Budget-Friendly Generation, Biochemical Analyses, and Lentiviral Transduction of Patient-Derived Colon Organoids.

For the past decade, three-dimensional (3D) culture models have been emerging as powerful tools in translational research to overcome the limitations of two-dimensional cell culture models. Thanks to their ability to recapitulate the phenotypic and molecular heterogeneity found in numerous organs, organoids have been used to model a broad range of tumors, such as colorectal cancer. Several approaches to generate organoids exist, with protocols using either pluripotent stem cells, embryonic stem cells, or organ-restricted adult stem cells found in primary tissues, such as surgical resections as starting material. The latter, so-called patient-derived organoids (PDOs), have shown their robustness in predicting patient drug responses compared to other models. Because of their origin, PDOs are natural offspring of the patient tumor or healthy surrounding tissue, and therefore, have been increasingly used to develop targeted drugs and personalized therapies. Here, we present a new protocol to generate patient-derived colon organoids (PDCOs) from tumor and healthy tissue biopsies. We emphasize budget-friendly and reproducible techniques, which are often limiting factors in this line of research that restrict the development of this 3D-culture model to a small number of laboratories worldwide. Accordingly, we describe efficient and cost-effective techniques to achieve immunoblot and high-resolution microscopy on PDCOs. Finally, a novel strategy of lentiviral transduction of PDCOs, which could be applied to all organoid models, is detailed in this article. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Establishment of PDCOs from biopsies Basic Protocol 2: Long-term maintenance and expansion of PDCOs in BME domes Basic Protocol 3: Cryopreservation and thawing of PDCOs Basic Protocol 4: Lentiviral transduction of PDCOs Basic Protocol 5: Immunoblot and evaluation of variability between donors Basic Protocol 6: Immunofluorescence labeling and high-resolution microscopy of PDCOs Basic Protocol 7: Transcriptomic analyses of PDCOs by RT-qPCR.

The application of decision tree model based on clinicopathological risk factors and pre-operative MRI radiomics for predicting short-term recurrence of glioblastoma after total resection: a retrospective cohort study.

To develop a decision tree model based on clinical information, molecular genetics information and pre-operative magnetic resonance imaging (MRI) radiomics-score (Rad-score) to investigate its predictive value for the risk of recurrence of glioblastoma (GBM) within one year after total resection. Patients with pathologically confirmed GBM at Huashan Hospital, Fudan University between November 2017 and June 2020 were retrospectively analyzed, and the enrolled patients were randomly divided into training and test sets according to the ratio of 3:1. The relevant clinical and MRI data of patients before, after surgery and follow-up were collected, and after feature extraction on preoperative MRI, the LASSO filter was used to filter the features and establish the Rad-score. Using the training set, a decision tree model for predicting recurrence of GBM within one year after total resection was established by the C5.0 algorithm, and scatter plots were generated to evaluate the prediction accuracy of the decision tree during model testing. The prediction performance of the model was also evaluated by calculating area under the receiver operating characteristic (ROC) curve (AUC), ACC, Sensitivity (SEN), Specificity (SPE) and other indicators. Besides, two external validation datasets from Wuhan union hospital and the second affiliated hospital of Xuzhou Medical University were used to verify the reliability and accuracy of the prediction model. According to the inclusion and exclusion criteria, 134 patients with GBM were finally identified for inclusion in the study, and 53 patients recurred within one year after total resection, with a mean recurrence time of 5.6 months. According to the importance of the predictor variables, a decision tree model for predicting recurrence based on five important factors, including patient age, Rad-score, O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation, pre-operative Karnofsky Performance Status (KPS) and Telomerase reverse transcriptase (TERT) promoter mutation, was developed. The AUCs of the model in the training and test sets were 0.850 and 0.719, respectively, and the scatter plot showed excellent consistency. In addition, the prediction model achieved AUCs of 0.810 and 0.702 in two external validation datasets from Wuhan union hospital and the second affiliated hospital of Xuzhou Medical University, respectively. The decision tree model based on clinicopathological risk factors and preoperative MRI Rad-score can accurately predict the risk of recurrence of GBM within one year after total resection, which can further guide the clinical optimization of patient treatment decisions, as well as refine the clinical management of patients and improve their prognoses to a certain extent.

CropQuant-Air: an AI-powered system to enable phenotypic analysis of yield- and performance-related traits using wheat canopy imagery collected by low-cost drones.

