Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction and Feature Importance Analysis for Severity of COVID-19 in South Korea Using Artificial Intelligence: Model Development and Validation

Background The number of deaths from COVID-19 continues to surge worldwide. In particular, if a patient’s condition is sufficiently severe to require invasive ventilation, it is more likely to lead to death than to recovery. Objective The goal of our study was to analyze the factors related to COVID-19 severity in patients and to develop an artificial intelligence (AI) model to predict the severity of COVID-19 at an early stage. Methods We developed an AI model that predicts severity based on data from 5601 COVID-19 patients from all national and regional hospitals across South Korea as of April 2020. The clinical severity of COVID-19 was divided into two categories: low and high severity. The condition of patients in the low-severity group corresponded to no limit of activity, oxygen support with nasal prong or facial mask, and noninvasive ventilation. The condition of patients in the high-severity group corresponded to invasive ventilation, multi-organ failure with extracorporeal membrane oxygenation required, and death. For the AI model input, we used 37 variables from the medical records, including basic patient information, a physical index, initial examination findings, clinical findings, comorbid diseases, and general blood test results at an early stage. Feature importance analysis was performed with AdaBoost, random forest, and eXtreme Gradient Boosting (XGBoost); the AI model for predicting COVID-19 severity among patients was developed with a 5-layer deep neural network (DNN) with the 20 most important features, which were selected based on ranked feature importance analysis of 37 features from the comprehensive data set. The selection procedure was performed using sensitivity, specificity, accuracy, balanced accuracy, and area under the curve (AUC). Results We found that age was the most important factor for predicting disease severity, followed by lymphocyte level, platelet count, and shortness of breath or dyspnea. Our proposed 5-layer DNN with the 20 most important features provided high sensitivity (90.2%), specificity (90.4%), accuracy (90.4%), balanced accuracy (90.3%), and AUC (0.96). Conclusions Our proposed AI model with the selected features was able to predict the severity of COVID-19 accurately. We also made a web application so that anyone can access the model. We believe that sharing the AI model with the public will be helpful in validating and improving its performance.
COVID-19, Diabetes, and Associated Health Outcomes in China: Results from a Nationwide Survey of 10 545 Adults

Abstract This study examined the associations between diabetes and self-reported/familial COVID-19 infection and investigated health-related outcomes among those with diabetes during China’s nationwide quarantine. The 2020 China COVID-19 Survey was administered anonymously via social media (WeChat). It was completed by 10 545 adults in all of mainland China’s 31 provinces. The survey consisted of 74 items covering sociodemographic characteristics, preventive measures for COVID-19, lifestyle behaviors, and health-related outcomes during the period of quarantine. Regression models examined associations among study variables. Diabetes was associated with a six-fold increased risk of reporting COVID-19 infection among respondents or their family members. Among people with diabetes, individuals who rarely wore masks had double the risk of suspected COVID-19 infection compared with those who always wore masks, with an inverse J-shaped relationship between face mask wearing and suspected COVID-19 infection. People with diabetes tended to have both poor knowledge of COVID-19 and poor compliance with preventive measures, despite perceiving a high risk of personal infection (40.0% among respondents reporting diabetes and 8.0% without diabetes). Only 54–55% of these respondents claimed to consistently practice preventive measures, including wearing face masks. Almost 60% of those with diabetes experienced food or medication shortages during the quarantine period, which was much higher than those without diabetes. Importantly, respondents who experienced medication shortages reported a 63% higher COVID-19 infection rate. Diabetes was associated with an increased risk of self-reported personal and family member COVID-19 infection, which is mitigated by consistent use of face masks.
SKSV: ultrafast structural variation detection from circular consensus sequencing reads

SUMMARY Circular consensus sequencing (CCS) reads are promising for the comprehensive detection of structural variants (SVs). However, alignment-based SV calling pipelines are computationally intensive due to the generation of complete read-alignments and its post-processing. Herein, we propose a SKeleton-based analysis toolkit for Structural Variation detection (SKSV). Benchmarks on real and simulated datasets demonstrate that SKSV has an order of magnitude of faster speed than state-of-the-art SV calling approaches, moreover, it achieves higher F1 scores for various types of SVs. AVAILABILITY SKSV is available from https://github.com/ydLiu-HIT/SKSV. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Starch damage in wheat flours: a comparison of enzymatic, iodometric, and near-infrared reflectance techniques.

