Contributors: Ruff, Zachary J., Lesmeister, Damon B., Duchac, Leila S., Padmaraju, Bharath K., Sullivan, Christopher M.
... This repository contains all the code and data necessary to replicate the results presented in Ruff et al. "Automated identification of avian vocalizations with deep convolutional neural networks", currently in revision, and is published in support of that manuscript. The folder includes several Python scripts, our trained convolutional neural network (CNN), and a set of 164,210 spectrogram images that were reviewed to generate CNN performance metrics. We include the CNN's predicted class scores for the test images as well as the set of labels assigned to the same images by experienced human technicians. We will update this description with a link to the article upon publication. As presented, the CNN is designed to accept grayscale PNG images at 500x129 resolution and will generate a set of seven class scores for each image. Class scores are the softmax activation from the final (seven unit) fully-connected layer of the CNN. Scores are bounded between 0 and 1 and sum to 1 for each image. This means target classes are implicitly treated as mutually exclusive (i.e., each image belongs to exactly one class), although in reality some images contain calls from >1 target species. The different scripts and their functions are as follows: - Code used to construct and train the CNN is in Owl_CNN_train_model.py - Code to generate spectrograms with randomized parameters based on tagged calls in audio files is in Owl_CNN_generate_training_data.py - Code to generate random spectrograms from a set of audio files (used to generate training data for the Noise class) can be generated with Owl_CNN_make_noise_data.py - Code used to process raw audio files, including segmenting them into 12 s clips, generating spectrograms, and generating class scores using a pre-trained CNN is in Owl_CNN_process_audio.py - Code to generate class scores for an existing set of spectrogram images using a pre-trained CNN are in Owl_CNN_process_images.py Our seven target classes are as follows: AEAC - Northern saw-whet owl, Aegolius acadicus. BUVI - Great horned owl, Bubo virginianus. GLGN - Northern pygmy-owl, Glaucidium gnoma. MEKE - Western screech-owl, Megascops kennicottii. STOC - (Northern) spotted owl, Strix occidentalis caurina. STVA - Barred owl, Strix varia. Noise - Catch-all for any clip that did not contain vocalizations of at least one of the six owl species listed above. The CNN was trained for 100 epochs and saved only after epochs in which validation loss improved. Loss was measured as categorical cross-entropy. The CNN was last saved at epoch 97 with reported metrics: Training loss = 0.218 Training accuracy = 0.972 Validation loss = 0.165 Validation accuracy = 0.987 Although this code has been tested and works on our system, we make no guarantee that it will work for others without modification. Created using Python version 2.7.14, TensorFlow version 1.2.1, Keras version 2.2, and SoX version 14.4. Code was developed by Bharath Padmaraju, Zack Ruff, and Chris Sullivan. Questions and comments may be directed to zjruff at gmail dot com. Zack Ruff 15 July 2019
Contributors: SXS Collaboration
... Simulation of a black-hole binary system evolved by the SpEC code.
FADN data on the support under the CAP delimited for LAU2 (NUTS2) regions in the EU Member States for the 2007-2013 programming period
Contributors: Pawel Chmielinski, Aleksandra Pawłowska, Monika Bocian
... Ready to use FADN dataset on the support under the CAP in 2007-2013 delimited for LAU2 (NUTS2) regions in the EU Member States. Investigation of the interaction between Cohesion and Rural Policies requires analysing comparable data. However, the CAP data are usually collected at the national level. The FADN database is the only data source for analysing the impact of agricultural policy instruments on the economic situation of farms. However, the regional breakdown of FADN data in some countries does not correspond to the NUTS2 breakdown for which cohesion policy is defined. The provided FADN data delimitation uses a methodology that takes into account the range of impact and features specific to a given region. Because the research shows a very strong relationship between the amount of support under the CAP and the number and size of farms on a given area, this criterion was used to delimit FADN data for particular LAU2 (NUTS2) regions, while maintaining the allocation to individual measures. FADN data aggregated (averaged) to the level of FADN regions and economic size classes were used. Each FADN region has been assigned a corresponding NUTS2 region (or regions) according to the classification in 2010 in which the full census of the farm structure survey was carried out. The delimitation of FADN data to NUTS2 regions was based on weights constructed on the basis of Eurostat data on utilised agricultural area and number of holdings in 2010. In each economic size class, each FADN region consisted of the sum of the NUTS2 regions weighted by the utilised agricultural area. The result of each FADN variable was the sum of its values in each economic size class, weighted by the total number of holdings in each class. This database has served as a basis for two articles, one validating the assumptions of the NUTS2 (LAU) delimitation of the FADN regions and the other using the database to compare synergies and trade-offs between cohesion policy and the common agricultural policy.
