Miracle-dz/UniFAR-FTUs huggingface dataset:
Local climate adaptation and gene flow in the native range of two co‐occurring fruit moths with contrasting invasiveness

Invasive species pose increasing threats to global biodiversity and ecosystems. While previous studies have characterized successful invaders based on ecological traits, characteristics related to evolutionary processes have rarely been investigated. Here we compared gene flow and local adaptation using demographic analyses and outlier tests in two co‐occurring moth pests across their common native range of China, one of which (the peach fruit moth, Carposina sasakii) has maintained its native distribution, while the other (the oriental fruit moth, Grapholita molesta) has expanded its range globally during the past century. We found that both species showed a pattern of genetic differentiation and an evolutionary history consistent with a common southwestern origin and northward expansion in their native range. However, for the noninvasive species, genetic differentiation was closely aligned with the environment, and there was a relatively low level of gene flow, whereas in the invasive species, genetic differentiation was associated with geography. Genome scans indicated stronger patterns of climate‐associated loci in the noninvasive species. While strong local adaptation and reduced gene flow across its native range may have decreased the invasiveness of C. sasakii, this requires further validation with additional comparisons of invasive and noninvasive species across their native range.
Genetic and phenotypic parameters for Aleutian disease tests and their correlations with pelt quality, reproductive performance, packed-cell volume, and harvest length in mink.

Aleutian disease (AD), caused by the Aleutian mink disease virus (AMDV), is a major health concern that results in global economic losses to the mink industry. The unsatisfactory outcome of the culling strategy, immunoprophylaxis, and medical treatment in controlling AD have urged mink farmers to select AD resilient mink based on several detection tests, including enzyme-linked immunosorbent assay (ELISA), counterimmunoelectrophoresis (CIEP), and iodine agglutination test (IAT). However, the genetic analysis of these AD tests and their correlations with pelt quality, reproductive performance, packed-cell volume (PCV), and harvest length (HL) have not been investigated. In this study, data on 5,824 mink were used to estimate the genetic and phenotypic parameters of four AD tests, including two systems of ELISA, CIEP, and IAT, and their genetic and phenotypic correlations with two pelt quality, five female reproductive performance, PCV, and HL traits. Significances (P<0.05) of fixed effects (sex, year, dam age, and color type), covariates (age at harvest and blood sampling ), and random effects (additive genetic, permanent environmental, and maternal effects) were determined under univariate models using ASReml 4.1 software. The genetic and phenotypic parameters for all traits were estimated under bivariate models using ASReml 4.1 software. Estimated heritabilities (±SE) were 0.39±0.06, 0.61±0.07, 0.11±0.07, and 0.26±0.05 for AMDV antigen-based ELISA (ELISA-G), AMDV capsid protein-based ELISA, CIEP, and IAT, respectively. The ELISA-G also showed a moderate repeatability (0.58±0.04) and had significant negative genetic correlations (±SE) with reproductive performance traits (from -0.41±0.16 to -0.49±0.12), PCV (-0.53±0.09), and HL (-0.45±0.16). These results indicated that ELISA-G had the potential to be applied as an indicator trait for genetic selection of AD resilient mink in AD endemic ranches, and therefore help mink farmers to reduce the adverse effects caused by AD.
Progression in Moyamoya Disease: Clinical Features, Neuroimaging Evaluation, and Treatment

Moyamoya disease (MMD) is a chronic cerebrovascular disease characterized by progressive stenosis of the arteries of the circle of Willis, with the formation of collateral vascular network at the base of the brain. Its clinical manifestations are complicated. Numerous studies have attempted to clarify the clinical features of MMD, including its epidemiology, genetic characteristics, and pathophysiology. With the development of neuroimaging techniques, various neuroimaging modalities with different advantages have deepened the understanding of MMD in terms of structural, functional, spatial, and temporal dimensions. At present, the main treatment for MMD focuses on neurological protection, cerebral blood flow reconstruction, and neurological rehabilitation, such as pharmacological treatment, surgical revascularization, and cognitive rehabilitation. In this review, we discuss recent progress in understanding the clinical features, in the neuroimaging evaluation and treatment of MMD.
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database

