bluuebunny/crossref_metadata_2025 huggingface dataset:
Beyond pathogens: the intriguing genetic legacy of endogenous retroviruses in host physiology
Authors: da Silva Amanda Lopes , Guedes Bruno Luiz Miranda , Santos Samuel Nascimento , Correa Giovanna Francisco , Nardy Ariane , Nali Luiz Henrique da Silva , Bachi Andre Luis Lacerda , Romano Camila Malta
Published: April 2024

The notion that viruses played a crucial role in the evolution of life is not a new concept. However, more recent insights suggest that this perception might be even more expansive, highlighting the ongoing impact of viruses on host evolution. Endogenous retroviruses (ERVs) are considered genomic remnants of ancient viral infections acquired throughout vertebrate evolution. Their exogenous counterparts once infected the host’s germline cells, eventually leading to the permanent endogenization of their respective proviruses. The success of ERV colonization is evident so that it constitutes 8% of the human genome. Emerging genomic studies indicate that endogenous retroviruses are not merely remnants of past infections but rather play a corollary role, despite not fully understood, in host genetic regulation. This review presents some evidence supporting the crucial role of endogenous retroviruses in regulating host genetics. We explore the involvement of human ERVs (HERVs) in key physiological processes, from their precise and orchestrated activities during cellular differentiation and pluripotency to their contributions to aging and cellular senescence. Additionally, we discuss the costs associated with hosting a substantial amount of preserved viral genetic material.
Spatial downscaling analysis of GPM IMERG precipitation dataset based on multiscale geographically weighted regression model: a case study of the Inner Mongolia Reach of the Yellow River basin
Authors: Tu Lihui , Duan Limin
Published: April 2024

The Inner Mongolia Reach of the Yellow River Basin is characterized by a relative scarcity of meteorological stations. While satellite precipitation products can complement observations from meteorological stations, their limited spatial resolution restricts their efficacy in regional studies. This study utilizes the GPM IMERG precipitation dataset, considering various factors that influence the spatial distribution of precipitation, such as the Normalized Difference Vegetation Index (NDVI), elevation, slope, aspect, and topographical relief, to construct a multiscale geographically weighted regression (MGWR) model. A spatial downscaling method for the GPM IMERG precipitation dataset is proposed, and its reliability is validated through an accuracy assessment. Moreover, the scale differences in the impact of different factors on the spatial pattern of precipitation in the Inner Mongolia Reach of the Yellow River Basin are scrutinized. The results indicate that: 1) The downscaled GPM IMERG precipitation data (1 km × 1 km) exhibit enhanced accuracy compared to the pre-downscaled data (approximately 11 km × 11 km). The correlation coefficient, Bias, and RMSE of the annual precipitation data after downscaling of GPM IMERG are 0.865, 6.05%, and 68.50 mm/year, respectively. For the monthly downscaled precipitation data, the correlation coefficient, Bias, and RMSE are 0.895, 6.09%, and 16.25 mm/month, respectively. The downscaled GPM IMERG precipitation dataset exhibit high accuracy on both annual and monthly temporal scales. 2) Different factors demonstrate localized effects on precipitation in both dry and wet years. Elevation is the dominant factor influencing the spatial heterogeneity of annual precipitation. The findings from this study can provide technical support for hydrological modeling, drought monitoring, and water resource management in data-scarce areas of the Inner Mongolia Reach of the Yellow River Basin.
Genetic infrapopulation sizes in blood parasites: a pilot quantification of the bottleneck in louse fly vectors
Authors: Fischer Kai , Chakarov Nayden
Published: April 2024

Introduction

Bottleneck events are crucial for the strength of genetic drift, selection and speed of evolution. They are believed to play a particularly prominent role for parasitic infrapopulations, inhabiting single host individuals, which are often established by very few parasite individuals during transmission. In vector-borne pathogens, the bottlenecking effects can even be serialized through repeated filtering of parasitic stages at different tissues and organs of the vector. Using qPCR we aimed to quantify the number of potentially transmittable sporozoites of the hemosporidian blood parasite Haemoproteus columbae in the specialized vector louse flies Pseudolynchia canariensis which transmit these parasites between house pigeon hosts Columba livia.

Results

Based on qPCR measurements of organ-derived DNA of individual louse flies, we estimate that the midgut of these vectors contains on average 20 parasites, the hindgut and other intestines ca. 50 parasites and the salivary glands ca. 5 parasite cells. Nearly one third of all vector individuals appeared to lack parasite DNA, despite having only infected hosts as blood meal sources. The magnitude of parasite numbers in midgut and salivary glands tended to correlate positively.

