The 50 most-cited articles in PeerJ, 2022

Animal vocalisations and natural soundscapes are fascinating objects of study, and contain valuable evidence about animal behaviours, populations and ecosystems. They are studied in bioacoustics and ecoacoustics, with signal processing and analysis an important component. Computational bioacoustics has accelerated in recent decades due to the growth of affordable digital sound recording devices, and to huge progress in informatics such as big data, signal processing and machine learning. Methods are inherited from the wider field of deep learning, including speech and image processing. However, the tasks, demands and data characteristics are often different from those addressed in speech or music analysis. There remain unsolved problems, and tasks for which evidence is surely present in many acoustic signals, but not yet realised. In this paper I perform a review of the state of the art in deep learning for computational bioacoustics, aiming to clarify key concepts and identify and analyse knowledge gaps. Based on this, I offer a subjective but principled roadmap for computational…

BACKGROUND: Markerless motion capture has the potential to perform movement analysis with reduced data collection and processing time compared to marker-based methods. This technology is now starting to be applied for clinical and rehabilitation applications and therefore it is crucial that users of these systems understand both their potential and limitations. This literature review aims to provide a comprehensive overview of the current state of markerless motion capture for both single camera and multi-camera systems. Additionally, this review explores how practical applications of markerless technology are being used in clinical and rehabilitation settings, and examines the future challenges and directions markerless research must explore to facilitate full integration of this technology within clinical biomechanics. METHODOLOGY: A scoping review is needed to examine this emerging broad body of literature and determine where gaps in knowledge exist, this is key to developing motion capture methods that are cost effective and practically relevant to clinicians, coaches and…

Background: The environmental pollution by microplastics is a global problem arising from the extensive production and use of plastics. Small particles of different plastics, measured less than 5 mm in diameter, are found in water, air, soil, and various living organisms around the globe. Humans constantly inhale and ingest these particles. The associated health risks raise major concerns and require dedicated evaluation. Objectives: In this review we systematize and summarize the effects of microplastics on the health of different animals. The article would be of interest to ecologists, experimental biologists, environmental physicians, and all those concerned with anthropogenic environmental changes. Methodology: We searched PubMed and Scopus from the period of 01/2010 to 09/2021 for peer-reviewed scientific publications focused on (1) environmental pollution with microplastics; (2) uptake of microplastics by humans; and (3) the impact of microplastics on animal health. Results: The number of published studies considering the effects of microplastic particles on aquatic organisms…

Principal Component Analysis (PCA) is one of the most broadly used statistical methods for the ordination and dimensionality-reduction of multivariate datasets across many scientific disciplines. Trivial PCs can be estimated from data sets without any correlational structure among the original variables, and traditional criteria for selecting non-trivial PC axes are difficult to implement, partially subjective or based on ad hoc thresholds. PCAtest is an R package that implements permutation-based statistical tests to evaluate the overall significance of a PCA, the significance of each PC axis, and of contributions of each observed variable to the significant axes. Based on simulation and empirical results, I encourage R users to routinely apply PCAtest to test the significance of their PCA before proceeding with the direct interpretation of PC axes and/or the utilization of PC scores in subsequent evolutionary and ecological analyses.

Abstract As generalized linear mixed-effects models (GLMMs) have become a widespread tool in ecology, the need to guide the use of such tools is increasingly important. One common guideline is that one needs at least five levels of a random effect. Having such few levels makes the estimation of the variance of random effects terms (such as ecological sites, individuals, or populations) difficult, but it need not muddy one’s ability to estimate fixed effects terms – which are often of primary interest in ecology. Here, I simulate ecological datasets and fit simple models and show that having too few random effects terms does not influence the parameter estimates or uncertainty around those estimates for fixed effects terms. Thus, it should be acceptable to use fewer levels of random effects if one is not interested in making inference about the random effects terms (i.e. they are ‘nuisance’ parameters used to group non-independent data). I also use simulations to assess the potential for pseudoreplication in (generalized) linear models (LMs), when random effects are explicitly…

Tissue regeneration after body injury has always been a complex problem to resolve for mammals. In adult mammals, the repair process after tissue injury is often accompanied by continuous and extensive fibrosis, which leads to scars. This process has been shown to severely hinder regeneration. Macrophages, as widely distributed innate immune cells, not only play an important role in various pathological processes, but also participate in the repair process before tissue regeneration and coordinate the regeneration process after repair. This review will discuss the various forms and indispensability of macrophages involved in repair and regeneration, and how macrophages play a role in the repair and regeneration of different tissues.

