bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regression mathematical models of the number of small mammals in the Kaluga region of the Russian Federation
Authors: Vasilevich F I , Kalmykov V V , Nikanorova A M , Koroleva E V , Grossman M F 
Published: September 2021

Abstract
An analytical review of mathematical model of the dynamics of the population of small mammals, feeders for ixodic ticks, is presented. Rodents are an essential link in the circulation of agents of numerous zoonoses, as a result, a constant natural nidality within a specific area is maintained. Small mammals also serve as host feeders for a number of hematophagous arthropods, which are natural reservoirs of causative agents of dangerous infections and invasions. Muroid rodents are the most numerous mammals that inhabit the territory of the Russian Federation. A combination of natural disease foci often occurs as a result of territorial convergence and the existence of common vectors and carriers in the same area. Tularemia can be combined with plague, pseudotuberculosis, listeriosis, leptospirosis, pasteurellosis, etc. Small mammals are also involved in the circulation of encephalitis virus, viral hemorrhagic fever, orthohantavirus, Lyme disease, toxoplasmosis, leishmaniasis, babesiosis, anaplasmosis, and many other diseases affecting animals and humans. All the above mentioned diseases require continuous monitoring of the population dynamics of small mammals within a specific natural and climatic area under study. Mathematical models of the dynamics of population of small mammals make it possible to effectively forecast outbreaks of natural focal diseases without significant financial investments. An accurate forecast will provide an opportunity to be prepared and will enable a prompt response to the epizootological situation. The purpose of the study is to develop mathematical models of the population of small mammals in the Kaluga region acting as ixodid tick host feeders, therefore making it possible to estimate the probability of outbreaks of vector-borne zoonoses. The obtained mathematical models enable the risk quantification of outbreaks of vector-borne zoonoses without incurring costs associated with field study and allow to implement competent, timely and effective preventive measures.
Influence of ultrasound and extraction conditions on the intensity of extraction of anthocyanin pigment from berry raw materials
Authors: Chesnokova N Y , Levochkina L V , Prikhod’ko Y V , Kuznetsova A A , Chebukin P A 
Published: September 2021

Abstract
The effect of ultrasound and extraction conditions on the degree of anthocyanin pigment extraction from berry raw materials has been studied. It has been shown that the use of ultrasound for extraction allows increasing the anthocyanin pigment yield. The ultrasound-assisted water extraction at 25°C for 30 minutes increases the yield of pigment in aqueous solution by 22 %. The increase in the ultrasound-assisted extraction temperature to 65°C reduces the extraction time down to 15 minutes. It has been shown that the use of ultrasound reduces the extraction degree in 96 % ethanol and in the ethanol/water/hydrochloric acid system and increases the amount of anthocyanin pigment into the solution containing water as an extraction agent. In this case, the use of the ultrasound-assisted extraction reduces the anthocyanin pigment extraction time to 20 minutes with the use of the 96 % ethanol as an extraction agent, and to 15 minutes in an aqueous solution. The study of the ultrasound-assisted extraction effect, as well as the frequency and power of ultrasonic vibrations on the anthocyanin pigment extraction intensity has shown that the indirect ultrasound-assisted extraction (ultrasonic bath) with the ultrasound exposure frequency of 35 kHz and the power of 80 W allows allocating the anthocyanin pigment to the fullest extent possible within 30 minutes. With the direct ultrasound exposure (ultrasonic homogenizer) with the frequency of 20 kHz and the power of 75 W, the extraction time with an aqueous solution is reduced to 15 minutes, and with 96 % ethanol - to 20 minutes.
Development and application of iron supplements, and principles of iron deficiency anemia therapy in fur farming
Authors: Balakirev N A , Maksimov V I , Deltsov A A 
Published: September 2021

Abstract
A key factor in the non-infectious disease of iron deficiency anemia, which slows down the growth and development of fur farming species, is metabolic disturbance of iron in the body, which leads to deprivation of condition and quality of furs. It has been shown that the use of supplements of ferrous and ferric iron leads to damage not only to the structural elements of the gastrointestinal tract, but also to other systems and organs, which is due to the fact that in the absence of oxygen in the tissues, the reduction of iron from the ferric form to the ferrous form with further transfer electrons from ferrous iron to hydrogen peroxide causes the formation of a hydroxyl radical, which launches a program for self-destruction. Several factors are proposed to solve the problem, including usage of iron supplements for oral use in fur farming - industry where they are not used enough, and conduction of research on development and study of the effect of physiologically-pharmacologically active compounds based on a polymer (iron-hydroxide polymantose) on fur animals for treatment and prevention of microelemetosis. It is being solved by the collective of the Department of Physiology, Pharmacology and Toxicology of Moscow state Academy of Veterinary Medicine and Biotechnology by K.I. Scriabin in cooperation with research and production company LLC Firm "A-BIO" on the basis of an analysis of literary and patent sources, production technologies, pharmacological characteristics of ongoing research to develop and study the effect of physiologically and pharmacologically active compounds based on polymer (iron-hydroxide polymantose) on fur animals in the treatment and prevention of iron deficiency anemia.
Specific features of aerobic energy exchange in crucian carp females during the spawning season
Authors: Kulachenko I V , Kulachenko V P , Kirienko A V 
Published: September 2021