Abstract Post-translational modifications (PTMs) are ubiquitous and essential for protein function and signaling, motivating the need for sustainable benefit and open models of web databases. Highly conserved O-GlcNAcylation is a case example of one of the most recently discovered PTMs, investigated by a growing community. Historically, details about O-GlcNAcylated proteins and sites were dispersed across literature and in non-O-GlcNAc-focused, rapidly outdated or now defunct web databases. In a first effort to fill the gap, we recently published a human O-GlcNAcome catalog with a basic web interface. Based on the enthusiasm generated by this first resource, we extended our O-GlcNAcome catalog to include data from 42 distinct organisms and released the O-GlcNAc Database v1.2. In this version, more than 14 500 O-GlcNAcylated proteins and 11 000 O-GlcNAcylation sites are referenced from the curation of 2200 publications. In this article, we also present the extensive features of the O-GlcNAc Database, including the user-friendly interface, back-end and client–server interactions. We particularly emphasized our workflow, involving a mostly automatized and self-maintained database, including machine learning approaches for text mining. We hope that this software model will be useful beyond the O-GlcNAc community, to set up new smart, scientific online databases, in a short period of time. Indeed, this database system can be administrated with little to no programming skills and is meant to be an example of a useful, sustainable and cost-efficient resource, which exclusively relies on free open-source software elements (www.oglcnac.mcw.edu).
Association of serum vitamin D levels with disease severity, systemic inflammation, prior lung function loss and exacerbations in a cohort of patients with chronic obstructive pulmonary disease (COPD)

Background Vitamin D deficiency has been associated with chronic disorders including chronic obstructive pulmonary disease (COPD) but the relationships with inflammation, exacerbations and disease progression remain unclear. Methods In this monocentric cross-sectional observational study we analyzed the disease status, systemic inflammation, prior exacerbation frequency and loss in lung function in relation to serum 25-hydroxyvitamin D (25-OHD) levels in a cohort of 94 patients with COPD. Serum 25-OHD, C-reactive protein, interleukin-6 and tumor necrosis factor-α were quantified. Exacerbation frequencies and sunlight exposure were assessed. These parameters were analyzed in correlation to the current forced expiratory volume in 1 s (FEV1), the individual average 3-year FEV1 decline and the Global Initiative for Chronic Obstructive Lung Disease (GOLD) stage. Results We observed fair correlation between serum 25-OHD and the current FEV1 (r=0.38, P<0.001). Furthermore, mean serum 25-OHD was significantly altered between patients of GOLD stages I–IV (P=0.013). There was weak negative correlation of 25-OHD and the average annual change of the FEV1 (r=−0.26, P<0.05). Furthermore, we observed fair negative correlation between 25-OHD and C-reactive protein (r=−0.32, P<0.01) as well as weak negative correlation with interleukin-6 (r=−0.23, P<0.05). While the exacerbation frequency significantly differed between GOLD stages (P=0.04), there was no direct association between exacerbations and 25-OHD levels. Conclusion Our data confirm frequent vitamin D deficiency in COPD and point out correlations between 25-OHD levels, systemic inflammation, disease severity and progression.
Phylogenomics and biogeography of Cunoniaceae (Oxalidales) with complete generic sampling and taxonomic realignments