As one of the most consumed stable foods around the world, wheat plays a crucial role in ensuring global food security. The ability to quantify key yield components under complex field conditions can help breeders and researchers assess wheat's yield performance effectively. Nevertheless, it is still challenging to conduct large-scale phenotyping to analyse canopy-level wheat spikes and relevant performance traits, in the field and in an automated manner. Here, we present CropQuant-Air, an AI-powered software system that combines state-of-the-art deep learning (DL) models and image processing algorithms to enable the detection of wheat spikes and phenotypic analysis using wheat canopy images acquired by low-cost drones. The system includes the YOLACT-Plot model for plot segmentation, an optimised YOLOv7 model for quantifying the spike number per m2 (SNpM2) trait, and performance-related trait analysis using spectral and texture features at the canopy level. Besides using our labelled dataset for model training, we also employed the Global Wheat Head Detection dataset to incorporate varietal features into the DL models, facilitating us to perform reliable yield-based analysis from hundreds of varieties selected from main wheat production regions in China. Finally, we employed the SNpM2 and performance traits to develop a yield classification model using the Extreme Gradient Boosting (XGBoost) ensemble and obtained significant positive correlations between the computational analysis results and manual scoring, indicating the reliability of CropQuant-Air. To ensure that our work could reach wider researchers, we created a graphical user interface for CropQuant-Air, so that non-expert users could readily use our work. We believe that our work represents valuable advances in yield-based field phenotyping and phenotypic analysis, providing useful and reliable toolkits to enable breeders, researchers, growers, and farmers to assess crop-yield performance in a cost-effective approach.

Assessment and modeling of effluent quality, economic benefits, and greenhouse gas reduction for receiving brewery wastewater on A2O by GPS-X.

Recently, breweries have been allowed to discharge brewery wastewater (BWW) to the sewage pipe network to alleviate the shortage of carbon sources of municipal wastewater treatment plants (MWTPs) under the premise of signing a contract with MWTPs in some countries. This study aims to provide a model-based method for MWTPs to evaluate the threshold, the effluent risk, the economic benefits, and the potential greenhouse gas (GHG) emissions reduction of receiving BWW. In this research, a simulation model of an anaerobic-anoxic-oxic process (A2O) receiving BWW was established based on the data of a real MWTP and brewery using GPS-X. The sensitivity factors of 189 parameters were analyzed, and several sensitive parameters were calibrated stably and dynamically. By analyzing the errors and standardized residuals, the calibrated model was proved to be high-quality and reliable. In the next phase, the impact of receiving BWW on the A2O was evaluated in terms of effluent quality, economic benefits, and GHG emissions reduction. The results showed that receiving a certain amount of BWW can effectively reduce the carbon source cost and GHG emissions for the MWTP compared with adding methanol. Though the chemical oxygen demand (COD), biochemical oxygen demand in five days (BOD5), and total nitrogen (TN) in the effluent increased in various degrees, the effluent quality still met the discharge standard implemented by the MWTP. The study can also facilitate the modeling work for many researchers and promote more kinds of food production wastewater to be treated equally.

Development of an audiological assessment and diagnostic model for high occupational noise exposure.

PURPOSE: To explore the diagnostic auditory indicators of high noise exposure and combine them into a diagnostic model of high noise exposure and possible development of hidden hearing loss (HHL). METHODS: We recruited 101 young adult subjects and divided them according to noise exposure history into high-risk and low-risk groups. All subjects completed demographic characteristic collection (including age, noise exposure, self-reported hearing status, and headset use) and related hearing examination. RESULTS: The 8 kHz (P = 0.039) and 10 kHz (P = 0.005) distortion product otoacoustic emission amplitudes (DPOAE) (DPs) in the high-risk group were lower than those in the low-risk group. The amplitudes of the summating potential (SP) (P = 0.017) and action potential (AP) (P = 0.012) of the electrocochleography (ECochG) in the high-risk group were smaller than those in the low-risk group. The auditory brainstem response (ABR) wave III amplitude in the high-risk group was higher than that in the low-risk group. When SNR = - 7.5 dB (P = 0.030) and - 5 dB (P = 0.000), the high-risk group had a lower speech discrimination score than that of the low-risk group. The 10 kHz DPOAE DP, ABR wave III amplitude and speech discrimination score under noise with SNR = - 5 dB were combined to construct a combination diagnostic indicator. The area under the ROC curve was 0.804 (95% CI 0.713-0.876), the sensitivity was 80.39%, and the specificity was 68.00%. CONCLUSIONS: We expect that high noise exposure can be detected early with this combined diagnostic indicator to prevent HHL or sensorineural hearing loss (SNHL). TRIAL REGISTRATION NUMBER/DATE OF REGISTRATION: ChiCTR2200057989, 2022/3/25.

