bluuebunny/crossref_metadata_2025 huggingface dataset:
Reactivations of Latent Viral Infections Are Associated with an Increased Thr389 p70S6k Phosphorylation in Peripheral Lymphocytes of Renal Transplant Recipients
Authors: Cherneha Maxim , Korth Johannes , Kaulfuß Meike , Trilling Mirko , Widera Marek , Rohn Hana , Dolff Sebastian , Babel Nina , Hoerning André , Kribben Andreas , Witzke Oliver
Published: March 2021

Reactivations of BK polyoma virus (BKPyV) and human cytomegalovirus (HCMV) frequently cause life- and graft-threatening complications after renal transplantation. Both viruses are dependent on the mTOR pathway for replication. In this study we investigated the association of viral replication with mTOR activity in peripheral lymphocytes of renal transplant recipients. A flow-cytometry based assay for the measurement of Thr389 p70S6k phosphorylation, a surrogate marker of the mTOR pathway was established. Forty-eight adult renal transplant recipients were recruited to measure p70S6k activity in their peripheral blood mononuclear cells. This data set in conjunction with information concerning previous replication of BKPyV and HCMV was examined for correlations. Episodes of BKPyV replication were significantly associated with increased p70S6k phosphorylation in CD4+ T lymphocytes (p = 0.0002) and CD19+ B lymphocytes (p = 0.0073). HCMV infection of patients with a high-risk HCMV constellation of donor and recipient (D+/R−) was associated with increased p70S6k phosphorylation in CD19+ B lymphocytes (p = 0.0325). These associations were found to be independent of the trough levels of the immunosuppressive drugs. Conclusion: P70S6k phosphorylation in peripheral lymphocytes is associated with BKPyV reactivations and to a lesser extent with HCMV infections in renal transplant recipients.
The place of neurotrophic therapy in the concept of stimulation of secondary angiogenesis in acute focal cerebral ischemia
Authors: Lychko V.S.
Published: March 2021

The features of changes in the structural and functional characteristics of brain tissue were studied in 60 outbred male Wistar rats during modelling of acute focal cerebral ischemia (AFCI) in the dynamics of treatment with human cryopreserved cord blood serum (CCBS). Electronic and optical microscopic examination of the sensorimotor area of the cerebral cortex was performed. All animals were divided into three groups: the first (control) group consisted of intact rats without trauma and treatment; the second group consisted of animals after modelling AFCI without treatment; third group consisted of rats after modelling AFCI, which were injected by CCBS. Each group consisted of 20 animals. Material for morphological examination was taken after administration of CCBS solution to animals with the model of AFCI at 12, 24, 72 hours and 7th days after the start of the experiment. The average area of perivascular spaces, which is an indicator of vasogenic oedema in rats of group 2 was 45 times higher than in rats of group 1. In contrast, in rats of group 3 with CCBS, this figure was exceeded 37 times. The average area of pericellular spaces, indicating the degree of cytotoxic oedema, in animals of group 2 on the 7th day after AFCI was almost 23 times higher than the results of group 1. This figure in rats of group 3 was increased 20 times compared with data in group 2. Against the background of the use of this drug, there were signs of reactive changes in endothelial cells in the form of an increase in the number of ribosomes and polysomes in the cytoplasm, a decrease in the degree of perivascular oedema of brain tissue by 21.4 %. The surface area of endothelial cells in the zone of AFCI on the 7th day of the experiment in animals that additionally received CCBS was (1483.00±26.48) μm2, which indicates a positive anti-inflammatory effect of the drug. On the 7th day of the experiment in group 3 rats by optical microscopy was found to increase the density of cerebral capillaries compared with group 2, which indicates the stimulation of the restoration of the ultrastructure of damaged capillaries, increase their density, the formation of new capillaries under the components of CCBS.
Omniscience, Free Will, and Religious Belief
Authors: Nartey Emmanuel
Published: March 2021

In this paper, I examine a standard foreknowledge argument and some interesting ways of handling it, along with some criticisms. I argue that there are philosophically interesting notions of free will that are compatible with determinism. These are the notions of free will that matter to ordinary life, and I argue that these generate a way for a philosophically interesting understanding of free will to be compatible with belief in God’s infallible foreknowledge. I discuss two key questions—the empirical question and the divine interference question—that are often neglected in the contemporary debate on foreknowledge and free will. Finally, I provide some answers to these questions that I hope can advance the debate.
First demonstration of X-band AlGaN/GaN high electron mobility transistors using free-standing AlN substrate over 15 W mm−1 output power density
Authors: Ozaki Shiro , Yaita Junya , Yamada Atsushi , Kumazaki Yusuke , Minoura Yuichi , Ohki Toshihiro , Okamoto Naoya , Nakamura Norikazu , Kotani Junji
Published: March 2021

