bluuebunny/crossref_metadata_2025 huggingface dataset:
Efecto del tiempo y temperatura en la deshidratación de oca (Oxalis Tuberosa Mol.) Mediante lecho fluidizado para la obtención de harina
Authors: Ore Areche Franklin , Aguirre Huayhua Lissete Lourdes , Ticsihua Huaman Jovencio
Published: March 2021

La región andina es conocida por ser cuna de algunos cultivos andinos de importancia mundial como la papa, oca, olluco y mashua. La oca es un tubérculo muy extendido en los Andes, por ser un producto tradicional, ancestral de sabor agradable, es uno de los alimentos más apreciados en la alimentación del sector rural. La Oxalis tuberosa Mol. Representa una buena fuente de antioxidantes por lo que puede considerarse como una excelente opción de materia prima para la elaboración de alimentos funcionales. Los objetivos de la investigación realizada fueron: evaluar las propiedades fisicoquímicas de la harina de oca, evaluar las propiedades químico proximal de la harina de oca y realizar el análisis microbiológico de la harina de oca (variedad rosada) deshidratado en lecho fluidizado a diferentes temperaturas (60, 70 y 80 °C) por un tiempo de 60 minutos a cada uno. Se empezó obteniendo las harinas, paro lo cual se seleccionó, soleo, limpió, lavo, cortó, escaldo, deshidrato, enfrió, molió, tamizo y envaso. En la caracterización fisicoquímica se hizo el análisis proximal, se determinó el pH y acidez mediante valoración volumétrica, se utilizó el método refractométrico para medir la concentración de azúcar, para el análisis microbiológico, la muestra se obtuvo al azar. Los resultados del análisis químico proximal realizados fueron: humedad, grasa, proteína, fibra, ceniza y carbohidratos, los cuales no muestran diferencias significativas entre ellos, los resultados microbiológicos indican que la harina de oca se encuentra dentro de los parámetros microbiológicos dados por DIGESA (2000), Se puede destacar que la harina de oca mantiene las características organolépticas propias del producto para su uso agroindustrial.
Persons and Things in Marseille and Lucca, 1300–1450
Authors: Smail Daniel Lord
Published: March 2021

In later medieval Europe, a rising tide of wealth changed the material regime and, with it, the relationships that defined the matrix of persons and things. Some of our best evidence for the changes afoot in the era can be found in the massive documentation generated by the legal institutions of the period. Featured in this chapter are household inventories and inventories of debt collection from the cities of Marseille and Lucca. Although the things found in these documents are not tangible, the approach known as “documentary archaeology” allows us to treat the words that describe them as fragments or traces left by things that once existed. Many of the things found in people’s houses were used for the purposes of social distinction, whether that means the individual pursuit of prestige or status, through competitive consumption and display, or a group’s pursuit of group identity, through the display of badges or totems that define membership in a group. The use of materiality for the purposes of distinction has a deep natural history. But in exploring distinction, it is important to bear in mind that prestige goods had other affordances and lent themselves to other ends. Particularly prominent in many human societies, including that of later medieval Europe, is the capacity for things to serve as stores of value. Also important is the fact that people form emotional connections with things. The complex nature of the relationship between people and things in the later Middle Ages is best understood if we treat things as part of the extended phenotype of persons, or as part of a matrix or network that treats both humans and things as equivalent nodes.
Clinical-neurological features of prematurely born children with hypoxic-ischemic lesions of the central nervous system
Authors: Vareshniuk O.V. , Vyun V.V.
Published: March 2021

The clinical and neurological features of prematurely born children with perinatal hypoxic-ischemic lesions of the central nervous system were studied. A comprehensive examination of 79 preterm infants of both sexes who underwent perinatal hypoxic-ischemic lesions of the central nervous system was performed. 37.9 % of the surveyed were diagnosed with spastic cerebral palsy, 20.3 % were diagnosed with spastic diplegia, 27.8 % were diagnosed with childhood hemiplegia, hydrocephalus was acquired in 13.9 % as a result of non-traumatic intraventricular hemorrhage. In 10.3 % of children, severe movement disorders (patients with spastic cerebral palsy and acquired hydrocephalus without surgery) were noted, 37.7 % of the examined did not master walking (patients with spastic diplegia, spastic cerebral palsy and acquired hydrocephalus operated on after 6 months of life), 35.5 % of children have mastered walking with assistive devices (patients with spastic diplegia and acquired hydrocephalus operated on up to 6 months of age), 16.5 % of children have mastered walking without restrictions (children with childhood hemiplegia and acquired hydrocephalus, operated on up to 6 months of age). Characteristic structural changes in perinatal hypoxic-ischemic lesions of the central nervous system are periventricular leukomalacia of the II–III degree and intraventricular hemorrhage of the I–III degree. The study of somatosensory evoked potentials conducted in the course of the work showed that at the 3rd, 4th levels of disorders of motor functions by GMFCP, there is a significant decrease in the function of conducting along the somatosensory pathway, depression of the amplitude of the peaks. It has been established, that in the structure of severe motor disorders in children with perinatal hypoxic-ischemic lesions of the central nervous system, violations of arbitrary regulation of movements and postural control are significant. A clear manifestation of the close correlation between motor function impairment, cognitive activity and anxiety level in the examined children has been established, which testifies to the negative impact of a negative emotional state on the development of a child with severe motor disorders.
Diagnostics of collateral circulation during revascularization of cerebral arteries
Authors: Pulyaeva I.S.
Published: March 2021

