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2,863 results for “Challenge”
Appendix to the paper titled: Which teamwork challenges do computing students face in a project-based learning course in research methods?
<p>Instructions on reflection reports, interview guide, and example student projects.</p>
Model files and output seismograms for Seismic Wavefield Modelling of Enceladus: challenges and opportunities presented by a 3D ice shell (Dapré & Irving)
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MLOps Education - Challenges and Recommendations
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Climate-Driven Range Shifts and Conservation Challenges for Brown Bears in Türkiye
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Data and figures for "Evolving interdisciplinary contributions to global societal challenges: A 50-year overview"
<div>This package accompanies the <a href="https://doi.org/10.1016/j.wdp.2025.100728">paper</a> titled <em>"Evolving interdisciplinary contributions to global societal challenges: A 50-year overview",</em> available on arXiv. The datasets and figures included are derived from data obtained through the <a href="https://openalex.org">OpenAlex</a> API. For further details, please refer to the original <a href="https://doi.org/10.1016/j.wdp.2025.100728">paper</a>. <h2>Suppl_data_1.csv</h2> Domains are labelled by 𝛼 = 1, ..., 4, where 1: Life Sciences, 2: Social Sciences, 3: Physical Sciences, and 4: Health Sciences. <p> </p> <table> <tbody> <tr> <td><strong>pyear</strong></td> <td>Year of publication</td> </tr> <tr> <td><strong>nwork</strong></td> <td>Number of publications, indexed in OpenAlex</td> </tr> <tr> <td><strong>nwork𝛼</strong></td> <td>Number of publications in domain 𝛼, indexed in OpenAlex</td> </tr> <tr> <td><strong>nIDR</strong></td> <td> <p>Number of publications with ’multi-/inter-/trans-disciplinar*’ in Title or Abstract, indexed in OpenAlex</p> </td> </tr> <tr> <td><strong>nIDR𝛼</strong></td> <td>Number of publications in domain 𝛼 with ’multi-/inter-/trans-disciplinar*’ in Title or Abstract, indexed in OpenAlex</td> </tr> <tr> <td><strong>%nIDR </strong></td> <td>Ratio of nIDR to nwork (in %) </td> </tr> <tr> <td><strong>%nIDR𝛼 </strong></td> <td>Ratio of nIDR𝛼 to nwork𝛼 (in %)</td> </tr> </tbody> </table> <p> </p> <h2>Suppl_data_2.csv</h2> Disciplines (the level-0 concepts defined in OpenAlex) are labelled by k = 1, ..., 19, where 1: Political Science, 2: Philosophy, 3: Economics, 4: Business, 5: Psychology, 6: Mathematics, 7: Medicine, 8: Biology, 9: Computer Science, 10: Geology, 11: Chemistry, 12: Art, 13: Sociology, 14: Engineering, 15: Geography, 16: History, 17: Materials Science, 18: Physics, and 19: Environmental Science. <p> </p> </div> <div> <div> <table> <tbody> <tr> <td><strong>idwork</strong></td> <td>Work identifier starting with ‘W’, as defined in OpenAlex</td> </tr> <tr> <td><strong>pyear</strong></td> <td>Year of publication</td> </tr> <tr> <td><strong>citation</strong></td> <td>Number of citations, as of April 2024, indexed in OpenAlex</td> </tr> <tr> <td><strong>discip<em>k</em></strong></td> <td>Score of affinity to each of the level-0 concepts defined in OpenAlex (<em>k</em> = 1, ..., 19)</td> </tr> <tr> <td> <p><strong>SDG<em>m</em></strong></p> </td> <td> <p>Score of affinity to each of the United Nations’ Sustainable Development Goals (SDGs) (<em>m</em> = 1, ..., 17)</p> </td> </tr> </tbody> </table> </div> <div> <p> </p> </div> </div>
Challenges in alpine soil recovery: the minor effect of grass restoration on microbial resource limitation
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Data from: Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.
