bnstruct: an R package for Bayesian Network structure learning in the presence of missing data.

Abstract Motivation A Bayesian Network is a probabilistic graphical model that encodes probabilistic dependencies between a set of random variables. We introduce bnstruct, an open source R package to (i) learn the structure and the parameters of a Bayesian Network from data in the presence of missing values and (ii) perform reasoning and inference on the learned Bayesian Networks. To the best of our knowledge, there is no other open source software that provides methods for all of these tasks, particularly the manipulation of missing data, which is a common situation in practice. Availability and Implementation The software is implemented in R and C and is available on CRAN under a GPL licence. Supplementary information Supplementary data are available at Bioinformatics online

Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

Abstract Background Targeted amplicon sequencing of the 16S ribosomal RNA gene is one of the key tools for studying microbial diversity. The accuracy of this approach strongly depends on the choice of primer pairs and, in particular, on the balance between efficiency, specificity and sensitivity in the amplification of the different bacterial 16S sequences contained in a sample. There is thus the need for computational methods to design optimal bacterial 16S primers able to take into account the knowledge provided by the new sequencing technologies. Results We propose here a computational method for optimizing the choice of primer sets, based on multi-objective optimization, which simultaneously: 1) maximizes efficiency and specificity of target amplification; 2) maximizes the number of different bacterial 16S sequences matched by at least one primer; 3) minimizes the differences in the number of primers matching each bacterial 16S sequence. Our algorithm can be applied to any desired amplicon length without affecting computational performance. The source code of the developed algorithm is released as the mopo16S software tool (Multi-Objective Primer Optimization for 16S experiments) under the GNU General Public License and is available at http://sysbiobig.dei.unipd.it/?q=Software#mopo16S. Conclusions Results show that our strategy is able to find better primer pairs than the ones available in the literature according to all three optimization criteria. We also experimentally validated three of the primer pairs identified by our method on multiple bacterial species, belonging to different genera and phyla. Results confirm the predicted efficiency and the ability to maximize the number of different bacterial 16S sequences matched by primers

Farming largemouth bass (Micropterus salmoides) with lettuce (Lactuca sativa) and radicchio (Cichorium intybus) in aquaponics: effects of stocking density on fish growth and quality, and vegetable production

