bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical performance of a novel and rapid bioassay for detection of thyroid-stimulating immunoglobulins in Graves’ orbitopathy patients: a comparison with two commonly used immunoassays
Authors: Hötte Gijsbert J. , de Bie Maaike , de Keizer Ronald O.B. , Kolijn P. Martijn , Drexhage Roosmarijn C. , Veenbergen Sharon , Versnel Marjan A. , van Hagen P. Martin , Paridaens Dion , Dik Willem A.
Published: September 2024

Background

For the selective detection of thyroid-stimulating hormone receptor antibodies with stimulating properties (thyroid-stimulating immunoglobulins; TSI), a novel and rapid bioassay (Turbo TSI) has been introduced. We evaluate the clinical performance of Turbo TSI in Graves’ orbitopathy (GO) patients and compare it to a bridge-based TSI binding immunoassay and third generation TSH-R-binding inhibitory immunoglobulins (TBII) assay. Also, we investigate the association of Turbo TSI and TBII measurements with GO activity and severity, as well as response to intravenous methylprednisolone (IVMP), and compare results to previous findings on the bridge-based TSI binding immunoassay.

Methods

Turbo TSI, TBII and bridge-based TSI binding immunoassay measurements were performed in biobank serum from 111 GO patients and control cases (healthy controls [HC; n=47], primary Sjögren’s disease [SD; n=10], systemic sclerosis [SSc; n= 10], systemic lupus erythematosus [SLE; n=10]). Clinical characteristics and response to treatment were retrospectively retrieved from GO patient files.

Results

Turbo TSI had the highest sensitivity (97.3%) and negative predictive value (96.1%), while bridge-based TSI binding immunoassay showed the highest specificity (100%) and positive predictive value (100%). Differentiating GO patients from control cases, receiver operating characteristic (ROC) analysis showed an area under the curve (AUC) of 98.5%, 95.7% and 99.8% for Turbo TSI, TBII and bridge-based TSI binding immunoassay, respectively. Turbo TSI (p<0.001) and TBII (p<0.01) levels were higher in patients with active compared to inactive GO. Correlation with CAS was stronger for Turbo TSI (r=0.42) than TBII (r=0.25). No statistically significant differences were observed in IVMP responders vs. non-responders for Turbo TSI (p=0.092) and TBII (p=0.21). For identifying active GO, an AUC of 75% with Turbo TSI and 67% with TBII was found. For IVMP response, AUC was 66.3% with Turbo TSI and 62.1% with TBII. In multivariate logistic regression analyses, both assays were independently associated with disease activity (p<0.01 for both assays) and IVMP response (p<0.01 for Turbo TSI; p<0.05 for TBII).

Conclusions

The new Turbo TSI functional bioassay has good clinical performance. Although turbo TSI is a stronger marker of activity and IVMP response than TBII, results are comparable to our previously published findings on the bridge-based TSI binding immunoassay.
Pregnane X receptor reduces particulate matter-induced type 17 inflammation in atopic dermatitis
Authors: Lee Ji Su , Lee Youngae , Jang Sunhyae , Oh Jang-Hee , Lee Dong Hun , Cho Soyun
Published: September 2024

Background

Epidemiological evidence suggests that particulate matter (PM) exposure can trigger or worsen atopic dermatitis (AD); however, the underlying mechanisms remain unclear. Recently, pregnane X receptor (PXR), a xenobiotic receptor, was reported to be related to skin inflammation in AD.

Objectives

This study aimed to explore the effects of PM on AD and investigate the role of PXR in PM-exposed AD.

Methods

In vivo and in vitro AD-like models were employed, using BALB/c mice, immortalized human keratinocytes (HaCaT), and mouse CD4+ T cells.

Results

Topical application of PM significantly increased dermatitis score and skin thickness in AD-like mice. PM treatment increased the mRNA and protein levels of type 17 inflammatory mediators, including interleukin (IL)-17A, IL-23A, IL-1β, and IL-6, in AD-like mice and human keratinocytes. PM also activated PXR signaling, and PXR knockdown exacerbated PM-induced type 17 inflammation in human keratinocytes and mouse CD4+ T cells. In contrast, PXR activation by rifampicin (a human PXR agonist) reduced PM-induced type 17 inflammation. Mechanistically, PXR activation led to a pronounced inhibition of the nuclear factor kappa B (NF-κB) pathway.

Conclusion

In summary, PM exposure induces type 17 inflammation and PXR activation in AD. PXR activation reduces PM-induced type 17 inflammation by suppressing the NF-κB signaling pathway. Thus, PXR represents a promising therapeutic target for controlling the PM-induced AD aggravation.
Exploring the gut microbiota of healthy captive Asian elephants from various locations in Yunnan, China
Authors: Wang Yuhan , Wang Yixuan , Zhou Jiuxuan , Bao Mingwei , Shah Taif , Yang Song , Zheng Jing , Li Qian , Hou Yutong , Wang Binghui , Yuan Ruiling
Published: September 2024

Introduction

The Asian elephant (Elephas maximus) is a giant herbivore classified as an endangered wildlife species by the International Union for Conservation of Threatened Species.This study aims to investigate and compare the core gut microbiota of captive Asian elephants from three different locations in Yunnan Province, China, to explore the impact of environmental and husbandry factors on microbial diversity.