Discussion

Our results indicate, potential severe bottlenecking of parasite populations during individual transmission events and a probable effect of individual vector immunity on this variable. However, this may be partly alleviated by the coloniality of house pigeons, the frequency of louse flies and their daily feeding events in most populations, leading to repeated transmission opportunities, decreased quasi-vertical transmission between parents and offspring and probable panmixia of Haemoproteus columbae lineages. Many of these mechanisms might not apply in other host-vector systems. We propose several additional molecular and microscopical tools to improve the accuracy of estimating parasite population sizes in vectors and call for more estimations in different vector species to better understand the co-evolution between malaria-like blood parasites and their avian and insect hosts.
Exploring the mechanisms behind swimming performance limits to ocean warming and acidification in the Atlantic king scallop, Pecten maximus
Authors: Bock Christian , Götze Sandra , Pörtner Hans O. , Lannig Gisela
Published: April 2024

Recently, we could show that scallops show limitations of muscular performance like a reduced force under ocean warming and acidification. However, the underlying mechanisms at the cellular level are not completely understood. Metabolomics has become a valuable tool to evaluate the responses of marine organisms to various stressors. In the present study we therefore used a semi-targeted, multi tissue NMR based metabolomic approach to analyze metabolite patterns in the Atlantic king scallop, Pecten maximus, that were long-term acclimated to different end of century conditions of ocean warming (OW), ocean acidification (OA) and their combination (OWA). We investigated tissue specific metabolic profiles and metabolite concentrations in frozen tissues from gills, mantle and phasic and tonic adductor muscle of P. maximus under present conditions using 1H-HR-MAS NMR spectroscopy. A set of 33 metabolites revealed a clear tissue-specific pattern which can be attributed to the individual functions of the respective tissue type. We then evaluated the impact of OW, OA and OWA on the metabolic profiles of the different tissues. OW was the main driver of the changes in metabolites. In particular, energy-related metabolites seem to play an important role in the physiological response of scallops to OW and OWA. In combination with pathway analysis and network exploration we propose a possible correlation between metabolic changes in the adductor muscle and limited swimming performance of P. maximus under future climate. While the metabolic response of the phasic muscle seems to mainly depend on net consumption of energy related metabolites such as ATP and phospho-L-arginine, the tonic muscle seems to rely on metabolizing specific amino acids and beta-oxidation to account for the elevated energetic requirements under ocean warming and acidification.
The influence of the pollination compatibility type on the pistil S-RNase expression in European pear (Pyrus communis)
Authors: Claessen Hanne , Palmers Han , Keulemans Wannes , Van de Poel Bram , De Storme Nico
Published: April 2024

The S-RNase gene plays an essential role in the gametophytic self-incompatibility (GSI) system of Pyrus. It codes for the stylar-expressed S-RNase protein which inhibits the growth of incompatible pollen tubes through cytotoxicity and the induction of programmed cell death in the pollen tube. While research on the Pyrus GSI system has primarily focused on the S-RNase gene, there is still a lack of insight into its spatiotemporal expression profile and the factors that regulate it. Previous studies have suggested that S-RNase expression in the style is influenced by pollination and is dependent on the compatibility type. We here continue on this basic hypothesis by analyzing the spatiotemporal expression of the S-RNase alleles in Pyrus communis “Conference” styles in response to different types of pollination; namely, upon full- and semi-compatible pollination and upon incompatible selfing. The results revealed that temporal dynamics of S-RNase expression are influenced by the pollen’s compatibility type, indicating the presence of a signaling mechanism between pollen and style to control S-RNase production during pollen tube growth. In our experiment, S-RNase expression continuously decreased after cross-pollination and in the unpollinated control. However, after a fully incompatible pollination, S-RNase expression remained constant. Finally, semi-compatible pollination showed a initially constant S-RNase expression for both alleles followed by a strong decrease in expression. Based on these results and previous findings, we propose a regulatory mechanism to explain the effect of pollination and the associated compatibility type on S-RNase expression in the style. This proposed mechanism could be used as a starting point for future research.
Eco-fascism: an oxymoron? Far-right nationalism, history, and the climate emergency
Authors: Conversi Daniele
Published: April 2024

Can we conceive of a continuity in the way right-wing nationalisms address environmental issues from the origins of fascism to the currently ongoing global “polycrisis”? This article explores the use of the term “eco-fascism” in connection with the climate crisis and considers the political relationship between ecologism and the contemporary far right through a historical perspective, seeking to determine persisting patterns in the relationship between the far right and the environment. Section 1 travels back to the historical origins of this relationship between nationalism, fascism and the environment, arguing that the conceptions of nature adopted and nourished by fascism had scarcely anything to do with ecology in its contemporary meaning. Section 2 explores the most well-known and consolidated studies on the relationship between the far right and climate change denialism, identifying a broad consensus that unites scholars from various disciplines on the density, intensity and persistence of this political relationship in the current millennium. The article concludes by underlining the irreality, falsifiability and internal contradictions of the notion of “eco-fascism” at a time when right-wing regimes have seized power in many countries through the use of vocabularies and sentiments in defense of the territory and its resources, but with a substantial refusal to tackle global environmental problems.
Early dynamic changes to monocytes following major surgery are associated with subsequent infections
Authors: Snow Timothy Arthur Chandos , Waller Alessia V. , Loye Richard , Ryckaert Francis , Cesar Antonio , Saleem Naveed , Roy Rudra , Whittle John , Al-Hindawi Ahmed , Das Abhishek , Singer Mervyn , Brealey David , Arulkumaran Nishkantha ,   the University College London Hospitals Critical Care Research Team
Published: April 2024

Background

Post-operative infections are a common cause of morbidity following major surgery. Little is understood about how major surgery perturbs immune function leading to heightened risk of subsequent infection. Through analysis of paired blood samples obtained immediately before and 24 h following surgery, we evaluated changes in circulating immune cell phenotype and function across the first 24 h, to identify early immune changes associated with subsequent infection.

