Miracle-dz/UniFAR-FTUs huggingface dataset:
Load Distribution-Based Research on a Cascading Failure Model of Network Public Opinion Dissemination

Research of network cascading failures is a heavily researched topic in network science research. The expression of a network cascading failure mechanism by a dynamic equation has become a basic mode for research of cascading failures. With the promotion of complexity and intelligent of nodes, it is difficult to reflect the evolution of the actual large network state objectively that only considering the coupling relationship among nodes from one network. To describe the dissemination process of network public opinion more accurately, this paper proposes a failure propagation model of network public opinion dissemination based on load spatial distribution, in which evolutional behaviors of nodes were expanded to overall evolutional behaviors of a network based on network coupling relations, and difficulty of analysis and solution was reduced through periodic iteration and feature value decomposition of network adjacent matrixes. Experimental results verify the feasibility and validity of this method. Failure analysis of the computer network also indicates that node behaviors could facilitate weakening of effects generated from attacks and failures. Meanwhile, weakening of nodes could effectively reduce the network sensitivity to deliberate attacks.
Association of Metabolic, Inflammatory, and Tumor Markers With Circulating Tumor Cells in Metastatic Breast Cancer

Abstract Background Circulating tumor cells (CTCs) are associated with worse prognosis in metastatic breast cancer (BC). We evaluated the association of metabolic, inflammatory, and tumor markers with CTCs in women with metastatic BC before commencing a new systemic therapy. Methods Ninety-six patients with newly diagnosed or progressing metastatic BC without current diabetes or use of anti-inflammatory agents were recruited from four Ontario hospitals. Women provided fasting blood for measurement of metabolic, inflammatory, and tumor markers and CTCs. CTCs were assayed within 72 hours of collection using CellSearch. Other blood was frozen at –80°C, and assays were performed in a single batch. Associations between CTC counts with study factors were evaluated using Spearman correlation, and the chi-square or Fisher exact test. All statistical tests were two-sided and P value ≤ . 05 was considered statistically significant. Results The median age was 60.5 years; 90.6% were postmenopausal. The cohort included hormone receptor–positive (87.5%), HER2–positive (15.6%), and triple-negative (10.4%) BCs. Patients were starting firstline (35.5%), second-line (26.0%), or third-or-later-line therapy (38.5%). CTC counts (per 7.5 mL of blood) ranged from 0 to 1238 (median 2); an elevated CTC count, defined as five or more CTCs, was detected in 42 (43.8%) patients. Those with liver metastases (vs not) more frequently had an elevated CTC count (59.0% vs 33.3%, P = .02). CTCs were significantly associated with C-reactive protein (R = .22, P = .02), interleukin (IL)-6 (R = .25, P = .01), IL-8 (R = .38, P = .0001), plasminogen activator inhibitor 1 (R = .31, P = .001), carcinoembryonic antigen (R = .31, P = .002), and cancer antigen 15-3 (R = .40, P = .0001) and inversely associated with body mass index (R = –.23, P = .02) and leptin (R = –.26, P = .01). Conclusions CTC counts were positively associated with tumor and inflammatory markers and inversely associated with some metabolic markers, potentially reflecting tumor burden and cachexia.
Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility

Murine models have become essential tools for understanding the complex interactions between gut microbes, their hosts, and disease. While many intra-facility factors are known to influence the structure of mouse microbiomes, the contribution of inter-facility variation to mouse microbiome composition, especially in the context of disease, remains under-investigated. We replicated microbiome experiments using identical mouse lines housed in two separate animal facilities and report drastic differences in composition of microbiomes based upon animal facility of origin. We observed facility-specific microbiome signatures in the context of a disease model [the Ednrb (endothelin receptor type B) Hirschsprung disease mouse] and in normal C57BL/6J mice. Importantly, these facility differences were independent of cage, sex, or sequencing-related influence. In addition, we investigated the reproducibility of microbiome dysbiosis previously associated with Ednrb-/- (knock-out; KO) mice. While we observed genotype-based differences in composition between wild-type (WT) and KO mice, these differences were inconsistent with the previously reported conclusions. Furthermore, the genotype-based differences were not identical across animal facilities. Despite this, through differential abundance testing, we identified several conserved candidate taxa and candidate operational taxonomic units that may play a role in disease promotion or protection. Overall, our findings raise the possibility that previously reported microbiome-disease associations from murine studies conducted in a single facility may be heavily influenced by facility-specific effects. More generally, these results provide a strong rationale for replication of mouse microbiome studies at multiple facilities, and for the meticulous collection of metadata that will allow the confounding effects of facility to be more specifically identified.
A Large Endoplasmic Reticulum-Resident Pool of TRPM1 in Retinal ON-Bipolar Cells

