Improved seed health tests for Xanthomonas axonopodis pv. phaseoli in common bean

Xanthomonas axonopodis pv. phaseoli and X. axonopodis pv. phaseoli var. fuscans are important seedborne pathogens of Phaseolus vulgaris. In order to maintain seed quality and meet phytosanitary requirements, accurate seed health testing methods are critical. Currently employed selective-media-based methods for these pathogens include several variations in extraction procedures. In order to optimize pathogen extraction from P. vulgaris seeds, we assessed the influence of different extraction steps on the sensitivity of X. axonopodis pv. phaseoli detection, including incubation time/temperature, vacuum extraction and centrifugation of seed extract. The results showed that vacuum extraction and centrifugation of seed extracts increased sensitivity, and the highest sensitivity was obtained with the 3-hour vacuum extraction at room temperature followed by centrifugation. These results were confirmed on seventy 1000-seed subsamples from 14 different naturally infested seedlots. Our results suggest that a 3-hour vacuum extraction followed by centrifugation would be a valuable modification of the current method approved by the International Seed Testing Association (ISTA). Based on DNA sequence information from RAPD fragments generated from X. axonopodis pv.phaseoli and X. axonopodis pv.phaseoli var. fuscans, real-time PCR methods were developed for detection and quantification of the pathogens in or on seeds. Assay specificity was tested against DNA of several Xanthomonas species and pathovars of X. axonopodis. None of the closely related Xanthomonas strains were amplified using this PCR assay. The detection limit of the TaqMan assay for purified DNA and cells was 20 fg and 20 CFU per 25 μl PCR reaction mixture, respectively. A linear model was developed for seed contamination level in relation to amplification cycles based on sensitivity tests on seed samples spiked with inoculated seeds. seedlots On naturally infested Phaseolus vulgaris seedlots, real-time PCR detection was more sensitive than the selective medium assay. Real-time PCR should be useful for rapid, highly sensitive and specific detection of these seedborne pathogens to ensure seed quality control and meet phytosanitary regulations. To my knowledge this is the first published real-time PCR assay developed for X. axonopodis pv. phaseoli and X. axonopodis pv. phaseoli var. fuscans. Seed transmission frequency and survival in storage were compared between both common blight pathogens from different geographic origins. Xanthomonas axonopodis pv. phaseoli var. fuscans isolates had a higher percentage of seed-seedling transmission than X. axonopodis pv. phaseoli isolates (P\u3c0.001). Both variants reduced seedling emergence compared to the noninoculated control, and X. axonopodis pv. phaseoli var. fuscans isolates reduced seedling emergence more than X. axonopodis pv. phaseoli (P\u3c0.001). The incidence of bacterial blight symptoms was higher in seedlings from X. axonopodis pv. phaseoli var. fuscans inoculated seeds than in seedlings from seeds inoculated with X. axonopodis pv. phaseoli (P\u3c0.001). Real-time PCR showed that a higher percentage of seedlings were infected with X. axonopodis pv. phaseoli var. fuscans than X. axonopodis pv. phaseoli. PCR results also revealed symptomless infection of seedlings. Survival (population size) of both bacteria on stored seeds was monitored over time using real-time PCR. Survival did not differ significantly between the two variants and real-time PCR gave higher population size estimates than a culture plating test after three months in storage (P\u3c0.05)

Artifact Restoration in Histology Images with Diffusion Probabilistic Models

Histological whole slide images (WSIs) can be usually compromised by artifacts, such as tissue folding and bubbles, which will increase the examination difficulty for both pathologists and Computer-Aided Diagnosis (CAD) systems. Existing approaches to restoring artifact images are confined to Generative Adversarial Networks (GANs), where the restoration process is formulated as an image-to-image transfer. Those methods are prone to suffer from mode collapse and unexpected mistransfer in the stain style, leading to unsatisfied and unrealistic restored images. Innovatively, we make the first attempt at a denoising diffusion probabilistic model for histological artifact restoration, namely ArtiFusion.Specifically, ArtiFusion formulates the artifact region restoration as a gradual denoising process, and its training relies solely on artifact-free images to simplify the training complexity.Furthermore, to capture local-global correlations in the regional artifact restoration, a novel Swin-Transformer denoising architecture is designed, along with a time token scheme. Our extensive evaluations demonstrate the effectiveness of ArtiFusion as a pre-processing method for histology analysis, which can successfully preserve the tissue structures and stain style in artifact-free regions during the restoration. Code is available at https://github.com/zhenqi-he/ArtiFusion.Comment: Accepted by MICCAI202

The existence of positive solution for an elliptic problem with critical growth and logarithmic perturbation