Methods

We conducted a prospective observational study of adult patients undergoing major elective gastrointestinal, gynecological, or maxillofacial surgery requiring planned admission to the post-anesthetic care unit. Patients were followed up to hospital discharge or death. Outcome data collected included mortality, length of stay, unplanned intensive care unit admission, and post-operative infections (using the standardized endpoints in perioperative medicine–core outcome measures for perioperative and anesthetic care criteria). Peripheral blood mononuclear cells were isolated prior to and 24 h following surgery from which cellular immune traits including activation and functional status were assessed by multi-parameter flow cytometry and serum immune analytes compared by enzyme-linked immunosorbent assay (ELISA).

Results

Forty-eight patients were recruited, 26 (54%) of whom developed a post-operative infection. We observed reduced baseline pre- and post-operative monocyte CXCR4 and CD80 expression (chemokine receptors and co-stimulation markers, respectively) in patients who subsequently developed an infection as well as a profound and selective post-operative increase in CD4+ lymphocyte IL-7 receptor expression in the infection group only. Higher post-operative monocyte count was significantly associated with the development of post-operative infection (false discovery rate < 1%; adjusted p-value = 0.001) with an area under the receiver operating characteristic curve of 0.84 (p < 0.0001).

Conclusion

Lower monocyte chemotaxis markers, higher post-operative circulating monocyte counts, and reduced co-stimulatory signals are associated with subsequent post-operative infections. Identifying the underlying mechanisms and therapeutics to reverse defects in immune cell function requires further exploration.
Extracellular vesicles in neuroblastoma: role in progression, resistance to therapy and diagnostics
Authors: Dhamdhere Mayura R. , Spiegelman Vladimir S.
Published: April 2024

Neuroblastoma (NB) is the most common extracranial solid pediatric cancer, and is one of the leading causes of cancer-related deaths in children. Despite the current multi-modal treatment regimens, majority of patients with advanced-stage NBs develop therapeutic resistance and relapse, leading to poor disease outcomes. There is a large body of knowledge on pathophysiological role of small extracellular vesicles (EVs) in progression and metastasis of multiple cancer types, however, the importance of EVs in NB was until recently not well understood. Studies emerging in the last few years have demonstrated the involvement of EVs in various aspects of NB pathogenesis. In this review we summarize these recent findings and advances on the role EVs play in NB progression, such as tumor growth, metastasis and therapeutic resistance, that could be helpful for future investigations in NB EV research. We also discuss different strategies for therapeutic targeting of NB-EVs as well as utilization of NB-EVs as potential biomarkers.
Global status and trends of gastric cancer and gastric microbiota research: a bibliometric analysis
Authors: Ke Yujia , Tan Cheng , Zhen Junhai , Dong Weiguo
Published: April 2024

Background

Numerous studies have cast light on the relationship between the gastric microbiota and gastric carcinogenesis. In this study, we conducted a bibliometric analysis of the relevant literature in the field of gastric cancer and the gastric microbiota and clarified its research status, hotspots, and development trends.

Materials and methods

Publications were retrieved from the Web of Science Core Collection on 18 July 2023. CiteSpace 6.2.R4, VOSviewer 1.6.19.0, and Biblioshiny were used for the co-occurrence and cooperation analyses of countries, institutions, authors, references, and keywords. A keyword cluster analysis and an emergence analysis were performed, and relevant knowledge maps were drawn.

Results

The number of published papers in this field totaled 215 and showed an increasing trend. The analysis of funding suggested that the input in this field is increasing steadily. China had the highest number of publications, while the United States had the highest betweenness centrality. Baylor College of Medicine published the most articles cumulatively. Both Ferreira RM and Cooker OO had the highest citation frequency. The journal Helicobacter showed the most interest in this field, while Gut provided a substantial research foundation. A total of 280 keywords were obtained using CiteSpace, which were primarily focused on the eradication and pathogenic mechanisms of Helicobacter pylori, as well as the application of the gastric microbiota in the evaluation and treatment of gastric cancer. The burst analysis suggested that in the future, research may focus on the application of gastric microorganisms, particularly Fusobacterium nucleatum, in the diagnosis and treatment of gastric cancer, along with their pathogenic mechanisms.

Conclusion

Current studies have been tracking the eradication of Helicobacter pylori and its pathogenic mechanisms, as well as changes in the gastric microbiota during gastric carcinogenesis. Future research may focus on the clinical application and pathogenesis of stomach microorganisms through bacteria such as Fusobacterium nucleatum.
Improving precision management of anxiety disorders: a Mendelian randomization study targeting specific gut microbiota and associated metabolites
Authors: Xu Ming-Min , Qiu Wen-Hui , Ma Qing-Yu , Yu Zhi-Yun , Yang Wen-Miao , Hu Tian-Nuo , Guo Yu , Chen Xiao-Yin
Published: April 2024

Background

There is growing evidence of associations between the gut microbiota and anxiety disorders, where changes in gut microbiotas may affect brain function and behavior via the microbiota-gut-brain axis. However, population-level studies offering a higher level of evidence for causality are lacking. Our aim was to investigate the specific gut microbiota and associated metabolites that are closely related to anxiety disorders to provide mechanistic insights and novel management perspectives for anxiety disorders.