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Contributors: Semyon Tikhonov, Alexey A. Mitsyuk
... This repository contains data that was used to carry out experiments as well as the results of these experiments. File names are presented in the following format: LM2-[repair method]-[b/f]-[number of experiment], where: - repair method may take values "Greedy" or "Smart". "Greedy" means that the repair method of the model was greedy algorithm working with maximal decomposition. "Smart" means that the repair method was greedy algorithm as well, with the difference of decomposition method being the developed one. - "b" (broken) means that the model has not undergone repair. "f" (fixed) means that the file presents a repaired model (the one which fits the initial log perfectly). - number of experiment ranging from 1 to 10. This repository also contains the following files: - LM2-CL.xes - the initial LM2 model log; - LM2-CM.pnml - the initial LM2 model; - LM2-Greedy-data.txt - auto-generated measurements of greedy approach performance; - LM2-Smart-data.txt - auto-generated measurements of smart (developed) approach perfomance.
Contributors: Bird, Philippa K, McEachan, Rosemary R. C., Mon-Williams, Mark, Small, Neil, West, Jane, Whincup, Peter, Wright, John, Andrews, Elizabeth, Barber, Sally E, Hill, Liam J B
... Background: Born in Bradford (BiB) is a prospective multi-ethnic pregnancy and birth cohort study that was established to examine determinants of health and development during childhood and, subsequently, adult life in a deprived multi-ethnic population in the north of England. Between 2007 and 2010, the BiB cohort recruited 12,453 women who experienced 13,776 pregnancies and 13,858 births, along with 3353 of their partners. Forty five percent of the cohort are of Pakistani origin. Now that children are at primary school, the first full follow-up of the cohort is taking place. The aims of the follow-up are to investigate the determinants of children's pre-pubertal health and development, including through understanding parents' health and wellbeing, and to obtain data on exposures in childhood that might influence future health.Methods: We are employing a multi-method approach across three data collection arms (community-based family visits, school based physical assessment, and whole classroom cognitive, motor function and wellbeing measures) to follow-up over 9000 BiB children aged 7–11 years and their families between 2017 and 2021. We are collecting detailed parent and child questionnaires, cognitive and sensorimotor assessments, blood pressure, anthropometry and blood samples from parents and children. Dual x-ray absorptiometry body scans, accelerometry and urine samples are collected on subsamples. Informed consent is collected for continued routine data linkage to health, social care and education records. A range of engagement activities are being used to raise the profile of BiB and to disseminate findings.Discussion: Our multi-method approach to recruitment and assessment provides an efficient method of collecting rich data on all family members. Data collected will enhance BiB as a resource for the international research community to study the interplay between ethnicity, socioeconomic circumstances and biology in relation to cardiometabolic health, mental health, education, cognitive and sensorimotor development and wellbeing.
Contributors: Michiel de Jong
... Dutch slide deck designed for a workshop on the Open Educational Practice of co-creating a course with students by writing an open textbook. Deze powerpoint presentatie is toegepast in een workshop op de SURF onderwijsdagen in 2018. Deze workshop introduceert twee aspecten van Open Education.: Het open textbook en co-creatie van leermaterialen. Het open textbook is een Open Educational Resource (OER). Het open textbook is dynamische onderwijsliteratuur die gemakkelijk bewerkbaar is door de auteur zelf, maar ook door anderen, naar hete 5R model voor OER van David Wiley. Co-creatie van leermaterialen wordt in deze workshop geintroduceerd, door deelnemers uit te dagen een cursus te ontwerpen waarbij zij als docent samen met hun studenten een open textbook ontwerpen. Dit wordt gedaan aan de hand van een drietal casussen.