Methods

We collected fecal samples from 29 captive Asian elephants from three locations and performed full-length 16S rRNA gene sequencing. Microbial diversity was assessed using alpha diversity (Chao1 and Shannon indexes) and beta diversity (Bray-Curtis and Euclidean distance metrics). Principal coordinate analysis (PCoA) was used to visualize microbial variation among groups.

Results

Alpha diversity analysis showed that the microbial diversity in the Yexianggu group was higher than that in the other groups. Bray-Curtis and Euclidean metrics revealed significant differences among the microbial communities. Bacteroidetes and Firmicutes, which are key cellulose-degrading bacteria, were the dominant phyla in all groups. Synergistaceae was the most abundant family in the Menghai group, while Lachnospiraceae and Pirellulaceae were more abundant in the Yexianggu and Yuantongshan groups, respectively. Genus p-1008-a5-gut-group was more abundant in Yexianggu, and Prevotella was predominant in Menghai.

Discussion

These results indicate that habitat and husbandry practices significantly influence the gut microbiota of captive Asian elephants. The identification of bacterial species such as Lactobacillus fermentum, Clostridium neonatale, Enterococcus mundtii, Klebsiella huaxiensis, Corynebacterium nasicanis, and Streptococcus equinus highlights the potential role of specific microbes in maintaining host-microbial interactions. Promoting microbial diversity through improved captive conditions could enhance the health of these endangered animals.
Genomic profiling and spatial SEIR modeling of COVID-19 transmission in Western New York
Authors: Bard Jonathan E. , Jiang Na , Emerson Jamaal , Bartz Madeleine , Lamb Natalie A. , Marzullo Brandon J. , Pohlman Alyssa , Boccolucci Amanda , Nowak Norma J. , Yergeau Donald A. , Crooks Andrew T. , Surtees Jennifer A.
Published: September 2024

The COVID-19 pandemic has prompted an unprecedented global effort to understand and mitigate the spread of the SARS-CoV-2 virus. In this study, we present a comprehensive analysis of COVID-19 in Western New York (WNY), integrating individual patient-level genomic sequencing data with a spatially informed agent-based disease Susceptible-Exposed-Infectious-Recovered (SEIR) computational model. The integration of genomic and spatial data enables a multi-faceted exploration of the factors influencing the transmission patterns of COVID-19, including genetic variations in the viral genomes, population density, and movement dynamics in New York State (NYS). Our genomic analyses provide insights into the genetic heterogeneity of SARS-CoV-2 within a single lineage, at region-specific resolutions, while our population analyses provide models for SARS-CoV-2 lineage transmission. Together, our findings shed light on localized dynamics of the pandemic, revealing potential cross-county transmission networks. This interdisciplinary approach, bridging genomics and spatial modeling, contributes to a more comprehensive understanding of COVID-19 dynamics. The results of this study have implications for future public health strategies, including guiding targeted interventions and resource allocations to control the spread of similar viruses.
Trust of inpatient physicians among parents of children with medical complexity: a qualitative study
Authors: Dewan Tammie , Whiteley Andrea , MacKay Lyndsay Jerusha , Martens Rachel , Noel Melanie , Barnard Chantelle , Jordan Isabel , Janvier Anne , Thorne Sally
Published: September 2024

Background

Trust is a foundation of the therapeutic relationship and is associated with important patient outcomes. Building trust between parents of children with medical complexity (CMC) and physicians during inpatient care is complicated by lack of relational continuity, cumulative (sometimes negative) parent experiences and the need to adjust roles and expectations to accommodate parental expertise. This study's objective was to describe how parents of CMC conceptualize trust with physicians within the pediatric inpatient setting and to provide recommendations for building trust in these relationships.

Methods

Interviews with 16 parents of CMC were completed and analyzed using interpretive description methodology.

Results

The research team identified one overarching meta theme regarding factors that influence trust development: situational awareness is needed to inform personalized care of children and families. There were also six major themes: (1) ensuring that the focus is on the child and family, (2) respecting both parent and physician expertise, (3) collaborating effectively, (4) maintaining a flow of communication, (5) acknowledging the impact of personal attributes, and (6) recognizing issues related to the healthcare system.

Discussion

Many elements that facilitated trust development were also components of patient- and family-centered care. Parents in this study approached trust with inpatient physicians as something that needs to be earned and reciprocated. To gain the trust of parents of CMC, inpatient physicians should personalize medical care to address the needs of each child and should explore the perceptions, expertise, and previous experiences of their parents.
The foundation of the rhubarb industry economy: investigating metabolites disparities of rhubarb between varieties and growing environments on the Tibetan plate
Authors: Zou Jinpeng , Wu Wei , Wang Fang , Hou Kai
Published: September 2024

Objective

In Tibetan dietary and folk medicine practices, Rheum austral is commonly used as an alternative to Rheum tanguticum, and there is a prevailing belief that wild rhubarb should not be substituted by its cultivated counterpart. However, these traditions are not supported by scientific evidence, particularly concerning the differences in endogenous metabolites between cultivated and wild rhubarbs, as well as between officially recognized and non-official rhubarbs. These uncertainties have also been hindering the vertical integration development of the local rhubarb industry.

