bluuebunny/crossref_metadata_2025_split huggingface dataset:
Network Pharmacology and Pharmacological Evaluation Reveals the Mechanism of the Sanguisorba Officinalis in Suppressing Hepatocellular Carcinoma
Authors: Jiang Nan , Li Hong , Sun Yueshan , Zeng Jing , Yang Fei , Kantawong Fahsai , Wu Jianming 
Published: March 2021

Background:Sanguisorba Officinalis L. (SO) is a well-known traditional Chinese medicine (TCM), commonly applied to treat complex diseases, such as anticancer, antibacterial, antiviral, anti-inflammatory, anti-oxidant and hemostatic effects. Especially, it has been reported to exert anti-tumor effect in various human cancers. However, its effect and pharmacological mechanism on hepatocellular carcinoma (HCC) remains unclear.Methods: In this study, network pharmacology approach was applied to characterize the underlying mechanism of SO on HCC. Active compounds and potential targets of SO, as well as related genes of HCC were obtained from the public databases, the potential targets and signaling pathways were determined by protein-protein interaction (PPI), gene ontology (GO) and pathway enrichment analyses. And the compound-target and target-pathway networks were constructed. Subsequently, in vitro experiments were also performed to further verify the anticancer effects of SO on HCC.Results: By using the comprehensive network pharmacology analysis, 41 ingredients in SO were collected from the corresponding databases, 12 active ingredients screened according to their oral bioavailability and drug-likeness index, and 258 potential targets related to HCC were predicted. Through enrichment analysis, SO was found to show its excellent therapeutic effects on HCC through several pathways, mainly related to proliferation and survival via the EGFR, PI3K/AKT, NFκB and MAPK signaling pathways. Additionally, in vitro, SO was found to inhibit cell proliferation, induce apoptosis and down-regulate cell migration and invasion in various HCC cells. Moreover, western blot analysis showed that SO treatment down-regulated the expression of p-EGFR, p-PI3K, p-AKT, p-NFκB and p-MAPK proteins in HepG2 cells. These results validated that SO exerted its therapeutic effects on HCC mainly by the regulation of cell proliferation and survival via the EGFR/MAPK and EGFR/PI3K/AKT/NFκB signaling pathways.Conclusion: Taken together, this study, revealed the anti-HCC effects of SO and its potential underlying therapeutic mechanisms in a multi-target and multi-pathway manner.
Structural and Functional Properties of Subsidiary Atrial Pacemakers in a Goat Model of Sinus Node Disease
Authors: Soattin Luca , Borbas Zoltan , Caldwell Jane , Prendergast Brian , Vohra Akbar , Saeed Yawer , Hoschtitzky Andreas , Yanni Joseph , Atkinson Andrew , Logantha Sunil Jit , Borbas Balint , Garratt Clifford , Morris Gwilym Matthew , Dobrzynski Halina 
Published: March 2021

BackgroundThe sinoatrial/sinus node (SAN) is the primary pacemaker of the heart. In humans, SAN is surrounded by the paranodal area (PNA). Although the PNA function remains debated, it is thought to act as a subsidiary atrial pacemaker (SAP) tissue and become the dominant pacemaker in the setting of sinus node disease (SND). Large animal models of SND allow characterization of SAP, which might be a target for novel treatment strategies for SAN diseases.MethodsA goat model of SND was developed (n = 10) by epicardially ablating the SAN and validated by mapping of emergent SAP locations through an ablation catheter and surface electrocardiogram (ECG). Structural characterization of the goat SAN and SAP was assessed by histology and immunofluorescence techniques.ResultsWhen the SAN was ablated, SAPs featured a shortened atrioventricular conduction, consistent with the location in proximity of atrioventricular junction. SAP recovery time showed significant prolongation compared to the SAN recovery time, followed by a decrease over a follow-up of 4 weeks. Like the SAN tissue, the SAP expressed the main isoform of pacemaker hyperpolarization-activated cyclic nucleotide-gated channel 4 (HCN4) and Na+/Ca2+ exchanger 1 (NCX1) and no high conductance connexin 43 (Cx43). Structural characterization of the right atrium (RA) revealed that the SAN was located at the earliest activation [i.e., at the junction of the superior vena cava (SVC) with the RA] and was surrounded by the paranodal-like tissue, extending down to the inferior vena cava (IVC). Emerged SAPs were localized close to the IVC and within the thick band of the atrial muscle known as the crista terminalis (CT).ConclusionsSAN ablation resulted in the generation of chronic SAP activity in 60% of treated animals. SAP displayed development over time and was located within the previously discovered PNA in humans, suggesting its role as dominant pacemaker in SND. Therefore, SAP in goat constitutes a promising stable target for electrophysiological modification to construct a fully functioning pacemaker.
Health Literacy and Health Behavior Among Women in Ghazni, Afghanistan
Authors: Harsch Stefanie , Jawid Asadullah , Jawid Ebrahim , Saboga-Nunes Luis , Sørensen Kristine , Sahrai Diana , Bittlingmayer Uwe H. 
Published: March 2021

