There You Are! Automated Detection of Indris’ Songs on Features Extracted from Passive Acoustic Recordings

From MDPI via Jisc Publications RouterHistory: received 2022-12-07, rev-recd 2022-12-21, accepted 2022-12-28, collection 2023-01, epub 2023-01-09Peer reviewed: TrueAcknowledgements: Acknowledgments: We are grateful to the local field guides and the assistants that helped during the data collection. We also wish to thank the GERP (Groupe d’Étude et de Recherche sur les Primates de Madagascar) for their unfailing support during the research activities and to the Parco Natura Viva for the financial and technical assistance. Data collection was carried out under research permits No. 118/19/MEDD/SG/DGEF/DSAP/DGRNE, 284/19/MEDD/SG/DGEF/DSAP/DGRNE, and 338/19/MEDD/G/DGEF/DSAP/DGRNE issued by the Ministère de l’Environnement et du Développement Durable (MEDD). Data collection in 2021 did not require a permit because it was only performed by Malagasy citizens.Article version: VoRPublication status: PublishedFunder: University of TorinoFunder: Parco Natura Viva—Garda Zoological ParksFunder: UIZA—the Italian Association of Zoos and AquariaSimple Summary: Identifying vocalisations of given species from passive acoustic recordings is a common step in bioacoustics. While manual labelling and identification are widespread, this approach is time-consuming, prone to errors, and unsustainable in the long term, given the vast amount of data collected through passive monitoring. We developed an automated classifier based on a convolutional neural network (CNN) for passive acoustic data collected via an in situ monitoring protocol. In particular, we aimed to detect the vocalisations of the only singing lemur, Indri indri. Our network achieved a very high performance (accuracy >90% and recall >80%) in song detection. Our study contributes significantly to the automated wildlife detection research field because it represents a first attempt to combine a CNN and acoustic features based on a third-octave band system for song detection. Moreover, the automated detection provided insights that will improve field data collection and fine-tune conservation practices. Abstract: The growing concern for the ongoing biodiversity loss drives researchers towards practical and large-scale automated systems to monitor wild animal populations. Primates, with most species threatened by extinction, face substantial risks. We focused on the vocal activity of the indri (Indri indri) recorded in Maromizaha Forest (Madagascar) from 2019 to 2021 via passive acoustics, a method increasingly used for monitoring activities in different environments. We first used indris’ songs, loud distinctive vocal sequences, to detect the species’ presence. We processed the raw data (66,443 10-min recordings) and extracted acoustic features based on the third-octave band system. We then analysed the features extracted from three datasets, divided according to sampling year, site, and recorder type, with a convolutional neural network that was able to generalise to recording sites and previously unsampled periods via data augmentation and transfer learning. For the three datasets, our network detected the song presence with high accuracy (>90%) and recall (>80%) values. Once provided the model with the time and day of recording, the high-performance values ensured that the classification process could accurately depict both daily and annual habits of indris‘ singing pattern, critical information to optimise field data collection. Overall, using this easy-to-implement species-specific detection workflow as a preprocessing method allows researchers to reduce the time dedicated to manual classification

New genetic loci link adipose and insulin biology to body fat distribution.

Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic outcomes, independent of overall adiposity. To increase our understanding of the genetic basis of body fat distribution and its molecular links to cardiometabolic traits, here we conduct genome-wide association meta-analyses of traits related to waist and hip circumferences in up to 224,459 individuals. We identify 49 loci (33 new) associated with waist-to-hip ratio adjusted for body mass index (BMI), and an additional 19 loci newly associated with related waist and hip circumference measures (P < 5 × 10(-8)). In total, 20 of the 49 waist-to-hip ratio adjusted for BMI loci show significant sexual dimorphism, 19 of which display a stronger effect in women. The identified loci were enriched for genes expressed in adipose tissue and for putative regulatory elements in adipocytes. Pathway analyses implicated adipogenesis, angiogenesis, transcriptional regulation and insulin resistance as processes affecting fat distribution, providing insight into potential pathophysiological mechanisms

