Miracle-dz/UniFAR-FTUs huggingface dataset:
Solubility Prediction from Molecular Properties and Analytical Data Using an In-phase Deep Neural Network (Ip-DNN)

Materials informatics is an emerging field that allows us to predict the properties of materials and has been applied in various research and development fields, such as materials science. In particular, solubility factors such as the Hansen and Hildebrand solubility parameters (HSPs and SP, respectively) and Log P are important values for understanding the physical properties of various substances. In this study, we succeeded at establishing a solubility prediction tool using a unique machine learning method called the in-phase deep neural network (ip-DNN), which starts exclusively from the analytical input data (e.g., NMR information, refractive index, and density) to predict solubility by predicting intermediate elements, such as molecular components and molecular descriptors, in the multiple-step method. For improving the level of accuracy of the prediction, intermediate regression models were employed when performing in-phase machine learning. In addition, we developed a website dedicated to the established solubility prediction method, which is freely available at “http://dmar.riken. jp/matsolca/”.
Non-anesthetist-administered moderate sedation with midazolam and fentanyl for outpatient MRI-aided hybrid intracavitary and interstitial brachytherapy in cervix cancer: a single-institution experience

Purpose The aim of the study was to determine the feasibility of interstitial brachytherapy under non-anesthetist-administered moderate sedation, to identify factors influencing the insertion, and the total procedural time. Material and methods A total of 47 insertions with hybrid intracavitary and interstitial applicators were performed in 23 patients from March 2017 to March 2020. Moderate sedation was achieved with intravenous midazolam and fentanyl administered by non-anesthetist. Insertion time and procedural time was recorded. Univariate and multivariate analysis were performed to evaluate the impact of different factors on insertion and procedural time. Results A total of 238 needles (range, 2-8 per insertion) were implanted, with an average insertion depth of 30 mm (range, 20-40 mm). The mean doses for midazolam and fentanyl were 3 mg (standard deviation [SD] = 1) and 53.3 mcg (SD = 23.9) per insertion, respectively. The median insertion time was 30 minutes (interquartile range [IQR] = 22-40), and the median total procedural time was 4.3 hours (IQR = 3.6-5.2). First time insertion, insertions performed before 2019, and higher midazolam dose were associated with significantly longer insertion time, whereas longer insertion time, MRI-based planning, and insertions performed before 2019 were associated with significantly longer total procedural time. Conclusions Outpatient interstitial brachytherapy with non-anesthetist-administered sedation is achievable and well-tolerated. This method may significantly lessen the burden on hospital resources and has the potential to be cost-effective.
Dynamic Protective Effect of Chinese Herbal Prescription, Yiqi Jiedu Decoction, on Testis in Mice with Acute Radiation Injury

Objective A Chinese herbal prescription, Yiqi Jiedu (YQJD) decoction, is used for injuries caused by radiotherapy. This study aimed to investigate the dynamic protective effects of YQJD decoction in mice on radiation damage at different time points of the testis. Methods The 200 male Balb/c mice were randomly divided into 5 groups (blank, model, Anduolin, low-dose YQJD, and high-dose YQJD groups). Blank and model groups were all given stomach deionized water. Anduolin group and high and low dose of Chinese herb groups were treated with Chinese material medical decoction compound for 2 weeks before being irradiated. Except for the blank group, other groups were given whole-body one-time irradiation of 5.5 Gy 60Co gamma rays. Histopathology examination of testes was conducted on the 1st, 7th, 21st, and 35th day after irradiation, respectively. Indexes of sperm motility rate, sperm count, serum levels of testosterone (T), estradiol (E2), follicle-stimulating hormone (FSH), and luteinizing hormone (LH) were also measured correspondingly. Result Compared to 1 day and 7 days after irradiation, most of the indexes, including testis index, sperm motility, and count, were decreased on the 21st and 35th day in all irradiated groups. However, compared with the model group, the indexes to assess sperm quality and the morphological structures of testis in low-dose and high-dose YQJD groups were significantly recovered on the 21st and 35th days. Additionally, reproductive hormones, including testosterone and estradiol, were recovered more in low-dose and high-dose YQJD groups on the 21st and 35th days. Conclusion The YQJD decoction is able to accelerate the recovery of sperm indexes, testosterone, and estradiol levels of sex hormones in mice after irradiation and demonstrated good protective effects on the testis.
Establishment of a modified percutaneous CT-guided paraspinal intramuscular VX-2 squamous cell carcinoma dual tumor model in rabbits