Method

This study used summary-level data from publicly available Genome-Wide Association Studies (GWAS) for 119 bacterial genera and the phenotype “All anxiety disorders” to reveal the causal effects of gut microbiota on anxiety disorders and identify specific bacterial genera associated with anxiety disorders. A two-sample, bidirectional Mendelian randomization (MR) design was deployed, followed by comprehensive sensitivity analyses to validate the robustness of results. We further conducted multivariable MR (MVMR) analysis to investigate the potential impact of neurotransmitter-associated metabolites, bacteria-associated dietary patterns, drug use or alcohol consumption, and lifestyle factors such as smoking and physical activity on the observed associations.

Results

Bidirectional MR analysis identified three bacterial genera causally related to anxiety disorders: the genus Eubacterium nodatum group and genus Ruminococcaceae UCG011 were protective, while the genus Ruminococcaceae UCG011 was associated with an increased risk of anxiety disorders. Further MVMR suggested that a metabolite-dependent mechanism, primarily driven by tryptophan, tyrosine, phenylalanine, glycine and cortisol, which is consistent with previous research findings, probably played a significant role in mediating the effects of these bacterial genera to anxiety disorders. Furthermore, modifying dietary pattern such as salt, sugar and processed meat intake, and adjusting smoking state and physical activity levels, appears to be the effective approaches for targeting specific gut microbiota to manage anxiety disorders.

Conclusion

Our findings offer potential avenues for developing precise and effective management approaches for anxiety disorders by targeting specific gut microbiota and associated metabolites.
Multi-pathological contributions toward atrophy patterns in the Alzheimer’s disease continuum
Authors: Mohanty Rosaleena , Ferreira Daniel , Westman Eric
Published: April 2024

Introduction

Heterogeneity in downstream atrophy in Alzheimer’s disease (AD) is predominantly investigated in relation to pathological hallmarks (Aβ, tau) and co-pathologies (cerebrovascular burden) independently. However, the proportional contribution of each pathology in determining atrophy pattern remains unclear. We assessed heterogeneity in atrophy using two recently conceptualized dimensions: typicality (typical AD atrophy at the center and deviant atypical atrophy on either extreme including limbic predominant to hippocampal sparing patterns) and severity (overall neurodegeneration spanning minimal atrophy to diffuse typical AD atrophy) in relation to Aβ, tau, and cerebrovascular burden.

Methods

We included 149 Aβ + individuals on the AD continuum (cognitively normal, prodromal AD, AD dementia) and 163 Aβ− cognitively normal individuals from the ADNI. We modeled heterogeneity in MRI-based atrophy with continuous-scales of typicality (ratio of hippocampus to cortical volume) and severity (total gray matter volume). Partial correlation models investigated the association of typicality/severity with (a) Aβ (global Aβ PET centiloid), tau (global tau PET SUVR), cerebrovascular (total white matter hypointensity volume) burden (b) four cognitive domains (memory, executive function, language, visuospatial composites). Using multiple regression, we assessed the association of each pathological burden and typicality/severity with cognition.

Results

(a) In the AD continuum, typicality (r = −0.31, p < 0.001) and severity (r = −0.37, p < 0.001) were associated with tau burden after controlling for Aβ, cerebrovascular burden and age. Findings imply greater tau pathology in limbic predominant atrophy and diffuse atrophy. (b) Typicality was associated with memory (r = 0.49, p < 0.001) and language scores (r = 0.19, p = 0.02). Severity was associated with memory (r = 0.26, p < 0.001), executive function (r = 0.24, p = 0.003) and language scores (r = 0.29, p < 0.001). Findings imply better cognitive performance in hippocampal sparing and minimal atrophy patterns. Beyond typicality/severity, tau burden but not Aβ and cerebrovascular burden explained cognition.

Conclusion

In the AD continuum, atrophy-based severity was more strongly associated with tau burden than typicality after accounting for Aβ and cerebrovascular burden. Cognitive performance in memory, executive function and language domains was explained by typicality and/or severity and additionally tau pathology. Typicality and severity may differentially reflect burden arising from tau pathology but not Aβ or cerebrovascular pathologies which need to be accounted for when investigating AD heterogeneity.
Brain alterations in adolescents with first-episode depression who have experienced adverse events: evidence from resting-state functional magnetic resonance imaging
Authors: Xia Xiaodi , Tang Jinxiang , Peng Yadong , Liu Ying , Chen Yingying , Yuan Meng , Yu Renqiang , Hou Xiao , Fu Yixiao
Published: April 2024

Introduction

Adverse life events constitute primary risk factors for major depressive disorder (MDD), influencing brain function and structure. Adolescents, with their brains undergoing continuous development, are particularly susceptible to enduring impacts of adverse events.

Methods

We investigated differences and correlations among childhood trauma, negative life events, and alterations of brain function in adolescents with first-episode MDD. The study included 23 patients with MDD and 19 healthy controls, aged 10–19 years. All participants underwent resting-state functional magnetic resonance imaging and were assessed using the beck depression inventory, childhood trauma questionnaire, and adolescent self-rating life events checklist.

Results

Compared with healthy controls, participants with first-episode MDD were more likely to have experienced emotional abuse, physical neglect, interpersonal relationship problems, and learning stress (all p’ < 0.05). These adverse life events were significantly correlated with alterations in brain functions (all p < 0.05).

