Embedding attribute grammars and their extensions using functional zippers

Attribute grammars are a suitable formalism to express complex software language analysis and manipulation algorithms, which rely on multiple traversals of the underlying syntax tree. Attribute grammars have been extended with mechanisms such as reference, higher order and circular attributes. Such extensions provide a powerful modular mechanism and allow the specification of complex computations. This paper studies an elegant and simple, zipper-based embedding of attribute grammars and their extensions as first class citizens. In this setting, language specifications are defined as a set of independent, off-the-shelf components that can easily be composed into a powerful, executable language processor. Techniques to describe automatic bidirectional transformations between grammars in this setting are also described. Several real examples of language specification and processing programs have been implemented. (C) 2016 Elsevier B.V. All rights reserved.This author is supported by ERDF - European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT - Fundacao para a Ciencia e a Tecnologia (Portuguese Foundation for Science and Technology) within project ON.2 IC&DT Programa Integrado "BEST CASE - Better Science Through Cooperative Advanced Synergetic Efforts (Ref. BIM-2013_BestCase_RL3.2_UMINHO) and project FATBIT - Foundations, Applications and Tools for Bidirectional Transformation (Ref. FCOMP-01-0124-FEDER-020532).This author is partially supported by NSF Award #1047961

Generating attribute grammar-based bidirectional transformations from rewrite rules

Higher order attribute grammars provide a convenient means for specifying uni-directional transformations, but they provide no direct support for bidirectional transformations. In this paper we show how rewrite rules (with non-linear right hand sides) that specify a forward/get transformation can be inverted to specify a partial backward/put transformation. These inverted rewrite rules can then be extended with additional rules based on characteristics of the source language grammar and forward transformations to create, under certain circumstances, a total backward transformation. Finally, these rules are used to generate attribute grammar specifications implementing both transformations.This work is partly funded by the following projects: European Regional Development Fund (ERDF) through the program COMPETE, project reference FCOMP-01-0124-FEDER-020532, by the North Portugal Regional Operational Programme (ON.2 - O Novo Norte); under the National Strategic Reference Framework (NSRF), through the ERDF, project reference RL3 SENSING NORTE-07-0124-FEDER-000058; by the Portuguese Government through FCT (Foundation for Science and Technology); by the U.S. National Science Foundation (NSF) award No. 0905581 and 1047961; and by the FLAD/NSF program Portugal-U.S. Research Networks 2011

Mixed methods evaluation of targeted selective anthelmintic treatment by resource-poor smallholder goat farmers in Botswana

AbstractDue to the threat of anthelmintic resistance, livestock farmers worldwide are encouraged to selectively apply treatments against gastrointestinal nematodes (GINs). Targeted selective treatment (TST) of individual animals would be especially useful for smallholder farmers in low-income economies, where cost-effective and sustainable intervention strategies will improve livestock productivity and food security. Supporting research has focused mainly on refining technical indicators for treatment, and much less on factors influencing uptake and effectiveness. We used a mixed method approach, whereby qualitative and quantitative approaches are combined, to develop, implement and validate a TST system for GINs in small ruminants, most commonly goats, among smallholder farmers in the Makgadikgadi Pans region of Botswana, and to seek better understanding of system performance within a cultural context. After the first six months of the study, 42 out of 47 enrolled farmers were followed up; 52% had monitored their animals using the taught inspection criteria and 26% applied TST during this phase. Uptake level showed little correlation with farmer characteristics, such as literacy and size of farm. Herd health significantly improved in those herds where anthelmintic treatment was applied: anaemia, as assessed using the five-point FAMACHA© scale, was 0.44–0.69 points better (95% confidence interval) and body condition score was 0.18–0.36 points better (95% C.I., five-point scale) in treated compared with untreated herds. Only targeting individuals in greatest need led to similar health improvements compared to treating the entire herd, leading to dose savings ranging from 36% to 97%. This study demonstrates that TST against nematodes can be implemented effectively by resource-poor farmers using a community-led approach. The use of mixed methods provides a promising system to integrate technical and social aspects of TST programmes for maximum uptake and effect

The South African SHARE-TAVI registry: incidence and risk factors leading to conduction disturbances requiring permanent pacemaker implantation

Background: One of the most common complications post transcatheter aortic valve implantation (TAVI) is the development of heart block requiring permanent pacemaker implantation (PPM). The incidence of PPM in international registries ranges from 13% - 17.5%. Methods: The aim of this observational study was to report the PPM rate in the SHARE-TAVI registry and determine the clinical, electrocardiographic and procedural predictors of PPM as well as the effect of PPM on clinical outcomes. Results: Three hundred and fi ve subjects were analysed. The PPM rate was 9%. Third degree atrioventricular block at the time of implant was the most common indication for PPM. Self-expanding valves (PPM rate 14% vs. 6% for balloon-expandable valves, p=0.02) were correlated with the need for PPM. Baseline ECG predictors of PPM were axis deviation, QRS duration and conduction delay, most notably a pre-existing right bundle branch block (OR 15.88, p<0.01). PPM infl uenced functional class at 30 days, but not the need for repeat hospitalisation or mortality at 30-day and 1-year follow-up. Conclusions: A PPM rate lower than that reported in large international registries was found. Predictors of PPM and the infl uence of PPM on outcomes were similar to those reported in the international data