Background:Health literacy is a determinant of health and assessed globally to inform the development of health interventions. However, little is known about health literacy in countries with one of the poorest health indicators worldwide, such as Afghanistan. Studies worldwide demonstrate that women play a key role in developing health literacy. Hence, this study's purpose is to explore health literacy of women in Afghanistan and the associated factors.Methods:From May to June 2017, we randomly recruited 7–10 women per day at the hospital in Ghazni, a representative province of Afghanistan. Two trained female interviewers interviewed 322 women (15–61 years old) orally in Dari or Pashto on a voluntary basis and assessed their health literacy using the HLS-EU-Q16, associated socio-demographics, and health behavior.Results:Health literacy of women (among educated and illiterates) is low even compared to other Asian countries. Health literacy is linked to age and education. We found mixed evidence of the relationship between health literacy and contextual factors, help-seeking, and health-related behavior.Conclusion:This study provides novel data on health literacy and astonishing insights into its association with health behavior of women in Afghanistan, thus contributing to health status. The study calls for recognition of health literacy as a public health challenge be addressed in Afghanistan and other low-income countries affected by crises.
Inter-evaluator and Intra-evaluator Reliability of a Software Program Used to Extract Kinematic Variables Obtained by an Extremity-Mounted Inertial Measurement Unit System in Sound Horses at the Trot Under Soft and Hard Ground Conditions and Treadmill Exercise
Authors: Schwarz Julia , Vidondo Beatriz , Maninchedda Ugo E. , Sprick Miriam , Schöpfer Melina C. , Cruz Antonio M. 
Published: March 2021

Objective:To assess the inter-evaluator and intra-evaluator reliability of a software program used to extract kinematic variables by a commercially available extremity-mounted inertial measurement unit system in sound horses at the trot under soft and hard ground conditions and treadmill exercise.Animals:Thirty adult, sound and healthy French Montagne stallions.Procedures:Data collection was performed with six IMUs strapped to the distal, metacarpal, metatarsal and tibial regions of every horse. Per surface (treadmill, soft and hard ground) 10 stallions were trotted three times. Prior to the analysis done by six evaluators (three experienced, three inexperienced) the data was blinded and copied three times. For every analysis a minimum of five strides had to be selected. To assess the intra- and inter-evaluator reliability a selection of gait variables was used to calculate intra and inter correlation coefficients (ICCs) as well as variance partitioning coefficients (VPCs).Results:All of the tested gait variables showed high levels of reliability. There was no mentionable difference considering the correlation coefficients between the intra and inter reliability as well as between the three different surfaces. VPCs showed that the factor horse is by far the most responsible for any appearing variance. The experience of the evaluator had no influence on the results.Conclusions and Clinical Relevance:The software program tested in this study has a high inter- and intra-evaluator reliability under the chosen conditions for the selected variables and acts independent of the ground situation and the experience of the evaluator. On the condition of a correct application it has the potential to become a clinically relevant and reliable gait analysis tool.
Arrheniusite-(Ce), CaMg[(Ce7Y3)Ca5](SiO4)3(Si3B3O18)(AsO4)(BO3)F11, a New Member of the Vicanite Group, from the Östanmossa Mine, Norberg, Sweden
Authors: Holtstam Dan , Bindi Luca , Bonazzi Paola , Förster Hans-Jürgen , Andersson Ulf B. 
Published: March 2021