Transcriptome Shotgun Sequencing (RNA-seq) has been readily embraced by geneticists and molecular ecologists alike. As with all high-throughput technologies, it is critical to understand which analytic strategies are best suited and which parameters may bias the interpretation of the data. Here we use a comprehensive simulation approach to explore how various features of the transcriptome (complexity, degree of polymorphism π, alternative splicing), technological processing (sequencing error ε, library normalization) and bioinformatic workflow (de novo vs. mapping assembly, reference genome quality) impact transcriptome quality and inference of differential gene expression (DE). We find that transcriptome assembly and gene expression profiling (edgeR vs. baySeq software) works well even in the absence of a reference genome, and is robust across a broad range of parameters. We advise against library normalization, and in most situations advocate mapping assemblies to an annotated genome of a divergent sister clade, which generally outperformed de novo assembly (Trans-Abyss, Trinity, SOAPdenovo-Trans). Transcriptome complexity (size, paralogs, alternative splicing isoforms) negatively affected the assembly and DE profiling, whereas the effects of sequencing error and polymorphism were almost negligible. Finally, we highlight the challenge of gene name assignment for de novo assemblies, the importance of mapping strategies, and raise awareness of challenges associated with the quality of reference genomes. Overall, our results have significant practical and methodological implications, and can provide guidance in the design and analysis of RNA-seq experiments, particularly for organisms where genomic background information is lacking.
Data from: Promise and challenge of DNA barcoding in Venus slipper (Paphiopedilum)
Orchidaceae are one of the largest families of flowering plants, with over 27,000 species described and all orchids are listed in CITES. Moreover, the seedlings of orchid species from the same genus are similar. The objective of DNA barcoding is rapid, accurate, and automated species identification, which may be used to identify illegally traded endangered species from vegetative specimens of Paphiopedilum (Venus slipper), a flagship group for plant conservation with high ornamental and commercial values. Here, we selected eight chloroplast barcodes and nrITS to evaluate their suitability in Venus slippers. The results indicate that all tested barcodes had no barcoding gap and the core plant barcodes showed low resolution for the identification of Venus slippers (18.86%). Of the single-locus barcodes, nrITS is the most efficient for the species identification of the genus (52.27%), whereas matK + atpF-atpH is the most efficient multi-locus combination (28.97%). Therefore, we recommend the combination of matK + atpF-atpH + ITS as a barcode for Venus slippers. Furthermore, there is an upper limit of resolution of the candidate barcodes, and only half of the taxa with multiple samples were identified successfully. The low efficiency of these candidate barcodes in Venus slippers may be caused by relatively recent speciation, the upper limit of the barcodes, and/or the sampling density. Although the discriminatory power is relatively low, DNA barcoding may be a promising tool to identify species involved in illegal trade, which has broad applications and is valuable for orchid conservation.
Data from: Challenges and solutions for analyzing dual RNA-seq data for non-model host/pathogen systems
1. Dual RNA-seq simultaneously profiles the transcriptomes of a host and pathogen during infection and may reveal the mechanisms underlying host-pathogen interactions. Dual RNA-seq is inherently a mixture of transcripts from at least two species (host and pathogen), so this mixture must be computationally sorted into host and pathogen components. Sorting relies on aligning reads to respective reference genomes, which may be unavailable for both species in non-model host-pathogen pairs. This lack of genomic resources may present challenges to applying dual RNA-seq to non-model systems. 2. We assessed the accuracy of alignments of dual RNA-seq when using the genomic resources of a closely-related species to the species of interest by simulating datasets of mixed transcripts from a host and pathogen. Specifically, we compared how different aligners performed across different proportions of pathogen to host transcripts and across variation in the genetic distance between the pathogen genome and reference genome. We performed extensive analyses for a host plant with fungal pathogen, and then we extended the plant-fungus results by repeating key analyses in vertebrate (human)-fungus and vertebrate-bacterium systems. 3. Aligners that were able to map pathogen transcripts to the reference genome of a species closely related to the pathogen (a "related reference genome") also mismapped transcripts originating from the host to the pathogen's related reference genome, which results in regions where this occurred being quantified as overexpressed. If a host reference genome was available, we show that to minimize host transcript mismapping while retaining the ability to map pathogen transcripts, one could concatenate it with the pathogen's related reference genome, then map transcripts to the concatenated genomes. If a host genome was unavailable, assembling reads de novo prior to aligning substantially decreased host read mismapping, while retaining the ability to map pathogen transcripts to a related reference genome. 4. The application of dual RNA-seq to organisms without reference genomes is currently limited. We propose an analytical workflow that leverages the genomic resources of species closely related to species of interest to facilitate application of dual RNA-seq to reveal the mechanisms of host-pathogen interactions across a wider array of systems.