Prediction and attenuation of seasonal spillover of parasites between wild and domestic ungulates in an arid mixed-use system

Transmission of parasites between host species affects host population dynamics, interspecific competition, and ecosystem structure and function. In areas where wild and domestic herbivores share grazing land, management of parasites in livestock may affect or be affected by sympatric wildlife due to cross-species transmission.We develop a novel method for simulating transmission potential based on both biotic and abiotic factors in a semi-arid system in Botswana. Optimal timing of antiparasitic treatment in livestock is then compared under a variety of alternative host scenarios, including seasonally migrating wild hosts.In this region, rainfall is the primary driver of seasonality of transmission, but wildlife migration leads to spatial differences in the effectiveness of treatment in domestic animals. Additionally, competent migratory wildlife hosts move parasites across the landscape.Simulated transmission potential matches observed patterns of clinical disease in livestock in the study area. Increased wildlife contact is correlated with a decrease in disease, suggesting that non-competent wild hosts may attenuate transmission by removing infective parasite larvae from livestock pasture.Optimising the timing of treatment according to within-year rainfall patterns was considerably more effective than treating at a standard time of year. By targeting treatment in this way, efficient control can be achieved, mitigating parasite spillover from wildlife where it does occur. Synthesis and applications. This model of parasite transmission potential enables evidence-based management of parasite spillover between wild and domestic species in a spatio-temporally dynamic system. It can be applied in other mixed-use systems to mitigate parasite transmission under altered climate scenarios or changes in host ranges

The Ursinus Weekly, November 1, 1973

UN Day held at UC • USGA-Union lock horns over new rep. position • SFARC elections held; warning system set • Protheatre productions scheduled for weekend • Musicians initiated into Pi Nu Epsilon • Editorial: The American Film Theatre; New furniture in Wilkinson lounge • Letters to the editor: Jazz fan responds; Starving student complains; Mr. Self speaks • Alumni corner • Jazz: Herman Herd in motion • Faculty Portrait: Dr. Peter G. Jessup • A discourse on mental divorce • Billy Jack • Ursinus downs U of P; then falls to Rams • Bears lose fifth game to a tough Widener teamhttps://digitalcommons.ursinus.edu/weekly/1004/thumbnail.jp

Low-cost molecular methods to characterise gastrointestinal nematode co-infections of goats in Africa

AVAILABILITY OF DATA AND MATERIALS : Raw diagnostic, DNA extraction, and PCR data are shown in Additional file 1: Table S1. All other original results including tabulated data, PCR results, and other materials are available on request where not included in the manuscript.SUPPLEMENTARY INFORMATION : ADDITIONAL FILE 1. TABLE S1. Raw baseline data on DNA extraction, quality, quantity and yield. ADDITIONAL FILE 2. TABLE S2. Primers and cycling conditions used for each PCR technique. ADDITIONAL FILE 3. TABLE S3. Nemabiome raw read results from Eurofins 2nd PCR amplicon sequencing. ADDITIONAL FILE 4. TABLE S4. DNA extraction costs. ADDITIONAL FILE 5. TABLE S5. HRMC peak temperatures and Singleplex PCR relative species abundance. ADDITIONAL FILE 6. TABLE S6. Proportional read differences between Mothur and DADA2 nemabiome pipelines. ADDITIONAL FILE 7. FILE S1. 72-well gel electrophoresis comb design. ADDITIONAL FILE 8. FIGURES S1–S5. FIGURE S1: Assessing quality of DNA extraction methods. FIGURE S2: Assessing GIN species detection likelihoods by DNA extraction method and infection intensity. FIGURE S3: High-resolution melt curves with pan-nematode ITS-2 primers. FIGURE S4: Nemabiome ITS-2 amplicon with the DADA2 IDTAXA pipeline. FIGURE S5: Cross-validation of PCR methods with nemabiome using the DADA2 IDTAXA pipeline.BACKGROUND : Veterinary diagnostics aid intervention strategies, track zoonoses, and direct selective breeding programs in livestock. In ruminants, gastrointestinal nematode (GIN) parasites are a major cause of production losses, but morphologically similar species limit our understanding of how specific GIN co-infections impact health in resource-limited settings. To estimate the presence and relative abundance of GINs and other helminths at the species level, we sought to develop a low-cost and low-resource molecular toolkit applied to goats from rural Malawi smallholdings. METHODS : Goats were subjected to health scoring and faecal sampling on smallholdings in Lilongwe district, Malawi. Infection intensities were estimated by faecal nematode egg counts with a faecal subsample desiccated for DNA analysis. Two DNA extraction methods were tested (low-resource magbead kit vs high-resource spin-column kit), with resulting DNA screened by endpoint polymerase chain reaction (PCR), semi-quantitative PCR, quantitative PCR (qPCR), high-resolution melt curve analysis (HRMC), and ‘nemabiome’ internal transcribed spacer 2 (ITS-2) amplicon sequencing. RESULTS : Both DNA isolation methods yielded comparable results despite poorer DNA purity and faecal contaminant carryover from the low-resource magbead method. GINs were detected in 100% of samples regardless of infection intensity. Co-infections with GINs and coccidia (Eimeria spp.) were present in most goats, with GIN populations dominated by Haemonchus contortus, Trichostrongylus colubriformis, Trichostrongylus axei, and Oesophagostomum columbianum. Both multiplex PCR and qPCR were highly predictive of GIN species proportions obtained using nemabiome amplicon sequencing; however, HRMC was less reliable than PCR in predicting the presence of particular species. CONCLUSIONS : These data represent the first ‘nemabiome’ sequencing of GINs from naturally infected smallholder goats in Africa and show the variable nature of GIN co-infections between individual animals. A similar level of granularity was detected by semi-quantitative PCR methods, which provided an accurate summary of species composition. Assessing GIN co-infections is therefore possible using cost-efficient low-resource DNA extraction and PCR approaches that can increase the capacity of molecular resources in areas where sequencing platforms are not available; and also open the door to affordable molecular GIN diagnostics. Given the diverse nature of infections in livestock and wildlife, these approaches have potential for disease surveillance in other areas.The Biotechnology and Biological Sciences Research Council.https://parasitesandvectors.biomedcentral.com/am2024Veterinary Tropical DiseasesSDG-02:Zero HungerSDG-03:Good heatlh and well-bein

