ClimMob: Software to support experimental citizen science in agriculture.

Experimental citizen science offers new ways to organize on-farm testing of crop varieties and other agronomic options. Its implementation at scale requires software that streamlines the process of experimental design, data collection and analysis, so that different organizations can support trials. This article considers ClimMob software developed to facilitate implementing experimental citizen science in agriculture. We describe the software design process, including our initial design choices, the architecture and functionality of ClimMob, and the methodology used for incorporating user feedback. Initial design choices were guided by the need to shape a workflow that is feasible for farmers and relevant for farmers, breeders and other decision-makers. Workflow and software concepts were developed concurrently. The resulting approach supported by ClimMob is triadic comparisons of technology options (tricot), which allows farmers to make simple comparisons between crop varieties or other agricultural technologies tested on farms. The software was built using Component-Based Software Engineering (CBSE), to allow for a flexible, modular design of software that is easy to maintain. Source is open-source and built on existing components that generally have a broad user community, to ensure their continuity in the future. Key components include Open Data Kit, ODK Tools, PyUtilib Component Architecture. The design of experiments and data analysis is done through R packages, which are all available on CRAN. Constant user feedback and short communication lines between the development teams and users was crucial in the development process. Development will continue to further improve user experience, expand data collection methods and media channels, ensure integration with other systems, and to further improve the support for data-driven decision-making.

Reconfigurable Magnonic Crystals Based on Imprinted Magnetization Textures in Hard and Soft Dipolar-Coupled Bilayers.

Reconfigurable magnetization textures offer control of spin waves with promising properties for future low-power beyond-CMOS systems. However, materials with perpendicular magnetic anisotropy (PMA) suitable for stable magnetization-texture formation are characterized by high damping, which limits their applicability in magnonic devices. Here, we propose to overcome this limitation by using hybrid structures, i.e., a PMA layer magnetostatically coupled to a low-damping soft ferromagnetic film. We experimentally show that a periodic stripe-domain texture from a PMA layer is imprinted upon the soft layer and induces a nonreciprocal dispersion relation of the spin waves confined to the low-damping film. Moreover, an asymmetric bandgap features the spin-wave band diagram, which is a clear demonstration of collective spin-wave dynamics, a property characteristic for magnonic crystals with broken time-reversal symmetry. The composite character of the hybrid structure allows for stabilization of two magnetic states at remanence, with parallel and antiparallel orientation of net magnetization in hard and soft layers. The states can be switched using a low external magnetic field; therefore, the proposed system obtains an additional functionality of state reconfigurability. This study offers a link between reconfigurable magnetization textures and low-damping spin-wave dynamics, providing an opportunity to create miniaturized, programmable, and energy-efficient signal processing devices operating at high frequencies.

Two-Step Resist Deposition of E-Beam Patterned Thick Py Nanostructures for X-ray Microscopy.

Patterned elements of permalloy (Py) with a thickness as large as 300 nm have been defined by electron beam lithography on X-ray-transparent 50 nm thick membranes in order to characterize their magnetic structure via Magnetic Transmission X-ray Microscopy (MTXM). To avoid the situation where the fragility of the membranes causes them to break during the lithography process, it has been found that the spin coating of the resist must be applied in two steps. The MTXM results show that our samples have a central domain wall, as well as other types of domain walls, if the nanostructures are wide enough.

Effects of virtual reality associated with serious games for upper limb rehabilitation inpatients with multiple sclerosis: randomized controlled trial.

