bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of Rainfall Variability on Rural Tea Roads in Kericho, Kenya
Authors: Koech Nancy Chemutai , Letema Sammy C. , Koske James Kibii 
Published: March 2021

Climate variability is a global phenomenon that is posing a threat to the infrastructure and agricultural sector. Intense precipitation often results in the deterioration of rural road infrastructure resulting in inaccessibility. Rainfall and temperature data from 1989 to 2019 was obtained from Kenya Meteorological Department. Data on Greenleaf and cost of repairs and maintenances are from selected tea factories managed by Kenya Tea Development Agency. Data on perception is based on a questionnaire survey of 398 randomly selected tea farmers. Results show that climate variability is experienced in Kericho (p < 0.005). There is a varsity variation in mean maximum temperatures F(0.05, 29) ꞊ 5.564 (p ꞊ 0.009) and mean minimum temperature F(29) =8.503 (p ꞊ 0.000). However, the linear regression analysis shows that rainfall has decreased (y ꞊ 2.5476x - 40.778) while the temperature has increased (y ꞊ 0.028x - 0.4473). There is a significant positive correlation between the amount of rainfall and cost of repairs and maintenances for five factories (r ꞊ 0.122, r = 0.046, r = 0.029, r = 0.255) except one (r = -.261, p ꞊ .466). Therefore, the climate has significantly varied from 1989-2019 and heavy rains occur periodically that damage rural tea roads, thus impacting negatively on tea transportation. There is a need, therefore, for heavy investment of emergency funds for repair and maintenance of rural tea roads based on rainfall variability and heavy rain return period pattern.
Comparative analysis of regional chemotherapy methods on an experimental rat model with peritoneal carcinomatosis
Authors: Zakharenko Aleksandr , Beliaev Mikhail , Bagnenko Sergei , Vervekin Ilia , Iukina Galina , Tamazian Nina , Novikova Anastasiia , Paltyshev Ilia 
Published: March 2021

Peritoneal carcinomatosis is a variant of implantation metastasis of tumors sprouting the serous membrane of an organ. At the moment, the most effective treatment for this disease is regional chemotherapy. Systemic chemotherapy is not effective enough. The standard for the treatment of peritoneal carcinomatosis was cytoreductive interventions followed by open or closed hypertermic intraperitoneal chemoperfusion (HIPEC) or pressurized intraperitoneal aerosol chemotherapy (PIPAC).
Purpose of the study: in an animal experiment to compare the efficacy and safety of regional chemotherapy methods HIPEC and PIPAC
Materials and methods: the study was conducted on 44 rats of Wistar females. To simulate carcinomatosis, a strain of ascites ovarian tumor (OA) from the Russian Oncology Cancer Research Center N.N. Petrova. was used. The safety of the technique was evaluated clinically and based on laboratory blood tests. Efficiency - based on mass spectrometry, pathomorphological data and in assessing the life expectancy of animals.
Results: the conducted methods HIPEC (open, closed) and PIPAC have shown their safety in experiments on laboratory animals. The closed HIPEC technique is most effective. The analysis of the incidence of postoperative complications demonstrated a greater aggressiveness of open and closed techniques compared to the more “sparing” PIPAC method.
Conclusions: the experiment showed comparable safety of all animals tested. Due to the peculiarities of the technique, the PIPAC method can be used as an option for multi-stage treatment in cases where CPC and HIPEC are not possible due to a high index of peritoneal carcinomatosis, and as a neoadjuvant treatment to prevent peritoneal carcinomatosis. In any case, the prospects for using this method require further research.
Semiempirical Modeling of the Atmospheres of the M Dwarf Exoplanet Hosts GJ 832 and GJ 581
Authors: Tilipman Dennis , Vieytes Mariela , Linsky Jeffrey L. , Buccino Andrea P. , France Kevin 
Published: March 2021

