AN ANALYSIS OF THE QUALITY OF THYROID CANCER WEBSITES

Objective: This study evaluated online thyroid cancer patient information quality. This is essential, given increasing patient use of online health information.Methods: A total of 100 thyroid cancer websites, representing those patients find first, were identified using Google and two meta-search engines. Content accuracy and patient-evaluable quality markers, including attribution, currency, structure, and content comprehensiveness and readability, were assessed with a previously validated standardized rating tool, developed using design-based methods. Accuracy was defined compared to standard, peer-reviewed medical resources, UpToDate and the National Comprehensive Cancer Network. Responses to general and personal “patient” questions were evaluated for promptness and accuracy.Results: Of 100 websites, only 26% stated authorship, and 56% cited sources. Seventy-four percent had dates of creation or last update, with only half of those dates occurring within the past 2 years. Websites most often discussed the definition (94%), diagnosis (92%), and treatment (94%) of thyroid cancer, but diagnosis and treatment were also most frequently incomplete or inaccurate: diagnosis information was complete and accurate 50% of the time, and treatment 47%. Only 2% of websites were comprehensible without high school education. Of 83 websites contacted with “patient” questions, 50 replied, 48 within 1 week.Conclusion: Thyroid cancer information is widely available online, but quality varies. Sites often lack markers for patients to assess quality, and content may be difficult to understand. Information is frequently incomplete, particularly on topics important to patients, such as diagnosis and treatment. Educational resource developers may fill these gaps, and healthcare providers can direct thyroid cancer patients to reliable online resources.Abbreviation: NCCN = National Comprehensive Cancer Network     

Zoology www guide

In almost every branch of zoology the internet is now a vital place for posting up-to-date status reports on all kind of animal groups and research areas. Many websites not only provide the latest on taxonomy, ecology and distribution, but also include valuable background information and details of experimental procedures as well as discussion forums. For the zoologist the online world seems to hold everything from acarology to otoliths. To show what impressive things can be done in communicating and facilitating research in zoology, given a little initiative and perseverance, we will introduce websites that find fresh ways to approach their subjects and that may, in some way or another, inspire zoologists. Readers are welcome to join in this process for future editions of Zoology www guides and should send their website suggestions to tbosch@zoologie.uni-kiel.de. In this issue the focus is on molluscs.     

Next‐generation field courses: Integrating Open Science and online learning

As Open Science practices become more commonplace, there is a need for the next generation of scientists to be well versed in these aspects of scientific research. Yet, many training opportunities for early career researchers (ECRs) could better emphasize or integrate Open Science elements. Field courses provide opportunities for ECRs to apply theoretical knowledge, practice new methodological approaches, and gain an appreciation for the challenges of real‐life research, and could provide an excellent platform for integrating training in Open Science practices. Our recent experience, as primarily ECRs engaged in a field course interrupted by COVID‐19, led us to reflect on the potential to enhance learning outcomes in field courses by integrating Open Science practices and online learning components. Specifically, we highlight the opportunity for field courses to align teaching activities with the recent developments and trends in how we conduct research, including training in: publishing registered reports, collecting data using standardized methods, adopting high‐quality data documentation, managing data through reproducible workflows, and sharing and publishing data through appropriate channels. We also discuss how field courses can use online tools to optimize time in the field, develop open access resources, and cultivate collaborations. By integrating these elements, we suggest that the next generation of field courses will offer excellent arenas for participants to adopt Open Science practices.     

Inhibition of dinoflagellate growth by extracts of barley straw (Hordeum vulgare)

Growth of dinoflagellates representing three orders, the Gymnodiniales,Peridiniales, and the Prorocentrales was examined following treatment withbarley straw extract. Selected dinoflagellate taxa showed growth responsessimilar to those reported for freshwater algae including: inhibition(Gyrodinium galatheanum, Gymnodiniumsanguineum, Heterocapsa triquetra andH. pygmaea); stimulation (Gyrodinium instriatum,Prorocentrum minimum and P. micans); and no effect(Gyrodinium estuariale, G. uncatenum,Ceratium furca, Peridinium sp.).Although barley straw extracts do not appear to have value as a universalmanagement tool for dinoflagellates, they may have potential in management ofspecific taxa and possibly taxonomic groups.     