Thirty-two flour samples were used to evaluate three methods for determining starch damage: an iodometric method presented by the Tripette/Renaud (Chopin) Company using their SD4 instrument; an enzymatic method marketed by the MegaZyme Company; and a rapid colorimetric method. These methods were compared to the approved AACC method 76-30A and the Farrand method as to their ease of use, precision, and accuracy. For all except the Chopin method, comparative coefficients of determinations (r 2 ) greater than 0.90 were obtained. For the Chopin method, the r 2 value ranged from 0.78 to 0.82, depending on the method used for the comparison. When data for soft wheats were excluded, the Chopin method also had r 2 values of greater than 0.90. In a separate study, damaged starch values were determined on 187 flour samples (covering two crop years) by the appruved AACC and Farrand methods, giving a coefficient of determination of 0.95. The regression equation generated was used to evaluate near-infrared spectroscopy as another method for starch damage determination, and resulted in a coefficient of determination of 0.90 between the laboratory value and the near-infrared predicted values
Draft nuclear genome and complete mitogenome of the Mediterranean corn borer, Sesamia nonagrioides, a major pest of maize

Abstract The Mediterranean corn borer (Sesamia nonagrioides, Noctuidae, Lepidoptera) is a major pest of maize in Europe and Africa. Here, we report an assembly of the nuclear and mitochondrial genome of a pool of inbred males and females third-instar larvae, based on short- and long-read sequencing. The complete mitochondrial genome is 15,330 bp and contains all expected 13 and 24 protein-coding and RNA genes, respectively. The nuclear assembly is 1021 Mb, composed of 2553 scaffolds and it has an N50 of 1105 kb. It is more than twice larger than that of all Noctuidae species sequenced to date, mainly due to a higher repeat content. A total of 17,230 protein-coding genes were predicted, including 15,776 with InterPro domains. We provide detailed annotation of genes involved in sex determination (doublesex, insulin-like growth factor 2 mRNA-binding protein, and P-element somatic inhibitor) and of alpha-amylase genes possibly involved in interaction with parasitoid wasps. We found no evidence of recent horizontal transfer of bracovirus genes from parasitoid wasps. These genome assemblies provide a solid molecular basis to study insect genome evolution and to further develop biocontrol strategies against S. nonagrioides.
Antisocial personality disorder as a predictor of polydrug use: a longitudinal study of the dual mediating roles of deviant peer association and self-control among juvenile offenders

Abstract Background Antisocial personality disorder (APD) has been linked to increased risk for polydrug use (PU). However, there is a dearth of research focusing on the mechanisms underlying this risk. Aims To examine the relationship between APD and PU; to test for the mediating effects of deviant peer association (DVA) and self-control in this relationship; to determine if the magnitudes of observed mediation effects are equivalent. Methods The Pathways to Desistance data were analyzed. Generalized structural equation modeling tested for direct and mediating relationships. Mediation effect equivalence was tested using a Clogg Z test. Results Antisocial personality disorder was associated with increased drug use heterogeneity (coefficient = 0.479; CI = 0.107–0.851). This was significantly mediated by self-control and DVA. The magnitude of the mediation was significantly stronger for the self-control path (self-control coefficient = 0.233; CI = 0.044–0.422; DVA coefficient = 0.134; CI = 0.028–0.241). Conclusion While both self-control and DVA were found to be important for explaining PU in APD, it may be beneficial to focus on self-control to address this problem.
The Integrin Signaling Network Promotes Axon Regeneration via the Src–Ephexin–RhoA GTPase Signaling Axis

