First Report of Gnomoniopsis idaeicola Causing Cane Wilt and Canker in Commercial Blackberry Fields in Oregon

Oregon is the leading producer of blackberries in the United States (USDA 2021). In November 2020, we visited a seven-year-old, 5.6 HA field of thornless trailing cultivar ‘Columbia Star’ in Marion County, Oregon in response to grower reports of rapid plant death that they called ‘Blackberry Collapse.’ The pattern of disease in the field was semi-circular patches of dead plants. We estimate that ca. 17% of the plants were killed. Symptoms included fewer and stunted primocanes, floricane reddening, premature floricane senescence, or elliptical or irregular brown to purple cane lesions often near the base of necrotic petioles clasping the cane. Twenty-two cane lesions were collected, surface-disinfested, and placed on potato dextrose agar with streptomycin. In addition to common Rubus cane pathogens (Kalmusia coniothyrium, Botrytis spp., Diaporthe spp., and Seimatosporium lichenicola), Gnomoniopsis idaeicola was isolated from 23% of the samples. After isolation of G. idaeicola from ‘Columbia Star’, we also isolated the pathogen from symptomatic ‘Black Diamond’ blackberry in fields in Washington and Linn Counties in Oregon. G. idaeicola grew as white- to cream-colored circular colonies on the agar surface with sparse to dense aerial hyphae. Some isolates produced cream-colored exudate from irregular conidiomata. Conidia were single-celled, hyaline, oval to ellipsoid, and ranged from 4.9 to 6.9 µm long and 1.2 to 2.5 µm wide (n = 100). Perithecia and ascospores were not seen on canes or in culture; molecular methods were used to identify the fungus. Genomic DNA was extracted from nine isolates and β-tubulin, ITS region, and tef-1α were amplified using the primers and conditions described by Walker et al. (2010). Amplicons were Sanger sequenced in both directions by the Core Facilities of the Center for Quantitative Life Sciences of Oregon State University, Corvallis, OR. Sequences were deposited in GenBank (β-tubulin OK539758-OK539766; ITS OK348854-OK348862; tef-1α OK539767-OK539775). β-tubulin sequences (737 bp) were 100% identical to sequence of G. idaeicola from Rubus procerus, Oregon (GU320783). ITS sequences (518 bp) were 99.2 to 100% identical to G. idaeicola CBS125674T (GU320796). tef-1α sequences (860 bp) were 99.9 to 100% identical with reference sequences of G. idaeicola. Phylogenetic analyses of concatenated sequences using Tamura-Nei neighbor-joining (Tamura et al. 2004) confirmed identity. Pathogenicity of G. idaeicola isolates was tested in repeated experiments on four to five detached ‘Black Diamond’ primocanes and potted ‘Columbia Star’ plants with 4 mm hyphal plugs placed on fresh wounds and wrapped in parafilm; controls were treated with sterile agar plugs (Ellis et al. 1984; Stevanović et al. 2019). By 14 days, in each experiment, expanding necrotic lesions were observed on canes inoculated with G. idaeicola, but not with sterile agar plugs. ITS-sequence of fungi isolated from lesions confirmed identity as G. idaeicola, fulfilling Koch’s postulate. G. idaeicola was described as a new species by Walker et al. (2010) from perithecia collected from wild Rubus spp. in the Pacific Northwest. Despite its presence on native Rubus, G. idaeicola has not been reported in commercial blackberry fields in OR. Stevanović et al. (2019) identified G. idaeicola as an important pathogen causing canker, wilt, and death of blackberry in Serbia. Surveys of Oregon blackberry fields for G. idaeicola are ongoing, along with research on the epidemiology and management of this emerging pathogen.