Event-Triggered Control for Markov Jump Systems Subject to Mismatched Modes and Strict Dissipativity.

In order to save network resources of discrete-time Markov jump systems, an event-triggered control framework is employed in this article. The threshold parameter in the event-triggered mechanism is designed as a diagonal matrix in which all elements can be adjusted according to system performance requirements. The hidden Markov model is introduced to characterize the asynchronization between the controller and controlled system. The effect of randomly occurring gain fluctuations is taken into account during the controller design. For the purpose of guaranteeing that the closed-loop system is stochastically stable and satisfies the strictly (D1,D2,D3)-γ- dissipative performance, sufficient conditions are constructed by employing the Lyapunov function and stochastic analysis. After linearization, the proposed controller gains are obtained by solving the linear matrix inequalities. Ultimately, a practical example of the dc motor device is used to illustrate the effectiveness of the proposed new design technique.

Performance-Based Assessment of Bridges with Novel SMA-Washer-Based Self-Centering Rocking Piers.

This study discussed a novel self-centering rocking (SCR) bridge system equipped with shape memory alloy (SMA)-based piers, with a particular focus on the benefit of the SCR bridge system in a life-cycle context. The study commences with an introduction of the SCR bridge system; subsequently, a life-cycle loss and resilience assessment framework for the SCR bridge system is presented. Specifically, the seismic fragility, resilience, and life-cycle loss associated with the SCR and conventional bridge systems were addressed. The proposed life-cycle assessment framework was finally applied to two highway bridges with and without SMA washer-based rocking piers, considering the representative hazard scenarios that could happen within the investigated regions. The results revealed that the novel SCR pier bridge system slightly increased the bearing displacement but extensively reduced the pier curvature ductility due to the rocking mechanism. The SCR bridge system kept a lower life-cycle loss level and exhibited more resilient performance than the conventional bridge, especially in the region with higher seismic intensities. Indirect loss can be significantly larger than the direct loss, specifically for the earthquakes with a relatively low probability of occurrence. The SCR bridge system outperformed the conventional system in terms of recovery time, where a quick recovery after an earthquake and drastically decreased the social and economic losses.

N-doped and activated porous biochar derived from cocoa shell for removing norfloxacin from aqueous solution: Performance assessment and mechanism insight.

Environmental pollution has worsened as a result of antibiotic overuse. Nitrogen doping of biochar increases its ability to adsorb antibiotics and has been widely applied as an adsorbent. In this study, we synthesized nitrogen-doped biochar (N-A) from cocoa shell wastes calcined with urea and sodium bicarbonate (NaHCO3) as nitrogen sources and green activators, respectively. An analysis of the biochar morphology, structure, specific surface area, and functional groups provided an understanding of its properties. As indicated by increased surface area, micropores, and surface functional groups, biochar was enhanced in its performance for norfloxacin adsorption when activated using NaHCO3 and nitrogen doped. Adsorption experiments revealed that N-A biochar at 700 and 400 °C had a high adsorption capacity for NOR of 134 mg/g (N-A-CSB700) and 112.31 mg/g (N-A-CSB400) when compared to pristine biochar at 59.27 mg/g (CSB700) and 56.34 mg/g (CSB400), indicating that N-A doped modification on biochar greatly improved adsorption capacity. The Langmuir model demonstrated better NOR adsorption isotherms. The pseudo-second order and Elovich models closely followed the adsorption kinetics. Further investigations were conducted to determine how environmental factors influence biochar interaction with NOR. The results indicated a stable NOR removal efficiency was kept at a wide pH range, whereas the ionic strength inhibited the NOR adsorption process. The investigation into the sorption mechanism revealed that pore filling, H-bonding, π-π EDA interactions, ion exchange, and electrostatic attraction may all be implicated in the NOR adsorption process. Specifically, pore filling played the dominant role for N-A-CSB700, while N-A-CSB400 sorption occurred mainly via H-bonding. Since N-A-CSB700 doped biochar combines high adsorption capacity with a low inhibition effect of environmental factors (Na+/Ca2+), it has a high potential for future practical applications as an environmentally sustainable alternative. It uses low-cost solid waste to produce an adsorbent to cope with emerging contaminants such as antibiotics.