Abstract
Stellar ultraviolet (UV) radiation drives photochemistry, and extreme-ultraviolet (EUV) radiation drives mass loss in exoplanet atmospheres. However, the UV flux is partly unobservable due to interstellar absorption, particularly in the EUV range (100–912 Å). It is therefore necessary to reconstruct the unobservable spectra in order to characterize the radiation environment of exoplanets. In the present work, we use a radiative transfer code SSRPM to build one-dimensional semiempirical models of two M dwarf exoplanet hosts, GJ 832 and GJ 581, and synthesize their spectra. SSRPM is equipped with an extensive atomic and molecular database and full-NLTE capabilities. We use observations in the visible, ultraviolet, and X-ray ranges to constrain atmospheric structures of the modeled stars. The synthesized integrated EUV fluxes are found to be in good agreement with other reconstruction techniques, but the spectral energy distributions disagree significantly across the EUV range. More than two-thirds of the EUV flux is formed above 105 K. We find that the far-ultraviolet (FUV) continuum contributes 42%–54% of the entire FUV flux between 1450 and 1700 Å. The comparison of stellar structures of GJ 832 and GJ 581 suggests that GJ 832 is a more magnetically active star, which is corroborated by other activity indicators.
Dissecting the Supercritical Filaments Embedded in the 0.5 pc Subsonic Region of Barnard 5
Authors: Schmiedeke Anika , Pineda Jaime E. , Caselli Paola , Arce Héctor G. , Fuller Gary A. , Goodman Alyssa A. , Maureira María José , Offner Stella S. R. , Segura-Cox Dominique , Seifried Daniel 
Published: March 2021

Abstract
We characterize in detail the two ∼0.3 pc long filamentary structures found within the subsonic region of Barnard 5. We use combined Robert C. Byrd Green Bank Telescope and Very Large Array observations of the molecular lines NH3(1,1) and (2,2) at a resolution of 1800 au, as well as James Clerk Maxwell Telescope continuum observations at 850 and 450 μm at a resolution of 4400 and 3000 au, respectively. We find that both filaments are highly supercritical with a mean mass per unit length, M/L, of ∼80 M
⊙ pc−1 after background subtraction, with local increases reaching values of ∼150 M
⊙ pc−1. This would require a magnetic field strength of ∼500 μG to be stable against radial collapse. We extract equidistant cuts perpendicular to the spine of the filament and fit a modified Plummer profile as well as a Gaussian to each of the cuts. The filament widths (deconvolved FWHM) range between 6500 and 7000 au (∼0.03 pc) along the filaments. This equals ∼twice the radius of the flat inner region. We find an anticorrelation between the central density and this flattening radius, suggestive of contraction. Further, we also find a strong correlation between the power-law exponent at large radii and the flattening radius. We note that the measurements of these three parameters fall in a plane and derive their empirical relation. Our high-resolution observations provide direct constraints on the distribution of the dense gas within supercritical filaments showing pre- and protostellar activity.
A Model for the Coupled Eruption of a Pseudostreamer and Helmet Streamer
Authors: Wyper P. F. , Antiochos S. K. , DeVore C. R. , Lynch B. J. , Karpen J. T. , Kumar P. 
Published: March 2021

Abstract
A highly important aspect of solar activity is the coupling between eruptions and the surrounding coronal magnetic field topology, which determines the trajectory and morphology of the event and can even lead to sympathetic eruptions from multiple sources. In this paper, we report on a numerical simulation of a new type of coupled eruption, in which a coronal jet initiated by a large pseudostreamer filament eruption triggers a streamer-blowout coronal mass ejection (CME) from the neighboring helmet streamer. Our configuration has a large opposite-polarity region positioned between the polar coronal hole and a small equatorial coronal hole, forming a pseudostreamer flanked by the coronal holes and the helmet streamer. Further out, the pseudostreamer stalk takes the shape of an extended arc in the heliosphere. We energize the system by applying photospheric shear along a section of the polarity inversion line within the pseudostreamer. The resulting sheared-arcade filament channel develops a flux rope that eventually erupts as a classic coronal-hole-type jet. However, the enhanced breakout reconnection above the channel as the jet is launched progresses into the neighboring helmet streamer, partially launching the jet along closed helmet streamer field lines and blowing out the streamer top to produce a classic bubble-like CME. This CME is strongly deflected from the jet’s initial trajectory and contains a mixture of open and closed magnetic field lines. We present the detailed dynamics of this new type of coupled eruption, its underlying mechanisms, and the implications of this work for the interpretation of in situ and remote-sensing observations.
Nonlinear Simulation of Ionospheric Irregularities at Mars
Authors: Jiang Chunhua , Yokoyama Tatsuhiro , Wei Lehui , Yang Guobin , Zhao Zhengyu 
Published: March 2021