54 patients with acute stroke were examined and treated: 12 patients were treated by thrombolytic therapy and/or thrombectomy, 22 patients were treated by endarterectomy from the internal carotid artery, and 20 patients were treated by anticoagulant, nootropic and antiplatelet therapy. Collateral blood circulation of blood vessels and foci of cerebral ischemia in ischemic stroke were examined in all patients to select a treatment method. The effect of collateral circulation in patients with recanalization of the carotid and cerebral arteries on the outcome of acute stroke treatment was analyzed. According to such parameters of neuroimaging as a large nucleus and poor collaterals, 25 out of 54 patients did not respond to revascularizing therapy, which was proved by CT data and a slight regression of neurological deficit within 14 days. Patients with a large nucleus and poor collateral circulation do not respond to revascularization surgery. Compared groups of patients according to CT data. It was found that the level of development of collaterals was associated with better clinical results. Adequate collateral circulation can help maintain tissue viability in the absence of recanalization. The choice of revascularization method depends on the state of collateral circulation, the size of the ischemic focus (according to CT, MRI) and the duration of treatment from the onset of stroke. Diagnosis of ischemia should begin with MRI angiography on the first day or CT angiography from the second day, which will allow assessing the level of collaterals, giving an idea of ​​collateral perfusion in patients and the size of the lesion.
Usos de Foucault, Deleuze y Derrida en la crítica literaria argentina (1980-2010)
Authors:   , Incaminato Natalí Antonella
Published: March 2021

La tesis se enfoca en el estudio de los usos de Michel Foucault, Jacques Derrida, y Gilles Deleuze en textos de crítica literaria argentina del período comprendido por los años que van de 1980 a 2010. El corpus está conformado por El género gauchesco. Un tratado sobre la patria (1988), El cuerpo del delito. Un manual (1999), Aquí América latina. Una especulación (2010), de Josefina Ludmer; Críticas (2000) y una serie de artículos de Jorge Panesi; Médicos maleantes y maricas. Higiene, criminología y homosexualidad en la construcción de la nación Argentina (1995) de Jorge Salessi; La chancha con cadenas (1994), Clases. Literatura y disidencia (2005) Fantasmas. Imaginación y sociedad (2009) de Daniel Link; Manuel Puig: La conversación infinita (2001) de Alberto Giordano; Las vueltas de César Aira (2002) de Sandra Contreras y Un desierto para la nación. La escritura del vacío (2010) de Fermín Rodríguez. El análisis lleva a cabo una lectura cercana que describe y construye hipótesis sobre las operaciones críticas, las torsiones y reapropiaciones de los conceptos filosóficos en las escrituras críticas argentinas, en el marco de las relaciones entre literatura y filosofía.
Dysbiosis of intestinal microbiota in autism spectrum disorders: new horizons in search for pathogenetic approaches to therapy. Part 1. Features of intestinal microbiota in autism spectrum disorders
Authors: Blagonravova A. S. , Zhilyaeva T. V. , Kvashnina D. V.
Published: March 2021

The first part of the literature review on the role of intestinal microbiota dysbiosis in the pathogenesis of autism spectrum disorders (ASD) includes recent data published in the literature on the features of the quantitative and qualitative composition of the intestinal microbiota in patients with autism. It was shown that an excessive presence of Clostridium was detected in ASD, and evidence was presented showing the possible participation of these bacteria in the development of autism symptoms. Contradictory research results on an increase in a number of other pathogenic bacteria and, conversely, a decrease in the number of bacteria necessary to maintain the normal functioning of the intestine and the host organism as a whole are presented. The possible role of Candida albicans in ASD, requiring further study, is reported. Possible causes of contradictions in the results of studies on this topic are discussed.
PENGARUH KONSEP DIRI DAN KOMPETENSI TERHADAP KOMITMEN ORGANISASI PADA PT. BAROKAH UTAMA KARYA MEDAN
Authors: Asnora Fadzil Hanafi , Fitria Eva , Indra Aulia
Published: March 2021

Dari penelitian awal yang peneliti lakukan, lemahnya karyawan dalam membangun keyakinan (building trust), yaitu interaksi dengan individu lain dan membangun rasa yakin terhadap perusahaan. Kekhawatiran dan rasa kurang yakin yang menyebabkan komitmen karyawan terganggu, selain akibat dari belum mampu memfokuskan waktu dan tenaga pada tugas serta pekerjaan yang berakibat ada aspek pekerjaan yang terabaikan, juga karena masih ada karyawan yang belum mampu menerima tanggung-jawab dari hasil kerja orang lain baik positif maupun negatif, hal ini disebabkan karena masih ada karyawan yang belum mampu menyusun suatu kriteria atau prosedur kerja untuk mencapai kualitas, produktivitas, dan layanan kerja yang dibutuhkan. Tujuan penelitian ini adalah untuk mengetahui pengaruh konsep diri dan kompetensi terhadap komitmen organisasi pada PT. Barokah Utama Karya Medan. Jumlah sampel dalam penelitian ini adalah berjumlah 93 orang dengan menggunakan teknik sampel jenuh. Teknik analisis yang digunakan adalah regresi linier berganda. Hasil penelitian menunjukkan bahwa secara langsung tidak terdapat pengaruh signifikansi konsep diri terhadap komitmen organisasi. Secara langsung terdapat pengaruh signifikansi kompetensi terhadap komitmen organisasi.
New Algorithm for Upgrading of Portal Radiation Monitors with Plastic Detectors
Authors: Stavrov Andrey
Published: March 2021