Axon regeneration is an evolutionarily conserved process essential for restoring the function of damaged neurons. In Caenorhabditis elegans hermaphrodites, initiation of axon regeneration is regulated by the RhoA GTPase–ROCK (Rho-associated coiled-coil kinase)–regulatory nonmuscle myosin light-chain phosphorylation signaling pathway. However, the upstream mechanism that activates the RhoA pathway remains unknown. Here, we show that axon injury activates TLN-1/talin via the cAMP–Epac (exchange protein directly activated by cAMP)–Rap GTPase cascade and that TLN-1 induces multiple downstream events, one of which is integrin inside-out activation, leading to the activation of the RhoA–ROCK signaling pathway. We found that the nonreceptor tyrosine kinase Src, a key mediator of integrin signaling, activates the Rho guanine nucleotide exchange factor EPHX-1/ephexin by phosphorylating the Tyr-568 residue in the autoinhibitory domain. Our results suggest that the C. elegans integrin signaling network regulates axon regeneration via the Src–RhoGEF–RhoA axis. SIGNIFICANCE STATEMENT The ability of axons to regenerate after injury is governed by cell-intrinsic regeneration pathways. We have previously demonstrated that the Caenorhabditis elegans RhoA GTPase–ROCK (Rho-associated coiled-coil kinase) pathway promotes axon regeneration by inducing MLC-4 phosphorylation. In this study, we found that axon injury activates TLN-1/talin through the cAMP–Epac (exchange protein directly activated by cAMP)–Rap GTPase cascade, leading to integrin inside-out activation, which promotes axonal regeneration by activating the RhoA signaling pathway. In this pathway, SRC-1/Src acts downstream of integrin activation and subsequently activates EPHX-1/ephexin RhoGEF by phosphorylating the Tyr-568 residue in the autoinhibitory domain. Our results suggest that the C. elegans integrin signaling network regulates axon regeneration via the Src–RhoGEF–RhoA axis.
Population pharmacokinetics of free flucloxacillin in patients treated with oral flucloxacillin plus probenecid

Oral flucloxacillin may be coadministered with probenecid to reduce flucloxacillin clearance and increase attainment of pharmacokinetic–pharmacodynamic (PK/PD) targets. The aims of this study were to develop a population PK model of free flucloxacillin when administered orally with probenecid, and to identify optimal dosing regimens for this combination.
How to Select the Lower Instrumented Vertebra in Traditional Growing Rods Index Surgery

ABSTRACT Background: There are still no consensus criteria on how to select the lower instrumented vertebra (LIV) for traditional growing rods (TGRs) at index surgery. The aim was to evaluate whether the criteria used for adolescent idiopathic scoliosis fusion adapts to early onset scoliosis (EOS). Methods: Retrospective analysis of prospectively longitudinal collected data in a consecutive cohort of patients with EOS treated with TGR, expanding from index surgery to 2 years after graduation. The LIV was analyzed regarding its relation to the stable vertebra (SV), substantially touched vertebra (STV), and not STV (NSTV). Failure of LIV selection was considered when revision surgery with distal extension was needed during follow up, due to adding on (ΔLIV tilt > 10°). Results: A total of 25 patients met inclusion criteria. Mean age was 8.6 ± 3 (at index surgery), 15.1 ± 1.8 (at graduation), and 17.8 ± 1.6 (at final follow up). The most frequent LIV at index surgery was L3 (13/25); in 13 cases, STV was selected as LIV; in 7, it was NSTV; and in 5, SV on the standard postero-anterior radiographs. During follow up, a significant increase in the mean LIV tilt (P = .049) and distal junctional angle (P = .017) was found. Nine of the 25 patients (36%) developed adding on: 20% (1/5) of those with LIV at SV, 38.5% (5/13) at STV, and 42.8% (3/7) at NSTV. Of those 9 cases of adding on, only four needed distal extension (mean LIV tilt = 17.6°): 2 STV patients (15.4%), and 2 NSTV patients (28.6%). None of the patients with the LIV chosen at SV needed distal extension due to adding on. Conclusions: The more cranial the selection of the LIV above the SV, the higher the risk of adding on and of revision surgery with distal extension during follow up. Saving motion segments could be justified by choosing STV as LIV because the need for distal extension is not high, and it can be scheduled during lengthening procedures or at graduation surgery. Level of Evidence: 4. Clinical Relevance: Choosing the correct LIV in TGR index surgery is crucial to have a secure distal foundation, control and correct the deformity during growth, and save distal segments to allow growth and mobility.
Polyaniline coated poly(butyl methacrylate) core-shell particles