We consider the existence and nonexistence of positive solution for the following Br\'ezis-Nirenberg problem with logarithmic perturbation: \begin{equation*} \begin{cases} -\Delta u={\left|u\right|}^{{2}^{\ast }-2}u+\lambda u+\mu u\log {u}^{2} &x\in \Omega, \quad \;\:\, u=0& x\in \partial \Omega, \end{cases} \end{equation*} where $\Omega$ $\subset$ $\R^N$ is a bounded smooth domain, $\lambda, \mu \in \R$, $N\ge3$ and ${2}^{\ast }:=\frac{2N}{N-2}$ is the critical Sobolev exponent for the embedding $H^1_{0}(\Omega)\hookrightarrow L^{2^\ast}(\Omega)$. The uncertainty of the sign of $s\log s^2$ in $(0, +\infty)$ has some interest in itself. We will show the existence of positive ground state solution which is of mountain pass type provided $\lambda\in \R, \mu>0$ and $N\geq 4$. While the case of $\mu<0$ is thornier. However, for $N=3,4$ $\lambda\in (-\infty, \lambda_1(\Omega))$, we can also establish the existence of positive solution under some further suitable assumptions. And a nonexistence result is also obtained for $\mu<0$ and $-\frac{(N-2)\mu}{2}+\frac{(N-2)\mu}{2}\log(-\frac{(N-2)\mu}{2})+\lambda-\lambda_1(\Omega)\geq 0$ if $N\geq 3$. Comparing with the results in Br\'ezis, H. and Nirenberg, L. (Comm. Pure Appl. Math. 1983), some new interesting phenomenon occurs when the parameter $\mu$ on logarithmic perturbation is not zero

Breaking up with my idol: A qualitative study of the psychological adaptation process of renouncing fanship

Introduction:This study aimed to explore the psychological adaptation process of renouncing fanship due to para-loveshock in the context of fandom culture.MethodsWe adopted netnography to explore social media platforms used by fans in China (Weibo, WeChat, and Douban) as research fields for 3 years.Results(1) The process of “breaking up with” or renouncing an idol can be divided into three phases: the resistance phase with acute stress, the negotiation phase with bargaining, and the recovery phase with attachment reconstruction. In the resistance phase, fans displayed acute stress responses due to loveshock in psychological, physical, and behavioral aspects. In the negotiation phase, fans faced four barriers to renouncement: cognitive dissonance, emotional attachment, behavioral dependence, and social threat. They bargained within the three types of cognitive framework before deciding to “leave” or “re-follow” their idol. In the recovery phase, fans adopted two types of strategies to promote recovery: healing the past and facing the future. Healing the past involved public outcry, sharing their breakup plans, cognitive reconstruction, and seeking closure to the fan role. Facing the future involved switching environments, seeking new interests, and inhibiting the re-intrusion of trauma cues. (2) Internal factors affecting the psychological adaptation process of renouncement include the level of initiative, attribution styles, experience, attachment status and core belief systems, and alternative lifestyles; external factors include social support, peer pressure from the fan community, life stressors, and types and impact of traumatic events. (3) Based on the two dimensions of orientation and commitment, fans were classified into four types: short-term rational, short-term passionate, bounded loyal, and unconditionally loyal, corresponding to non-traumatic, stressful, accumulated, and traumatic breakup processes, respectively. (4) The post-renouncement growth of fans mainly manifested in the development of mental modes, coping skills toward trauma, emotional adaptation experience, and behavior patterns.ImplicationsThis investigation of the recovery process from para-loveshock after renouncement of fanship can provide theoretical and practical insights into the development of psychological resilience for fans, reduction of the psychological distress and negative outcomes, and public governance on social media platform and cyber pop culture industry

Achieving short-cut nitrification and denitrification in modified intermittently aerated constructed wetland

This study aim to enhance nitrogen removal performance via shifting nitrogen removal pathway from nitrate to nitrite pathway. It was demonstrated that nitrite pathway was successfully and stably achieved in CWs by using modified intermittent aeration control with aeration 20 min/non-aeration 100 min and reducing DO concentration during aeration, nitrite in the effluent could accumulate to over 70% of the total oxidized nitrogen. Q-PCR analysis showed that nitrifying microbial communities were optimized under the alternating anoxic and aerobic conditions, ammonia oxidizing bacteria increased from 7.15 x 10(6) to 8.99 x 10(6) copies/g, while nitrite oxidizing bacteria decreased approximately threefold after 234 days operation. Most importantly, high nitrogen removal efficiency with ammonium removal efficiency of 94.6%, and total nitrogen removal efficiency of 82.6% could be achieved via nitrite pathway even under carbon limiting conditions. In comparison to the nitrate pathway, the nitrite pathway could improve the TN removal by about 55%. (C) 2017 Elsevier Ltd. All rights reserved.</p

Pathogenic Mutations in Cancer-Predisposing Genes: A Survey of 300 Patients with Whole-Genome Sequencing and Lifetime Electronic Health Records