The new algorithm for portal radiation monitors with plastic detectors is discussed in the paper. It is based on optimization of the value of smoothing for count rate profiles, alarming thresholds and so called energy windows. Implementation of this algorithm provides increasing of probability of detection of the radioactive sources including those which are masked by NORM under suppression of natural background. The verification of radioactive sources and NORM on the base of analysis of count rate profiles for point and distributed sources is discussed in the first part.
Method of Non-Destructive Measurement of Natural Radionuclides Concentration in Building Materials
Authors: Vasil'ev Aleksey , Ekidin Aleksey , Pyshkina Mariya , Malinovskiy Georgiy , Onischenko Aleksandra , Yarmoshenko Il'ya , Zhukovskiy Mihail
Published: March 2021

A method for non-destructive monitoring of the content of natural radionuclides in building materials has been developed. Spectrum measurements of gamma radiation are carried out with a pre-calibrated field gamma spectrometer. The calculation of the average specific activity of natural radionuclides in building materials is carried out by comparing the calculated flux density of unscattered gamma quanta normalized to the specific activity, and the experimentally measured count rates in the photopeak. calculated for the geometry of the room under study and the location of the detector. Application of the developed method makes it possible to estimate the average activity of natural radionuclides in building materials without destruction.
The molecular mechanisms of multidrug resistance of human glioblastomas
Authors: Chernov Alexandr , Baldueva Irina , Nekhaeva Tatyana , Galimova Elvira , Alaverdian Diana , Shamova Olga
Published: March 2021

In review discusses the phenomenon of drug resistance of GB in the context of the expression of ABC family transporter proteins and the processes of proliferation, angiogenesis, recurrence and death. The emphasis is on the identifying for molecular targets among growth factors, receptors, signal transduction proteins, microRNAs, transcription factors, proto-oncogenes, tumor suppressor genes and their polymorphic variants (SNPs) for the development and creation of targeted anticancer drugs.
Superior vena cava resection and plastic repair as a part of surgical and combined treatment of lung cancer
Authors: Levchenko Evgeny , Ergnyan Stepan , Shutov Vitalii , Krotov Nikolai , Levchenko Nikita , Yurin Roman , Murtazin Azat , Shabinskaya Viktoriya
Published: March 2021

This article summarizes our own experience of reconstructive operations with resection and plastic repair of the superior vena cava in the field of locally advanced lung cancer surgery. Both technical aspects and methodological approaches of this type of combined interventions are described in detail. Data from 45 patients who underwent wedge (21) and circular (24) superior vena cava resections were analyzed. In most (65%) cases, venous resection and reconstruction were combined with multi-organ resections of other anatomical structures of the chest cavity. 87% of patients received combined treatment in different directions. Postoperative complications were registered in 40% of cases, and the mortality rate was 13%. The unfavorable postoperative prognostic factors were followings: old age, pneumonectomy, combination of vein angioplasty with carinal resection. The 5-year survival rate was 18.5%, with a median survival of 19.4 + 4.6 months. The results allow us to recommend such operations in highly specialized clinics that have extensive experience in tracheobronchial angioplastic surgery and highly-qualified anesthesia care providers. Multimodal treatment allows to achieve satisfactory long-term results.
Detektieren ermüdungsbedingter Spannstahlbrüche mittels Rissmonitoring im Versuch und am Bauwerk/Detection of fatigue induced fracture of prestressing steel by means of monitoring of experiment and structure
Authors: Heinrich Jens , Maurer Reinhard , Leckey Kevin , Müller Christine H. , Ickstadt Katja
Published: March 2021

An einer Spannbetonbrücke wurden systematische Rissbildungen mit Rissbreiten bis zu 0,5 mm im Bereich der Momentennullpunkte aus ständigen Lasten festgestellt. Diese waren eine Folge der seinerzeit nicht berücksichtigten Zwangsschnittgrößen infolge Temperatur (ΔTM). Aus den Rissen resultierte in der Folge eine Gefährdung der Spannglieder durch Ermüdung. Auch mit genaueren Methoden konnte kein ausreichender Ermüdungswiderstand nachgewiesen werden. Dazu kam der schlechte bauliche Gesamtzustand. Daher wurde vom Baulastträger ein möglichst kurzfristiger Ersatzneubau beschlossen, bis zu dessen Zeitpunkt die Tragsicherheit des Bauwerks sichergestellt werden musste. Zu diesem Zweck erfolgte ein kontinuierliches Rissmonitoring für die kritischen Bereiche. Die Grundlage für dessen Bewertung bildeten Ermüdungsversuche an Spannbetonbauteilen an der TU Dortmund. Dabei ist es gelungen, einzelne Drahtbrüche während des laufenden Versuchs zuverlässig zu identifizieren und ein Prognoseverfahren für die Restlebensdauer zu entwickeln. Über die Erfahrungen und Schwierigkeiten diese Methoden auf ein reales Bauwerk zu übertragen, wird berichtet.
Coping Strategies in Professional Activities of Educational Psychologists
Authors: Казаренков В.И. , Карнелович М.М. , Казаренкова Т.Б.
Published: March 2021