Abstract The chemical signal of light onset, a decrease in glutamate release from rod and cone photoreceptors, is processed by a postsynaptic G protein signaling cascade in ON-bipolar cells (BPCs). The metabotropic glutamate receptor mGluR6, along with other cascade elements, is localized synaptically at the BPC dendritic tips. The effector ion channel protein transient receptor potential melastatin-1 (TRPM1), in contrast, is located not only at the dendritic tips but also in BPC bodies and axons. Little is known about the intracellular localization of TRPM1, or its trafficking route to the dendritic tip plasma membrane. Recombinant TRPM1 expressed in mammalian cells colocalized with endoplasmic reticulum (ER) markers, with little or none detected at the plasma membrane. In mouse retina, somatic TRPM1 was similarly intracellular, and not at the plasma membrane. Labeling of ER membranes by expression of a fluorescent marker showed that in BPCs the ER extends into axons and dendrites, but not dendritic tips. In cell bodies, TRPM1 colocalized with the ER, and not with the Golgi apparatus. Fluorescence protease protection (FPP) assays with TRPM1-GFP fusions in heterologous cells revealed that the N and C termini are both accessible to the cytoplasm, consistent with the transmembrane domain topology of related TRP channels. These results indicate that the majority of TRPM1 is present in the ER, from which it can potentially be transported to the dendritic tips as needed for ON light responses. The excess of ER-resident TRPM1 relative to the amount needed at the dendritic tips suggests a potential new function for TRPM1 in the ER.
Global Hippocampal Volume Reductions and Local CA1 Shape Deformations in Amyotrophic Lateral Sclerosis

There is increasing evidence for hippocampal involvement in Amyotrophic Lateral Sclerosis (ALS). Recent neuroimaging studies have been focused on disease-related hippocampal volume alterations while changes in hippocampal shape have been investigated less frequently. Here, we aimed to characterize the patterns of hippocampal degeneration using both an automatic and manual volumetric and surface-based approach in a group of 31 patients with ALS and 29 healthy controls. Irrespective of the segmentation type, left, and right hippocampal volumes were significantly reduced in ALS compared to controls. Local shape alterations were identified in the hippocampal head region of patients with ALS that corresponds to the cornu ammonis field 1 (CA1), a region known to be involved in novelty detection, memory processing, and integration of hippocampal input and output information. The results suggest a global hippocampal volume loss in ALS that is complemented by local shape deformations in a highly interconnected region within the hippocampus.
Few-Shot Adaptation for Multimedia Semantic Indexing

We propose a few-shot adaptation framework, which bridges zero-shot learning and supervised many-shot learning, for semantic indexing of image and video data. Few-shot adaptation provides robust parameter estimation with few training examples, by optimizing the parameters of zero-shot learning and supervised many-shot learning simultaneously. In this method, first we build a zero-shot detector, and then update it by using the few examples. Our experiments show the effectiveness of the proposed framework on three datasets: TRECVID Semantic Indexing 2010, 2014, and ImageNET. On the ImageNET dataset, we show that our method outperforms recent few-shot learning methods. On the TRECVID 2014 dataset, we achieve 15.19~% and 35.98~% in Mean Average Precision under the zero-shot condition and the supervised condition, respectively. To the best of our knowledge, these are the best results on this dataset.
Identification of Odorant-Binding Proteins (OBPs) and Functional Analysis of Phase-Related OBPs in the Migratory Locust

