bluuebunny/crossref_metadata_2025 huggingface dataset:
Viewpoint of al-Darqu?n? regarding uncertain singularity of transmitter from most frequent ?m?m: Descriptive study
Authors: Al-Haq Ikram , Kharroub Dr. Abdelhamid
Published: March 2021

The Taffarud or singurality in ?ad?th sciences is one of the important and most critical type. Therefore, scholars of the ?ad?th paid it much attention and wrote number of books on the account of “al-Afr?d and al-Ghar?b a??d?th”. Many scholars like ?m?m al-Daraqu?n?, ?m?m al-Bazz?r, al-?m?m al-?abr?n? and other critics composed books on this subject. The discussion about the narrator’s uniqueness and singularity compared to other narrators from his sheikh who has many students, includes in the issue of reasoning, that a transmitter narrates a ?ad?th from that sheikh which his peers do not know about it. If a transmitter who is unique in its narration and also contains the critics of the scholars is called “Taffarud” which comes with different conditions in terms of acceptance and rejection. In that case, it is not acceptable to consider those terms as a totality and whoever takes it as such will be mistaken, as these rules must be understood in the light of the scholar’s understandings and their intention of usage. Otherwise we will eventually deviate from their methodology. This research is divided into an introduction, two articles, and a conclusion. As for the introduction, author defined the “taffarud” literally and lexically. In the first section, author explained the opinions of critics regarding; not to accept the uniqueness of the narrators narrating from a lot others. In the second section, author conducted an applied study on the transmitters who are not likely to be accepted in their narrations from the one who narrates a lot. As well as, author mentioned the conclusion and stidy results.
Arabic Language as Source of Qur’anic Exegeses: Study of Ghulam Ahmad Pervaiz’s Arguments
Authors: Razzaq Dr. Abdul , Iqbal Dr. Zafar
Published: March 2021

Principles of Quranic exegesis are illustration of Qur’an, gradually by Qur’an, Hadith, sayings of companions of holy prophet (SAW), Arabic literature, as well as rational reasoning. Study of Quranic commentaries reveals that, although, there is a consensus on these principles being used for Quranic exegeses but there are variations in understanding and application of these. In this context, the commentaries also differ from one scholar to other. One of these scholars is Ghulam Ahmad Pervaiz, author of Urdu exegesis of Qur’an, whose understanding and application of these principles completely differ from mainstream scholars. Pervaiz used the Arabic language and dictionary meanings as a basic source of Quranic exegeses, while other use it as secondary source. Similarly, Pervaiz rejected the principle of Quranic exegesis ‘illustration by Hadith’. This article discussed the validity and authenticity of Arabic language as a source of Quranic exegesis and Pervaiz’s application of it by disagreeing with mainstream scholars. Analysis made based on basic exegesis principles and historical traditional literature.
MENGUKUR DAMPAK KETERAMPILAN KERJA DAN KOMPENSASI MASA COVID-19 DALAM MENINGKATKAN PRODUKTIVITAS KERJA KARYAWAN
Authors: Febriani Budi , Harahap Aziddin , Simanjuntak Daslan
Published: March 2021

Covid-19 telah memberikan pelajaran penting bagi perusahaan-perusahaan terkaita hubungannya dengan pengelolaan SDM-nya, banyak perusahaan awalnya kewalahan menghadapi guncangan covid-19 terutama dalam memperhatikan keterampilan kerja dan kompensasi hingga hubungannya terhadap produktivitas kerja. Kemajuan perusahaan bergantung pada produktivitas kerja yang dihasilkan karyawannya melalui keterampilan kerja dan kompensasi yang diterimanya. Hasil penelitian ini membuktikan bahwa keterampilan kerja karyawan dimasa covid-19 masih memiliki  hubungan yang kuat dengan produktivitas kerja, sedangkan kompensasi tidak memiliki hubungan yang baik dalam peningkatan produktivitas kerja.
PENGARUH MEDIA PEMBELAJARAN ONLINE DALAM PEMAHAMAN DAN MINAT BELAJAR MAHASISWA PADA BIDANG STUDI AKUTANSI DI FEB UNIVERSITAS LABUHANBATU
Authors: Nasution Siti Lam'ah , Windari Furi , Harahap Syaiful Zuhri , Elvina Elvina
Published: March 2021

