclusions of this article will be made available by the authors, without undue reservation.YH and XQ: methodology, software, validation, writing – original draft, and writing – review and editing. JL: methodology, software, and validation. RY: methodology and software. FuW: software. YL and SZ: project administration. FaW: writing – review and editing. WQ: project administration, writing – original draft, and writing – review and editing. All authors contributed to the article and approved the submitted version.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Theranostic imaging, as a rapidly expanding facet of molecular imaging, also creates new possibilities to deploy treatment options targeting TME by delivering therapeutic agents or disruptive photothermal and photodynamic energy. The advanced molecular and theranostic imaging tools and approaches presented in this special issue, including one review article, one mini review article, and two original research articles, offer an overview and a few examples of such applications.Tumor microenvironment (TME) plays key roles in cancer development, prognosis and responses to treatments. However, given its heterogeneity and complex interactions/interplays with other malignant processes, investigating TME requires systematical and preferably non-disruptive approaches. Molecular imaging enables visualizing, characterizing, and even quantitatively measuring specific biological and molecular processes Li et al. provided a latest overview of the recent progress of breast cancer treatments, including the predictive biomarkers, immune checkpoint blockades, cancer vaccines, and adoptive cell therapy, which directly or indirectly changed TME to exert the efficacy. In this mini review article, the authors highlighted the potential of nanotechnology to monitor and control the tumor immune microenvironment. Gao et al. introduced the therapeutic applications of gold nanoparticles in cancer treatment and discussed the potential of using stimuli-responsive strategies to respond to TME and to increase the transport efficacy. Serval unique properties, such as localized surface plasma resonance and stimuli-responsive properties to hypoxia and acidic pH, making gold nanoparticles promising for transport therapeutic drugs to TME. In a research report, Heaster et al. demonstrated intravital metabolic autofluorescence imaging can be used to resolve the dynamic macrophage function and reveal the heterogeneity of macrophage between normal and cancerous microenvironments in vivo. This method enabled autofluorescence imaging to monitor macrophage behavior in response to treatment, which would be helpful to identify new targets for drug development. Finally, Wang et al. present a rationally designed sandwich nanostructure of gold-graphene hybrid material that can be used for photoacoustic image-guided photothermal therapy. The imaging-guided photothermal therapy could precisely control the temperature of the tumor and potentially alter the TME through the disruption of its specific components.Focusing on immune therapy that aims to reverse the immune-suppressive TME, As this Research Topic on this issue covers the recent advances in molecular and theranostic imaging of TME, it should be noted that the potential of nanotechnology and molecular imaging applications in imaging and modulation of TME has yet to be fully explored. The editors hope that the selected articles on this Research Topic will inspire future work to further advance and expand molecular and theranostic imaging in studying TME and beyond.


Toxins is to present a modern understanding of the various aspects of the molecular mechanisms underlying the action of animal venoms and their constituents.Animal venoms comprise numerous toxin families, consisting mainly of peptides and proteins. In prey, these toxins affect various vitally important systems that may result in severe illness or death. During evolution, toxins acquired the ability to bind selectively and with high affinity to different biological targets in organisms. However, at present, not all toxin targets have been identified, and not all the molecular mechanisms underlying the effects of toxins are understood. This understanding is very important for the efficient treatment of envenomation, which still continues to be a significant problem. On the other hand, the high selectivity and efficiency of toxins make them valuable molecular tools for fundamental research. Moreover, toxins with known mechanisms of action may serve as templates for drug development. All this suggests that studying the molecular mechanisms of action of animal venoms and their toxins is a very challenging and important task. The aim of this Special Issue of Structures and molecular mechanisms of action vary greatly among toxins from different animals. Venomous animals can be found among representatives of various types, classes, orders, families and genera. This diversity is reflected in the articles published in this Special Issue. There are articles that deal with the toxins from insects, spiders, scorpions, octopuses, toads, frogs, and snakes. The topics range from initial characterization of biological activity of toxins to detailed investigation of the mechanism of action at the level of viruses, cells, organs, or live animal. Different methods to study the biological activity were applied, including molecular modeling, electrophysiology, spectroscopy (NMR), molecular biology etc.Rhinella horribilis, more than 50 compounds  are identified using HPLC-MS/MS [R. schneideri demonstrates an insecticidal activity towards Nauphoeta cinerea cockroaches [R. icterica secretion done by the same group [R. icterica is also studied using avian preparations [In this Special Issue, several articles are focused on the characterization of venoms and poisons from species not studied earlier. Thus, three papers describe the effects of toad poisons. For example, in the parotoid gland secretion of the toad LC-MS/MS . The seckroaches . Togetheme group , this maarations . After sCalliophis, which is the most basal branch of the family Elapidae [Calliophis species (C. bivirgatus) contains