В статье рассматриваются проблемные вопросы психологии совладания субъекта со стрессовыми ситуациями в профессиональной сфере жизнедеятельности.
Предмет исследования — совладание педагогов-психологов со стрессом в профессиональной деятельности. Цель исследования — определить влияние стратегий совладающего поведения на развитие профессионального стресса у педагогов-психологов.
Методы исследования: тестирование, методы описательной статистики, множественный регрессионный анализ, U-критерий Манна — Уитни.
Приведены результаты эмпирического исследования профессионального стресса и копинга у педагогов-психологов, работающих в системе общего среднего образования Российской Федерации и Республики Беларусь. Раскрыты уровни выраженности стресса и специфические особенности копинга со стрессорами в деятельности у педагогов-психологов с разной длительностью стажа профессиональной деятельности.
Результаты исследования свидетельствуют о необходимости обучения педагогов-психологов навыкам саморегуляции эмоциональных состояний для повышения стрессоустойчивости и могут использоваться при разработке программ профилактики эмоционального выгорания и стрессовых состояний у представителей социономических профессий.

The article treats some problematic issues of coping with stressful situations in career-related situations.
The object of the research is educational psychologists’ coping skills that help them cope with stress in their professional activities. The aim of the research is to identify the influence of coping strategies on the development of occupational stress in educational psychologists.
The methods of the research are the following: test, descriptive statistics, multiple regression analysis, the Mann-Whitney U test.
The article provides the results of an empirical research of occupational stress and coping strategies in educational psychologists working in the system of compulsory secondary education in the Russian Federation and the Republic of Belarus. The article reveals the levels of stress manifestation and specific coping strategies in educational psychologists with different professional records.
The results of the research show that it is essential that educational psychologists should be taught to self-regulate their emotional conditions and cope with stressful situations in an effective way. The results of the research can be used to develop a training course aimed at preventing emotional burnout and stress in representatives of socionomic professions.
Antibakterijski učinak preparata
„Sanosil super25“ na višestruko rezistentne bakterije Acinetobacter baumannii i Klebsiella
pneumoniae
Authors: Kovačić Ana , Hrenović Jasna , Goić-Barišić Ivana , Barišić Miroslav
Published: March 2021

Višestruko rezistentne bakterije, uzročnici hospitalnih
infekcija, kao što su Acinetobacter
baumannii i Klebsiella pneumoniae,
predstavljaju globalni problem 21. stoljeća. Osobito zabrinjava sve učestalija
pojava otpornosti ovih mikroorganizama na komercijalno dostupne dezinficijense.
Cilj našeg istraživanja bio je utvrditi učinkovitost dezinfekcije proizvoda
„Sanosil super25“, u odnosu na vodikov peroksid i to na višestruko rezistentne
izolate A. baumannii i K. pneumoniae. Ispitane su vrijednosti
MTC (maksimalno tolerirajuća koncentracija); MIC (minimalna inhibirajuća
koncentracija) i MBC (minimalna baktericidna koncentracija). MTC Sanosila
(<1.25 ppm) bila je dvostruko manja u odnosu na vodikov peroksid. MIC-e
Sanosila (1.25 ili <1.25 ppm) su bile 4 puta manje u odnosu na vodikov
peroksid. MBC koja rezultira izostankom vijabilnih bakterija za Sanosil je bila
<1.25 ppm već nakon 5 min kontakta, što je barem 8 puta niža koncentracija u
odnosu na vodikov peroksid. Rezultati su pokazali da je Sanosil super25 bio
učinkovitiji u sve tri kategorije, u odnosu na vodikov peroksid.
Accretion Geometry in the Hard State of the Black Hole X-Ray Binary MAXI J1820+070
Authors: Zdziarski Andrzej A. , Dziełak Marta A. , Marco Barbara De , Szanecki Michał , Niedźwiecki Andrzej
Published: March 2021

We study X-ray spectra from the outburst rise of the accreting black hole binary MAXI J1820+070. We find that models having the disk inclinations within those of either the binary or the jet imply significant changes of the accretion disk inner radius during the luminous part of the hard spectral state, with that radius changing from >100 to ∼10 gravitational radii. The main trend is a decrease with the decreasing spectral hardness. Our analysis requires the accretion flow to be structured, with at least two components with different spectral slopes. The harder component dominates the bolometric luminosity and produces strong, narrow, X-ray reflection features. The softer component is responsible for the underlying broader reflection features. The data are compatible with the harder component having a large scale height, located downstream the disk truncation radius, and reflecting mostly from remote parts of the disk. The softer component forms a corona above the disk up to some transition radius. Our findings can explain the changes of the characteristic variability timescales, found in other works, as being driven by the changes of the disk characteristic radii.
Predicting classifications in marine biomonitoring with supervised machine learning: how much data is required?
Authors: Dully Verena , Wilding Tom , Mühlhaus Timo , Stoeck Thorsten
Published: March 2021

