Adaptive Factorization Network: Learning Adaptive-Order Feature Interactions

Various factorization-based methods have been proposed to leverage second-order, or higher-order cross features for boosting the performance of predictive models. They generally enumerate all the cross features under a predefined maximum order, and then identify useful feature interactions through model training, which suffer from two drawbacks. First, they have to make a trade-off between the expressiveness of higher-order cross features and the computational cost, resulting in suboptimal predictions. Second, enumerating all the cross features, including irrelevant ones, may introduce noisy feature combinations that degrade model performance. In this work, we propose the Adaptive Factorization Network (AFN), a new model that learns arbitrary-order cross features adaptively from data. The core of AFN is a logarithmic transformation layer to convert the power of each feature in a feature combination into the coefficient to be learned. The experimental results on four real datasets demonstrate the superior predictive performance of AFN against the start-of-the-arts.Comment: Accepted by AAAI'2

Related consistent lures increase the judgment of multiplication facts: Evidence using event-related potential technique

Simple multiplication errors are primarily shown in whether the lures are related to the operands (relatedness, such as 3 × 4 = 15 vs. 17) or whether the same decades are shared with the correct answers (consistency, such as 3 × 4 = 16 vs. 21). This study used a delayed verification paradigm and event-related potential technique to investigate the effects of relatedness and consistency in simple multiplication mental arithmetic for 30 college students in an experiment of presenting probes in auditory channels. We found that, compared to the related inconsistent lures, the related consistent lures showed significantly faster reaction time and induced significantly large amplitudes of N400 and late positive component. The findings suggest that related consistent lures are less affected by the activation diffusion of the arithmetic problem, and the credibility of being perceived as the correct answer is less; the lures related to operands and sharing the same decades with the accurate results can promote the judgment of multiplication mental arithmetic, and the results support the Interacting Neighbors Model

Biological and genomic analysis of a symbiotic nitrogen fixation defective mutant in Medicago truncatula

Medicago truncatula has been selected as one of the model legume species for gene functional studies. To elucidate the functions of the very large number of genes present in plant genomes, genetic mutant resources are very useful and necessary tools. Fast Neutron (FN) mutagenesis is effective in inducing deletion mutations in genomes of diverse species. Through this method, we have generated a large mutant resource in M. truncatula. This mutant resources have been used to screen for different mutant using a forward genetics methods. We have isolated and identified a large amount of symbiotic nitrogen fixation (SNF) deficiency mutants. Here, we describe the detail procedures that are being used to characterize symbiotic mutants in M. truncatula. In recent years, whole genome sequencing has been used to speed up and scale up the deletion identification in the mutant. Using this method, we have successfully isolated a SNF defective mutant FN007 and identified that it has a large segment deletion on chromosome 3. The causal deletion in the mutant was confirmed by tail PCR amplication and sequencing. Our results illustrate the utility of whole genome sequencing analysis in the characterization of FN induced deletion mutants for gene discovery and functional studies in the M. truncatula. It is expected to improve our understanding of molecular mechanisms underlying symbiotic nitrogen fixation in legume plants to a great extent

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

A novel preoperative image-guided localization for small pulmonary nodule resection using a claw-suture device

Abstract Video-assisted thoracoscopic surgery (VATS) provides better option concerning pathological diagnosis and curative intention of small pulmonary nodules (SPNs) that are sometimes challenging to localize. We assess the safety and feasibility of a new localization technique for SPNs, and report experience accumulated over time. A retrospective review of the new claw-suture localization cases between February 2018 and May 2023 was performed. Nodules were localized by a novel system that has an anchor claw and a tri-colored suture, guided by computed tomography (CT). Localization and operative procedure outcomes were then assessed. A total of 590 SPNs were localized from 568 patients before operation. The median nodule size was 0.70 cm (range, 0.3–2.0 cm). The claw-suture localization was successful without dislodgment or device fracture in 574 of 590 lesions (97.3%). Failures included not meeting target distance between claw and lesion (n = 13 [2.2%]), and device displacement (n = 3 [0.5%]). Complications requiring no further medical intervention included asymptomatic pneumothorax (n = 68 [11.5%]), parenchymal hemorrhage (n = 51 [8.6%]), and hemothorax (n = 1 [0.2%]) with the exception of pleural reaction observed in 2 cases (0.3%). Additionally, the depth of pulmonary nodules was significantly associated with the occurrence of pneumothorax (P = 0.036) and parenchymal hemorrhage (P = 0.000). The median duration of the localization was 12 min (range, 7–25 min). No patient complained of remarkable pain during the entire procedure. Retrieve of device after operation was 100%. The new localization technique is a safe, feasible, and well-tolerated method to localize SPNs for VATS resection