In this letter, we successfully achieved high-power radio frequency (RF) operation of AlGaN/GaN high electron mobility transistors (HEMTs) fabricated on free-standing AlN substrate at X-band. The developed HEMT on AlN substrate comprised a 200 nm thick GaN channel and AlGaN buffer with an Al composition of 30%. Thanks to high breakdown voltage of the HEMT on AlN substrate, we successfully demonstrated 15.2 W mm−1 output power density at operating voltages of 70 V even without device technologies such as source-field plate and optimization of device dimension. Our results show that the potential of GaN HEMTs on AlN substrate as next-generation high-power RF devices.
Implementing Facial Recognition by Interfacing MATLAB Along with Arduino
Authors:   Department of Electrical and Electronics Engineering, Sri Ramakrishna Institute of Technology, India., Ramkumar E. , Guna T. ,   Department of Electronics and Communication Engineering, Sri Ramakrishna Institute of Technology, India., Dharshan S.M. ,   Department of Mechanical Engineering, Sri Ramakrishna Institute of Technology, India., Ramanan V.S. Ashok ,   Department of Mechanical Engineering, Sri Ramakrishna Institute of Technology, India.
Published: March 2021

Facial recognition has become one of the recent trends in attracting abundant attention within the society of social media network. The face is flat and therefore needs plenty of mathematical computations. Facial knowledge has become one in every of the foremost necessary biometric, we tend to witness it from the day-to-day gadgets like mobile phones. Every transportable electronic device currently being discharged includes a camera embedded in it. Network access management via face recognition not solely makes hackers just about not possible to steal one’s “password”, however conjointly will increase the user-friendliness in human-computer interaction. For the applications of videophone and conference, the help of face recognition conjointly provides an additional economical secret writing theme. Face detection technologies are employed in an oversized kind of applications like advertising, diversion, video secret writing, digital cameras, CCTV police investigation, and even in military use. Totally different algorithms are used for biometric authentication. The Kanade-Lucas-Tomasi rule makes use of abstraction common intensity transformation to direct the deep explore for the position that shows the simplest match. Another common face detection rule is that the Viola-Jones rule that’s the foremost wide used face detection rule. It’s employed in most digital cameras and mobile phones to notice faces. It uses cascades to notice edges just like the nose, the ears, etc. Hence, during this paper, we’ve got planned the Viola-Jones rule because the best one supported our application. The rule is employed within the biometric authentication of individuals and also the pictures are kept during processing. The kept information is employed for recognizing the faces and if the information matches, an impression signal is given to the controller. The MATLAB software is employed to relinquish control signals to the motor, which is employed for gap and shutting the door. The input image is fed by a digital camera and also the image is processed within MATLAB. The output is given to the external controller interfaced with MATLAB. The image process field has several sub-fields, biometric authentication is one in each of them because it gains additional quality for security functions these days. The planned system can be employed in residential buildings, malls, and industrial sectors. Thus, this technique is helpful for homemakers to be safer in their homes.
ANALYSIS OF PARADIGM SHIFT AND IRRATIONALITY IN THOMAS KUHN’S PHILOSOPHY OF SCIENCE
Authors: Yıkmış Göksel
Published: March 2021

In this article, I will explore Kuhn’s arguments concerning his
claims of “paradigm shift in science is irrational”. First, I will do this by
looking into Kuhn’s opinions about paradigms, normal science, and
revolutions by taking reference to his writings. Second, I will try to
understand influences and ideas located in “The Structure of Scientific
Revolutions”. Third, I will look into the scientific examples that related to
Kuhn’s claims about paradigm changes as irrational. I considered the
paramount importance of historical and well-known examples in science.
This is as to why and how Kuhn has concluded and understood the stages
and effects of paradigm changes are irrational in the collective thinking of
the masses in the science world. To get the bottom of Kuhn’s claims in the
light of wider scientific changes, I will try to demonstrate relationships
between Kuhn’s specific notions and these scientific examples. To do this,
I came up with the main question and two close objectives so that complete
the article in a manner that the article focuses on deeper layers of Kuhn’s
claims how paradigm changes in science are irrational.
An In-Situ Study on The Specimen Size Effects on Compressive Strength for Different Strength Concretes
Authors: TEKİN İlker
Published: March 2021

The compressive strength of concrete is the most basic and considerable material property while reinforced concrete structures are designed. It has become a problem to use this value, however, because the control specimen sizes and shapes from country to country may be dissimilar. The study presents the results of an experiment that examined the effect of specimen size on the different classes of compressive strengths of concrete. The study included casting specimens, cubes, and six different classes of the concrete mixture. Compression tests were conducted at the age of 3, 7, and 28 days on 150 mm & 100 mm cube samples. The fresh properties of concrete were measured by slump and unit weights tests. Moreover, the specimen size of concrete has an important role both on the compressive strength and capacity of a curing cabinet. Correlations between compressive strengths and sizes of specimens are compatible for classes of structural concretes. Therefore, it can be used in curing cabinet varying sizes of concretes like 150 mm & 100 mm cube samples. Although almost 220 concrete specimens sized of 150 mm cube can be poured in curing tank, roughly 585 concrete specimens can be poured with using 100 mm cube concrete specimens. The most convenient size resulted from this study is suggested as 100 mm sized cubic specimen that it promote to change the law for concrete both curing and compressive strength test.
Surgical tactics for «near-complete» rectal cancer response to neoadjuvant therapy: total mesorectumectomy or local excision?
Authors: Karachun Alexey , Samsonov Denis
Published: March 2021