BACKGROUND: Dexterity and activities of daily living limitations on the upper limb (UL) represent one of the most common problems in patients with multiple sclerosis (MS). The aim of this study was to evaluate the effectiveness of the specially developed Serious Games that make use of the Leap Motion Controller (LMC) as main user interface for improving UL grip muscle strength, dexterity, fatigue, quality of life, satisfaction and compliance. METHODS: A single-blinded randomized controlled trial was conducted. The sample was randomized into two groups: an experimental group who received treatment based on serious games designed by the research team using the developed LMC based Serious Games for the UL plus conventional rehabilitation, and a control group who received the same conventional rehabilitation for the UL. Both groups received two 60 min sessions per week over a ten-week period. Grip muscle strength, coordination, speed of movements, fine and gross UL dexterity, fatigue, quality of life, satisfaction and compliance were assessed in both groups pre-treatment, post-treatment and in a follow-up period of 1 month without receiving any treatment. RESULTS: In the experimental group compared to the control group, significant improvements were observed in the post-treatment assessment for coordination, speed of movements, fine and gross UL dexterity. Also, significant results were found in the follow-up in coordination, speed of movements, fine and gross for the more affected side. CONCLUSIONS: An experimental protocol using an LMC based Serious Games designed for UL rehabilitation showed improvements for unilateral gross manual dexterity, fine manual dexterity, and coordination in MS patients with high satisfaction and excellent compliance. TRIAL REGISTRATION: This randomized controlled trial has been registered at ClinicalTrials.gov Identifier: NCT04171908 , Nov 2019.

The Impact of a Novel Immersive Virtual Reality Technology Associated with Serious Games in Parkinson's Disease Patients on Upper Limb Rehabilitation: A Mixed Methods Intervention Study.

BACKGROUND: Parkinson's disease is a neurodegenerative disorder that causes impaired motor functions. Virtual reality technology may be recommended to optimize motor learning in a safe environment. The objective of this paper was to evaluate the effects of a novel immersive virtual reality technology used for serious games (Oculus Rift 2 plus leap motion controller-OR2-LMC) for upper limb outcomes (muscle strength, coordination, speed of movements, fine and gross dexterity). Another objective was to obtain qualitative data for participants' experiences related to the intervention. METHODS: A mixed methods intervention (embedded) study was used, with a qualitative design after a technology intervention (quantitative design). The intervention and qualitative design followed international guidelines and were integrated into the method and reporting subheadings. RESULTS: Significant improvements were observed in strength (p = 0.028), fine (p = 0.026 to 0.028) and gross coordination dexterity, and speed movements (p = 0.039) in the affected side, with excellent compliance (100%) and a high level of satisfaction (3.66 ± 0.18 points out of the maximum of 4). No adverse side effects were observed. Qualitative findings described patients' perspectives regarding OR2-LMC treatment, facilitators and barriers for adherence, OR2-LMC applications, and treatment improvements. CONCLUSIONS: The intervention showed positive results for the upper limbs, with elements of discordance, expansion, and confirmation between qualitative and quantitative results.

Leap motion controlled video game-based therapy for upper limb rehabilitation in patients with Parkinson's disease: a feasibility study.

BACKGROUND: Non-immersive video games are currently being used as technological rehabilitation tools for individuals with Parkinson's disease (PD). The aim of this feasibility study was to evaluate the effectiveness of the Leap Motion Controller® (LMC) system used with serious games designed for the upper limb (UL), as well as the levels of satisfaction and compliance among patients in mild-to-moderate stages of the disease. METHODS: A non-probabilistic sampling of non-consecutive cases was performed. 23 PD patients, in stages II-IV of the Hoehn & Yahr scale, were randomized into two groups: an experimental group (n = 12) who received treatment based on serious games designed by the research team using the LMC system for the UL, and a control group (n = 11) who received a specific intervention for the UL. Grip muscle strength, coordination, speed of movements, fine and gross UL dexterity, as well as satisfaction and compliance, were assessed in both groups pre-treatment and post-treatment. RESULTS: Within the experimental group, significant improvements were observed in all post-treatment assessments, except for Box and Blocks test for the less affected side. Clinical improvements were observed for all assessments in the control group. Statistical intergroup analysis showed significant improvements in coordination, speed of movements and fine motor dexterity scores on the more affected side of patients in the experimental group. CONCLUSIONS: The LMC system and the serious games designed may be a feasible rehabilitation tool for the improvement of coordination, speed of movements and fine UL dexterity in PD patients. Further studies are needed to confirm these preliminary findings.

Crop variety management for climate adaptation supported by citizen science.