Discussion

This study contributes novel evidence on the underlying process between adverse life events, brain function, and depression, emphasizing the significant neurophysiological impact of environmental factors.
Cannabis use and mood disorders: a systematic review
Authors: Sorkhou Maryam , Dent Eliza L. , George Tony P.
Published: April 2024

Background

Problematic cannabis use is highly prevalent among people with mood disorders. This underscores the need to understand the effects of cannabis and cannabinoids in this population, especially considering legalization of recreational cannabis use.

Objectives

We aimed to (1) systematically evaluate cross-sectional and longitudinal studies investigating the interplay between cannabis use, cannabis use disorder (CUD), and the occurrence of mood disorders and symptoms, with a focus on major depressive disorder (MDD) and bipolar disorder (BD) and; (2) examine the effects of cannabis on the prognosis and treatment outcomes of MDD and BD.

Methods

Following PRISMA guidelines, we conducted an extensive search for English-language studies investigating the potential impact of cannabis on the development and prognosis of mood disorders published from inception through November 2023, using EMBASE, PsycINFO, PubMed, and MEDLINE databases.

Results

Our literature search identified 3,262 studies, with 78 meeting inclusion criteria. We found that cannabis use is associated with increased depressive and manic symptoms in the general population in addition to an elevated likelihood of developing MDD and BD. Furthermore, we observed that cannabis use is linked to an unfavorable prognosis in both MDD or BD.

Discussion

Our findings suggest that cannabis use may negatively influence the development, course, and prognosis of MDD and BD. Future well-designed studies, considering type, amount, and frequency of cannabis use while addressing confounding factors, are imperative for a comprehensive understanding of this relationship.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023481634.
A review of mathematical modeling of bone remodeling from a systems biology perspective
Authors: Cook Carley V. , Lighty Ariel M. , Smith Brenda J. , Ford Versypt Ashlee N.
Published: April 2024

Bone remodeling is an essential, delicately balanced physiological process of coordinated activity of bone cells that remove and deposit new bone tissue in the adult skeleton. Due to the complex nature of this process, many mathematical models of bone remodeling have been developed. Each of these models has unique features, but they have underlying patterns. In this review, the authors highlight the important aspects frequently found in mathematical models for bone remodeling and discuss how and why these aspects are included when considering the physiology of the bone basic multicellular unit, which is the term used for the collection of cells responsible for bone remodeling. The review also emphasizes the view of bone remodeling from a systems biology perspective. Understanding the systemic mechanisms involved in remodeling will help provide information on bone pathology associated with aging, endocrine disorders, cancers, and inflammatory conditions and enhance systems pharmacology. Furthermore, some features of the bone remodeling cycle and interactions with other organ systems that have not yet been modeled mathematically are discussed as promising future directions in the field.
A Novel DC Electroosmotic Micromixer Based on Helical Vortices
Authors: Saravanakumar Sri Manikandan , Jamshidi Seresht Mohsen , Izquierdo Ricardo , Cicek Paul-Vahe
Published: April 2024

This work introduces a novel direct current electroosmosis (DCEO) micromixer designed for rapid and efficient fluid mixing. This micromixer demonstrates excellent capability, achieving approximately 98.5% mixing efficiency within a one-second timespan and 99.8% efficiency within two seconds, all within a simple channel of only 1000 µm in length. A distinctive feature of this micromixer is its ability to generate robust and stable helical vortices by applying a controlled DC electric field. Unlike complex, intricate microfluidic designs, this work proposes a simple yet effective approach to fluid mixing, making it a versatile tool suitable for various applications. In addition, through simple modifications to the driving signal configuration and channel geometry, the mixing efficiency can be further enhanced to 99.3% in one second.
Effects of Pitch Stabilization Buffer on the Dynamic Performance of Frame-Type Landing Gear
Authors: Shi Xiazheng , Yu Anyuan , Nie Hong , Zhang Ming , Gui Xiwen , Yang Shaofei , Zheng Yuting , Liu Tianxing
Published: April 2024

During the landing and taxiing process of aircraft, the frame-type landing gear (FTLG) usually generates large pitch vibrations under external excitation. Excessive vibration increases localized loads on the landing gear, which may lead to localized failure of the structure. To minimize this undesirable vibration, a passive oil–pneumatic pitch-stabilizing buffer (PSB) is designed in this paper to provide pitch damping. This paper applies the basic principles of dynamics to establish a dynamic model of FTLG considering the influence of PSB. And based on the design of experiments (DOE) method, by changing the filling parameters and structural parameters of PSB, the results of the changes of the frame vibration angle, angular velocity, and landing gear load are obtained, so as to analyze the effects of different parameters on the dynamic performance of the landing gear in the landing and taxiing process. The results demonstrate that increasing the oil damping coefficient of PSB and decreasing the installation angle of PSB on the main strut during the landing period resulted in less frame vibration and lower wheelset load ratios, but increased the landing overloads of landing gears. In the taxiing phase, increasing the PSB air spring stiffness can effectively reduce the frame vibration caused by the uneven road surface. The PSB structural parameters have little effect on the dynamic performance of FTLG.
Data Assimilation of Ideally Expanded Supersonic Jet Using RANS Simulation for High-Resolution PIV Data
Authors: Ozawa Yuta , Nonomura Taku
Published: April 2024