Premise Cunoniaceae are a family of shrubs and trees with 27 genera and ca. 335 species, mostly confined to tropical and wet temperate zones of the southern hemisphere. There are several known issues regarding generic limits, and the family also displays a number of intriguing long‐range disjunctions. Methods We performed a phylogenomic study using the universal Angiosperms353 probe set for targeted sequence capture. We sampled 37 species covering all genera in the Cunoniaceae, and those in the three closely related families of the crown Oxalidales (Brunelliaceae, Cephalotaceae, and Elaeocarpaceae). We also performed analyses for molecular dating and ancestral area reconstruction. Results We recovered the topology (Cunoniaceae, (Cephalotaceae, (Brunelliaceae, Elaeocarpaceae))) and a well‐resolved genus‐level phylogeny of Cunoniaceae with strongly supported clades corresponding to all previously recognized tribes. As previously suspected, the genera Ackama and Weinmannia were recovered as paraphyletic. Australasia was inferred as the likely ancestral area for the family. Conclusions The current distribution of Cunoniaceae is best explained by long‐distance dispersal with a few possible cases of Australasian–American vicariance events. Extinctions may have been important in determining the mostly Oceanian distribution of this family while some genera in the tribe Cunonieae and in New Caledonia have undergone recent bursts of diversification. New generic diagnoses, 80 new combinations, and one new name are provided for a recircumscribed Ackama (including Spiraeopsis), a much smaller Weinmannia (mostly New World), and a resurrected Pterophylla to accommodate Old World taxa previously in Weinmannia.
Boosting with heterologous vaccines effectively improves protective immune responses of the inactivated SARS-CoV-2 vaccine

ABSTRACT Since the outbreak of COVID-19, a variety of vaccine platforms have been developed. Amongst these, inactivated vaccines have been authorized for emergency use or conditional marketing in many countries. To further enhance the protective immune responses in populations that have completed vaccination regimen, we investigated the immunogenic characteristics of different vaccine platforms and tried homologous or heterologous boost strategy post two doses of inactivated vaccines in a mouse model. Our results showed that the humoral and cellular immune responses induced by different vaccines when administered individually differ significantly. In particular, inactivated vaccines showed relatively lower level of neutralizing antibody and T cell responses, but a higher IgG2a/IgG1 ratio compared with other vaccines. Boosting with either recombinant subunit, adenovirus vectored or mRNA vaccine after two-doses of inactivated vaccine further improved both neutralizing antibody and Spike-specific Th1-type T cell responses compared to boosting with a third dose of inactivated vaccine. Our results provide new ideas for prophylactic inoculation strategy of SARS-CoV-2 vaccines.
The effect of the enhanced recovery after surgery program on lung cancer surgery: a systematic review and meta-analysis

Background Lung cancer is one of the most common causes of cancer-related death worldwide. The enhanced recovery after surgery (ERAS) program is an effective evidence-based multidisciplinary protocol of perioperative care. However, the roles of ERAS in lung cancer surgery remain unclear. This systematic review and meta-analysis aimed to investigate the short-term impact of the ERAS program on lung resection surgery, especially in relation to postoperative complications. Methods A systematic literature search of PubMed, EMBASE, and the Cochrane Library databases until October 2020 was performed to identify the studies that implemented an ERAS program in lung cancer surgery. The studies were selected and subjected to data extraction by 2 reviewers independently, which was followed by quality assessment. A random effects model was used to calculate overall effect sizes. Risk ratio (RR), risk difference (RD), and standardized mean difference (SMD) with 95% confidence interval (CI) served as the summary statistics for meta-analysis. Subgroup analysis and sensitivity analysis were subsequently performed. Results A total of 21 studies with 6,480 patients were included. The meta-analysis indicated that patients in the ERAS group had a significantly reduced risk of postoperative complications (RR =0.64; 95% CI: 0.52 to 0.78) and shortened postoperative length of stay (SMD=−1.58; 95% CI: −2.38 to −0.79) with a significant heterogeneity. Subgroup analysis showed that the risks of pulmonary (RR =0.58; 95% CI: 0.45 to 0.75), cardiovascular (RR =0.73; 95% CI: 0.59 to 0.89), urinary (RR =0.53; 95% CI: 0.32 to 0.88), and surgical complications (RR =0.64; 95% CI: 0.42 to 0.97) were significantly lower in the ERAS group. No significant reduction was found in the in-hospital mortality (RD =0.00; 95% CI: −0.01 to 0.00) and readmission rate (RR =1.00; 95% CI: 0.76 to 1.32). In the qualitative review, most of the evidence reported significantly decreased hospitalization costs in the ERAS group. Conclusions The implementation of an ERAS program for surgery of lung cancer can effectively reduce risks of postoperative complications, length of stay, and costs of patients who have undergone lung cancer surgery without compromising their safety.
Value of radiomics model based on multi-parametric magnetic resonance imaging in predicting epidermal growth factor receptor mutation status in patients with lung adenocarcinoma