Background: Throughout biology, multiple sequence alignments (MSAs) form the basis of much investigation into biological features and relationships. These alignments are at the heart of many bioinformatics analyses. However, sequences in MSAs are often incomplete or very divergent, which can lead to poor alignment and large gaps. This slows down computation and can impact conclusions without being biologically relevant. Cleaning the alignment by removing common issues such as gaps, divergent sequences, large insertions and deletions and poorly aligned sequence ends can substantially improve analyses. Manual editing of MSAs is very widespread but is time-consuming and difficult to reproduce. Results: We present a comprehensive, user-friendly MSA trimming tool with multiple visualisation options. Our highly customisable command line tool aims to give intervention power to the user by offering various options, and outputs graphical representations of the alignment before and after processing to give the user a clear overview of what has been removed. The main functionalities of the…

Background: Poor mental health among university students remains a pressing public health issue. Over the past few years, digital health interventions have been developed and considered promising in increasing psychological wellbeing among university students. Therefore, this umbrella review aims to synthesize evidence on digital health interventions targeting university students and to evaluate their effectiveness. Methods: A systematic literature search was performed in April 2021 searching PubMed, Psychology and Behavioural Science Collection, Web of Science, ERIC, and Scopus for systematic reviews and meta-analyses on digital mental health interventions targeting university students. The review protocol was registered in the International Prospective Register of Systematic Reviews PROSPERO [CRD42021234773]. Results: The initital literature search resulted in 806 records of which seven remained after duplicates were removed and evaluated against the inclusion criteria. Effectiveness was reported and categorized into the following six delivery types: (a) web-based,…

Summary: Bulked segregant analysis implemented in MutMap and QTL-seq is a powerful and efficient method to identify loci contributing to important phenotypic traits. However, the previous pipelines were not user-friendly to install and run. Here, we describe new pipelines for MutMap and QTL-seq. These updated pipelines are approximately 5-8 times faster than the previous pipeline, are easier for novice users to use, and can be easily installed through bioconda with all dependencies. Availability: The new pipelines of MutMap and QTL-seq are written in Python and can be installed via bioconda. The source code and manuals are available online (MutMap: https://github.com/YuSugihara/MutMap, QTL-seq: https://github.com/YuSugihara/QTL-seq).

Several independent comparisons indicate regenerative farming practices enhance the nutritional profiles of crops and livestock. Measurements from paired farms across the United States indicate differences in soil health and crop nutrient density between fields worked with conventional (synthetically-fertilized and herbicide-treated) or regenerative practices for 5 to 10 years. Specifically, regenerative farms that combined no-till, cover crops, and diverse rotations-a system known as Conservation Agriculture-produced crops with higher soil organic matter levels, soil health scores, and levels of certain vitamins, minerals, and phytochemicals. In addition, crops from two regenerative no-till vegetable farms, one in California and the other in Connecticut, had higher levels of phytochemicals than values reported previously from New York supermarkets. Moreover, a comparison of wheat from adjacent regenerative and conventional no-till fields in northern Oregon found a higher density of mineral micronutrients in the regenerative crop. Finally, a comparison of the unsaturated fatty acid…

Allergic rhinitis (AR) is a common disorder of the upper airway, while asthma is a disease affecting the lower airway and both diseases are usually comorbid. Interleukin (IL)-4 and IL-13 are critical cytokines in the induction of the pathogenic Th2 responses in AR and asthma. Targeting the IL-4/IL-13 axis at various levels of its signaling pathway has emerged as promising targeted therapy in both AR and asthma patient populations. In this review, we discuss the biological characteristics of IL-4 and IL-13, their signaling pathways, and therapeutic antibodies against each cytokine as well as their receptors. In particular, the pleiotropic roles of IL-4 and IL-13 in orchestrating Th2 responses in AR and asthma patients indicate that dual IL-4/IL-13 blockade is a promising therapeutic strategy for both diseases.

RNA viruses encoding a polymerase gene (riboviruses) dominate the known eukaryotic virome. High-throughput sequencing is revealing a wealth of new riboviruses known only from sequence, precluding classification by traditional taxonomic methods. Sequence classification is often based on polymerase sequences, but standardised methods to support this approach are currently lacking. To address this need, we describe the polymerase palmprint, a segment of the palm sub-domain robustly delineated by well-conserved catalytic motifs. We present an algorithm, Palmscan, which identifies palmprints in nucleotide and amino acid sequences; PALMdb, a collection of palmprints derived from public sequence databases; and palmID, a public website implementing palmprint identification, search, and annotation. Together, these methods demonstrate a proof-of-concept workflow for high-throughput characterisation of RNA viruses, paving the path for the continued rapid growth in RNA virus discovery anticipated in the coming decade.

The roles of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) in improving nutrition uptake and soil quality have been well documented. However, few studies have explored their effects on root morphology and soil properties. In this study, we inoculated Elymus nutans Griseb with AMF and/or PGPR in order to explore their effects on plant growth, soil physicochemical properties, and soil enzyme activities. The results showed that AMF and/or PGPR inoculation significantly enhanced aboveground and belowground vegetation biomass. Both single and dual inoculations were beneficial for plant root length, surface area, root branches, stem diameter, height, and the ratio of shoot to root, but decreased root volume and root average diameter. Soil total nitrogen, alkaline phosphatase, and urease activities showed significant growth, and soil electrical conductivity and pH significantly declined under the inoculation treatments. Specific root length showed a negative correlation with belowground biomass, but a positive correlation with root length and root…

The content and the ratio of soluble sugars and organic acids in fruits are significant indicators for fruit quality. They are affected by multiple environmental factors, in which water-deficient is the most concern. Previous studies found that the content of soluble sugars and organic acids in fruit displayed great differences under varied water stress. It is important to clarify the mechanism of such difference and to provide researchers with systematic knowledge about the response to drought stress and the mechanism of sugar and acid changes in fruits, so that they can better carry out the study of fruit quality under drought stress. Therefore, the researchers studied dozens of research articles about the content of soluble sugar and organic acid, the activity of related metabolic enzymes, and the expression of related metabolic genes in fruits under water stress, and the stress response of plants to water stress. We found that after plants perceived and transmitted the signal of water deficit, the expression of genes related to the metabolism of soluble sugars and organic acids…

