bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerating the Automated Detection, Counting and Measurements of Reproductive Organs in Herbarium Collections in the Era of Deep Learning
Authors: Mora-Fallas Adán , Goëau Hervé , Mazer Susan , Love Natalie , Mata-Montero Erick , Bonnet Pierre , Joly Alexis 
Published: June 2019

Millions of herbarium records provide an invaluable legacy and knowledge of the spatial and temporal distributions of plants over centuries across all continents (Soltis et al. 2018). Due to recent efforts to digitize and to make publicly accessible most major natural collections, investigations of ecological and evolutionary patterns at unprecedented geographic scales are now possible (Carranza-Rojas et al. 2017, Lorieul et al. 2019). Nevertheless, biologists are now facing the problem of extracting from a huge number of herbarium sheets basic information such as textual descriptions, the numbers of organs, and measurements of various morphological traits. Deep learning technologies can dramatically accelerate the extraction of such basic information by automating the routines of organ identification, counts and measurements, thereby allowing biologists to spend more time on investigations such as phenological or geographic distribution studies.
Recent progress on instance segmentation demonstrated by the Mask-RCNN method is very promising in the context of herbarium sheets, in particular for detecting with high precision different organs of interest on each specimen, including leaves, flowers, and fruits. However, like any deep learning approach, this method requires a significant number of labeled examples with fairly detailed outlines of individual organs. Creating such a training dataset can be very time-consuming and may be discouraging for researchers. We propose in this work to integrate the Mask-RCNN approach within a global system enabling an active learning mechanism (Sener and Savarese 2018) in order to minimize the number of outlines of organs that researchers must manually annotate. The principle is to alternate cycles of manual annotations and training updates of the deep learning model and predictions on the entire collection to process. Then, the challenge of the active learning mechanism is to estimate automatically at each cycle which are the most useful objects that must be manually extracted in the next manual annotation cycle in order to learn, in as few cycles as possible, an accurate model.
We discuss experiments addressing the effectiveness, the limits and the time required of our approach for annotation, in the context of a phenological study of more than 10,000 reproductive organs (buds, flowers, fruits and immature fruits) of Streptanthus tortuosus, a species known to be highly variable in appearance and therefore very difficult to be processed by an instance segmentation deep learning model.
TaxonWorks 1.0?
Authors: Yoder Matthew , Dmitriev Dmitry , Pereira José Luis , Flood James , Tucker James , Pereira Hernán , Beckman Marilyn 
Published: June 2019

TaxonWorks is an open-source workbench for biodiversity researchers. With several years of development behind it, we highlight its present status, and discuss if and when it makes sense to release a version 1.0, i.e. software completed to specific stage. TaxonWorks' scope is broad; it seeks to touch nearly all areas that might be of interest to taxonomists, i.e. those who integrate everything that is known about a taxon into a single resource. Its role as a software platform is placed in a broader context, where many instances of TaxonWorks each can support multiple research projects. Instances may be supported by individuals or organizations. A suite of technical tools including containerization and unit tests facilitate collaboration at many different levels. TaxonWorks is a research tool, mechanisms for analyzing the results of data curation including its application programing interface are described.
The long-term development of TaxonWorks is supported by an endowment to the Species File Group. Its source is available on Github.
Biodiversity Data Integration: The significance of data resolution and domain
Authors: König Christian , Weigelt Patrick , Schrader Julian , Taylor Amanda , Kattge Jens , Kreft Holger 
Published: June 2019