Penerapan dan pelaksanaan pembelajaran jarak jauh (online) disetiap lembaga pendidikan khususnya pada perguruan tinggi merupakan aplikasi dan tidak lanjut dari peraturan yang dikeluarkan pemerintah melalui kementrian pendidikan nasional. Peraturan ini dikeluarkan dalam rangka meminimalisir penyebaran wabah Covie19. Pembelajaran jarak jauh sebenarnya bukanlah hal yang baru dalam dunia pendidikan. Pembelajaran jarak jauh sudah dilaksanakan sebelum adanya wabah Covid19 di Indonesia. Pembelajaran jarak jauh sebelumnya dilaksanakan dengan E-learning yang terintegrasi dengan pembelajaran tatap muka (luring). Akan tetapi pembelajaran jarak jauh saat ini dilakukan secara berkelanjutan sehingga berpotensi memberikan efek atau pengaruh psikologis pada mahasiswa, sehingga pemahaman dan minat belajarnya menjadi menurun. Untuk itu seorang tenaga pendidik (Dosen) harus mampu memilih media yang tepat untuk digunakan dalam pelaksanaan pembelajaran jarak jauh, seorang dosen harus memperteimbangkan metode dan media pembelajaran yang tepat untuk dapat meningkatkan pemahaman mahasiswa pada materi pembelajaran dan mempertahankan motivasi belajarnya. Penelitian ini bertujuan untuk mengeahui pengaruh pembelajaran online dalam pemahaman dan minat belajar mahasiswa pada bidang studi akuntansi. Hasil penelitian menunjukkan bahwa mahasiswa program studi akuntansi Universitas labuhanbatu tidak menyukai atau tidak senang dengan sistem pembelajaran online (daring) yang diterapkan khusunya pada pembelajaran materi akuntansi. Mahasiswa kurang memahami materi pembelajaran akuntansi yang dilakukan secara daring sebab, materi tidak tersampaikan dengan tuntas akibat gangguan jaringan internet yang tidak stabil dan media pembelajaran yang terbatas pada mahasiswa. Minat belajar mahasiswa pada materi akuntansi sangat kuat, akan tetapi dengan metode dan sistem pembelajaran daring membuat tingkat pemahaman mahasiswa pada materi akuntansi masih terbatas.
An Enhanced Spice and 3D Modelling for Standard Servomotors
Authors: Dondon Philippe , Bulucea C. A.
Published: March 2021

Servomotors are widely used and well known by hobbyists for control of small scale radio controlled boats, cars or planes. The control is done using a simple PWM signal modulation, easily compatible with a 2 or 4 channels remote control system. As hobbyists are generally simple users, a light knowledge is generally enough to drive this kind of motor. However, in some electronic applications, we need deeper information on servomotors behaviour. Unfortunately, servo manufacturers never give detailed datasheet and no information is available on various WEB sites. Thus, we present in this paper, a SPICE modelling for hobbyist servomotor. Simulation and practical experimentations are done to validate the modelling. Finally, an additional lively 3D modelling is proposed and a concrete didactical application is described before conclusion
CLASSIFICATION OF COVID-19 SYMPTOM FOR CHATBOT USING BERT
Authors: Park H. , Moon G. , Kim K.
Published: March 2021

Coronavirus disease (COVID-19) is a significant disaster worldwide from December 2019 to the present. Information on the COVID-19 is grasped through news media or social media, and researchers are conducting various research. This is because we are trying to shorten the time to be aware of the COVID-19 disaster situation. In this paper, we build a chatbot so that it can be used in emergencies using the COVID-19 data set and investigate how the analysis is changing the situation with deep learning.
Development of method for creating tumor xenograft model with porous metal scaffold
Authors: Protasova Tatyana , Goncharova Anna , Lukbanova Ekaterina , Volovik Vyatcheslav , Mindar Mariya , Khodakova Dariya , Volkova Anastasia , Zaikina Ekaterina , Chapek Sergei , Karnaukhov Nikolai , Potemkin Dmitry , Vasilchenko Nikita , Maksimov Aleksei
Published: March 2021

Aim of the study – the development of a method for obtaining a tumor xenograft model by a subcutaneous transplantation of a porous metal scaffold populated with cultured human lung carcinoma cells.
Material and methods. The study included 14 athymic male Balb c/nude mice aged 8-90 weeks, weighing 20-24 g. All animals received injections with cultured human A549 lung carcinoma cells subcutaneously into the right anterolateral area of the back. In animals of the main group (gr.1, n=4), scaffolds with a pore diameter of 0.5 mm made of titanium-aluminum-vanadium alloy using an industrial 3D printer served as carriers of tumor cells. Scaffolds were seeded with 3 million A549 culture cells, and were implanted into the recipient animals after the 7-day incubation. Results were compared with the results of the tumor culture transplantation with Matrigel (100 mcL) in two groups of animals with varying cell suspension dosages: the maximum vaccination dose for in vivo (10×106 cells per mouse, gr.2, n=5) and half the maximum dose (5×106 respectively, gr.3, n=5). Then, the dynamics of tumor growth in the groups of experimental mice was monitored for 55 days: xenograft volumes were calculated using the Shrek’s formula for an ellipsoid. At the end of the experiment, the animals were euthanized by cervical dislocation.
Results. Monitoring of the dynamics of xenograft volumes demonstrated the maximal values in mice with implanted scaffolds. The slowest xenograft growth was registered in animals with the maximum vaccination dose of tumor cells with Matrigel. Histological study showed that tumor material obtained from all animals corresponded to A549 lung carcinoma.
Conclusions. Porous metal scaffolds, previously incubated with A549 culture cells and implanted subcutaneously in athymic Balb c/nude mice, allows obtaining rapidly growing xenografts with histologically confirmed correspondence to the original tumor.
Glioma C6 perivascular changes of invasion structural parameters variation (research study).
Authors: Kostenikov Nikolay , Dubrovskaya Violetta , Kovanko Elena , Mirolyubova Olga , Mukhina Marina , Ilyushchenko Yury , Stanzhevsky Andrei , Maistrenko Dmitry
Published: March 2021

A comparative study of the structural characteristics of microvessels with a perivascular arrangement of tumor cells and microvessels with normal structure located in the peritumoral zones of an intracranially implanted glioblastoma ("glioma C6") was conducted. The study was performed on rats. Morphometric method was used to determine the area, internal diameter and length of microvessels for 21 days after the introduction of tumor cells into the brain of rats. Changes in the structure of microvessels with glioblastoma cells were registered throughout the entire observation period. The active role of perivascularly located tumor cells in the transformation of the structure and properties of microvessels involved in the process of glioblastoma invasion into brain tissue is considered.