a unique toxin  that acts on the voltage-gated sodium (NaV) channels. Based on the analysis done in the study, it was hypothesized that elongated glands in Calliophis species may have evolved together with NaV channel toxins.One paper focuses on the molecular evolution of three-finger toxins (3FTX) in the snake genus Elapidae . It is sNaja melanoleuca cobra venom revealed the structural elements involved in the interaction of toxins with nicotinic acetylcholine receptors (nAChRs) and GABAA receptors [A receptor. From the venom of the scorpion Buthus martensii, the new toxin BmK NSPK was isolated [Cyriopagopus longipes and characterized [About one third of the Special Issue papers deal mainly with the structural and functional characterization of new toxins. These toxins were isolated from the venoms of snakes, scorpions, spiders, centipedes, and wasps, as well as the poison of a frog. Thus, the investigation of novel three-finger neurotoxins from eceptors . The resisolated . The toxcterized . Among sSicarius thomisoides spider is characterized with that of the Loxosceles laeta spider [S. thomisoides venom can seriously harm people. An acyl-activating enzyme (4-coumarate:CoA ligase-like protein) was cloned from the venom apparatus of the endoparasitoid wasp Tetrastichus brontispae (Hymenoptera: Eulophidae) [Octodonta nipae that damages several species of palm trees. The molecular mechanism of the enzyme activity may involve the regulation of host immunity through fatty acid metabolism-derived signaling pathways. From the cDNA library of the venom glands of centipede Scolopendra hainanum, a kazal-type serine protease inhibitor (ShSPI) was identified [Ki values of 225.8 nM and 12.6 nM, respectively. As elastases are involved in several important physiological cascades, the identified inhibitor may be regarded as a candidate to develop a drug for cardiopulmonary diseases. From the poison of the frog Amolops jingdongensis, a prokineticin homolog Bv8-A was isolated and characterized [In a comparative study, the venom of the Chilean a spider . The eleophidae) . A recomentified . ShSPI eTityus serrulatus scorpion’s envenomation effects. The study aimed to investigate that hyperglycemia due to scorpion envenomation may involve inflammatory signaling in the pancreas showed that T. serrulatus venom indeed induced the production of IL-1α and IL-1β in the pancreas, which provoked nitric oxide (NO) production and edema in β-cells in islets [Latoia consocia living in Southwest China showed that it induced severe acute pain behaviors after intraplantar injection into the hind paws of mice [Protobothrops mucrosquamatus and Trimeresurus stejnegeri venoms, C-type lectin-like proteins mucetin and stejnulxin isolated from these venoms were studied [Protobothrops mucrosquamatus and Trimeresurus stejnegeri venoms make them similar in immobilization activity to Naja atra venom, albeit through a different mechanism. The paper by Kuo et al. [A great deal of papers in the Special Issue are focused on the molecular mechanisms underlying biological effects of animal venoms and toxins. The investigated effects are very diverse and ranged from antiviral and anticancer activities to hyperglycemia caused by scorpion envenomation. Thus, a life-threatening transitory hyperglycemia is among the n islets . The aut of mice . The stu studied . It was o et al.  describeTetrahymena pyriformis revealed the high activity of cobra venoms [T. pyriformis. A life-threatening infectious disease caused by parasitic protozoa of the genus Plasmodium  is malaria. To overcome antimalarial drug resistance , the derecently , an anti studied . It was Octopus kaurna-derived peptide, Octpep-1, was investigated [The Special Issue did not remain without a description of such an important property of animal toxins as anticancer activity. To identify new drug candidates against melanoma, the molecular mechanism of action of the stigated . It was 31P-NMR and 1H-NMR spectroscopy, the effects of cardiotoxins CTI and CTII on phospholipid packing and dynamics in model phosphatidylcholine membranes that mimic a phospholipid composition in the outer mitochondrial membrane (OMM) was analyzed. To study the molecular mechanisms by which CTII and CTI bind to a phospholipid membrane, molecular dynamics and molecular docking were applied. As a result, a conceptual model that explains a molecular mechanism by which cobra venom cardiotoxins interact with mitochondrial membranes was proposed.Two papers in the Special Issue deal with the molecular mechanisms of interaction of 3FTXs with their targets. Thus, 3FTXs interaction with nAChR was studied via a homology modeling and protein docking protocol . UtiliziCupiennius salei formed complexes. In addition, through the use of the voltage clamp technique in the oocytes of Xenopus laevis, it was shown that a combined application of two neurotoxins of different types has a much more pronounced cytolytic effect than each of the toxins alone, and toxicity to Drosophila melanogaster greatly increased at the combined application of two toxins. Thus, the high cytolytic activity of Cupiennius salei venom was explained by the merge of two different toxins.Quite an interesting molecular mechanism for the potentiation of venom toxicity to insect was discovered in the work by Clémençon et al. . It was In conclusion, the papers in the Special Issue addressing the different aspects of animal venoms contribute to a deeper understanding of their molecular composition and the biological activity of the constituent toxins. Some papers, including in particular those describing the antimicrobial and anticancer properties of toxins and their analogs, bring us closer to the development of new modern drugs. Other papers demonstrating the underlying molecular mechanisms of action of venoms and toxins reveal the fundamental basis for the functioning of various vital systems in living organisms. Thus, animal toxins have a large, not yet fully disclosed potential for use both as molecular tools for the study of physiological processes and as a basis for the design of new drugs. Both these spheres deserve further extensive and rigorous investigation.