Methods

In this study, ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UHPLC-QTOFMS) and biostatistical analysis were employed to systematically and comprehensively investigate the chemical constituents of rhubarbs from various sources, focusing on the differences in metabolic components between cultivated and wild rhubarbs.

Results

The metabolic differences in rhubarb from various varieties and environments are pronounced. Among them, 39 differential metabolites were identified between cultivated R. tanguticum and wild R. tanguticum. cultivated R. tanguticum is rich in emodin, physcion, and rhapontigenin, whereas wild R. tanguticum exhibits a higher concentration of rhaponticin and is particularly abundant in anthraquinone compounds. Additionally, 33 differential metabolites distinguished wild R. tanguticum from wild R. austral, with R. austral being rich in stilbene derivatives and wild R. tanguticum predominantly containing coumarins. The correlations among these differential metabolites have also been further explored and presented.

Conclusion

The metabolic disparities between cultivated and wild rhubarb varieties are substantial, with wild rhuabarb containing higher levels of effective components than its cultivated counterparts. However, wild varieties face issues with component instability and resource depletion, while cultivated varieties exhibit more stable effective components. Given these significant differences in metabolic components, it is essential to differentiate rhubarbs from various species and growing conditions to suit specific medicinal and dietary purposes effectively. This paper can lay a theoretical foundation for the vertical integration development of the rhubarb industry in Tibetan areas.
Adaptive design of long-focal-length freeform off-axis reflective space cameras with lightweight and integration of primary/tertiary mirror
Authors: Sun Yiwei , Wei Yangjie , Zhao Ji
Published: September 2024

With advancements in freeform surface design and manufacturing, applying freeform surfaces to space cameras is an effective method to further enhance imaging quality. However, existing design methods for freeform space cameras rarely consider imaging quality, system size, and manufacturing constraints simultaneously during design. This study proposes an adaptive design method for long-focal-length freeform off-axis reflective space cameras with lightweight and primary/three mirror integration, which balances system size and ease of manufacturing while ensuring good imaging quality. First, a method for adaptive configuration of the structural parameter search spaces is proposed, so that the search spaces for structural parameters are dynamically generated based on different design requirements of long-focal-length off-axis space cameras with various structures. Then, a multiple-parameter objective function is constructed, and the structural parameters for the off-axis space camera are determined through a search process to balance imaging quality, lightweight requirements and manufacturing demands. Finally, the improved Wassermann–Wolf (W-W) method is employed to optimize the mirrors into freeform surfaces, further enhancing the imaging quality of the designed space camera. Experimental results demonstrate that the proposed method can adaptively generate reasonable structural parameter search spaces while maintaining high imaging quality, facilitating the acquisition of a lightweight and easily manufacturable freeform off-axis reflective space camera. This method exhibits strong dynamic adaptability and low reliance on prior experience, providing a new insight for the design of space cameras.
Ionic regulatory strategies of crabs: the transition from water to land
Authors: Lucu Čedomil , Turner Lucy M.
Published: September 2024

Terrestrial crabs (brachyurans and anomurans) have invaded land following a variety of pathways from marine and/or via freshwater environments. This transition from water to land requires physiological, ecological, and behavioral adaptations to allow the exploitation of these new environmental conditions. Arguably, the management of salt and water balance (e.g., osmoregulation) is integral for their survival and success in an environment where predominantly low-salinity aquatic (e.g., freshwater) water sources are found, sometimes in only minimal amounts. This requires a suite of morphological and biochemical modifications, especially at the branchial chamber of semi-terrestrial and terrestrial crabs to allow reprocessing of urine to maximize ion uptake. Using knowledge gained from electrophysiology, biochemistry, and more recent molecular biology techniques, we present summarized updated models for ion transport for all major taxonomic groups of terrestrial crabs. This is an exciting and fast-moving field of research, and we hope that this review will stimulate further study. Terrestrial crabs retain their crown as the ideal model group for studying the evolutionary pathways that facilitated terrestrial invasion.
Heart-specific expression of the green fluorescent protein gene in avian embryos by administration of recombinant adenovirus type-5 vector into the embryonic blood vessel
Authors: Choi Wonjun , Lee Joonbum , Kim Dong-Hwan , Ma Evan , Suh Yeunsu , Lee Sang-Suk , Lee Kichoon
Published: September 2024

Genetic modification in vivo could provide direct functions of genes that could potentially contribute to diverse areas of research including genetics, developmental biology, and physiology. It has been reported that genes of interest could be introduced via recombinant adenovirus type 5 (Ad5) in poultry. Successful gene delivery to mammal fetuses in utero promises substantial progress in clinical and developmental biology, but it is limited because of difficulties in injecting specific sites and invasiveness. On the other hand, developing avian embryos are easily accessible by making a window on the eggshell. Therefore, the objective of this study is to determine permissive embryonic stages for gene transfer into specific avian tissue/organs by injection of Ad5 containing the green fluorescent protein (GFP) gene into blood vessels. At 2 d of post-injection, a strong GFP signal was predominantly identified in the heart of chicken embryos injected at Hamilton–Hamburger (HH) 14, 15, 16 and17 stages with the percentages (44%, 53%, 25%, and 14%, respectively) of GFP positive embryos. In quail embryos, the injection at the HH 15 resulted in heart-specific expression of GFP. Western blot analysis revealed that GFP was exclusively expressed in the avian hearts. These results suggest that the GFP gene is specifically delivered to the avian embryonic hearts when Ad5 is injected through the blood vessel at HH 14–17. This adenoviral transduction of genes of interest in avian embryonic hearts can provide new models for understanding functions of genetic factors on embryonic heart development and unravel genetic etiology of congenital heart diseases.
Unveiling the diversification and dispersal of the Lewinskya firma complex (Orthotrichaceae, Bryophyta) across Africa and India
Authors: Lara Francisco , Díaz San Román Raúl , Fernández-Mazuecos Mario , Calleja Juan Antonio , Flagmeier Maren , Mazimpaka Vicente , Garilleti Ricardo , Draper Isabel
Published: September 2024