Key words: glioblastoma, microvessels, morphometry, peritumoral zones.
Structural composition and clinical features of dermatological patients with keratinocytic skin tumors
Authors: Khasanov Rustem , Faizullina Elena , Khismatulina Irina , Murtazin Azat
Published: March 2021

Basal cell skin cancer (BCС) is the most common malignancy that is found in dermatological practice. The purpose of the study: to determine the structure of clinical manifestations of BCС in ambulant dermatological patients. The study was conducted from 2015 to 2017 in a private clinic in Kazan, which has a license to provide medical care in the specialties "dermatovenerology" and "surgery". We studied the results of examination of 2730 patients with skin tumors available in outpatient cards. 101 patients with histologically verified BCС were examined, including 29% of men (n=29) and 71% of women (n=72), the average age was 59.7±14.9 years (median – 61.5 years). The percentage of patients with BCС among patients with all skin malignancies at the dermatological reception was 95.3% (n=101). Most often, patients aged 60-74 years suffered from BCС: women – in 21.0% (n=21) and men – in 16.0% (n=16), respectively. The proportion of women aged 45-59 years was significantly higher – 20.0%, than the proportion of men – 9.0% (p<0.05). Men were significantly more likely to see a dermatologist – 55.0% in less than a year from the onset of the disease, than women – 21.4% (p<0.01). The proportion of women (44.6%) who noted the appearance of a tumor over a long period (≥5 years) was significantly less than the proportion of men 15.0% (p<0.05). The most common variant of BCС was the nodular form n=77 (76.2%), in which the primary elements of 80.5% were identified by dermatologists as single 5-10 mm papules. The oculo-fronto-nasal region was involved in the pathological process in 47.5% (n=48) of cases, which is significantly more frequent than in other localisations (p<0.05). Dermatoscopy improved the visualization of the atypical vascular network.
Synthesis and properties of oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing adenine, guanine, or 5-methylcytosine nucleobases
Authors: Horie Naohiro , Yamaguchi Takao , Kumagai Shinji , Obika Satoshi
Published: March 2021

Chemical modifications have been extensively used for therapeutic oligonucleotides because they strongly enhance the stability against nucleases, binding affinity to the targets, and efficacy. We previously reported that oligonucleotides modified with an N-methylguanidine-bridged nucleic acid (GuNA[Me]) bearing the thymine (T) nucleobase show excellent biophysical properties for applications in antisense technology. In this paper, we describe the synthesis of GuNA[Me] phosphoramidites bearing other typical nucleobases including adenine (A), guanine (G), and 5-methylcytosine (mC). The phosphoramidites were successfully incorporated into oligonucleotides following the method previously developed for the GuNA[Me]-T-modified oligonucleotides. The binding affinity of the oligonucleotides modified with GuNA[Me]-A, -G, or -mC toward the complementary single-stranded DNAs or RNAs was systematically evaluated. All of the GuNA[Me]-modified oligonucleotides were found to have a strong affinity for RNAs. These data indicate that GuNA[Me] could be a useful modification for therapeutic antisense oligonucleotides.
Students’ Emotions as a Factor of their Professional Competence Development
Authors: Гапонова С.А. , Ловков С.Г.
Published: March 2021

В статье рассматривается вопрос о факторах, влияющих на развитие настоящего профессионализма, неразрывно связанного с профессиональной направленностью личности, субъектным отношением к деятельности.
Одной из психических структур, связывающих профессиональное и личностное, являются профессиональные представления.
Анализ современных эмпирических исследований показывает, что значительное развитие профессиональные представления получают во время обучения в системе высшего образования. Однако это развитие имеет значительные резервы.
Гипотеза исследования состоит в том, что существуют факторы, значительно замедляющие развитие у студентов профессиональных представлений в процессе обучения. На основе анализа особенностей развития профессиональных представлений было выдвинуто предположение, что одним из таких факторов является частое возникновение у них негативных эмоциональных состояний. Для подтверждения этой гипотезы со студентами были проведены занятия по формированию навыка совладания с негативными переживаниями. В результате развитие профессиональных представлений у них значительно ускорилось. Таким образом, возникновение негативных переживаний, связанных
с процессом обучения, является фактором, существенно замедляющим развитие профессиональных представлений.