Marine coastal ecosystems offer numerous ecosystem services and are therefore subject to a variety of stressors from anthropogenic activities. Environmental biomonitoring programs for effective management and conservation of coastal marine ecosystems are therefore crucial. Traditional monitoring has been based on macrofauna indices which are laborious and require expert knowledge. Recently, eDNA metabarcoding has become increasingly popular as it does not involve macrofauna species identification and is therefore cost and time inexpensive. Studies have shown that ecosystem monitoring based on eDNA metabarcoding is feasible and random forest (RF) algorithms can predict various biological indices, and therefore ecosystem health. To propose adequate designs for future eDNA metabarcoding-based marine coastal monitoring surveys, the aim of the study is to find out (1) What is the lower limit of reads for accurate RF predictions in coastal marine monitoring using microbial communities? (2) Is this limit the same for different monitoring targets? To achieve this goal, we exploited four different Illumina amplicon datasets obtained from bacterial communities in different costal environments. From these datasets, we predicted different objectives relevant for biomonitoring. For each dataset, those corresponding prediction objectives (labels) were predicted using amplicon sequence variants (ASVs) as features. After construction of RF models using all available sequences of a dataset (full model, serving as benchmark for targeted prediction accuracy), we then successively down-sampled each dataset to lower sequence numbers. Prediction accuracies of the reduced models were then compared to the accuracies of the full models to assess the minimum number of features to obtain the targeted prediction accuracy. Our results show that there is no general answer to question (1) and that (2) the limit varies between different monitoring targets. We have identified the most informative criteria that are relevant to assess the sequencing depth required to predict a biomonitoring category using RF. This may guide future study designs and may help to estimate and control costs in applied routine DNA-based biomonitoring using RF to predict the biomonitoring target. In our contribution we will elucidate and discuss these criteria.
Evaluating the impact of sampling strategies and bioinformatics on ethanol-based DNA metabarcoding
Authors: Martins Filipa MS , Fonseca Nuno A , Egeter Bastian , Pinto Joana , Assunção Tiago , Chaves Cátia , Sousa Pedro , Jesus Joaquim , Beja Pedro
Published: March 2021

Recent developments on ethanol-based DNA (etDNA) metabarcoding have shown that it is possible to extract meaningful information about macroinvertebrate community diversity and composition from the ethanol used to preserve bulk samples. The major advantages of this molecular approach are the reduced processing time and costs, and the possibility to keep specimens intact for other experiments. Yet, organisms with highly sclerotised exoskeleton or that are rare in the sample have been found to release a lower amount of DNA into solution and tend to be consistently missed by etDNA metabarcoding, thereby compromising the viability of the method. Few studies have shown that the first steps of the metabarcoding workflow are crucial for the good performance of etDNA-based assays, such as the decision on storage time before sampling and the ethanol phase to be analysed, the inclusion of pre-treatment strategies (i.e., freezing), and the choice of the DNA extraction protocol. In this study, we aimed to evaluate the combined effect of various technical choices on the performance of etDNA metabarcoding, considering factors such as sample volume, ethanol phase of sorted and unsorted samples, pre-capture treatments (evaporation vs filtration) and bioinformatic pipelines. Through the application of decision-tree models, our preliminary data revealed that the increase of volume (by itself) is enough to improve PCR amplification yields and proportion of families matching the morphological identifications, with great impact on the detection of hard-bodied and cased taxa. Also, no major differences among phases with or without a sorting step nor among bioinformatic pipelines were detected, particularly at higher volumes. Our results suggest that the higher performance (with lower observed variation) in taxonomic detection at higher volumes is likely a consequence of a higher availability of longer fragments of DNA in solution. This study highlights the importance of understanding the impact of technical choices to improve the efficiency of a DNA-based method, and reinstates etDNA metabarcoding as a potential method in the context of biomonitoring.
Analyzing multiple stressor effects on EPT taxa in a mesocosm experiment with DNA metabarcoding
Authors: Werner Marie-Thérése , Beermann Arne , Elbrecht Vasco , Zizka Vera , Leese Florian
Published: March 2021

Multiple stressors diversely and often adversely affect stream ecosystems around the globe. Therefore, understanding multiple stressor effects on different organisms is essential for a better ecosystem understanding, an accurate water quality assessment and improved ecosystem management. However, while multiple stressor effects should be assessed at species level this taxonomic resolution is often not achieved e.g. for stream macroinvertebrates. Due to their high abundance and diversity, species-level identification is often not feasible with morphology‑based approaches. DNA metabarcoding represents an alternative approach for studying multiple stressor interactions at species level.

In an outdoor experiment over 10,000 specimens from the insect orders Ephemeroptera, Plecoptera and Trichoptera (EPT), which are routinely used as bioindicators, and their responses to stressors were studied. In the experiment salinity, fine sediment deposition and flow velocity were manipulated in a full‑factorial design in 64 mesocosms with two microhabitats each (streambed and leaf litter), resulting in eight replicates per treatment. DNA metabarcoding revealed 122 EPT Operational Taxonomic Units (OTUs), from which the most abundant 27 alone showed 14 different response patterns to the applied stressors. The high taxonomic resolution achieved by DNA metabarcoding revealed species specific stressor responses that were hidden at a lower taxonomic resolution. As a prominent example, Rhithrogena semicolorata responded negatively to fine sediment deposition and flow velocity reduction, while Ecdyonurus torrentis (both Heptageniidae, Ephemeroptera) was insensitive to experimental manipulation, highlighting different stressor responses among species within the same family (Fig. 1, Beermann et al. 2020).