Improving the amount of organic carbon in soils is an attractive alternative to partially mitigate climate change. However, the amount of carbon that can be potentially added to the soil is still being debated, and there is a lack of information on additional storage potential on global cropland. Soil organic carbon (SOC) sequestration potential is region-specific and conditioned by climate and management but most global estimates use fixed accumulation rates or time frames. In this study, we model SOC storage potential as a function of climate, land cover and soil. We used 83,416 SOC observations from global databases and developed a quantile regression neural network to quantify the SOC variation within soils with similar environmental characteristics. This allows us to identify similar areas that present higher SOC with the difference representing an additional storage potential. We estimated that the topsoils (0-30 cm) of global croplands (1,410 million hectares) hold 83 Pg C. The additional SOC storage potential in the topsoil of global croplands ranges from 29 to 65 Pg C.…

Background: Single camera markerless motion capture has the potential to facilitate at home movement assessment due to the ease of setup, portability, and affordable cost of the technology. However, it is not clear what the current healthcare applications of single camera markerless motion capture are and what information is being collected that may be used to inform clinical decision making. This review aims to map the available literature to highlight potential use cases and identify the limitations of the technology for clinicians and researchers interested in the collection of movement data. Survey Methodology: Studies were collected up to 14 January 2022 using Pubmed, CINAHL and SPORTDiscus using a systematic search. Data recorded included the description of the markerless system, clinical outcome measures, and biomechanical data mapped to the International Classification of Functioning, Disability and Health Framework (ICF). Studies were grouped by patient population. Results: A total of 50 studies were included for data collection. Use cases for single camera markerless…

Background Progressive overload is a principle of resistance training exercise program design that typically relies on increasing load to increase neuromuscular demand to facilitate further adaptations. However, little attention has been given to another way of increasing demand—increasing the number of repetitions. Objective This study aimed to compare the effects of two resistance training programs: (1) increasing load while keeping repetition range constant vs (2) increasing repetitions while keeping load constant. We aimed to compare the effects of these programs on lower body muscle hypertrophy, muscle strength, and muscle endurance in resistance-trained individuals over an 8-week study period. Methods Forty-three participants with at least 1 year of consistent lower body resistance training experience were randomly assigned to one of two experimental, parallel groups: A group that aimed to increase load while keeping repetitions constant (LOAD: n = 22; 13 men, nine women) or a group that aimed to increase repetitions while keeping load constant (REPS: n = 21; 14 men, seven…

BACKGROUND: Ground reaction forces (GRFs) are important for understanding human movement, but their measurement is generally limited to a laboratory environment. Previous studies have used neural networks to predict GRF waveforms during running from wearable device data, but these predictions are limited to the stance phase of level-ground running. A method of predicting the normal (perpendicular to running surface) GRF waveform using wearable devices across a range of running speeds and slopes could allow researchers and clinicians to predict kinetic and kinematic variables outside the laboratory environment. PURPOSE: We sought to develop a recurrent neural network capable of predicting continuous normal (perpendicular to surface) GRFs across a range of running speeds and slopes from accelerometer data. METHODS: Nineteen subjects ran on a force-measuring treadmill at five slopes (0°, ±5°, ±10°) and three speeds (2.5, 3.33, 4.17 m/s) per slope with sacral- and shoe-mounted accelerometers. We then trained a recurrent neural network to predict normal GRF waveforms frame-by-frame. The…

Abstract Paper describes a data-driven framework based on spatio-temporal ensemble machine learning to produce distribution maps for 16 forest tree species (Abies alba Mill., Castanea sativa Mill. , Corylus avellana L., Fagus sylvatica L., Olea europaea L., Picea abies L. H. Karst., Pinus halepensis Mill., Pinus nigra J. F. Arnold, Pinus pinea L., Pinus sylvestris L., Prunus avium L., Quercus cerris L., Quercus ilex L., Quercus robur L., Quercus suber L. and Salix caprea L.) at high spatial resolution (30 m). Tree occurrence data for a total of 3 million of points was used to train different Machine Learning (ML) algorithms: random forest, gradient-boosted trees, generalized linear models, k-nearest neighbors, CART and an artificial neural network. A stack of 585 coarse and high resolution covariates representing spectral reflectance (Landsat bands, spectral indices; time-series of seasonal composites), different biophysical conditions (i.e. temperature, precipitation, elevation, lithology) and biotic competition (other species distribution maps) was used as predictors for realized…

Over the past decade, concerns over microplastic pollution in the marine ecosystem has increasingly gained more attention, but research investigating the ingestion of microplastics by marine fish in Malaysia is still regrettably lacking. This study investigated the microplastic presence, abundance, and morphological types within the guts of four species of commercial marine fish ( Atule mate, Crenimugil seheli, Sardinella fimbriata and Rastrelliger brachysoma ) caught in seawater off the coast of Malaysia’s Northwest Peninsular. A total of 72 individual commercial marine fish guts from four species (fish per species n = 18) were examined. Remarkably, this study found that 100% of the samples contained microplastics. A total number of 432 microplastics (size < 5 mm) from the four species were found in the excised marine fish guts. The most common type of microplastic discovered was fragment, which accounted for 49.5% of all microplastics present. The gut microplastic content differed between species. Sardinella fimbriata recorded the greatest amount of microplastic ingestion, with an…