Educational value assessment of YouTube surgical videos of tension-free vaginal tape obturator (TVT-O) and trans-obturator vaginal tape (TOT).

BACKGROUND: YouTube, as a widely used video website around the world, contains a large number of surgical teaching videos, providing a good platform for doctors to learn surgery, but its content and quality are uneven. Tension-free vaginal tape obturator (TVT-O) and trans-obturator vaginal tape (TOT) are common surgical methods for the treatment of stress urinary incontinence (SUI), and there are many videos on YouTube teaching these procedures. We aimed to assess the educational value of surgical videos of TVT-O and TOT on YouTube. METHODS: A comprehensive search was conducted for "tension-free vaginal tape obturator" and "trans-obturator vaginal tape" on YouTube on August 22. After referring to LAParoscopic surgery Video Educational GuidelineS (LAP-VEGaS) and previous studies, we developed a checklist containing 5 major items and 18 minor items. SPSS 26 was applied to data and correlation analysis. RESULTS: A total of 36 videos were assessed. The average number of days available was 1,956.6 days (range, 190-4,152 days) and the average length was 9.7 min (range, 1.8-73.6 min, SD: 13.65). Video definition is divided into high, moderate and low, accounting for 22%, 36% and 42% respectively. The average score of the included videos was 7.39 (range, 3-16, SD: 3.57). The correlation analysis indicated that the video quality score has a certain correlation with the length of the video, but has no significant correlation with other factors and there was no significant correlation between audience likes and other factors. CONCLUSIONS: On YouTube, we still lack high educational value videos about TVT-O and TOT, and the existing videos are deficient in the explanation of critical steps, the key points of patients' perioperative management, and the application of auxiliary teaching tools. This further indicates the importance of improving educational videos of surgery, and an authoritative checklist for urologic surgery.

Educational value assessment of YouTube surgical videos of green light laser vaporization of the prostate.

Background: YouTube is commonly used by doctors to learn surgery. To date, no studies have evaluated the quality of videos on photoselective vaporization of the prostate (PVP) for benign prostatic hyperplasia (BPH) on YouTube. Our aim was to assess the educational value of YouTube videos regarding PVP. Methods: "Green light laser vaporization of the prostate" and "photoselective vaporization of the prostate (PVP)" were searched by 2 authors on YouTube on February 14, 2022. Based on the Laparoscopic Surgery Video Educational Guidelines and previous studies, a checklist that included 4 major and 16 minor items was developed. SPSS version 26 (IBM Corp., Armonk, NY, USA) was used to analyze the data using correlation analysis. Results: A total of 74 surgical videos were assessed. The mean number of days available for educational videos was 2,607 days (range, 156-5,854 days), with the earliest videos dating back to 2006 and the latest to 2021. The average length was 12.69 minutes (range, 0.73-123.7, SD 21.25). The majority of videos originated in the United States, and the video definition was divided into high, moderate, and low, accounting for 21.6%, 66.2%, and 12.2% of the videos, respectively. The average numbers of likes and dislikes for videos were 34.26 (SD 87.96) and 0, respectively. The average score of the videos was 6.65 (range, 2-12, SD 2.79). The correlation analysis indicated that the number of views of these videos was related to the number of online days and likes. The scores of videos were related to the number of likes, and the annual average number of views was related to both the number of views and the number of surgeon likes. Conclusions: There is a lack of high-quality surgical videos of green laser vaporization of the prostate on YouTube. More detailed explanations of the key steps of the operation are needed. We hope that more videos with higher educational value will be published in the future to help surgeons master this technology.

Examining the functional range of commercially available low-cost airborne particle sensors and consequences for monitoring of indoor air quality in residences.

Low-cost airborne particle sensors are gaining attention for monitoring human exposure to indoor particulate matter. This study aimed to establish the concentrations at which these commercially available sensors can be expected to report accurate concentrations. We exposed five types of commercial integrated devices and three types of "bare" low-cost particle sensors to a range of concentrations generated by three different sources. We propose definitions of upper and lower bounds of functional range based on the relationship between a given sensor's output and that of a reference instrument during a laboratory experiment. Experiments show that the lower bound can range from approximately 3 to 15 µg/m3 . At greater concentrations, sensor output deviates from linearity at approximately 300-3000 µg/m3 . We also conducted a simulation campaign to analyze the effect of this limitation on functional range on the accuracy of exposure readings given by these devices. We estimate that the upper bound results in minimal inaccuracy in exposure quantification, and the lower bound can result in as much as a 50% error in approximately 10% of US homes.