The article focuses on factors that influence the development of professional competencies, promotes people’s professional improvement, their involvement in their work.
Professional insights serve as a bridge between the personal and the professional.
The analysis of modern empirical research shows that higher education efficiently promotes the development of people’s professional insights. It also shows that people’s professional development has significant reserves. The hypothesis of the research consists in the assumption that there are certain factors that hinder the development of students’ professional insights in the process of education. The analysis of the peculiarities of professional insights development enables the authors of the article to assume that one of the factors is students’ predisposition towards negative emotions. To prove the hypothesis, students were engaged into learning activities aimed at the development of coping skills. The experiment showed that students’ professional insights were developed more efficiently and rapidly. Therefore, negative emotions associated with the process of education are a factor that significantly hinders the development of students’ professional insights.
The first record of Catocala helena Eversmann, 1856 (Lepidoptera, Erebidae) in Europe with notes on its distribution in Russia
Authors: Knyazev Svyatoslav A. , Gorbunov Pavel Yu. , Melyakh Sergey F. , Nedoshivina Svetlana V. , Grebennikov Nikolai D. , Matov Alexey Yu.
Published: March 2021

First record of the nemoral Eastern Palaearctic species Catocala helena Eversmann, 1856 is reported from Samara Region as new to Europe. New localities in the South Urals and West Siberia are reported for the first time. The present records expand the species distribution for more than 2500 km to the west. The general species’ distribution and bionomics is provided. Species’ habitats in the South Urals are illustrated.
Evaluating Opioid Dispensing Rates among Pediatrics and Young Adults based on CURES Data Reporting in California from 2015-2019
Authors: Phan Michael , Wong Courtney , Tomaszewski Daniel , Kain Zeev , Jenkins Brooke , Donaldson Candice , Fortier Michelle
Published: March 2021

Background
Receipt of opioid prescriptions in pediatric and young adult patients may be a risk factor for future opioid misuse. Data from prescription drug monitoring programs provide insight on outpatient opioid use. In our study, we analyzed the opioid dispensing rates for pediatrics and young adults in California.
Methods
A secondary analysis was performed from 2015-2019 using Controlled Utilization Review and Evaluation System data. This database provides dispensing data of controlled substances in California. Patients younger than 25 years who were prescribed opiates were analyzed by county. We further divided them into two groups (children: ≤14 years; adolescents and young adult: 15-24 years). Descriptive statistics and heat maps were used to illustrate the trends in opioid usage among different age groups.
Results
The overall percentages for the number of opioids being dispensed to patients aged <25 years have decreased over the past four years. In 2015, 6 out of 58 counties in California were considered “high-rate” with >2.9% of opioids dispensed to patients younger than 25 years old; in 2019, this number reduced to zero. Patients 25 and older received a higher proportion of opioids compared to younger populations; in 2019, 35.91% of opioids were dispensed to patients 45-64, and 8.92% to patients younger than 25.
Conclusion
Pediatric opioid prescriptions have declined over the recent years. However, a high degree of variability of prescription rates between demographic counties was noted. More studies are warranted in order to understand this discrepancy in opioid prescribing among pediatric and young adult patients.
Comparing metatranscriptomics, PCR-based methods, and morphology in estimating diversity and composition of zooplankton mock communities
Authors: Lopez Mark Louie , Lin Ya-Ying , Machida Ryuji
Published: March 2021

Studying complex metazoan communities requires taxonomic expertise and laborious work if done using the traditional morphological approach. Nowadays, the popular use of molecular25 based methods accompanied by massively parallel sequencing (MPS) provides rapid and higher resolution diversity analyses. However, diversity estimates derived from the molecular-based approach can be biased by the co-detection of environmental DNA (eDNA), pseudogene contamination, and PCR amplification biases. Here, we constructed microcrustacean zooplankton mock communities to compare species diversity and composition estimates from PCR-based methods using genomic (gDNA) and complementary DNA (cDNA), metatranscriptomic transcripts, and morphology data. Mock community analyses show that gDNA mitochondrial cytochrome c oxidase I (mtCOI) amplicons inflate species richness due to environmental and nontarget species sequence contamination. Significantly higher amplicon sequence variant (ASV) and nucleotide diversity in gDNA amplicons than cDNA indicated the presence of putative pseudogenes. Last, PCR-based methods failed to detect the most abundant species in mock communities due to priming site mismatch. Overall, metatranscriptomic transcripts provided estimates of species richness and composition that closely resembled morphological data. The use of metatranscriptomic transcripts was further tested in field samples. The results showed that it could provide consistent species diversity estimates among biological and technical replicates while allowing monitoring of the zooplankton temporal species composition changes using different mitochondrial markers. These findings show that community characterization based on metatranscriptomic transcripts reflects the actual community more than PCR-based approaches.
Circumglobal distribution of fish environmental DNA in coral reefs
Authors: Mathon Laetitia , Marques Virginie , Mouillot David , Albouy Camille , Andrello Marco , Baletaud Florian , Borrero-Pérez Giomar , Dejean Tony , Edgar Graham J. , Grondin Jonathan , Guerin Pierre-Edouard , Hocdé Régis , Juhel Jean-Baptiste , Kadarusman Kadarusman , Maire Eva , Mariani Gael , McLean Matthew , Polanco F Andrea , Pouyaud Laurent , Stuart-Smith Rick D. , Sugeha Hagi Yulia , Valentini Alice , Vigliola Laurent , Vimono Indra B. , Pellissier Loic , Manel Stephanie
Published: March 2021

Coral reefs host the highest fish diversity on Earth despite covering less than 0.1% of the ocean’s seafloor. At the same time they are also extremely threatened. Data syntheses over decades of surveys estimate the total number of coral reef fishes to vary from 2,400 to 8,000 species distributed among roughly 100 families. But this diversity remains largely unknown.