Many decades of improvement in cacao have aided to obtain cultivars with characteristics of tolerance to diseases, adaptability to different edaphoclimatic conditions, and higher yields. In Ecuador, as a result of several breeding programs, the clone CCN 51 was obtained, which gradually expanded through the cacao-production regions of Ecuador, Colombia, Brazil and Peru. Recognized for its high yield and adaptability to different regions and environments, it has become one of the most popular clones for breeding programs and cultivation around the world. This review aims to summarize the current evidence on the origin, genetics, morphological, volatile compounds, and organoleptic characteristics of this clone. Physiological evidence, production dynamics, and floral biology are also included to explain the high yield of CCN 51. Thus, characteristics such as osmotic adjustment, long pollen longevity, and fruit formation are further discussed and associated with high production at the end of the dry period. Finally, the impact of this popular clone on the current and future cacao…

Fungal contamination of animal feed can severely affect the health of farm animals, and result in considerable economic losses. Certain filamentous fungi or molds produce toxic secondary metabolites known as mycotoxins, of which aflatoxins (AFTs) are considered the most critical dietary risk factor for both humans and animals. AFTs are ubiquitous in the environment, soil, and food crops, and aflatoxin B 1 (AFB 1 ) has been identified by the World Health Organization (WHO) as one of the most potent natural group 1A carcinogen. We reviewed the literature on the toxic effects of AFB 1 in humans and animals along with its toxicokinetic properties. The damage induced by AFB 1 in cells and tissues is mainly achieved through cell cycle arrest and inhibition of cell proliferation, and the induction of apoptosis, oxidative stress, endoplasmic reticulum (ER) stress and autophagy. In addition, numerous coding genes and non-coding RNAs have been identified that regulate AFB 1 toxicity. This review is a summary of the current research on the complexity of AFB 1 toxicity, and provides insights…

Food safety is a significant challenge worldwide, from plantation to cultivation, especially for perishable products such as tomatoes. New eco-friendly strategies are needed, and beneficial microorganisms might be a sustainable solution. This study demonstrates bacteria activity in the tomato plant rhizosphere. Further, it investigates the rhizobacteria’s structure, function, and diversity in soil. Rhizobacteria that promote the growth and development of tomato plants are referred to as plant growth-promoting bacteria (PGPR). They form a series of associations with plants and other organisms in the soil through a mutualistic relationship where both parties benefit from living together. It implies the antagonistic activities of the rhizobacteria to deter pathogens from invading tomato plants through their roots. Some PGPR are regarded as biological control agents that hinder the development of spoilage organisms and can act as an alternative for agricultural chemicals that may be detrimental to the health of humans, animals, and some of the beneficial microbes in the rhizosphere…

Mountains are highly diverse in areal extent, geological and climatic context, ecosystems and human activity. As such, mountain environments worldwide are particularly sensitive to the effects of anthropogenic climate change (global warming) as a result of their unique heat balance properties and the presence of climatically-sensitive snow, ice, permafrost and ecosystems. Consequently, mountain systems-in particular cryospheric ones-are currently undergoing unprecedented changes in the Anthropocene. This study identifies and discusses four of the major properties of mountains upon which anthropogenic climate change can impact, and indeed is already doing so. These properties are: the changing mountain cryosphere of glaciers and permafrost; mountain hazards and risk; mountain ecosystems and their services; and mountain communities and infrastructure. It is notable that changes in these different mountain properties do not follow a predictable trajectory of evolution in response to anthropogenic climate change. This demonstrates that different elements of mountain systems exhibit…

BACKGROUND: Rainfed agriculture plays key role in ensuring food security and maintain ecological balance. Especially in developing areas, most grain food are produced rainfed agricultural ecosystem. Therefore, the increase of crop yields in rainfed agricultural ecosystem becomes vital as well as ensuring global food security. METHODS: The potential roles of arbuscular mycorrhizal fungi (AMF) in improving crop yields under rainfed condition were explored based on 546 pairs of observations published from 1950 to 2021. RESULTS: AMF inoculation increased 23.0% crop yields based on 13 popular crops under rainfed condition. Not only was crop biomass of shoot and root increased 24.2% and 29.6% by AMF inocula, respectively but also seed number and pod/fruit number per plant were enhanced markedly. Further, the effect of AMF on crop yields depended on different crop groups. AMF improved more yield of N-fixing crops than non-N-fixing crops. The effect of AMF changed between grain and non-grain crops with the effect size of 0.216 and 0.352, respectively. AMF inoculation enhances stress…

Background: Hyperuricemia and gout are a group of disorders of purine metabolism. In recent years, the incidence of hyperuricemia and gout has been increasing, which is a severe threat to people's health. Several studies on hyperuricemia and gout in proteomics and metabolomics have been conducted recently. Some literature has identified biomarkers that distinguish asymptomatic hyperuricemia from acute gout or remission of gout. We summarize the physiological processes in which these biomarkers may be involved and their role in disease progression. Methodology: We used professional databases including PubMed, Web of Science to conduct the literature review. This review addresses the current landscape of hyperuricemia and gout biomarkers with a focus on proteomics and metabolomics. Results: Proteomic methods are used to identify differentially expressed proteins to find specific biomarkers. These findings may be suggestive for the diagnosis and treatment of hyperuricemia and gout to explore the disease pathogenesis. The identified biomarkers may be mediators of the link between…