An evaluation of educators’ views on the e-Bug resources in England

Introduction: e-Bug is an international educational resource for young people covering microbes, hygiene and antibiotics. e-Bug supports NICE guidance on changing public behaviour around antibiotic use. This study aimed to determine educators’ views of the e-Bug teacher resources to inform further development and dissemination of e-Bug. Methods: Age appropriate e-Bug resource packs were posted to every primary school (N = 19,142) and secondary school (N = 5637) in England with a cover letter signed by the Chief Medical Officer, Chief Executive of PHE and e-Bug Project Lead inviting educators to complete an online survey to evaluate the e-Bug resources. The online survey consisted of nine questions and took approximately 15 min to complete. Results: 695 participants completed the online survey. 94% of participants rated the e-Bug resource as excellent or good; one fifth of respondents used the e-Bug resources at least termly. Educators who used e-Bug rated the different lesson plans as excellent or good including ‘Introduction to Microbes’ (98%) and ‘Hand Hygiene’ (95%). Educators provided suggestions for the development of additional lessons plans. Conclusions: Educators view e-Bug as a valuable resource for teaching children about hygiene and antibiotics. Further e-Bug promotion and resource development is required to increase awareness and usage in schools.     

Data acquisition and management software for camera trap data: A case study from the TEAM Network

Camera traps and the images they generate are becoming an essential tool for field biologists studying and monitoring terrestrial animals, in particular medium to large terrestrial mammals and birds. In the last five years, camera traps have made the transition to digital technology, where these devices now produce hundreds of instantly available images per month and a large amount of ancillary metadata (e.g., date, time, temperature, image size, etc.). Despite this accelerated pace in the development of digital image capture, field biologists still lack adequate software solutions to process and manage the increasing amount of information in a cost efficient way. In this paper we describe a software system that we have developed, called DeskTEAM, to address this issue. DeskTEAM has been developed in the context of the Tropical Ecology Assessment and Monitoring Network (TEAM), a global network that monitors terrestrial vertebrates. We describe the software architecture and functionality and its utility in managing and processing large amounts of digital camera trap data collected throughout the global TEAM network. DeskTEAM incorporates software features and functionality that make it relevant to the broad camera trapping community. These include the ability to run the application locally on a laptop or desktop computer, without requiring an Internet connection, as well as the ability to run on multiple operating systems; an intuitive navigational user interface with multiple levels of detail (from individual images, to whole groups of images) which allows users to easily manage hundreds or thousands of images; ability to automatically extract EXIF and custom metadata information from digital images to increase standardization; availability of embedded taxonomic lists to allow users to easily tag images with species identities; and the ability to export data packages consisting of data, metadata and images in standardized formats so that they can be transferred to online data warehouses for easy archiving and dissemination. Lastly, building these software tools for wildlife scientists provides valuable lessons for the ecoinformatics community.     

Phytochemical data parallel morpho-colorimetric variation in Polygala flavescens DC.

Abstract

Phytochemical data, integrated with other sources of information, represent a valuable tool helping to solve different kinds of taxonomic problems in plant systematics. In the present study, a comparative investigation, in order to clarify the systematic relationships of the three subspecies currently recognized within the Italian endemic Polygala flavescens, was carried out. Preliminarily, a morphometric and colorimetric analysis, in order to test the degree of morphological distinctiveness among the taxa, was performed. Then, a phytochemical analysis based both on volatile and non-volatile compounds was obtained. Concerning the morpho-colorimetric analysis, our results confirm most of the characters as useful to discriminate the three subspecies. In addition, some volatile and non-volatile compounds are good taxonomic markers. Morpho-colorimetric variation is clearly paralleled by phytochemical results, confirming the value of this kind of data to infer relationships in plant systematics. Based on these results, we support a taxonomic treatment at subspecific level for the involved taxa. Finally, based on the most significant morphological characters, a revision of herbarium specimens allowed to redefine the distribution pattern of the three subspecies. Accordingly, the range of P. flavescens subsp. maremmana is limited to Mt. Argentario (southern Tuscany) only. A key is also reported for the identification of the three subspecies.     

One species in eight: DNA barcodes from type specimens resolve a taxonomic quagmire

Each holotype specimen provides the only objective link to a particular Linnean binomen. Sequence information from them is increasingly valuable due to the growing usage of DNA barcodes in taxonomy. As type specimens are often old, it may only be possible to recover fragmentary sequence information from them. We tested the efficacy of short sequences from type specimens in the resolution of a challenging taxonomic puzzle: the Elachista dispunctella complex which includes 64 described species with minuscule morphological differences. We applied a multistep procedure to resolve the taxonomy of this species complex. First, we sequenced a large number of newly collected specimens and as many holotypes as possible. Second, we used all >400 bp examine species boundaries. We employed three unsupervised methods (BIN, ABGD, GMYC) with specified criteria on how to handle discordant results and examined diagnostic bases from each delineated putative species (operational taxonomic units, OTUs). Third, we evaluated the morphological characters of each OTU. Finally, we associated short barcodes from types with the delineated OTUs. In this step, we employed various supervised methods, including distance‐based, tree‐based and character‐based. We recovered 658 bp barcode sequences from 194 of 215 fresh specimens and recovered an average of 141 bp from 33 of 42 holotypes. We observed strong congruence among all methods and good correspondence with morphology. We demonstrate potential pitfalls with tree‐, distance‐ and character‐based approaches when associating sequences of varied length. Our results suggest that sequences as short as 56 bp can often provide valuable taxonomic information. The results support significant taxonomic oversplitting of species in the Elachista dispunctella complex.     