Crop adaptation to climate change requires accelerated crop variety introduction accompanied by recommendations to help farmers match the best variety with their field contexts. Existing approaches to generate these recommendations lack scalability and predictivity in marginal production environments. We tested if crowdsourced citizen science can address this challenge, producing empirical data across geographic space that, in aggregate, can characterize varietal climatic responses. We present the results of 12,409 farmer-managed experimental plots of common bean (Phaseolus vulgaris L.) in Nicaragua, durum wheat (Triticum durum Desf.) in Ethiopia, and bread wheat (Triticum aestivum L.) in India. Farmers collaborated as citizen scientists, each ranking the performance of three varieties randomly assigned from a larger set. We show that the approach can register known specific effects of climate variation on varietal performance. The prediction of variety performance from seasonal climatic variables was generalizable across growing seasons. We show that these analyses can improve variety recommendations in four aspects: reduction of climate bias, incorporation of seasonal climate forecasts, risk analysis, and geographic extrapolation. Variety recommendations derived from the citizen science trials led to important differences with previous recommendations.

3D reconstruction of magnetization from dichroic soft X-ray transmission tomography.

The development of magnetic nanostructures for applications in spintronics requires methods capable of visualizing their magnetization. Soft X-ray magnetic imaging combined with circular magnetic dichroism allows nanostructures up to 100-300 nm in thickness to be probed with resolutions of 20-40 nm. Here a new iterative tomographic reconstruction method to extract the three-dimensional magnetization configuration from tomographic projections is presented. The vector field is reconstructed by using a modified algebraic reconstruction approach based on solving a set of linear equations in an iterative manner. The application of this method is illustrated with two examples (magnetic nano-disc and micro-square heterostructure) along with comparison of error in reconstructions, and convergence of the algorithm.

Reducing progoitrin and enriching glucoraphanin in Brassica napus seeds through silencing of the GSL-ALK gene family.

The hydrolytic products of glucosinolates in brassica crops are bioactive compounds. Some glucosinolate derivatives such as oxazolidine-2-thione from progoitrin in brassica oilseed meal are toxic and detrimental to animals, but some isothiocyanates such as sulforaphane are potent anti-carcinogens that have preventive effects on several human cancers. In most B. rapa, B. napus and B. juncea vegetables and oilseeds, there is no or only trace amount of glucoraphanin that is the precursor to sulforaphane. In this paper, RNA interference (RNAi) of the GSL-ALK gene family was used to down-regulate the expression of GSL-ALK genes in B. napus. The detrimental glucosinolate progoitrin was reduced by 65 %, and the beneficial glucosinolate glucoraphanin was increased to a relatively high concentration (42.6 µmol g(-1) seed) in seeds of B. napus transgenic plants through silencing of the GSL-ALK gene family. Therefore, there is potential application of the new germplasm with reduced detrimental glucosinolates and increased beneficial glucosinolates for producing improved brassica vegetables.

A physical map of Brassica oleracea shows complexity of chromosomal changes following recursive paleopolyploidizations.

BACKGROUND: Evolution of the Brassica species has been recursively affected by polyploidy events, and comparison to their relative, Arabidopsis thaliana, provides means to explore their genomic complexity. RESULTS: A genome-wide physical map of a rapid-cycling strain of B. oleracea was constructed by integrating high-information-content fingerprinting (HICF) of Bacterial Artificial Chromosome (BAC) clones with hybridization to sequence-tagged probes. Using 2907 contigs of two or more BACs, we performed several lines of comparative genomic analysis. Interspecific DNA synteny is much better preserved in euchromatin than heterochromatin, showing the qualitative difference in evolution of these respective genomic domains. About 67% of contigs can be aligned to the Arabidopsis genome, with 96.5% corresponding to euchromatic regions, and 3.5% (shown to contain repetitive sequences) to pericentromeric regions. Overgo probe hybridization data showed that contigs aligned to Arabidopsis euchromatin contain ~80% of low-copy-number genes, while genes with high copy number are much more frequently associated with pericentromeric regions. We identified 39 interchromosomal breakpoints during the diversification of B. oleracea and Arabidopsis thaliana, a relatively high level of genomic change since their divergence. Comparison of the B. oleracea physical map with Arabidopsis and other available eudicot genomes showed appreciable 'shadowing' produced by more ancient polyploidies, resulting in a web of relatedness among contigs which increased genomic complexity. CONCLUSIONS: A high-resolution genetically-anchored physical map sheds light on Brassica genome organization and advances positional cloning of specific genes, and may help to validate genome sequence assembly and alignment to chromosomes.All the physical mapping data is freely shared at a WebFPC site (http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/; Temporarily password-protected: account: pgml; password: 123qwe123.

