To evaluate the performance of the Prostate Health Index (PHI) in magnetic resonance imaging-transrectal ultrasound (MRI-TRUS) fusion prostate biopsy for the detection of clinically significant ...prostate cancer (csPCa). We prospectively enrolled 164 patients with at least one Prostate Imaging Reporting and Data System version 2 (PI-RADS v2) ≥ 3 lesions who underwent MRI-TRUS fusion prostate biopsy. Of the PSA-derived biomarkers, the PHI had the best performance in predicting csPCa (AUC 0.792, CI 0.707-0.877) in patients with PI-RADS 4/5 lesions. Furthermore, the predictive power of PHI was even higher in the patients with PI-RADS 3 lesions (AUC 0.884, CI 0.792-0.976). To minimize missing csPCa, we used a PHI cutoff of 27 and 7.4% of patients with PI-RADS 4/5 lesions could have avoided a biopsy. At this level, 2.0% of cases with csPCa would have been missed, with sensitivity and NPV rates of 98.0% and 87.5%, respectively. However, the subgroup of PI-RADS 3 was too small to define the optimal PHI cutoff. PHI was the best PSA-derived biomarker to predict csPCa in MRI-TRUS fusion prostate biopsies in men with PI-RADS ≥ 3 lesions, especially for the patients with PI-RADS 3 lesions who gained the most value.
MicroRNAs (miRNAs) are small non-coding RNA molecules capable of negatively regulating gene expression to control many cellular mechanisms. The miRTarBase database ...(http://mirtarbase.mbc.nctu.edu.tw/) provides the most current and comprehensive information of experimentally validated miRNA-target interactions. The database was launched in 2010 with data sources for >100 published studies in the identification of miRNA targets, molecular networks of miRNA targets and systems biology, and the current release (2013, version 4) includes significant expansions and enhancements over the initial release (2010, version 1). This article reports the current status of and recent improvements to the database, including (i) a 14-fold increase to miRNA-target interaction entries, (ii) a miRNA-target network, (iii) expression profile of miRNA and its target gene, (iv) miRNA target-associated diseases and (v) additional utilities including an upgrade reminder and an error reporting/user feedback system.
Rational syntheses under controllable reducing conditions in the preparation of superatoms with cluster electron number not exceeding two are challenging. Herein a dithiolate‐stabilized two‐electron ...silver nanocluster, Ag10{S2P(OiPr)2}8 (1), is isolated via a self‐redox reaction of Ag7(H){S2P(OiPr)2}6 without adding extra reducing agents. The metal framework of Ag7, a bicapped trigonal bipyramid, is highly correlated to that of Ag10, suggesting Ag7(H){S2P(OiPr)2}6 acts as both reducing agent and template in cluster growth. 1 is highly fluorescent at ambient temperature and TD‐DFT calculations indicate that the emission is of 1Px→1S nature.
A self‐redox reaction of Ag7(H){S2P(OiPr)2}6 leads to the formation of a highly emissive, two‐electron Ag nanocluster, Ag10{S2P(OiPr)2}8, without adding extra reducing agents. The metal framework of Ag7, a bicapped trigonal bipyramid, is highly correlated to that of Ag10, suggesting Ag7(H){S2P(OiPr)2}6 acts as both reducing agent and template in cluster growth.
Information on biodiversity is essential to evaluate the ecological status of coral reefs. Sounds produced by reef-associated organisms have been used as a biodiversity indicator. However, the ...interference from abiotic sounds and the lack of a comprehensive audio library have impeded effective evaluation. This study investigated the application of underwater soundscapes as a remote-sensing method to detect biological and anthropogenic activities. Using techniques including the visualization of long-duration recordings, source separation, and clustering, soundscapes were separated into sounds of anthropogenic and biological sources. Our results revealed the dynamics of biological sounds among coral reefs off Sesoko Island, Okinawa, Japan. Biological sounds were much more prominent in shallow-water reefs than in upper-mesophotic reefs, but their spectral features and compositions differed. The shallow-water reefs were dominated by broadband sounds of crustaceans and low-frequency transient fish calls, whereas the upper-mesophotic reefs were characterized by a diverse array of fish choruses and transient sounds. We also discovered that shipping noise heavily interfered with the soundscapes from the upper-mesophotic reefs and represented an invisible threat to life in the low-light habitat. The applied techniques of soundscape information retrieval revealed the distinct ecological status of coral reefs and the behavior change of sound-producing organisms in high temporal resolution. Implementation of soundscape monitoring can generate ecological information on habitat quality, reef biodiversity, human activities, and their interactions. Global collaboration on underwater soundscapes will establish a data-informed platform and help stakeholders assess the resilience of coral reefs to environmental and anthropogenic stressors.
