bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of trends and location of organic crop production in European countries
Authors: Zaruk N F , Kagirova M V , Kharitonova A E , Romantseva Yu N , Kolomeeva E S 
Published: July 2023

Abstract
The article is devoted to the study of the features of the development and location of organic crop production in Europe. The authors considered the dynamics of the main indicators characterizing the size of organic land use in general for a set of countries, the scale of production in terms of the main resource; a comparative analysis was carried out by countries. The location of the organic crop production in general, as well as by groups of crops, was assessed, a relationship was found with the location of traditional agricultural production. 34 countries of Europe were chosen as the object of study. The main methods that made it possible to identify trends in organic production and location features were analytical alignment of the time series by the least squares method, statistical groupings, calculation and analysis of structural series, rank correlation; a graphical method of presenting the results of the study was also used. The results obtained by the authors are used to develop a methodology for determining the optimal distribution of crop production across territories, taking into account the existing specialization of traditional agriculture within countries with a large extent and at the international level.
Study of the problems and consequences of the use of reclamation fund lands of the forest-steppe of the Chelyabinsk region, allocated as unowned
Authors: Sinyavskiy I V , Sinyavkaya T A 
Published: July 2023

Abstract
The purpose of the conducted research was to identify unowned land plots of the reclamation fund of the forest-steppe of the Chelyabinsk region that are currently not used for crop production, to determine the main reasons for their long-fallow condition, to develop measures to facilitate their involvement in agricultural turnover. To achieve this goal, objects were identified in the field routes, their ecological condition was assessed based on the obtained agrochemical parameters. Methods and techniques defined by the state standards of the Russian Federation were used during laboratory studies. For the first time, a comprehensive indicator was used to assess the unowned territories of the reclamation fund, which makes it possible to assess in detail the ecological state and potential fertility of the soil, the soil-ecological index (PEI), with reference to the conditions of the evolution of the soils of the Southern Urals, the level of effective fertility was estimated by basic agrochemical parameters through the expected yield of spring wheat as a diagnostic crop. The ecological and production potentials of unowned lands of the reclamation fund have been determined, 4 categories have been identified, all surveyed plots belong to categories 1, 2, and 3, which indicates their high production potential and the possibility of their effective use with minor adjustments of a number of parameters by agrotechnical techniques. Proposals have been developed for their further effective use, including technological techniques and organizational and economic measures contributing to soil formation with high ecological and production potential.
Devices for monitoring the humidity of agricultural products
Authors: Kalandarov P I , Ikramov G I , Mukimov Z M 
Published: July 2023

Abstract
This article deals with the problem of studying methods for automatic measurement of electrophysical characteristics of granular materials in the process of technological control using the dielcometric method, based on the interaction of the electric field of the primary transducer with matter. The principle of operation of the information-measuring system is analyzed, the functional scheme of the dielcometric system ispresented with a linear switching of channels, as well as improving the accuracy of measurement by eliminating technical errors, simplifying the measuring scheme and increasing the reliability of the functioning of the entire device.
Intelligent forecasting of growth and development of fruit trees by deep learning recurrent neural networks
Authors: Kabildjanov A S , Okhunboboeva Ch Z , Yo Ismailov S 
Published: July 2023

Abstract
The questions of intellectual forecasting of dynamic processes of growth and development of fruit trees are considered. The average growth rate of shoots of apple trees of the «Renet Simirenko» variety was predicted. Forecasting was carried out using a deep learning recurrent neural network LSTM in relation to a one-dimensional time series, with which the specified parameter was described. The implementation of the recurrent neural network LSTM was carried out in the MATLAB 2021 environment. When defining the architecture and training of the LSTM recurrent neural network, the Deep Network Designer application was used, which is included in the MATLAB 2021 extensions and allows you to create, visualize, edit and train deep learning networks. The recurrent neural network LSTM was trained using the Adam method. The results obtained in the course of predicting the average growth rate of apple shoots using a trained LSTM recurrent neural network were evaluated by the root-mean-square error RMSE and the loss function LOSS.
Production of organic onion products during forcing for green onion in a protected ground
Authors: Yu Vaulin A 
Published: July 2023

Abstract
The article presents the experiment data on growing organic products of green onion in protected ground on various substrates. They prove that onion forcing on the variant with humus provides a significant increase in yield from 23 to 97% compared to other variants of the experiment. Also, this option provided a significant 10 to 25% increase in the green onion yield from the weight of onions planted for forcing, and in addition, it also accelerated the time for receiving finished products from 7 to 12 days. Such indicators allowed the option with humus not only to get a larger amount of high-quality biologically complete green onion products, but also to do it with incomparably higher economic indicators than other options.
The microplastics pollution in agricultural soils global trends and prospects research: bibliometric analysis
Authors: Nosova A O , Uspenskaya M V 
Published: July 2023