Data assimilation using particle image velocimetry (PIV) and Reynolds-averaged Navier–Stokes (RANS) simulation was performed for an ideally expanded supersonic jet flying at a Mach number of 2.0. The present study aims to efficiently reconstruct all the physical quantities in the aeroacoustic fields that match well with a realistic, experimentally obtained flow field. The two-dimensional, two-component PIV measurement was applied to the jet axis plane, and the time-averaged velocity field was obtained using single-pixel ensemble correlation. Two-dimensional axisymmetric RANS simulation using the Menter shear stress transport (SST) model was also performed, and the parameters of the SST model were optimized via data assimilation using the ensemble Kalman filter. The standard deviation of the observation noise σ, which is a parameter of the ensemble Kalman filter, is estimated by the previously proposed method (Nakamura et al., Low-Grid-Resolution-RANS-Based Data Assimilation of Time-Averaged Separated Flow Obtained by LES. Int. J. Comp. Fluid. Dyn., 2022), and its effectiveness was investigated for the first time. This method effectively estimated the magnitude of σ at each generation without tuning the hyperparameters. The assimilated flow fields exhibited similar flow structures observed in PIV such as the potential core length or shear layer. Therefore, the present framework can be used to estimate time-averaged full flow fields that match well with experimentally observed flow fields, and has the potential to construct a database for the Navier-Stokes-based stability analysis that requires a full flow field.
Design and Test of Hydraulic Driving System for Undercarriage of Paddy Field Weeder
Authors: Xiao Maohua , Zhao Yuxiang , Wang Hongxiang , Xu Xiaomei , Bartos Petr , Zhu Yejun
Published: April 2024

In response to challenges such as inadequate driving stability and power in traditional weeding machinery, we designed and investigated a hydraulic chassis tailored for paddy field operations. Utilizing SolidWorks and RecurDyn V9R4 software, we obtained linear driving and steering curves to model and simulate the dynamics of the mower chassis. Through the AMESim software, we further modeled and simulated the hydraulic chassis system, focusing on the hydraulic characteristics of the components relevant to its operation. Subsequently, we developed a hydraulic-driven paddy weeder and conducted tests to evaluate the linear deviation and paddy slip rates. Our findings indicate that the designed hydraulic weeder chassis exhibits commendable dynamic performance and driving stability, with the actual average deviation and paddy slip rates measured at 2.61% and 3.59%, respectively. These results underscore the efficacy of our approach in addressing the challenges inherent in traditional weeding machinery and highlight the potential of hydraulic systems in enhancing agricultural operations.
Nitrogen Addition Decreased Respiration and Heterotrophic Respiration but Increased Autotrophic Respiration in a Cabbage (Brassica pekinensis Rupr) Experiment in the Northeast Plains
Authors: Jiang Xinming , Yan Xu , Liu Shuyan , Fu Lili , Gao Xiaomei , Huang Dongyan
Published: April 2024

Farmland soil respiration (Rs) significantly impacts the global carbon (C) cycle. Although nitrogen (N) can promote crop growth and increase yields, its relationship with Rs and its constituents, including autotrophic respiration (Ra) and heterotrophic respiration (Rh), remains unclear. Therefore, a field study was carried out in a cabbage (Brassica pekinensis Rupr) system to probe the impact of N addition on Rs, Ra, and Rh. Five levels of N addition, including 0 kg N hm−2·yr−1 (N0), 50 kg N hm−2·yr−1 (N50), 100 kg N hm−2·yr−1 (N100), 150 kg N hm−2·yr−1 (N150), and 200 kg N hm−2·yr−1 (N200), started in March 2022. The Rs (Ra and Rh) and soil samples were measured and collected twice a month. The findings revealed the following: (1) N fertilizer enhanced Ra while reducing Rs and Rh; (2) soil temperature (ST), belowground net primary productivity (BNPP), soil inorganic N (SIN), and soil total C/total N (C/N) were the significant elements influencing Ra, and microbial biomass carbon (MBC), SIN, and microbial diversity (MD) were the primary factors influencing Rh; (3) partial least squares-path models (PLS-PM) showed that ST and SIN directly impacted Rh, while ST and BNPP tangentially influenced Ra; (4) 150 kg N hm−2·yr−1 was the ideal N addition rate for the cabbage in the region. In summary, the reactions of Ra and Rh to N fertilizer in the Northeast Plains are distinct. To comprehend the underlying processes of Rs, Ra, and Rh, further long-term trials involving various amounts of N addition are required, particularly concerning worsening N deposition.
Food Authentication: The Detection of Arbutus unedo and Olea europaea Leaves as an Admixture of Oregano Using LAMP- and Duplex LAMP-Based Test Systems with Lateral-Flow Assays
Authors: Holz Nathalie , Wax Nils , Illarionov Boris A. , Iskhakova Margarita , Fischer Markus
Published: April 2024

The Mediterranean herb oregano is one of the most frequently adulterated foods. Often morphologically similar leaf material is used as a filler, which can generally be detected using DNA-based methods. Loop-mediated isothermal amplification (LAMP) has high potential for point-of-care testing as it requires only a simple device for sample incubation and is less sensitive to inhibition by co-isolated metabolites compared to conventional PCRs (polymerase chain reactions). In this work, we have developed two LAMP assays for the specific detection of the adulterants olive (Olea europaea) and strawberry tree (Arbutus unedo). The combination with a rapid isolation protocol and LFAs (Lateral-flow assays) as a visualization technique provides a reliable indication of possible adulteration. It has also been shown that it is possible to estimate the level of contamination and to perform the LAMP/LFA assay with DNA isolation in less than 30 min. As a further option, a duplex LAMP/LFA assay was developed that allows both contaminants to be detected in parallel, making the rapid test system even more cost-effective and user-friendly.
Identification and Expression Pattern Analysis of the SOS Gene Family in Tomatoes
Authors: Huang Jiahui , Liu Jiayu , Jiang Fangling , Liu Min , Chen Zheng , Zhou Rong , Wu Zhen
Published: April 2024