Intercontinental disjunctions are one of the most attractive and interesting biogeographical patterns. Bryophytes often exhibit such distributions, which is partly explained by their great ability to disperse over long distances. However, such intercontinental ranges are sometimes a distorted reality caused by the existence of unnoticed species. This study investigates whether the disjunction between East Africa and southern India of the moss Lewinskya firma reflects the genuine distribution of a single species or implies pseudo-cryptic species (whose morphological differentiation is subtle and have therefore been masked). An integrative taxonomic approach combining morphological and molecular methods (genotyping by sequencing, GBS) was used, based on a representation of samples specifically collected from all the major mountainous regions where this moss occurs. Two species, L. firma s. str. and L. afroindica sp. nov. are involved, whose ranges completely overlap in East Africa, although genetic distance and morphological differences in leaf apex shape, vaginula hairs shape and papillosity, spore ornamentation and peristome constitution and ornamentation allow distinguishing both. In addition, the range of L. afroindica extends into both southern Africa and southern India. The phylogenetic reconstruction obtained shows a certain degree of differentiation of the Indian populations, although they are yet morphologically indistinguishable from African populations. The results thus highlight both the existence of overlooked species and the complexity of bryophyte biogeography.
Identification of candidate genes and development of KASP markers for soybean shade-tolerance using GWAS
Authors: Jia Qianru , Hu Shengyan , Li Xihuan , Wei Libin , Wang Qiong , Zhang Wei , Zhang Hongmei , Liu Xiaoqing , Chen Xin , Wang Xuejun , Chen Huatao
Published: September 2024

Shade has a direct impact on photosynthesis and production of plants. Exposure to shade significantly reduces crops yields. Identifying shade-tolerant genomic loci and soybean varieties is crucial for improving soybean yields. In this study, we applied a shade treatment (30% light reduction) to a natural soybean population consisting of 264 accessions, and measured several traits, including the first pod height, plant height, pod number per plant, grain weight per plant, branch number, and main stem node number. Additionally, we performed GWAS on these six traits with and without shade treatment, as well as on the shade tolerance coefficients (STCs) of the six traits. As a result, we identified five shade-tolerance varieties, 733 SNPs and four candidate genes over two years. Furthermore, we developed four kompetitive allele-specific PCR (KASP) makers for the STC of S18_1766721, S09_48870909, S19_49517336, S18_3429732. This study provides valuable genetic resources for breeding soybean shade tolerance and offers new insights into the theoretical research on soybean shade tolerance.
Modeling of Supercooled Large Droplet Physics in Aircraft Icing
Authors: Özgen Serkan , Sarıbel Eda Bahar
Published: September 2024

This paper aims to investigate phenomena that are related to SLD conditions in aircraft icing including gravity, non-spherical droplets, droplet breakup and droplet splash using an in-house computational tool. The in-house computational tool involves four modules for the computation of the flow field, droplet trajectories, convective heat transfer coefficients and ice growth rates. Droplet trajectories are computed using the Lagrangian approach, while ice growth rates are calculated using the Extended Messinger Model. In order to extend the capabilities of the computational tool to include SLD-related phenomena, empirical models that represent SLD physics are implemented. An extensive study has been performed using MS317 and NACA0012 airfoils, that aims to bring out the relative importance of the SLD-related phenomena, particularly on water catch rates and ice formation. The results of the study pointed to some important new conclusions that may shed further light on SLD physics. For example, multiple droplet breakup has been observed under certain conditions and droplet breakup emerged as a more important effect than previously reported. It was also seen that droplet splash influences both the energy balance and the mass balance in the icing process, which has been shown to have an important effect on the final ice shape, especially for very large droplets.
Optimizing Nitrogen Fertilization to Maximize Yield and Bioactive Compounds in Ziziphora clinopodioides
Authors: Hazrati Saeid , Mousavi Zahra , Mollaei Saeed , Sedaghat Mojde , Mohammadi Marzieh , Pignata Giuseppe , Nicola Silvana
Published: September 2024