荨麻科楼梯草属植物瘦果的补充描述

楼梯草属植物的瘦果具有较高的形态多样性,可作为种类鉴定的重要依据.然而,中国超过半数楼梯草属植物缺少瘦果形态信息.该研究通过野外考察、标本查阅以及光镜和扫描电镜的观察,对七种楼梯草属植物的瘦果进行了补充描述,并提供了墨线图和照片.该研究结果对该属的进一步分类修订提供了有价值的信息.     

Revised dinoflagellate phylogeny inferred from molecular analysis of large-subunit ribosomal RNA gene sequences

The nucleotide sequence analysis of the PCR products corresponding to the variable large-subunit rRNA domains D1, D2, D9, and D10 from ten representative dinoflagellate species is reported. Species were selected among the main laboratory-grown dinoflagellate groups: Prorocentrales, Gymnodiniales, and Peridiniales which comprise a variety of morphological and ecological characteristics. The sequence alignments comprising up to 1,000 nucleotides from all ten species were employed to analyze the phylogenetic relationships among these dinoflagellates. Maximum parsimony and neighbor joining trees were inferred from the data generated and subsequently tested by bootstrapping. Both the D1/D2 and the D9/D10 regions led to coherent trees in which the main class of dinoflagellates, Dinophyceae, is divided in three groups: prorocentroid, gymnodinioid, and peridinioid. An interesting outcome from the molecular phylogeny obtained was the uncertain emergence of Prorocentrum lima. The molecular results reported agreed with morphological classifications within Peridiniales but not with those of Prorocentrales and Gymnodiniales. Additionally, the sequence comparison analysis provided strong evidence to suggest that Alexandrium minutum and Alexandrium lusitanicum were synonymous species given the identical sequence they shared. Moreover, clone Gg1V, which was determined Gymnodinium catenatum based on morphological criteria, would correspond to a new species of the genus Gymnodinium as its sequence clearly differed from that obtained in G. catenatum. The sequence of the amplified fragments was demonstrated to be a valuable tool for phylogenetic and taxonomical analysis among these highly diversified species. Correspondence to: J. M. Bautista     

Public access for teaching genomics,proteomics, and bioinformatics

When the human genome project was conceived, its leaders wanted all researchers to have equal access to the data and associated research tools. Their vision of equal access provides an unprecedented teaching opportunity. Teachers and students have free access to the same databases that researchers are using. Furthermore, the recent movement to deliver scientific publications freely has presented a second source of current information for teaching. I have developed a genomics course that incorporates many of the public-domain databases, research tools, and peer-reviewed journals. These online resources provide students with exciting entree into the new fields of genomics, proteomics, and bioinformatics. In this essay, I outline how these fields are especially well suited for inclusion in the undergraduate curriculum. Assessment data indicate that my students were able to utilize online information to achieve the educational goals of the course and that the experience positively influenced their perceptions of how they might contribute to biology.     

Webalert of waste management

Waste is unwanted or useless material. It is widely recognized that waste materials are valuable resources, whilst there is debate as to how this value is best realized. Re-use, recycling and energy recovery are being applied to regulated wastes. Yet, while recycling and re-use are increasing, the overall amounts of waste are still growing, and there is an increasing demand for primary resources and stress on eco-systems. In this webalert, we will focus on some important websites which provide readers with more informative resources related to waste management.     

Photosharing websites may improve Hemiptera biodiversity knowledge and conservation

Internet photosharing websites is a very recent and powerful tool for the study of biodiversity, and a meeting point of general public fond of nature and professional naturalists. The article discusses when an uploaded picture is scientifically valuable, and the benefits of structured hosting websites for the most fruitful information retrieval. Examples are given of faunistic, biological, ecological and conservation results concerning Hemiptera provided by information download from photosharing websites.     