Recent years have seen an explosion in the availability of biodiversity data describing the distribution, function, and evolutionary history of life on earth. Integrating these heterogeneous data remains a challenge due to large variations in observational scales, collection purposes, and terminologies. Here, we conceptualize widely used biodiversity data types according to their domain (what aspect of biodiversity is described?) and informational resolution (how specific is the description?)(Fig. 1). Applying this framework to major data providers in biodiversity research reveals a strong focus on the disaggregated end of the data spectrum, e.g. point occurrence data or trait measurements, whereas aggregated data types, e.g. floras or taxonomic monographs, remain largely under-utilized. We discuss the implications of this imbalance for the scope and representativeness of current macroecological research and lay out how an explicit consideration of domain and resolution can inform data collection, mobilization, imputation, and integration.
We use two case studies to substantiate our points. In the first case study, we show how coarse-grained regional plant checklists can be used to predict global growth form spectra at high spatial resolutions. Our predictions are highly consistent with fine-grained empirical data based on point occurrence records and vegetation plots. While such dis-aggregated data produce reliable results only for a limited set of well-covered regions, aggregated data types can provide critical information for the extrapolation of biodiversity patterns into less well-sampled regions. In the second case study, we revisit the latitudinal gradient in seed mass, which has been reported to exhibit a 320-fold decrease between 0 and 60 degrees latitude as well as a sharp, 7-fold drop at the edge of the tropics. Re-assessing this relationship using an independent dataset revealed a much more moderate, 11-fold decrease of seed mass towards the poles with little evidence for any abrupt changes. We show that the original results, which were based on relatively sparse, disaggregated data, are confounded by substantial biases in the representation of biomes and growth forms. This, we argue, amplified the magnitude and distorted the shape of the latitudinal gradient in seed mass.
In summary, this talk aims to provide both theoretical and practical arguments for a more integrated biodiversity data landscape, which utilizes the strengths and weaknesses of multiple data types across multiple domains and resolutions in order to produce more robust, comprehensive and informative macroecological inferences.
PlutoF: Biodiversity data management platform for the complete data lifecycle
Authors: Kõljalg Urmas , Abarenkov Kessy , Zirk Allan , Runnel Veljo , Piirmann Timo , Pöhönen Raivo , Ivanov Filipp 
Published: June 2019

PlutoF online platform (https://plutof.ut.ee) is built for the management of biodiversity data. The concept is to provide a common workbench where the full data lifecycle can be managed and support seamless data sharing between single users, workgroups and institutions. Today, large and sophisticated biodiversity datasets are increasingly developed and managed by international workgroups. PlutoF's ambition is to serve such collaborative projects as well as to provide data management services to single users, museum or private collections and research institutions.
Data management in PlutoF follows a logical order of the data lifecycle Fig. 1. At first, project metadata is uploaded including the project description, data management plan, participants, sampling areas, etc. Data upload and management activities then follow which is often linked to the internal data sharing. Some data analyses can be performed directly in the workbench or data can be exported in standard formats. PlutoF includes also data publishing module. Users can publish their data, generating a citable DOI without datasets leaving PlutoF workbench. PlutoF is part of the DataCite collaboration (https://datacite.org) and so far released more than 600 000 DOIs. Another option is to publish observation or collection datasets via the GBIF (Global Biodiversity Information Facility) portal. A. new feature implemented in 2019 allows users to publish High Throughput Sequencing data as taxon occurrences in GBIF. There is an additional option to send specific datasets directly to the Pensoft online journals. Ultimately, PlutoF works as a data archive which completes the data life cycle.
In PlutoF users can manage different data types. Most common types include specimen and living specimen data, nucleotide sequences, human observations, material samples, taxonomic backbones and ecological data. Another important feature is that these data types can be managed as a single datasets or projects.
PlutoF follows several biodiversity standards. Examples include Darwin Core, GGBN (Global Genome Biodiversity Network), EML (Ecological Metadata Language), MCL (Microbiological Common Language), and MIxS (Minimum Information about any (x) Sequence).
LinBi: Linking biodiversity and culture information
Authors: Huybrechts Pieter , Alonso-Sánchez Felix , Böttinger Petra , Dillen Mathias , Groom Quentin , Hanquart Nicole , Koch Walter , Gordon Martin , Mergen Patricia 
Published: June 2019