Challenging the established order: innovating clinical trials for amyotrophic lateral sclerosis
<p><span><span><span><span><span><span><span><span><span><span><span>Development of effective treatment for amyotrophic lateral sclerosis (ALS) has been hampered by disease heterogeneity,a limited understanding of underlying pathophysiology and methodological design challenges. Here we have evaluated two major themes in the design of pivotal, phase 3 clinical trials for ALS: (1) patient selection and (2) analytical strategy, and discussed potential solutions with the European Medicines Agency (EMA). Several design considerations were assessed using data from five placebo-controlled clinical trials (N = 988), four population-based cohorts (N = 5,100), and 2,436 placebo-allocated patients from the PRO-ACT database. The validity of each proposed design modification was confirmed by means of simulation and illustrated for a hypothetical setting. Compared to classical trial design, the proposed design modifications reduce the sample size by 30.5% and placebo exposure time by 35.4%. By making use of prognostic survival models, one creates a potential to include a larger proportion of the population and maximize generalizability. We propose a flexible design framework which naturally adapts the trial duration when inaccurate assumptions are made at the design stage such as the enrollment or survival rate. In case of futility, the follow-up time is shortened and patient exposure to ineffective treatments or placebo is minimized. For diseases such as ALS, optimizing the use of resources, widening eligibility criteria and minimizing the exposure to futile treatments and placebo is critical to the development of effective treatments. Our proposed design modifications could circumvent important pitfalls and may serve a blueprint for future clinical trials in this population.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Using local ecological knowledge to build mutualistic networks in hyper-diverse and logistically challenging ecosystems
<p>1. Collecting interaction data to build frugivory or seed dispersal networks is logistically challenging in ecosystems that have very high plant and animal diversity and/or where fieldwork is difficult or dangerous. Consequently, the majority of available networks are from ecosystems with low species diversity or they represent a sub-set of the community. </p> <p>2. Here, we propose an approach using local ecological knowledge (LEK) of indigenous communities to build interaction databases and weighted networks that would otherwise be difficult to achieve with direct observations. Indigenous communities live and work in many hyper-diverse ecosystems and the people within these communities often have detailed knowledge of ecological processes. </p> <p>3. Working in a Sundaland biodiversity hotspot – Royal Belum State Park, Peninsular Malaysia – we used field data, visually-oriented interviews with indigenous people (Orang Asli, in the Jahai and Temiar ethnic subgroups), and published records to collate interactions, and their frequency of occurrence of animal fruit consumption and seed dispersal. </p> <p>4. We documented 2060 fruit consumption and 1330 seed dispersal interactions among 164 plant species and 34 animal taxa, the latter representing groups of closely related species or individual species. The majority of the interactions (97%) were identified by the LEK interviews, with the additional methods (field data and published records) used to support and marginally expand the interview data. The metrics for the networks we built reflect those of networks structured by biological mechanisms, supporting the validity of our novel method. </p> <p>5. Local ecological knowledge is highly relevant for building detailed databases for mutualistic interactions in hyper-diverse and/or challenging ecosystems. Such ecosystems are among the most vulnerable on earth, harbouring ecological interactions that are often poorly documented at a community-level. We show how LEK can broaden our knowledge of such sensitive ecosystems, but our approach is useful for any ecosystem where people retain rich local ecological knowledge.</p>
A rapid review about software analytics tools architectures and challenges to apply in a company
<p>A rapid review about software analytics tools architectures and challenges to apply in a company</p>
Figure 1 from: Atanasov PY, Moneva-Sakelarieva MG, Kobakova YA, Ivanova SA, Obreshkova DP, Petkova VB, Becheva MV (2021) COVID-19 as a concomitant diagnosis and the emergencies behind COVID-19 mask – a real challenge that requires a multidisciplinary view of the patient. Pharmacia 68(3): 603-606. https://doi.org/10.3897/pharmacia.68.e71287
Figure 1 Number of examined patients in a multidisciplinary emergency department for the period 2018–2020.