Sexuality in animals is a rather stable trait, with the male genetic determinant operating in a female background, but is more complex in flowering plants.Hermaphroditism (perfect flowers with both sexes expressed) is recognized as being the most ancient state in the evolution of Angiosperms. It has evolved into monoecism  and gymnodioecism , which in turn has evolved to dioecism . These transitions could have occurred many times, with reversion to hermaphroditism occurring frequently as well.Pistacia vera). Dioecy occurs in 5–6% of flowering plants but could reach 20% among the crop species and is therefore of economic interest, prompting this Frontiers Research Topic.This complex and unstable sexuality of plants has attracted the interest of scientists since 1,715 when Sébastien Vaillant, botanist at the “Jardin Royal des Plantes médicinales” (now “Le Jardin des Plantes”) in Paris, hypothesized the occurrence of sexual dimorphism in pistachio (Diospyros) and date palm (Phoenix).The Research Topic was launched in July 2019 and collected 115 potential contributors, most of which became irresponsive after the spread of Sars-Cov-2 pandemic. However, we are happy, as editors, to have collected two excellent reviews and original papers on persimmon , where recombination between the sex-determinants is suppressed, or through an epistatic genetic interaction, that would not require linkage.Indeed, dioecy might have developed from hermaphroditism through the intermediate step of gynodioeciousness  or through monoecy. The evolution of dioecy from monoecy would require a single gene that determines the sexual orientation, independent of the number of genes that control the development of stamens and carpels.Cronk and Müller, who analyzed species like Diospyros, Populus, and Salix. The authors point out that the separation of unisexual flowers has already occurred in the monoecious ancestor; therefore, the evolution toward dioecy may be a simple matter of separating pre-existing epistatic regulatory architecture to different individuals, which may be accomplished by a single master regulator gene (the ARR17 gene for Populus and the MeGI gene for Diospyros), either in a hemizygous state or toggled on–off by a suppressor .This aspect of dioecy has been revised for this Research Topic by Phoenix.The Research Topic includes two valuable papers on persimmon and date palm. The first of two was preceded in the literature by several papers of the same authors on the complex, and in some instances incomplete, dioecy of this crop; while the second one introduces for the first time a molecular analysis of the SDR in Masuda et al. provides a deep insight into Diospyros, a genus that contains around 450 different species all dioecious or sub-dioecious and is becoming a model for the study of the fine tuning of sex expression. The authors focused on a transition out of dioecy into monoecy in hexaploid Diospyros kaki , which is based on their previous study for epigenetic silencing of the sex determinants, OGI and MeGI. They studied a cultivar with high-frequent male flowers, uncovering the mechanism by which the epigenetic silencing of MeGI/OGI is regulated. The male-rich cultivar showed strong DNA methylation in the OGI promoter, as well as in other female-rich cultivars, while OGI expression in the male-rich cultivar is released from silencing. Further transcriptomic approaches suggested gene networks relating stress- or jasmonate signal might involve the release of OGI silencing via chromatin remodeling or histone-methylations. Masuda et al. provided an insight into the molecular mechanism to generate a well-balanced monoecious system evolved from dioecy.The contribution from Torres et al. who reported updated information on date palm (Phoenix dactylifera), the most recent species on which the gender control has been explored at the molecular level. In date palm, there is the classical X/Y chromosome system, but the evolution of the Y chromosome, in absence of recombination, has led to a large-scale re-arrangement of the sex-determining region, detected by the analysis of the density of k-mers in the assembled scaffolds of the SDR region sequenced in three different male genotypes. The degeneration of the non-recombining Y-region is known among the evolutionists as the “Muller's ratchet”, according to which the lack of recombination (the “ratchet”) forces the degeneration of the region. Torres et al. provide experimental evidence of this evolutionary mechanism.The last paper included in this Research Topic on dioecy is from All authors listed have made a substantial, direct and intellectual contribution to the work, and approved it for publication.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Molecular descriptors offer numerical readouts based onmolecular properties and provide a fertile ground for developing quickscreening platforms. Thus, a study was conducted with 14 monomers/repeatingblocks of polymeric chains, namely, oxazoline, acrylamide, vinylpyrrolidone,glycerol, acryloyl morpholine, dimethyl acrylamide, hydroxypropylmethacrylamide, hydroxyethyl methacrylamide, sialic acid, carboxybetaineacrylamide, carboxybetaine methacrylate, sulfobetaine methacrylate,methacryloyloxyethyl phosphorylcholine, and vinyl-pyridinio propanesulfonate,capable of imparting hydrophilicity to a surface when assembled aspolymeric brushes. Employing free, Web-based, and user-friendly platforms,such as SwissADME and ChemMine tools, a series of molecular descriptorsand Tanimoto coefficient of molecular pairs were determined, followedby hierarchical clustering analyses. Molecular pairs of oxazoline/dimethylacrylamide, hydroxypropyl methacrylamide/hydroxyethyl methacrylamide,acrylamide/glycerol, carboxybetaine acrylamide/vinyl-pyridinio propanesulfonate,and sulfobetaine methacrylate/methacryloyloxyethyl phosphorylcholinewere clustered together. Similarly, the molecular pair of hydroxypropylmethacrylamide/hydroxyethyl methacrylamide demonstrated a high Tanimotocoefficient of >0.9, whereas the pairs oxazoline/vinylpyrrolidone,acrylamide/dimethyl acrylamide, acryloyl morpholine/dimethyl acrylamide,acryloyl morpholine/hydroxypropyl methacrylamide, acryloyl morpholine/hydroxyethylmethacrylamide, carboxybetaine methacrylate/sulfobetaine methacrylate,and