Phylogenetic incongruence between dinoflagellate endosymbionts (Symbiodinium) and their host foraminifera (Sorites): small-subunit ribosomal RNA gene sequence evidence

Phototrophic dinoflagellate zooxanthellae commonly occur as endosymbionts in many planktic and certain benthic foraminifera (soritids). Many taxonomic issues and specific identities of foraminiferal dinoflagellates are not yet resolved. To assess taxonomic affinities among other dinoflagellates, we have determined the complete nucleotide sequence of the small-subunit rRNA coding region from Symbiodinium sp., an endosymbiotic dinoflagellate of the larger foraminifer Sorites orbiculus. The poly merase chain reaction was adopted for the in vitro amplification of ribosomal DNA, utilizing primers complementary to conserved regions. PCR-amplified DNA was directly sequenced and the sequence was aligned to all complete 18S-rDNA dinoflagellate sequences currently available through GenBank. Apicomplexan, ciliate, chromistacean, and rhodophycean sequences were added to infer across-kingdom phylogenetic relationships. Phylogenetic analysis of aligned nucleotide sequences produced a single most parsimonious tree (generated by the branch and bound method of PAUP). The inferred phylogeny indicates that the dinoflagellate extracted from the foraminifer Sorites orbiculus is a sister taxon to the symbiont present in the larger foraminifera Marginopora kudakajimaensis, but only distantly related to the dinoflagellate isolated from the soritid Amphisorus hemprichii. The sequence heterogeneity demonstrates a high degree of genetic diversity among Symbiodinium-like zooxanthellae and re-emphasizes that they are a variety of distinct entities.The inferred molecular phylogenetic relationships among symbiotic dinoflagellates are not congruent with the foraminiferal phylogeny based on cladistic methodology. The lack of correlation between the evolutionary history of dinoflagellate symbionts and their foraminiferal hosts argues against co-evolution. This lack of co-evolution implies that flexible recombinations among hosts and symbionts are evolutionarily favorable over permanently associated lineages, at least in these benthic foraminifera.     

淫羊藿属分类学研究:进展、问题与展望

淫羊藿是我国特有且传统的重要药用植物,逐渐步入大宗品种行列。物种的准确鉴定是药效保障和用药安全的前提,为促进其资源的合理开发和利用,该文对淫羊藿属分类学研究进行系统梳理,并对其中存在的问题及存疑类群进行阐述。淫羊藿属共发表68种,中国58种(85.3%),其中57种为特有分布,具有显著的资源优势。淫羊藿属中国类群的分类学研究较为特殊,共26种集中发表于1990s,共31种(53.4%)为国外研究者命名,且绝大多数依据少量栽培个体命名。由于缺乏广泛的形态调查和性状变异分析,导致大量类群的形态描述不准确或不全面,后续20个类群被归并或降级。依据栽培个体命名的类群是补充描述和分类修订的重点。花色、根茎类型、花茎叶的数量及着生方式等性状在中国类群中存在广泛变异。经分类修订后,该属目前包括46种、1亚种和2变种。淫羊藿属中国组类群仍处于活跃进化中,其形态变异复杂,种间关系无法得到解决,为该属分类的最大挑战。但种质资源的研究和利用需要建立在清晰的分类学基础上。未来研究应基于居群调查,完善各物种的形态描述;在此基础上,整合形态变异特征、地理分布格局和基因序列特征,检测自然种间杂交事件,从而揭示物种的...     

UniEuk: Time to Speak a Common Language in Protistology!

Universal taxonomic frameworks have been critical tools to structure the fields of botany, zoology, mycology, and bacteriology as well as their large research communities. Animals, plants, and fungi have relatively solid, stable morpho‐taxonomies built over the last three centuries, while bacteria have been classified for the last three decades under a coherent molecular taxonomic framework. By contrast, no such common language exists for microbial eukaryotes, even though environmental ‘‐omics’ surveys suggest that protists make up most of the organismal and genetic complexity of our planet's ecosystems! With the current deluge of eukaryotic meta‐omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist ‐omics age to the fragile, centuries‐old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information. UniEuk is an open, inclusive, community‐based and expert‐driven international initiative to build a flexible, adaptive universal taxonomic framework for eukaryotes. It unites three complementary modules, EukRef, EukBank, and EukMap, which use phylogenetic markers, environmental metabarcoding surveys, and expert knowledge to inform the taxonomic framework. The UniEuk taxonomy is directly implemented in the European Nucleotide Archive at EMBL‐EBI, ensuring its broad use and long‐term preservation as a reference taxonomy for eukaryotes.     

A taxonomic wish-list for community ecology

Community ecology seeks to explain the number and relative abundance of coexisting species. Four research frontiers in community ecology are closely tied to research in systematics and taxonomy: the statistics of species richness estimators, global patterns of biodiversity, the influence of global climate change on community structure, and phylogenetic influences on community structure. The most pressing needs for taxonomic information in community ecology research are usable taxonomic keys, current nomenclature, species occurrence records and resolved phylogenies. These products can best be obtained from Internet-based phylogenetic and taxonomic resources, but the lack of trained professional systematists and taxonomists threatens this effort. Community ecologists will benefit most directly from research in systematics and taxonomy by making better use of resources in museums and herbaria, and by actively seeking training, information and collaborations with taxonomic specialists.