Construction of a Prognostic Prediction Model of Patients with Pathologic N0 in Resected Invasive Mucinous Adenocarcinoma of the Lung

Background and objective Invasive mucinous adenocarcinoma (IMA) was a rare and specific type of lung adenocarcinoma, which was often characterized by fewer lymphatic metastases. Therefore, it was difficult to evaluate the prognosis of these tumors based on the existing tumor-node-metastasis (TNM) staging. So, this study aimed to develop Nomograms to predict outcomes of patients with pathologic N0 in resected IMA. Methods According to the inclusion criteria and exclusion criteria, IMA patients with pathologic N0 in The Affiliated Lihuili Hospital of Ningbo University (training cohort, n=78) and Ningbo No.2 Hospital (validation cohort, n=66) were reviewed between July 2012 and May 2017. The prognostic value of the clinicopathological features in the training cohort was analyzed and prognostic prediction models were established, and the performances of models were evaluated. Finally, the validation cohort data was put in for external validation. Results Univariate analysis showed that pneumonic type, larger tumor size, mixed mucinous/non-mucinous component, and higher overall stage were significant influence factors of 5-year progression-free survival (PFS) and overall survival (OS). Multivariate analysis further indicated that type of imaging, tumor size, mucinous component were the independent prognostic factors for poor 5-year PFS and OS. Moreover, the 5-year PFS and OS rates were 62.82% and 75.64%, respectively. In subgroups, the survival analysis also showed that the pneumonic type and mixed mucinous/non-mucinous patients had significantly poorer 5-year PFS and OS compared with solitary type and pure mucinous patients, respectively. The C-index of Nomograms with 5-year PFS and OS were 0.815 (95%CI: 0.741-0.889) and 0.767 (95%CI: 0.669-0.865). The calibration curve and decision curve analysis (DCA) of both models showed good predictive performances in both cohorts. Conclusion The Nomograms based on clinicopathological characteristics in a certain extent, can be used as an effective prognostic tool for patients with pathologic N0 after IMA resection

CircBCAR3 accelerates esophageal cancer tumorigenesis and metastasis via sponging miR-27a-3p

Abstract Rationale Circular RNAs (circRNAs) have been demonstrated to contribute to esophageal cancer progression. CircBCAR3 (hsa_circ_0007624) is predicted to be differentially expressed in esophageal cancer by bioinformatics analysis. We investigated the oncogenic roles and biogenesis of circBCAR3 in esophageal carcinogenesis. Methods Functions of circBCAR3 on cancer cell proliferation, migration, invasion, and ferroptosis were explored using the loss-of-function assays. A xenograft mouse model was used to reveal effects of circBCAR3 on xenograft growth and lung metastasis. The upstream and downstream mechanisms of circBCAR3 were investigated by bioinformatics analysis and confirmed by RNA immunoprecipitation and luciferase reporter assays. The dysregulated genes in hypoxia-induced esophageal cancer cells were identified using RNA-seq. Results CircBCAR3 was highly expressed in esophageal cancer tissues and cells and its expression was increased by hypoxia in vitro. Silencing of circBCAR3 repressed the proliferation, migration, invasion, and ferroptosis of esophageal cancer cells in vitro, as well as inhibited the growth and metastasis of esophageal xenograft in mice in vivo. The hypoxia-induced promotive effects on esophageal cancer cell migration and ferroptosis were rescued by circBCAR3 knockdown. Mechanistically, circBCAR3 can interact with miR-27a-3p by the competitive endogenous RNA mechanism to upregulate transportin-1 (TNPO1). Furthermore, our investigation indicated that splicing factor quaking (QKI) is a positive regulator of circBCAR3 via targeting the introns flanking the hsa_circ_0007624-formed exons in BCAR3 pre-mRNA. Hypoxia upregulates E2F7 to transcriptionally activate QKI. Conclusion Our research demonstrated that splicing factor QKI promotes circBCAR3 biogenesis, which accelerates esophageal cancer tumorigenesis via binding with miR-27a-3p to upregulate TNPO1. These data suggested circBCAR3 as a potential target in the treatment of esophageal cancer. Graphical Abstract Hypoxia induces the upregulation of E2F7, which transcriptionally activates QKI in esophageal cancer cells. QKI increases the formation of circBCAR3 by juxtaposing the circularized exons. CircBCAR3 binds with miR-27a-3p to promote TNPO1 expression. CircBCAR3 promoted the proliferation, migration, invasion, and ferroptosis of esophageal cancer cells by miR-27a-3p