glycerol/hydroxypropyl methacrylamide had a Tanimoto coefficientof >0.8. The analyzed data not only demonstrated the ability ofsuch  Moreover, the high reactivity ofNPs opens a wide range of opportunities for bioconjugation, for example,with homing peptides like Arg-Gly-Asp7 orligands like folic acid8 to target pathologicsites in the body, such as tumors known to over-express folate receptorsor integrins on the walls of leaky intratumoral vasculature.9The use of nanoparticles (NPs) as drug delivery systems (DDSs)has increased considerably in the past few decades.10 It is established that the nanoparticulate surfacechemistry determines its behavior within biological systems , has emerged as anattractive strategy toward developing NPs that can negotiate withphysiological barriers,13 such as the gutmucus layer.14A key message that distills out upon scrutinyof the literatureon nano-DDSs is the importance of surface chemistry in nano-bio interactions. systems 1, includ15 Given that mucus has evolvedinto a formidable physiological barrier over epochs, such unprecedentedmucopermeation demonstrated by the viruses has intrigued researchers,although the mechanism is still unclear. It is known that virusesexhibit a high surface density of polar groups, and there is a growingconsensus that the cloak of polar groups surrounding the viruses causesa hydrophilic brush effect,16 where it drags a meniscus of water with it while permeating themucus.17 As a result, the mucoadhesionof the viral particles is deterred, and viral mobility inside mucuscan proceed  unhindered.To a certain extent, the concept of coating NP surfaces with hydrophilicmolecules while designing mucopermeative nano-DDSs was inspired bythe examples of viruses. It was noted that viruses, such as poliovirus,Norwalk virus, or respiratory syncytial virus, can freely diffusethrough the mucus barrier .18 Mucin fibers form a complexnetwork with interspersed pores that act as a sieve and prevent particulatematerials from permeating unless smaller than the pores.19 However, these pores are not static, and theirdimensions keep fluctuating (10–500 nm) based on multiple factors,including pathophysiological state, site, degree of desiccation, oroxidation.20 Moreover, the mucin fibersharbor cationic and anionic sites arranged in tandem that, based onelectrostatic interactions, act as traps for charged NPs. Thus, uponmeeting mucus, NPs, unlike viruses, typically adhere and get sloughedoff with the superficial mucus layers recycled within the body, forexample, every 3–4 h in the case of gut mucus.21Mucin, a zwitterionic fibrillarglycoprotein biopolymer, formsmost of the mucus’s solid components and supports its characteristichydrogel form.accelerated blood clearance phenomenon.23 Such brisk sieving is induced by the activation of the reticuloendothelialsystem in the body, releasing macrophages to phagocytose the NPs circulatingin the bloodstream.24 Instant coating ofthe NPs with opsonins  present in theblood by surface adsorption initiates the cascade of macrophagic invasion.25 Rapid phagocytosis ensures that a significantfraction, sometimes more than 90%, of the injected NPs are withdrawnfrom the blood and sequestered into the liver, lungs, spleen, andbone marrow.26 Hence, the administerednano-DDSs, despite mechanisms promoting accumulation into tumor sites,such as the enhanced permeation and retention effect,27 fail to achieve an adequate therapeutic concentrationinside a tumor.Another challenge with nano-DDSs is their rapid filtrationfromblood after intravenous administration—widely known as the 28 Thus, the plasma half-life of the nano-DDSsis prolonged. The current strategy of achieving that relies fundamentallyon modulating the surface chemistry via conjugation, either by covalentbonding or by surface adsorption. PEGylation,29 achieved mostly through surface conjugation, elucidates the hydrophilicbrush effect and induces mucopermeation. However, as a molecule, PEGis biopersistent and can induce allergic reactions in the host body.33 Moreover, PEGylation is not a facile technique and, at times, requiresharsh reaction conditions that might be deleterious toward a labiledrug payload.Imparting surface polarity to the NPs is knownto deter mucoadhesion,facilitate the mobility of such stealth NPs in a mucus mesh, and resistthe opsonization of NPs once introduced into the blood.N-vinylpyrrolidone) (PVP), polyglycerol (PG), and polyacrylamide(PAA) has been probed.34 Similarly, natural and zwitterionic polymers have also been explored. However, such investigationshave led to the challenge of screening and shortlisting the rightcandidate(s) from an extensive list of low molecular weight moleculesor ranking a library of surface ligands based on their hydrophilicitywhile taking biocompatibility into account.Currently, a search is ongoing to find suitablereplacements ofPEG that can be used for surface functionalization of NPs. For example,a series of hydrophilic polymers like polyoxazoline (POZ), poly, are free, simple, intuitive, and user-friendly and run with anintegrated platform for drawing chemical structures or inserting asimplified molecular-input line-entry system (SMILES) of molecules.36 If necessary, more advanced molecular simulationtools, such as open-source PaDEL, which calculates 1875 descriptors(1444 1D and 2D descriptors plus 431 3D descriptors) along with 12molecular fingerprints, can be employed.37An interesting wayto make such a choice is to rely on the moleculardescriptors that signify a molecule’s physicochemical attributeshttp://www.scbdd.com/chemdes/; Computational Biology & Drug Design Group, School of PharmaceuticalSciences, Central South University, China), are also emerging.38 These integrated Web platforms can provide awealth of information about molecules in spreadsheets that can furtherbe used for clustering analyses. Determining molecular similaritybased on the Tanimoto coefficient is an interesting way of comparing a library of molecules.39 Taken together, the data points form an integralpart of cheminformatics and quantitative structure–activityrelationship-based studies with implications for designing nano-DDSs.Free Web-based computational platforms to determine thousandsofmolecular descriptors, such as ChemDes , acrylamide (AA), vinylpyrrolidone(VP), glycerol (Gly), acryloyl morpholine (AcM), dimethyl acrylamide(DMA), hydroxypropyl methacrylamide (HPMA), hydroxyethyl methacrylamide(HEMA), sialic acid (SA), carboxybetaine acrylamide (CBAA), carboxybetainemethacrylate (CBMA), sulfobetaine methacrylate (SBMA), methacryloyloxyethylphosphorylcholine (MPC), and vinyl-pyridinio propanesulfonate (VPPS).2.2www.swissadme.ch)—a free Web tool developed and maintained by the Swiss Instituteof Bioinformatics—to generate the SMILES and evaluate the pharmacokinetics,drug-likeness, and medicinal chemistry of the molecules. Upon loadingthe molecular structures of the monomers, the SwissADME suite wasrun to obtain a set of molecular descriptors asserting the physicochemicalproperties , lipophilicity , solubility , pharmacokinetics , drug-likeness ,and medicinal chemistry (lead-likeness and synthetic accessibility).The obtained data set for each monomer was collated as spreadsheetsfor further analyses.Chemical structures of the monomers were drawn in ChemDraw Ultra and savedas ChemDraw (.cdx) files. Later, the structures were uploaded in theSwissADME user interface (2.3http://www.swisstargetprediction.ch/) linked to the SwissADME Web application followed by the selectionof Homo sapiens (humans) as targetspecies and running the program.41 Target moleculeswith the highest probabilities were noted.The molecular SMILES of the 14 monomers were uploadedinto the onlineSwissTargetPrediction suite (2.4https://chemminetools.ucr.edu/)—a free Web-based application developed by researchers fromthe University of California Riverside —to analyzeand cluster small molecules.42 The molecularstructures of the 14 monomers were fed into the system by insertingSMILES, followed by activating the Similarity Workbench suite withinthe application. The coefficient was calculated by measuring c/(a + b + c), where c denotes the number of features sharedby both the molecules, whereas a and b represent unique features present in each molecule. The monomerswere compared in pairs, and the Tanimoto coefficient was measuredbased on the maximum common substructure algorithm.43The Tanimoto coefficient wasdetermined by the ChemMine tools  under pre-decided settings . Furthermore, a heatmap was developed after plotting theTanimoto coefficient data matrix in OriginPro 2015.33.1The details ofthe 14 monomers chosen are shown in 3.2Section S1) was subjected to hierarchical clustering, and a dendrogramwas generated (The data set of molecular descriptors(enerated 2. The SA3.3Section S2)—derived from a paired comparisonof the 14 monomers—is shown in The molecular similarity plottedas a heatmap based on the Tanimoto coefficient data matrix .Another interesting example can be the pair of OZ and VP that, despitesharing molecular similarity, did not demonstrate a high Tanimotocoefficient, such as >0.9. It can be attributed to the differencein molecular configurations: OZ is a linear molecule, while VP harborsa heterocyclic backbone with a carbonyl group attached to it. Thus,the correlation between the Tanimoto coefficient and hierarchicalclustering is not linear, although it often does follow a patternor trend. For instance, HPMA and HEMA were clustered together whilealso having a high Tanimoto coefficient (0.92).It is crucial to understand thedifference between the Tanimotocoefficient and hierarchical clustering based on molecular descriptors.While both these operations try to assess molecular similarity, theresults need not be identical. Two molecules with a considerable Tanimotocoefficient (≥0.6) do not necessarily depict a high similarityin the hierarchical clustering method and The subtle discrepancybetween the Tanimoto coefficient and hierarchicalclustering algorithm arises from the difference in how they are measured.While the Tanimoto coefficient is determined purely based on the molecularstructure, the data set of molecular descriptors tries to representa snapshot of the physicochemical behavior of the molecule. Hence,an analysis of molecules based on molecular descriptors and any similarityidentified based on them bears more relevance in drug designing. Onthe other hand, the Tanimoto coefficient is easy to calculate, requiresless computation, and provides a fast screening of a range of smallermolecules based on structural similarity that, at times, may comein handy while designing experiments or selecting chains for surfacegrafting.48 It is also crucial to screen the descriptorsas current tools can offer thousands of them. It is prudent to gatherthe important ones as otherwise the system risks being overwhelmed.Such screening of molecular descriptors will be influenced by thetype of molecules being investigated and the information that the in silico platform is expected to deliver.It is worth mentioning that the molecular descriptorsincludedhere were mostly 1D and 2D descriptors, while a more detailed studyrequires 3D descriptors. However, that will be a calculation-intensiveand time-consuming process, and at least from an initial screeningperspective, hardly provides an edge over 1D and 2D descriptors.glioblastoma multiforme—an aggressivebrain tumor with a grave prognosis.49 Moreover,an idea of the suitability to act as a P-gp substrate also estimateswhether surface grafting of a molecule will deliver a therapeuticeffect in resistant cancer cells where P-gp is a major mechanism drivingdrug resistance.50Moleculardescriptors also provide a decent understanding of somekey features of a grafted molecule, such as its solubility and bioavailability.These parameters are crucial while designing surface-functionalizednano-DDSs, especially for intravenous administration. Predictionsare also made on the drug’s potential to be absorbed from thegut, act as a P-gp substrate, or permeate the BBB. Having an initialidea on these essential surface properties of the NPs certainly assistsin designing advanced DDSs, especially aiming for oral delivery ortargeting the central nervous system, for example, while trying tounload a drug cargo at the brain from an encapsulated nano-DDS inthe case of Intriguingly,the molecular descriptors can also imply the targetmolecules expected to bind or interact with the monomers once theyare grafted on an NP. It is generally accepted that structurally similarmolecules engage the same or similar targets. Hence, a molecular