Miracle-dz/UniFAR-FTUs huggingface dataset:
A Robust Cover Song Identification System with Two-Level Similarity Fusion and Post-Processing

Similarity measurement plays an important role in various information retrieval tasks. In this paper, a music information retrieval scheme based on two-level similarity fusion and post-processing is proposed. At the similarity fusion level, to take full advantage of the common and complementary properties among different descriptors and different similarity functions, first, the track-by-track similarity graphs generated from the same descriptor but different similarity functions are fused with the similarity network fusion (SNF) technique. Then, the obtained first-level fused similarities based on different descriptors are further fused with the mixture Markov model (MMM) technique. At the post-processing level, diffusion is first performed on the two-level fused similarity graph to utilize the underlying track manifold contained within it. Then, a mutual proximity (MP) algorithm is adopted to refine the diffused similarity scores, which helps to reduce the bad influence caused by the “hubness” phenomenon contained in the scores. The performance of the proposed scheme is tested in the cover song identification (CSI) task on three cover song datasets (Covers80, Covers40, and Second Hand Songs (SHS)). The experimental results demonstrate that the proposed scheme outperforms state-of-the-art CSI schemes based on single similarity or similarity fusion.
Matching Biomedical Ontologies via a Hybrid Graph Attention Network

Biomedical ontologies have been used extensively to formally define and organize biomedical terminologies, and these ontologies are typically manually created by biomedical experts. With more biomedical ontologies being built independently, matching them to address the problem of heterogeneity and interoperability has become a critical challenge in many biomedical applications. Existing matching methods have mostly focused on capturing features of terminological, structural, and contextual semantics in ontologies. However, these feature engineering-based techniques are not only labor-intensive but also ignore the hidden semantic relations in ontologies. In this study, we propose an alternative biomedical ontology-matching framework BioHAN via a hybrid graph attention network, and that consists of three techniques. First, we propose an effective ontology-enriching method that refines and enriches the ontologies through axioms and external resources. Subsequently, we use hyperbolic graph attention layers to encode hierarchical concepts in a unified hyperbolic space. Finally, we aggregate the features of both the direct and distant neighbors with a graph attention network. Experimental results on real-world biomedical ontologies demonstrate that BioHAN is competitive with the state-of-the-art ontology matching methods.
Interplay between innate immunity and the viral oncoproteins Tax and HBZ in the pathogenesis and therapeutic response of HTLV-1 associated adult T cell leukemia

The Human T-cell Leukemia virus type 1 (HTLV-1) causes an array of pathologies, the most aggressive of which is adult T-cell leukemia (ATL), a fatal blood malignancy with dismal prognosis. The progression of these diseases is partly ascribed to the failure of the immune system in controlling the spread of virally infected cells. HTLV-1 infected subjects, whether asymptomatic carriers or symptomatic patients are prone to opportunistic infections. An increasing body of literature emphasizes the interplay between HTLV-1, its associated pathologies, and the pivotal role of the host innate and adoptive immune system, in shaping the progression of HTLV-1 associated diseases and their response to therapy. In this review, we will describe the modalities adopted by the malignant ATL cells to subvert the host innate immune response with emphasis on the role of the two viral oncoproteins Tax and HBZ in this process. We will also provide a comprehensive overview on the function of innate immunity in the therapeutic response to chemotherapy, anti-viral or targeted therapies in the pre-clinical and clinical settings.
A prediction model of pulmonary hypertension in preterm infants with bronchopulmonary dysplasia