Share and protect our health data: an evidence based approach to rare disease patients' perspectives on data sharing and data protection - quantitative survey and recommendations
Contributors: Courbier, Sandra, Dimond, Rebecca, Bros-Facer, Virginie
... Background: The needs and benefits of sharing health data to advance scientific research and improve clinical benefits have been well documented in recent years, specifically in the field of rare diseases where knowledge and expertise are limited and patient populations are geographically dispersed. Understanding what patients want and need from rare disease research and data sharing is important to ensure their participation and engagement in the process, and to ensure that these wishes and needs are embedded within research design. EURORDIS-Rare Diseases Europe regularly surveys the rare disease community to identify its perspectives and needs on a number of issues in order to represent rare disease patients and be their voice within European and International initiatives and policy developments.Here, we present key findings from a large quantitative survey conducted with patients with rare diseases and family members as part of a continuous evidence-based advocacy process developed at EURORDIS. The aim of this survey was to explore patient and family perspectives on data sharing and data protection in research and healthcare settings and develop relevant recommendations to support shaping of future data sharing initiatives in rare disease research.This survey, translated into 23 languages, was carried out via the Rare Barometer Programme and was designed to be accessible to a diverse population with a wide range of education backgrounds. It was widely disseminated via patient organisations worldwide to ensure that a wide range of voices and experiences were represented.Main findings: Rare disease patients, regardless of the severity of their disease and their socio-demographic profile, are clearly supportive of data sharing to foster research and improve healthcare. However, rare disease patients' willingness to share their data does come with specific requirements in order to respect their privacy, choices and needs for information regarding the use of their data.Conclusions: To ensure sustainability and success of international data sharing initiatives in health and research for rare diseases, appropriate legislations need to be implemented and multi-stakeholder efforts need to be pursued to foster cultural and technological changes enabling the systematic integration of patients' preferences regarding sharing of their own health data.
Catastrophic health expenditure and impoverishment in households of persons with depression: a cross-sectional, comparative study in rural Ethiopia
Contributors: Hailemichael, Yohannes, Hanlon, Charlotte, Tirfessa, Kebede, Docrat, Sumaiyah, Alem, Atalay, Medhin, Girmay, Lund, Crick, Chisholm, Dan, Fekadu, Abebaw, Hailemariam, Damen
... Background: The extent of catastrophic health expenditure and impoverishment associated with depression in low-and middle-income countries is not known. The aim of this study was to estimate the incidence and intensity of catastrophic out-of-pocket (OOP) health expenditure, level of impoverishment and coping strategies used by households of persons with and without depression in a rural Ethiopian district.Methods: A comparative cross-sectional survey was conducted, including 128 households of persons with depression and 129 households without. Depression screening was conducted using the Patient Health Questionnaire, nine item version (PHQ-9). People in the depression group were classified into high and low disability groups based on the median value on the World Health Organization Disability Assessment Schedule (WHODAS) polytomous summary score.Health expenditure greater than thresholds of 10 and 25% of total household consumption was used for the primary analyses. The poverty headcount, poverty gap and normalized poverty gap were estimated using retrospective recall of total household expenditure pre- and post-OOP payments for health care. Linear probability model using binreg command in STATA with rr option was used to estimate risk ratio for the occurrence of outcomes among households with and without depression based on level of disability.Results: Catastrophic OOP payments at any threshold level for households with depression and high disability were higher than control households. At the 10% threshold level, 24.0% of households of persons with depression and high disability faced catastrophic payments compared with 15.3% for depression and low disability and 12.1% for control households (p = 0.041). Depression and high disability level was an independent predictor of catastrophic OOP payments: RR 2.1; 95% CI:1.1, 4.6.An estimated 5.8% of households of persons with depression and high disability were pushed into poverty because of paying for health care compared with 3.5% for households of persons with depression and low disability and 2.3% for control households (p = 0.039).Conclusions: Households of people with depression and high disability were more likely to face catastrophic expenditures and impoverishment from OOP payments. Financial protection interventions through prepayment schemes, exemptions and fee waiver strategies need to target households of persons with depression.