Even for well-studied organisms such as EPT taxa, this study shows that DNA metabarcoding has the potential to depict response patterns at species or OTU level despite high specimen abundance. Consequently, DNA metabarcoding promises to be a rewarding method when investigating and assessing multiple stressor effects on stream water quality.
TaxonTableTools - A comprehensive, platform-independent graphical user interface software to explore and visualise DNA metabarcoding data
Authors: Macher Till-Hendrik , Beermann Arne , Leese Florian
Published: March 2021

DNA-based identification methods, such as DNA metabarcoding, are increasingly used as biodiversity assessment tools in research and environmental management. Although powerful analysis software exists to process raw data, the translation of sequence read data into biological information and downstream analyses may be difficult for end users with limited expertise in bioinformatics. Thus, the need for easy-to-use, graphical user interface (GUI) software to analyze and visualize DNA metabarcoding data is growing. Here we present TaxonTableTools (TTT), a new platform-independent GUI that aims to fill this gap by providing simple, reproducible analysis and visualization workflows. The input format of TTT is a so-called "TaXon table". This data format can easily be generated within TTT from two common file formats that can be obtained using various published DNA metabarcoding pipelines: a read table and a taxonomy table. TTT offers a wide range of processing, filtering and analysis modules. The user can analyze and visualize basic statistics, such as read proportion per taxon, as well as more sophisticated visualizations such as interactive Krona charts for taxonomic data exploration, or complex parallel category diagrams to assess species distribution patterns. Venn diagrams can be calculated to compare taxon overlap among replicates, samples, or analysis methods. Various ecological analyses can be produced directly, including alpha or beta diversity estimates, rarefaction analyses, and principal coordinate or non-metric multidimensional scaling plots. The taxonomy of a data set can be validated via the Global Biodiversity Information Facility (GBIF) API to check for synonyms and spelling mistakes. Furthermore, geographical distribution data can be automatically downloaded from GBIF. Additionally, TTT offers a conversion tool for DNA metabarcoding data into formats required for traditional, taxonomy-based analyses performed by regulatory bioassessment programs. Beyond that, TTT is able to produce fully interactive html-based graphics that can be analyzed in any web browser. The software comes with a manual and tutorial, is free and publicly available through GitHub (https://github.com/TillMacher/TaxonTableTools) or the Python package index (https://pypi.org/project/taxontabletools/).
The first step towards a DNA barcode reference database for mayflies (Ephemeroptera) of Slovakia
Authors: Macko Patrik , Derka Tomáš , Čiampor Jr Fedor , Čiamporová-Zaťovičová Zuzana
Published: March 2021

Mayflies (Ephemeroptera) represent a small but diverse order of amphibiotic insects, whose larvae contribute to several essential processes in freshwater habitats, such as bioturbation and bioirrigation, decomposition, nutrient cycling, and also serve as a primary source of nutrients for numerous organisms. Due to their cosmopolitan distribution and high-quality water requirements, they are also important indicators of ecosystem health and an integral part of biomonitoring protocols. Although the Slovak mayfly fauna is well researched, studies on genetic diversity, including DNA barcoding, are still lacking. The absence of the comprehensive DNA barcode reference libraries from various biogeographical regions and the presence of so-called cryptic lineages may prevent further efficient use and application of new approaches to aquatic ecosystem biomonitoring (Biomonitoring 2.0) based on eDNA analyses. Therefore, in the initial stage of our research, we bring the first insight into the genetic diversity of mayflies (based on mtDNA COI-5P barcoding fragment) from 47 localities of Slovakia mostly situated in the biogeographically significant Western Carpathians' territory. A total of 403 sequences of 42 morphologically determined species were added to the BOLD (Barcode of Life Data System) database, representing more than 1/3 of the mayfly fauna of Slovakia and covering 10 of 16 families. Sequences of these species were finally assigned to 62 BINs (Barcode Index Numbers) in BOLD (Fig. 1), whereby sequences of 12 species were divided into more than one BIN, indicating the presence of cryptic lineages. The largest number of BINs was represented by widely distributed species such as Baetis rhodani Pictet, 1843-1845 (6 BINs), Habroleptoides confusa Sartori & Jacob, 1986 (4 BINs) and Ecdyonurus venosus (Fabricius, 1775) (3 BINs). The sequences of the remaining nine species were split into two BINs. Maximum intraspecific variability (calculated by K2P) of some representatives was surprisingly high [e.g., E. venosus – 27.1 %; Baetis muticus (Linneaus, 1758) – 23.6 %; Caenis luctuosa (Burmeister, 1839) – 23.34 %, Baetis rhodani – 18.66 % and B. vernus Curtis, 1834 – 15.25 %] and far exceeded the level of intraspecific variability of the COI fragment based on the BOLD standards. The sequences of 23 individuals determined as Habroleptoides confusa, Baetis rhodani, B. buceratus Eaton, 1870, Caenis beskidensis Sowa, 1973 and Torleya major (Klapálek, 1905) created seven unique BINs, which represent the distant phylogenetic lineages of already existing BINs, that are currently unique to Slovakia. The coexistence of Baetis rhodani individuals of two different BINs was confirmed at five localities. Our study indicates clear importance of more detailed sampling and DNA barcoding due to the presence of unexpected intraspecific genetic diversity of mayflies captured in a relatively small area of the Western Carpathians.
Establishing (e)DNA-Methods for Governmental Biomonitoring Efforts and Ecological Assessment in German Federal Waterways
Authors: Schmidt Saskia , Mora Demetrio , Krenek Sascha , Kleinteich Julia , Schöll Franz , Fischer Helmut
Published: March 2021

The German Federal Institute of Hydrology (BfG, for its acronym in German) is the nationwide advising departmental research institution regarding hydrology, water use and quality, ecology and water protection of the German Federal Waterways that comprise inland waterways as well as marine coastal waters.