Polymorphic chloroplast microsatellite markers in the octoploid Lepidium meyenii (Brassicaceae) and cross-species amplification in Lepidium.

PREMISE OF THE STUDY: As a crop and medicinal plant, the octoploid Andean endemic Lepidium meyenii suffers from taxonomic uncertainty. Few molecular markers are available to genotype individuals or track gene flow in wild and cultivated material. • METHODS AND RESULTS: Using available sequence data, eight cpSSR primer pairs were developed for L. meyenii. Levels of polymorphism checked in 56 individual L. meyenii, including cultivated and wild material, revealed that the number of alleles per locus ranged from three to five, and intrapopulation allele frequencies ranged from 0.071 to 1.0. Polymerase-chain-reaction screens using our cpSSR primers in 27 other Lepidium species and three Coronopus species suggested a high degree of interspecific amplification. • CONCLUSIONS: These polymorphic cpSSR markers should prove useful in characterizing genetic variation among cultivated and wild L. meyenii. Additionally, interspecific amplifications suggest that these markers will be useful for the study of related taxa.

Comparative sequence analysis for Brassica oleracea with similar sequences in B. rapa and Arabidopsis thaliana.

We sequenced five BAC clones of Brassica oleracea doubled haploid 'Early Big' broccoli containing major genes in the aliphatic glucosinolate pathway, and comparatively analyzed them with similar sequences in A. thaliana and B. rapa. Additionally, we included in the analysis published sequences from three other B. oleracea BAC clones and a contig of this species corresponding to segments in A. thaliana chromosomes IV and V. A total of 2,946 kb of B. oleracea, 1,069 kb of B. rapa sequence and 2,607 kb of A. thaliana sequence were compared and analyzed. We found conserved collinearity for gene order and content restricted to specific chromosomal segments, but breaks in collinearity were frequent resulting in gene absence likely not due to gene loss but rearrangements. B. oleracea has the lowest gene density of the three species, followed by B. rapa. The genome expansion of the Brassica species, B. oleracea in particular, is due to larger introns and gene spacers resulting from frequent insertion of DNA transposons and retrotransposons. These findings are discussed in relation to the possible origin and evolution of the Brassica genomes.

High-density Brassica oleracea linkage map: identification of useful new linkages.

We constructed a 1,257-marker, high-density genetic map of Brassica oleracea spanning 703 cM in nine linkage groups, designated LG1-LG9. It was developed in an F2 segregating population of 143 individuals obtained by crossing double haploid plants of broccoli "Early-Big" and cauliflower "An-Nan Early". These markers are randomly distributed throughout the map, which includes a total of 1,062 genomic SRAP markers, 155 cDNA SRAP markers, 26 SSR markers, 3 broccoli BAC end sequences and 11 known Brassica genes: BoGSL-ALK, BoGSL-ELONG, BoGSL-PROa, BoGSL-PROb, BoCS-lyase, BoGS-OH, BoCYP79F1, BoS-GT (glucosinolate pathway), BoDM1 (resistance to downy mildew), BoCALa, BoAP1a (inflorescence architecture). BoDM1 and BoGSL-ELONG are linked on LG 2 at 0.8 cM, making it possible to use the glucosinolate gene as a marker for the disease resistance gene. By QTL analysis, we found three segments involved in curd formation in cauliflower. The map was aligned to the C genome linkage groups and chromosomes of B. oleracea and B. napus, and anchored to the physical map of A. thaliana. This map adds over 1,000 new markers to Brassica molecular tools.

Comparative analysis of methylthioalkylmalate synthase (MAM) gene family and flanking DNA sequences in Brassica oleracea and Arabidopsis thaliana.