Objective Pulmonary hypertension (PH) is a severe cardiovascular complication of bronchopulmonary dysplasia (BPD) that contributes to the high mortality rates for preterm infants. The objective of this study is to establish a prediction model of BPD-associated PH (BPD-PH) by integrating multiple predictive factors for infants with BPD. Method A retrospective investigation of the perinatal clinical records and data of echocardiography in all the preterm infants with BPD was performed from January 2012 to December 2019. A prediction model of BPD-PH was established based on the univariate and multivariate logistic regression analysis of the clinical data and evaluated by using the area under the receiver operating characteristic (ROC) curve (AUC), combined with the Hosmer–Lemeshow (HL) test. Internal validation was performed with bootstrap resampling. Result A total of 268 infants with BPD were divided into the BPD-PH group and the no-PH group. Multivariate logistic regression analysis showed that the independent predictive factors of BPD-PH were moderate to severe BPD, small for gestational age, duration of hemodynamically significant patent ductus arteriosus ≥ 28 days, and early PH. A prediction model was established based on the β coefficients of the four predictors. The area under the ROC curve of the prediction model was 0.930. The Hosmer–Lemeshow test (p = 0.976) and the calibration curve showed good calibration. Conclusion The prediction model based on the four risk factors predicts the development of BPD-PH with high sensitivity and specificity and might help clinicians to make individualized interventions to minimize the disease risk.
Fusing attention mechanism with Mask R-CNN for instance segmentation of grape cluster in the field

Accurately detecting and segmenting grape cluster in the field is fundamental for precision viticulture. In this paper, a new backbone network, ResNet50-FPN-ED, was proposed to improve Mask R-CNN instance segmentation so that the detection and segmentation performance can be improved under complex environments, cluster shape variations, leaf shading, trunk occlusion, and grapes overlapping. An Efficient Channel Attention (ECA) mechanism was first introduced in the backbone network to correct the extracted features for better grape cluster detection. To obtain detailed feature map information, Dense Upsampling Convolution (DUC) was used in feature pyramid fusion to improve model segmentation accuracy. Moreover, model generalization performance was also improved by training the model on two different datasets. The developed algorithm was validated on a large dataset with 682 annotated images, where the experimental results indicate that the model achieves an Average Precision (AP) of 60.1% on object detection and 59.5% on instance segmentation. Particularly, on object detection task, the AP improved by 1.4% and 1.8% over the original Mask R-CNN (ResNet50-FPN) and Faster R-CNN (ResNet50-FPN). For the instance segmentation, the AP improved by 1.6% and 2.2% over the original Mask R-CNN and SOLOv2. When tested on different datasets, the improved model had high detection and segmentation accuracy and inter-varietal generalization performance in complex growth environments, which is able to provide technical support for intelligent vineyard management.
The effects of nursing work environment on patient safety in Saudi Arabian hospitals

Purpose This study aims to investigate the impact of the nursing work environment on patients’ safety in Saudi Arabian hospitals. Methods This study used a cross-sectional design for collecting the data related to the nursing work environment and patients’ safety from nursing staff in Saudi Arabian hospitals. The survey questionnaire included in this study has two pre-validated questionnaires including practice environment scale-nursing work index questionnaire and hospital’s survey on patients’ safety developed by Surveys on Patients Safety Culture. The survey link was forwarded to HR administrators of 96 hospitals in Saudi Arabia, which included 72 public hospitals, 23 private hospitals, and one public-private hospital. Three hundred sixty-nine responses were received. After removing the incomplete responses, 357 responses were considered for the data analysis, in which t-tests and Pearson’s correlation techniques were adopted. Results Strongest correlations were identified between resource adequacy and work area (r = 0.763, p < 0.01), “participation in management and leadership” and work area (r = 0.712, p < 0.01), “participation in management and leadership” and supervisor/managers’ approaches (r = 0.731, p < 0.01), and “nursing care and inter-disciplinary relationships and frequency of events” (r = 0.701, p < 0.01). Conclusion The nursing work environment factors, especially participation, management and leadership, nursing care, inter-disciplinary relationships, and resource adequacy have to be improved in order to improve the patients’ safety.
Genetic Configuration of Genomic Resistance Islands in Acinetobacter baumannii Clinical Isolates From Egypt