(L.) Merrill] is a predominant edible plant and a major supply of plant protein worldwide. Global demand for soybean keeps increasing as its seeds provide essential proteins, oil, and nutraceuticals. In a quest to meet heightened demands for soybean, it has become essential to introduce agro-technical methods that promote adaptability to complex environments, improve soybean resistance to abiotic stress , and increase productivity. Plant growth regulators are mainly exploited to achieve this due to their crucial roles in plant growth and development. Increasing research suggests the influence of plant growth regulators on soybean growth and development, yield, quality, and abiotic stress responses. In an attempt to expatiate on the topic, current knowledge, and possible applications of plant growth regulators that improve growth and yield have been reviewed and discussed. Notably, the application of plant growth regulators in their appropriate concentrations at suitable growth periods relieves abiotic stress thereby increasing the yield and yield components of soybean. Moreover, the…

Background Cassava ( Manibot esculenta Crantz) is one of the most important among tuber crops. The amount of nitrogen fertilizer used for cassava production is relatively high (400 kg ha −1 ), but there are few studies on biological nitrogen fixation in this crop. Therefore, it is particularly important to study whether cassava and microorganisms have the associated nitrogen-fixing and other promoting effects of endophytic bacteria. Methods We screened 10 endophytic bacteria using the nitrogen-free culture method from the roots of seven cassava cultivars, and the nitrogenase activity of the A02 strain was the highest 95.81 nmol mL −1 h −1 . The A02 strain was confirmed as Microbacteriaceae, Curtobacterium using 16S rRNA sequence alignment. The biological and morphological characteristics of strain A02 were further analyzed. Results The experimental results showed that the biomass of roots, stems, and leaves of cassava inoculated with A02 increased by 17.6%, 12.6%, and 10.3%, respectively, compared to that of the control (without A02 inoculation). These results were not only related…

The physiological demands of soccer challenge the entire spectrum of the response capacity of the biological systems and fitness requirements of the players. In this review we examined variations and evolutionary trends in body composition, neuromuscular and endurance-related parameters, as well as in game-related physical parameters of professional players. Further, we explore aspects relevant for training monitoring and we reference how different training stimulus and situational variables ( e.g ., competition exposure) affect the physiological and performance parameters of players. Generally, improvements of small magnitude in non- (non-CMJ) and countermovement-based jumps (CMJ Based ) and in the sprint acceleration (ACC Phase ) and maximal velocity phase (MV Phase ) are observed from start of preparation phase (PPS) to beginning of competition phase (BCP). A greater magnitude of increases is observed in physiological and endurance performance measures within this period; moderate magnitude in sub-maximal intensity exercise (velocity at fixed blood lactate concentrations; V…

Background Positional data have been used to capture physical and tactical factors in football, however current research is now looking to apply spatiotemporal parameters from an integrative perspective. Thus, the aim of this article was to systematically review the published articles that integrate physical and tactical variables in football using positional data. Methods and Materials Following the Preferred Reporting Item for Systematic Reviews and Meta-analyses (PRISMA), a systematic search of relevant English-language articles was performed from earliest record to August 2021. The methodological quality of the studies was evaluated using the modified Downs and Black Quality Index (observational and cross-sectional studies) and the Physiotherapy Evidence Database (PEDro) scale (intervention studies). Results The literature search returned 982 articles (WoS = 495; PubMed = 232 and SportDiscus = 255). After screening, 26 full-text articles met the inclusion criteria and data extraction was conducted. All studies considered the integration of physical and tactical variables in…

Ferroptosis is a mode of cell death that occurs in myocardial infarction (MI). Signals emanating from apoptotic cells are able to induce macrophage polarization through exosome-loading cargos, which plays a vital role in the process of disease. However, whether ferroptotic cardiomyocytes derived exosome (MI-Exo) during MI act on macrophage polarization and its mechanism remain unclear. In this study, a MI mouse model was established, and cardiac function evaluation and pathological staining were performed. The effect of MI-Exo on polarization of RAW264.7 cells was assessed by the expression of IL-10 and NOS2. Ferroptosis inhibitor of ferrostatin-1 was used to verify whether MI-Exo function was dependents on ferroptosis. Cardiac function and myocardial histomorphology were markedly impaired and massive immune cell infiltration in MI mice, compared with the sham group. The significantly increased MDA content and Fe 2+ accumulation in the heart tissue of MI mice suggested cardiomyocyte ferroptosis. Compared with the sham group, the expression of M1 marker NOS2 was significantly…

Roots assist plants in absorbing water and nutrients from soil. Thus, they are vital to the survival of nearly all land plants, considering that plants cannot move to seek optimal environmental conditions. Crop species with optimal root system are essential for future food security and key to improving agricultural productivity and sustainability. Root systems can be improved and bred to acquire soil resources efficiently and effectively. This can also reduce adverse environmental impacts by decreasing the need for fertilization and fresh water. Therefore, there is a need to improve and breed crop cultivars with favorable root system. However, the lack of high-throughput root phenotyping tools for characterizing root traits in situ is a barrier to breeding for root system improvement. In recent years, many breakthroughs in the measurement and analysis of roots in a root system have been made. Here, we describe the major advances in root image acquisition and analysis technologies and summarize the advantages and disadvantages of each method. Furthermore, we look forward to the…