The Federal Waterways of Germany are important habitats and distribution corridors for aquatic biodiversity. However, the ecology of these large rivers is heavily impacted by shipping, hydromorphological alterations, chemical pollution and the distribution and establishment of invasive species. All these factors have led to a decline of native biodiversity and ecological status. Since the 1970s, tremendous efforts have been undertaken to restore water quality and biodiversity. Continuous monitoring and assessment of both chemical components and biological quality elements (BQEs) required by law should indicate the success or failure of restoration measures as well as ongoing and future ecological consequences of multiple stakeholders’ interests and demands.

Standardized ecological assessment procedures are already in place for both rivers and streams. However, these widely used procedures have several shortcomings and require a high level of taxonomic competence, which is being lost at an increasing rate. DNA and environmental DNA (eDNA)-based methods, such as DNA barcoding and (e)DNA metabarcoding, are promising alternatives to overcome the impediments to the morphology-based identification of organisms. But, these new methods need to be tailored to the challenges of large river bioassessment. The implementation of such state-of-the-art methods for future biomonitoring and ecological assessment efforts in large rivers should therefore ultimately serve the legal requirements regarding the EU Water Framework Directive (WFD) and promote the application of (e)DNA methods from basic and applied research to water managers and regulatory authorities.

Here we present the goals and approaches of our ongoing project that are 1) to create standard operation procedures (SOPs) for (e)DNA analyses for large rivers and 2) update or establish new methods for biodiversity assessment and biomonitoring (e.g. presence-absence analyses) of the federal waterways; and 3) to transfer the gained knowledge to water managers and practitioners. To accomplish these goals, the focus of our research relies on the BQEs fish and macrozoobenthos (led by Saskia Schmidt), as well as phytobenthos and phytoplankton (led by Demetrio Mora).
Comparing total RNA sequencing and metagenomics pipelines for multi-domain taxonomic profiling: implications for ecological assessments
Authors: Hempel Christopher , Harvie Julia , Hleap Lozano Jose , Wright Natalie , Adamowicz Sarah , Steinke Dirk
Published: March 2021

Ecological assessments are necessary to evaluate the status of our deteriorating ecosystems, however, assessment methods traditionally omit most microbes because unicellular organisms are challenging to identify. This omission is not ideal, as microbes might be better indicators for changes in environmental conditions than taxa traditionally used. DNA- and RNA-based techniques are increasingly applied for ecological assessments to overcome this challenge but require more testing and optimization. In this study, we compare metagenomics and total RNA sequencing (total RNA-Seq) for their taxonomic profiling performance for microbial communities. We applied both techniques on two sample sets, 1) a commercially available microbial mock community consisting of eight bacterial and two eukaryotic species, and 2) a display tank water sample. We processed the data using 1,532 bioinformatics pipelines and evaluated each workflow, i.e., the combination of sample type (metagenomics or total RNA-Seq) and pipeline, in terms of their accuracy and precision. This talk will showcase preliminary results and highlight differences in workflow performances. A recommended workflow to maximize taxonomic profiling accuracy of microbial communities will also be presented.
Decona: From demultiplexing to consensus for Nanopore amplicon data
Authors: Oosterbroek Saskia , Doorenspleet Karlijn , Nijland Reindert , Jansen Lara
Published: March 2021

Sequencing of long amplicons is one of the major benefits of Nanopore technologies, as it allows for reads much longer than Illumina. One of the major challenges for the analysis of these long Nanopore reads is the relatively high error rate. Sequencing errors are generally corrected by consensus generation and polishing. This is still a challenge for mixed samples such as metabarcoding environmental DNA, bulk DNA, mixed amplicon PCR’s and contaminated samples because sequence data would have to be clustered before consensus generation.

To this end, we developed Decona (https://github.com/Saskia-Oosterbroek/decona), a command line tool that creates consensus sequences from mixed (metabarcoding) samples using a single command. Decona uses the CD-hit algorithm to cluster reads after demultiplexing (qcat) and filtering (NanoFilt). The sequences in each cluster are subsequently aligned (Minimap2), consensus sequences are generated (Racon) and finally polished (Medaka). Variant calling of the clusters (Medaka) is optional. With the integration of the BLAST+ application Decona does not only generate consensus sequences but also produces BLAST output if desired. The program can be used on a laptop computer making it suitable for use under field conditions.

Amplicon data ranging from 300-7500 nucleotides was successfully processed by Decona, creating consensus sequences reaching over 99,9% read identity. This included fish datasets (environmental DNA from filtered water) from a curated aquarium, vertebrate datasets that were contaminated with human sequences and separating sponge sequences from their countless microbial symbionts.