In Acinetobacter baumannii (A. baumannii), a wide repertoire of resistance genes is often carried within genomic resistance islands (RIs), particularly in high-risk global clones (GCs). As the first in Egypt, the current study aimed at exploring the diversity and genetic configuration of RIs in the clinical isolates of A. baumannii. For this purpose, draft genomes of 18 isolates were generated by Illumina sequencing. Disk diffusion susceptibility profiling revealed multidrug resistance (MDR) and extensive drug resistance (XDR) phenotypes in 27.7 and 72.2%, respectively. The highest susceptibility was noted for tigecycline (100.0%) followed by colistin (94.4%), for which an MIC50 of 0.25 μg/ml was recorded by the broth microdilution assay. Sequence typing (ST) showed that the majority of the isolates belonged to high-risk global clones (GC1, GC2, and GC9). A novel Oxford sequence type (ST2329) that also formed a novel clonal complex was submitted to the PubMLST database. A novel blaADC variant (blaADC−258) was also identified in strain M18 (ST85Pas/1089Oxf). In addition to a wide array of resistance determinants, whole-genome sequencing (WGS) disclosed at least nine configurations of genomic RIs distributed over 16/18 isolates. GC2 isolates accumulated the largest number of RIs (three RIs/isolate) followed by those that belong to GC1 (two RIs/isolate). In addition to Tn6022 (44.4%), the comM gene was interrupted by AbaR4 (5.5%) and three variants of A. baumannii genomic resistance island 1(AbGRI)-type RIs (44.4%), including AbaR4b (16.6%) and two novel configurations of AbGRI1-like RIs (22.2%). Three of which (AbaR4, AbaR4b, and AbGRI1-like-2) carried blaOXA−23 within Tn2006. With less abundance (38.8%), IS26-bound RIs were detected exclusively in GC2 isolates. These included a short version of AbGRI2 (AbGRI2-15) carrying the genes blaTEM−1 and aphA1 and two variants of AbGRI3 RIs carrying up to seven resistance genes [mphE-msrE-armA-sul1-aadA1-catB8-aacA4]. Confined to GC1 (22.2%), sulfonamide resistance was acquired by an ISAba1 bracketed GIsul2 RI. An additional RI (RI-PER-7) was also identified on a plasmid carried by strain M03. Among others, RI-PER-7 carried the resistance genes armA and blaPER−7. Here, we provided a closer view of the diversity and genetic organization of RIs carried by a previously unexplored population of A. baumannii.
Neural activity during solo and choral reading: A functional magnetic resonance imaging study of overt continuous speech production in adults who stutter

Previous neuroimaging investigations of overt speech production in adults who stutter (AWS) found increased motor and decreased auditory activity compared to controls. Activity in the auditory cortex is heightened, however, under fluency-inducing conditions in which AWS temporarily become fluent while synchronizing their speech with an external rhythm, such as a metronome or another speaker. These findings suggest that stuttering is associated with disrupted auditory motor integration. Technical challenges in acquiring neuroimaging data during continuous overt speech production have limited experimental paradigms to short or covert speech tasks. Such paradigms are not ideal, as stuttering primarily occurs during longer speaking tasks. To address this gap, we used a validated spatial ICA technique designed to address speech movement artifacts during functional magnetic resonance imaging (fMRI) scanning. We compared brain activity and functional connectivity of the left auditory cortex during continuous speech production in two conditions: solo (stutter-prone) and choral (fluency-inducing) reading tasks. Overall, brain activity differences in AWS relative to controls in the two conditions were similar, showing expected patterns of hyperactivity in premotor/motor regions but underactivity in auditory regions. Functional connectivity of the left auditory cortex (STG) showed that within the AWS group there was increased correlated activity with the right insula and inferior frontal area during choral speech. The AWS also exhibited heightened connectivity between left STG and key regions of the default mode network (DMN) during solo speech. These findings indicate possible interference by the DMN during natural, stuttering-prone speech in AWS, and that enhanced coordination between auditory and motor regions may support fluent speech.
Online learning satisfaction and its associated factors among international students in China