pairwith a high Tanimoto coefficient is expected to demonstrate similartarget binding. An excellent example can be the pair of SBMA and CBMAwith a Tanimoto coefficient of ∼0.73. These molecules werepredicted to bind similar proteins, including GPCR, phosphatase, andproteases. Similarly, both AA and DMA, with a Tanimoto coefficientof ∼0.78, were predicted to bind oxidoreductases.H. sapiens), house mouse (Mus musculus), andthe brown rat (Rattus norvegicus).The model was validated by investigating its predictive capacity onan external test set of 500 compounds chosen randomly from the ChEMBL24database.38 The computational tools used in the study,including the estimation of molecular similarity and target prediction,were designed on molecular structure and reactivity that remains afundamental pillar of understanding nature. A strong validation basedon experimental data has guided the development of these insilico platforms. Thus, the predictions were made based onthe knowledge that was supported with experimental data.TheSwiss Prediction Tool assesses the macromolecular targets ofa small molecule (bioactive) based on an extensive database comprisingof 370,000 known bioactives on >3000 proteins from three differentspecies, namely, humans . Theseparameters present a numerical readout that can further be used tocluster molecules based on structural similarity and physicochemicalproperties. Moreover, the descriptors can offer an adequate understandingof how these molecules will influence the behavior of an NP in a nano–biointerface, including information on solubility, ability to permeatethe BBB, gut absorption, and molecular targets. The study, comprisinga set of 14 monomers, highlighted the utility of such molecular descriptorsin screening surface ligands with implications for translation.Gaining control over the surface chemistry ofengineered NPs holdsthe key toward developing effective nano-DDSs. Imparting polarityby grafting hydrophilic polymeric chains, such as PEG, has emergedas an attractive strategy toward designing nano-DDSs that, apart frombeing effective, can also negotiate physiological barriers like mucus.However, the range of molecular candidates for such surface graftingis diverse, and performing a thorough investigation on each of themis realistically not feasible. To this end, a study comprising 14monomers/repeating blocks of polymer chains  was undertaken with the extraction of a range ofmolecular descriptors followed by hierarchical clustering and determinationof the Tanimoto coefficient of molecular pairs. Hierarchical clusteringplaced the molecular pairs of oxazoline/dimethyl acrylamide, hydroxypropylmethacrylamide/hydroxyethyl methacrylamide, acrylamide/glycerol, carboxybetaineacrylamide/vinyl-pyridinio propanesulfonate, and sulfobetaine methacrylate/methacryloyloxyethylphosphorylcholine in same clades. Similarly, the pairs of hydroxypropylmethacrylamide/hydroxyethyl methacrylamide demonstrated a Tanimotocoefficient of >0.9. A high Tanimoto coefficient of >0.8 wasnotedfor oxazoline/vinylpyrrolidone, acrylamide/dimethyl acrylamide, acryloylmorpholine/dimethyl acrylamide, acryloyl morpholine/hydroxypropylmethacrylamide, acryloyl morpholine/hydroxyethyl methacrylamide, carboxybetainemethacrylate/sulfobetaine methacrylate, and glycerol/hydroxypropylmethacrylamide. Current


Molecular modeling is widely utilized in subjects including but not limited to physics, chemistry, biology, materials science and engineering. Impressive progress has been made in development of theories, algorithms and software packages. To divide and conquer, and to cache intermediate results have been long standing principles in development of algorithms. Not surprisingly, most important methodological advancements in more than half century of molecular modeling are various implementations of these two fundamental principles. In the mainstream classical computational molecular science, tremendous efforts have been invested on two lines of algorithm development. The first is coarse graining, which is to represent multiple basic particles in higher resolution modeling as a single larger and softer particle in lower resolution counterpart, with resulting force fields of partial transferability at the expense of some information loss. The second is enhanced sampling, which realizes “dividing and conquering” and/or “caching” in configurational space with focus either on reaction coordinates and collective variables as in metadynamics and related algorithms, or on the transition matrix and state discretization as in Markov state models. For this line of algorithms, spatial resolution is maintained but results are not transferable. Deep learning has been utilized to realize more efficient and accurate ways of “dividing and conquering” and “caching” along these two lines of algorithmic research. We proposed and demonstrated the local free energy landscape approach, a new framework for classical computational molecular science. This framework is based on a third class of algorithm that facilitates molecular modeling through partially transferable in resolution “caching” of distributions for local clusters of molecular degrees of freedom. Differences, connections and potential interactions among these three algorithmic directions are discussed, with the hope to stimulate development of more elegant, efficient and reliable formulations and algorithms for “dividing and conquering” and “caching” in complex molecular systems. Statistics from a Web of Science  or sunctions ,49,50: tunctions . It is wunctions ,53,54. OPairwise approximations are usually adopted for its computational convenience, both in terms of dramatically reduced computational cost and tremendously smaller  number of necessary parameters to be fit in FF parameterization. It is widely acknowledged that construction of traditional FF  is a laComplexity of molecular systems is rooted in their molecular interactions, which engender complex and non-linear correlations among molecular degrees of freedom (DOFs). Consequently, effective number of DOFs are greatly reduced. Therefore, complex molecular systems are confined to manifolds  of much In stochastic trajectory generation by Monte Carlo (MC) simulations or candidate structural model proposal in protein structure prediction and refinement (or other similar scenarios), new configuration proposal is carried out in NHDS. A lot of effort is inevitably wasted due to sampling outside the actual manifold occupied by the target molecular system. Such wasting may be avoided if we understood all correlations. However, understanding all correlations implicates accurate description of global free energy landscape (FEL) and there is no need to investigate it further. Due to preference of lower energy configurations by typical importance sampling strategies , stochastic trajectories tend to be trapped in local minima of FEL. This is especially true for complex molecular  systems which have hierarchical rugged FEL with many local minima ,64. In tTo cope with fundamental difficulties in molecular modeling, two distinct lines of methodological development (CG and ES) based on DC and “caching” strategies have been conducted and tremendous progress has been made in understanding of molecular systems. As summarized below:Atomistic FF parameterization is the most well established coarse graining based on time scale separation between each nuclei and its surrounding electrons. Theoretically, MMFFs are potential of mean force (PMF) obtained by averaging over many electronic DOFs for given atomic configurations. In practice, due to the fact that ab initio calculations are expensive and may have significant error when level of theory (and/or basis set) is not sufficient, reference data usually include results from both quantum mechanical (QM) calculations and well-established experimental data ,66,67. TV and The united atom model (UAM) is the next step in coarse graining , where htion see  for essetion see .Another simple and powerful type of CG model for biomolecular systems is Gō model ,99 and es. DC strategy is first applied by dividing s into windows, information for each window is then partially “cached” by corresponding bias potentials and local statistics. Later on, adaptive US (AUS) [Umbrella sampling (US)  is probaUS (AUS) ,109 and US (AUS)  were devUS (AUS) ,112 was US (AUS) ,114,115 US (AUS) ,117,118.US (AUS) ,121,122.essed as :(3)p0(s)The starting point of these “caching” algorithms is specification of reaction coordinates (RC) or collective variables (CVs), which is a very challenging task for complex molecular systems in many cases. Traditionally, principle component analysis (PCA)  is the mApparently, RC and/or CV based ES is a different path for facilitate simulation of complex molecular systems on longer time scales from coarse graining. One apparent plus side is that these algorithms are “in resolution” as no systematic discarding of molecular DOFs occur. With specification of RC and/or CVs, computational resource is presumably directed toward the most interesting dynamics of the target molecular system, and RC and/or CV maybe repetitively refined to obtain mechanistic understanding of interested molecular processes. However, the down side is that “cached” information on local configurational space is not transferable to other similar molecular systems. While rigorous transferability may not be easily established for any CG FF, practical utility of CG FF for molecular systems with similar composition and thermodynamic conditions have been quite common and useful . Therefot and j after an implied lag time  ,136,137,The advantage of not needing RC/CV does not come for free but with accompanying difficulties. Firstly, one has to distribute start points of trajectories to statistically important and different part of configurational space, then select proper  partition of configurational space into discrete states. This is the key step of DC strategy in MSM. No formal rule is available and experience is important. In many cases some try and error is necessary. Secondly, within each discrete state at a given level of hierarchy, equilibration is assumed to be achieved instantly and this assumption causes systematic discretization error, which fortunately may be controlled with proper partition and sufficiently long lag time . ApparenAnother important class of enhanced sampling is to facilitate sampling with non-Boltzmann distributions and restore property at targeted thermodynamic condition through proper reweight . Most ouFixed functional form and pairwise approximation of non-bonded interactions are two major factors limiting the accuracy of molecular interaction description in both atomistic and some CG FF. Neural network (NN) has capability of approximating arbitrary functions and therefore has potential to address these two issues. Not surprisingly, significant progress has been made in this regard as summarized by recent excellent reviews ,156,157.Just as in the case of traditional FF, transferability and accuracy is always a tradeoff. More transferability implicates less attention is paid to “cache” detailed differences among different molecular systems, hence less accuracy. Exploration in this regard, however, remains not as much as necessary ,165,166.As in the case of constructing atomic level potentials, machine learning has been applied to address two outstanding pending issues in coarse graining, which are definition of CG sites/particles and parameterization of corresponding interactions between/among these sites/particles. Traditional CG FF, suffers from both pairwise approximation and, for some, accuracy ceiling of simple fixed functional forms which are easy to fit. By using more complex  potentials with a machine learning fitting process, Chan et al.  developeTo overcome difficulties of earlier nonlinear CV construction algorithms ,128,130 N DOFs, this LFEL approach may be expressed as:N-DOF molecular system is reorganized into M overlapping regions  and is extremely difficult, if ever possible, to be calculated directly. However, GCF is a unnormalized probability distribution, when all molecular DOFs in local terms are (approximately) sampled according to GCF, then we do not need GCF explicitly anymore (Equations (12) and  of distributions for faster/discarded DOFs with proper CG FF, and thus has the inevitable cost of losing resolution (information), accompanied by the desired attribute of  transferability to various extent. ES reduces lingering time of molecular systems in local minima through “caching” visited local configurational space, which is