Figure 1 from: Diakova AV, Polilov AA (2021) Porous or non-porous? The challenge of studying unusual placoid sensilla of Megaphragma wasps (Hymenoptera, Trichogrammatidae) with electron microscopy. In: Proshchalykin MYu, Gokhman VE (Eds) Hymenoptera studies through space and time: A collection of papers dedicated to the 75th anniversary of Arkady S. Lelej. Journal of Hymenoptera Research 84: 69-73. https://doi.org/10.3897/jhr.84.68707
Figure 1 Structure and ultrastructure of unusual placoid sensella (PS) in female Megaphragma amalphitanumA–GSEMH 3D-reconstruction I, JFIB-SEMA third flagellomere bearing PSB, CPS wall sputtered with gold, sputtering thickness 20–25 nm D, EPS wall sputtered with chromium in ESEM mode F, GPS wall sputtered with gold, sputtering thickness 15 nm, orbital rotation with an inclination of up to 45° I cross section through the middle of PSJ cross section through the outgrowth of PSH three-dimensional reconstruction of PS and one of the sensory neurons. Abbreviations: cu – cuticle, de – dendrite, le – ledge, nb – neuron body. Arrows designate the locations of the pores.
Figs. 19–24 in Redescription of Archaeoscelio Brues and Description of Three New Genera of Scelionidae (Hymenoptera): A Challenge to the Definition of the Family
Figs. 19–24. Cobaloscelio speculifer Johnson and Masner, n.sp. 19, Holotype and paratype males, holotype at upper left (OSUC 83622). 20, Lateral habitus, holotype male. 21, Dorsal habitus, paratype male. Apparent sculpture on mesonotum and head is an artifact. 22, Ventral habitus, paratype male. 23, Paratype female, frontolateral view (OSUC 67849). 24, Female, lateral habitus (OSUC 67849). Scale bars in millimeters.
Figure 12 in New organic-walled Foraminifera (Protista) from the ocean's deepest point, the Challenger Deep (western Pacific Ocean)
Figure 12. Resigella bilocularis sp. nov. Scanning electron micrographs. A, general view; note collapsed initial chamber. B, detail of same specimen showing agglutinated coating of organic wall; note that the grains become more prominent towards proximal part of chamber. C–H, damaged specimen; the initial chamber has been lost. C, general view; areas within boxes are shown in more detail in E–H. D, surface of proximal part of chamber showing agglutinated grains. E, surface towards posterior end of chamber showing agglutinated grains and smoother, intervening areas; box indicates area shown in detail in F. F, detail of organic wall with mesh-like structures and a few flat areas. G, H, surface towards distal part of chamber showing smooth, flake-like features separated by areas with a fine, mesh-like structure. The flake-like features in F–H are probably clay particles.
Figure 13 in New organic-walled Foraminifera (Protista) from the ocean's deepest point, the Challenger Deep (western Pacific Ocean)
Figure 13. Resigella bilocularis sp. nov. Scanning electron micrographs. A, aperture of specimen shown in Figure 12C. B, general view of specimen with intact intial chamber and broken second chamber. C, D, broken cross-section of test wall showing organic layer overlain by agglutinated grains. E, F, general view of test and detail of organic surface with flake-like features (probably clay particles) separated by mesh-like structures.