Background The epidermal growth factor receptor (EGFR) is an important therapeutic target for patients with non-small-cell lung cancer (NSCLC). Radiomics and radiogenomics have emerged as attractive research topics aiming to extract mineable high-dimensional features from medical images and show potential to correlate with the gene mutation. Herein, we aim to develop a magnetic resonance imaging (MRI)-based radiomics model for pretreatment prediction of the EGFR status in patients with lung adenocarcinoma. Methods A total of 92 patients with pathologically confirmed lung adenocarcinoma were retrospectively enrolled in this study. EGFR genotype was analyzed by sequence testing. All patients were randomized into training and test group in a 7:3 ratio using the R software. Radiomics features were extracted from T2 weighted imaging (T2WI), diffusion-weighted imaging (DWI), and apparent diffusion coefficient (ADC); radiomics signatures were built using the least absolute shrinkage and selection operator (LASSO) and logistic regression. Preoperative clinical factors and image features associated with EGFR were also evaluated. A nomogram including sex, smoking status, and radiomics signatures was constructed. A total of five radiomics models were built, and the area under the curve (AUC) was used to evaluate their performance of EGFR mutation prediction. Results Among the three single-sequence models, the ADC model showed the best prediction performance. The AUCs of the ADC, DWI, T2WI prediction model in the test cohort were 0.805 (95% CI: 0.610 to 1.000), 0.722 (95% CI: 0.519 to 0.924), and 0.655 (95% CI: 0.438 to 0.872), respectively. Compared with the single-sequence model, the multi-sequence prediction model showed better performed [AUCtest =0.838 (95% CI: 0.685 to 0.992)]. The AUC of the nomogram in the training group was 0.925 (95% CI: 0.855 to 0.994) and 0.727 (95% CI: 0.531 to 0.924) in the test group, respectively. Conclusions The radiomics model based on MRI might have the potential to predict EGFR mutation in patients with lung adenocarcinoma. The multi-sequence model had better performance than other models.
Psychological distress in the context of the COVID-19 pandemic: the joint contribution of intolerance of uncertainty and cyberchondria

Abstract Objective To explore the direct and indirect associations between intolerance of uncertainty, health anxiety (HA), and psychological distress through problematic internet use (PIU) and cyberchondria, both before and during the first months of the COVID-19 pandemic. Design Two Italian samples were enrolled via an online questionnaire. Sample 1 (N = 556; 69.3% females, Mage 29.6 years, SD = 13.2) was recruited in non-pandemic times, whereas Sample 2 (N = 575; 74% females, Mage 31.9 years, SD = 13.4) was recruited during the COVID-19 lockdown. Main outcome measures Self-report measures assessing HA and psychological distress. Results Two distinct path analyses showed that intolerance of uncertainty was directly associated with HA and psychological distress in both samples. Moreover, cyberchondria partially mediated the relationship between intolerance of uncertainty and HA and PIU partially mediated the relationship between intolerance of uncertainty and psychological distress in both samples. The link between cyberchondria and psychological distress was significant in Sample 2 but non-significant in Sample 1. The model accounted for a substantial variance of HA and psychological distress in both samples. Conclusion Our findings suggest that problematic online behaviors might exacerbate the negative consequences of intolerance of uncertainty in terms of higher levels of HA and psychological distress both in pandemic and non-pandemic contexts.
Simplifying ignition delay prediction for homogeneous charge compression ignition engine design and control