A Novel Nanobody Targeting Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Receptor-Binding Domain Has Potent Cross-Neutralizing Activity and Protective Efficacy against MERS-CoV.

The newly emerged Middle East respiratory syndrome coronavirus (MERS-CoV) continues to infect humans and camels, calling for efficient, cost-effective, and broad-spectrum strategies to control its spread. Nanobodies (Nbs) are single-domain antibodies derived from camelids and sharks and are potentially cost-effective antivirals with small size and great expression yield. In this study, we developed a novel neutralizing Nb (NbMS10) and its human-Fc-fused version (NbMS10-Fc), both of which target the MERS-CoV spike protein receptor-binding domain (RBD). We further tested their receptor-binding affinity, recognizing epitopes, cross-neutralizing activity, half-life, and efficacy against MERS-CoV infection. Both Nbs can be expressed in yeasts with high yield, bind to MERS-CoV RBD with high affinity, and block the binding of MERS-CoV RBD to the MERS-CoV receptor. The binding site of the Nbs on the RBD was mapped to be around residue Asp539, which is part of a conserved conformational epitope at the receptor-binding interface. NbMS10 and NbMS10-Fc maintained strong cross-neutralizing activity against divergent MERS-CoV strains isolated from humans and camels. Particularly, NbMS10-Fc had significantly extended half-life in vivo; a single-dose treatment of NbMS10-Fc exhibited high prophylactic and therapeutic efficacy by completely protecting humanized mice from lethal MERS-CoV challenge. Overall, this study proves the feasibility of producing cost-effective, potent, and broad-spectrum Nbs against MERS-CoV and has produced Nbs with great potentials as anti-MERS-CoV therapeutics.IMPORTANCE Therapeutic development is critical for preventing and treating continual MERS-CoV infections in humans and camels. Because of their small size, nanobodies (Nbs) have advantages as antiviral therapeutics (e.g., high expression yield and robustness for storage and transportation) and also potential limitations (e.g., low antigen-binding affinity and fast renal clearance). Here, we have developed novel Nbs that specifically target the receptor-binding domain (RBD) of MERS-CoV spike protein. They bind to a conserved site on MERS-CoV RBD with high affinity, blocking RBD's binding to MERS-CoV receptor. Through engineering a C-terminal human Fc tag, the in vivo half-life of the Nbs is significantly extended. Moreover, the Nbs can potently cross-neutralize the infections of diverse MERS-CoV strains isolated from humans and camels. The Fc-tagged Nb also completely protects humanized mice from lethal MERS-CoV challenge. Taken together, our study has discovered novel Nbs that hold promise as potent, cost-effective, and broad-spectrum anti-MERS-CoV therapeutic agents.

Annual financial impact of thyroidectomies for nodular thyroid disease in China.

A large proportion of patients with thyroid nodules in China undergo thyroidectomy in order to get confirmatory histology diagnosis. The financial impact of this modality remains to be investigated. To evaluate rationality of performing thyroidectomy without a routine FNA preoperatively from the economic perspective, we conducted a retrospective, observational study of all archival thyroidectomies with records of cost per stay (CPS), cost per day (CPD) and length of stay (LOS) from 2008 to 2013 in the First Affiliated Hospital of Nanjing Medical University. We compared all the parameters between cancer and non-cancer thyroidectomies. We recruited 6, 140 thyroidectomies with valid records of CPS, CPD and LOS in this period. The CPS of cancer thyroidectomy was significantly higher than non-cancer thyroidectomy. The percentage of cancer thyroidectomy increased from 26.5% to 41.6%. The percentage of annual cost of cancer thyroidectomies rose from 30.2% to 45.2%. The LOS for cancer and non-cancer thyroidectomy decreased while the CPD increased in the past six years. The estimated national cost in 2012 for all thyroidectomies would be USD 1.86 billion with USD 1.09 billion for non-cancer thyroidectomies. We have witnessed great improvement in the healthcare for patients with thyroid nodules in China. However, given limited healthcare resources, currently thyroid FNA for more precise preoperative diagnosis may help to curb the rapidly increasing demand in healthcare costs in the future for nodular thyroid disease in China.