Ziziphora clinopodioides L. is a valuable medicinal and aromatic plant; however, its special requirements for proper growth and enhanced secondary metabolite composition have limited its production and availability. The lack of appropriate fertilizer dosage recommendations is one of these limiting factors for ex situ conservation and large-scale cultivation. This study investigated the effects of nitrogen (N) fertilization on Z. clinopodioides in both open field and unheated greenhouse conditions. The determined research factor was N dosage (0, 40, 80, and 120 kg N ha−1 in the field) and (0, 200, 400, and 600 mg N pot−1 in the greenhouse). It was found that Z. clinopodioides plants could grow successfully outside their natural habitat with sufficient N fertilization yielding a satisfactory amount of metabolites per plantation area. Specifically, among the tested dosages, the 120 kg N ha−1 (which showed no significant difference from 80 kg N ha−1) and 400 mg N pot−1 fertilizers increased the aboveground dry and fresh biomass, essential oil (EO) content, and yield. Nitrogen fertilization showed a direct correlation with menthone, neo-menthol, menthol, pulegone, E-ocimenone, and spathulenol, but a negative correlation with α-pinene, β-pinene, limonene, 1,8-cineol, trans-pulegol, and iso-menthone. This study is the first to evaluate the effects of N fertilization on the genus Ziziphora. The results indicate that utilizing N fertilizer at a moderate rate (80 kg N ha−1 in the field and 400 mg N pot−1 in the greenhouse) can improve the agronomic traits and EO of Z. clinopodioides.
Non-Commodity Agricultural Price Hedging with Minimum Tracking Error Portfolios: The Case of Mexican Hass Avocado
Authors: Torre-Torres Oscar V. De la , del Río-Rama María de la Cruz , José Álvarez-García
Published: September 2024

The present paper tests the use of an agricultural futures minimum tracking error portfolio to replicate the price of the Mexican Hass avocado (a non-commodity). The motivation is that this portfolio could be used to balance the basis risk that the avocado price hedge issuer could face. By performing a backtest of a theoretical avocado producer from January 2000 to September 2023, the results show that the avocado producer could hedge the avocado price by 94%, with the hedge offered by a theoretical financial or government institution. Also, this issuer could balance the risk of such a hedge by buying a coffee–sugar futures portfolio. The cointegrated or long-term relationship shows that using such a futures portfolio is useful for Mexican Hass avocado price hedging. This paper stands as one of the first in testing futures portfolios to offer a synthetic hedge of non-commodities through a commodities’ futures portfolio.
Estimate of Genetic Parameters for Pre-Weaning Growth Traits and Kleiber Ratio in Palestinian Sheep Breeds
Authors: Salman Muayad , Ben Souf Ikram , Khnissi Samia , Halaweh Wael , M’Hamdi Naceur
Published: September 2024

Data on 1440 Awassi (AW), 2114 Assaf (AF), 261 Crossbred (XB), and 439 Improved Awassi (IA) lamb genotypes from 689 AW, 1009 AF, 105 XB, and 195 IA dams, and 152 sires, obtained from three geographical districts in the West Bank and collected between 2010 and 2015, were analyzed to estimate (co)variance components and genetic parameters for pre-weaning growth traits, including birth weight (BW), weaning weight (WW), pre-weaning average daily gain (PADG), and Kleiber ratio (KR). Explanatory statistical analyses employed the least squares method of the following factors: lamb genotype, mating type (natural mating or artificial insemination), lamb sex, and birth type, on lamb pre-weaning growth traits. The estimation of genetic parameters was performed by an animal model in Restricted Maximum Likelihood (REML) The heritability estimates for lamb traits showed that AF lambs had the highest heritability for KR 0.62, while IA lambs had a relatively high heritability for PADG 0.42. In terms of genetic correlations, the correlation between birth weight and PADG was strongest in AW 0.80, and IA lambs had a negative genetic correlation between BW and WW −0.28. For maternal genetic correlations, AF lambs exhibited a high maternal correlation between BW and WW 0.78, and AW lambs had a strong maternal correlation between PADG and KR 0.57. Phenotypic correlations were particularly strong in XB lambs between BW and KR 0.79. It was concluded that IA lambs had higher BW, and AF lambs excelled in WW and PADG. These results indicated the potential for genetic improvement in feed efficiency among AF lambs, whereas AW lambs exhibited a stronger environmental influence on growth traits.
Socio-Economic Viability of the High Nature Value Farmland under the CAP 2023–2027: The Case of a Sub-Mediterranean Region in Slovenia
Authors: Šumrada Tanja , Erjavec Emil , Šilc Urban , Žgajnar Jaka
Published: September 2024

Our study aimed to analyse socio-economic sustainability and the drivers of land abandonment in the Kras region of Slovenia, a representative eastern Mediterranean farmland area. We also sought to provide policy recommendations for supporting biodiversity conservation and facilitating the sustainable transition of similar High Nature Value (HNV) farming systems across Europe. The Slovenian Typical Farm Model (SiTFarm) was used to assess the economic performance of representative livestock and wine-growing farm types. Additionally, in-depth interviews with farmers were conducted to understand their perspectives on these farming systems and their preferences for alternative management strategies and policy instruments. Our findings indicate that, due to the introduction of basic income support for sustainability and complementary voluntary coupled payments, budgetary support for the livestock sector in the region is projected to increase by 27–55% in estimated gross margins during the 2023–2027 Common Agricultural Policy (CAP) period, depending on the farm type. Furthermore, farms can enhance their economic performance by converting to organic farming and enrolling in agri-environmental schemes that promote extensive grasslands management, which is crucial for biodiversity conservation. This suggests that Slovenia’s current CAP strategic plan adequately addresses the maintenance of the existing farming systems. However, the region faces significant challenges, particularly in restructuring small farms and adding value to primary farm products. These issues appear to be insufficiently addressed by the current CAP strategic plan, implying that limited progress is expected in mitigating land abandonment in the long term. Comprehensive strategies for the development of feasible HNV farming systems, aligned with biodiversity conservation recommendations, and a well-managed system of supporting institutions and policy instruments is needed to facilitate more market-oriented and sustainable development of agriculture at the local level.
Organic Management Mediates Multifunctionality Responses to Land Conversion from Longan (Dimocarpus longan) to Tea Plantations at the Aggregate Level
Authors: Shan Ying , Yue Zhengfu , Zhou Guangfan , Wei Chaoxian , Wu Dongming , Liu Beibei , Li Qinfen , Wang Jinchuang , Zou Yukun
Published: September 2024