Challenges of students and residents of human medicine in the first four months of the fight against the Covid-19 pandemic – Implications for future waves and scenarios
<p><strong>Introduction:</strong> In the fight against the Covid-19 pandemic, medical students and residents are expected to adapt and contribute in a healthcare environment characterized by ever-changing measures and policies. The aim of this narrative review is to provide a summary of the literature that addresses the challenges of students and residents of human medicine in the first four months of the fight against the Covid-19 pandemic in order to identify gaps and find implications areas for improvement within the current situation and for potential future scenarios. <br> <strong>Methods:</strong> We performed a systematic literature search and content analysis (CA) of articles available in English language that address the challenges of students and residents of human medicine in the first four months of the fight against the Covid-19 pandemic.<br> <strong>Results:</strong> We retrieved 82 articles from a wide range of journals, professional backgrounds and countries. CA identified five recurring subgroup topics: «faculty preparation», «uncertaintiesy and mental health», «clinical knowledge», «rights and obligations» and «(self-) support and supply». Within these subgroups the main concerns of «(re)deployment», «interruption of training and career», «safety issues», «transmission of disease», and «restricted social interaction» were identified as potential stressors that hold a risk for fatigue, loss of morale and burnout.<br> <strong>Discussion:</strong> Students and residents are willing and able to participate in the fight against Covid-19 when provided with appropriate deployment to areas of need, thorough supervision, legal guidance, Personal Protective Equipment (PPE)safety measures and, clinical necessary knowledge, thorough supervision, social integration and mental health support. Preceding interviews to decide on reasonable voluntary deployment, the use of new technology and frequent feedback communication with faculties, educators and policymakers can further help with a successful and sustainable integration of students and residents in the fight against the pandemic.Faculties and policymakers should be in close contact with the youngest in training and be cognizant of their concerns and intrinsic creativity on the scenario. The use of new technology for interaction and knowledge provision, preceding interviews to decide on reasonable voluntary deployment and the provision of mental health support seem important measures to aid students and residents in the fight against the current pandemic.<br> <strong>Conclusion:</strong> It is critical that faculties, educators and policymakers have a better thorough understanding of the needs and concerns of medical trainees during this pandemic times. Leaders should facilitate close communication with students and residents, value their intrinsic creativeness and regularly evaluate their needs in regards to deployment, knowledge aspects, safety measures, legal concerns and overall well-being.</p>
Figure 3 from: Maggioni T, Taverna A, Tatián M (2016) Redescription of the deep-sea colonial ascidian Synoicum molle (Herdman, 1886): first record since its original finding during the Challenger Expedition. Zoosystematics and Evolution 92(2): 181-185. https://doi.org/10.3897/zse.92.9521
Figure 3 - Zooid of Synoicum molle. Only the initial and last sections of the post-abdomen are shown.
Figures 97-102 from: Huemer P, Karsholt O (2018) Revision of the genus Megacraspedus Zeller, 1839, a challenging taxonomic tightrope of species delimitation (Lepidoptera, Gelechiidae). ZooKeys 800: 1-278. https://doi.org/10.3897/zookeys.800.26292
Figures 97-102 Megacraspedus adults in dorsal view. 97M.tenuignathos sp. n. – Holotype, male, Morocco (RCAW) 98M.glaberipalpus sp. n. – Paratype, male, Morocco (NHMW) 99M.glaberipalpus sp. n. – Paratype, female, Morocco (NHMW) 100M.imparellus (Fischer von Röslerstamm, 1843) – male, Hungary (RCZT) 101M.imparellus (Fischer von Röslerstamm, 1843) – female, Hungary (RCZT) 102M.imparellus (Fischer von Röslerstamm, 1843) – male, Greece (ZMUC).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.