Ramucirumab plus docetaxel versus placebo plus docetaxel in patients with locally advanced or metastatic urothelial carcinoma after platinum-based therapy (RANGE): a randomised, double-blind, phase 3 trial

Few treatments with a distinct mechanism of action are available for patients with platinum-refractory advanced or metastatic urothelial carcinoma. We assessed the efficacy and safety of treatment with docetaxel plus either ramucirumab-a human IgG1 VEGFR-2 antagonist-or placebo in this patient population

The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome

Abstract Background Molecular alterations critical to development of cancer include mutations, copy number alterations (amplifications and deletions) as well as genomic rearrangements resulting in gene fusions. Massively parallel next generation sequencing, which enables the discovery of such changes, uses considerable quantities of genomic DNA (> 5 ug), a serious limitation in ever smaller clinical samples. However, a commonly available microarray platforms such as array comparative genomic hybridization (array CGH) allows the characterization of gene copy number at a single gene resolution using much smaller amounts of genomic DNA. In this study we evaluate the sensitivity of ultra-dense array CGH platforms developed by Agilent, especially that of the 1 million probe array (1 M array), and their application when whole genome amplification is required because of limited sample quantities. Methods We performed array CGH on whole genome amplified and not amplified genomic DNA from MCF-7 breast cancer cells, using 244 K and 1 M Agilent arrays. The ADM-2 algorithm was used to identify micro-copy number alterations that measured less than 1 Mb in genomic length. Results DNA from MCF-7 breast cancer cells was analyzed for micro-copy number alterations, defined as measuring less than 1 Mb in genomic length. The 4-fold extra resolution of the 1 M array platform relative to the less dense 244 K array platform, led to the improved detection of copy number variations (CNVs) and micro-CNAs. The identification of intra-genic breakpoints in areas of DNA copy number gain signaled the possible presence of gene fusion events. However, the ultra-dense platforms, especially the densest 1 M array, detect artifacts inherent to whole genome amplification and should be used only with non-amplified DNA samples. Conclusions This is a first report using 1 M array CGH for the discovery of cancer genes and biomarkers. We show the remarkable capacity of this technology to discover CNVs, micro-copy number alterations and even gene fusions. However, these platforms require excellent genomic DNA quality and do not tolerate relatively small imperfections related to the whole genome amplification.</p

Interval Changes in PSMA PET/CT During Radium-223 Therapy for Metastatic Bone Disease from Castration-Resistant Prostate Cancer

Background: Radium-223, an alpha-emitting therapeutic radiopharmaceutical, prolongs overall survival (OS) in patients with symptomatic bone-predominant metastatic castration-resistant prostate cancer (mCRPC). PSMA PET/CT is a molecular imaging tool for whole-body imaging of prostate cancer and may inform on the mechanisms of radium-223 activity and treatment resistance in mCRPC patients. Methods: In an open-label, single-arm, prospective trial, we enrolled patients with bone-predominant mCRPC to undergo baseline PSMA PET/CT, 6 cycles of radium-223, and post-therapy PSMA PET/CT. We assessed the relationship between multiple parameters of interval change on PSMA PET/CT on aPROMISE PSMA automated analysis and a human reader, and laboratory measurements. Results: Fourteen patients were enrolled and 9 patients completed both protocol-defined PSMA PET/CT. Of the 9 evaluable patients, 1 (11%) had a complete response and 8 (89%) had PSMA PET progressive disease. All patients showed decreases in PSMA uptake in some disease sites evident on the baseline scan. The change in overall burden of disease on PSMA PET was more strongly correlated with changes in PSA (ρ = 0.95) than ALP (ρ = 0.62). Progression in bone was a common finding on post-treatment PSMA PET/CT. Conclusion: PSMA PET was able to assess response in individual lesions during radium-223 therapy in mCRPC patients. PSMA PET responses in previously established disease sites were universal, but most patients also showed overall PSMA PET progression during 6 cycles of radium-223. Given high correlation with changes in PSA, PSMA PET may be of limited value in follow-up during or after radium-223 in bone-predominant mCRPC. Graphical abstract: [Figure not available: see fulltext.