The successes of neoadjuvant therapy for locally advanced rectal cancer, which can sometimes achieve significant tumor regression, suggests that the performance of total mesorectumectomy in certain categories of such patients may be excessive. The rapid development of minimally invasive surgical technologies designed to limit the trauma due to the intervention, reduce the risk of postoperative complications, improve the quality of life and increase the proportion of sphincter-preserving operations, initiated several studies investigating the results of local excision of irradiated tumors of rectal cancer. This review article considers the published results of such studies, the problems, and prospects of this surgical strategy. The search of scientific literature was carried out using the PubMed database.
C³-Projekt – Erfolgreiche Partnerschaft für Innovation im Bauwesen
Authors: Lieboldt M. , Tietze M. , Schladitz F.
Published: March 2021

Mit dem Projekt Carbon Concrete Composite (kurz: C³-Projekt), dem derzeit größten Forschungsprojekt im deutschen Bauwesen, soll eine wirtschaftliche Anwendung eines Hochleistungswerkstoffs im Massenmarkt möglich werden. Die grundlegenden Ideen zu C³ wurden in Dresden und Aachen geboren und basieren auf der Erforschung von Textilbeton. Gerade im Bauwesen gestaltet sich die Einführung innovativer Ideen aufgrund normativer und baurechtlicher Beschränkungen oft schwierig und sehr zeitintensiv. Mit dem C³-Projekt bietet sich die Chance, vielversprechende Ideen aus Forschung und Industrie schneller umzusetzen. Durch einen gezielt geförderten Technologietransfer kann ein beschleunigter Übergang in die Baupraxis vollzogen werden. Aktuell beschäftigen sich über 167 Partner aus Forschung, Wirtschaft, Verbänden und Vereinen an dem neuartigen Verbundwerkstoff. Die Projektziele sind mit dem Ausbau, der Ansiedlung und Neugründung von Unternehmen entlang der gesamten Wertschöpfungskette, von den Grundmaterialien bis zum fertigen Bauwerk, verbunden. Das Bundesministerium für Bildung und Forschung (BMBF) fördert das Projekt im Rahmen der Initiative „Zwanzig20 – Partnerschaft für Innovation“ mit bis zu 45 Millionen Euro. Hinzu kommen circa 15 Millionen Euro Eigenmittel der beteiligten Partner. Neben der geschichtlichen Entwicklung liefert der Artikel einen Überblick über das breite Inhaltsspektrum des Großforschungsprojektes C³.
Versuche zur Querkraftverstärkung mit Carbonbeton/Test results to shear strengthening with carbon reinforced concrete
Authors: May Sebastian , Schumann Alexander , Bergmann Sarah , Curbach Manfred , Hegger Josef
Published: March 2021

Im Rahmen des Forschungsprojektes C³ – Carbon Concrete Composite wurden Querkraftversuche an Plattenbalken mit zwei unterschiedlichen Geometrien und Carbonbetonverstärkung durchgeführt. Insgesamt wurden fünf Referenz- und 25 verstärkte Bauteile im Vier-Punkt-Biegeversuch getestet. Variiert wurden das Carbongelege selbst, die Verstärkungskonfiguration am Steg, die Lagenanzahl, Anordnung und Ausrichtung des Carbongeleges in der Verstärkungsschicht sowie die Schubschlankheit. Zudem wurde der Einfluss einer Vorschädigung des Grundkörpers vor dem Verstärken betrachtet. Die Carbonbetonverstärkung bewirkte eine Steigerung der Bruchlast um 25 % bis 42 %, was die Eignung dieser Querkraftverstärkungsmethode belegt.
Current Understanding of Epidemiology and Clinical Manifestation of Coronavirus Disease 2019 (COVID-19)
Authors: Lukić Ljiljana , Dušek Davorka
Published: March 2021

Since it emerged in China in the late 2019, the SARS-CoV-2 virus has spread throughout the world and caused the newest pandemic. The epidemiological characteristics of the virus and the clinical manifestations of the COVID-19 disease are currently being studied. The new data is emerging continuously but not yet fully understood. So far, we have
learned a lot about the virus and the disease but more research is needed as many issues are still being explored.
Commissioning the H i Observing Mode of the Beam Former for the Cryogenically Cooled Focal L-band Array for the GBT (FLAG)
Authors: Pingel N. M. , Pisano D. J. , Ruzindana M. , Burnett M. , Rajwade K. M. , Black R. , Jeffs B. , Warnick K. F. , Lorimer D. R. , Roshi D. Anish , Prestage R. , McLaughlin M. A. , Agarwal D. , Chamberlin T. , Hawkins L. , Jensen L. , Marganian P. , Nelson J. D. , Shillue W. , Smith E. , Simon B. , Tonder V. Van , White S.
Published: March 2021

We present the results of commissioning observations for a new digital beam-forming back end for the Focal plane L-band Array for the Robert C. Byrd Green Bank Telescope (FLAG), a cryogenically cooled Phased Array Feed (PAF) with the lowest measured T
sys/η of any PAF outfitted on a radio telescope to date. We describe the custom software used to apply beam-forming weights to the raw element covariances to create research-quality spectral-line images for the new fine-channel mode, study the stability of the beam weights over time, characterize FLAG’s sensitivity over a frequency range of 150 MHz, and compare the measured noise properties and observed distribution of neutral hydrogen emission from several extragalactic and Galactic sources with data obtained with the current single-pixel L-band receiver. These commissioning runs establish FLAG as the preeminent PAF receiver currently available for spectral-line observations on the world’s major radio telescopes.
Unlocking Starlight Subtraction in Full-data-rate Exoplanet Imaging by Efficiently Updating Karhunen–Loève Eigenimages
Authors: Long Joseph D. , Males Jared R.
Published: March 2021