Gene BoGSL-PRO is associated with presence of 3-carbon side-chain glucosinolates (GSL). This gene is a member of the methylthioalkylmalate synthase (MAM) gene family. A BAC clone of Brassica oleracea, B21F5, containing this gene, was sequenced, annotated and compared to its corresponding region in Arabidopsis thaliana. Twelve protein-coding genes and 10 transposable elements were found in this clone. The corresponding region in A. thaliana chromosome I has 14 genes and no transposable elements. Analysis of MAM gene family in both species, which also include genes controlling 4-carbon side-chain GSL, separated the genes in two groups based on exon numbers and function. Phylogenetic analysis of the amino acid sequences encoded by these genes suggest that these two groups were produced by a duplication that must have occurred before the divergence of the Rosid and Asterid lineages of angiosperms. Comparison with putative orthologs from several prokaryotes further suggest that the members of the gene family with 10 exons, which encode proteins involved in 4-carbon side-chain GSL biosynthesis, were derived via truncation of the 3' end from ancestral genes more similar in length to those with 12 exons, which encode proteins involved in 3-carbon side-chain GSL biosynthesis. Lower gene density in B. oleracea compared to A. thaliana is due in part to presence of transposable elements (TE) mostly in inter-genic regions.

Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A. thaliana.

We compared the sequence of a 96.7 Kb-long BAC clone (B 19 N 3) from Brassica oleracea (broccoli) with its corresponding regions in Arabidopsis thaliana. B 19 N 3 contains eight genes and 15 transposable elements (TEs). The first two genes in this clone, Bo 1 and Bo 2, have its corresponding region at the end of chromosome V of Arabidopsis (24 Mb). The third gene, Bo 3, corresponds to an ortholog at the opposite end (2.6 Mb) of the same chromosome. The other five genes, Bo 4 to Bo 8 also have a corresponding region on the same chromosome but at 7.7 Mb . These five genes are colinear with those found in the corresponding region of Arabidopsis, which contains, however, 15 genes. Therefore, a cluster of 10 genes is missing in B. oleracea clone (B 19 N 3). All five genes in common have the same order and orientation in the genomes of both species. Their 36 exons constituting the eight homologous genes have high conservation in size and sequence identity in both species. Among these, there is a major gene involved in aliphatic glucosinolate biosynthesis, Bo GSL-ELONG (Bo 4). Similar to A. thaliana, this gene, has a tandem duplicate, Bo 5. A contig for this region was constructed by primer walking and BAC-end-sequencing, revealing general gene colinearity between both species. During the 20 million years separating A. thaliana from B. oleracea from a common ancestor both genomes have diverged by chromosomal rearrangements and differential TE activity. These events, in addition to changes in chromosome number are responsible for the evolution of the genomes of both species. In spite of these changes, both species conserve general colinearity for their corresponding genes.

Comparative analysis of a Brassica BAC clone containing several major aliphatic glucosinolate genes with its corresponding Arabidopsis sequence.

We compared the sequence of a 101-kb-long bacterial artificial chromosome (BAC) clone (B21H13) from Brassica oleracea with its homologous region in Arabidopsis thaliana. This clone contains a gene family involved in the synthesis of aliphatic glucosinolates. The A. thaliana homologs for this gene family are located on chromosome IV and correspond to three 2-oxoglutarate-dependent dioxygenase (AOP) genes. We found that B21H13 harbors 23 genes, whereas the equivalent region in Arabidopsis contains 37 genes. All 23 common genes have the same order and orientation in both Brassica and Arabidopsis. The 16 missing genes in the broccoli BAC clone were arranged in two major blocks of 5 and 7 contiguous genes, two singletons, and a twosome. The 118 exons comprising these 23 genes have high conservation between the two species. The arrangement of the AOP gene family in A. thaliana is as follows: AOP3 (GS-OHP) - AOP2 (GS-ALK) - pseudogene - AOP1. In contrast, in B. oleracea (broccoli and collard), two of the genes are duplicated and the third, AOP3, is missing. The remaining genes are arranged as follows: Bo-AOP2.1 (BoGSL-ALKa) - pseudogene - AOP2.2 (BoGSL-ALKb) - AOP1.1 - AOP1.2. When the survey was expanded to other Brassica accessions, we found variation in copy number and sequence for the Brassica AOP2 homologs. This study confirms that extensive rearrangements have taken place during the evolution of the Brassicacea at both gene and chromosomal levels.