Decona considerably simplifies and speeds up post sequencing processes, providing consensus sequences and BLAST output through a single command. Classifying consensus sequences instead of raw sequences improves classification accuracy and drastically decreases the amount of sequences that need to be classified. Overall it is a user friendly option for researchers with limited knowledge of script based data processing.
Application of eDNA method in the detection of Cordulegaster (Insecta: Odonata) species
Authors: Fekete Judit , Buchner Dominik , Leese Florian , Padisák Judit , Várbíró Gábor
Published: March 2021

The aim of this pilot study was to investigate the potential of eDNA techniques to detect the presence of the two dragonfly species Cordulegaster heros and Cordulegaster bidentata. Both species are classified as “near threatened” according to the IUCN Red List and are strictly protected in several countries. Monitoring these species with traditional sampling methods is often difficult, time-consuming and invasive. In this pilot study, we first collected tissue samples from C. heros and C. bidentata to sequence the traditional DNA-barcode gene fragment COI. We then collected further dragonfly COI sequences from BOLD to design species-specific primers. This, however, was impossible given the enormous variability of COI. Therefore, we refrained from species-specific eDNA assays and followed eDNA metabarcoding protocol using universal (BF2/BF2) and a newly designed dragonfly specific primer. For the evaluation of the method, we took water samples from places where Cordulegaster specimens are known to occur. After the extraction, we used two sequential PCR steps for obtaining the desired amplicon (two-step PCR) using universal primers in the first step, and group (dragonfly) specific primers or universal primers. Amplicons were sequenced on an Illumina MiSeq platform and then analysed the data with the JAMP pipeline. With the newly designed primers and we could effectively detect the targeted dragonfly species from tissue samples, and also from filtered environmental samples. The detection of the species with the traditional method is time consuming and involves the destruction of the specimens. In comparison, with the eDNA method we could easily detect these near threatherned odonates and other dragonfly species in a non-invasive way.
A reliable DNA barcode reference library for the identification of benthic invertebrates: essential for biomonitoring of the North Sea
Authors: Christodoulou Magdalini , van der Hoorn Berry , Van den Bulcke Laure , Derycke Sofie , De Backer Annelies , Kröncke Ingrid , Martinez Arbizu Pedro
Published: March 2021

Benthic macroinvertebrates are key components in environmental impact assessments. Nevertheless, their use as bioindicators can be constrained by the time- and cost-consuming processes needed for their morphological identification. The recent advances in high-throughput sequencing, particularly DNA metabarcoding can provide an alternative to morphology-based approaches. The main limitation for DNA-based tools to be implemented in biomonitoring projects is the considerable investment needed to build high-quality and curated taxonomic reference DNA sequence libraries for species identification. To begin addressing this shortage, Interreg NSR project GEANS aim in developing a curated DNA reference library based on mitochondrial cytochrome c oxidase subunit I (COI) for the North Sea macrobenthos that will serve as the backbone of all the molecular protocols. For the collection of the macroinvertebrates, a targeted sampling campaign is underway across the North Sea Region, while existing collections are being scanned. Macrobenthic specimens are being processed following a series of standardised work flows covering sampling, morphological identifications, molecular lab processing and data handling. GEANS' reference library, currently holds DNA barcodes for 3443 specimens collected from various areas of the North Sea. In total 11 phyla, 28 classes, 80 orders, 280 families, 428 genera and 586 species (37 non-indigenous species) are represented within the library. Species-level identification is taxonomically verified for over 90 % of the species, while genus-level identifications are verified for almost 100 % of the genera. GEANS reference library covers so far over 30 % of North Sea species and its constantly enriched. All specimens are photographed and together with the accompanying sequences, collection and taxonomic data are archived in a dedicate BOLD project. Voucher specimens and DNA extracts are archived at three different institutes in Germany (Senckenberg am Meer), the Netherlands (Naturalis) and Belgium (ILVO). Once available, this DNA-library will be based on taxonomically well-curated specimens and it will support the implementation of fast, cost-efficient and reliable DNA-based identifications and subsequently environmental health assessments in the North Sea.
Targeted Next Generation Sequencing improves detection and quantification of rare species from eDNA
Authors: Westfall Kristen , Therriault Thomas , Abbott Cathryn
Published: March 2021

Targeted species detection from eDNA is central to identifying and quantifying rare (i.e. invasive or endangered) species to inform conservation and resource management. Here we introduce a new targeted Next Generation Sequencing (tNGS) assay that shows improved detection relative to quantitative (q)PCR at low eDNA concentrations and increased precision to detect spatial variation in eDNA concentration related to species abundance. We compare the tNGS and qPCR methods using invasive European green crab (Carcinus maenas) in the northeast Pacific Ocean as a test case, and find that crab abundance measured by traditional trapping is significantly correlated with eDNA concentration across multiple sites for both methods. However, the tNGS assay outperformed qPCR in all tests: (1) increased precision of eDNA concentration estimation; (2) a 7-10% increase in detection probability at low abundance sites; and (3) greater power to detect spatial variation in eDNA concentration. The accuracy of predicting green crab abundance from eDNA concentration increased with the number of field replicates sampled and did not change appreciably over a tidal cycle. Green crab eDNA concentration behaving similarly to abundance measured from trapping demonstrates great promise for this tool to be implemented for early detection and routine monitoring surveys. The tNGS assay is easily accessible for surveying other species with existing qPCR assays and can thus be potentially important for detection and quantification of any species of high interest to management.