Starlight subtraction algorithms based on the method of Karhunen–Loève eigenimages have proved invaluable to exoplanet direct imaging. However, they scale poorly in runtime when paired with differential imaging techniques. In such observations, reference frames and frames from which starlight is to be subtracted are drawn from the same set of data, requiring a new subset of references (and eigenimages) for each frame processed to avoid self-subtraction of the signal of interest. The data rates of extreme adaptive optics instruments are such that the only way to make this computationally feasible has been to downsample the data. We develop a technique that updates a precomputed singular value decomposition of the full data set to remove frames (i.e., a “downdate”) without a full recomputation, yielding the modified eigenimages. This not only enables analysis of much larger data volumes in the same amount of time, but also exhibits near-linear scaling in runtime as the number of observations increases. We apply this technique to archival data and investigate its scaling behavior for very large numbers of frames N. The resulting algorithm provides speed improvements of 2.6× (for 200 eigenimages at N = 300) to 140× (at N = 104) with the advantage only increasing as N grows. This algorithm has allowed us to substantially accelerate Karhunen–Loève image projection (KLIP) even for modest N, and will let us quickly explore how KLIP parameters affect exoplanet characterization in large-N data sets.
The Missing Cool Corona in the Flat Magnetic Field around Solar Active Regions
Authors: Singh Talwinder , Sterling Alphonse C. , Moore Ronald L.
Published: March 2021

Solar Dynamics Observatory (SDO)/Atmospheric Imaging Assembly (AIA) images the full solar disk in several extreme-ultraviolet (EUV) bands that are each sensitive to coronal plasma emissions of one or more specific temperatures. We observe that when isolated active regions (ARs) are on the disk, full-disk images in some of the coronal EUV channels show the outskirts of the AR as a dark moat surrounding the AR. Here we present seven specific examples, selected from time periods when there was only a single AR present on the disk. Visually, we observe the moat to be most prominent in the AIA 171 Å band, which has the most sensitivity to emission from plasma at log10
T = 5.8. By examining the 1D line-of-sight emission measure temperature distribution found from six AIA EUV channels, we find the intensity of the moat to be most depressed over the temperature range log10
T ≈ 5.7–6.2 for most of the cases. We argue that the dark moat exists because the pressure from the strong magnetic field that splays out from the AR presses down on underlying magnetic loops, flattening those loops—along with the lowest of the AR’s own loops over the moat—to a low altitude. Those loops, which would normally emit the bulk of the 171 Å emission, are restricted to heights above the surface that are too low to have 171 Å emitting plasmas sustained in them, according to Antiochos & Noci, while hotter EUV-emitting plasmas are sustained in the overlying higher-altitude long AR-rooted coronal loops. This potentially explains the low-coronal-temperature dark moats surrounding the ARs.
Chandra Probes the X-Ray Variability of M51 ULX-7: Evidence of Propeller Transition and X-Ray Dips on Orbital Periods
Authors: Vasilopoulos Georgios , Koliopanos Filippos , Haberl Frank , Treiber Helena , Brightman Murray , Earnshaw Hannah P. , Gúrpide Andrés
Published: March 2021

We report on the temporal properties of the ultraluminous X-ray (ULX) pulsar M51 ULX-7 inferred from the analysis of the 2018–2020 Swift/X-ray Telescope monitoring data and archival Chandra data obtained over a period of 33 days in 2012. We find an extended low flux state, which might be indicative of propeller transition, lending further support to the interpretation that the neutron star is rotating near equilibrium. Alternatively, this off-state could be related to a variable superorbital period. Moreover, we report the discovery of periodic dips in the X-ray light curve that are associated with the binary orbital period. The presence of the dips implies a configuration where the orbital plane of the binary is closer to an edge-on orientation, and thus demonstrates that favorable geometries are not necessary in order to observe ULX pulsars. These characteristics are similar to those seen in prototypical X-ray pulsars such as Her X-1 and SMC X-1 or other ULX pulsars such as NGC 5907 ULX1.
Correction to the Photometric Colors of the Gaia Data Release 2 with the Stellar Color Regression Method
Authors: Niu Zexi , Yuan Haibo , Liu Jifeng
Published: March 2021

The second Gaia data release (DR2) delivers accurate and homogeneous photometry data of the whole sky of an exquisite quality, reaching down to the unprecedented millimagnitude (mmag) level for the G, G
RP, and G
BP passbands. However, the presence of magnitude-dependent systematic effects at the 10 mmag level limits its power in scientific exploitation. In this work, using about a half million stars in common with the LAMOST DR5, we apply the spectroscopy-based stellar color regression method to calibrate the Gaia G − G
RP and G
BP − G
RP colors. With an unprecedented precision of about 1 mmag, systematic trends with G magnitude are revealed for both colors in great detail, reflecting changes in instrument configurations. Color-dependent trends are found for the G
BP − G
RP color and for stars brighter than G ∼ 11.5 mag. The maximum correction term of the calibration is about 20 mmag in general and varies by a few mmag/mag. A revised color–color diagram of Gaia DR2 is given, and some applications are briefly discussed.
Coronal Wave Trains and Plasma Heating Triggered by Turbulence in the Wake of a CME
Authors: Ye Jing , Cai Qiangwei , Shen Chengcai , Raymond John C. , Mei Zhixing , Li Yan , Lin Jun
Published: March 2021