The LinBi project aims to enhance the discoverability of digitized objects from natural history collections hosted by institutes all over Europe. This enhancement is achieved by publishing new and enriched content to the Europeana collections platform. The use of simple vocabularies and machine-readable metadata encourages reuse and has the additional advantage of facilitating the clustering of interesting content for user groups beyond biodiversity and natural history researchers. Linking the collections of Europe together in an openly-available platform and sharing our common cultural and natural heritage with a broad audience will increase the public’s awareness of biodiversity collections. Furthermore, it will help us reach out to new user groups such as teachers, journalists and artists, who were previously unaware of, or distant from, our collections.
Suitable content was selected and harmonized for interlinking with Europeana. Contributions include a large quantity of herbarium sheets, digitized glass plate negatives taken between 1880 and 1930 and a portrait collection dating from the late 19th and early 20th century. With the help of the DoeDat crowdsourcing platform, existing metadata were enriched and mobilized to allow for publication in the form of open linked data.
The integration of geographical data and common names allows the Europeana platform to link scientific specimens with literature and fine art from different collections and to guide users to interesting and inspiring content via themed virtual exhibitions. One such theme is composed of content from the "Wild Roses of Crépin" collection, which will be enriched by pictures of living plants, herbarium specimens and illustrations old and modern. A second content cluster consists of an enriched and curated collection of botanical illustrations originating from a corpus of special and rare books ranging from the 15th to 19th centuries. Careful curation increases the potential for re-use and provides additional oppertunities for the general public to interact with this collection.
The LinBi platform has the long-term ambition of forming a sustainable and open source solution integrated into the Europeana Core Service. This will further improve cooperation between institutes by building international infrastructure and networks, thus contributing to a more open cross-border society.
Assessment of drug utilization pattern of steroids in a district general hospital in Amravati region
Authors: Shende Mulchand , Ghutke Bhupesh , Panekar Dhanshree , Kachewar Aparna 
Published: June 2019

Introduction: Rational use of corticosteroids is very important in the long term for improving patient safety. The main objective of the study was to analyze the prescribing patterns of steroids in a district general hospital, Amravati.
Materials and methods: A prospective observational study was carried out over a period of six months in a district general hospital. All patients receiving any category of steroid therapy were enrolled, and the prescribing tapering patterns of steroids were reviewed. The demographic data, disease data and data on the utilization of various steroids were analyzed, and the knowledge of the patients was assessed by using a Michigan questionnaire.
Results and discussion: 179 patients were recruited for the study. Steroids were prescribed for various (29.6%) respiratory conditions, (10.1%) CVS diseases, (11.7%) CNS, (1.6%) in hepatic disorders, (1.1%) musculoskeletal disorders, (3.4%) skeletal disorders, (0.6%) renal impairments, (3.9%) GI disorders, (19.0%) skin diseases and (19.0%) other diseases. The utilization of steroid dexamethasone was the most commonly prescribed to 111 patients (63.8%) followed by hydrocortisone (57 patients, 32.8%) and prednisolone (6 patients, 3.4 %). Dexamethasone was most commonly associated with adverse effects (1.8% of such as headaches, abdominal pains, and rashes), followed by prednisolone (0.8% of such as facial swelling), clobetasol (0.4%) and fluticasone (0.4 %).
Conclusions: Very little variation was found in the prescription pattern amongst the healthcare professionals. Most of the drugs were prescribed rationally; the significance of the study is to improve the patient safety in the long-term use of steroid therapy by observing the prescribing patterns as irrational use of steroids can increase the risk of adverse effects.
Tratamiento de la prensa sobre el viaje del rey don Juan Carlos a Estados Unidos el 2 de junio de 1976
Authors: Tenorio Maciá José Carlos 
Published: June 2019

L’objet principal de cette recherche est d’étudier la figure du roi Juan Carlos I et le rôle de la presse pendant les premiers moments de la transition démocratique espagnole. Pour cela, nous avons analysé comment les principaux journaux espagnols ont couvert le voyage de LL. MM. le roi et la reine aux États-Unis en 1976, afin que nous puissions déterminer si la couverture médiatique correspondait à l’importance que cet événement a eu sur l’évolution de l’Espagne vers la démocratie. Nous avons également cherché à établir des points communs et des divergences dans le traitement de l’information de chaque journal à travers une étude individualisée. Pour ce faire, nous avons utilisé les archives numériques des journaux ABC, El País et La Vanguardia, en commençant notre analyse une semaine avant l’arrivée des monarques aux États-Unis et en la prolongeant jusqu’à une semaine après (du 26 mai au 9 juin). Nous avons observé que tous les journaux examinés ont accordé une importance particulière à cette visite, bien que chacun l'ait couverte et traitée de manière différente.
Famille et pouvoir dans le monde franc (VIIe-Xe siècle)
Authors: Le Jan Régine 
Published: June 2019

La société médiévale est née à l'époque carolingienne... Durant cette période charnière, un lent mouvement de fond a conduit au gouvernement par conseil des grands et au développement des liens de fidélité, à la conjugalisation du modèle familial et au renforcement des liens verticaux et hiérarchiques à l’intérieur des groupements de parenté aristocratiques. La famille carolingienne et les familles royales qui lui ont succédé sont issues de l’aristocratie franque qui apparaît au fil de l’étude comme l’observatoire privilégié de toutes les transformations sociales.