The tremendous boost in next generation sequencing and in the "omics" technologies makes it possible to characterize the human gut microbiome-the collective genomes of the microbial community that reside in our gastrointestinal tract. Although some of these microorganisms are considered to be essential regulators of our immune system, the alteration of the complexity and eubiotic state of microbiota might promote autoimmune and inflammatory disorders such as diabetes, rheumatoid arthritis, Inflammatory bowel diseases (IBD), obesity, and carcinogenesis. IBD, comprising Crohn's disease and ulcerative colitis, is a gut-related, multifactorial disease with an unknown etiology. IBD presents defects in the detection and control of the gut microbiota, associated with unbalanced immune reactions, genetic mutations that confer susceptibility to the disease, and complex environmental conditions such as westernized lifestyle. Although some existing studies attempt to unveil the composition and functional capacity of the gut microbiome in relation to IBD diseases, a comprehensive picture of the…

Background: Sleep quality plays a principal role in the protection of health. There is an increasing number of studies in the literature demonstrating that internet addiction and smartphone addiction impair sleep quality. However, the number of studies on Turkish adolescents is very limited. Therefore, this study examined the effects of internet addiction and smartphone addiction on sleep quality among Turkish adolescents. Methods: Participants in this cross-sectional study were 910 adolescents aged 13–18 years. Data were collected with the Short Internet Addiction Test, Smartphone Addiction Scale, and Pittsburgh Sleep Quality Index. In addition, a questionnaire was used to gather information about the demographic, socioeconomic, and health-related characteristics. Pearson’s Chi-square test, Chi-square test for trend, Mann–Whitney U test, logistic regression analysis, and Spearman’s correlation analysis were used in the analysis. Results: The sleep quality of 58.7% of the adolescents was poor. Additionally, girls and adolescents ≥16 years old had poor sleep quality. Sleep quality…

A spatiotemporal machine learning framework for automated prediction and analysis of long-term Land Use/Land Cover dynamics is presented. The framework includes: (1) harmonization and preprocessing of spatial and spatiotemporal input datasets (GLAD Landsat, NPP/VIIRS) including five million harmonized LUCAS and CORINE Land Cover-derived training samples, (2) model building based on spatial k-fold cross-validation and hyper-parameter optimization, (3) prediction of the most probable class, class probabilities and model variance of predicted probabilities per pixel, (4) LULC change analysis on time-series of produced maps. The spatiotemporal ensemble model consists of a random forest, gradient boosted tree classifier, and an artificial neural network, with a logistic regressor as meta-learner. The results show that the most important variables for mapping LULC in Europe are: seasonal aggregates of Landsat green and near-infrared bands, multiple Landsat-derived spectral indices, long-term surface water probability, and elevation. Spatial cross-validation of the model indicates…

Background The presence of plastic particles in freshwater species is becoming a global concern owing to the potential impact on food security and human health. In this study, we investigated the presence microplastics (MPs) in two economically important freshwater species: the giant freshwater prawn ( Macrobrachium rosenbergii ) and the white leg shrimp ( Litopenaeus vannamei ) cultured in a polyculture pond in the central part of Thailand. Methods The gastrointestinal tract (GT) of 300 giant freshwater prawn (160 female and 140 male) and 150 white leg shrimp specimens were investigated for the presence of MPs. Results From the pooled samples, a total of 1,166 MP items were identified. Specifically, the GTs of female and male freshwater prawns and white leg shrimps contained an average of 33.31 ± 19.42, 33.43 ± 19.07, and 11.00 ± 4.60 MP items per individual, respectively. Further, their mean MP contents per g of gut material were 32.66 ± 5.10, 32.14 ± 4.85, and 10.28 ± 1.19 MP items, respectively. In the GT of these species, MPs with sizes in the range 500–1000 µm, were…

ABSTRACT Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur–bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19 th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most detailed morphological assessment of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis , the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal…

Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison. However, much faster genome comparison tools have been appearing in the literature. In this study we tested the quality of different approaches for genome-based species delineation against ANI. To this end, we compared 1,189 Klebsiella genomes using measures calculated with Mash, Dashing, and DNA compositional signatures, all of which run in a fraction of the time required to obtain ANI. Receiver Operating Characteristic (ROC) curve analyses showed equal quality in species discrimination for ANI, Mash and Dashing, with Area Under the Curve (AUC) values above 0.99, followed by DNA signatures (AUC: 0.96). Accordingly, groups obtained at optimized cutoffs largely agree with species designation,…