Here, we investigated how environmental DNA (eDNA) could describe the distribution of fish diversity in coral reefs. We generated 504,457,267 raw 12S ribosomal DNA (rDNA) sequence reads from 251 samples (2,693 PCR replicates) collected at 25 sites in 145 stations covering five regions across the Indian, Pacific and Atlantic Oceans. Bioinformatic analysis clustered these sequences into 2,160 molecular operational taxonomic units (MOTUs) corresponding to distinct species (Marques 2020) We compared our results, with visual census surveys from Reef Life Survey, on 2,813 transects in tropical regions.

Our outcomes demonstrate the capacity of eDNA metabarcoding from water samples to reconstruct well-known biogeographic patterns of fish diversity on coral reefs, such as species richness gradients towards the coral triangle, and family proportion stability across sites (Bellwood and Hughes 2001). Additionally, eDNA survey data documented a higher fish species (16%) and family (50%) diversity than estimates obtained with underwater visual surveys carried out on 20 times more sites. MOTU richness per family retrieved with eDNA closely matched fish species richness within families recorded in visual census data. However, eDNA revealed higher richness of reef-associated species and species from adjacent habitats, of cryptobenthic or nocturnal species, but also of pelagic and wide-ranging species. eDNA survey data showed that fish diversity is characterized by spatially heterogeneous species assemblages among regions, with more dissimilarity among adjacent coral reefs than detected with visual survey data. Unlike visual surveys, eDNA metabarcoding revealed the same prevalence of rarity as expected under the neutral theory of biodiversity, suggesting the predominance of random processes and ecological equivalence within trophic groups at large scale to explain fish biodiversity patterns on coral reefs. Our study demonstrates how sequencing eDNA from water provides a rapid and effective approach to characterize and assess coral reef diversity across large spatial scales, thereby also uncovering hidden biodiversity patterns.
Challenges in building barcode reference libraries for marine invertebrates exemplified by the genus Prionospio (Annelida: Spionidae)
Authors: Hektoen Martin , Ekrem Torbjørn , Bakken Torkild
Published: March 2021

The completeness of reference libraries is often a limiting factor in the effectiveness of biomonitoring using molecular tools. The fact that these libraries are often built upon Sanger sequencing can create a substantial bias due to poor primer fits and unoptimized lab protocols. Some taxa of marine macroinvertebrates are known to be notoriously difficult to sequence using traditional, PCR-based means, and only about 15% of the known bioindicator species world-wide have publicly available sequences for any genetic marker (Aylagas et al. 2014). The Barcode of Life Data System (BOLD) indicates an amplification rate between 46% and 85% of the barcode region of COI for the most commonly used marine invertebrates that indicate pollution in the North East Atlantic (Capitellidae, Cirratulidae, Dorvilleidae, Spionidae and Tubificidae within Annelida, and Thyasiridae within Mollusca). A currently on-going integrative taxonomic study on Prionospio Malmgren, 1867 (Spionidae, Annelida) exemplifies the extensive issues of utilizing Sanger sequencing on marine invertebrates. The barcode region of COI was attempted amplified using five primer pairs: three designed to be universal for marine invertebrates (Folmer et al. 1994, Geller et al. 2013, Lobo et al. 2013), one specialized on polychaetes (Carr et al. 2011) and one self-designed. In addition, two DNA polymerases were tested (TaKaRa Ex Taq HS and Qiagen HotStarTaq) and three annealing temperatures. Only five sequences of COI were obtained from a total of 255 PCR reactions (2% success rate). Other genetic markers showed better amplification rates: 58% for 16S rDNA, and more than 90% success rates for 28S rDNA and Histone H3. This illustrates the importance of having more than one marker in mind when seeking to complete reference libraries, and the potential effectiveness of a multi-marker approach in molecular biomonitoring surveys. As sequencing costs decrease, utilizing shallow shotgun-based sequencing (genome skimming) on problematic groups such as Prionospio to bypass issues regarding unfit primers is also becoming a viable option.
Keystone species of coastal ecosystems from the Bay of Biscay
Authors: Garate Leire , Lanzén Anders
Published: March 2021

Estuarine and coastal ecosystems play a fundamental role in human activities. Since millions of people depend on the numerous resources they offer (i.e., fisheries, transportation, and recreational activities), these ecosystems are also exposed to a high anthropogenic pressure. In order to better monitor and regulate such pressures, it is critical to improve our understanding of the functioning of these ecosystems. This is especially important for microorganisms, considering, for instance, their important roles in biogeochemical cycles. In this study we investigate estuarine and coastal microbial communities along the coast of the Basque Country using eDNA metabarcoding of bacterioplankton and microbenthos samples along a time series, from locations that present different degrees of disturbance. Metabarcoding of the 16S and 18S rRNA gene was carried out, and the OTU and taxa tables generated were used to reconstruct ecological networks, representing potential biological interactions. These ecological networks were used to identify on one hand the species that play a major role in the maintenance of the whole community structure (keystones), and on the other, complex network modules affected by environmental impacts. Here, we define keystone taxa as those that presented the highest ratio between the degree of connectivity (number of associations they established within the network) and their relative abundance. The underlying aim of this study is to develop novel “bioindicators” based on taxa that are both sensitive to impacts and important for community structure.