Magnetohydrodynamic (MHD) turbulence plays an important role for the fast energy release and wave structures related to coronal mass ejections (CMEs). The CME plasma has been observed to be strongly heated during solar eruptions, but the heating mechanism is not understood. In this paper, we focus on the hot, dense region at the bottom of the CME and the generation of coronal wave trains therein using a high-resolution 2.5D MHD simulation. Our results show that the interaction between the tearing current sheet and the turbulence, including the termination shocks (TSs) at the bottom of the CME, can make a significant contribution to heating the CME, and the heating rate in this region is found to be greater than the kinetic energy transfer rate. Also, the turbulence can be somewhat amplified by the TSs. The compression ratio of the TS under the CME can exceed 4 due to thermal conduction, but such a strong TS is hardly detectable in all Solar Dynamics Observatory/Atmospheric Imaging Assembly bands. And turbulence is an indispensable source for the periodic generation of coronal wave trains around the CME.
Analysis of Smoking Behavior Risk Factors in Adolescent through Health Belief Model Approaches
Authors: Anhar Vina Yulia , Arifin Syamsul , Rahman Fauzie , Ridwan Agus Muhammad , Bohari Bohari
Published: March 2021

BACKGROUND: Teenagers who smoke are very susceptible to product degradation which is seen in the low quality of human resources. Identification of risk factors needed as a first step before health interventions to prevent and reduce smoking rates in adolescents.
AIM: This study aims to analyze the risk factors for smoking behavior in adolescents through the health believe model approach.
METHODS: The design of this study is observational using a cross-sectional approach with the sample size, namely, 156 respondents. The instrument planned to be used in this study is a questionnaire that has been tested for validity and reliability. This study has received permission from relevant parties, including having received approval from the ULM FK Ethics Commission. The variables to be studied are, dependent: Smoking and independent behavior: Gender, knowledge, attitude, parental influence, peer influence, and cigarette advertising. The data analysis used Chi-square test and Fisher’s exact test with a significance level of p < 0.05.
RESULTS: Frequency distribution, 139 (89.1%) respondents do not smoke, 81 (51.9%) respondents were female, 147 (5.8%) respondents are well-informed, and 141 (90.4%) respondents have a positive attitude, the number of respondents who are not affected by the smoking behavior of the elderly is 142 people (91%). Number of respondents who are not affected by peer smoking behaviors is 150 people (96.2%) and 144 people (92.3%) of the respondents were exposed to cigarette advertisements in the high category. Statistical tests show that the variables that have a significant relationship with smoking behavior are gender (p = 0.000), attitude (p = 0.000), parental influence (p = 0.000), and cigarette advertising (p = 0.000).
CONCLUSIONS: There are four variables which have a relationship with smoking behavior, namely, there is a relationship between gender, attitude, the influence of parents, and cigarette advertising with smoking behavior.
Frozen Shoulder: Current Concept of Management
Authors: Sumarwoto Tito , Hadinoto Seti Aji , Roshada Musa Fasa
Published: March 2021

BACKGROUND: Frozen shoulder is a musculoskeletal disorder resulting from chronic inflammation of the capsule subsynovial layer and characterized with capsular thickening, progressive fibrosis, and contracture of the glenohumeral joint capsule. This condition is a relatively common condition that mimics other condition and its management requires deliberate consideration of patient’s condition.
REVIEW ARTICLE: This article reviews and summarize latest findings of frozen shoulder. The diagnosis of frozen shoulder is described from the patient history, physical examination in look, feel, and move sequence to the supporting examinations. The current evidence of managements of frozen shoulder is described, from the nonoperative to the surgical approach.
CONCLUSION: Most of frozen shoulder cases resolve spontaneously thus conservative treatment should be the first choice of frozen shoulder. However, for cases that failed with conservative treatment and had a debilitating effect to patient’s daily life or cases with history of surgery, operative treatment should be considered. Operative treatment is aimed to release the capsule either by manipulation under anesthesia, by arthroscopy, or by open surgery. Physical rehabilitation following every procedure is mandatory and key to maintain range of motion years following the surgery.
An assay validation framework to compare and evaluate targeted environmental DNA assays for routine species monitoring
Authors: Thalinger Bettina , Deiner Kristy , Harper Lynsey , Rees Helen , Blackman Rosetta , Sint Daniela , Traugott Michael , Goldberg Caren , Bruce Kat
Published: March 2021

Environmental DNA (eDNA) analysis utilises trace DNA released by organisms into their environment for species detection and is revolutionising non ‐ invasive species and biodiversity monitoring. However, this technology requires rigorous validation along the whole workflow – from field sampling to statistical analysis – to ensure appropriate and meaningful interpretation of results. Targeted eDNA assays are often validated within a specific system and with particular aims, but without fulfilling predefined criteria. Consequently, their applicability beyond initial development often remains undetermined. Additionally, there tends to be poor understanding of the uncertainties and limitations associated with already published assays and thus potentially inappropriate interpretation of the results they produce. The lack of a “gold standard” limits the incorporation of targeted eDNA assays into species monitoring and policy making by end-users and is therefore key for the future implementation of eDNA-based surveys.