SOSs are key genes in the SOS (salt overly sensitive) signaling pathway, which plays an important role in maintaining ion homeostasis in plants under salt stress. Our aim was to clarify the biological function of the SOS gene family in tomato plants. We identified 14 SpeSOS genes, 10 SpiSOS genes, 11 SpmSOS genes, 9 SlmSOS genes, and 11 SlySOS genes from the genomes of “LA0716” (Spe), “LA2093” (Spi), “LA1589” (Spm), “M82” (Slm), and “Heinz 1706” (Sly) separately. The SOS protein family in tomatoes was divided into five subgroups (SOS1, SOS2, SOS3, SOS4, and SOS5) through phylogenetic analysis. The SOS proteins of the same subgroup in tomatoes contained similar conserved domains and motif structures. A subcellular localization prediction showed that the SOS1, SOS3, and SOS5 proteins in tomatoes were located on the cell membrane, while the SOS2 and SOS4 proteins in tomatoes were located on the cytoplasm and chloroplast, respectively. SlSOS1 contained the most exons and introns (23 and 22, respectively), while SlSOS5 contained only one exon. Via the analysis of the cis-elements in the promoters of those SOS genes in tomatoes, several hormone-, light-, and abiotic stress-related cis-elements were found. In addition, qRT-PCR revealed that the SpeSOS, SpiSOS, and SlySOS genes were induced by salt stress with similar expression patterns. Additionally, the expressions of SOS1-1, SOS1-2, SOS2-2, SOS3-3, SOS4-1, and SOS5-2 were higher in salt-tolerant tomatoes compared with salt-sensitive tomatoes under salt stress. In the salt-sensitive “LA1698” tomato and salt-tolerant “LA0516” tomato, most SOS genes had the highest expression in the roots. The expressions of SOS1-1, SOS1-2, SOS2-1, SOS2-2, SOS3-2, SOS3-3, and SOS5-1 in the leaves of salt-tolerant tomatoes were significantly higher than those in salt-sensitive tomatoes. Thereby, the SOS genes in tomatoes were induced by salt stress, indicating that they participated in the regulation mechanism of tomato salt tolerance. This study laid the foundation for further study on the function of the SOS gene family and revealed the molecular mechanism of tomato salt resistance.
Impact of Pre-Plant Fertilizer Rates in Combination with Polysulphate® on Soil Nitrogen Distribution and Yield of Short-Day Strawberries (Fragaria × ananassa cv. Camarosa)
Authors: Lay-Walters Amanda , Heagy Kimberly , Woodley Alex , Hoffmann Mark
Published: April 2024

Strawberries are by far the most produced soft fruit (blueberries, raspberries, blackberries, and strawberries) worldwide, with China and the US being the two countries with the most production. In the US, strawberries reached a farm gate value of more than USD 3 billion in 2023 and are predominantly grown in the open field on an annual cycle in hilled-up soil beds using plastic mulch (plasticulture). This process relies on adequate pre-plant fertilizer application for plant establishment and fruit development. In North Carolina (US), it is current practice to apply pre-plant fertilizer containing 67 nitrogen (N) kg/ha; however, with increasing fertilizer costs and environmental concerns, questions remain as to whether or not pre-plant full-spectrum fertilizer rates can be reduced and substituted with organic low-N fertilizer sources, such as Polysulphate, without impacting yield or fruit quality. For this reason, field trials were established to evaluate the impact of pre-plant fertilizer rates on strawberry production (‘Camarosa’). Trials were conducted in the 2019–2020 and 2020–2021 seasons at two locations in North Carolina. The following N-rate pre-plant fertilizer treatments were applied: 80.1, 67.3, 54.1, 41.1, 33.6, 28.0, and 0 kg/ha. NO3 and NH4 content were frequently assessed in each replicate in the raised bed profile between planting and spring fertilizer application. Marketable and total strawberry yields were assessed over 6 weeks in the spring of 2020 and 2021. Our trial results showed that, especially in sandy soil, N rapidly declined under plastic within the first 8 weeks after pre-plant fertilizer application. However, no impact between pre-plant fertilizer rates and plant yield was observed. Treatments that contained Polysulphate and lower amounts of full-spectrum fertilizer showed significantly lower N concentrations in the soil while maintaining similar yields and fruit quality compared to grower-standard pre-plant fertilizer treatments. In summary, our results show that it is possible to reduce N content in pre-plant fertilizer by up to 50% compared to current recommendations without causing yield loss in short-day strawberry cultivars.
The Evaluation of Sweetcorn (Zea mays saccharata Sturt.) Infestation of Barnyardgrass (Echinochloa crus-galli) Depending on Weather Conditions and Crop Rotation
Authors: Majchrzak Leszek , Waligóra Hubert , Zawieja Bogna , Idziak Robert , Szulc Piotr
Published: April 2024