Abstract
The article provides the study of the features of aerobic energy metabolism in female crucian carp during the spawning season based on the amount of dissolved in water oxygen consumed according to the methods suggested in fish farming with reference to weight, length and surface area of the body, condition and weight of eggs. It has been shown that aerobic energy metabolism in female crucian carp with oxygen content in the water of the fishing area of 9.5 mg/l and a water temperature of 15 °C during the spawning season is characterized by a high positive correlation of the oxygen amount consumed with the mass, length and surface area of the body, moderate - with the gonads mass and moderately negative with condition, which corresponds to the spawning season and their reproductive potential in favorable environmental conditions.
To the issue of organization of the communication system in microorganisms
Authors: Mukhamadiev B T , Sharipov M Z 
Published: September 2021

Abstract
The role of EMF (electromagnetic field) in biological systems is considered in a large number of works performed by various foreign scientists. The energy imparted to the EMF system by the ELF (extremely low frequency) field is much less than the energy of thermal movements. But no work discusses the issues of impulse exchange in biological systems, and first of all, between the molecules of the (flexible) γ-protein and membranes that act as a capacitor of electrical impulses. The purpose of the article is to fill this gap in science by discussing the literature data on the effect of ELF and ULF (ultra-low frequency) EMFs on biological systems, primarily, the protein envelope of the virus + the host cell membrane.
Formation of a “cold” winter of shorebirds and waterfowl in the source and upper current of the river Angara (South Baikal) and its causes
Authors: Mel’nikov Yu , Kupchinskiy A , Fialkov V 
Published: September 2021

Abstract
On the basis of many years of research (1972-2019), the peculiarities of the formation of “cold” wintering of near-water and waterfowl in the source and upper reaches of the Angara river are considered. Despite the fact that it has been for a very long time studied, this issue has not yet received proper coverage in the scientific literature. Until now, there are different opinions about the reasons for its formation - sometimes very controversial, which requires a more complete analysis of the available materials. We found out that the formation of wintering is associated with delays in the departure of birds that have not accumulated a sufficient amount of plastic substances necessary for the continuation of migration. Late freezing source and upper course of the Angara river (mid-January - early February) allow birds to stay for a long time. Here, due to the huge mass of water heated in summer, which increases the temperature of the surface air layer in the late autumn and early winter periods, a thermal is refugium formed. However, by the time the birds are able to continue their migration, it becomes impossible. Permanent snow cover and very low air temperatures are in the surrounding areas established, and all lake systems freeze. This thermal refugium, into which birds, delayed with flight, gradually move, becomes an ecological trap, and the “cold” wintering itself is forced.
Prospects of application in the breeding Fragaria Orientalis Los. in the conditions of permafrost
Authors: Belevtsova V I , Sorokopudov V N , Mutuzova M Kh 
Published: September 2021

Abstract
This article discusses the issue of interspecific hybridization in the genus Fragaria L. under the conditions of Yakutia. The species of oriental strawberry - Fragaria Orientalis Los., which formed under severe natural selection conditions and possessed high ecological adaptability to local natural and climatic conditions, was used as the main form. Revealed high frost resistance, immunity, productivity, unpretentiousness, excellent taste, and aroma of fruits of the species of interest for breeding in extreme conditions. The purpose of the research is to create local varieties of strawberries that combine a high level of productivity and quality indicators with adaptability to a complex of biotic and abiotic environmental factors. The result of interspecific hybridization of strawberries was the creation of varieties with a complex of economically valuable traits: Sadovo-Spasskaya, Bersenevskaya, Vladyka Zosima. The high stability and productivity of the variety Sadovo-Spasskaya were noted. Early ripening, high winter hardiness, and high taste are characteristic of the Bersenevskaya variety. The Vladyka Zosima variety is distinguished by an early ripening period, high productivity in the year of planting, and a long fruiting period. The result of research from 1999 to 2020. the creation of diverse seedlings with different types and periods of fruiting, yield, and weight of fruits, varied in shape and taste, runners-forming with high winter hardiness began.
Opposition in a hybrid regime: The functions of opposition parties in Burkina Faso and Uganda
Authors: Bertrand Eloïse 
Published: September 2021