Background The rabbit VX-2 tumor model is a commonly used transplanted tumor model and is widely used in surgical, radiological, and interventional studies. Most of the known tumor models for each site are single solid tumors. This study aimed to establish an accurate and stable intramuscular dual tumor model guided by computed tomography (CT). Methods In this study, we compared three different inoculation methods to select the most appropriate dual tumor model. Six New Zealand White rabbits were used as tumor-carrying rabbits for tumor harvesting. Thirty rabbits were divided into three groups as experimental rabbits. Group A applied the tumor cell suspension method, in which the suspension was injected into the designated location with a syringe under CT guidance. Groups B and C used tumor tissue strips obtained in vivo or under direct in vitro vision. The tumor tissue strips were implanted into the designated locations using a guide needle under CT guidance. The differences in tumorigenic rate, the size difference between bilateral tumors, and metastasis between the three methods were compared. Results It was found that group A obtained a 100% tumor survival rate, but the size of the tumor was more variable, and needle tract implantation metastasis occurred in 5 cases. In group B, tumor tissue strips were taken in vivo for implantation, in which one case failed to survive. Tumor tissue strips in group C were obtained in vitro under direct vision. The tumor tissue strips obtained in vitro by puncture using a biopsy needle in group C had a 100% tumorigenicity rate and stable tumor size. No significant needle tract implantation metastases were found in either group B or C. The variance of tumor size obtained in group A was significantly higher than in groups B and C. The variance of tumor size in group C was the smallest. Group C had high tumorigenicity and a more stable size and morphology of the formed tumors. Conclusion The results showed that the method of obtaining tumor tissue strips using in vitro direct vision puncture and implanting them into the muscle with CT guidance and guide needles can establish an accurate and stable dual tumor model. This dual tumor model can provide substantial support for relevant preclinical studies.
Research on Characteristic of Chronic Spontaneous Urticaria Based on Multiscale Entropy

Chronic spontaneous urticaria (CSU) is a common skin disease which symptom is local pruritus and pain. In medicine, researchers take a certain point that the brain is the control center of CSU, but in previous experiments, the researchers found that cerebellum also had a certain effect on CSU. In order to find out the influence of CSU in the brain and cerebellum, we collected the brain resting-state fMRI data from 40 healthy controls and 32 CSU patients and used DPABI to preprocess. We calculated the entropy values of five scales by using multiscale entropy (MSE) and the average entropy values of two groups' BOLD signals; 15 regions with significant differences were found which not only had a more detailed impact in the brain but also had an impact in the cerebellum, such as precentral gyrus, lenticular putamen, and vermis of cerebellum. In addition, we found that compared with the healthy controls, the entropy values of CSU patients showed two trends which need further study. The advantage of our experiment is that the multiscale entropy value is used to get more influence regions of CSU in the brain and cerebellum. The results of this paper may provide some help for the pathological study of CSU.
Predicting Poor Outcome of COVID-19 Patients on the Day of Admission with the COVID-19 Score