Polyaniline coated poly(butyl methacrylate) core–shell particles were synthesized and formulated into electrically conductive colloidal inks appropriate for use in roll-to-roll printing. Since the first demonstration of an organic field-effect transistor, a specific interest in fabricating low-cost, large area organic electronics through the exploitation of conventional ink-jet, screen, or roll-to-roll printing technologies has developed. Using a commercial roll-to-roll printing press, interdigitated test figures were printed with the core–shell colloidal ink down to a line thickness of ca. 40 µm. The printed zones exhibited a conductivity of ca. 0.5 Ω−1 cm−1, though this conductivity could be modified by altering the composition of the ink to include more uncoated poly(butyl methacrylate) particles. Heating the printed zone above 35 °C allowed the core to flow, resulting in enhanced mechanical properties of the printed zone.
Overexpression of thioredoxin m in chloroplasts alters carbon and nitrogen partitioning in tobacco

Abstract In plants, there is a complex interaction between carbon (C) and nitrogen (N) metabolism, and its coordination is fundamental for plant growth and development. Here, we studied the influence of thioredoxin (Trx) m on C and N partitioning using tobacco plants overexpressing Trx m from the chloroplast genome. The transgenic plants showed altered metabolism of C (lower leaf starch and soluble sugar accumulation) and N (with higher amounts of amino acids and soluble protein), which pointed to an activation of N metabolism at the expense of carbohydrates. To further delineate the effect of Trx m overexpression, metabolomic and enzymatic analyses were performed on these plants. These results showed an up-regulation of the glutamine synthetase–glutamate synthase pathway; specifically tobacco plants overexpressing Trx m displayed increased activity and stability of glutamine synthetase. Moreover, higher photorespiration and nitrate accumulation were observed in these plants relative to untransformed control plants, indicating that overexpression of Trx m favors the photorespiratory N cycle rather than primary nitrate assimilation. Taken together, our results reveal the importance of Trx m as a molecular mediator of N metabolism in plant chloroplasts.
TRAIL‐Armed ER Nanosomes Induce Drastically Enhanced Apoptosis in Resistant Tumor in Combination with the Antagonist of IAPs (AZD5582)

Although mesenchymal stem cells (MSCs) can be engineered to deliver the TNF‐related apoptosis‐inducing ligand (TRAIL) as an effective anticancer therapy, the clinical application is hampered by the costly manufacturing of therapeutic MSCs. Therefore, it is needed to find an alternative cell‐free therapy. In this study, TRAIL‐armed endoplasmic reticulum (ER)‐derived nanosomes (ERN‐T) are successfully prepared with an average size of 70.6 nm in diameter from TRAIL transduced MSCs. It is demonstrated that the ERN‐T is significantly more efficient for cancer cell killing than the soluble recombinant TRAIL (rTRAIL). AZD5582 is an antagonist of the inhibitors of apoptosis proteins (IAPs), and its combination with ERN‐T induces strikingly enhanced apoptosis in cancerous but not normal cells. AZD5582 sensitizes resistant cancer cells to TRAIL through concomitant downregulation of IAP members like XIAP and the Bcl2 family member Mcl‐1. Intravenously infused ERN‐Ts accumulate in tumors for over 48 h indicating good tumor tropism and retention. The combination of ERN‐T and AZD5582 drastically promotes therapeutic efficacy comparing with the cotreatment by rTRAIL and AZD5582 in a subcutaneous MDA‐MB‐231 xenograft tumor model. The data thus demonstrate that ERN‐T can be a novel cell‐free alternative to TRAIL‐expressing MSC‐based anticancer therapy and its efficacy can be drastically enhanced through combination with AZD5582.
Lordosis Restoration With Midline Minimally Invasive Cortical Trajectory Screws (MidLF) and Transforaminal Interbody Fusion: A Safe Technique With a Short Stay