Abstract
Motivated by the observations and linear theory analysis of ionospheric irregularities at Mars, we performed numerical simulations of the nonlinear evolution of the electromagnetic gradient drift instability in the Martian ionospheric dynamo region. The seeding source of ionospheric irregularities is perturbation zonal neutral wind. We found that the perturbation electric fields induced by the gradient drift instability can convect lower density plasma into higher density plasma at higher altitudes. Then, the associated perturbation magnetic field and electric field can cause the velocity shear of the plasma, which induced the Kelvin–Helmholtz instability at higher altitude. The Kelvin–Helmholtz instabilities furthermore lead to smaller-scale irregularities in plasma density, magnetic field, and electric field in the Martial ionosphere. Key points: (1) Nonlinear simulation of small-scale ionospheric irregularities at Mars was present. (2) Ionospheric irregularities at Mars can be seeded by the perturbation neutral winds. (3) Model results are comparable to linear theory analysis and satellite observations.
Are multiplexed metabarcoding panels comparable to individual marker gene library preparations?
Authors: Eastwood Niamh , Orsini Luisa 
Published: March 2021

Analysis of multiple marker genes using metabarcoding of environmental DNA (eDNA) can offer information greater than that from sequencing single marker genes, such as responses from across the phylogenetic tree to environmental gradients (Cordier et al. 2019). Furthermore, multiple regions of the same gene can be sequenced to improve phylogenetic resolution (Fuks et al. 2018). However, separate amplification reactions and library preparation steps for each marker can be costly and time consuming.
Here, we have designed and optimised a multiplex panel of four marker genes (two regions of 18S rRNA gene, one region of the 16S rRNA gene and one region of the rbcL gene). By combining steps into a single reaction, the labwork required is decreased, reducing cost and time. This multiplex is compared with a widely available commercial microbial (bacterial and fungal) screening panel and individual library preparations of each marker gene.
New kid on the block: Research of alpine-lake macroinvertebrates in the Tatra Mountains enhanced by DNA barcoding and metabarcoding
Authors: Vargovčík Ondrej , Čiamporová-Zaťovičová Zuzana , Čiampor Jr Fedor 
Published: March 2021

State of ecosystems and biodiversity protection are becoming the key interests for modern society due to climate change and negative human impacts (Leese 2018). Environmental changes in freshwaters are indicated also by benthic communities, especially in sensitive ecosystems like alpine lakes (Fjellheim 2009). Moreover, remoteness and isolation of alpine lakes make them a source of biodiversity, which is worth conserving (Hamerlík 2014). A promising tool for efficient large-scale monitoring of aquatic communities is DNA metabarcoding (Leese 2018). In this study, we applied metabarcoding to analyse macrozoobenthos of 12 lakes in the Tatra Mountains, using benthic bulk samples and eDNA filtered from water (Fig. 1).
In compliance with recent publications, eDNA amplified with BF3/BR2 primers resulted in high percentage of non-invertebrate reads (Leese 2021). Based on in silico tests with the obtained sequences, we confirm that the recently developed EPTDr2n primer enables minimizing non-target amplification even with eDNA filtered from alpine-lake water (Elbrecht and Leese 2017). This ability is facilitated by 3’ end of the primer and we observed the two important mismatches in non-target sequences from our study (Leese 2021). Thus, our future analyses of eDNA (and bulk-sample fixative) will benefit from the new primer.
Concerning bulk samples, a wide range of invertebrate taxa was assigned to the OTUs and they showed good congruence with previous studies using morphological determination (e.g. Krno 2006). Certain differences with (and among) the previous records per lake were observed, which could suggest ecological changes, but at the moment the influence of sampling error cannot be excluded. In eDNA, several taxa were congruent with the previous records, but their amount and read abundance was considerably lower due to non-target amplification. Apart from that, filling gaps in barcoding databases remains one of our priorities, as identification to species or genus level was not yet possible for some invertebrate OTUs.
In addition, we subjected the NGS data to denoising and abundance-filtering in order to explore haplotype-level diversity (Andújar 2021). Although more comprehensive conclusions will be possible only after obtaining data from more lakes and years, already the two metabarcoding experiments presented here enabled us to efficiently detect within-species genetic diversity and identify a large variety of taxa, including groups that would otherwise be omitted or very challenging to identify. This underlines the potential of DNA methods to provide valuable ecological and biodiversity data across the tree of life for modern biomonitoring. This study was realized with support from VEGA 2/0030/17 and VEGA 2/0084/21.
Composition of diatom communities on travertine barriers of the Una River (Bosnia and Herzegovina) obtained by DNA metabarcoding and morphological analysis
Authors: Kamberović Jasmina , Gligora Udovič Marija , Kahlert Maria , Tapolczai Kálmán , Lukić Zorana , Ahmić Adisa , Dedić Anita , Kulaš Antonija , Kajan Katarina , Hanjalić Jasna , Lasić Lejla , Kalamujic Stroil Belma 
Published: March 2021