Soil aggregates, which are highly influenced by land conversion, play key roles in driving soil nutrient distribution and microbial colonization. However, the role of soil aggregates in shaping the responses of microbial community composition and multiple ecosystem functions, especially ecosystem multifunctionality (EMF), to land conversion remains poorly understood. In this study, we investigated the impact of the conversion of a longan orchard (LO) to a conventional tea plantation (CTP) and organic tea plantation (OTP) on soil EMF at the aggregate level and explored the underlying mechanism. Our results showed that EMF was significantly reduced in the conventional tea plantation, with 3.44, 1.79, and 1.24 times for large macro-, macro-, and micro-aggregates. In contrast, it was relatively preserved in the organic tea plantation. Notably, micro-aggregates with higher microbial biomass supported more EMF than larger aggregates under the land conversion conditions. The EMF associated with soil aggregates was found to be regulated by the differences in nutrient content and microbial community composition. Random forest analysis, redundancy analysis, and Pearson analysis indicated that both soil nutrient and microbial community composition within soil aggregates jointly determined EMF. This study highlights that soil aggregation influences the stratification of nutrients and microbial communities, which leads to the differing response of aggregate-related EMF to land conversion.
Biofumigation-Derived Soil Microbiome Modification and Its Effects on Tomato (Solanum lycopersicum L.) Health under Drought
Authors: Lee Dokyung , Park Tae-Hyung , Lim Kyeongmo , Jeong Minsoo , Nam GaYeon , Kim Won-Chan , Shin Jae-Ho
Published: September 2024

Tomato is an economically and nutritionally important crop and is vulnerable to drought. Under drought, soil microbes provide beneficial effects to plants and alleviate stress. We suggest a reconstruction of the soil microbiome using biofumigation, an organic farming method, to protect tomatoes. In this study, we treated soil in four ways with varied concentrations: biofumigation (BF0.5, BF1.0, and BF1.5), green manure treatment (GM0.5, GM1.0, and GM1.5), autoclaving (AT), and non-treatment (NT). Tomatoes were grown in each treated soil, subjected to water shortages, and were rewatered. We investigated plant phenotypes and soil properties, focused on microbial communities using the Illumina MiSeq® System. Relative Water Content and malondialdehyde were measured as plant stress. The results showed that the 1% biofumigation treatment had 105% and 108.8% RWC during drought and after rewatering, compared to the non-treated soil. The highest concentration, the 1.5% treatment, lowered RWC due to an excess of NO3−, K+, Ca2+, and decreased alpha diversity. Through PLS-PM, bacterial alpha diversity was found to be the largest factor in the increase in RWC (coefficient = 0.3397), and both biofumigant and green manure significantly increased the Shannon index and observed species. In addition, biofumigation increased beneficial functional genes (purine metabolism, pyrimidine metabolism, carbon fixation pathways, and zeatin bio-synthesis) of soil microorganisms (p value < 0.05, <0.01, >0.05, and <0.05, respectively). The 1% biofumigation treatment enriched the core five genera of the fungal network (Enterocarpus, Aspergillus, Leucothecium, Peniophora, and Wallemia) of the fungal network which might suppress the most dominant pathogen, Plectosphaerella. In conclusion, biofumigation-derived soil microbiome alterations have the potential to lower plant stress under drought.
The Genetic Diversity Assessment of Broomcorn Millet (Panicum miliaceum) and the Construction of a Mini-Core Collection
Authors: Ren Jiandong , Yu Xiaohan , Wang Xiaoxing , Wang Yue , Xin Xuxia , Wang Ruonan , Zhang Yingxing , Liu Minxuan , Xiang Jishan
Published: September 2024

Broomcorn millet (Panicum miliaceum L.) is a crop with a good ability to adapt to the environment. Over 8800 accessions have been collected in the national gene bank of China. The huge quantity of germplasms made it difficult for analysis and evaluation. Although a broomcorn millet core collection (CC) comprising 780 accessions was established, the number is still too large for researchers to explore in depth. In this study, the genetic diversity of 634 broomcorn millet accessions from the core collection was analyzed based on SSR markers. A mini-core collection (MC) containing 256 accessions was extracted. The mini-core collection accounted for less than half of the original core collection and only about 2.8% of the total resources but still provided a good representation. In addition, the results of this study validated that Shanxi is the origin of broomcorn millet, and accessions from the South region may contain novel genes. In conclusion, this study provides a comprehensive characterization of the genetic diversities of broomcorn millet core collection in China. Moreover, an MC may aid in reasonably and efficiently selecting materials for broomcorn millet breeding as researchers could screen for aimed genetic characters within a smaller scope.
A Hierarchical Feature-Aware Model for Accurate Tomato Blight Disease Spot Detection: Unet with Vision Mamba and ConvNeXt Perspective
Authors: Shi Dongyuan , Li Changhong , Shi Hui , Liang Longwei , Liu Huiying , Diao Ming
Published: September 2024