Famille large-famille étroite, parenté cognatique-parenté agnatique ? L’auteur dépasse ces débats traditionnels en mettant en relation les fondements sociaux et culturels du pouvoir avec les mécanismes de la filiation, de l’alliance et de la résidence. Fondamentalement cognatique mais de plus en plus fermement centré sur le couple conjugal, le système de parenté a évolué au rythme des transformations sociales et politiques, tout en participant lui-même à la dynamique du changement social.

Le présent ouvrage met en lumière mutations et permanences. La montée des Carolingiens et le système politique qu’ils mettent en place aux VIIIe et XIe siècles tirent parti de la hiérarchisation de l’aristocratie et l’accélèrent. Sous le contrôle du roi et de l’Église, l’équilibre social et politique repose désormais sur des groupements que structurent l’alliance, l’amitié et la fidélité. La rupture de l’ordre carolingien et la promotion de la militia à la fin du IXe siècle, l’apparition de lignages organisés autour d’un honor transmis en ligne directe, la nouvelle définition du rôle de la femme et de la parenté agnatique au Xe siècle n’y changent rien : l’alliance et la fidélité restent les fondements des équilibres locaux.
Development and Characterization of a Preclinical Model for the Evaluation of CD205-Mediated Antigen Delivery Therapeutics in Type 1 Diabetes
Authors: Schloss Jennifer , Ali Riyasat , Babad Jeffrey , Guerrero-Ros Ignacio , Pongsachai Jillamika , He Li-Zhen , Keler Tibor , DiLorenzo Teresa P 
Published: June 2019

Abstract
Dendritic cells (DCs) are crucial for the production of adaptive immune responses to disease-causing microbes. However, in the steady state (i.e., in the absence of an infection or when Ags are experimentally delivered without a DC-activating adjuvant), DCs present Ags to T cells in a tolerogenic manner and are important for the establishment of peripheral tolerance. Delivery of islet Ags to DCs using Ag-linked Abs to the DC endocytic receptor CD205 has shown promise in the NOD mouse model of type 1 diabetes (T1D). It is important to note, however, that all myeloid DCs express CD205 in humans, whereas in mice, only one of the classical DC subsets does (classical DC1; CD8α+ in spleen). Thus, the evaluation of CD205-targeted treatments in mice will likely not accurately predict the results observed in humans. To overcome this challenge, we have developed and characterized a novel NOD mouse model in which all myeloid DCs transgenically express human CD205 (hCD205). This NOD.hCD205 strain displays a similar T1D incidence profile to standard NOD mice. The presence of the transgene does not alter DC development, phenotype, or function. Importantly, the DCs are able to process and present Ags delivered via hCD205. Because Ags taken up via hCD205 can be presented on both class I and class II MHC, both CD4+ and CD8+ T cells can be modulated. As both T cell subsets are important for T1D pathogenesis, NOD.hCD205 mice represent a unique, patient-relevant tool for the development and optimization of DC-directed T1D therapies.
Thymus-Derived Regulatory T Cells Exhibit Foxp3 Epigenetic Modification and Phenotype Attenuation after Mating in Mice
Authors: Moldenhauer Lachlan M. , Schjenken John E. , Hope Christopher M. , Green Ella S. , Zhang Bihong , Eldi Preethi , Hayball John D. , Barry Simon C. , Robertson Sarah A. 
Published: June 2019