Advanced combustion engine concepts, such as the homogeneous charge compression ignition engine, rely on chemical kinetics for their proper operation. Accurate prediction and control of auto ignition time scales are therefore key issues. Real-time prediction and control of ignition using detailed chemical kinetic models is difficult due to the large size of such mechanisms that calls for high computational costs. Ignition models in the form of correlations can overcome these challenges, as long as they are able to predict the time scales that would be obtained using a detailed chemical kinetic model. In this work, a correlation approach based on detailed chemical models is used to simplify the determination of chemical time scales associated with kinetically controlled combustion events. Detailed combustion mechanisms for biodiesel surrogate (methyl decanoate), gasoline surrogates (isooctane/n-heptane/toluene), bio-alcohol (n-octanol) and ethanol/gasoline surrogate blends from the literature are used to generate ignition databases for correlation development, taking into account complex ignition behavior such as pressure-dependent limits of negative temperature coefficient kinetics. We further employ the Livengood–Wu integral method to assess the ability of the resulting correlations to predict ignition in cases where the temperature and pressure are changing prior to ignition. The integral method is compared with results of a single-zone adiabatic homogeneous charge compression ignition engine model simulation using the detailed chemical kinetic model. It is found that the simplified correlations accurately reproduce the predictions of the detailed chemical kinetic models at an insignificant computational cost relative to the detailed simulations. The correlation approach presented here can also be applied to experimental ignition data, as far as these are obtained in a manner that covers a wide range of the relevant parameters with minimal experimental uncertainties. This work enables the incorporation of realistic chemical kinetic effects in the computational analysis and control of kinetically controlled combustion systems.
An evaluation of the reporting quality in clinical practice guidelines for hepatocellular carcinoma using the RIGHT checklist

Background Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide. Clinical practice guidelines (CPGs) on the prevention, surveillance, diagnosis and management of HCC are essential to guide clinical practice. The objective of this study was to evaluate the reporting quality of the most recent CPGs for HCC published worldwide. Methods We systematically searched literature databases and websites of guideline development organizations and medical associations to extract CPGs on HCC published between January 2018 and December 2020. We evaluated the reporting quality using the Reporting Items for practice Guidelines in Healthcare (RIGHT) statement. We assessed for each of the 35 RIGHT checklist items whether the guidelines reported the corresponding information. We calculated the mean (± standard error of the mean, SEM) percentages of the guidelines’ compliance with the items (reporting rate), both overall and for each of the seven domains of the RIGHT checklist. Results We identified 22 guidelines, of which three (14%) were written in Chinese and 19 (86%) in English. The mean ±SEM overall reporting rate in the twenty-two guidelines was 56%±4%. The reporting rates of the seven domains were the following: basic information 81%±3%, background 58%±6%, evidence 58%±6%, recommendations 59%±5%, review and quality assurance 34%±10%, funding and declaration and management of interests 39%±4%, and other information 23%±6%. Conclusions The reporting quality of the recently published guidelines for HCC was suboptimal. While there is no doubt about the great value of the CPGs’ recommendations in clinical practice, the reporting in CPGs for HCC still needs improvement.
Phase II single-arm study of brentuximab vedotin in Chinese patients with relapsed/refractory classical Hodgkin lymphoma or systemic anaplastic large cell lymphoma

ABSTRACT Background Relapsed/refractory (R/R) classical HL (cHL) and systemic anaplastic large-cell lymphoma (sALCL) treatment options are limited in China. There is a need for new therapies. Research design and methods This single-arm, open-label, multicenter, Phase II study assessed efficacy, safety, and pharmacokinetics of single-agent brentuximab vedotin in Chinese patients with R/R cHL or sALCL. Patients received brentuximab vedotin 1.8 mg/kg by intravenous infusion on Day 1 of 3-week cycles (maximum 16 cycles). Results Patients (N = 39) received a median of 10 cycles (range: 2–16) of brentuximab vedotin. The objective response rate was 69% (95% CI: 52–83%), with 27 patients achieving objective responses (complete response: n = 11 [28%]; partial response: n = 16 [41%]). Median duration of response, progression-free survival and overall survival were 12.1 months, 13.5 months (95% CI: 6.8 months–not estimable) and not reached after a median follow-up of 16.6 months. Brentuximab vedotin was well tolerated with no on-study deaths. AEs were generally manageable and reversible. No new safety signals were identified. Pharmacokinetics were consistent with those previously described in Western populations. Conclusion Brentuximab vedotin had a positive benefit–risk profile for Chinese patients with R/R cHL or sALCL, confirming it as a potential treatment option. Clinical trial registration www.clinicaltrials. gov identifier is NCT02939014.