Tomato blight significantly threatened tomato yield and quality, making precise disease detection essential for modern agricultural practices. Traditional segmentation models often struggle with over-segmentation and missed segmentation, particularly in complex backgrounds and with diverse lesion morphologies. To address these challenges, we proposed Unet with Vision Mamba and ConvNeXt (VMC-Unet), an asymmetric segmentation model for quantitative analysis of tomato blight. Built on the Unet framework, VMC-Unet integrated a parallel feature-aware backbone combining ConvNeXt, Vision Mamba, and Atrous Spatial Pyramid Pooling (ASPP) modules to enhance spatial feature focusing and multi-scale information processing. During decoding, Vision Mamba was hierarchically embedded to accurately recover complex lesion morphologies through refined feature processing and efficient up-sampling. A joint loss function was designed to optimize the model’s performance. Extensive experiments on both tomato epidemic and public datasets demonstrated VMC-Unet superior performance, achieving 97.82% pixel accuracy, 87.94% F1 score, and 86.75% mIoU. These results surpassed those of classical segmentation models, underscoring the effectiveness of VMC-Unet in mitigating over-segmentation and under-segmentation while maintaining high segmentation accuracy in complex backgrounds. The consistent performance of the model across various datasets further validated its robustness and generalization potential, highlighting its applicability in broader agricultural settings.
Agronomic and Phytochemical Characterization of Chickpea Local Genetic Resources for the Agroecological Transition and Sustainable Food Systems
Authors: Abou Chehade Lara , Tavarini Silvia , Bozzini Maria Francesca , Koskey Gilbert , Caturegli Lisa , Antichi Daniele , Angelini Luciana G.
Published: September 2024

Legume crops play a key role in hastening both the agroecological and protein transition and improving the sustainability of cropping systems. Among legumes, chickpea (Cicer arietinum L.) is a valuable source of protein, fibers, and nutraceutical compounds, providing important agri-environmental effects. Nevertheless, few studies have explored the effect of genetic characteristics on production and quality traits in chickpea. Chickpea landraces seem particularly interesting for their positive agronomic and quality characteristics, opening the door for innovation in sustainable food systems. Thus, the present study aimed to characterize two chickpea Tuscan landraces (Rugoso della Maremma and Cappuccio della Valtiberina) in comparison with widely distributed commercial chickpea varieties (Ares, Maragià, Pascià, Principe, Reale, Sultano, and Vittoria). Our findings highlighted positive agronomic traits of landraces in terms of seed yield and yield components, demonstrating performance that is either superior or comparable to commercial varieties. Notably, Cappuccio della Valtiberina showed the highest 1000-seed weight (425.50 g), followed by Maragià (432.92 g), Principe (392.32 g), and Reale (382.79 g), and the highest harvest index (0.55), similar to Reale (0.55). Overall, landraces achieved 18.75% higher yields than commercial varieties. Regarding chickpea quality, landraces exhibited profiles comparable to those of commercial genotypes in terms of protein and oil content, as well as nutraceuticals. Interestingly, the two landraces had the most favorable ω-6/ω-3 ratios (Cappuccio della Valtiberina, 12.45; Rugoso della Maremma, 13.71) among the genotypes except for Maragià (11.78), indicating better nutritional quality compared to commercial varieties (>14.00). These results demonstrated that landraces could offer promising prospects for future chickpea breeding programs, aiding in the selection of genotypes capable of adapting to changing growing conditions and supporting the development of sustainable food systems.
Effects of Combined Application of Organic and Inorganic Fertilizers on Physical and Chemical Properties in Saline–Alkali Soil
Authors: Yu Dandan , Miao Qingfeng , Shi Haibin , Feng Zhuangzhuang , Feng Weiying
Published: September 2024

To mitigate the issues of severe farmland soil salinization, the environmental degradation stemming from the overuse of chemical fertilizers, and suboptimal soil composition, a study was conducted to investigate the influence of different types and ratios of organic fertilizers on the physical and chemical attributes of saline–alkali soil. This study aimed to investigate the relationship between different types and proportions of organic fertilizers, soil moisture, organic fertilizer application rates, organic carbon molecular structure, and the soil environment in saline–alkali soils. Reducing the application of chemical fertilizers and substituting them with organic fertilizers can improve the soil quality of saline–alkali lands. The results indicated that replacing a part of the urea with organic fertilizer in saline–alkali farmland reduced the soil salinity by 11.1 to 22.8% in the 0–60 cm soil layer, decreased the soil pH by 0.11 to 1.52%, and increased the soil redox potential (Eh) values by 2.5 to 4.3% in the 0–20 cm layer of the mild and moderate saline–alkali soils. It also decreased the accumulation of the soil organic matter (OM) during the growing season. Compared to commercial organic fertilizers, natural organic fertilizers increased the accumulation of the soil soluble carbon (DOC) and nitrogen (DON), resulting in less soil salinity accumulation. When commercial organic fertilizer was applied in a 1:1 ratio with inorganic fertilizer, the salt accumulation was minimized. Compared to conventional fertilization, organic fertilizer reduced the accumulation of the NH4+-N (ammonium nitrogen) and NO3−-N (nitrate nitrogen) in the soil by 3.1 to 22.6%. In comparison to conventional chemical fertilizers, the application of organic fertilizer in the mild and moderate saline–alkali soils increased the accumulation of the DOC, DON, microbial biomass carbon (MBC), microbial biomass nitrogen (MBN), and microbial quotient during the grain-filling stage. Specifically, it increased the DOC, DON, and DOC/DON by 12.7 to 26.7%, 12 to 59.3%, and 15.2 to 35.5%, respectively. The application of commercial organic fertilizer in the mild saline–alkali soils increased the MBC, MBN, MBC/SOC, and MBN/TN by 37.1, 65.6, 36.7, and 4.7%, respectively. Through analyzing the relative proportions of soil surface organic carbon functional groups during the grain filling period, we observed that, after the application of organic fertilizer, the OM in the mildly salinized soils primarily originated from terrestrial plant litter, whereas, in moderately salinized soils, the OM was mainly derived from microbial sources.
Improving Distantly Supervised Relation Extraction with Multi-Level Noise Reduction
Authors: Song Wei , Yang Zijiang
Published: September 2024