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Underwater soundscapes, though invisible, are crucial in shaping the biodiversity of marine ecosystems by acting as habitat‐specific settlement cues for larvae. The deep sea has received little ...attention in soundscape research, but it is being targeted for mineral extraction to feed the ever‐growing needs of our society. Anthropogenic impacts on soundscapes influence the resilience of key shallow‐water habitats, and the same likely applies to the deep. Japan is a forerunner in deep‐sea mining, but virtually no deep soundscape baselines exist for Japanese waters. Here, we report baseline soundscapes from four deep‐sea locations in Japan, including the Suiyo Seamount hydrothermal vent, the abyssal plain around the Minamitorishima Island home to manganese nodule fields and muds rich in rare‐earth elements, twilight depths off Sanriku, as well as a typical bathyal system in Suruga Bay. Long‐duration audio recordings were visualized and factorized by an unsupervised machine learning model, revealing differing characteristics among the habitats. Two locations near the coast are highly influenced by shipping noise. The Suiyo vent is characterized by low‐frequency sounds from venting, and the abyssal Minamitorishima is quiet with a flat spectral shape. Noise from observation platforms is likely sufficient to alter soundscape characteristics, especially in offshore locations, suggesting offshore mining‐targeted areas are susceptible to impacts from anthropogenic noise. We argue that the monitoring of soundscapes is an indispensable component for assessing potential mining impacts on deep‐sea ecosystems. Our results establish reference points for future soundscape monitoring and assessment in Japanese waters as well as similar ecosystems globally.
Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or ...culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA), Atypical, and leukocytes). Computer-assisted semen analysis (CASA) was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%), Pseudomonas (9.85%), Prevotella (8.51%) and Gardnerella (4.21%). The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6%) were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
A comprehensive assessment of ecosystem dynamics requires the monitoring of biological, physical and social changes. Changes that cannot be observed visually may be trackable acoustically through ...soundscape analysis. Soundscapes vary greatly depending on geophysical events, biodiversity and human activities. However, retrieving source‐specific information from geophony, biophony and anthropophony remains a challenging task, due to interference by simultaneous sound sources. Audio source separation is a technique that aims to recover individual sound sources when only mixtures are accessible. Here, we review techniques of monoaural audio source separation with the fundamental theories and assumptions behind them. Depending on the availability of prior information about the source signals, the task can be approached as a blind source separation or a model‐based source separation. Most blind source separation techniques depend on assumptions about the behaviour of the source signals, and their performance may deteriorate when the assumptions fail. Model‐based techniques generally do not require specific assumptions, and the models are directly learned from labelled data. With the recent advances of deep learning, the model‐based techniques can yield state‐of‐the‐art separation performance, accordingly facilitate content‐based audio information retrieval. Source separation techniques have been adopted in several ecoacoustic applications to evaluate the contributions from biodiversity and anthropogenic disturbance to soundscape dynamics. They can also be employed as nonlinear filters to improve the recognition of bioacoustic signals. To effectively retrieve ecological information from soundscapes, source separation is a crucial tool. We believe that the future integrations of ecological hypotheses and deep learning can realize a high‐performance source separation for ecoacoustics, and accordingly improve soundscape‐based ecosystem monitoring. Therefore, we outline a roadmap for applying source separation to assist in soundscape information retrieval and hope to promote cross‐disciplinary collaboration.
Retrieving source‐specific information from geophony, biophony and anthrophony from soundscapes remains a challenging task. This study reviews modern techniques of monoaural audio source separation with their assumptions and limitations. The review shows that source separation techniques are crucial for assisting the evaluation of soundscape dynamics, and the automated recognition of biological sounds. Future integrations of ecological observations and hypotheses into deep learning can realize a high‐performance source separation for ecoacoustics, and accordingly improve soundscape‐based ecosystem monitoring.