Abstract
Microplastics are a relatively new environmental problem with many blind spots. There is more and more evidence that the contamination of agricultural soils with this pollutant can lead to negative consequences for soil properties, microflora and the soil animals and plants vital activity. Bibliometrics can help to understand global research trends and academic collaboration networks. In this article, a bibliometric analysis of the topic of microplastics pollution in agricultural soils was carried out, the publication activity dynamics was determined, and a map of cooperation between the most active countries was built. A bibliographic map was created, which made it possible to identify six main thematic areas of research. This study can be used in planning and conducting research in Russia.
Biodegradable food packaging as a criterion for ensuring food safety
Authors: Minina N N , Sinelnikova O V 
Published: July 2023

Abstract
Product packaging is important today as protection and as attracting attention to the product. However, packaging should, first of all, protect products from the negative effects of the environment and prevent rapid deterioration of products. The composition and types of packaging material are regulated in all countries. Most of the food packaging is made of various types of plastic, because it has many positive properties that characterize the packaging, but the degradation period of plastic packaging is about 200 years. Plastic waste breaks down into the smallest particles and is included in the food chain, causing great harm to every link, including humans. The most promising direction today is the synthesis of biodegradable polymers. Of particular interest is the creation of biodegradable multifunctional packaging materials based on biopolymers that contain antimicrobial compounds and antioxidants. This type of packaging is a multilayer film consisting of a base (matrix) and various fillers. The matrix usually includes hydrocolloids (polysaccharides and proteins), lipids or some combined materials. The most promising direction in the manufacture of biodegradable packaging is the creation of polymer nanocomposites, the matrix of which is based on polysaccharides, and the additions are combined nanofibers, which can be represented by gelatin or cellulose, and a filler represented by inorganic nanoparticles (metal oxides). Such packages significantly increase the shelf life of food products, and accordingly make products safer and of higher quality. However, such materials require further study, because their effect on the human body is unknown. In the last decade, biodegradable packages have been developed that increase the shelf life of products with temperature fluctuations, reduce the number of microorganisms and, accordingly, extend the shelf life of products. Scientists have developed methods for obtaining biodegradable packages from protein hydrolysates of keratin-containing raw materials and waste from sugar beet factories. This direction in the production of biodegradable packages is the most promising, because firstly, production waste is disposed of, secondly, food packaging is produced that does not harm human health and extends the shelf life of products, thirdly, such packaging has a short degradation period, does not harm natural ecosystems and is safely included in food chains.
Micro-morphological adaptations and tolerance assessment of selected vascular plant species exposed to vehicular exhausts
Authors: Shakeel Tufail , Hussain Manzoor , Shah Ghulam Mujtaba , Zeb Bibi Saima 
Published: July 2023

Abstract
The vehicular exhausts on roadsides negatively affect living organisms and disturb their environment. These negative impacts of vehicular exhausts on plants demand a scientific investigation of roadside plants in Abbottabad, Pakistan. So, this observational and experimental study was conducted to evaluate the effect of vehicular exhausts on morphology, epidermal structure and biochemical characteristics of leaves of plants near roadsides and compared with the non-polluted site. The quantitative morphological parameters: leaf area, length of petiole and vein-to-vein difference along with anatomical attributes such as stomata and epidermal cells were recorded. Compared to non-polluted areas, the chlorophyll content of plant leaves from polluted areas was higher. The results indicate that vehicular exhaust negatively affects leaf morphology and increases the Stomatal number at adaxial (front surface) of leaves. The air pollution tolerance index evaluated Melia azedarach and Salix angustifolia as tolerant tree species and Rumex dentatus, Amaranthus viridis and Sonchus hydrophilus as tolerant herbaceous species. In order to survive in polluted environments, this study demonstrated that plants go through adaptive processes.
Impact of drought and salt stress on galactinol and raffinose family oligosaccharides in common bean (Phaseolus vulgaris)
Authors: de Koning Ramon , Wils Gertjan E , Kiekens Raphaël , De Vuyst Luc , Angenon Geert 
Published: July 2023