Results of two seawater communities, one from offshore waters and the other from the coast, showed similar bacterial composition at family level, dominated by Flavobacteraceae and Rhodobacteraceae. Nevertheless, their ecological network properties differed strongly: for a similar number of taxa that established associations, the conectance was similar in both communities, but the number of associations in the coastal community was twice as high as for the offshore one, resulting in a higher modularity. Identified keystone taxa were taxonomically different between both communities: those from the coastal community belonged to Protobacteria, Bacteroidetes, Firmicutes, and Fusobacteria phyla, while the keystones from the offshore community belonged to Proteobacteria, Actinobacteria, Chloroflexi, Thaumarchaeota, PAUC34f and Verrucomicrobia. Moreover, we identified “connector” taxa that presented the highest values of betweenness centrality. These taxa, without having a high degree of connectivity, may be important for the interaction structure because they connect modules, i.e., highly connected subnetworks within the whole network. Further, hierarchical clustering was performed to identify seasonal trends and to better understand the associations retrieved. Taxa with different seasonal preference often grouped together in the same modules, which indicates that modularity was not caused primarily by seasonality.
Alpine freshwater fish biodiversity assessment: an intercalibration test for metabarcoding method set up
Authors: Riccioni Giulia , Domaizon Isabelle , Gandolfi Andrea , Pindo Massimo , Vautier Marine , Kurmayer Rainer , Hufnagl Peter , Dobrovolny Stefanie , Vasselon Valentin , Rund Hans , Bylemans Jonas , Tang Cuong , Wanzenböck Josef
Published: March 2021

Environmental DNA (eDNA) based methods (Fig. 1) are proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC) especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. Freshwater fish are actively involved in aquatic ecosystems functioning and diversity, contributing to the health, well-being and economy in every geographic realm. Unfortunately, many freshwater fish are experiencing critical population decline with risk of local or global extinction because of intense anthropogenic pressure. Within the EU project Eco-AlpsWater, advanced high throughput sequencing (HTS) techniques are used to improve the traditional WFD monitoring approaches by using environmental DNA (eDNA) collected in Alpine waterbodies. To evaluate the performance of the metabarcoding approach specifically designed to measure freshwater fish biodiversity in Alpine lakes and rivers, an intercalibration test was performed. This exercise forecasted the use of mock samples containing either tissue-extracted DNA of different target species or water collected from aquaculture tanks to mimic real environmental water sampling and processing. Moreover, three water samples collected in Lake Bourget (France) were used to compare the efficiency of taxonomic assignments in natural and mock community samples. Our results highlighted a good efficiency of the molecular laboratory protocols for HTS and a good amplification success of the selected primers, providing essential information concerning the taxonomic resolution of the 12S mitochondrial marker. As further confirmation, different concentration of species DNA in the mock samples were well represented by the relative read abundance. This preliminary test confirmed the applicability of eDNA metabarcoding analyses for the biomonitoring of freshwater fish inhabiting Alpine and perialpine lakes and rivers.
Development of specific markers for the detection of Tolypella canadensis eDNA in water samples
Authors: Wiebe Christina , Nowak Petra , Schubert Hendrik
Published: March 2021

Assessing the biodiversity of an ecosystem plays a major role in ecosystem management. However, proper determination on species-level is often tricky when morphological features are scarce and especially rare species require huge sampling efforts to be detected in the aquatic realm. As an alternative to conventional methods, environmental samples can be examined via the eDNA method, allowing for large-scale integration as well as taxa resolution independent from expression of morphological characters. However, to apply this technique genetic markers that are specific to a species or at least a genus are required. Such markers until now have been successfully developed only for a few well studied taxonomic groups like, e.g., fishes and amphibians, but are still missing for others, especially plants and algae (e.g. Bista et al. 2017).

This project focusses on the development of species-specific markers for the macrophytic green algae Tolypella canadensis (Characeae, Charophyta), a rare alga preferring deep water and known so far mainly from remote places. Tolypella canadensis is a circumpolar species and prefers oligotrophic lakes, where it grows in depths up to 13 m (Langangen 2002; Romanov and Kopyrina 2016). In addition, proper determination of Tolypella-species is a field of a few specialists, further complicating monitoring or even detection of this rare species.

The design of the species-specific primers was based on reference nucleotide sequences of the chloroplast genes rbcL, psbC and atpB and of the ribosomal internal transcribed spacer regions ITS1 and ITS2, obtained from GenBank (Perez et al. 2017). To determine the specificity of the newly designed primers, DNA isolates obtained from T. canadensis specimens collected from the Torneträsk (Sweden, 2018) and other charophyte species were prepared in different proportions. The sensitivity of the primers was experimentally assayed by using serial dilutions of T. canadensis DNA. Additionally, a mock test comprised of a sample with the DNA of several charophyte species was conducted and finally, the markers were tested on environmental samples from the Torneträsk.

Tolypella canadensis-specific primers of the ITS2 region yielded positive PCR amplifications of one single band when T. canadensis was present in a sample. Cross-amplification was not found during the mock test; other charophyte species did not yield positive amplification. The eDNA samples from the Torneträsk validated the performance of the ITS2 marker.