Here, we present a framework (https://edna-validation.com/) and user-friendly criteria for the classification of assays, which is based on previous validation efforts. A 5 ‐ level assay validation scale (“incomplete” to “operational”) was defined by reviewing the current eDNA literature and conducting a meta-analysis on sampling, laboratory practices, detection limits, and detection probabilities. The so far published single species eDNA assays were reviewed for their performance in this new framework and we identified steps within the validation process that often remain untouched. Finally, we provide guidance for end ‐ users as to which criteria are most important for validation and suggest how results obtained from assays at different levels of the validation scale should be interpreted.
An account of epiphytic diatoms in mediterranean wetlands: comparing morphological and molecular assessments
Authors: Borrego-Ramos María , Bécares Eloy , García-García Pedro , Nistal Alejandro , Blanco Saúl
Published: March 2021

Benthic diatoms are well known bioindicators of water quality, used in many aquatic ecosystems. Since diatom-based monitoring of water quality is required by European legislation, the search for methods that facilitate this task has become more relevant. The aim of this study was to test the reliability of DNA metabarcoding combined with high-throughput sequencing (HTS) techniques in the bioassessment of 22 Mediterranean shallow ponds in Spain. For each pond, Trophic Diatom Index (TDI) was calculated from inventories obtained by using light microscopy, and then molecular (HTS) methods. Ponds were subsequently classified into five water quality classes. Our results showed a good correspondence between both methods, especially after applying a correction factor depending on the biovolume of the cells. This correspondence led to the assignment to the same quality class in 59% of the ponds. The determination and quantification of valves or DNA sequences was one of the main pitfalls, mainly those related to the variability in the relative abundances of some species. Accordingly, ponds with similar relative abundances for the dominant species were assigned to the same quality class. Moreover, other difficulties leading the discrepancies were the misidentification of some species due to the presence of semi-cryptic taxa, the incompleteness of the reference database and the bioinformatic protocol. Therefore, the validation of DNA-based methods for the identification of freshwater diatoms represents an important goal, as an alternative to traditional ones in Mediterranean shallow ponds.
Wet grinding of invertebrate bulk samples – a scalable and cost-efficient protocol for metabarcoding and metagenomics
Authors: Buchner Dominik , Haase Peter , Leese Florian
Published: March 2021

DNA metabarcoding is an efficient tool to characterize invertebrate species composition in environmental samples. Most metabarcoding protocols for invertebrate bulk samples start with sample homogenization, followed by DNA extraction, amplification of a specific marker region and sequencing on a high-throughput sequencer.

Many of the above-mentioned laboratory steps have been verified thoroughly and best practice strategies exist. Giving the amount of research done to validate almost all laboratory steps of metabarcoding workflows it is surprising that there is no clear recommendation for the basis of almost all metabarcoding studies: the homogenization of samples itself.

For homogenization, different devices are used that can be divided into two major categories: bead mills and blenders. While bead-mills accelerate small, hard particles in a closed container or tube to break down specimens into small tissue fragments, blenders work with a rapidly rotating blades that reliably slice specimens as well as other substrate of the sample. Both methods are currently used in metabarcoding studies and have downsides to consider.

Bead-mills rely on single-use plastics and therefore produce a lot of waste and are expensive. In addition to that, processing times can go up to 30 minutes making them unsuitable for large scale studies. Blenders on the other hand offer the opportunity to be cleaned and can handle larger sample volumes in shorter time, with an increased risk of cross-contamination.

We here aimed to develop a fast, robust, cheap and reliable sample homogenization protocol that overcomes the above-mentioned limitations of both methods, i.e. does not produce difficult to discard waste and avoid single-use plastics while reducing overall costs. We tested the performance of the new protocol using six sorted Malaise trap insect samples and six unsorted stream macroinvertebrate kick-net samples. We used 14 technical replicates of each sample and many negative controls per sample (Fig. 1) to quantify impacts of i) insufficient homogenization and ii) possible sources of cross-contamination.

Our results show that homogenization is sufficient after 3 minutes of homogenization. Rinsing the blender with water is sufficient in most cases but leads to low read-numbers in some of the negative controls. These could be further reduced by rinsing the blender with self-made drain-safe sterilization solution based on bleach but far less corrosive than pure bleach. Our results suggest that rinsing 1-2 times for 20 seconds is sufficient to avoid any cross-contamination.