ABSTRACT
Arrheniusite-(Ce) is a new mineral (IMA 2019-086) from the Östanmossa mine, one of the Bastnäs-type deposits in the Bergslagen ore region, Sweden. It occurs in a metasomatic F-rich skarn, associated with dolomite, tremolite, talc, magnetite, calcite, pyrite, dollaseite-(Ce), parisite-(Ce), bastnäsite-(Ce), fluorbritholite-(Ce), and gadolinite-(Nd). Arrheniusite-(Ce) forms anhedral, greenish-yellow translucent grains, exceptionally up to 0.8 mm in diameter. It is optically uniaxial (–), with ω = 1.750(5), ε = 1.725(5), and non-pleochroic in thin section. The calculated density is 4.78(1) g/cm3. Arrheniusite-(Ce) is trigonal, space group R3m, with unit-cell parameters a = 10.8082(3) Å, c = 27.5196(9) Å, and V = 2784.07(14) Å3 for Z = 3. The crystal structure was refined from X-ray diffraction data to R1 = 3.85% for 2286 observed reflections [Fo &gt; 4σ(Fo)]. The empirical formula for the fragment used for the structural study, based on EPMA data and results from the structure refinement, is: (Ca0.65As3+0.35)Σ1(Mg0.57Fe2+0.30As5+0.10Al0.03)Σ1[(Ce2.24Nd2.13La0.86Gd0.74Sm0.71Pr0.37)Σ7.05(Y2.76Dy0.26Er0.11Tb0.08Tm0.01Ho0.04Yb0.01)Σ3.27Ca4.14]Σ14.46(SiO4)3[(Si3.26B2.74)Σ6O17.31F0.69][(As5+0.65Si0.22P0.13)Σ1O4](B0.77O3)F11; the ideal formula obtained is CaMg[(Ce7Y3)Ca5](SiO4)3(Si3B3O18)(AsO4)(BO3)F11. Arrheniusite-(Ce) belongs to the vicanite group of minerals and is distinct from other isostructural members mainly by having a Mg-dominant, octahedrally coordinated site (M6); it can be considered a Mg-As analog to hundholmenite-(Y). The threefold coordinated T5 site is partly occupied by B, like in laptevite-(Ce) and vicanite-(Ce). The mineral name honors C.A. Arrhenius (1757–1824), a Swedish officer and chemist, who first discovered gadolinite-(Y) from the famous Ytterby pegmatite quarry.
Improved freshwater macroinvertebrate detection from environmental DNA through minimized nontarget amplification
Authors: Sander Mandy , Beermann Arne , Buchner Dominik , Elbrecht Vasco , Haase Peter , Zizka Vera , Leese Florian 
Published: March 2021

Environmental DNA (eDNA) metabarcoding is a new, promising, and non-invasive method to detect biodiversity in aquatic environments. So far, it has mainly been used to screen for fish and amphibian diversity and rarely to detect macroinvertebrates. Typically, DNA metabarcoding relies on PCR amplification of a fragment of the mitochondrial cytochrome c oxidase I (COI) gene with degenerate primers. In comparison to other genes like 16S, COI has a greater taxonomic resolution and availability of an extensive reference database. Benthic stream invertebrates are of critical importance for regulatory biomonitoring, but when using universal primers on eDNA isolated from water, the number of reads and OTUs is “watered down”. This means the target taxa, macroinvertebrates, are underrepresented in comparison to other nontarget taxa, e. g. algae, bacteria, and fungi.
The aim of the project was to design an insect-specific primer, which minimizes nontarget amplification. Therefore, data from a time series of 15 months at the Kinzig (Hesse), a silica-rich low-mountain-range stream, which is part of the Rhine‑Main‑Observatory (LTER site) was generated using the universal primers BF2/BR2. With this data we identified the most abundant nontarget taxa and designed a new reverse primer (EPTDr2n) with 3’ ‐ specificity toward benthic invertebrate taxa. Primer specificity was validated in silico together with universal forward primer fwhF2 using available data from GenBank and BOLD. 20 eDNA samples from the Kinzig River and its tributaries were then used to test the new primer in situ together with primer fwhF2.
The new primer combination showed a much higher amplification of benthic invertebrates, insects in particular, than two other universal primer pairs for both, number of target reads (fwhF2/EPTDr2n: 99.6% versus BF2/BR2: 25.89% and fwhF2/fwhR2n: 39.04%; Fig. 1) and number of target species (fwhF2/EPTDr2n: 305 versus BF2/BR2: 113 and fwhF2/fwhR2n: 185). Additionally, the number of benthic invertebrate species exceeded even the number of 153 species identified by expert taxonomists at nearby sites across two decades of sampling. While several taxa reported, like a few trichopteran genera, flatworms, and some crustaceans, were not found, the primer shows greatly improved results for eDNA metabarcoding of benthic invertebrates(Leese et al. 2021).
A pilot for implementing environmental DNA (eDNA) based methods into environmental and biomonitoring
Authors: Laamanen Tiina , Norros Veera , Suikkanen Sanna , Tolkkinen Mikko , Vuorio Kristiina , Vihervaara Petteri , Sirkiä Päivi , Jørgensen Kirsten , Kortelainen Pirkko , Reunamo Anna , Järvinen Marko , Meissner Kristian 
Published: March 2021