The process of travertine formation and carbonate deposition in the rivers is unique, delicate, and depends on the activity of algae and mosses. Although diatoms have been used extensively in hydrobiological studies, the comparative analysis data on diatom communities of the travertine barriers in karstic rivers are still scarce.
The study aimed to detect the diatom composition on travertine barriers in the Una River, the large karstic river in Bosnia and Herzegovina. An integrated classical morphological identification approach with metabarcoding was applied on eight samples across the river length profile. Morphological analyses were performed using both light and scanning electron microscopes. Subsequent DNA metabarcoding of the chloroplastic gene 312bp rbcL was done. The DADA2 pipeline was used for the bioinformatic treatment of the demultiplexed MiSeq reads to infer Amplicon Sequence Variants (ASVs). ASVs were taxonomically assigned using the Diat.barcode v7 reference database.
A total of 126 species were identified using the morphological approach, while 133 ASVs were taxonomically assigned to 58 unique taxa with the molecular approach. Diatom community structures in terms of molecular and morphological approaches were congruent with 49 shared species. Species from genera Gomphonema, Navicula and Encyonema were less assigned in molecular analysis.
The most abundant taxa in the Una River are alkaliphilous, belonging to the genera Gomphonema, Nitzshia and Navicula. Although specific for their extremely good chemical status, the travertine barriers of the Una River are largely inhabited with meso-eutraphentic taxa.
There's always a better way: The application of eDNA to effectively assess biodiversity
Authors: Roy Prabir , Thiess Mary 
Published: March 2021

Our ecosystem monitoring methodologies focus on data collection for reporting purposes that may not serve to identify the systematic causes of ecological change. Managers need precise and timely information at appropriate scales to build ecosystem resilience.
Traditional species detection methodologies offer little information when species abundance are low, especially in large water ecosystems such as the Great Lakes. Species not found during monitoring doesn’t necessarily mean that species are absent. Moreover, even if a change in the ecosystem is detected, it is often not possible to determine its cause at a spatiotemporal scale or a trophic cascade level. As a result, we often find ourselves being reactive in our mitigation measures. Before irreversible change occurs, we must be guided by a better understanding of the actual ecological landscape which Environmental DNA (eDNA) may help provide.
eDNA is a potential tool to effectively overcome traditional species survey limitations currently in use at many Parks Canada sites (Supplemental file 1). As various organisms interact with the environment, DNA is expelled and accumulates in their surroundings. Such samples can be analyzed by high-throughput DNA sequencing methods for rapid measurement and monitoring of biodiversity. Access to this genetic information makes a critical contribution to the understanding of population size, species distribution, and population dynamics for species not well documented. Despite the increasing use of eDNA in conservation practice, it requires further methodological improvement for greater influence on management decisions. The tool requires standardized protocols based on site-specific covariates and objectives.
We’re working to tackle the challenge with 2 objectives: (1) to combine traditional biomonitoring knowledge and metagenomics to further develop eDNA as a reliable sampling tool for Parks Canada and (2) to support site-specific monitoring objectives for species-at-risk, invasive species, aquatic species inventories, and/or culturally significant species. The overall goal is to increase our capacity to make more informed, timely, regionally-coordinated conservation decisions through the rapid and sensitive species detection methods offered by eDNA.
DNA barcodes for UK freshwater arthropod species: coverage, quality and implications
Authors: Davidson Liz 
Published: March 2021