ABSTRACT Background: The minimally invasive cortical trajectory screw (MidLF) technique has been described accompanied with posterolateral interbody fusion (PLIF). We present our 2-year results of a hybrid technique to show that using transforaminal interbody fusion (TLIF) rather than PLIF in conjunction with MidLF is a less invasive and safe technique. Methods: We retrospectively identified 25 patients who underwent MidLF with TLIF from July 2015 through September 2017. The surgical technique was the same for each, with radiological, clinical, and patient-reported outcome data collected and analyzed at a 2-year follow-up. Results: The cohort showed a mean age of 55 (35–85) years. The length of hospital stay was between 1 and 4 days, with an average of 2.7 days. Postoperatively, lordosis across the motion segment fused increased by a mean of 7.3° (0°–24°), mean pelvic incidence was 53°(31°–80°), and pelvic tilt reduced by an average of 3.5° (0°–11°). The Oswestry Disability Index improved from 34 preoperatively to 19 postoperatively. Visual analogue pain score–leg improved by 4.7 points, from 6 down to 1. One patient showed delayed wound healing. There were no incidences of neurological injury or durotomy. Conclusions: Our data suggests that MidLF with TLIF is both less invasive than traditional techniques and safe. It restores lordosis, requires less exposure and retraction of neural elements than the more widely used PLIF, and shows early discharge and satisfactory medium-term patient-reported outcomes. Level of Evidence: 3. Clinical Relevance: The MidLF technique with PLIF is less invasive than traditional techniques, restores alignment and shows satisfactory medium term results.
Semi-supervised learning for the study of structural formation in colloidal systems via image recognition

The analysis of the structural formation of colloidal systems using machine learning techniques has recently attracted much attention. In many of these studies, local bond-order parameters (LBOPs) were employed as descriptors, where such LBOPs are suitable mainly for the detection of crystal structures. On the other hand, image-based convolutional neural networks (CNNs) are quite effective in detecting not only crystals but also random structures, and the author demonstrated their efficiency in a previous paper. However, in supervised learning, it is difficult to obtain a correct result when there is an unexpected new phase that was unknown when training the CNN. In this paper, we propose a hybrid scheme that consists of supervised and unsupervised learning techniques, employing two different approaches: image-based CNN and generalized LBOP. The proposed method was applied to two-dimensional colloidal systems, and its efficiency was demonstrated.
A model for phenotyping crop fractional vegetation cover using imagery from unmanned aerial vehicles.

Fractional vegetation cover (FVC) is the key trait of interest for characterizing crop growth status in crop breeding and precision management. Accurate quantification of FVC among different breeding lines, cultivars, and growth environments is a challenging task, especially because of the large spatiotemporal variability in complex field conditions. This study presents an ensemble modeling strategy for phenotyping crop FVC from unmanned aerial vehicle (UAV)-based multispectral images by coupling PROSAIL with gap probability model (PROSAIL-GP). Seven field experiments for four main crops were conducted, and canopy images were acquired using a UAV platform equipped with RGB and multispectral cameras. The PROSAIL-GP model successfully retrieved FVC in oilseed rape (Brassica napus L.) with coefficient of determination, root mean square error (RMSE), and relative RMSE (rRMSE) of 0.79, 0.09, and 18%, respectively. The robustness of the proposed method was further examined with rice (Oryza sativa L.), wheat (Triticum aestivum L.), and cotton (Gossypium hirsutum L.), and the high accuracy of FVC retrieval was obtained with rRMSE of 12%, 6%, and 6%, respectively. The findings suggest that the proposed method can efficiently retrieve crop FVC from UAV images at a high spatiotemporal domain, which would be a promising tool for precision crop breeding.
Examination of Cancer and Aging Through Activities of Daily Living: A National Health and Aging Trends Study Analysis

Objectives: This study longitudinally examined how older adult cancer survivors perceive disability in activities of daily living over time compared to older adults who have not had cancer. Methods: This was a secondary analysis of the National Health and Aging Trends Study examining participants with a new cancer diagnosis and age-, gender-, and comorbidity-matched comparison participants without a history of cancer. Generalized linear mixed models examined time and group interaction and main effects in disability. Results: There was a significant main effect of time (F 4,771 = 12.81; p < .0001) demonstrating increasing disability levels for both groups. There were significant group differences, with higher disability in the cancer group than the comparison group (β = 0.628, SE = 0.263; t = 2.39, p = 0.017). Discussion: Although perceived disability was greater immediately following cancer diagnosis, older adult cancer survivors and comparison participants appear to have similar perceived disability over time.