Olfactory plasticity, which is one of the major characteristics of density-dependent phase polyphenism, plays critical roles in the large-scale aggregation formation of Locusta migratoria. It is still unknown whether odorant-binding proteins (OBPs) are involved in phase-related olfactory plasticity of locusts, despite the confirmed involvement of several types of olfactory perception genes. In this study, we performed a large-scale search for OBPs and verified their expression patterns in the migratory locust. We identified 17 OBPs in the L. migratoria genome, of which 10 were novel, and we found their scattering distribution characteristics by mapping the genomic loci. Next, we revealed that these OBPs with close phylogenic relationships displayed similar tissue-specific expression profiles by a combined analysis of qRT-PCR and phylogenetic tree reconstruction. In all identified locust OBPs, seven OBPs showed differential mRNA expression levels in antenna tissue between gregarious and solitarious nymphs. Six of these seven OBPs displayed higher mRNA expression in the antennae of gregarious nymphs. The mRNA expression of LmigOBP2 and LmigOBP4 increased during gregarization and decreased during solitarization. RNAi experiments confirmed that only LmigOBP4 regulates the behavioral traits to affect gregarious behavior. These results demonstrated that OBPs also play important roles in the regulation of phase-related behavior of the locusts.
A Novel UDP-Glycosyltransferase of Rhodiola crenulata Converts Tyrosol to Specifically Produce Icariside D2

Rhodiola crenulata is a Tibetan native herbal plant belonging to the family of Crassulaceae, which produces the pharmaceutical icariside D2 with the activities of inhibiting angiotensin-converting enzyme and killing leukemia cancer cells. In this study, we functionally characterized a novel UDP-glycosyltransferase (RcUGT1) that converted tyrosol to specifically produce icariside D2 from R. crenulata at molecular and biochemical levels. RcUGT1 was highly expressed in flowers and roots, while the icariside D2 content was much higher in stems than that in other organs, suggesting the potential translocation of icariside D2 from flowers and roots to stems. The high production of icariside D2 in stems provided a reasonable suggestion to farmers to harvest stems instead of roots for icariside D2 production. Enzymatic assays of recombinant RcUGT1 indicated that it converted tyrosol to specifically form icariside D2, with the values of Km 0.97±0.10 mM, Vmax 286±8.26 pKat/mg, Kcat 0.01552 s−1, and Kcat/Km 159.55 s−1 M−1. Functional identification of RcUGT1 facilitated the icariside D2 production through metabolic engineering in plants or synthetic biology in microbes.
Sequence to Logic with Copy and Cache

Generating logical form equivalents of human language is a fresh way to employ neural architectures where long short-term memory effectively captures dependencies in both encoder and decoder units. The logical form of the sequence usually preserves information from the natural language side in the form of similar tokens, and recently a copying mechanism has been proposed which increases the probability of outputting tokens from the source input through decoding. In this paper we propose a caching mechanism as a more general form of the copying mechanism which also weighs all the words from the source vocabulary according to their relation to the current decoding context. Our results confirm that the proposed method achieves improvements in sequence/token-level accuracy on sequence to logical form tasks. Further experiments on cross-domain adversarial attacks show substantial improvements when using the most influential examples of other domains for training.
Hybrid Scene Compression for Visual Localization

Localizing an image w.r. t. a 3D scene model represents a core task for many computer vision applications. An increasing number of real-world applications of visual localization on mobile devices, e.g., Augmented Reality or autonomous robots such as drones or self-driving cars, demand localization approaches to minimize storage and bandwidth requirements. Compressing the 3D models used for localization thus becomes a practical necessity. In this work, we introduce a new hybrid compression algorithm that uses a given memory limit in a more effective way. Rather than treating all 3D points equally, it represents a small set of points with full appearance information and an additional, larger set of points with compressed information. This enables our approach to obtain a more complete scene representation without increasing the memory requirements, leading to a superior performance compared to previous compression schemes. As part of our contribution, we show how to handle ambiguous matches arising from point compression during RANSAC. Besides outperforming previous compression techniques in terms of pose accuracy under the same memory constraints, our compression scheme itself is also more efficient. Furthermore, the localization rates and accuracy obtained with our approach are comparable to state-of-the-art feature-based methods, while using a small fraction of the memory.
Noise Adaptive Speech Enhancement using Domain Adversarial Training