Problem-Solving in a Pandemic: How the Creation of a New Workflow Improved the Quality and Timeliness of Remote Core Descriptions

The COVID-19 pandemic limited global travel and access to core facilities. However, by adopting an innovative remote core description workflow, potential delays to an important reservoir characterisation study were avoided and mitigated. Over c.1700ft of middle Miocene core from an Onshore well in Abu Dhabi was described using high-resolution core photos, CT scans and CCA data. Detailed (1:20ft scale) descriptions of heterogeneous, mixed lithology sediments from a gas reservoir were produced. The aim when developing the workflow was not to try and replicate the process of in-person core description, but to create a workflow that could be executed remotely, whilst maintaining technical standards. Ideally, we wanted to find a solution that also had the potential to improve the overall quality of core description, by integrating more data from the onset. The workflow used a matrix to generate a confidence score for the description of each cored interval. Factors such as core condition were considered, which highly influences the extractable core information. The confidence score was used to make decisions, such as whether an in-person review of the core was necessary, especially where core condition was below a reasonable threshold. This helped prioritise cored intervals for review, ensuring time in the core store was focused, and allowed accuracy and reliability of the remote description to be assessed. The 4-phase workflow is summarised as: Image extraction of white light (WL), ultraviolet (UV) and computed tomography (CT) core images. Digital chart creation, core-to-log shifts and sample selection: Wireline data, CCA data and core images loaded Core images used to determine core-to-log shifts Thin section, SEM and XRD samples selected Remote core description: Conducted using all core imagery, CCA and wireline data Thin section, SEM and XRD data were used to refine the description when they became available A confidence score was given to each cored interval QC and finalization: Using the results from phase 3, a selection of cored intervals for in-person review was made. Intervals included those with a poor match between remote description and petrographic data, or areas with a low confidence score. Following the review, charts were finalised and quality-checked for data export Using this workflow, ensured work on an important study could continue during the pandemic. Such an approach has continued value for future studies as it increases efficiency and accounts for more data to be considered in core description prior to viewing the core in-person; it has been used on recent studies with great success. Another benefit to this approach is that less time in the core store is required, reducing potential HSE risks and helping to manage core store availability in busy facilities.

Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses

Motivation: Core sequencing facilities produce huge amounts of sequencing data that need to be analysed with automated workflows to ensure reproducibility and traceability. Eoulsan is a versatile open-source workflow engine meeting the needs of core facilities, by automating the analysis of a large number of samples. Its core design separates the description of the workflow from the actual commands to be run. This originality simplifies its usage as the user does not need to handle code, while ensuring reproducibility. Eoulsan was initially developed for bulk RNA-seq data, but the transcriptomics applications have recently widened with the advent of long-read sequencing and single-cell technologies, calling for the development of new workflows. Result: We present Eoulsan 2, a major update that (i) enhances the workflow manager itself, (ii) facilitates the development of new modules, and (iii) expands its applications to long reads RNA-seq (Oxford Nanopore Technologies) and scRNA-seq (Smart-seq2 and 10x Genomics). The workflow manager has been rewritten, with support for execution on a larger choice of computational infrastructure (workstations, Hadoop clusters, and various job schedulers for cluster usage). Eoulsan now facilitates the development of new modules, by reusing wrappers developed for the Galaxy platform, with support for container images (Docker or Singularity) packaging tools to execute. Finally, Eoulsan natively integrates novel modules for bulk RNA-seq, as well as others specifically designed for processing long read RNA-seq and scRNA-seq. Eoulsan 2 is distributed with ready-to-use workflows and companion tutorials. Availability and implementation: Eoulsan is implemented in Java, supported on Linux systems and distributed under the LGPL and CeCILL-C licenses at: http://outils.genomique.biologie.ens.fr/eoulsan/. The source code and sample workflows are available on GitHub: https://github.com/GenomicParisCentre/eoulsan. A GitHub repository for modules using the Galaxy tool XML syntax is further provided at: https://github.com/GenomicParisCentre/eoulsan-tools

Versatile, do-it-yourself, low-cost spinning disk confocal microscope

Confocal microscopy is an invaluable tool for 3D imaging of biological specimens, however, accessibility is often limited to core facilities due to the high cost of the hardware. We describe an inexpensive do-it-yourself (DIY) spinning disk confocal microscope (SDCM) module based on a commercially fabricated chromium photomask that can be added on to a laser-illuminated epifluorescence microscope. The SDCM achieves strong performance across a wide wavelength range (~400-800 nm) as demonstrated through a series of biological imaging applications that include conventional microscopy (immunofluorescence, small-molecule stains, and fluorescence in situ hybridization) and super-resolution microscopy (single-molecule localization microscopy and expansion microscopy). This low-cost and simple DIY SDCM is well-documented and should help increase accessibility to confocal microscopy for researchers.