Background Agricultural plastic mulches offer great benefits such as higher yields and lower pesticide use. Yet, plastic mulches may disintegrate over time and fragment into smaller debris. Such plastic debris is expected to remain in the field after removal of the plastic mulch and thus contributes to soil contamination with plastics. Method To investigate this, we collected soil samples at 0–10 cm and 10–40 cm depth from three fields covered with black mulch film for three consecutive years. Three fields without any reported plastic use served as control. Visual plastic debris > 1 cm (macroplastics) was collected from the soil surface. Mesoplastics between 2 mm and 1 cm were density separated from the sampled soil using saturated NaCl solution and analyzed by Fourier-transform infrared spectroscopy. Debris ≤ 2 mm (microplastics) was dispersed from 50 g soil using sodium hexametaphosphate solution followed by the aforementioned density separation. The separated polyethylene (PE), polypropylene (PP), and polystyrene (PS) were quantified via solvent-based pyrolysis–gas…

The rapid spread of the coronavirus since its first appearance in 2019 has taken the world by surprise, challenging the global economy, and putting pressure on healthcare systems across the world. The introduction of preventive vaccines only managed to slow the rising death rates worldwide, illuminating the pressing need for developing effective antiviral therapeutics. The traditional route of drug discovery has been known to require years which the world does not currently have. In silico approaches in drug design have shown promising results over the last decade, helping to decrease the required time for drug development. One of the vital non-structural proteins that are essential to viral replication and transcription is the SARS-CoV-2 main protease (Mpro). Herein, using a test set of recently identified COVID-19 inhibitors, a pharmacophore was developed to screen 20 million drug-like compounds obtained from a freely accessible Zinc database. The generated hits were ranked using a structure based virtual screening technique (SBVS), and the top hits were subjected to in-depth…

Background Transcutaneous auricular vagus nerve stimulation (taVNS) stimulating the auricular branch of the vagus nerve along a well-defined neuroanatomical pathway, has promising therapeutic efficacy. Potentially, taVNS can modulate autonomic responses. Specifically, taVNS can induce more consistent parasympathetic activation and may lead to increased heart rate variability (HRV). However, the effects of taVNS on HRV remain inconclusive. Here, we investigated changes in HRV due to brief alteration periods of parasympathetic-vagal cardiac activity produced by taVNS on the cymba as opposed to control administration via the helix. Materials and Methods We compared the effect of 10 min of active stimulation (i.e., cymba conchae) to sham stimulation (i.e., helix) on peripheral cardiovascular response, in 28 healthy young adults. HRV was estimated in the time domain and frequency domain during the overall stimulation. Results Although active-taVNS and sham-taVNS stimulation did not differ in subjective intensity ratings, the active stimulation of the cymba led to vagally mediated HRV…

Background The aim of this study was two-fold: (i) analyze the within-group physical fitness adaptations promoted by a detraining period (4 weeks) followed by an intervention period (4 weeks) using small-sided games (SSGs) or running-based high intensity interval training (HIIT); and (ii) analyze the between-group differences aiming to identify the effectiveness of each training intervention on the physical fitness of youth male soccer players. Methods This study followed a randomized parallel study design. Forty male soccer players (age: 16.4 ± 0.5 years old) were assessed three times: (i) baseline; (ii) after 4 weeks of detraining; and (iii) after a retraining period of 4 weeks. After returning from detraining, players were randomized to an SSG-based training intervention ( n = 20) or running-based HIIT ( n = 20). Interventions lasted 4 weeks, with a training frequency of three sessions per week. At all timepoints, players were assessed by: (i) anthropometry (height, body mass, fat mass (FM)), countermovement jump (CMJ), standing broad jump (SBJ), triple hop jump (THJ), linear…

Fritillaria wilt is a kind of soil-borne disease that causes a large reduction in the yield of Fritillaria ussuriensis . The diversity and structure of the soil microbial community are important factors affecting the health of Fritillaria ussuriensis . The analysis of the microbial community in the diseased and healthy soils provided a theoretical basis for revealing the pathological mechanism and prevention of Fritillaria wilt disease. In the present study, we sequenced the soil microorganisms from healthy (H), pathology (P) and blank (B) soil samples by Illumina MiSeq. Determined the soil physicochemical properties respectively, analyzed the soil microbial diversity and structure, and constructed single factor co-correlation networks among microbial genera. The results showed that Ascomycota (48.36%), Mortierellomycota (23.06%), Basidiomycota (19.00%), Proteobacteria (31.74%), and Acidobacteria (20.95%) were dominant in the soil. The diversity of healthy soil was significantly greater than that of diseased soil samples (P and B) ( P < 0.05). The populations of Fusarium and…

DNA barcoding is critical to conservation and biodiversity research, yet public reference databases are incomplete. Existing barcode databases are biased toward cytochrome oxidase subunit I (COI) and frequently lack associated voucher specimens or geospatial metadata, which can hinder reliable species assignments. The emergence of metabarcoding approaches such as environmental DNA (eDNA) has necessitated multiple marker techniques combined with barcode reference databases backed by voucher specimens. Reference barcodes have traditionally been generated by Sanger sequencing, however sequencing multiple markers is costly for large numbers of specimens, requires multiple separate PCR reactions, and limits resulting sequences to targeted regions. High-throughput sequencing techniques such as genome skimming enable assembly of complete mitogenomes, which contain the most commonly used barcoding loci ( e.g., COI, 12S, 16S), as well as nuclear ribosomal repeat regions ( e.g., ITS1&2, 18S). We evaluated the feasibility of genome skimming to generate barcode references databases for marine…