In this study, we propose a novel noise adaptive speech enhancement (SE) system, which employs a domain adversarial training (DAT) approach to tackle the issue of a noise type mismatch between the training and testing conditions. Such a mismatch is a critical problem in deep-learning-based SE systems. A large mismatch may cause a serious performance degradation to the SE performance. Because we generally use a well-trained SE system to handle various unseen noise types, a noise type mismatch commonly occurs in real-world scenarios. The proposed noise adaptive SE system contains an encoder-decoder-based enhancement model and a domain discriminator model. During adaptation, the DAT approach encourages the encoder to produce noise-invariant features based on the information from the discriminator model and consequentially increases the robustness of the enhancement model to unseen noise types. Herein, we regard stationary noises as the source domain (with the ground truth of clean speech) and non-stationary noises as the target domain (without the ground truth). We evaluated the proposed system on TIMIT sentences. The experiment results show that the proposed noise adaptive SE system successfully provides significant improvements in PESQ (19.0%), SSNR (39.3%), and STOI (27.0%) over the SE system without an adaptation.
A Panel of MicroRNA Signature as a Tool for Predicting Survival of Patients with Urothelial Carcinoma of the Bladder

Introduction and Objectives MicroRNA (miRNA) expression is altered in urologic malignancies, including urothelial carcinoma of the bladder (UCB). Individual miRNAs have been shown to modulate multiple signaling pathways that contribute to BC. To identify a panel of miRNA signature that can predict aggressive phenotype from normal nonaggressive counterpart using miRNA expression levels and to assess the prognostic value of this specific miRNA markers in patients with UCB. Methods To determine candidate miRNAs as prognostic biomarkers for dividing aggressive type of UCB, miRNA expression was profiled in patients' samples with an aggressive phenotype or nonaggressive phenotype using 3D-Gene miRNA labeling kit (Toray, Japan). To create a prognostic index model, we used the panel of 9-miRNA signature based on Cancer Genome Atlas (TCGA) data portal (TCGA Data Portal (https://tcgadata.nci.nih.gov/tcga/tcgaHome2.jsp)). miRNA expression data and corresponding clinical data, including outcome and staging information of 84 UCB patients, were obtained. The Kaplan-Meier and log-rank test were performed to quantify the survival functions in two groups. Results Deregulation of nine miRNAs (hsa-miR-99a-5p, hsa-miR-100-5p, hsa-miR-125b-5p, hsa-miR-145-5p, hsa-miR-4324, hsa-miR-34b-5p, hsa-miR-29c-3p, hsa-miR-135a-3p, and hsa-miR-33b-3p) was determined in UCB patients with aggressive phenotype compared with nonaggressive subject. To validate the prognostic power of the nine-signature miRNAs using the TCGA dataset of bladder cancer, the survival status and tumor miRNA expression of all 84 TCGA UCB patients were ranked according to the prognostic score values. Of nine miRNAs, six were associated with high risk (hsa-miR-99a-5p, hsa-miR-100-5p, hsa-miR-125b-5p, hsa-miR-4324, hsa-miR-34b-5p, and hsa-miR-135a-3p) and three were shown to be protective (hsa-miR-145-5p, hsa-miR-29c-3p, and hsa-miR-33b-3p). Patients with the high-risk miRNA signature exhibited poorer OS than patients expressing the low-risk miRNA profile (HR = 7.05, p < 0.001). Conclusions The miRNA array identified nine dysregulated miRNAs from clinical samples. This panel of nine-miRNA signature provides predictive and prognostic value of patients with UCB.
Immune profiling of microsatellite instability-high and polymerase ε (POLE)-mutated metastatic colorectal tumors identifies predictors of response to anti-PD-1 therapy.