Survey of aliphatic glucosinolates in Sicilian wild and cultivated Brassicaceae.

In the frame of the activities carried out to exploit Sicilian local cultivars of brassicas, we focused our attention on some of the potential health compounds of various local cruciferous crops. These compounds are of interest to improve the quality of the produce with the aim to develop new cultivars capable of providing functional foods able to prevent disease. In this context, we surveyed for the presence of specific glucosinolates in local cultivars of broccoli, cauliflower, kale, and in some wild species widespread in Sicily, using as control various commercial cultivars. Glucosinolate composition varied extensively among species and crops of the same species, such as cauliflower, broccoli and kale. Cultivar variation for glucosinolate profile was also observed for some crops. For example, Sicilian cultivars of cauliflower possessing colored curds displayed a high content of glucosinolates, glucoraphanin in particular, compared to white curd commercial cultivars. Also some wild species had a high content of other glucosinolates.

Genetic analysis, expression and molecular characterization of BoGSL-ELONG, a major gene involved in the aliphatic glucosinolate pathway of Brassica species.

We cloned a major aliphatic glucosinolate (GSL) gene, BoGSL-ELONG in Brassica oleracea, using the Arabidopsis sequence database. We based our work on an Arabidopsis candidate gene forming part of a gene family coding for isopropyl malate synthetase-like enzymes (IPMS). This gene is presumably responsible for synthesis of GSL possessing side chains consisting of four carbons (4C). The similarity of the Brassica homolog IPMS-Bo from broccoli to its Arabidopsis counterpart IPMS-At was on the order of 78%, both sharing the same number of exons. A nonfunctional allele of the BoGSL-ELONG gene from white cauliflower, based on the absence of 4C GSL in this crop, displayed a 30-bp deletion, which allowed us to develop a codominant marker for 4C-GSL. Gene expression analysis based on RT-PCR revealed a splicing site mutation in the white cauliflower allele. This resulted in a longer transcript containing intron 3, which failed to excise. Perfect cosegregation was observed for broccoli and cauliflower alleles at the IPMS-Bo gene and 4C-GSL content, strongly indicating that this gene indeed corresponds to BoGSL-ELONG. Cloning of two other major genes, BoGSL-ALK and BoGSL-PRO, is underway. The availability of these genes and BoGSL-ELONG is essential for the manipulation of the aliphatic GSL profile of B. oleracea.

Inheritance of Resistance to Celery mosaic virus in Celery.

Screening of the Apium germ plasm collection for resistance to Celery mosaic virus (CeMV) revealed four resistant accessions: a celeriac, a feral celery line, and two wild celery species. The feral celery, which is genetically closest to cultivated celery, A. graveolens var. dulce, was used to generate backcross and F2 progenies to determine the inheritance of the resistance. Resistance was recessive and determined by a single locus named cmv. The simple inheritance of this trait will allow the development of celery lines resistant to CeMV.

La campaña mundial de erradicación de la viruela: papel de la Organización Panamericana de la Salud en el Perú / The world campaign of erradication of the smallpox: role of the Pan-American Health Organization, Peru

Al asumir Fred L. Soper la dirección de la Organización Panamericana de la Salud se captaron recursos financieros hacia el continente americano para erradicar las enfermedades transmisibles. El Programa Continental de Erradicación que se inició en el Perú en 1949, adiestró personal y mejoró los laboratorios para la preparación de la vacuna antivariólica en America Latina. Se trataba de producir una vacuna más resistencia al calor en las zonas tropicales remotas, donde no habían posibilidades de conservarla en refrigeración constante y facilitar su transporte con el fin de realizar programas uniformes de vacunación en masa. El laboratorio del Instituto Nacional de Salud, pudo contar con cantidades suficientes de vacuna liofilizada para el Programa Nacional de Erradicación de Viruela e incluso para enviar a otros países. Este laboratorio se convirtió en un centro piloto en el que se entrenaron técnicos y profesionales de otros paises. El Perú contribuyó al Programa Mundial de Erradicación de la Viruela con 3,000.000 de dosis.