Abstract
Regulatory T cells (Tregs) are essential for maternal tolerance in allogeneic pregnancy. In preeclampsia, Tregs are fewer and display aberrant phenotypes, particularly in the thymic Treg (tTreg) compartment, potentially because of insufficient priming to male partner alloantigens before conception. To investigate how tTregs as well as peripheral Tregs (pTregs) respond to male partner seminal fluid, Foxp3+CD4+ Tregs were examined in the uterus and uterus-draining lymph nodes in virgin estrus mice and 3.5 d postcoitum. Mating elicited 5-fold increases in uterine Tregs accompanied by extensive Treg proliferation in the uterus-draining lymph nodes, comprising 70% neuropilin 1+ tTregs and 30% neuropilin 1− pTregs. Proliferation marker Ki67 and suppressive competence markers Foxp3 and CTLA4 were induced after mating in both subsets, and Ki67, CTLA4, CD25, and GITR were higher in tTregs than in pTregs. Analysis by t-stochastic neighbor embedding confirmed phenotypically distinct tTreg and pTreg clusters, with the proportion of tTregs but not pTregs among CD4+ T cells expanding in response to seminal fluid. Bisulphite sequencing revealed increased demethylation of the Treg-specific demethylation region in the Foxp3 locus in tTregs but not pTregs after mating. These data show that tTregs and pTregs with distinct phenotypes both respond to seminal fluid priming, but the Foxp3 epigenetic signature is uniquely increased in tTregs. We conclude that reproductive tract tTregs as well as pTregs are sensitive to local regulation by seminal fluid, providing a candidate mechanism warranting evaluation for the potential to influence preeclampsia susceptibility in women.
Determining a diagnostic algorithm for hyperinsulinaemia
Authors: Crofts Catherine A.P. , Schofield Grant , Wheldon Mark C. , Zinn Caryn , Kraft Joseph R. 
Published: June 2019

Background: Ascertaining Kraft dynamic insulin response patterns following a 3-h 100 g oral glucose tolerance test seems to be the most reliable method for diagnosing hyperinsulinaemia. However, this test may be too resource-intensive for standard clinical use.Aim: This study aims to see if Kraft patterns can be accurately predicted using fewer blood samples with sensitivity and specificity analyses.Setting: St Joseph Hospital, Chicago, Illinois, United States and Human Potential Centre, Auckland University of technology, Auckland, New Zealand.Method: We analysed the results of 4185 men and women with a normal glucose tolerance, who had a 100 g oral glucose tolerance test with Kraft pattern analysis. Participants were dichotomised into normal–low insulin tolerance (Kraft I or V patterns) or hyperinsulinaemia (Kraft IIA–IV patterns). Sensitivity and specificity analysis was applied to available variables (including age, body mass index, fasting insulin or glucose) both individually and in combination.Results: Out of a maximal combined sensitivity and specificity score of 2.0, 2-h insulin level 45 µU/mL attained the highest score (1.80). Two-hour insulin also attained the highest sensitivity ( 30 µU/mL, 0.98) and the highest specificity ( 50 µU/mL, 0.99) scores. Combining the 2-h insulin with other variables reduced the sensitivity and/or specificity. Dynamic measures had a better combined sensitivity and specificity compared to fasting or anthropological measures.Conclusion: People with a 2-h plasma insulin level 30 µU/mL are unlikely to be hyperinsulinaemic. Given that first-line treatment is lifestyle modification, we recommend that a 2-h plasma insulin level 30 µU/mL following a 100 g oral glucose tolerance test be used to identify the hyperinsulinaemic individual.
Rise Up!
Authors: Jones Chris 
Published: June 2019

Penned by one of America’s best-known daily theatre critics and organized chronologically, this lively and readable book tells the story of Broadway’s renaissance from the darkest days of the AIDS crisis, via the disaster that was Spiderman: Turn off the Dark through the unparalleled financial, artistic and political success of Lin-Manuel Miranda’s Hamilton. It is the story of the embrace of risk and substance. In so doing, Chris Jones makes the point that the theatre thrived by finally figuring out how to embrace the bold statement and insert itself into the national conversation - only to find out in 2016 that a hefty sector of the American public had not been listening to what it had to say.
Chris Jones was in the theatres when and where it mattered. He takes readers from the moment when Tony Kushner’s angel crashed (quite literally) through the ceiling of prejudice and religious intolerance to the triumph of Hamilton, with the coda of the Broadway cast addressing a new Republican vice-president from the stage. That complex performance - at once indicative of the theatre’s new clout and its inability to fully change American society for the better - is the final scene of the book.