The improvements of the protocol in terms of speed, ease of handling, overall reduction of costs as well as the documented reliability and robustness make it an important candidate for sample homogenization after sampling in particular for large-scale and regulatory metabarcoding biodiversity assessments and monitoring programs.
The amount of environmental DNA increases with freshwater crayfish density and over time
Authors: Wallinger Corinna , Sint Daniela , Kolp Bernhard , Füreder Leopold , Traugott Michael
Published: March 2021

eDNA analysis is ideally suited to monitor the occurrence of endangered or invasive species because of its non-invasive nature and high sensitivity. European freshwater crayfish are threatened across the whole continent. Classical crayfish monitoring is challenging and time consuming due to their nocturnal activity and hidden lifestyle. Therefore, eDNA-based monitoring of native as well as invasive species seems to be of great benefit for the conservation of the native species and it has indeed been increasingly applied in recent years. Nevertheless, comparably little is known on the relationship between eDNA concentration and crayfish population densities, a prerequisite for estimating population size based on eDNA measurements. Here, we performed laboratory experiments to investigate the relationship between the concentration of crayfish eDNA and population densities - measured as crayfish size and biomass. There was a strong correlation between the two measurements. Moreover, the amount of eDNA increased at least during the first three days after crayfish stocking in the aquarium. The experiments also indicate, that crayfish activity might have a strong influence on the eDNA signal strength. Our findings will significantly contribute to an optimization of the monitoring of freshwater crayfish via the analysis of eDNA and therefore be important for the conservation of these threatened species.
Getting rid of rain and stars: mitigating inhibition effects in ddPCR assays, the case of the invasive crayfish Pacifastacus leniusculus in the streams of Luxembourg
Authors: Porco David , Hermant Sylvie , Purnomo Chanistya , Horn Mario , Marson Guy , Colling Guy
Published: March 2021

ddPCR is getting more and more popular in the field of eDNA-based aquatic monitoring. Even if emulsion PCR used in ddPCR confers a partial resistance to inhibition due to the high number of reactions for the same sample (between 10K and 20K), it is not impervious to it. Inhibition impacts the fluorescence amplitude of positive droplets, affecting both their dispersion and their position relatively to the negative droplets cloud. This fluctuation could jeopardize the use of a shared threshold among several samples and thus the objective assignation of the positive droplets.

This is even more critical for low concentration samples such as eDNA samples: the positive droplets are scarce and it is thus crucial to objectively discriminate if they can be counted as positive by establishing an appropriate threshold. Another issue is the artifactual generation of high fluorescence droplets that could be counted as positive with a single threshold solution.

Here we propose a double threshold method to take both high fluorescence droplets and PCR inhibition impact into account allowing for an objective sorting of the positive and negative droplets in ddPCR assays.
Functional traits link anthropogenic impact and disturbance regimes driving ecosystem function in a floodplain wetland complex
Authors: Rideout Natalie , Compson Zacchaeus , Monk Wendy , Hajibabaei Mehrdad , Porter Teresita , Wright Michael , Baird Donald
Published: March 2021

Floodplains are disturbance-driven ecosystems with high spatial and temporal habitat diversity, making them both highly productive and hosts to high biodiversity. The unpredictable timing of flood and drought years creates a mosaic of habitat patches at different stages of succession, while water level fluctuation directly influences macrophyte community dynamics, and thus habitat structure. This habitat complexity and diversity of disturbance regimes makes floodplains an ideal ecosystem in which to examine the links between biodiversity, traits and ecosystem function. With up to 90% of floodplains in North America and Europe altered to the point of functional extinction, it is particularly imperative to study and conserve those that remain intact, such as the Lower Saint John River and its associated floodplain, including the Grand Lake Meadows and Portobello Creek wetland complex. Despite the rise in trait-based science, taxonomic resolution has imposed limitations, especially in wetland and floodplain ecosystems where communities are vastly understudied compared to their riverine counterparts. Compared to traditional biomonitoring, DNA-based biomonitoring from high-throughput genomics sequencing methods is powerful in that it can reliably characterize community composition in unprecedented detail, allowing us to assess how disturbance and environmental filters interact with invertebrate traits and ecosystem function. Using structural equation analysis, we take a whole ecosystem approach to examine ecosystem health across a floodplain disturbance gradient. We focus chiefly on how anthropogenic alteration within watersheds affects downstream floodplain wetlands, how the resulting patch diversity shapes communities and, finally, how those communities influence ecosystem function through trait diversity metrics. We also examine and compare which traits are associated with crucial ecosystem gradients.
Development of eDNA tools for the detection of marine invasive non-native species to support European flat oyster (Ostrea edulis) restoration projects.
Authors: Markus Sean , Matejusova Iveta , Douglas Alex , Sanderson William
Published: March 2021

The European flat oyster (Ostrea edulis) is an important keystone species in Scottish coastal waters. However due to anthropogenic pressures, significant reductions to oyster beds have been observed across Europe. In Scotland, several projects are currently aiming to restore European flat oyster habitats through the translocation of juvenile oysters from various sources including hatcheries and aquaculture. However, translocation of shellfish is not risk free and can increase the risk of accidental translocation of invasive non-native species (INNS). If INNS become established outside of their native range they can cause irreversible harm to native organisms and habitats. This study aims to develop molecular tools to detect environmental DNA of INNS which can be potentially associated with the translocation of live shellfish stocks. We have developed a species-specific real-time PCR assay for detection of Pacific oyster (Crassostrea gigas) and tested its sensitivity in a large-scale replicated mesocosm based experiment with varying densities of C.gigas. A secondary objective of the experiment was to assess the detection of another invasive species, the carpet sea squirt Didemnum vexillum which was cohabited with C. gigas. We aim to quantify the detection probability of increasing densities of C. gigas from repeat water samples and qPCR replicates. This project also aims to investigate the feasibility of using portable, real-time sequencing technologies such as the Oxford Nanopore MinION to develop robust tools to support native oyster restoration programmes.
Towards a simple way to collect eDNA using a 3D-printed passive sampler
Authors: Verdier Héloïse , Konecny Lara , Marquette Christophe , Lefebure Tristan
Published: March 2021