Background COVID-19 may result in multiorgan failure and death. Early detection of patients at risk may allow triage and more intense monitoring. The aim of this study was to develop a simple, objective admission score, based on laboratory tests, that identifies patients who are likely going to deteriorate. Methods This is a retrospective cohort study of all COVID-19 patients admitted to a tertiary academic medical center in New York City during the COVID-19 crisis in spring 2020. The primary combined endpoint included intubation, stage 3 acute kidney injury (AKI), or death. Laboratory tests available on admission in at least 70% of patients (and age) were included for univariate analysis. Tests that were statistically or clinically significant were then included in a multivariate binary logistic regression model using stepwise exclusion. 70% of all patients were used to train the model, and 30% were used as an internal validation cohort. The aim of this study was to develop and validate a model for COVID-19 severity based on biomarkers. Results Out of 2545 patients, 833 (32.7%) experienced the primary endpoint. 53 laboratory tests were analyzed, and of these, 47 tests (and age) were significantly different between patients with and without the endpoint. The final multivariate model included age, albumin, creatinine, C-reactive protein, and lactate dehydrogenase. The area under the ROC curve was 0.850 (CI [95%]: 0.813, 0.889), with a sensitivity of 0.800 and specificity of 0.761. The probability of experiencing the primary endpoint can be calculated as p=e(−2.4475+0.02492age − 0.6503albumin+0.81926creat+0.00388CRP+0.00143LDH)/1+e(−2.4475+ 0.02492age − 0.6503albumin+0.81926creat+0.00388CRP+0.00143LDH). Conclusions Our study demonstrated that poor outcome in COVID-19 patients can be predicted with good sensitivity and specificity using a few laboratory tests. This is useful for identifying patients at risk during admission.
The complete chloroplast genome of a purple Ethiopian rape (Brassica carinata: Brassicaceae) from Guizhou Province, China and its phylogenetic analysis

Abstract Brassica carinata A. Braun (Ethiopian rape), which was derived from the interspecific hybridization between B. nigra and B. oleracea, is used as both an oilseed and a leafy vegetable. The complete chloroplast (cp) genome of a purple B. carinata was obtained. This cp genome has a typical quadripartite structure and is 153,641 bp in length. The GC content of the cp genome is 36.39%. A total of 113 genes were predicted on this cp genome, including 79 protein coding, 4 rRNA, and 30 tRNA genes. Among these genes, 18 genes were duplicated (7 tRNAs, 4 rRNAs, and 7 protein coding genes). Sixty-eight SSR loci, including 11 compound SSRs, were identified in this cp genome by MISA. The phylogenetic tree analysis fully resolved B. carinata in a clade with B. nigra. This study provides important information for future evolution, genetic and molecular biology studies of B. carinata.
Cafeteria Diet-Induced Metabolic and Cardiovascular Changes in Rats: The Role of Piper nigrum Leaf Extract

Background Cafeteria diet is known to induce excessive body fat accumulation (obesity) that could cause metabolic and cardiovascular changes and even death. The increase in prevalence over time and the failure in treatment options make obesity a real public health problem. The present study assessed the preventive effect of the hydro-ethanolic extract of the Piper nigrum leaf on the development of metabolic and cardiovascular changes in cafeteria diet fed Wistar rats. Methods Thirty-six male rats were divided into 5 groups of 6 rats each: a normal control group (Nor.), a negative control group (Neg.), two groups administered different doses of extract in mg/kg (E250 and E500), and a group administered atorvastatin 10 mg/kg (Ator., reference drug). The animals were fed with experimental diets (standard and cafeteria) for a period of 5 weeks. Food and water intake were assessed daily, and the body weight assessed weekly. At the end of the feeding, plasma lipid profile and markers of hepatic and renal function were assessed. Furthermore, the relative weights of the adipose tissue and the organs were assessed. The liver, kidneys, and heart homogenates were assessed for markers of oxidative stress while the aorta was histopathologically examined. Results Cafeteria diet-induced weight gain of 30% and increased triglyceride, total cholesterol, and low-density lipoprotein cholesterol level of more than 50%. Equally, an increase in the relative weight of accumulated adipose tissues of more than 90%, oxidative stress, and alteration in the organ structure were visible in cafeteria diet fed rats (Neg). Treatment with P. nigrum extract significantly prevented weight gain, dyslipidemia, oxidative stress, and alteration in the architecture of the aorta. The effect of P. nigrum extract was comparable to that of the reference drug. Conclusion Piper nigrum leaf may prevent weight gain and possess cardioprotective activity with a strong antioxidant activity.
Beyond generative models: superfast traversal, optimization, novelty, exploration and discovery (STONED) algorithm for molecules using SELFIES