Background: Distantly supervised relation extraction (DSRE) aims to identify semantic relations in large-scale texts automatically labeled via knowledge base alignment. It has garnered significant attention due to its high efficiency, but existing methods are plagued by noise at both the word and sentence level and fail to address these issues adequately. The former level of noise arises from the large proportion of irrelevant words within sentences, while noise at the latter level is caused by inaccurate relation labels for various sentences. Method: We propose a novel multi-level noise reduction neural network (MLNRNN) to tackle both issues by mitigating the impact of multi-level noise. We first build an iterative keyword semantic aggregator (IKSA) to remove noisy words, and capture distinctive features of sentences by aggregating the information of keywords. Next, we implement multi-objective multi-instance learning (MOMIL) to reduce the impact of incorrect labels in sentences by identifying the cluster of correctly labeled instances. Meanwhile, we leverage mislabeled sentences with cross-level contrastive learning (CCL) to further enhance the classification capability of the extractor. Results: Comprehensive experimental results on two DSRE benchmark datasets demonstrated that the MLNRNN outperformed state-of-the-art methods for distantly supervised relation extraction in almost all cases. Conclusions: The proposed MLNRNN effectively addresses both word- and sentence-level noise, providing a significant improvement in relation extraction performance under distant supervision.
Fault Classification of 3D-Printing Operations Using Different Types of Machine and Deep Learning Techniques
Authors: Kumar Satish , Sayyad Sameer , Bongale Arunkumar
Published: September 2024

Fused deposition modeling (FDM), a method of additive manufacturing (AM), comprises the extrusion of materials via a nozzle and the subsequent combining of the layers to create 3D-printed objects. FDM is a widely used method for 3D-printing objects since it is affordable, effective, and easy to use. Some defects such as poor infill, elephant foot, layer shift, and poor surface finish arise in the FDM components at the printing stage due to variations in printing parameters such as printing speed, change in nozzle, or bed temperature. Proper fault classification is required to identify the cause of faulty products. In this work, the multi-sensory data are gathered using different sensors such as vibration, current, temperature, and sound sensors. The data acquisition is performed by using the National Instrumentation (NI) Data Acquisition System (DAQ) which provides the synchronous multi-sensory data for the model training. To induce the faults, the data are captured under different conditions such as variations in printing speed, temperate, and jerk during the printing. The collected data are used to train the machine learning (ML) and deep learning (DL) classification models to classify the variation in printing parameters. The ML models such as k-nearest neighbor (KNN), decision tree (DT), extra trees (ET), and random forest (RF) with convolutional neural network (CNN) as a DL model are used to classify the variable operation printing parameters. Out of the available models, in ML models, the RF classifier shows a classification accuracy of around 91% whereas, in the DL model, the CNN model shows good classification performance with accuracy ranging from 92 to 94% under variable operating conditions.
Behavioral Assessment Reveals GnRH Immunocastration as a Better Alternative to Surgical Castration
Authors: Lin Liuxia , Xu Mengsi , Ma Jian , Du Chunmei , Zang Yaxin , Huang Amei , Wei Chen , Gao Qinghua , Gan Shangquan
Published: September 2024

Castration is often employed in animal management for reproductive control. However, it is important to evaluate its impact on animal welfare. In this study, we developed rat models for both surgical (n = 6) and GnRH immunocastration (n = 6) to assess the effects of these castration methods on physiological and behavioral characteristics. The novel GnRH-based vaccine significantly increased serum GnRH antibody levels and drastically reduced testosterone, with the testes shrinking to one-fifth the size of those in the control group, thereby halting spermatogenesis at the secondary spermatocyte stage. Behavioral evaluations demonstrated that sexual behavior was significantly suppressed in both surgically and immunologically castrated groups compared to the control, confirming the effectiveness of both methods. However, psychological tests revealed significant signs of depression and social deficits in the surgically castrated group, whereas the behavior of the GnRH-immunocastrated group did not significantly differ from the control. Furthermore, no significant differences in learning and memory were observed among the three groups in the water maze test. Compared to surgical castration, GnRH immunocastration offers effective results and better animal welfare, providing a more humane alternative for livestock management.