Background: It is unclear whether and how whole-genome sequencing (WGS) data can be used to implement genomic medicine. Our objective is to retrospectively evaluate whether WGS can facilitate improving prevention and care for patients with susceptibility to cancer syndromes. Methods and Findings: We analyzed genetic mutations in 60 autosomal dominant cancer-predisposition genes in 300 deceased patients with WGS data and nearly complete long-term (over 30 years) medical records. To infer biological insights from massive amounts of WGS data and comprehensive clinical data in a short period of time, we developed an in-house analysis pipeline within the SeqHBase software framework to quickly identify pathogenic or likely pathogenic variants. The clinical data of the patients who carried pathogenic and/or likely pathogenic variants were further reviewed to assess their clinical conditions using their lifetime EHRs. Among the 300 participants, 5 (1.7%) carried pathogenic or likely pathogenic variants in 5 cancer-predisposing genes: one in APC, BRCA1, BRCA2, NF1, and TP53 each. When assessing the clinical data, each of the 5 patients had one or more different types of cancers, fully consistent with their genetic profiles. Among these 5 patients, 2 died due to cancer while the others had multiple disorders later in their lifetimes; however, they may have benefited from early diagnosis and treatment for healthier lives, had the patients had genetic testing in their earlier lifetimes. Conclusions: We demonstrated a case study where the discovery of pathogenic or likely pathogenic germline mutations from population-wide WGS correlates with clinical outcome. The use of WGS may have clinical impacts to improve healthcare delivery

Personalized Prompt for Sequential Recommendation

Pre-training models have shown their power in sequential recommendation. Recently, prompt has been widely explored and verified for tuning in NLP pre-training, which could help to more effectively and efficiently extract useful knowledge from pre-training models for downstream tasks, especially in cold-start scenarios. However, it is challenging to bring prompt-tuning from NLP to recommendation, since the tokens in recommendation (i.e., items) do not have explicit explainable semantics, and the sequence modeling should be personalized. In this work, we first introduces prompt to recommendation and propose a novel Personalized prompt-based recommendation (PPR) framework for cold-start recommendation. Specifically, we build the personalized soft prefix prompt via a prompt generator based on user profiles and enable a sufficient training of prompts via a prompt-oriented contrastive learning with both prompt- and behavior-based augmentations. We conduct extensive evaluations on various tasks. In both few-shot and zero-shot recommendation, PPR models achieve significant improvements over baselines on various metrics in three large-scale open datasets. We also conduct ablation tests and sparsity analysis for a better understanding of PPR. Moreover, We further verify PPR's universality on different pre-training models, and conduct explorations on PPR's other promising downstream tasks including cross-domain recommendation and user profile prediction

Prevalence and clustering of metabolic risk factors for type 2 diabetes among Chinese adults in Shanghai, China

<p>Abstract</p> <p>Background</p> <p>Type 2 diabetes is becoming an epidemic in China. To evaluate the prevalence, clustering of metabolic risk factors and their impact on type 2 diabetes, we conducted a population-based study in Shanghai, China's largest metropolitan area.</p> <p>Methods</p> <p>From 2006 to 2007, 2,113 type 2 diabetes cases and 2,458 comparable controls of adults aged 40 to 79 years were enrolled. Demographic, lifestyle, and dietary factors were assessed via standardized questionnaires. Plasma, red and white blood cells were collected and stored for future studies. Anthropometric indices and biochemical intermediates (including blood pressure, fasting glucose, glycosylated hemoglobin, and blood lipids) were measured. The prevalence of metabolic syndrome were also compared following two criteria recommended by the Chinese Diabetes Society (CDS, 2004) and the National Cholesterol Education Program's Adult Treatment Panel III (ATP III, 2002).</p> <p>Results</p> <p>Prevalence of metabolic syndrome (62% vs. 15% using CDS criteria) and its individual components, including obesity (51% vs. 42%), hypertension (54% vs. 41%), hypertriglyceridemia (42% vs. 32%), and low high-density lipoprotein-cholesterol (HDL) levels (36% vs. 25%) were higher in diabetes cases than controls. Regardless of criteria used, those with impaired fasting glucose (IFG) had similarly high prevalence of metabolic syndrome as did diabetes cases. In a multiple logistic regression model adjusted for demographics and lifestyle risk factors, the odds ratios of diabetes (95% CI) were 1.23 (1.04-1.45) for overweight (28 >= BMI >= 24), 1.81 (1.45-2.25) for obesity (BMI > 28), 1.53 (1.30-1.80) for central obesity (waist circumference > 80 cm for woman or waist circumference > 85 cm for man), 1.36 (1.17-1.59) for hypertension (sbp/dbp >= 140/90 mmHg), 1.55 (1.32-1.82) for high triglycerides (triglycerides > 1.70 mmol/l) and 1.52 (1.23-1.79) for low HDL-C (HDL-C < 1.04 mmol/L).</p> <p>Conclusions</p> <p>These data indicate that multiple metabolic risk factors--individually or jointly--were more prevalent in diabetes patients than in controls. Further research will examine hypotheses concerning the high prevalence of IFG, family history, and central obesity, aiding development of multifaceted preventive strategies specific to this population.</p