Background Health care workers (HCWs) involved in day-to-day care and other healthcare activities play a significant role in biomedical waste (BMW) management. The World Health Organization stated some of the causes for the failure of BMW management, namely, lack of awareness of the health hazards related to BMW and inadequate trained HCWs in BMW management. The present study assessed knowledge, attitude, and practice (KAP) towards BMW management among the HCWs in northern Saudi Arabia. Methodology The present study assessed KAP through a self-administered and validated questionnaire. Using a multistage probability sampling method, 384 HCWs from different healthcare facilities participated in this survey. We performed binomial logistic regression analysis to find association between KAP subscales and sociodemographic characteristics. Spearman’s correlation test was performed to find the strength and direction of correlation ( rho ) between KAP scores. Results Of the population studied, high knowledge, attitude, and practice scores were found in 47.1%, 65.1%, and 49.5% of the HCWs,…

Heavy metal resistant bacteria are of great importance because they play a crucial role in bioremediation. In the present study, 11 bacterial strains isolated from industrial waste were screened under different concentrations of cadmium (Cd) (100 µM and 200 µM). Among 11 strains, the Cd tolerant Bacillus cereus (S6D1–105) strain was selected for in vitro and in vivo studies. B. cereus was able to solubilize potassium, and phosphate as well as produce protease and siderophores during plate essays. Moreover, we observed the response of hydroponically grown rice plants, inoculated with B. cereus which was able to promote plant growth, by increasing plant biomass, chlorophyll contents, relative water content, different antioxidant enzymatic activity such as catalase, superoxide dismutase, ascorbate peroxidase, polyphenol oxidase and phenylalanine ammonia-lyase and reducing malondialdehyde content in both roots and leaves of rice plants under Cd stress. Our results showed that the B. cereus can be used as a biofertilizer which might be beneficial for rice cultivation in Cd contaminated…

Environmental DNA (eDNA) metabarcoding is a powerful tool that can enhance marine ecosystem/biodiversity monitoring programs. Here we outline five important steps managers and researchers should consider when developing eDNA monitoring program: (1) select genes and primers to target taxa; (2) assemble or develop comprehensive barcode reference databases; (3) apply rigorous site occupancy based decontamination pipelines; (4) conduct pilot studies to define spatial and temporal variance of eDNA; and (5) archive samples, extracts, and raw sequence data. We demonstrate the importance of each of these considerations using a case study of eDNA metabarcoding in the Ports of Los Angeles and Long Beach. eDNA metabarcoding approaches detected 94.1% (16/17) of species observed in paired trawl surveys while identifying an additional 55 native fishes, providing more comprehensive biodiversity inventories. Rigorous benchmarking of eDNA metabarcoding results improved ecological interpretation and confidence in species detections while providing archived genetic resources for future analyses. Well…

The nitric oxide synthases (NOS; EC 1.14.13.39) use L-arginine as a substrate to produce nitric oxide (NO) as a by-product in the tissue microenvironment. NOS1 represents the predominant NO-producing enzyme highly enriched in the brain and known to mediate multiple functions, ranging from learning and memory development to maintaining synaptic plasticity and neuronal development, Alzheimer's disease (AD), psychiatric disorders and behavioral deficits. However, accumulating evidence indicate both canonical and non-canonical roles of NOS1-derived NO in several other tissues and chronic diseases. A better understanding of NOS1-derived NO signaling, and identification and characterization of NO-metabolites in non-neuronal tissues could become useful in diagnosis and prognosis of diseases associated with NOS1 expression. Continued investigation on the roles of NOS1, therefore, will synthesize new knowledge and aid in the discovery of small molecules which could be used to titrate the activities of NOS1-derived NO signaling and NO-metabolites. Here, we address the significance of NOS1 and…

Antimicrobial peptides (AMPs) are versatile molecules with broad antimicrobial activity produced by representatives of the three domains of life. Also, there are derivatives of AMPs and artificial short peptides that can inhibit microbial growth. Beyond killing microbes, AMPs at grow sub-inhibitory concentrations also exhibit anti-virulence activity against critical pathogenic bacteria, including ESKAPE pathogens. Anti-virulence therapies are an alternative to antibiotics since they do not directly affect viability and growth, and they are considered less likely to generate resistance. Bacterial biofilms significantly increase antibiotic resistance and are linked to establishing chronic infections. Various AMPs can kill biofilm cells and eradicate infections in animal models. However, some can inhibit biofilm formation and promote dispersal at sub-growth inhibitory concentrations. These examples are discussed here, along with those of peptides that inhibit the expression of traits controlled by quorum sensing, such as the production of exoproteases, phenazines, surfactants, toxins,…

KIAA1429 is a major m6A methyltransferase, which plays important biological and pharmacological roles in both human cancer or non-cancer diseases. KIAA1429 produce a tumorigenic role in various cancers through regulating DAPK3, ID2, GATA3, SMC1A, CDK1, SIRT1 and other targets, promoting cell proliferation, migration, invasion, metastasis and tumor growth . At the same time, KIAA1429 is also effective in non-tumor diseases, such as reproductive system and cardiovascular system diseases. The potential regulatory mechanism of KIAA1429 dependent on m6A modification is related to mRNA, lncRNA, circRNA and miRNAs. In this review, we summarized the current evidence on KIAA1429 in various human cancers or non-cancer diseases and its potential as a prognostic target.