Abstract
Due to climate change, farmers will face more extreme weather conditions and hence will need crops that are better adapted to these challenges. The raffinose family oligosaccharides (RFOs) could play a role in the tolerance of crops towards abiotic stress. To investigate this, we determined for the first time the importance of galactinol and RFOs in the roots and leaves of common bean under drought and salt stress conditions. Initially, the physiological characteristics of common bean under agronomically relevant abiotic stress conditions were investigated by measuring the growth rate, transpiration rate, chlorophyll concentration and membrane stability, allowing to establish relevant sampling points. Subsequently, the differential gene expression profiles of the galactinol and RFO biosynthetic genes and the amount of galactinol and RFO molecules were measured in the primary leaves and roots of Phaseolus vulgaris cv. CIAP7247F at these sampling points, using RT-qPCR and HPAEC-PAD, respectively. Under drought stress, the genes galactinol synthase 1, galactinol synthase 3 and stachyose synthase were significantly upregulated in the leaves and had a high transcript level in comparison with the other galactinol and RFO biosynthetic genes. This was in accordance with the significantly higher amount of galactinol and raffinose detected in the leaves. Under salt stress, raffinose was also present in a significantly higher quantity in the leaves. In the roots, transcript levels of the RFO biosynthetic genes were generally low and no galactinol, raffinose or stachyose could be detected. These results suggest that in the leaves, both galactinol and raffinose could play a role in the protection of common bean against abiotic stresses. Especially, the isoform galactinol synthase 3 could have a specific role during drought stress and forms an interesting candidate to improve the abiotic stress resistance of common bean or other plant species.
Tau-typing: a Nextflow pipeline for finding the best phylogenetic markers in the genome for molecular typing of microbial species
Authors: Seabolt Matthew H , Boddapati Arun K , Forstedt Joshua J , Konstantinidis Konstantinos T 
Published: July 2023

Abstract

Summary
Tau-typing is an integrated analysis pipeline for identifying genes or genomic segments whose phylogenetic resolving power most closely resembles the genome-wide resolving power of an input collection of genomes using the Kendall Tau rank correlation statistic. The pipeline is implemented in Nextflow and uses Docker and Singularity containers to ensure reliable scalability and reproducibility of results. This pipeline is particularly suitable for organisms for which whole-genome sequencing remains unaffordable or unscalable for routine applications, such as protozoan parasites which are not amenable to laboratory culture-based methods.

Availability and implementation
Tau-typing is freely available at https://github.com/hseabolt/tautyping. The pipeline is implemented in Nextflow with Singularity support.
A novel approach to T-cell receptor beta chain (TCRB) repertoire encoding using lossless string compression
Authors: Konstantinovsky Thomas , Yaari Gur 
Published: July 2023

Abstract

Motivation
T-cell receptor beta chain (TCRB) repertoires are crucial for understanding immune responses. However, their high diversity and complexity present significant challenges in representation and analysis. The main motivation of this study is to develop a unified and compact representation of a TCRB repertoire that can efficiently capture its inherent complexity and diversity and allow for direct inference.

Results
We introduce a novel approach to TCRB repertoire encoding and analysis, leveraging the Lempel-Ziv 76 algorithm. This approach allows us to create a graph-like model, identify-specific sequence features, and produce a new encoding approach for an individual’s repertoire. The proposed representation enables various applications, including generation probability inference, informative feature vector derivation, sequence generation, a new measure for diversity estimation, and a new sequence centrality measure. The approach was applied to four large-scale public TCRB sequencing datasets, demonstrating its potential for a wide range of applications in big biological sequencing data.

Availability and implementation
Python package for implementation is available https://github.com/MuteJester/LZGraphs.
‘Stab, chase me, mate with me, seduce me’: how widespread is traumatic insemination in Strepsiptera?
Authors: Jandausch Kenny , van de Kamp Thomas , Beutel Rolf G , Niehuis Oliver , Pohl Hans 
Published: July 2023

Abstract
Traumatic insemination refers to mating in which males pierce the female’s integument with his penis for insemination. Strepsiptera are often listed as an example for this mode of copulation. However, while traumatic insemination in Mengenillidae with free-living females is undisputed, its occurrence in Stylopidia with permanent endoparasitic females – 97% of the known species of Strepsiptera – has remained unclear. Rather, observations from a single study on Xenos vesparum (Xenidae) that questioned traumatic insemination in this species became generalized for Stylopidia. Here we show that integration of data from various imaging methods provides convincing evidence for traumatic insemination being phylogenetically widespread in Strepsiptera. Specifically, we provide the first evidence of injury wounds from traumatic insemination in species of Mengenillidae, Corioxenidae, Elenchidae, Halictophagidae and Xenidae. Using three-dimensional models of copulating pairs of Stylops ovinae (Stylopidae) and X. vesparum, we visualize the physical piercing of the female’s integument by the male’s penis. Finally, we show in species of Mengenillidae, Xenidae and Stylopidae that traumatic mating is associated with the injection of sperm in the female’s haemocoel. Our results significantly alter the understanding of the reproductive biology of Strepsiptera and imply that traumatic insemination has been the ancestral mode of copulation and retained in most, if not all, extant families.
Sex differences in innate and adaptive immunity impact fetal, placental, and maternal health
Authors: Baines Kelly J , West Rachel C 
Published: July 2023

