bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in long-term water quality changes in Ivan’kovo and Uglich reservoirs
Authors: Lomov V A , Georgiadi A G , Datsenko Y S , Danilenko A O 
Published: September 2021

Abstract
A comparative analysis of water quality indicators in the upper and lower parts of the Ivan’kovo and Uglich Reservoirs was carried out based on the analysis of long-term monitoring datasets on water quality condition in reservoirs. The observations were performed at the gauging stations of the State Observation Network and Mosvodokanal in the period from the mid-1980s to 2019 and 2004 accordingly. Over a long-term period, all studied hydrochemical indicators except for Zn and SO4 tend to decrease closer to the dam both in the Ivan’kovo and Uglich Reservoirs. Two periods with sufficiently different average values of considered parameters and their dynamics were distinguished for the Uglich Reservoir according to statistical analysis. A high level of pollution in the Uglich Reservoir is mainly associated with heavy metals (Cu, Zn, Fe), phenols and oil products and is typical for both the upper and lower parts of the reservoir. Such pattern is inherent to both heterogeneous periods (1985-2000 and 2001-2019) identified for the Uglich Reservoir. The main trends of long-term and seasonal variability in water quality of the Ivan’kovo and Uglich Reservoirs have been identified using the water pollution index.
Current hydroecological state of the Ural River in the lower reaches
Authors: Efimova L , Magritsky D , Kenzhebaeva A , Goncharov A 
Published: September 2021

Abstract
Climate and hydrological changes in the Ural River basin, together with water management activities determine the current hydroecological state of the river in its lower course. In comparison with the conventional natural background, the salinity of water in high water period increased by 2.5 times, in low water period- by 5-8 %. Contamination of the lower course of the river is caused by the inflow of pollutants from the upstream sections and the confluence of the polluted tributaries. In the area with no tributaries, the water is characterized as “standard-clean”. The saprobity indices, which characterize the content of organic substances in water, are located within the boundaries of the b-mesosaprobic zone, which characterize low level of water contamination. The content of dissolved oxygen indicates insufficient aeration of the river water during most of the year. The lowest oxygen content is observed during winter period.
Longitudinal patterns of different pollutant concentrations in the Setun River
Authors: Tereshina M , Erina O , Sokolov D , Shinkareva G , Vasilchuk J 
Published: September 2021

Abstract
As one of the most well-studied rivers of the Moscow megalopolis with diverse landscape and anthropogenic impact conditions on its watershed, the Setun River is a unique system suitable for complex urban geochemical research. Data of our ecological monitoring of 2019-2020 show elevated content of multiple elements, including nutrients and heavy metals, in its water throughout the year with several distinctive types of concentration distribution along the course of the river. These patterns correspond to various major impacts in the watershed: concentrations of P, N, Mn and sometimes As are the highest in the upper reaches due to proximity of a landfill and decrease downstream; Cu has a drastic concentration increase below an industrial park, and concentrations of various metals consistently increase downstream from highways and railroads despite the fact that the lower reaches are protected as a part of a wildlife sanctuary. Our findings may serve as a basis for optimizing the water quality monitoring within the framework of comprehensive research of pollution transport in water, soil and air of an urban watershed.
Estimation of the water quality of the Izhevsk Reservoir tributaries by macrozoobenthos indicators
Authors: Kholmogorova N V , Kargapoltseva I A 
Published: September 2021

Abstract
The species composition and quantitative indicators of macrozoobenthos of the main tributaries of the Izhevsk Reservoir were studied. The status of the rivers was assessed by bioindication methods. A significant simplification of the structure of the benthic communities in the lower reaches of the Luk and Podborenka rivers has been established. The Podborenka River is the most polluted of the tributaries of the Izhevsk Reservoir, and therefore, it is an important source of the deterioration of water quality in there.
Analysis of microplastic concentrations in water and bottom sediments as a new aspect of ecological monitoring
Authors: Ivanova E V , Pozdnyakov Sh R , Tikhonova D A 
Published: September 2021

Abstract
In this article we consider some features of spatial distribution of microplastic particles in water column and bottom sediments of Lake Ladoga based on results of research conducted in 2018-2019. This new type of contamination poses new threats to ecological conditions of water bodies. Considering the growing relevance of this problem, it is important to estimate genesis and scale of this contamination and its spatial and temporal distribution for developing recommendations for managing conditions of water bodies. It is advisable to add microplastic research including analysing microplastic concentrations and chemical composition of the particles to the system of ecological monitoring.
Inland water in Bosnia and Herzegovina
Authors: Drašković B , Gutalj M 
Published: September 2021