Environmental DNA has emerged as a revolutionary approach to monitor aquatic biodiversity. The study of the DNA released by macro-organisms in their habitat offers a fast, non-invasive and sensitive approach to monitor their presence. Despite its many advantages, methodological challenges limit the widespread use of eDNA. Among them, eDNA sampling represents one of the most challenging step. Often based on the filtration of a large volume of water, this process can be long and tedious, requiring human intervention and special care, and which is not applicable to a wide range of habitats. As an alternative to filtration, passive eDNA sampling using natural substrates appears to be a promising solution. This approach uses the natural properties of some minerals (eg. silica), organisms (eg. sponges) or even communities (e.g. biofilms) to collect and preserved eDNA. Yet, such approaches are difficult to standardize and may not be applicable in many habitats. To circumvent that problem, we have designed 3D-printed samplers made of hydroxyapatite (HAp samplers), a mineral known for its high binding affinity with DNA. The shape of the samplers has been designed to facilitate their handling in laboratory and field experiments. Here we describe and test the ability of HAp samplers to recover freshwater eDNA. We show that HAp samplers recover DNA with high efficiency and are effective even on small amounts of waterlouse eDNA. However, the eDNA recovery is also highly variable across experiments. We show that by understanding the physico-chemical interactions between DNA and the HAp sampler surface, we could improve the replicability of the process and provide a robust alternative to filtration.
Aquatic macroinvertebrates in Uruguayan rice agroecosystem
Authors: Bao Leticia , Martínez Sebastián , Cadenazzi Mónica , Urrutia Mónica , Seijas Lucía , Castiglioni Enrique
Published: March 2021

This work is a first approach to the knowledge of insects and other aquatic macroinvertebrates of rice agroecosystems from eastern Uruguay. The composition of the groups collected may represent an approximation to the knowledge of the quality of water sources associated with Uruguayan rice production. Sampling of aquatic macroinvertebrates was carried out during the grain-filling stage in crops without insecticide use, in three localities of Treinta y Tres Department. In each crop, macroinvertebrates were collected with a Surber-type network at the inlet and outlet of water to and from the paddy field and a neighbouring control area. Differences in morphospecies composition were found according to the location and source of water. Insecta was the most represented class in macroinvertebrate samplings (41.5%). Diptera (59.9%), Hemiptera (16.3%) and Ephemeroptera (14.0%) were the most abundant orders within insects. The Richness and Shannon Diversity Indices were higher than those recorded for similar studies in Costa Rica, Italy and Australia.
Vivre avec une maladie neuro-évolutive
Authors: Michon Agnès
Published: March 2021

L’identité se construit également sur les relations intersubjectives et c’est peut-être sur cette modification de la relation à l’autre qu’il faut nous interroger dans la maladie chronique et plus particulièrement dans la maladie d’Alzheimer.
Le bébé et les interactions précoces
Authors: Squires Claire
Published: March 2021

L’observation au cours des thérapies psychanalytiques avec des nourrissons On ne peut opposer l’observation d’un comportement extérieur à l’exploration d’un matériel inconscient qui s’effectuerait dans le cadre privilégié d’une cure psychanalytique. Au cours des thérapies psychanalytiques avec des nourrissons, le clinicien oscille entre le recueil des interactions manifestes entre la mère et le nourrisson et le dévoilement des fantasmes agis dans leur interrelation. Deux thérapies de nourrissons anorexxiques montrent comment le thérapeute imagine un espace de créativité au travers d’une dynamique relationnelle qui apparaît fondamentale pour le développement.
Une French touch dans l'analyse des politiques publiques ?
Authors: Hall Peter A.
Published: March 2021

Résumé In this round-table chapter, three political scientists whose works have had a great echo in France offer their differing views on French policy analysis, with a special emphasis on cognitive approaches. Each one reflects upon his/her reading and uses of French policy analysis developments, as well as on the ways in which their own work draws on French analyses. These three Anglo-Saxon perspectives constitute a unique and personal insight to the debate on the existence of a “French touch” in policy analysis.
Une French touch dans l'analyse des politiques publiques ?
Authors: Engeli Isabelle , Perrier Gwenaëlle
Published: March 2021

Résumé Ce chapitre analyse l’institutionnalisation de la recherche sur le genre et les politiques publiques en France, en faisant le lien avec le contexte politique et académique de cette institutionnalisation. Il met en avant les différents objets et perspectives d’analyse qui structurent ce champ de recherche, ainsi que leurs apports pour les études de genre et pour l’analyse des politiques publiques. Il fait le point sur les nouveaux défis de la recherche en genre et politique publique que sont la prise en compte de l’intersectionnalité, les enjeux relatifs à la sexualité et l’approche transsectorielle des politiques publiques.