The outbreak of the COVID-19 pandemic has caused a substantial transition of Chinese international education to online learning. This article discusses the impact of online learning from international students’ perspectives. Data were collected from exploratory interviews with a small group of international students at a research university and a nationwide survey involving 1,010 international students at 41 universities in China. A synthesis of the two studies’ findings pointed to low levels of online learning satisfaction, particularly among international students from Africa, those in undergraduate programs, those in life sciences and medical disciplines, and those studying at research-centered universities. Moreover, both studies revealed low emotional engagement significantly predicted international students’ online learning dissatisfaction. To enhance international students’ satisfaction, it is suggested that universities and teachers prioritize the building of student-centered online learning environments supporting international students’ emotional involvement and helping them feel a greater sense of belonging in online intercultural learning.
Carbon Ion Radiotherapy Induce Metabolic Inhibition After Functional Imaging-Guided Simultaneous Integrated Boost for Prostate Cancer

Purpose As local recurrence remains a challenge and the advantages of the simultaneous integrated boost (SIB) technique have been validated in photon radiotherapy, we applied the SIB technique to CIRT. The aim was to investigate the metabolomic changes of the CIRT with concurrent androgen deprivation therapy (ADT) in localized prostate cancer (PCa) and the unique metabolic effect of the SIB technique. Material and Methods This study enrolled 24 pathologically confirmed PCa patients. All patients went through CIRT with concurrent ADT. The gross target volume (GTV) boost was defined as positive lesions on both 68Ga-PSMA PET/CT and mpMRI images. Urine samples collected before and after CIRT were analyzed by the Q-TOF UPLC-MS/MS system. R platform and MetDNA were used for peak detection and identification. Statistical analysis and metabolic pathway analysis were performed on Metaboanalyst. Results The metabolite profiles were significantly altered after CIRT. The most significantly altered metabolic pathway is PSMA participated alanine, aspartate and glutamate metabolism. Metabolites in this pathway showed a trend to be better suppressed in the SIB group. A total of 11 identified metabolites were significantly discriminative between two groups and all of them were better down-regulated in the SIB group. Meanwhile, among these metabolites, three metabolites in DNA damage and repair related purine metabolism were down-regulated to a greater extent in the SIB group. Conclusion Metabolic dysfunction was one of the typical characteristics of PCa. CIRT with ADT showed a powerful inhibition of PCa metabolism, especially in PSMA participated metabolic pathway. The SIB CIRT showed even better performance on down-regulation of most metabolism than uniform-dose-distribution CIRT. Meanwhile, the SIB CIRT also showed its unique superiority to inhibit purine metabolism. PSMA PET/CT guided SIB CIRT showed its potentials to further benefit PCa patients.
Changes on the conformational and functional properties of soybean protein isolate induced by quercetin

The conformational changes and functional properties of SPI induced by quercetin was investigated via fourier transform infrared (FTIR) spectroscopy, fluorescence spectroscopy, circular dichroism (CD) spectroscopy and molecular docking. A decrease in the fluorescence intensity and a blue shift in the maximum wavelength were observed due to the binding process with fluorescent residues. The analysis of Stern-Volmer equation showed that the fluorescence quenching induced by quercetin took the form of static quenching, and the binding stoichiometry between SPI and quercetin was 1:1. The values of ΔH and ΔS were both positive illustrating that hydrophobic interaction was the primary binding force between quercetin and SPI. Results of FTIR and CD indicated that the binding with quercetin changed the secondary structure of SPI, resulting in a partially unfolded and more flexible structure. SDS-PAGE confirmed there was no covalent interaction between the two constituents. Molecular docking demonstrated that there were stable configurations and high matching degrees in both 11S and 7S proteins with quercetin via hydrogen bonds and hydrophobic interactions. Meanwhile, modification by quercetin enhanced the foaming and emulsifying capacities of SPI. These findings might provide theory reference for elucidation the mechanism of polyphenols-proteins interaction and development of related food additive products in future.
Niche-Neutral Continuum Seems to Explain the Global Niche Differentiation and Local Drift of the Human Digestive Tract Microbiome