Development of a decision support system for animal health management using geo-Information technology : a novel approach to precision livestock management

This article belongs to the Special Issue titled 'Advancing Animal Welfare: Precision Livestock Farming Technologies for Monitoring and Preventing Abnormal Behavior'.DATA AVAILABILITY STATEMENT : Data can be provided upon request to Corresponding Author.Livestock management is challenging for resource-poor (R-P) farmers due to unavailability of quality feed, limited professional advice, and rumor-spreading about animal health condition in a herd. This research seeks to improve animal health in southern Africa by promoting sericea lespedeza (Lespedeza cuneata), a nutraceutical forage legume. An automated geospatial model for precision agriculture (PA) can identify suitable locations for its cultivation. Additionally, a novel approach of radio-frequency identifier (RFID) supported telemetry technology can track animal movement, and the analyses of data using artificial intelligence can determine sickness of small ruminants. This RFID-based system is being connected to a smartphone app (under construction) to alert farmers of potential livestock health issues in real time so they can take immediate corrective measures. An accompanying Decision Support System (DSS) site is being developed for R-P farmers to obtain all possible support on livestock production, including the designed PA and RFID-based DSS.The USDA-NIFA (Capacity Building Grant).https://www.mdpi.com/journal/agricultureVeterinary Tropical DiseasesSDG-02:Zero HungerSDG-09: Industry, innovation and infrastructur

From plants to pixels : the role of artificial intelligence in identifying Sericea lespedeza in field-based studies

DATA AVAILABILITY STATEMENT : The data presented in this study are available on request from the corresponding author.The increasing use of convolutional neural networks (CNNs) has brought about a significant transformation in numerous fields, such as image categorization and identification. In the development of a CNN model to classify images of sericea lespedeza [SL; Lespedeza cuneata (Dum-Cours) G. Don] from weed images, four architectures were explored: CNN model variant 1, CNN model variant 2, the Visual Geometry Group (VGG16) model, and ResNet50. CNN model variant 1 (batch normalization with adjusted dropout method) demonstrated 100% validation accuracy, while variant 2 (RMSprop optimization with adjusted learning rate) achieved 90.78% validation accuracy. Pre-trained models, like VGG16 and ResNet50, were also analyzed. In contrast, ResNet50’s steady learning pattern indicated the potential for better generalization. A detailed evaluation of these models revealed that variant 1 achieved a perfect score in precision, recall, and F1 score, indicating superior optimization and feature utilization. Variant 2 presented a balanced performance, with metrics between 86% and 93%. VGG16 mirrored the behavior of variant 2, both maintaining around 90% accuracy. In contrast, ResNet50’s results revealed a conservative approach for class 0 predictions. Overall, variant 1 stood out in performance, while both variant 2 and VGG16 showed balanced results. The reliability of CNN model variant 1 was highlighted by the significant accuracy percentages, suggesting potential for practical implementation in agriculture. In addition to the above, a smart- phone application for the identification of SL in a field-based trial showed promising results with an accuracy of 98–99%. The conclusion from the above is that a CNN model with batch normalization has the potential to play a crucial role in the future in redefining and optimizing the management of undesirable vegetation.The USDA-National Institute of Food and Agriculture.https://www.mdpi.com/journal/agronomyVeterinary Tropical DiseasesSDG-09: Industry, innovation and infrastructureSDG-15:Life on lan