Abstract
Modern researches of the Earth’s surface by remote sensing are mainly based on photointerpretation of satellite images. Copernicus is the most important European program of satellite observation and monitoring in 33 countries of the European Union and 6 cooperating countries including Bosnia and Herzegovina. Within the program, there are several databases on inland waters, including EU-Hydro and Water and Wetness. Also, CORINE Land Cover is database containing water information within five main categories. The paper analyses data on water bodies that include lakes, reservoirs, rivers and wetlands. According to the EU-Hydro database for Bosnia and Herzegovina there are 251 water reservoirs with an area of at least 1 ha. The amount of precipitation is higher than the European average and density of the river network is relatively high. Since it is not a densely populated country, the amount of water per capita is 8 times larger in comparison with Germany or 3 times larger than in France. However, renewable water resources are not evenly distributed, neither temporally nor spatially, so this is a challenge for their management.
Regional characteristics of water use in conditions of water scarcity in steppe transboundary river basins (the Ural River basin as a case study)
Authors: Sivokhip Zh T , Pavleychik V M 
Published: September 2021

Abstract
The regional features of water use within the steppe biome and in conditions of water scarcity is analysed. It has established a steady trend of increasing summer temperature extremes and identified a trend in the seasonal distribution of precipitation. Rivers of the Ural River basin are found to be characterized by a decline in the percentage of spring flood runoff and an increase in the percentage of low-water seasonal runoff. This transformation of intra-annual flow is even more significant for rivers with a regulated regime. The paper defines also regional specific features concerning the use of water resources in the Ural River basin. In the Russian regions, the main portion of water resources is spent on industrial and utilities needs, and the minimum portion spent on the needs of agriculture. Another specific is a high portion of recycled water in the Russian regions, which confirms the rather efficient use of water resources in various economy sectors. The structure of water consumption in Kazakhstan regions is characterized by predominance of water use for industrial and utilities needs and preservation of a significant portion of water for agricultural supply. The results obtained show that an ambiguous and poorly predicted situation with water resources emerges in the transboundary basin of the Ural River. In this context, the priority task is to ensure the cost-effective and environmentally safe use of water resources in regions of the studied basin.
Zooplankton community structure in mouth areas of different rivers (tributaries of the lowland Cheboksary Reservoir, European Russia)
Authors: Zhikharev V S , Gavrilko D E , Shurganova G V 
Published: September 2021

Abstract
Main features of the structural organization of zooplankton communities are assessed for different morphological types of mouth areas found in tributaries of a lowland reservoir. It is shown that a river mouth with a distinguished delta is characterized by the highest species richness and diversity of all studied mouth types in both the free-flowing part of the stream and in the reservoir zone. In the transitional zone between the river and the reservoir, no statistically significant differences between zooplankton community structures of different types of river mouths were found, which can be explained by high heterogeneity of zooplankton communities in these zones, substantial shift in the dominant species composition, and higher quantitative development of zooplankton. The shift between dominance of various species in different river mouths was not uniform, but had a common direction – from the dominance of riverine rotifers to lacustrine crustacean species.
Hydrobiological and ichthyological features of the Shirokovsky Reservoir
Authors: Pozdeev I V , Kotelnikova V S , Ogorodov S P , Yu Krainev E , Bezmaternykh V V , Belyaeva P G 
Published: September 2021

Abstract
The characteristic of Shirokovsky Reservoir by communities of phytoplankton, zooplankton, benthic invertebrates, and fish is given. It is the first investigation of the reservoir since the building time of 1948. All levels of the ecosystem are impoverished as species compositions as functional groups. A considerable part of all communities is presented by riverine oxyphilous species. Any invasion species of algae, invertebrates, and fish haven’t registered. The maximal species richness and quantitative parameters of phytoplankton have been registered in the upper riverine part of the reservoir and were determined by Bacillariophyta (primarily centric species). The zooplankton complexes’ dominants were Bosmina longirostris, Daphnia galeata, and Mesocyclops leuckarti. Maximal quantity of zooplankton has been shown in the middle part of the waterbody. The species of oligochaetes Limnodrilus hoffmeisteri and chironomids Parakiefferiella coronata were the most important in benthic communities’ structure. Benthofauna species richness and quantity of benthic invertebrates have been maximal in the lower part of the reservoir. The most common fish species at the current period are dace, perch, and Siberian roach. The fish quantity has been the richest in the middle part of the reservoir with lots of shallow areas. Assessing the quantitative values, the Shirokovsky Reservoir was classified as an oligotrophic waterbody at present.
High resolution stereolithography fabrication of perfusable scaffolds to enable long-term meso-scale hepatic culture for disease modeling
Authors: Sphabmixay Pierre , Raredon Micha Sam Brickman , Wang Alex J-S , Lee Howon , Hammond Paula T , Fang Nicholas X , Griffith Linda G 
Published: September 2021