Abstract
Despite growing interest in party politics in Africa, the activities and roles of African opposition parties are still underexplored, especially in the context of one-party-dominant ‘hybrid’ regimes where they are allowed to operate but face a myriad of constraints. In these settings, opposition parties face a common dilemma: having to participate in the regime’s institutions and protest against them at the same time. Existing frameworks fail to provide a full and accurate picture of how opposition parties can erode the incumbent’s dominance and promote regime change. This article offers a novel functional framework, drawing from comparative research in Burkina Faso and Uganda. It identifies a set of three functions that opposition parties perform within a hybrid regime: denunciation, mobilization of dissent, and succession signalling. Understanding opposition parties’ functions in a hybrid regime through this alternative framework enables us to reconcile the seemingly contradictory behaviour of opposition parties that work both within and against the status quo and to better evaluate their role in this setting.
Soviet Secrecy: Toward a Social Map of Knowledge
Authors: Siddiqi Asif 
Published: September 2021

Abstract
This article offers a framework to model the epistemological terrain of the circulation and regulation of knowledge in late-period Soviet society. It proposes that secrecy and openness operated in a mutually constitutive “social map of knowledge” that was constantly shifting due to the inability to maintain secrecy as a stable category. Investigating the domain of Soviet science, this article sheds light on the work of institutions such as Glavlit, the state censorship authority, which supported the state’s goal to maintain the contours of secrecy as a static category by repeatedly issuing edicts and restructuring the apparatus of secrecy in the face of constant and destabilizing social, cultural, and technological pressures. This stable but volatile condition encouraged a common language of “speaking in secret” that cut across the Soviet social order. The “social map of knowledge” was one with high peaks, where valuable knowledge was placed in the hands of those with power, even as these peaks were under intense pressure to collapse from a parallel market of speculation marked by rumor, suspicion, and conspiracy theories. This form of “stable volatility” became impossible to maintain in the 1980s, when a deluge of information flooded Soviet society.
Evaluation of the Post-COVID Patient Prior to Elective Plastic Surgery: Developing an Evidence-Based Framework
Authors: Fiala Thomas , Fernau James , Singer Robert 
Published: September 2021

Abstract

Preoperative assessment of a potential surgical patient has long been a cornerstone of patient safety. As more patients get, and recover from, COVID, plastic surgeons will be faced with the challenge of evaluating the health status and operative risk of convalescent COVID patients who now desire elective surgery. A significant fraction of these patients, however, can have new or persistent health issues as a result of COVID-19, which can affect surgical safety. This paper briefly examines the current relevant literature regarding the post-COVID patient, reviews the waiting period for adequate recovery, and suggests an evidence-based framework for preoperative assessment, based on the severity of the prior COVID-19 episode, ongoing symptoms, and basic screening tests.

Level of Evidence: 4
sciCNV: high-throughput paired profiling of transcriptomes and DNA copy number variations at single-cell resolution
Authors: Mahdipour-Shirayeh Ali , Erdmann Natalie , Leung-Hagesteijn Chungyee , Tiedemann Rodger E 
Published: September 2021

Abstract
Chromosome copy number variations (CNVs) are a near-universal feature of cancer; however, their individual effects on cellular function are often incompletely understood. Single-cell ribonucleic acid (RNA) sequencing (scRNA-seq) might be leveraged to reveal the function of intra-clonal CNVs; however, it cannot directly link cellular gene expression to CNVs. Here, we report a high-throughput scRNA-seq analysis pipeline that provides paired CNV profiles and transcriptomes for single cells, enabling exploration of the effects of CNVs on cellular programs. RTAM1 and -2 normalization methods are described, and are shown to improve transcriptome alignment between cells, increasing the sensitivity of scRNA-seq for CNV detection. We also report single-cell inferred chromosomal copy number variation (sciCNV), a tool for inferring single-cell CNVs from scRNA-seq at 19–46 Mb resolution. Comparison of sciCNV with existing RNA-based CNV methods reveals useful advances in sensitivity and specificity. Using sciCNV, we demonstrate that scRNA-seq can be used to examine the cellular effects of cancer CNVs. As an example, sciCNV is used to identify subclonal multiple myeloma (MM) cells with +8q22–24. Studies of the gene expression of intra-clonal MM cells with and without the CNV demonstrate that +8q22–24 upregulates MYC and MYC-target genes, messenger RNA processing and protein synthesis, which is consistent with established models. In conclusion, we provide new tools for scRNA-seq that enable paired profiling of the CNVs and transcriptomes of single cells, facilitating rapid and accurate deconstruction of the effects of cancer CNVs on cellular programming.
BioDynaMo: a modular platform for high-performance agent-based simulation
Authors: Breitwieser Lukas , Hesam Ahmad , de Montigny Jean , Vavourakis Vasileios , Iosif Alexandros , Jennings Jack , Kaiser Marcus , Manca Marco , Di Meglio Alberto , Al-Ars Zaid , Rademakers Fons , Mutlu Onur , Bauer Roman 
Published: September 2021

Abstract

Motivation
Agent-based modeling is an indispensable tool for studying complex biological systems. However, existing simulation platforms do not always take full advantage of modern hardware and often have a field-specific software design.