Despite the perpetual darkness of the deep sea, contrasting the sunlit epipelagic waters, many deep‐sea organisms exhibit rhythmic activities. To discern environmental cues that may serve as ...entrainment signals for deep‐sea organisms, this study investigated the soundscape of the abyssal plain south of Minamitorishima Island. Our analysis revealed clear diel and seasonal patterns, primarily driven by evening fish choruses and marine mammal vocalizations. These evening choruses, discernible above the background noise, likely serve as a circadian time cue for organisms capable of perceiving them within the aphotic depths. In addition, the frequent detection of whistles and echolocation clicks suggests this region functions as a foraging ground for marine mammals. These acoustic cues might guide organisms with auditory capabilities toward habitats rich in sinking food debris and whale falls. By elucidating the ecological processes shaping abyssal soundscape dynamics, these findings open new directions for further exploration in deep‐sea chronobiology.
Soundscapes contain rich acoustic information associated with animal behaviours, environmental characteristics and human activities, providing opportunities for predicting biodiversity changes and ...associated drivers. However, assessing the diversity of animal vocalizations remains challenging due to the interference of environmental and anthropogenic noise. A tool for separating sound sources and delineating changes in acoustic signals is crucial for an effective assessment of acoustic diversity.
We present soundscape_IR, an open‐source Python toolbox dedicated to soundscape information retrieval in which nonnegative matrix factorization is applied. This toolbox provides algorithms for supervised and unsupervised source separation (SS). It also enables the use of a snapshot recording for model training and subsequently applying adaptive and semi‐supervised SS when target species produce sounds with varying features and when unseen sound sources are encountered.
Our results demonstrated that SS could enhance the vocalizations of target species, characterize the complexity of vocal repertoires and investigate the spatio‐temporal divergence of soundscapes. In tropical forest soundscapes, the application of SS effectively detected the rutting vocalizations of sika deer and revealed a graded structure in their acoustic characteristics. In subtropical estuarine soundscapes, SS automated the process of identifying distinct biotic and abiotic sounds, and the result uncovered divergent sound compositions between inshore and offshore waters.
Implementation of SS in soundscape analysis offers a promising method for streamlining the assessment of acoustic diversity in diverse environments. Future application of SS will open new directions to acoustically quantify ecological interactions across individual, species and ecosystem levels.
摘要
聲景中充滿了與動物行為、 環境特徵和人類活動相關的豐富訊息， 提供一個絕佳機會， 讓人們得以透過聲音預測生物多樣性的變化趨勢以及相關的驅動機制。 然而， 環境聲音和人為噪音的干擾導致動物聲音多樣性的分析極富挑戰性。 因此，一個能夠分離各種聲音並釐清音訊變化的分析工具， 對於分析聲音多樣性將有至關重要的幫助。
soundscape_IR 是一個 Python 開源工具箱， 運用非負矩陣分解法擷取聲景中的各種訊息， 其提供了基於監督式學習和非監督式學習的聲源分離演算法， 使用者也能夠透過一小段錄音訓練模型， 在後續的分析中， 運用適應性和半監督式聲源分離找出目標物種不同特徵的聲音和其他未曾遇過的聲音。
研究結果顯示， 聲源分離演算法可以在吵雜的錄音中強化目標物種的聲音訊號， 解析動物聲音曲譜的複雜性， 辨別聲景的時空變化趨勢。 在熱帶森林的聲景錄音中， 此工具可有效偵測梅花鹿的發情叫聲， 並揭露其聲學特徵的階層性結構。 在亞熱帶河口的聲景錄音中， 此工具可以自動存別出各種生物和非生物聲音， 揭露近岸和離岸水域在聲音組成的差異。
本研究開發的聲源分離演算法與分析工具提供一個極具前景的聲景研究方法， 能夠簡化聲音多樣性的評估過程， 未來可望有效協助研究者透過聲音訊息量化個體、 物種和生態系等各種層級的交互作用。
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