Abstract
Microphysiological systems (MPS), comprising human cell cultured in formats that capture features of the three-dimensional (3D) microenvironments of native human organs under microperfusion, are promising tools for biomedical research. Here we report the development of a mesoscale physiological system (MePS) enabling the long-term 3D perfused culture of primary human hepatocytes at scales of over 106 cells per MPS. A central feature of the MePS, which employs a commercially-available multiwell bioreactor for perfusion, is a novel scaffold comprising a dense network of nano- and micro-porous polymer channels, designed to provide appropriate convective and diffusive mass transfer of oxygen and other nutrients while maintaining physiological values of shear stress. The scaffold design is realized by a high resolution stereolithography fabrication process employing a novel resin. This new culture system sustains mesoscopic hepatic tissue-like cultures with greater hepatic functionality (assessed by albumin and urea synthesis, and CYP3A4 activity) and lower inflammation markers compared to comparable cultures on the commercial polystyrene scaffold. To illustrate applications to disease modeling, we established an insulin-resistant phenotype by exposing liver cells to hyperglycemic and hyperinsulinemic media. Future applications of the MePS include the co-culture of hepatocytes with resident immune cells and the integration with multiple organs to model complex liver-associated diseases
Condensed ECM-based nanofilms on highly permeable PET membranes for robust cell-to-cell communications with improved optical clarity
Authors: Choi Brian , Choi Jeong-Won , Jin Hyungwon , Sim Hye-Rim , Park Jung-Hoon , Park Tae-Eun , Kang Joo H 
Published: September 2021

Abstract
The properties of a semipermeable porous membrane, including pore size, pore density, and thickness, play a crucial role in creating a tissue interface in a microphysiological system (MPS) because it dictates multicellular interactions between different compartments. The small pore-sized membrane has been preferentially used in an MPS for stable cell adhesion and the formation of tissue barriers on the membrane. However, it limited the applicability of the MPS because of the hindered cell transmigration via sparse through-holes and the optical translucence caused by light scattering through pores. Thus, there remain unmet challenges to construct a compartmentalized MPS without those drawbacks. Here we report a submicrometer-thickness (∼500 nm) fibrous extracellular matrix (ECM) film selectively condensed on a large pore-sized track-etched (TE) membrane (10 µm-pores) in an MPS device, which enables the generation of functional tissue barriers simultaneously achieving optical transparency, intercellular interactions, and transmigration of cells across the membrane. The condensed ECM fibers uniformly covering the surface and 10 µm-pores of the TE membrane permitted sufficient surface areas where a monolayer of the human induced pluripotent stem cell-derived brain endothelial cells is formed in the MPS device. The functional maturation of the blood–brain barrier (BBB) was proficiently achieved due to astrocytic endfeet sheathing the brain endothelial cells through 10 µm pores of the condensed-ECM-coated TE (cECMTE) membrane. We also demonstrated the extravasation of human metastatic breast tumor cells through the human BBB on the cECMTE membrane. Thus, the cECMTE membrane integrated with an MPS can be used as a versatile platform for studying various intercellular communications and migration, mimicking the physiological barriers of an organ compartment.
Querying multiple sets ofP-values through composed hypothesis testing
Authors: Mary-Huard Tristan , Das Sarmistha , Mukhopadhyay Indranil , Robin Stéphane 
Published: September 2021