Results
We present a novel simulation platform called BioDynaMo that alleviates both of these problems. BioDynaMo features a modular and high-performance simulation engine. We demonstrate that BioDynaMo can be used to simulate use cases in: neuroscience, oncology and epidemiology. For each use case, we validate our findings with experimental data or an analytical solution. Our performance results show that BioDynaMo performs up to three orders of magnitude faster than the state-of-the-art baselines. This improvement makes it feasible to simulate each use case with one billion agents on a single server, showcasing the potential BioDynaMo has for computational biology research.

Availability and implementation
BioDynaMo is an open-source project under the Apache 2.0 license and is available at www.biodynamo.org. Instructions to reproduce the results are available in the supplementary information.

Supplementary information
Available at https://doi.org/10.5281/zenodo.5121618.
SGI: automatic clinical subgroup identification in omics datasets
Authors: Buyukozkan Mustafa , Suhre Karsten , Krumsiek Jan 
Published: September 2021

Abstract

Summary
The ‘Subgroup Identification’ (SGI) toolbox provides an algorithm to automatically detect clinical subgroups of samples in large-scale omics datasets. It is based on hierarchical clustering trees in combination with a specifically designed association testing and visualization framework that can process an arbitrary number of clinical parameters and outcomes in a systematic fashion. A multi-block extension allows for the simultaneous use of multiple omics datasets on the same samples. In this article, we first describe the functionality of the toolbox and then demonstrate its capabilities through application examples on a type 2 diabetes metabolomics study as well as two copy number variation datasets from The Cancer Genome Atlas.

Availability and implementation
SGI is an open-source package implemented in R. Package source codes and hands-on tutorials are available at https://github.com/krumsieklab/sgi. The QMdiab metabolomics data is included in the package and can be downloaded from https://doi.org/10.6084/m9.figshare.5904022.

Supplementary information
Supplementary data are available at Bioinformatics online.
Uterine cellular changes during mammalian pregnancy and the evolution of placentation
Authors: Dudley Jessica S , Murphy Christopher R , Thompson Michael B , McAllan Bronwyn M 
Published: September 2021

AbstractThere are many different forms of nutrient provision in viviparous (live-bearing) species. The formation of a placenta is one method where the placenta functions to transfer nutrients from mother to fetus (placentotrophy), to transfer waste from the fetus to the mother, and to perform respiratory gas exchange. Despite having the same overarching function, there are different types of placentation within placentotrophic vertebrates, and many morphological changes occur in the uterus during pregnancy to facilitate formation of the placenta. These changes are regulated in complex ways but are controlled by similar hormonal mechanisms across species. This review describes current knowledge of the morphological and molecular changes to the uterine epithelium preceding implantation among mammals. Our aim is to identify the commonalities and constraints of these cellular changes to understand the evolution of placentation in mammals and to propose directions for future research. We compare and discuss the complex modifications to the ultrastructure of uterine epithelial cells (UEC) and show that there are similarities in the changes to the cytoskeleton and gross morphology of the UEC, especially of the apical and lateral plasma membrane of the cells during the formation of a placenta in all eutherians and marsupials studied to date. We conclude that further research is needed to understand the evolution of placentation among viviparous mammals, particularly concerning the level of placental invasiveness, hormonal control, and genetic underpinnings of pregnancy in marsupial taxa.
Shareholder Voting and COVID-19: The China Experience
Authors: Xi Chao 
Published: September 2021

Abstract
Using state-of-the-art data-mining techniques, this research constructs a unique dataset comprising the votes cast by Chinese shareholders on 15,553 resolutions laid before 2,888 general meetings of Shanghai Stock Exchange-listed companies in the six-year period between 2015 and 2020. This research empirically depicts, for the first time, the manner in which minority shareholders exercise their rights to vote in China, presenting a counter-thesis to the conventional wisdom of shareholder passivity. In particular, this research offers a unique perspective on how the COVID-19 pandemic has influenced Chinese shareholders’ voting behaviour by focusing its empirical investigation on the 76-day time window from 23 January to 7 April 2020, during which period Wuhan, the epicentre of the COVID-19 outbreak in China, came under a mandatory lockdown order. Our findings offer strong empirical evidence that Chinese shareholders cast their votes in a characteristically more informed manner in the 2020 sample period than they did during the sample periods in the previous five years. The research highlights the potential of shareholder activism in economies where share ownership is concentrated. It also has implications for the ongoing discourse on virtual shareholder meetings and the shareholder franchise.