Inverse design allows the generation of molecules with desirable physical quantities using property optimization. Deep generative models have recently been applied to tackle inverse design, as they possess the ability to optimize molecular properties directly through structure modification using gradients. While the ability to carry out direct property optimizations is promising, the use of generative deep learning models to solve practical problems requires large amounts of data and is very time-consuming. In this work, we propose STONED – a simple and efficient algorithm to perform interpolation and exploration in the chemical space, comparable to deep generative models. STONED bypasses the need for large amounts of data and training times by using string modifications in the SELFIES molecular representation. First, we achieve non-trivial performance on typical benchmarks for generative models without any training. Additionally, we demonstrate applications in high-throughput virtual screening for the design of drugs, photovoltaics, and the construction of chemical paths, allowing for both property and structure-based interpolation in the chemical space. Overall, we anticipate our results to be a stepping stone for developing more sophisticated inverse design models and benchmarking tools, ultimately helping generative models achieve wider adoption.
Overexpression of RIPK4 Predicts Poor Prognosis and Promotes Metastasis in Ovarian Cancer

This study was conducted to evaluate the prognostic value of receptor-interacting protein kinase 4 (RIPK4) in ovarian cancer (OC) and its role in tumorigenesis. RNA expression and the corresponding clinical data were obtained from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. The relationship between clinical-pathological characteristics and RIPK4 expression was analyzed using the Wilcoxon signed-rank test and logistic regression. The Cox regression and the Kaplan-Meier method were used to evaluate the relationship between clinicopathological features and overall survival (OS). Gene set enrichment analysis (GSEA) was performed using Molecular Signatures Database. Scratch assay, transwell assay, and cell transfection were used to verify the function of RIPK4. Overexpression of RIPK4 was associated with the stage of OC and distant metastasis. Survival analysis revealed that patients with OC and higher expression of RIPK4 had a poorer prognosis. Univariate and multivariate analyses indicated that high expression of RIPK4 was associated with poor OS, as well as age and stage of OC. The areas under the curve (AUC) at 1, 4, and 8 years were 0.737, 0.634, and 0.669, respectively, according to the established OS prediction model. GSEA revealed that adherens junction, cadherin binding, and Wnt signaling pathway were enriched in the high RIPK4 expression group. Cell transfection confirmed RIPK4 was involved in the Wnt signaling pathway. RIPK4 can act as a potential prognostic molecular marker for poor survival in OC. Moreover, RIPK4 is associated with tumor metastasis and implicated in the regulation of the Wnt signaling pathway.
Using a mobile health app to improve patients’ adherence to hypertension treatment: a non-randomized clinical trial

Poor adherence to hypertension treatment increases complications of the disease and is characterized by a lack of awareness and acceptance of ongoing treatment. Mobile health (mHealth) apps can optimize processes and facilitate access to health information by combining treatment methods with attractive solutions. In this study, we aimed at verifying the influence of using an mHealth app on patients’ adherence to hypertension treatment, also examining how user experience toward the app influenced the outcomes. A total of 49 participants completed the study, men and women, diagnosed with hypertension and ongoing medical treatment. For 12 weeks, the control group continued with conventional monitoring, while the experimental group used an mHealth app. From the experimental group, at baseline, 8% were non-adherent, 64% were partial adherents and 28% were adherent to the treatment. Baseline in the control group indicated 4.2% non-adherents, 58.3% partial adherents, and 37.5% adherents. After follow-up, the experimental group had an increase to 92% adherent, 8% partially adherent, and 0% non-adherent (P < 0.001). In the control group, adherence after follow-up remained virtually the same (P ≥ 0.999). Results of user experience were substantially positive and indicate that the participants in the experimental group had a satisfactory perception of the app. In conclusion, this study suggests that using an mHealth app can empower patients to manage their own health and increase adherence to hypertension treatment, especially when the app provides a positive user experience.
Analysis of metallothioneins by mass spectrometry-based hyphenated techniques