AbstractMotivationCombining the results of different experiments to exhibit complex patterns or to improve statistical power is a typical aim of data integration. The starting point of the statistical analysis often comes as a set of P-values resulting from previous analyses, that need to be combined flexibly to explore complex hypotheses, while guaranteeing a low proportion of false discoveries.ResultsWe introduce the generic concept of composed hypothesis, which corresponds to an arbitrary complex combination of simple hypotheses. We rephrase the problem of testing a composed hypothesis as a classification task and show that finding items for which the composed null hypothesis is rejected boils down to fitting a mixture model and classifying the items according to their posterior probabilities. We show that inference can be efficiently performed and provide a thorough classification rule to control for type I error. The performance and the usefulness of the approach are illustrated in simulations and on two different applications. The method is scalable, does not require any parameter tuning, and provided valuable biological insight on the considered application cases.Availability and implementationThe QCH methodology is available in the qch package hosted on CRAN. Additionally, R codes to reproduce the Einkorn example are available on the personal webpage of the first author: https://www6.inrae.fr/mia-paris/Equipes/Membres/Tristan-Mary-Huard.Supplementary informationSupplementary data are available at Bioinformatics online.
pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification
Authors: Weeder Benjamin R , Wood Mary A , Li Ellysia , Nellore Abhinav , Thompson Reid F 
Published: September 2021

Abstract

Motivation
Proteasomal cleavage is a key component in protein turnover, as well as antigen processing and presentation. Although tools for proteasomal cleavage prediction are available, they vary widely in their performance, options and availability.

Results
Herein, we present pepsickle, an open-source tool for proteasomal cleavage prediction with better in vivo prediction performance (area under the curve) and computational speed than current models available in the field and with the ability to predict sites based on both constitutive and immunoproteasome profiles. Post hoc filtering of predicted patient neoepitopes using pepsickle significantly enriches for immune-responsive epitopes and may improve current epitope prediction and vaccine development pipelines.

Availability and implementation
pepsickle is open source and available at https://github.com/pdxgx/pepsickle.

Supplementary information
Supplementary data are available at Bioinformatics online.
mspack: efficient lossless and lossy mass spectrometry data compression
Authors: Hanau Felix , Röst Hannes , Ochoa Idoia 
Published: September 2021

Abstract

Motivation
Mass spectrometry (MS) data, used for proteomics and metabolomics analyses, have seen considerable growth in the last years. Aiming at reducing the associated storage costs, dedicated compression algorithms for MS data have been proposed, such as MassComp and MSNumpress. However, these algorithms focus on either lossless or lossy compression, respectively, and do not exploit the additional redundancy existing across scans contained in a single file. We introduce mspack, a compression algorithm for MS data that exploits this additional redundancy and that supports both lossless and lossy compression, as well as the mzML and the legacy mzXML formats. mspack applies several preprocessing lossless transforms and optional lossy transforms with a configurable error, followed by the general purpose compressors gzip or bsc to achieve a higher compression ratio.

Results
We tested mspack on several datasets generated by commonly used MS instruments. When used with the bsc compression backend, mspack achieves on average 76% smaller file sizes for lossless compression and 94% smaller file sizes for lossy compression, as compared with the original files. Lossless mspack achieves 10–60% lower file sizes than MassComp, and lossy mspack compresses 36–60% better than the lossy MSNumpress, for the same error, while exhibiting comparable accuracy and running time.

Availability and implementation
mspack is implemented in C++ and freely available at https://github.com/fhanau/mspack under the Apache license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Exercise effects on cardiovascular disease: from basic aspects to clinical evidence
Authors: Sanchis-Gomar Fabian , Lavie Carl J , Marín Jorge , Perez-Quilis Carme , Eijsvogels Thijs M H , O’Keefe James H , Perez Marco V , Blair Steven N 
Published: September 2021

AbstractCardiovascular (CV) disease (CVD) remains the leading cause of major morbidity and CVD- and all-cause mortality in most of the world. It is now clear that regular physical activity (PA) and exercise training (ET) induces a wide range of direct and indirect physiologic adaptations and pleiotropic benefits for human general and CV health. Generally, higher levels of PA, ET, and cardiorespiratory fitness (CRF) are correlated with reduced risk of CVD, including myocardial infarction, CVD-related death, and all-cause mortality. Although exact details regarding the ideal doses of ET, including resistance and, especially, aerobic ET, as well as the potential adverse effects of extreme levels of ET, continue to be investigated, there is no question that most of the world’s population have insufficient levels of PA/ET, and many also have lower than ideal levels of CRF. Therefore, assessment and promotion of PA, ET, and efforts to improve levels of CRF should be integrated into all health professionals’ practices worldwide. In this state-of-the-art review, we discuss the exercise effects on many areas related to CVD, from basic aspects to clinical practice.
Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices
Authors: Wolfe Marnin D , Chan Ariel W , Kulakow Peter , Rabbi Ismail , Jannink Jean-Luc 
Published: September 2021

AbstractDiverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).