Abstract
The differences between males and females begin shortly after birth, continue throughout prenatal development, and eventually extend into childhood and adult life. Male embryos and fetuses prioritize proliferation and growth, often at the expense of the fetoplacental energy reserves. This singular focus on growth over adaptability leaves male fetuses and neonates vulnerable to adverse outcomes during pregnancy and birth and can have lasting impacts throughout life. Beyond this prioritization of growth, male placentas and fetuses also respond to infection and inflammation differently than female counterparts. Pregnancies carrying female fetuses have a more regulatory immune response, whereas pregnancies carrying male fetuses have a stronger inflammatory response. These differences can be seen as early as the innate immune response with differences in cytokine and chemokine signaling. The sexual dimorphism in immunity then continues into the adaptive immune response with differences in T-cell biology and antibody production and transfer. As it appears that these sex-specific differences are amplified in pathologic pregnancies, it stands to reason that differences in the placental, fetal, and maternal immune responses in pregnancy contribute to increased male perinatal morbidity and mortality. In this review, we will describe the genetic and hormonal contributions to the sexual dimorphism of fetal and placental immunity. We will also discuss current research efforts to describe the sex-specific differences of the maternal–fetal interface and how it impacts fetal and maternal health.
Active surveillance of oesophageal cancer after response to neoadjuvant chemoradiotherapy: dysphagia is uncommon
Authors: Valkema Maria J , Spaander Manon C W , Boonstra Jurjen J , van Dieren Jolanda M , Hazen Wouter L , Erkelens G Willemien , Holster I Lisanne , van der Linden Andries , van der Linde Klaas , Oostenbrug Liekele E , Quispel Rutger , Schoon Erik J , Siersema Peter D , Doukas Michail , Eyck Ben M , van der Wilk Berend J , van der Sluis Pieter C , Wijnhoven Bas P L , Lagarde Sjoerd M , van Lanschot J Jan B 
Published: July 2023

Abstract

Background
Active surveillance is being investigated as an alternative to standard surgery after neoadjuvant chemoradiotherapy for oesophageal cancer. It is unknown whether dysphagia persists or develops when the oesophagus is preserved after neoadjuvant chemoradiotherapy. The aim of this study was to assess the prevalence and severity of dysphagia during active surveillance in patients with an ongoing response.

Methods
Patients who underwent active surveillance were identified from the Surgery As Needed for Oesophageal cancer (‘SANO’) trial. Patients without evidence of residual oesophageal cancer until at least 6 months after neoadjuvant chemoradiotherapy were included. Study endpoints were assessed at time points that patients were cancer-free and remained cancer-free for the next 4 months. Dysphagia scores were evaluated at 6, 9, 12, and 16 months after neoadjuvant chemoradiotherapy. Scores were based on the European Organisation for Research and Treatment of Cancer oesophago-gastric quality-of-life questionnaire 25 (EORTC QLQ-OG25) (range 0–100; no to severe dysphagia). The rate of patients with a (non-)traversable stenosis was determined based on all available endoscopy reports.

Results
In total, 131 patients were included, of whom 93 (71.0 per cent) had adenocarcinoma, 93 (71.0 per cent) had a cT3–4a tumour, and 33 (25.2 per cent) had a tumour circumference of greater than 75 per cent at endoscopy; 60.8 to 71.0 per cent of patients completed questionnaires per time point after neoadjuvant chemoradiotherapy. At all time points after neoadjuvant chemoradiotherapy, median dysphagia scores were 0 (interquartile range 0–0). Two patients (1.5 per cent) underwent an intervention for a stenosis: one underwent successful endoscopic dilatation; and the other patient required temporary tube feeding. Notably, these patients did not participate in questionnaires.

Conclusion
Dysphagia and clinically relevant stenosis are uncommon during active surveillance.
Visual experience-dependent development of ocular dominance columns in pigmented rats
Authors: Zhou Qiuying , Li Hangqi , Yao Songping , Takahata Toru 
Published: July 2023

Abstract
Despite previous agreement of the absence of cortical column structure in the rodent visual cortex, we have recently revealed a presence of ocular dominance columns (ODCs) in the primary visual cortex (V1) of adult Long-Evans rats. In this study, we deepened understanding of characteristics of rat ODCs. We found that this structure was conserved in Brown Norway rats, but not in albino rats; therefore, it could be a structure generally present in pigmented wild rats. Activity-dependent gene expression indicated that maturation of eye-dominant patches takes more than 2 weeks after eye-opening, and this process is visual experience dependent. Monocular deprivation during classical critical period strongly influenced size of ODCs, shifting ocular dominance from the deprived eye to the opened eye. On the other hand, transneuronal anterograde tracer showed a presence of eye-dominant patchy innervation from the ipsilateral V1 even before eye-opening, suggesting the presence of visual activity-independent genetic components of developing ODCs. Pigmented C57BL/6J mice also showed minor clusters of ocular dominance neurons. These results provide insights into how visual experience-dependent and experience-independent components both contribute to develop cortical columns during early postnatal stages, and indicate that rats and mice can be excellent models to study them.