This paper focuses on the weed species Echinochloa crus-galli, commonly known as barnyardgrass, which is a persistent threat to crop yield and quality, especially in maize (Zea mays) cultivation. It is one of the most problematic weeds in agricultural fields due to its aggressive growth, adaptability to different environmental conditions and prolific seed production. The incidence of Echinochloa crus-galli in maize fields has increased in recent years. This study aims to provide a comprehensive understanding of the characteristics and behavior of Echinochloa crus-galli, and to suggest effective measures to control it. This research on sweetcorn was conducted from 1992 to 2019 at the Research and Education Center Gorzyń, Złotniki branch, which belongs to the Poznań University of Life Sciences. The evaluation of weed infestation was carried out in experiments focusing on chemical weed control in maize. The experiments were designed as a one-factor randomised block design with four field replications. The condition and the degree of weed infestation (number of weeds and fresh weight of weeds) in the control plots was assessed on an annual basis at the end of June and in July. The aim of the study was to evaluate the dynamic changes in the status and extent of barnyardgrass (Echinochloa crus-galli) infestation in maize grown after various other crops in the Wielkopolska region, with a focus on the weather conditions. The study found that barnyardgrass was most likely to occur when maize was sown after winter wheat in a dry and warm year, and least likely when maize was grown in rotation after winter wheat in a cold year with average rainfall. The proportion of barnyardgrass weed mass in the total weed mass was significantly lower after winter rye than after winter wheat, winter oilseed rape and winter triticale. Further research into the biology and ecology of barnyardgrass is key to effectively controlling this weed and safeguarding sweetcorn yields.
Enhancing Rumen Fermentation and Bacteria Community in Sika Deer (Cervus nippon) through Varying Levels of Dragon Fruit Peel Polyphenolic Extract: An In Vitro Study
Authors: Ban Chao , Tian Xingzhou , Lu Qi , Lounglawan Pipat , Wen Guilan
Published: April 2024

The aim of this study is to investigate the effect of dragon fruit peel polyphenolic extract (DFPE) on gas production, rumen fermentation, and bacterial communities in sika deer using an in vitro technique. Three treatments with different DFPE levels (DFPE0, base diet; DFPE5, base diet + 5 mg/g DFPE; DFPE10, base diet + 10 mg/g DFPE, respectively; n = 6) were implemented. The phenolic composition of DFPE, gas production (GP), ammonia nitrogen (NH3-N), volatile fatty acid (VFA), and bacteria communities was evaluated after 24 h of incubation. The results showed that GP and NH3-N were reduced by DFPE supplementation. Total VFA, isovaleric acid, and valeric acid were increased (p < 0.05) by the addition of DFPE. No changes (p > 0.05) were observed in pH, acetic acid, propionic acid, isobutyric acid, butyric acid, and the ratio of acetic acid to propionic acid. Additionally, the alpha indexes, including Sobs, Shannon, and Ace, were increased by DFPE supplementation. Moreover, at the phylum level, DFPE supplementation increased (p = 0.01) Bacteroidota but reduced (p < 0.01) Firmicutes. At the genus level, compared to DFPE0, the DFPE10 had increased relative abundances of Rikenellaceae_RC9_gut_group (p < 0.01), norank_f_Muribaculaceae (p = 0.01), Lachnospiraceae_NK3A20_group (p < 0.01), Christensenellaceae_R-7_group (p < 0.01), and NK4A214_group (p < 0.01), decreased relative abundances of Streptococcus (p < 0.01), Oribacterium (p = 0.01), and Enterococcus (p < 0.01). Compared to DFPE0, DFPE5 had no change (p > 0.05) in all bacteria at the genus level except for decreased relative abundance of Enterococcus (p < 0.01). These results indicated that DFPE may be able to be used as a feed additive to enhance fermentation parameters and improve ruminal bacteria communities in Sika deer.
A Comprehensive Review of Recent Research into the Effects of Antimicrobial Peptides on Biofilms—January 2020 to September 2023
Authors: Fontanot Alessio , Ellinger Isabella , Unger Wendy W. J. , Hays John P.
Published: April 2024

Microbial biofilm formation creates a persistent and resistant environment in which microorganisms can survive, contributing to antibiotic resistance and chronic inflammatory diseases. Increasingly, biofilms are caused by multi-drug resistant microorganisms, which, coupled with a diminishing supply of effective antibiotics, is driving the search for new antibiotic therapies. In this respect, antimicrobial peptides (AMPs) are short, hydrophobic, and amphipathic peptides that show activity against multidrug-resistant bacteria and biofilm formation. They also possess broad-spectrum activity and diverse mechanisms of action. In this comprehensive review, 150 publications (from January 2020 to September 2023) were collected and categorized using the search terms ‘polypeptide antibiotic agent’, ‘antimicrobial peptide’, and ‘biofilm’. During this period, a wide range of natural and synthetic AMPs were studied, of which LL-37, polymyxin B, GH12, and Nisin were the most frequently cited. Furthermore, although many microbes were studied, Staphylococcus aureus and Pseudomonas aeruginosa were the most popular. Publications also considered AMP combinations and the potential role of AMP delivery systems in increasing the efficacy of AMPs, including nanoparticle delivery. Relatively few publications focused on AMP resistance. This comprehensive review informs and guides researchers about the latest developments in AMP research, presenting promising evidence of the role of AMPs as effective antimicrobial agents.