The human digestive tract (DT) is differentiated into diverse niches and harbors the greatest microbiome diversity of our bodies. Segata et al. (2012) found that the microbiome of diverse habitats along the DT may be classified as four categories or niches with different microbial compositions and metabolic potentials. Nonetheless, few studies have offered theoretical interpretations of the observed patterns, not to mention quantitative mechanistic parameters. Such parameters should capture the essence of the fundamental processes that shape the microbiome distribution, beyond simple ecological metrics such as diversity or composition descriptors, which only capture the manifestations of the mechanisms. Here, we aim to get educated guesses for such parameters by adopting an integrated approach with multisite neutral (MSN) and niche-neutral hybrid (NNH) modeling, via reanalyzing Segata’s 16s-rRNA samples covering 10 DT-sites from over 200 healthy individuals. We evaluate the relative importance of the four essential processes (drift, dispersal, speciation, and selection) in shaping the microbiome distribution and dynamics along DT, which are assumed to form a niche-neutral continuum. Furthermore, the continuum seems to be hierarchical: the selection or niche differentiations seem to play a predominant role (> 90% based on NNH) at the global (the DT metacommunity) level, but the neutral drifts seem to be prevalent (> 90% based on MSN/NNH) at the local sites except for the gut site. An additional finding is that the DT appears to have a fifth niche for the DT microbiome, namely, Keratinized gingival (KG), while in Segata’s original study, only four niches were identified. Specifically, in Segata’s study, KG was classified into the same niche type including buccal mucosa (BM), hard palate (HP), and KG. However, it should be emphasized that the proposal of the fifth niche of KG requires additional verification in the future studies.
Oral anticoagulant decreases stroke recurrence in patients with atrial fibrillation detected after stroke

Background Atrial fibrillation detected after stroke (AFDAS) has a lower risk of ischemic stroke recurrence than known atrial fibrillation (KAF). While the benefit of oral anticoagulants (OAC) for preventing ischemic stroke recurrence in KAF is well established, their role in patients with AFDAS is more controversial. This study aimed to evaluate the association between OAC use and the risk of recurrent ischemic stroke in patients with AFDAS in a real-world setting. Methods This nationwide retrospective cohort study was conducted using the Taiwan National Health Insurance Research Database. Patients hospitalized with a first-ever ischemic stroke and AFDAS confirmed within 30 days after hospitalization were assigned to OAC and non-OAC cohorts. Inverse probability of treatment weighting was applied to balance the baseline characteristics of the cohorts. The primary outcome was ischemic stroke recurrence. Secondary outcomes were intracranial hemorrhage (ICH), death, and the composite outcome of “ischemic stroke recurrence, ICH, or death. ” Multivariate Cox proportional hazard models were used to estimate adjusted hazard ratios (aHR) and 95% confidence intervals (CI). Results A total of 4,508 hospitalized patients with stroke and AFDAS were identified. Based on OAC use, 2,856 and 1,652 patients were assigned to the OAC and non-OAC groups, respectively. During the follow-up period (median duration, 2.76 years), the OAC cohort exhibited a lower risk of ischemic stroke recurrence (aHR, 0.84; 95% CI, 0.70–0.99), death (aHR, 0.65; 95% CI, 0.58–0.73), and composite outcome (aHR, 0.70; 95% CI, 0.63–0.78) than did the non-OAC cohort. The risk of ICH (aHR, 0.96; 95% CI, 0.62–1.50) was not significantly different between the two cohorts. Conclusion OAC use in patients with AFDAS was associated with reduced risk of ischemic stroke recurrence, without an increased risk of ICH. This supports current guidelines recommending OACs for secondary stroke prevention in patients with AF, regardless of the time of diagnosis.
Why should sarcopenic obesity be included in a routine assessment during weight-management programmes?

COPYRIGHT © 2022 El Ghoch and Pellegrini. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. TYPE Opinion PUBLISHED 22 July 2022 DOI 10.3389/fendo.2022. 962895