Contributors: Coen, Olivier, Lu, Jing, Xu, Wenjia, De Vos, Delphine, Péchoux, Christine, Domergue, Frédéric, Grain, Damaris, Lepiniec, Loïc, Magnani, Enrico
... Background: In flowering plants, proper seed development is achieved through the constant interplay of fertilization products, embryo and endosperm, and maternal tissues. Communication between these compartments is supposed to be tightly regulated at their interfaces. Here, we characterize the deposition pattern of an apoplastic lipid barrier between the maternal inner integument and fertilization products in Arabidopsis thaliana seeds.Results: We demonstrate that an apoplastic lipid barrier is first deposited by the ovule inner integument and undergoes de novo cutin deposition following central cell fertilization and relief of the FERTILIZATION INDEPENDENT SEED Polycomb group repressive mechanism. In addition, we show that the WIP zinc-finger TRANSPARENT TESTA 1 and the MADS-Box TRANSPARENT TESTA 16 transcription factors act maternally to promote its deposition by regulating cuticle biosynthetic pathways. Finally, mutant analyses indicate that this apoplastic barrier allows correct embryo sliding along the seed coat.Conclusions: Our results revealed that the deposition of a cutin apoplastic barrier between seed maternal and zygotic tissues is part of the seed coat developmental program.
A nemertean excitatory peptide/CCHamide regulates ciliary swimming in the larvae of Lineus longissimus
Contributors: Thiel, Daniel, Bauknecht, Philipp, Jékely, Gáspár, Hejnol, Andreas
... Background: The trochozoan excitatory peptide (EP) and its ortholog, the arthropod CCHamide, are neuropeptides that are only investigated in very few animal species. Previous studies on different trochozoan species focused on their physiological effect in adult specimens, demonstrating a myo-excitatory effect, often on tissues of the digestive system. The function of EP in the planktonic larvae of trochozoans has not yet been studied.Results: We surveyed transcriptomes from species of various spiralian (Orthonectida, Nemertea, Brachiopoda, Entoprocta, Rotifera) and ecdysozoan taxa (Tardigrada, Onychophora, Priapulida, Loricifera, Nematomorpha) to investigate the evolution of EPs/CCHamides in protostomes. We found that the EPs of several pilidiophoran nemerteans show a characteristic difference in their C-terminus. Deorphanization of a pilidiophoran EP receptor showed, that the two splice variants of the nemertean Lineus longissimus EP activate a single receptor. We investigated the expression of EP in L. longissimus larvae and juveniles with customized antibodies and found that EP positive nerves in larvae project from the apical organ to the ciliary band and that EP is expressed more broadly in juveniles in the neuropil and the prominent longitudinal nerve cords. While exposing juvenile L. longissimus specimens to synthetic excitatory peptides did not show any obvious effect, exposure of larvae to either of the two EPs increased the beat frequency of their locomotory cilia and shifted their vertical swimming distribution in a water column upwards.Conclusion: Our results show that EP/CCHamide peptides are broadly conserved in protostomes. We show that the EP increases the ciliary beat frequency of L. longissimus larvae, which shifts their vertical distribution in a water column upwards. Endogenous EP may be released at the ciliary band from the projections of apical organ EP positive neurons to regulate ciliary beating. This locomotory function of EP in L. longissimus larvae stands in contrast to the repeated association of EP/CCHamides with its myo-excitatory effect in adult trochozoans and the general association with the digestive system in many protostomes.