Abstract As a kind of cysteine-rich protein, metallothioneins (MTs) play an important role in metal-related biochemical pathways, including homeostasis of essential metals, detoxification of heavy metals, and scavenging of free radicals. The analysis of MTs is challenging due to the complexity of the sample matrix, the coexisting isoforms, and easy destruction of the integrity of metal–MTs complexes during processing. Mass spectrometry (MS)-based hyphenated techniques, such as high-performance liquid chromatography (HPLC) or capillary electrophoresis (CE) combined with inductively coupled plasma (ICP)-MS or electrospray ionization (ESI)-MS have become the most effective methods for MT analysis because they can provide comprehensive information on MTs, including the amount, the metal components, and the isoforms. In this review, we summarize the analysis of MTs using MS-based hyphenated techniques. The use of ICP-MS and ESI-MS as well as matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF)-MS are stated. The combination of CE or HPLC with ICP-MS and ESI-MS for the analysis of MTs isoforms is discussed. Four HPLC separation modes, including size exclusion chromatography (SEC), anion-exchange chromatography (AEC), reversed phase liquid chromatography (RPLC), and hydrophilic interaction liquid chromatography (HILIC), are elaborated. The coupling of RPLC with ICP-MS and ESI-MS in parallel for the analysis of MT subisoforms is especially highlighted.
Rehabilitation of patients after COVID-19 recovery: An experience at the Physical and Rehabilitation Medicine Institute and Lucy Montoro Rehabilitation Institute

OBJECTIVES: As patients recovering from the novel coronavirus disease 2019 (COVID-19) present with physical, respiratory, cognitive, nutritional, and swallowing-related impairments and mental health complications, their rehabilitation needs are complex. This study aimed to describe the demographic, clinical, and functional status after the discharge of COVID-19 survivors who underwent intensive multidisciplinary inpatient rehabilitation at the Physical and Rehabilitation Medicine Institute of the University of Sao Paulo Medical School General Hospital and Lucy Montoro Rehabilitation Institute. We determined the most important factors related to the length of inpatient rehabilitation treatment and present the functional outcomes. METHODS: This was a retrospective study based on electronic medical records. In addition to the severity of COVID-19 and length of hospital stay for the management of COVID-19 and comorbidities, we collected sociodemographic data including age, sex, height, and weight. Functional assessments were performed using the Functional Independence Measure (FIM); Short Physical Performance Battery; Montreal Cognitive Assessment; Depression, Anxiety and Stress Scale; Revised Impact of Events Scale; bioelectrical impedance; Functional Oral Intake Scale; oropharyngeal dysphagia classification; and nutritional assessment. RESULTS: There was a significant improvement in FIM before and after inpatient rehabilitation treatment (p<0.0001). Muscle strength and walking capacity were significantly improved (p<0.01). The most important factors related to the length of inpatient rehabilitation treatment were improvement in FIM scores (Spearman's r=0.71) and gain in lean mass (Spearman's r=0.79). CONCLUSIONS: Rehabilitation of patients after COVID-19 recovery improves their functional status and should be considered in the post-acute phase for selected patients with COVID-19.
Screening for Colour Developer and Optimization of Reaction Conditions for Fast Determination of Basic Orange II in Foods

Using the ability of basic orange Ⅱ to develop color,a fast method was presented for the determination of this dye. The optimal conditions for color development were investigated. A reagent system composed of potassium ferricyanide and Iron (Ⅲ) was found to the best color developer through comparative analysis of color developing effects of different color developers and observation of absorbance change,and the optimal ratio of potassium ferricyanide solution (3 g/L) to ferric chloride solution (4.5 g/L) was 1:1. The optimal reaction conditions were determined based on absorbance at 755 nm wavelength as follows:color developer amount,0.7 mL; and reaction temperature,50 ℃ for a reaction duration of 20 min.
Determination of Camptothecin in Leaves of Camptotheca Acuminata Decne. by HPLC

A simple, rapid and sensitive method for the determination of camptothecin in leaves of Camptotheca acuminata Decne.was established. Camptothecin in the leaves was ultrasonically extracted with 61% alcohol at 50 ℃ for 10 min, and determined by high performance liquid chromatography. The camptothecin was separated on a Techsphere ODS column(25 cm×4.6 mm ID, 5 μm) at 25 ℃, using acetonitrile-water(4∶6 by volume) system with 1.0 mL/min as the mobile phase, and detected at 254 nm. Relative standard deviation of 2.5%(n=6) and average recovery of 96% for the method were found.