Background Microsatellite instability-high (MSI-H) and polymerase ε (POLE)-mutated metastatic colorectal cancer (mCRC) represent hypermutated and ultramutated tumor phenotypes, respectively, that may predict benefit to checkpoint blockade [anti-programmed cell death 1 (PD-1)/programmed death ligand 1 (PD-L1)]. Methods Immune profiling through multispectral fluorescent immunohistochemistry (IHC) using a multi-marker staining panel was performed on pretreatment tumor specimens from a cohort of MSI-H or POLE-mutated mCRC patients treated with PD-1 blockade at our institution to identify candidate predictors of response to checkpoint inhibitors. Results From 4/2013 to 1/2017, a total of 237 mCRC patients with molecularly profiled tumors were screened. Five MSI-H and three POLE-mutated mCRC patients were treated with checkpoint inhibitors. Immune profiling identified higher CD8+ tumor-infiltrating lymphocytes (TILs) within the tumor microenvironment (TME) of responders (CR or PR as best response) than nonresponders (SD or PD as best response). Responders had significantly higher densities of CD8+ PD-1+ TILs than nonresponders (P=0.0007). PD-L1 expression (P=0.73), CD4+ T-cell density (P=0.39), and CD4+ FOXP3+ T-cell density (P=0.68) did not significantly differ, but the percentage of CD4+ Tbet+ T-cells (Th1 phenotype) was also significantly higher in responders than nonresponders (P=0.0007). Conclusions Higher densities of CD8+ TILs, PD-1-expressing CD8+ TILs, and tumor-infiltrating immune cells with a Th1 phenotype in the TME may predict response to checkpoint inhibitors in MSI-H and POLE-mutated mCRC.
Biostimulant Potential of Humic Acids Extracted From an Amendment Obtained via Combination of Olive Mill Wastewaters (OMW) and a Pre-treated Organic Material Derived From Municipal Solid Waste (MSW)

Olive mill wastewaters (OMW) contain significant levels of phenolic compounds with antimicrobial/phytotoxic activity and high amounts of undecomposed organic matter that may exert negative effects on soil biology. Among OMW detoxification techniques, those focusing on oxidative degradation of phenolic compounds are relevant. The composting (bio-oxidation) process in particular, exploits exothermic oxidation reactions by microorganisms to transform the organic matrix of OMW into an amendment biologically stable and feasible to use in agriculture. This process consists of an active phase during which organic compounds are rapidly decomposed, and a curing phase characterized by a slow breakdown of the remaining materials with the formation of humic substances (HS) as by-products. In this study, bio-oxidation of OMW was performed using a pre-treated organic material derived from municipal solid waste (MSW). The obtained amendment (OMWF) was stable and in accordance with the legislative parameters of mixed organic amendments. HS were then extracted from OMWF and MSW (control amendment, Amd-C), and differences in structural properties of their humic acid (HA) fraction were highlighted via spectroscopy (Fourier Transform Infrared) and Dynamic Light Scattering. To assay a potential use of HA as biostimulants for crops, 12-day old Zea Mays L. plants were supplied with HA at 0.5 mg and 1 mg C L-1 for 2 days. HA from both amendments increased plant growth, but HA from OMWF was more effective at both dosages (plus 35–37%). Also, HA from OMWF enhanced both nitrogen assimilation and glycolysis by increasing the activity of nitrate reductase (∼1.8–1.9 fold), phosphoglucose isomerase (PGI) (∼1.8–2 fold) and pyruvate kinase (PK) (∼1.5–1.8 fold), while HA from Amd-C targeted glycolysis preferentially. HA from OMWF, however, significantly stimulated plant nutrition only at lower dosage, perhaps because certain undetermined compounds from detoxified OMW and incorporated in HA altered the root membrane permeability, thus preventing the increase of nutrient uptake. Conversely, HA from Amd-C increased nutrient accumulation in maize at both dosages. In conclusion, our results indicate that the amendment obtained via OMW composting using MSW had a reduced pollution load in terms of phenolic compounds, and HA extracted from OMWF could be used as valuable biostimulants during maize cultivation.