Environmental DNA (eDNA) and other molecular based approaches are revolutionizing the field of biomonitoring. These approaches undergo rapid modifications, and it is crucial to develop the best practices by sharing the newest information and knowledge. In our ongoing project we:

assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE;

identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring;

promote information exchange on eDNA methods and

advance future research efforts both within SYKE and with our national and international partners.

assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE;
identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring;
promote information exchange on eDNA methods and
advance future research efforts both within SYKE and with our national and international partners.

Scientific background

Well-functioning and intact natural ecosystems are essential for human well-being, provide a variety of ecosystem services and contain a high diversity of organisms. However, human activities such as eutrophication, pollution, land-use or invasive species, are threatening the state and functioning of ecosystems from local to global scale (e.g. Benateau et al. 2019; Reid et al. 2018; Vörösmarty et al. 2010). New molecular techniques in the field and in the laboratory have enabled sampling and identification of much of terrestrial, marine and freshwater biodiversity. These include environmental DNA (eDNA, e.g. Valentini et al. 2016) and bulk-sample DNA metabarcoding approaches (e.g. Elbrecht et al. 2017) and targeted RNA-based methods (e.g. Mäki and Tiirola 2018). The eDNA technique uses DNA that is released from organisms into their environment, from which a signal of organisms’ presence in the system can be obtained. For example, in aquatic ecosystems, eDNA is typically extracted from sediment or filtered water samples (e.g. Deiner et al. 2016), and this approach is distinguished from bulk DNA metabarcoding, where organisms are directly identified from e.g. complete biological monitoring samples (e.g. Elbrecht et al. 2017). Despite the demonstrated potential of environmental and bulk-sample DNA metabarcoding approaches in recent years, there are still significant bottlenecks to their routine use that need to be addressed (e.g. Pawlowski et al. 2020).

Methods and implementati
on

The project is divided into three work packages: WP1 Gathering existing knowledge, identifying knowledge gaps and proposing best practices, WP2 Roadmap to implementation and WP3 eDNA monitoring pilot. Please see more details in the Fig. 1
Aquatic biofilms can act as natural environmental DNA samplers
Authors: Rivera Sinziana , Vasselon Valentin , Rimet Frederic , Bouchez Agnès 
Published: March 2021

Diatoms, macroinvertebrates and fish communities are widely used for the assessment of the ecological status of rivers and lakes. Metabarcoding studies of these communities are usually performed from “bulk” samples in the case of diatoms and macroinvertebrates; and from water samples in the case of fish.
Recent studies, suggest that aquatic biofilms can physically act as environmental catchers of environmental DNA (eDNA) (e.g. Mariani et al. 2019). Thus, we propose an alternative metabarcoding approach to study macroinvertebrates and fishes directly from this matrix.
The capacity of aquatic biofilms to catch macroinvertebrate eDNA was tested from a previous study in Mayotte Island were both biofilm samples and macroinvertebrate morphological inventories were available at same river sites (Rivera et al. 2021). First, macroinvertebrate specimens were identified based on their morphological characteristics. Second, DNA was extracted from biofilms, and macroinvertebrate communities were targeted using a standard COI barcode. The resulting morphological and molecular inventories were compared. Our results showed that both methods provided comparable structures and diversities for macroinvertebrate communities when using unassigned OTUs suggesting that macroinvertebrate DNA is present in biofilms and representative of the communities. However, after taxonomic assignment of OTUs, diversity and richness were no longer correlated. Indeed, many constraints were observed as the need for: a) more specific primers to avoid co-amplification of untargeted taxa inhabiting biofilms, b) primers targeting shorter barcodes to sequence more easily degraded eDNA that may be captured in biofilms, and c) a reference database well adapted to our tropical study sites. Finally, even if the results of this first study were encouraging, we wanted to test the biofilm approach on organisms that do not inhabit this environmental matrix in order to be able to distinguish between intra or extra-cellular DNA.
Based on these observations, a second study looking for a fish eDNA signal in aquatic biofilms was performed. Environmental biofilm and water samples were collected in parallel at littoral sites at Lake Geneva. DNA was extracted from these samples, and fish communities were targeted using a standard 12S barcode. The molecular inventories derived from the biofilm and the water samples were compared. Both methods provide comparable floristic lists, providing a novel approach for ecological studies related to fish phenology using eDNA in biofilms.
Our results open the door to the study of diatoms, macroinvertebrates and fish communities through metabarcoding from a single matrix reducing sampling efforts and costs.
Diat.barcode: a DNA tool to decipher diatom communities for the evaluation environmental pressures
Authors: Rimet Frederic , Chonova Teofana , Gassiole Gilles , Kahlert Maria , Keck François , Kelly Martyn , Kulikovskiy Maxim , Mann David , Pfannkuchen Martin , Baričević Ana , Trobajo Rosa , Vasselon Valentin , Zimmermann Jonas , Wetzel Carlos , Bouchez Agnès 
Published: March 2021