usually defined by relevant DC strategies, with biasing potentials. When compared with CG, there is no resolution loss. However, “cached” manifold of configurational space is molecular process specific and thus not transferable at all. In molecular modeling community, these two lines of methodologies are developed quite independently. Nevertheless, one might want to ask why not have both advantages in one method, that is to reduce repetitive local sampling without loss of resolution and with “cached” results being partially transferable. The local free energy landscape (LFEL) approach  is propoessed as:P(M≤N)Ri=P and . While wBoth terms may be learned from either experimental or computational datasets, as long as they are sufficiently representative and reliable. The first term in Equation  is the lpredictioncenter.org/casp14/index.cgi (accessed on 15 February 2021)), our method ranked the the first for the 13 targets with start GDT-TS score larger than 60. We expect incorporation of complete heavy atom information and local prior terms to further improve this method in the future. GSFE theory in particular and the LFEL approach in general, are certainly extendable to modeling of other soft matter molecular systems.A particular implementation of the LMLA-GSFE for protein structure refinement with residues defined as comprising unit was conducted . In thisastRelax ) and thoastRelax . In the All of these algorithms have a common goal of accelerating computation of a joint distribution for a given molecular system at some target resolution, albeit from distinct perspectives. The fundamental underpinning is the fact that molecular correlations among its various DOFs limit a molecular system to a manifold of significantly lower dimension. Both ES and CG in the FF framework and the LFEL approach are distinct strategies to “cache” manifolds from either configurational space  or physiBoth MSM and RC/CV based ES are designed to first describe local parts of the approximate manifold in the configurational space formed by all molecular DOFs of the target molecular system. Information for such local configurational space is partially “cached” either as bias potentials or transition counts, which are further processed to map FEL and dynamics of interested molecular processes. Computational process (or educated guess) for establishment of RC/CVs is essentially “caching” results from sampling/guessing local parts of the configurational as approximate relevant manifold B. SubseqIn contrast, both CG in the FF framework and the LFEL approach are motivated to “cache” relevant information on the complete configurational distribution for local clusters of molecular DOFs. Such local clusters are building blocks for many similar molecular systems  and consequently have limited and approximate transferability. In CG, strongly correlated local clusters of molecular DOFs are represented as a single particle, complex many body correlations/interactions of CG particles within selected cutoff distances are represented by simplified CG FF in a lower resolution and longer range correlations/interactions are incorporated either through more coarser CG models or by separate long-range interaction computation. In LMLA-GSFE implementation of LFEL, all complex many body correlations within selected regions  are decomposed into two terms in Equation , local lThe first step of CG is to partition atoms/particles of high resolution representation into highly correlated local clusters that will be represented by corresponding single CG particles, and moderately correlated regions define interaction cutoff for CG particles; The second step is to select a site  to represent the corresponding highly correlated cluster; The third step is to select functional forms to describe molecular interactions among newly defined CG particles, and parameters are optimized by selected loss functions  baseThese three lines of algorithms may be combined to facilitate molecular modeling. For example, one might first utilize deep learning based near quantum accuracy many body FF to perform atomistic simulations for protein molecular systems, and then extracting local distributions properly with some form of LFEL, which may potentially be utilized to simulate protein molecular systems with near-quantum accuracy and at regular amino-acid based CG or even much faster speed! Similarly, one may extract and “cache” large body of information from residue level CG simulations with proper LFEL implementation, which may be utilized to achieve ultra CG (UCG) efficiency with residue resolution. Application of CV and MSM based ES algorithm for CG models is straight forward. Combination of LFEL with CV or MSM based ES is more subtle and yet to be investigated.The application of “dividing and conquering” and “caching” principle in development of molecular modeling algorithms is briefed. Historically, coarse graining and enhanced sampling have been two independent lines of methodological development in the mainstream FF framework. While they share the common goal of reducing local sampling, the formulations are completely different with distinct (dis)advantages. Coarse graining obtains partial transferable FFs but loses resolution, enhanced sampling retains resolution but results are not transferable. The LFEL approach suggests a third strategy to directly approximate global joint distribution by superposition of LFEL, which may be learned from available dataset of either experimental or computational origin. Through integration of coordinate transformation, autodifferentiation and neural network implementation of GSFE, our recent work of protein structure refinement demonstrated that simultaneous realization of transferable in-resolution “caching” of local sampling is not only feasible, but also highly efficient due to replacement of local sampling by differentiation. It is hoped that this review stimulates further development of better “dividing and conquering” strategies for complex molecular systems through more elegant, efficient and accurate ways of “caching” potentially repetitive computations in molecular modeling at various spatial and temporal scales. With diverse molecular systems , specialization of methodology is essential to take advantage of distinct constraints and characteristics.