The T. canadensis-specific marker designed in this project was proven to be sensitive and accurate. It could be recommended as a useful tool to detect the presence of T. canadensis DNA, even at low concentration and in complex samples containing other charophyte species.
AquaBOL.SK - how far have we come with the Slovak reference barcode database since DNAqua-Net was launched?
Authors: Čiamporová-Zaťovičová Zuzana , Macko Patrik , Šamulková Michaela , Vargovčík Ondrej , Bozáňová Jana , Čiampor Jr Fedor
Published: March 2021

Essential for implementation of molecular tools in bioassessments are comprehensive databases with high-quality reference DNA sequence data. A recent survey arising from the DNAqua-Net EU COST Action WG1 has revealed significant gaps in the barcode reference data of aquatic biota both on a taxonomic and a geographical level (Weigand 2019). Although reference barcode libraries of all main freshwater groups are continuously improved through a number of national DNA-barcoding campaigns, still little data is available from Central and Eastern Europe.

In Slovakia, the barcode coverage of the aquatic biota was very low when DNAqua-Net started. At the end of 2016 only 165 public records (60 OTUs) were available in BOLD (< 3 % of aquatic macroinvertebrates reported from Slovakia), and most of them were mined from GenBank. This led us to launch the campaign “Barcoding aquatic biota of Slovakia” (www.AquaBOL.SK), aiming to improve this unpleasant state. Since many common species in Slovakia are covered by barcodes from other countries, initially we focused on least explored habitat types within Europe - alpine glacial lakes in Tatra Mts and karstic springs. Both are located in Western and Slovak part of Eastern Carpathians, which are considered one of the most valuable biodiversity centers in Europe. More than 2700 sequences of COI-5P (337 BINs), originating in Slovakia, are currently in our dataset. Mostly they represent aquatic insects (86 %) and crustaceans (12 %), followed by minor taxonomic groups. From insects, the best covered orders are Coleoptera (43 % of sequences, 21% of species), followed by Trichoptera (22 % of sequences, 24 % of species) and Ephemeroptera (18 % of sequences, 33 % of species). And even if other groups (Hemiptera, Plecoptera) represent only around 5 % of all sequences each, their species coverage is already 21 % or 28 %, respectively. Relatively high number of unique BINs (35 out of 337) from our area, and separate intraspecific lineages within BINs of many widespread species, supports the premise that the Western Carpathians belong to the most important biodiversity hotspots.

Our local reference database, continuously updated, is useful for the analysis and interpretation of metabarcoding data - a prerequisite for effective and nondestructive monitoring of aquatic biotopes including vulnerable, threatened, and protected habitats. It is also beneficial for a number of other purposes such as taxonomic revisions and phylogenetic analyses. This contribution was partially supported by VEGA2/0030/17, VEGA2/0084/2021 and COST CA15219.
eDNA reveals widespread presence of marine fish in the Panama Canal
Authors: Schreiber Lennart , Castellanos-Galindo Gustavo , Robertson D. Ross , Torchin Mark , Chavarria Karina , Laakmann Silke , Saltonstall Kristin
Published: March 2021

Shipping corridors can be hotspots for biological invasions as they connect the world’s oceans and dissolve dispersal barriers between these aquatic systems. As a consequence, multiple opportunities for biotic exchange arise and the resulting establishment of non-native species often causes adverse ecological and economic impacts. In this study, a combined effort of traditional gillnetting and eDNA-based surveys was implemented to characterize the fish community of the Panama Canal, which is a key region for biotic exchange as it connects the Pacific and Atlantic Oceans in Central America. The Canal was recently expanded and new lock systems installed potentially providing novel opportunities for fish to enter the Canal. Using COI metabarcoding, we detected a total of 142 taxa, including thirteen potentially new records for the freshwater part of the Canal. Furthermore, we found evidence for the presence of 16 Atlantic and 10 Pacific non-native marine fish inside different sections of the Canal. Identifications based on molecular data did not cover all species caught with gillnets, but generally provided a more complete image of the fish fauna. Diversity indices based on eDNA surveys revealed significant differences across different sections of the Canal reflecting in part the prevailing environmental conditions. The observed changes in the fish community may be attributed to the recent expansion of the lock systems, which facilitates species migration directly by enlarging the canal entrances on either side of the Isthmus and indirectly by allowing more salt water to enter the Canal and thus increasing the overall salinity. Given the potential ecological and socio-economic consequences of non-native species crossing the Canal and establishing in the ocean basins on either end, it seems advisable to evaluate limiting salt water intrusion as well as implementing additional barriers to species dispersal (acoustic/electric/chemical deterrents) as a precautionary measure.
Effects of anthropogenic pressures on diatom communities using morphological and molecular approaches
Authors: Teixeira Marco , Almeida Salomé , Feio Maria , Mortágua Andreia , Sales Manuela
Published: March 2021

The relevance of molecular composition of diatom assemblages to detect river impairment caused by different intensive land uses (industrial, agricultural, and urbanization) was tested in this study with data from two rivers (Ferreira and Sousa rivers) and 21 sampling sites located in the north of Portugal. The Water Framework Directive (WFD) gives the legal basis for the use of this ecological indicator for water quality assessment (Vasselon et al. 2017 ). However, the morphological identification and count of diatoms using the light microscope requires a high level of expertise, is time-consuming and costly (Valentin et al. 2019). DNA metabarcoding combined with high-throughput sequencing techniques (HTS), offers a promising alternative to classic methodologies, reducing time and costs (Mortágua et al. 2019 ). Thus, here we compared the response of the two approaches in terms of ecological assessments (IPS Ecological Quality Ratios) to the different types of pressures felt in the 21 sites.