A Classification of Japanese Nursing Homes on the Spatial Layouts of Common Facilities: An analysis using Space Syntax Theory

This article analyzes the spatial layout in Japanese nursing homes, and to clarify the core space and spatial characteristics of the common facility. By using the Space Syntax DepthMapX tool, we analyzed 62 nursing homes from Japanese architecture publications. Then, we use the spatial integration metric to identify the core space and transition of the common core facilities. The result shows the core space changed from the corridor in the 1980s to the hall nowadays; the community space and physical training room have also become the common core facility in Japanese nursing homes. Keywords: Common Space, Core Space, Nursing Home, Space Syntax, Depth Map. eISSN 2514-751X © 2021. The Authors. Published for AMER ABRA by E-International Publishing House, Ltd., UK. This is an open-access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Peer-review under responsibility of AMER (Association of Malaysian Environment-Behaviour Researchers), ABRA (Association of Behavioural Researchers on Asians/Africans/Arabians) and cE-Bs (Centre for Environment-Behaviour Studies), Faculty of Architecture, Planning & Surveying, Universiti Teknologi MARA, Malaysia. DOI: https://doi.org/10.21834/ajebs.v6i18.379

Civil airline fare prediction with a multi-attribute dual-stage attention mechanism

Airfare price prediction is one of the core facilities of the decision support system in civil aviation, which includes departure time, days of purchase in advance and flight airline. The traditional airfare price prediction system is limited by the nonlinear interrelationship of multiple factors and fails to deal with the impact of different time steps, resulting in low prediction accuracy. To address these challenges, this paper proposes a novel civil airline fare prediction system with a Multi-Attribute Dual-stage Attention (MADA) mechanism integrating different types of data extracted from the same dimension. In this method, the Seq2Seq model is used to add attention mechanisms to both the encoder and the decoder. The encoder attention mechanism extracts multi-attribute data from time series, which are optimized and filtered by the temporal attention mechanism in the decoder to capture the complex time dependence of the ticket price sequence. Extensive experiments with actual civil aviation data sets were performed, and the results suggested that MADA outperforms airfare prediction models based on the Auto-Regressive Integrated Moving Average (ARIMA), random forest, or deep learning models in MSE, RMSE, and MAE indicators. And from the results of a large amount of experimental data, it is proven that the prediction results of the MADA model proposed in this paper on different routes are at least 2.3% better than the other compared models.

Remote Exploration of Experimental Biophysical Instrumentation in Core Facilities

ABSTRACT Biophysics is defined by the experimental data that are collected on an extensive array of powerful and elegant tools. To solve important problems in biophysics, an understanding of the capabilities and limitations of the current instrumental methods is needed. Although lecture-based courses can instruct students on the physical principles of biophysical instrumentation, the actual practical use of instrumentation can seem far from the concepts taught through presentations or books. Traditionally, laboratory courses can expose students to hands-on use and understanding of experimental methods. During the COVID-19 pandemic, laboratory-based courses were challenging or, at times, prohibited. The educational aim of this article is to connect the instrumental concepts learned in lecture to the use of instruments for experiments when students are unable to go into laboratory environments. I present a low-stakes assignment for students to explore the biophysical instrumentation at core facilities. Prompts were provided to guide students through methods and challenges when using an instrument in a laboratory. These were then shared in a group environment so students could learn about multiple instruments in a single class and further benefit from social interactions with their peers, combating isolation during remote courses. Beyond remote instruction during COVID-19, this assignment can be applicable to future courses where laboratory work is cost-, time-, or location-prohibitive. Adaptations for in-person instruction are also discussed.