DNA-based identification methods have been shown to have high detection capability and reduced costs compared to traditional methods and can also enable the detection of species that might be missed using traditional methods (e.g. rare species, cryptic species, larval stages). The success of DNA-based identification is dependent on the ‘DNA barcodes’ of target species being present in a barcode reference database. In order to use DNA-based identification methods to assess and monitor UK freshwater arthropods for biodiversity and ecological quality assessments, it is vital that comprehensive reference databases are available. Incomplete reference databases result in many sequences derived from metabarcoding not being assigned to species.
Two current projects aim to create collections of high-quality sequences from expertly identified specimens of UK species. The Darwin Tree of Life project aims to sequence the genomes of all the eukaryotic species in Britain and Ireland and FreshBase aims to create a genomic reference collection for UK freshwater invertebrates. The Barcode of Life Data System (BOLD) is one of the main reference databases for animal barcodes. Prioritising the sequencing of UK freshwater arthropod species that are not yet represented in BOLD, would enable more complete identification of UK freshwater biodiversity using metabarcoding and would enable the development of primers to target specific arthropod groups or species.
We analysed the coverage of UK freshwater arthropod species in BOLD. Our analyses show that coverage varies between taxonomic groups and large proportions of sequences in some orders are only represented by privately stored sequences in BOLD. Analyses of intra- and inter-specific variation in sequences stored in BOLD show that misidentifications or errors can reduce the barcode gap in some species which could cause difficulties in accurately identifying sequences derived from metabarcoding. Representation in BOLD by specimens from the UK is extremely low and analyses show that high geographic variation in sequences in some species could be important for accurate DNA-based identification of UK species. Our results have implications for prioritising the sequencing of UK freshwater arthropods and for the quality control of stored sequences in order to reduce the occurrence of misidentifications and errors that could impact the accuracy of DNA-based identification.
The use of eDNA and DNA metabarcoding in monitoring the ecological condition of Norwegian lakes
Authors: Atienza Casas Sara , Majaneva Markus , Jensen Thomas , Davey Marie , Fossøy Frode , Bækkelie Knut , Gjelland Karl Øystein , Schartau Ann , Ekrem Torbjørn 
Published: March 2021

Biodiversity assessments using molecular identification of organisms through high-throughput sequencing techniques have been a game changer in ecosystem monitoring, providing increased taxonomic resolution, more objective identifications, potential cost reductions, and reduced processing times. The use of DNA metabarcoding of bulk samples and environmental DNA (eDNA) is now widespread but is not yet universally implemented in national monitoring programs. While bulk sample metabarcoding involves extraction of DNA from organisms in a sample, eDNA analysis involves obtaining DNA directly from environmental samples, which can include microorganisms, meiofauna-size taxa and macrofauna traces such as larval stages, skin and hair cells, gametes, faeces and free DNA bound to particles.
In Norway, freshwater biomonitoring in compliance with the EU Water Framework Directive (WFD) is conducted on several administrative levels, including national monitoring programs for running water, small and large lakes. These programs typically focus on a fraction of the actual biodiversity present in the monitored habitats (Weigand 2019). DNA metabarcoding of both bulk samples and eDNA samples are relevant tools for future freshwater biomonitoring in Norway.
The aim of this PhD project is to develop assessment protocols based on DNA-metabarcoding and eDNA of benthic invertebrates, microcrustaceans and fish that can be used as standard biomonitoring tools to assess the ecological condition of lakes. The main topics addressed will be:
- Development of protocols throughout the eDNA-metabarcoding workflow (i.e. sampling, filtration, preservation, extraction, amplification and sequencing) suitable to execute biodiversity assessments and determine the ecological status of lakes.
- Comparison of the results obtained using molecular tools and traditional morphology-based approaches in order to assess the feasibility of such techniques to be incorporated as standard biomonitoring tools, such as the ones implemented under the provisions of the WFD.
- Evaluate the effect of improved taxonomic resolution from molecular techniques on determining the ecological status of lakes, both by broadening the number of taxa analyzed and by identifying more taxa to species level.
- Assess the feasibility of using eDNA extracted from water samples, taken at different depths and fish densities, to measure fish abundance/biomass as a proxy to calculate the ecological quality indices regulated in the WFD.
- Analyze the coverage and resolution provided by reference libraries for certain taxa, such as crustacea, in order to assess the reliability and precision of taxonomic assignments.