Submitted 2020-06-30 | Accepted 2020-09-01 | Available 2020-12-01https://doi.org/10.15414/afz.2020.23.mi-fpap.79-87The present study assessed the effects of two initial stocking densities (low – LD, 4.23 kg m-3, moderate – MD, 8.05 kg m-3) on growth, health and fillet quality of largemouth bass (Micropterus salmoides), and on yield of lettuce (Lactuca sativa) and radicchio (Cichorium intybus group Rubifolium) produced in a low-tech recirculating aquaponic system. A total of 104 largemouth bass (initial body weight: 236 ± 38 g) were randomly stocked in eight 500 L tanks (four per stocking density) and monitored during a 70-day period. Vegetables yield was similar in LD and MD groups. Lettuce yield (6.33 kg m-2) was in line with typical values, whereas radicchio showed a negligible yield (1.34 kg m-2). Likewise, fish final weight (263 g, on average), specific growth rate (0.17% d-1), feed conversion ratio (2.72), and mortality (4.8%) did not differ between treatments. Fish morphometric indices, slaughter results and fillet quality were not affected by stocking density. In conclusion, the production of lettuce was successful in the tested system, whereas the production of radicchio did not achieve satisfactory results. Growth performances of the largemouth bass were poor and further investigations are required to optimize the rearing of this fish species in low-tech aquaponic systems.Keywords: largemouth bass, lettuce, radicchio, water quality, flesh qualityReferencesBAßMANN, B. et al. (2017). Stress and welfare of African catfish (Clarias gariepinus Burchell, 1822) in a coupled aquaponic system. Water, 9(7), 504. https://doi.org/10.3390/w9070504BROWN, T. G. et al. (2009). Biological synopsis of largemouth bass (Micropterus salmoides). Canadian Manuscript Report of Fisheries and Aquatic Sciences, 2884, v + 27 p.CHAVES-POZO, E. et al. (2019). An overview of the reproductive cycle of cultured specimens of a potential candidate for Mediterranean aquaculture, Umbrina cirrosa. Aquaculture, 505, 137–149. https://doi.org/10.1016/j.aquaculture.2019.02.039CHEN, Y. et al. (2020). Effects of dietary fish oil replacement by soybean oil and L-carnitine supplementation on growth performance, fatty acid composition, lipid metabolism and liver health of juvenile largemouth bass, Micropterus salmoides. Aquaculture, 516, 734596. https://doi.org/10.1016/j.aquaculture.2019.734596PANTANELLA, E. et al. (2012). Aquaponics vs. hydroponics: production and quality of lettuce crop. Acta Horticulturae, 927, 887-893. https://doi.org/10.17660/ActaHortic.2012.927.109RAHMAN, M. M (2015). Role of common carp (Cyprinus carpio) in aquaculture production systems. Frontiers in Life Science, 8(4), 399–410. https://doi.org/10.1080/21553769.2015.1045629RAKOCY, J. E. (2012). Aquaponics: integrating fish and plant culture. In: Tidwell J.H. (Ed), Aquaculture production systems. India: Wiley-Blackwell (pp. 343–386). https://doi.org/10.1002/9781118250105.ch14SAS (Statistical Analysis System). 2013. SAS/STAT(R) 9.2 User’s Guide, second ed. SAS Institute Inc., Cary, NC, USA. Retrieved May 10, 2020 from http://support.sas.com/documentation/cdl/en/statug/63033/HTML/default/viewer.htm#glm_toc.htmSOMERVILLE, C. et al. (2014). Small-scale aquaponic food production. Integrated fish and plant farming. Rome: FAO Fisheries and Aquaculture Technical Paper No. 589. Retrieved May 15, 2020 from http://www.fao.org/3/a-i4021e.pdfSUÁREZ, M. D. et al. (2014). Influence of dietary lipids and culture density on rainbow trout (Oncorhynchus mykiss) flesh composition and quality parameter. Aquaculture Engineering, 63, 16–24. http://dx.doi.org/10.1016/j.aquaeng.2014.09.001SUN, J.-L. et al. (2020). Interactive effect of thermal and hypoxia on largemouth bass (Micropterus salmoides) gill and liver: Aggravation of oxidative stress, inhibition of immunity and promotion of cell apoptosis. Fish & Shellfish Immunology, 98, 923–936. https://doi.org/10.1016/j.fsi.2019.11.056TIDWELL, J. H. et al. (2000). Species profile – Largemouth bass. Southern Regional Aquaculture Center 722. Retrieved May 20, 2020 from http://aquaculture.ca.uky.edu/aquaculture-publications/12TIDWELL, J. H. et al. (2007). Effect of stocking density on growth and water quality for largemouth bass Micropterus salmoides growout in ponds. Journal of the World Aquaculture Society, 29, 79–83. https://doi.org/10.1111/j.1749-7345.1998.tb00302.xTYSON, R. V. et al. (2004). Reconciling water quality parameters impacting nitrification in aquaponics: the pH levels. In: Proceedings of the Florida State Horticultural Society 117, 79–83. Retrieved May 20, 2020 from https://journals.flvc.org/fshs/article/view/858557_11VITULE, J. R. S. et al. (2006). Introduction of the African catfish Clarias gariepinus (Burchell, 1822) into Southern Brazil. Biological Invasions, 8, 677–681. https://doi.org/10.1007/s10530-005-2535-8WANG, Y. et al. (2019). Effect of stocking density on growth, serum biochemical parameters, digestive enzymes activity and antioxidant status of largemouth bass, Micropterus salmoides. Pakistan Journal of Zoology, 51(4), 1509–1517. http://dx.doi.org/10.17582/journal.pjz/2019.51.4.1509.1517WATTS, C. et al. (2016). Evaluation of stocking density during second‐year growth of largemouth bass, Micropterus salmoides, raised indoors in a recirculating aquaculture system. Journal of the World Aquaculture Society, 47(4), 538–543. https://doi.org/10.1111/jwas.12315YILDIZ, H. Y. et al. (2017). Fish welfare in aquaponic systems: its relation to water quality with an emphasis on feed and faeces—A review. Water, 9(1), 13. https://doi.org/10.3390/w9010013YUAN, J. et al. (2019). Analysis of the growth performances, muscle quality, blood biochemistry and antioxidant status of Micropterus salmoides farmed in in-pond raceway systems versus usual-pond systems. Aquaculture, 511, 734241. https://doi.org/10.1016/j.aquaculture.2019.734241

Lightweight and Effective Convolutional Neural Networks for Vehicle Viewpoint Estimation From Monocular Images