Diatoms (Bacillariophyta) are ubiquitous microalgae, which present a huge taxonomic diversity, changing in correlation with differing environmental conditions. This makes them excellent ecological indicators for various ecosystems and ecological problematics (ecotoxicology, biomonitoring, paleo-environmental reconstruction …).
Current standardized methodologies for diatoms are based on microscopic determinations, which is time consuming and prone to identification uncertainties. DNA metabarcoding has been proposed as a way to avoid these flaws, enabling the sequencing of a large quantity of barcodes from natural samples. A taxonomic identity is given to these barcodes by comparing their sequences to a barcoding reference library. However, to identify environmental sequences correctly, the reference database should contain a representative number of reference sequences to ensure a good coverage of diatom diversity. Moreover, the reference database needs to be carefully taxonomically curated by experts, as its content has an obvious impact on species detection.
Diat.barcode is an open-access library for diatoms linking diatom taxonomic identities to rbcL barcode sequences (a chloroplast marker suitable for species-level identification of diatoms), which has been maintained since 2012. Data are accumulated from three sources: (1) the NCBI nucleotide database, (2) unpublished sequencing data of culture collections and more recently (3) environmental sequences. Since 2017, an international network of experts in diatom taxonomy curate this library. The last version of the database (version 9.2), includes 8066 entries that correspond to more than 280 different genera and 1490 different species. In addition to the taxonomic information, morphological features (e.g. biovolumes, chloroplasts, etc.), life-forms (mobility, colony-type) and ecological features (taxa preferences to pollution) are given.
The database can be downloaded from the website (www6.inrae.fr/carrtel-collection/Barcoding-database/) or directly through the R package diatbarcode. Ready-to-use files for commonly used metabarcoding pipelines (Mothur and DADA2) are also available.
How many Non-Indigenous Species occurring in the Mediterranean Sea can actually be identified through environmental DNA? A gap analysis of NIS DNA barcodes in the reference libraries
Authors: Pinna Maurizio , Zangaro Francesco , Tzafesta Eftychia , Specchia Valeria 
Published: March 2021

The Mediterranean Sea is known for hosting a high diversity of species, with more than 17,000 reported marine species, one fifth which are endemic. Moreover, the number of non-indigenous species (NIS) in the Mediterranean Sea is recently reported to be increasing. The monitoring and the distribution of NIS is a key requirement for the conservation and management of the ecosystems, as also foreseen by the regulation (EU) No 1143/2014 of the European Parliament and of the Council of 22 October 2014 on the prevention and management of the introduction and spread of invasive alien species. A promising innovative approach for the identification of species and biodiversity is the use of molecular tools (DNA barcoding and metabarcoding). Combined with environmental DNA (eDNA) extracted from environmental samples like water or sediment, traces of species can be identified. Currently, the main limitation in the use of molecular tools (DNA barcoding and metabarcoding, eDNA) for species identification is the incompleteness of the DNA barcode reference databases. We assessed the extent of gaps in DNA barcode reference libraries, using the most updated inventory of 666 confirmed alien species occurring in the Mediterranean Sea. Also, the availability of primers for the amplification process was investigated. 32.58% of these species lack DNA barcodes in the reference libraries. Also, 70% of the retrieved NIS in the DNA barcode libraries lack the public availability of the primers used for the amplification process.
The results of this study allow us to direct scientific efforts towards specific taxonomic groups in order to complete the NIS DNA barcode reference libraries and enable effective application of eDNA in investigations of the occurrence and the distribution of NIS in the Mediterranean Sea, and in the first sighting of still unknown NIS.