Diatoms were sampled at 21 sites located in the North of Portugal in autumn of 2019 (Fig. 1). Samples were submitted in parallel to the molecular and morphological analyses. The eDNA was extracted, PCR amplified (312 bp rbcL DNA barcode), and finally sequenced (Illumina MiSeq). The Mothur software was used to obtain the Operational Taxonomic Units (OTUs), which were then taxonomically assigned to the species through the R-Syst::diatom version 7.1 (Rimet et al. 2018) reference library. EQR values indicated a good correlation between morphological and molecular methods (Fig. 2). PCA analysis (Fig. 3 ) revealed that in urban, agricultural, and industrial areas there is a greater concentration of nutrients (phosphorus and nitrogen), organic matter, and heavy metals due to the discharge of urban/industrial effluents, while in places considered natural (without any type of anthropogenic pressure) we find low levels of these pollutants and high concentrations of dissolved oxygen (DO). The BEST (BIO-ENV) analysis (Tables 1, 2) shows in the case of the morphological approach, the combination of 4 environmental variables (NO₃⁻, Li, K, and Cu) is highly correlated with the biological patterns, and in the molecular approach the combination of only 2 of the environmental variables (Li and K), explains the distribution of diatom communities composition and has a slightly higher correlation. The morphological methodology seems to demonstrate a better response to urban pressures, mainly to effluent discharges, while the molecular one demonstrates a more diffuse response with special emphasis on good correlation with variables such as zinc and nitrate, which may also be related to effluent discharges and use of fertilizers in agriculture. However, it is necessary to improve the reference library so that there is a better response of the molecular methodology to the existing pressures.
Ichtyological diversity in a tropical nature reserve (Etang de Saint-Paul, Réunion Island) from environmental DNA (eDNA) metabarcoding
Authors: Nikolic Natacha , Corse Emmanuel , Juillet Nicolas
Published: March 2021

The aim of this study was to test whether the ichthyological diversity of one natural reserve in Reunion Island (Réserve de l'Etang de Saint-Paul) could be established with a molecular tool, environmental DNA (eDNA). We hence filtrated the water (2L) at 10 different areas around the reserve. For each sampling area, 12 PCR replicas were performed and the identification of fish species was carried out by metabarcoding through a primer over a mitochondrial region (12S). This study showed the importance of reference sequencing databases as well as improvements through phylogenetic analyses. This first fish study by eDNA in La Réunion also revealed the coherence of the distribution of species and their habitat.

See the Poster in Suppl. material 1.

Collection : 1st DNAQUA International Conference - poster session.
DNA barcoding reveals an unknown Chironomidae diversity from the freshwater biodiversity hot-spot: comparison between local and the European datasets
Authors: Gadawski Piotr , Montagna Matteo , Rossaro Bruno , Giłka Wojciech , Pesic Vladimir , Grabowski Michal , Magoga Giulia
Published: March 2021

In the present study, we developed and evaluated the first reference barcode library for non-biting midges (Diptera: Chironomidae) as flagship taxa of freshwater ecology from Skadar Lake system (Montenegro and Albania), a well-known hotspot of freshwater biodiversity composed by the young lake Skadar (originated 1200 before present) and by its old system of springs (originated during Pliocene). Using an expanded reference library and records deposited in Barcode of Life Database (BOLD), we estimated DNA barcoding efficiency for the European Chironomidae. Study provides COI barcodes for 770 Chironomidae individuals assigned, based on morphology, to 77 species collected in the Skadar Lake basin. Molecular analyses assigned sequences to 100 BINs and 104 OTUs (all records from this area are new for online repositories) and confirms the usefulness of DNA barcoding for the identification of non-biting midges. Additionally, we explored chironomid species distribution patterns in Europe using universal Barcode Index Number (BIN) with a discussion of problematic species groups, both for traditional taxonomy and DNA barcoding. The results of our study provide the first insight into the factual chironomid species diversity of the Lake Skadar basin, in comparison with chironomid fauna at the European scale. The results fill a significant gap in knowledge of biodiversity in the Balkan region. Based on the results of Chironomidae fauna investigation, we conclude that the Skadar Lake basin is now well sampled and such a high representation of species from various sampling sites provides reliable estimation of the non-biting midges fauna.
Transitions vers l'agriculture biologique
Authors: Lamine Claire , Bellon Stéphane
Published: March 2021

En écho aux chapitres précédents et aux enjeux développés dans le chapitre 1, ce chapitre présente une synthèse des conditions favorisant la conversion au niveau individuel, collectif, et territorial.
Évaluons, évoluons
Authors: Borin Christiane , Castellan Joëlle , Marcoux Alain
Published: March 2021

Ce chapitre s’ inscrit dans le prolongement du précédent et éclaire le processus d’ évaluation certificative du point de vue central des jurys et de leurs présidents. Il se base sur les témoignages de présidents de jury, exerçant ces fonctions au sein de diplômes différents de l’ enseignement secondaire (baccalauréat technologique et baccalauréat professionnel) et de l’ enseignement supérieur (brevet de technicien supérieur agricole). Il rend compte de l’ organisation de ces jurys, de leur déroulement, des difficultés qu’ils rencontrent et des solutions qu’ils élaborent. Il souligne surtout l’importance des présidents de jury sur les épaules desquels repose très largement la fiabilité de la certification.