Vehicle viewpoint estimation from monocular images is a crucial component for autonomous driving vehicles and for fleet management applications. In this paper, we make several contributions to advance the state-of-the-art on this problem. We show the effectiveness of applying a smoothing filter to the output neurons of a Convolutional Neural Network (CNN) when estimating vehicle viewpoint. We point out the overlooked fact that, under the same viewpoint, the appearance of a vehicle is strongly influenced by its position in the image plane, which renders viewpoint estimation from appearance an ill-posed problem. We show how, by inserting in the model a CoordConv layer to provide the coordinates of the vehicle, we are able to solve such ambiguity and greatly increase performance. Finally, we introduce a new data augmentation technique that improves viewpoint estimation on vehicles that are closer to the camera or partially occluded. All these improvements let a lightweight CNN reach optimal results while keeping inference time low. An extensive evaluation on a viewpoint estimation benchmark and on actual vehicle camera data shows that our method significantly outperforms the state-of-the-art in vehicle viewpoint estimation, both in terms of accuracy and memory footprint

Experimental Demonstration of Partially Disaggregated Optical Network Control Using the Physical Layer Digital Twin

Optical communications and networking are fast becoming the solution to support ever-increasing data traffic across all segments of the network, expanding from core/metro networks to 5G/6G front-hauling. Therefore, optical networks need to evolve towards an efficient exploitation of the infrastructure by overcoming the closed and aggregated paradigm, to enable apparatus sharing together with the slicing and separation of the optical data plane from the optical control. In addition to the advantages in terms of efficiency and cost reduction, this evolution will increase network reliability, also allowing for a fine trade-off between robustness and maximum capacity exploitation. In this work, an optical network architecture is presented based on the physical layer digital twin of the optical transport used within a multi-layer hierarchical control operated by an intent-based network operating system. An experimental proof of concept is performed on a three-node network including up to 1000 km optical transmission, open re-configurable optical add & drop multiplexers (ROADMs) and whitebox transponders hosting pluggable multirate transceivers. The proposed solution is based on GNPy as the optical physical layer digital twin and ONOS as intent-based network operating system. The reliability of the optical control decoupled by the data plane functioning is experimentally demonstrated exploiting GNPy as open lightpath computation engine and software optical amplifier models derived from the component characterization. Besides the lightpath deployment exploiting the modulation format evaluation given a generic traffic request, the architecture reliability is tested mimicking the use case of an automatic failure recovery from a fiber cut

Graphene Oxide Promotes Site-Selective Allylic Alkylation of Thiophenes with Alcohols

The graphene oxide (GO) assisted allylic alkylation of thiophenes with alcohols is presented. Mild reaction conditions and a low GO loading enabled the isolation of a range of densely functionalized thienyl and bithienyl compounds in moderate to high yields (up to 90%). The cooperative action of the Bronsted acidity, epoxide moieties, and pi-surface of the 2D-promoter is highlighted as crucial in the reaction course of the present Friedel-Crafts-type protocol

The need to improve access to rabies post-exposure vaccines: Lessons from Tanzania

Background Rabies is preventable through prompt administration of post-exposure prophylaxis (PEP) to exposed persons, but PEP access is limited in many rabies-endemic countries. We investigated how access to PEP can be improved to better prevent human rabies. Methods Using data from different settings in Tanzania, including contact tracing (2,367 probable rabies exposures identified) and large-scale mobile phone-based surveillance (24,999 patient records), we estimated the incidence of rabies exposures and bite-injuries, and examined health seeking and health outcomes in relation to PEP access. We used surveys and qualitative interviews with stakeholders within the health system to further characterise PEP supply and triangulate these findings. Results Incidence of bite-injury patients was related to dog population sizes, with higher incidence in districts with lower human:dog ratios and urban centres. A substantial percentage (25%) of probable rabies exposures did not seek care due to costs and limited appreciation of risk. Upon seeking care a further 15% of probable rabies exposed persons did not obtain PEP due to shortages, cost barriers or misadvice. Of those that initiated PEP, 46% did not complete the course. If no PEP was administered, the risk of developing rabies following a probable rabies exposure was high (0.165), with bites to the head carrying most risk. Decentralized and free PEP increased the probability that patients received PEP and reduced delays in initiating PEP. No major difficulties were encountered by health workers whilst switching to dose-sparing ID administration of PEP. Health infrastructure also includes sufficient cold chain capacity to support improved PEP provision. However, high costs to governments and patients currently limits the supply chain and PEP access. The cost barrier was exacerbated by decentralization of budgets, with priority given to purchase of cheaper medicines for other conditions. Reactive procurement resulted in limited and unresponsive PEP supply, increasing costs and risks to bite victims. Conclusion PEP access could be improved and rabies deaths reduced through ring-fenced procurement, switching to dose-sparing ID regimens and free provision of PEP